From cecile.madjar at mcin.ca Fri Nov 1 16:07:59 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Fri, 1 Nov 2019 16:07:59 -0400 Subject: [Loris-dev] LORIS Mondays assignment focus: testing and bug fixes for 22.0!! Message-ID: Hi everyone, Next week we will be focusing on finalizing the first round of testing for 22.0 and send bug fixes for release 22.0. Below is the list of items with their assignments categorized in *1) Testing* and *2) Issues to fix*. If you still have not tested your assigned module, *please test them as a priority on Monday!* *1) Testing:* A little reminder of the procedure for testing can be found in the instructions column of the Testing 22.0 project of the LORIS repository . Please make sure to: - add the "22.0 TESTING" label to the issues and PRs created for the testing/bug fixes of 22.0 - make sure to update the cards on the project Testing 22.0 on Github as follows: - drag the card to either "Fail" or "Success" columns after testing is completed - update the card with links to the issues and/or PRs you created *List of the modules that should be tested at the latest on Monday:* - publication: *Leigh Mac.* - new_profile: *Henri* - next_stage: *Nicolas* - server_processing_manager: *Jess* - survey_accounts: *Dave* - configuration: *Rida* - data_dictionary: *Henri* - login: *Nicolas* - imaging_browser: *John* (when test-loris-dev is updated) - data_team_helper: *Xavier* - genomic_browser: *Dave* - DQT: *C?cile* - instrument_manager: *Shen*, can you test it or give access to the backend of testing to *Justin* so he can test it? *2) Issues to fix for 22.0* These have been assigned per modules. Please work on them on Monday so that the issues found during the first round of testing can be quickly resolved. - *Bugs most likely related to the setup of the testing VM:* *Shen* - Instruments BMI bug (#5448 ) - Set up the media upload folder (#5455 , #5462 ) - *Install CentOS issues:* *Aliz?e* - Install error when schema sourcing fails (#5472 ) - Install CentOS: update documentation for httpd.conf (#5454 ) - Remove is-writable check for logs directory (#5382 ) - *document_repository:* *Zaliqa* - Files from all directories shown without filtering (#5449 ) - Duplicate file uploading (#5453 ) - User A edits while user B deletes (#5456 ) - No notifications sent to email (#5457 ) - *media:* *Henri* - Not all item included in .csv when table is downloaded (#5458 ) - Language option in edit page (#5459 ) - Force language selection when uploading a file (#5464 ) - Form not resetting after upload (#5363 ) - *statistics:* *Sruthy* - Total age average in months not calculated (#5466 ) - Behavioural statistics not updating when switching project (#5463 ) - Minor UI issue in dropdown in <900px wide screens (#5460 ) - *examiner:* *Sruthy* - saving examiner certification details gives 500 error (#5423 ) - *brainbrowser:* *C?cile* - No permissions for access restriction (#5473 ) - Minor UI improvements on Overlay Panel (#5469 ) - Loading slowness and lack of clarity when loading (#5474 ) - *dashboard:* *Justin* - New and pending imaging sessions are un-clickable (#5461 ) - *data_release:* *Justin* - no access point for regular users except manually type in URL (#5496 ) - *user_accounts:* *Nicolas* - Can set password and email to be the same (#5416 ) - PR to review and test for user account (#5426 ) - Abstract common functionality between Edit User and My Preferences( #5427 ) - Can set new password to be the same as current password (#5439 ) - Password auto-created is massive (#5440 ) - *candidate parameters:* *Jess* - Module broken (#5434 ) - *quality_control:* *John/Christine* - Arrows at top right of data table - hide all data (#5483 ) - BVL tab seems to be missing a status? (#5482 ) - Create RB test data (#5480 ) - *data_integrity_flag:* *Henri* - Filter link not fully working (#5479 ) - *mri_violation:* *C?cile* to sit with John for those issues - (#5422 ) - (#5421 ) - (#5420 ) - (#5419 ) - *new_profile:* *Rida* - If user assigned to 1 site, unhide site field and auto-populate default site (#5380 ) - *create_timepoint:* *Krishna* - Creating timepoint without selecting `Project` leads to 500 error ( #5418 ) - *dicom_archive:* *Krishna* - date format inconsistencies (#5443 ) - please double check that this is indeed an issue - test and review PR #5450 that fixes metadata not being display in the view details page - *test plan tickets:* *Corey* - (#5481 ) Can you work with *Christine* and *John* to create a proper test plan for the QC module? - Issue Tracker test plan to update (#5495 ) - *instrument_builder:* *Christine maybe you could help Corey clarify how to test that module?* - No cue for how to add and save rules (#5494 ) - No cue for how to Preview the instrument (#5493 ) - Item meaning confusing (#5488 ) - No cue for "Add Blank Line" (#5486 ) - No cue for "validate that not_answered option is added in the linst file for this question" (#5484 ) - *behavioural feedback:* *Xavier* - Issues with display and closing of threads after hitting 'Close' button (#5467 ) - (#5468 ) new feature - *imaging_uploader:* *Xavier* - can't show upload file in the front-end (#5413 ) - *help_editor:* *Xavier* - unable to edit help editor (#5446 ) Thank you all very much for your contribution! If you encounter any issues with your assignments, please contact Dave, Rida or C?cile so we can deal with those. Happy Postponed Halloween!! ????? C?cile -------------- next part -------------- An HTML attachment was scrubbed... URL: From joh17964 at umn.edu Mon Nov 4 14:53:43 2019 From: joh17964 at umn.edu (Eli Johnson) Date: Mon, 4 Nov 2019 13:53:43 -0600 Subject: [Loris-dev] LORIS Development Database Set Up Message-ID: Hi all, We are setting up a development server and database for our instance of LORIS. I am looking for advice on how to best set up and maintain a development database that replicates our production database. From discussion with Dave and Leigh at McGill, it sounds like we will want to clone our production database. This could be done via a mysqldump from the production database which is loaded into the development database. *Several specific questions*: 1. I imagine cloning the production database via mysqldump every time would take a bit of time with a larger database. Any advice on this process? Is mysqldump the best method or is there a recommended alternative method to do this? 2. Does anyone have scripts or tools they could share to help automate this process? 3. Will I need to completely clone the production database every time I want to update the development database or is there some way to update it incrementally? Any additional advice on best practices for this are appreciated! Thanks, Eli Eli Johnson Researcher Institute of Child Development University of Minnesota joh17964 at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From melanie.legault2 at mcgill.ca Tue Nov 5 09:11:23 2019 From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs) Date: Tue, 5 Nov 2019 14:11:23 +0000 Subject: [Loris-dev] LORIS Development Database Set Up In-Reply-To: References: Message-ID: Hello Eli, There is no need to create a new database dump from production every time you start a new project. If you do all you development on your dev instance before porting to production and keep this dev instance to the same release of LORIS as your prod, both database instance should have the same schema. It is also a good idea to test a new release of LORIS elsewhere than you production instance first to ensure there is no compatibility problem with your internal development before upgrading you production. As long as database schema modification are eventually applied to both instance, there is no need to use a datadump to re-synchronize. Of course the data itself would be out of date but it is normally not a problem for a development instance. M?lanie Legault | Software developer | Faculty of Medicine | McGill University 3801 University, Montr?al, QC H3A 2B4 ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Eli Johnson Sent: November 4, 2019 14:53 To: loris dev Subject: [Loris-dev] LORIS Development Database Set Up Hi all, We are setting up a development server and database for our instance of LORIS. I am looking for advice on how to best set up and maintain a development database that replicates our production database. From discussion with Dave and Leigh at McGill, it sounds like we will want to clone our production database. This could be done via a mysqldump from the production database which is loaded into the development database. Several specific questions: 1. I imagine cloning the production database via mysqldump every time would take a bit of time with a larger database. Any advice on this process? Is mysqldump the best method or is there a recommended alternative method to do this? 2. Does anyone have scripts or tools they could share to help automate this process? 3. Will I need to completely clone the production database every time I want to update the development database or is there some way to update it incrementally? Any additional advice on best practices for this are appreciated! Thanks, Eli Eli Johnson Researcher Institute of Child Development University of Minnesota joh17964 at umn.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Tue Nov 5 09:59:55 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 5 Nov 2019 14:59:55 +0000 Subject: [Loris-dev] LORIS Development Database Set Up In-Reply-To: References: Message-ID: Hi Eli - As a side note further to Melanie's answer -- If your intention is to test production-ready code updates on a current copy of your production data -- our practice as a Data Coordinating Centre is to set up a (third) "staging" environment to do this, in addition to production and development environments. Typically this staging environment is refreshed with a dump of the production database as often as needed/automated. We set up this 3-pronged system for most projects when we serve as DCC and can advise further. Best, Christine On Tue, Nov 5, 2019 at 9:11 AM Melanie Legault, Mrs > wrote: Hello Eli, There is no need to create a new database dump from production every time you start a new project. If you do all you development on your dev instance before porting to production and keep this dev instance to the same release of LORIS as your prod, both database instance should have the same schema. It is also a good idea to test a new release of LORIS elsewhere than you production instance first to ensure there is no compatibility problem with your internal development before upgrading you production. As long as database schema modification are eventually applied to both instance, there is no need to use a datadump to re-synchronize. Of course the data itself would be out of date but it is normally not a problem for a development instance. M?lanie Legault | Software developer | Faculty of Medicine | McGill University 3801 University, Montr?al, QC H3A 2B4 ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca > on behalf of Eli Johnson > Sent: November 4, 2019 14:53 To: loris dev > Subject: [Loris-dev] LORIS Development Database Set Up Hi all, We are setting up a development server and database for our instance of LORIS. I am looking for advice on how to best set up and maintain a development database that replicates our production database. From discussion with Dave and Leigh at McGill, it sounds like we will want to clone our production database. This could be done via a mysqldump from the production database which is loaded into the development database. Several specific questions: 1. I imagine cloning the production database via mysqldump every time would take a bit of time with a larger database. Any advice on this process? Is mysqldump the best method or is there a recommended alternative method to do this? 2. Does anyone have scripts or tools they could share to help automate this process? 3. Will I need to completely clone the production database every time I want to update the development database or is there some way to update it incrementally? Any additional advice on best practices for this are appreciated! Thanks, Eli Eli Johnson Researcher Institute of Child Development University of Minnesota joh17964 at umn.edu _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From ioannis at berkeley.edu Thu Nov 7 00:18:07 2019 From: ioannis at berkeley.edu (Ioannis Pappas) Date: Wed, 6 Nov 2019 21:18:07 -0800 Subject: [Loris-dev] loris server In-Reply-To: <20191107030327.GA7157@gaia.neuro.berkeley.edu> References: <20191104195851.GA4052@gaia.neuro.berkeley.edu> <20191104200859.GB27438@nx6.priv> <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu> Message-ID: Hi Christine and Julie. Yes it looks like that any attempt to configure something in the front-end results in the same page. I am sending this to the list (as you requested Christine) alongside the troubleshooting and discussion so far with Julie. Best wishes, Ioannis > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing Support wrote: > > hi Christine and Ioannis, > Ioannis, can you follow-up with Christine about using the front-end? > > We're using CentOS7.7 and loris-21.0.1. > > I confirmed that I could login as the mysql user (lorismyqsl) and change the 'url' config setting from 'http://loris.priv' to 'http://localhost', and back again. > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > | ConfigID | Name | Label | Value | Description | > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > | 44 | host | Host | loris.priv | Host | > | 45 | url | Main LORIS URL | http://loris.priv | Main URL where LORIS can be accessed | > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > MariaDB [loris_database]> UPDATE Config SET Value='http://localhost' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > Rows matched: 1 Changed: 1 Warnings: 0 > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > +----------+-------------------+-------------------+------------------+--------------------------------------+ > | ConfigID | Name | Label | Value | Description | > +----------+-------------------+-------------------+------------------+--------------------------------------+ > | 44 | host | Host | loris.priv | Host | > | 45 | url | Main LORIS URL | http://localhost | Main URL where LORIS can be accessed | > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > +----------+-------------------+-------------------+------------------+--------------------------------------+ > 3 rows in set (0.00 sec) > > best, > Julie > > > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: >> Hi Julie, >> Forgive my ambiguity - We run the community support listserv for >> developers, project administrators and sysadmins setting up LORIS, so that >> these users can contact our technical team for exactly such technical >> help. >> If it's ok with you, I'd encourage you subscribe to the listserv and >> contact our technical team that way for the same reason. >> (Note that front-end users of LORIS typically contact their project team >> for support, rather than us.) >> Given that your lorismysql user privileges seem appropriate ('UPDATE" is >> there, I mistyped 'INSERT" before) >> -- is there any other indication why the database record is not >> updating? >> In the front-end, can your 'admin' user effect any changes in (any) Config >> setting? >> In the back-end, when you tried updating a field using your >> lorismysql credential, what happened? >> Your front end is loading ok, and you can log in there, if I understood >> correctly. >> Thanks for letting us know these details at >> [1]loris-dev at bic.mni.mcgill.ca >> Please also include what version of LORIS you are installing, and on what >> OS version. >> Best, >> Christine >> On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI Computing Support >> <[2]support-cirl at berkeley.edu> wrote: >> >> Thank you Christine, >> I'm the linux sysadmin who installed the loris database for Ioannis. >> I'm not a loris user, however, so that makes it a little awkward for >> troubleshooting via the mailing list. I'm happy to help in whatever way >> I can. >> >> Regarding the database permissions, I ran: >> >> MariaDB [(none)]> show grants for 'lorismysql'@'%'; >> +--------------------------------------------------------------------------------+ >> | Grants for lorismysql@% >> | >> +--------------------------------------------------------------------------------+ >> | GRANT USAGE ON *.* TO 'lorismysql'@'%' >> | >> | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO >> 'lorismysql'@'%' | >> +--------------------------------------------------------------------------------+ >> 2 rows in set (0.00 sec) >> >> looking at the 'tips' section in the page you referred to... >> >> | 29 | base | Base | /srv/www/loris/ | The base >> filesystem path where LORIS is installed | >> | 31 | DownloadPath | Downloads | /srv/www/loris/ | Where >> files are downloaded >> >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> | ConfigID | Name | Label | Value | >> Description | >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> | 44 | host | Host | loris.priv | >> Host | >> | 45 | url | Main LORIS URL | >> [3]http://loris.priv | Main URL where LORIS can be accessed | >> | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | >> The *new* bug/issue tracker url | >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> >> apache config: >> >> Listen 80 >> User apache >> Group apache >> DocumentRoot "/srv/www/loris/htdocs" >> >> >> AllowOverride none >> Require all denied >> >> >> >> AllowOverride All >> Options Indexes FollowSymLinks >> Require all granted >> >> >> >> Options Indexes FollowSymLinks >> AllowOverride All >> Require all granted >> >> >> file permissions: >> >> # ls -ld /srv/www/loris/smarty/templates_c >> drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 >> /srv/www/loris/smarty/templates_c/ >> >> [root at loris loris]# ls -l /srv/www/loris/smarty/templates_c >> -rw-r--r-- 1 lorisadmin lorisadmin 2444 Oct 31 09:46 >> 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 >> 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep 7 18:39 >> 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3296 Sep 7 18:35 >> 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 5901 Sep 7 21:10 >> 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep 7 18:39 >> 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 874 Sep 10 11:01 >> 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 1101 Sep 10 10:58 >> 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 >> 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3590 Sep 7 18:39 >> a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep 7 21:08 >> a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 897 Sep 7 18:35 >> a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 9210 Sep 10 11:01 >> a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 8917 Sep 10 13:21 >> ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 4811 Sep 7 18:35 >> d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3309 Sep 10 11:02 >> d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 >> e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep 7 17:42 >> fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php >> >> thanks again! >> Julie >> >> On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: >>> Hi Ioannis,? >>> Thanks for your question.? >>> Given that the URL field is not updating, I suspect it's a database >>> back-end issue.? >>> Can you verify -- Has your mysql user lorismysql? been granted the >> "INSERT" >>> privilege for the right database? If not, that would result in an >> error >>> like the kind you are seeing.? >>> Also, if you wish to check your LORIS Configuration settings in the >>> backend database such as the URL field -- to see what was actually >> stored >>> in a given database field and should display in the Config >> module:? >>> You can run the queries listed in the "Troubleshooting >> Configuration >>> settings" section of our Github-wiki Setup Guide (under Project >>> Customization) :? >>> >> [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> Lastly, this question is perfectly appropriate for the loris-dev >> community >>> support listserv -- please [2]subscribe here and then email our >> technical >>> team your next question at? [3][5]loris-dev at bic.mni.mcgill.ca >> (after checking >>> any forwarded threads for sensitive info).? >>> We prefer to answer technical questions there for the benefit of >> the >>> community and other first-time users in the same position as >> yourself.? ? >>> Thanks and cheers,? >>> Christine? >>> On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD >>> <[4][6]ioannis at berkeley.edu> wrote: >>> >>> Hi Loris support.? >>> My name is ioannis Pappas, a post-doc at the D'Esposito lab >> stroke group >>> at UC Berkeley. With the kind of help of our sys admin? Julie >> (cc'ed) we >>> have set up our loris database in our cluster (she is the sudo >> user and >>> I am the admin user). >>> If you allow me, I would like to ask you about the first >> configuration >>> steps in the front end as they are described in the tutorial. We >> can >>> login to [5][7]http://loris and the front end normally. >>> However any update that I am trying to? perform in >> Admin->Configuration >>> doesn't work (e.g. updating the study name). It just refreshes >> the same >>> page. I am just wondering if there is an issue with writing in >> the >>> configuration file. >>> Here are the permissions setup for where Loris is installed. >>> chmod 777 /var/www/loris/smarty/templates_c >>> cd /srv/www/loris >>> chown -R lorisadmin:lorisadmin . >>> chmod -c -R a+r . >>> ? ? this command gives everyone read access, and outputs what >> changes >>> were made: >>> ? ? mode of ??./project?? changed from 0770 (rwxrwx---) to 0774 >>> (rwxrwxr--) >>> ? ? mode of ??./tools/logs?? changed from 0770 (rwxrwx---) to >> 0774 >>> (rwxrwxr--) >>> find . -type d -exec chmod a+x -c {} \; >>> ? ? this command gives everyone permission to open a directory, >> and >>> outputs what changes were made: >>> ? ? mode of ??./project?? changed from 0774 (rwxrwxr--) to 0775 >>> (rwxrwxr-x) >>> ? ? mode of ??./tools/logs?? changed from 0774 (rwxrwxr--) to >> 0775 >>> (rwxrwxr-x) >>> Hopefully? you can help me with this. I also subscribed to the >> mailing >>> list but I am not sure if this too much of a basic question for >> the >>> list. >>> Best wishes, >>> Ioannis >>> On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI Computing >> Support >>> <[6][8]support-cirl at berkeley.edu> wrote: >>> >>> Hi ioannis, maybe it's best to ask the developers? You can cc >> me if >>> you'd like. >>> On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas >> <[7][9]ioannis at berkeley.edu> >>> wrote: >>> >>> That did the trick Julie. Thank you! >>> >>> I am still trying to understand how configuration works >> though. For >>> example if I just try to change the name of the >>> study from the front end, I get nowhere (it just refreshes >> the same >>> page). >>> >>> I am not sure if this requires write permissions somewhere in >> a >>> config file/folder and that???s why it doesn???t update it. >>> >>> Best wishes, >>> Ioannis >>> >>> > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI Computing >>> Support <[8][10]support-cirl at berkeley.edu> wrote: >>> > >>> > just in case you're interested, these are the permission >> changes I >>> made: >>> > >>> > chmod 777 /var/www/loris/smarty/templates_c >>> > cd /srv/www/loris >>> > chown -R lorisadmin:lorisadmin . >>> > chmod -c -R a+r . >>> >? ? this command gives everyone read access, and outputs >> what >>> changes were made: >>> >? ? mode of ??./project?? changed from 0770 (rwxrwx---) to >> 0774 >>> (rwxrwxr--) >>> >? ? mode of ??./tools/logs?? changed from 0770 (rwxrwx---) >> to 0774 >>> (rwxrwxr--) >>> > find . -type d -exec chmod a+x -c {} \; >>> >? ? this command gives everyone permission to open a >> directory, and >>> outputs what changes were made: >>> >? ? mode of ??./project?? changed from 0774 (rwxrwxr--) to >> 0775 >>> (rwxrwxr-x) >>> >? ? mode of ??./tools/logs?? changed from 0774 (rwxrwxr--) >> to 0775 >>> (rwxrwxr-x) >>> > >>> > >>> > >>> > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: >>> >> Hi Julie. >>> >> I just tried and I still don???t get anything. I also >> tried >>> private mode in Firefox in case the empty page was cached. >>> >> Sorry for this. >>> >> >>> >> Best wishes, >>> >> Ioannis >>> >> >>> >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, HWNI >> Computing >>> Support <[9][11]support-cirl at berkeley.edu> wrote: >>> >>> >>> >>> hi Ioannis, >>> >>> no worries, I changed the following directory to 777: >>> >>> >>> >>> /var/www/loris/smarty/templates_c >>> >>> >>> >>> will you please check if that works? >>> >>> >>> >>> thanks! >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas PhD wrote: >>> >>>>? Hi Julie. >>> >>>>? Apologies for bugging you with this again. We tried >> now to >>> >>>>? access?? [1][10][12]http://loris?? >>> >>>>? and we are getting a?? blank page. I think the reason >> for this >>> is that we >>> >>>>? don't have read?? permissions to read from the >> template located >>> in >>> >>>>? /var/www/loris/smarty See here bottom of the >>> >>>>? page?? >>> >> [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> >>>>? I think, in general, I am a little bit confused as to >> what the >>> permissions >>> >>>>? should be for us that are not sudos. My understanding >> is that >>> if we don't >>> >>>>? have read or write permissions then we can't access or >> write >>> to >>> >>>>? /var/www/loris, meaning that we can't access or >> configure. >>> Should >>> >>>>? everything be chmod 777 for example??? >>> >>>>? Thank you very much once again. >>> >>>>? Best wishes, >>> >>>>? Ioannis >>> >>>>? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis Pappas PhD >>> >>>>? <[3][12][14]ioannis at berkeley.edu> wrote: >>> >>>> >>> >>>>? ? Thank you very much Julie. I appreciate this and I >> will dig >>> into Loris >>> >>>>? ? given your changes. Thank you so much for your >> help. >>> >>>>? ? Best wishes, >>> >>>>? ? Ioannis >>> >>>>? ? On Thu, Oct 31, 2019 at 12:48 PM Julie Ashworth, >> HWNI >>> Computing Support >>> >>>>? ? <[4][13][15]support-cirl at berkeley.edu> wrote: >>> >>>> >>> >>>>? ? ? hi Ioannis, >>> >>>> >>> >>>>? ? ? 1. I changed the permissions of /srv/www/loris >> to be owned >>> by >>> >>>>? ? ? lorisadmin. I reivewed my installation notes, >> and I did >>> this already >>> >>>>? ? ? when >>> >>>>? ? ? I installed the server. I'm not sure why they >> changed, so >>> it's >>> >>>>? ? ? probably a >>> >>>>? ? ? good idea to keep an eye on that. >>> >>>> >>> >>>>? ? ? 2. When I installed the loris software, I also >> installed a >>> mysql >>> >>>>? ? ? database as recommended in the instructions: >>> >>>> >>> >>>>? ? ? projectname: LORIS >>> >>>>? ? ? databasename: loris_database >>> >>>>? ? ? mysqluser: lorismysql >>> >>>>? ? ? frontend: lorisweb >>> >>>> >>> >>>>? ? ? 3. A couple of weeks ago, I moved Henrik's home >> directory >>> to >>> >>>>? ? ? /home/despoA, >>> >>>>? ? ? but I forgot to update loris. This is done now. >>> >>>> >>> >>>>? ? ? best, >>> >>>>? ? ? Julie >>> >>>> >>> >>>>? ? ? On 31-10-2019 11.15 -0700, Dr. Ioannis Pappas >> PhD wrote: >>> >>>>> ??? ??? Hi Julie. >>> >>>>> ??? ??? I hope you are well. We are trying to >> configure loris >>> that you >>> >>>>? ? ? kindly set >>> >>>>> ??? ??? up for us. >>> >>>>> ??? ??? I have a couple of questions for you if you >> allow me >>> so.?? >>> >>>>> ??? ??? 1) First, although we are logging into the >> front end >>> with admin >>> >>>>? ? ? username >>> >>>>> ??? ??? (lorisweb) and password, it seems that any >> kind of >>> update of >>> >>>>? ? ? configuration >>> >>>>> ??? ??? we are trying to do fails (meaning that if >> we, say, >>> change the >>> >>>>? ? ? name of the >>> >>>>> ??? ??? study and press "submit", this doesn't do >> anything-it >>> doesn't >>> >>>>? ? ? update). >>> >>>>> ??? ??? It's almost like our lorisweb user doesn't >> have write >>> privileges >>> >>>>? ? ? in the >>> >>>>> ??? ??? /var/www/loris/project (where I think every >>> configuration should >>> >>>>? ? ? be). >>> >>>>> ??? ??? This generalizes for everything that we are >> trying to do >>> in the >>> >>>>? ? ? front end. >>> >>>>> ??? ??? Clicking any instrument/tab in the front end >> doesn't >>> really point >>> >>>>? ? ? to >>> >>>>> ??? ??? anything.?? >>> >>>>> ??? ??? 2) Loris suggest doing configurations via >> SQL. Is it >>> possible to >>> >>>>? ? ? run SQL >>> >>>>> ??? ??? scripts in the backend >>> >>>>> ??? ??? 3) For some reason typing ssh lors for Henrik >> doesn't >>> directly >>> >>>>? ? ? take him to >>> >>>>> ??? ??? loris (it requires a password that is not the >> password >>> setup for >>> >>>>? ? ? the >>> >>>>> ??? ??? lorisweb user). Will you be able to fix this >> via your >>> sudo >>> >>>>? ? ? privileges? >>> >>>>> ??? ??? Thank you very much in advance for all your >> help Julie. >>> Let us >>> >>>>? ? ? know if >>> >>>>> ??? ??? this is something that shouldn't be directed >> to you (but >>> instead >>> >>>>? ? ? to the >>> >>>>> ??? ??? loris people).?? >>> >>>>> ??? ??? Best wishes, >>> >>>>> ??? ??? Ioannis >>> >>>>> ??? ??? On Mon, Sep 9, 2019 at 6:25 PM Julie >> Ashworth, HWNI >>> Computing >>> >>>>? ? ? Support >>> >>>>> ??? ??? <[1][5][14][16]support-cirl at berkeley.edu> >> wrote: >>> >>>>> >>> >>>>> ??? ??? ??? hi Henrik and Ioannis, >>> >>>>> ??? ??? ??? the loris server is available for you to >> use. >>> >>>>> >>> >>>>> ??? ??? ??? The servername is 'loris'. I created a >> directory >>> called >>> >>>>? ? ? /data/loris for >>> >>>>> ??? ??? ??? you to store data. You may create new >> folders in >>> /data/loris to >>> >>>>? ? ? organize >>> >>>>> ??? ??? ??? your data. >>> >>>>> >>> >>>>> ??? ??? ??? 1) secure shell or secure copy: >>> >>>>> ??? ??? ??? You can log in with the 'ssh' or 'scp' >> command from >>> your remote >>> >>>>? ? ? desktop >>> >>>>> ??? ??? ??? session. You don't need to authenticate >> to log in. >>> Maybe you'll >>> >>>>? ? ? use scp >>> >>>>> ??? ??? ??? to transfer data between your cluster >> account and the >>> loris >>> >>>>? ? ? server? >>> >>>>> ??? ??? ??? Please put the data in /data/loris, so I >> can make >>> backups more >>> >>>>? ? ? easily. >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? secure shell: >>> >>>>> ??? ??? ??? ??? ??? $ ssh loris >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? secure copy (change the names >> in brackets). Let >>> me know if >>> >>>>? ? ? I can >>> >>>>> ??? ??? ??? ??? ??? help with syntax: >>> >>>>> ??? ??? ??? ??? ??? $ scp -r >> loris:/data/loris/ >>> >>>>> >>> >>>>> ??? ??? ??? 2) front-end web interface.??? Open a >> web browser in >>> your remote >>> >>>>? ? ? desktop >>> >>>>> ??? ??? ??? session and enter the hostname: >>> >>>>> ??? ??? ??? [2][6][15][17]http://loris >>> >>>>> ??? ??? ??? I created an admin user called >> 'lorisweb'. I put the >>> password >>> >>>>? ? ? in >>> >>>>> ??? ??? ??? $HOME/newuser on the cluster. To see it, >> open a >>> terminal, and >>> >>>>? ? ? run: >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? $ cat $HOME/newuser >>> >>>>> >>> >>>>> ??? ??? ??? If other people need shell access to the >> webserver, >>> please let >>> >>>>? ? ? me know >>> >>>>> ??? ??? ??? so I can create a home directory for >> them. >>> >>>>> >>> >>>>> ??? ??? ??? We should eventually discuss backups. >>> >>>>> >>> >>>>> ??? ??? ??? best, >>> >>>>> ??? ??? ??? Julie >>> >>>>> >>> >>>>> References >>> >>>>> >>> >>>>> ??? ??? Visible links >>> >>>>> ??? ??? 1. >> mailto:[7][16][18]support-cirl at berkeley.edu >>> >>>>> ??? ??? 2. [8][17][19]http://loris/ >>> >>>>? ? ? ---end quoted text--- >>> >>>> >>> >>>> References >>> >>>> >>> >>>>? Visible links >>> >>>>? 1. [18][20]http://loris/ >>> >>>>? 2. >>> >> [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> >>>>? 3. mailto:[20][22]ioannis at berkeley.edu >>> >>>>? 4. mailto:[21][23]support-cirl at berkeley.edu >>> >>>>? 5. mailto:[22][24]support-cirl at berkeley.edu >>> >>>>? 6. [23][25]http://loris/ >>> >>>>? 7. mailto:[24][26]support-cirl at berkeley.edu >>> >>>>? 8. [25][27]http://loris/ >>> >>> ---end quoted text--- >>> >> >>> > ---end quoted text--- >>> >>> -- >>> [26][28]christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> References >>> >>> Visible links >>> 1. >> [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> 2. [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> 3. mailto:[31]loris-dev at bic.mni.mcgill.ca >>> 4. mailto:[32]ioannis at berkeley.edu >>> 5. [33]http://loris/ >>> 6. mailto:[34]support-cirl at berkeley.edu >>> 7. mailto:[35]ioannis at berkeley.edu >>> 8. mailto:[36]support-cirl at berkeley.edu >>> 9. mailto:[37]support-cirl at berkeley.edu >>> 10. [38]http://xn--loris-7qa/ >>> 11. [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> 12. mailto:[40]ioannis at berkeley.edu >>> 13. mailto:[41]support-cirl at berkeley.edu >>> 14. mailto:[42]support-cirl at berkeley.edu >>> 15. [43]http://loris/ >>> 16. mailto:[44]support-cirl at berkeley.edu >>> 17. [45]http://loris/ >>> 18. [46]http://loris/ >>> 19. [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> 20. mailto:[48]ioannis at berkeley.edu >>> 21. mailto:[49]support-cirl at berkeley.edu >>> 22. mailto:[50]support-cirl at berkeley.edu >>> 23. [51]http://loris/ >>> 24. mailto:[52]support-cirl at berkeley.edu >>> 25. [53]http://loris/ >>> 26. mailto:[54]christine.rogers at mcgill.ca >> ---end quoted text--- >> >> -- >> [55]christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> References >> >> Visible links >> 1. mailto:loris-dev at bic.mni.mcgill.ca >> 2. mailto:support-cirl at berkeley.edu >> 3. http://loris.priv/ >> 4. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >> 5. mailto:loris-dev at bic.mni.mcgill.ca >> 6. mailto:ioannis at berkeley.edu >> 7. http://loris/ >> 8. mailto:support-cirl at berkeley.edu >> 9. mailto:ioannis at berkeley.edu >> 10. mailto:support-cirl at berkeley.edu >> 11. mailto:support-cirl at berkeley.edu >> 12. http://xn--loris-era/ >> 13. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 14. mailto:ioannis at berkeley.edu >> 15. mailto:support-cirl at berkeley.edu >> 16. mailto:support-cirl at berkeley.edu >> 17. http://loris/ >> 18. mailto:support-cirl at berkeley.edu >> 19. http://loris/ >> 20. http://loris/ >> 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 22. mailto:ioannis at berkeley.edu >> 23. mailto:support-cirl at berkeley.edu >> 24. mailto:support-cirl at berkeley.edu >> 25. http://loris/ >> 26. mailto:support-cirl at berkeley.edu >> 27. http://loris/ >> 28. mailto:christine.rogers at mcgill.ca >> 29. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >> 30. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> 31. mailto:loris-dev at bic.mni.mcgill.ca >> 32. mailto:ioannis at berkeley.edu >> 33. http://loris/ >> 34. mailto:support-cirl at berkeley.edu >> 35. mailto:ioannis at berkeley.edu >> 36. mailto:support-cirl at berkeley.edu >> 37. mailto:support-cirl at berkeley.edu >> 38. http://xn--loris-7qa/ >> 39. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 40. mailto:ioannis at berkeley.edu >> 41. mailto:support-cirl at berkeley.edu >> 42. mailto:support-cirl at berkeley.edu >> 43. http://loris/ >> 44. mailto:support-cirl at berkeley.edu >> 45. http://loris/ >> 46. http://loris/ >> 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 48. mailto:ioannis at berkeley.edu >> 49. mailto:support-cirl at berkeley.edu >> 50. mailto:support-cirl at berkeley.edu >> 51. http://loris/ >> 52. mailto:support-cirl at berkeley.edu >> 53. http://loris/ >> 54. mailto:christine.rogers at mcgill.ca >> 55. mailto:christine.rogers at mcgill.ca > ---end quoted text--- From melanie.legault2 at mcgill.ca Thu Nov 7 07:33:56 2019 From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs) Date: Thu, 7 Nov 2019 12:33:56 +0000 Subject: [Loris-dev] loris server In-Reply-To: References: <20191104195851.GA4052@gaia.neuro.berkeley.edu> <20191104200859.GB27438@nx6.priv> <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu>, Message-ID: Hello, Changing the project name in the configuration page (https://loris.url/configuration/) of LORIS, only change the title of the project. To see this change, you have to log out of LORIS and then go back to the login page (https://.loris.url/). This is the only place you can find the project name (except from the configuration page). See ProjectName.png As for files permission, I would suggest a few change to improve security of you server. Some extra permissions where granted to help you but are not needed. * /srv/www/loris/smarty/templates_c/ should have ownership of lorisadmin:httpd and permission 770 (or 775) * srv/www/loris/project/ should have ownership lorisadmin:httpd and permission 770 (775) * All other files under loris should have lorisadmin:lorisadmin 755 Reading through this change of mail, I understand that you let Apache store file in /srv/www/loris | 31 | DownloadPath | Downloads | /srv/www/loris/ | Where >> files are downloaded Downloaded files should not be in the same tree as LORIS code. It should be in a separate structure where Apache will not try and do not have permission (in httpd.conf) to execute files. Kind regards, M?lanie Legault | Software developer | Faculty of Medicine | McGill University 3801 University, Montr?al, QC H3A 2B4 ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Ioannis Pappas Sent: November 7, 2019 0:18 To: loris-dev at bic.mni.mcgill.ca Cc: Julie Ashworth, HWNI Computing Support ; Christine Rogers, Ms. Subject: Re: [Loris-dev] loris server Hi Christine and Julie. Yes it looks like that any attempt to configure something in the front-end results in the same page. I am sending this to the list (as you requested Christine) alongside the troubleshooting and discussion so far with Julie. Best wishes, Ioannis > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing Support wrote: > > hi Christine and Ioannis, > Ioannis, can you follow-up with Christine about using the front-end? > > We're using CentOS7.7 and loris-21.0.1. > > I confirmed that I could login as the mysql user (lorismyqsl) and change the 'url' config setting from 'http://loris.priv' to 'http://localhost', and back again. > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > | ConfigID | Name | Label | Value | Description | > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > | 44 | host | Host | loris.priv | Host | > | 45 | url | Main LORIS URL | http://loris.priv | Main URL where LORIS can be accessed | > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > MariaDB [loris_database]> UPDATE Config SET Value='http://localhost' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > Rows matched: 1 Changed: 1 Warnings: 0 > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > +----------+-------------------+-------------------+------------------+--------------------------------------+ > | ConfigID | Name | Label | Value | Description | > +----------+-------------------+-------------------+------------------+--------------------------------------+ > | 44 | host | Host | loris.priv | Host | > | 45 | url | Main LORIS URL | http://localhost | Main URL where LORIS can be accessed | > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > +----------+-------------------+-------------------+------------------+--------------------------------------+ > 3 rows in set (0.00 sec) > > best, > Julie > > > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: >> Hi Julie, >> Forgive my ambiguity - We run the community support listserv for >> developers, project administrators and sysadmins setting up LORIS, so that >> these users can contact our technical team for exactly such technical >> help. >> If it's ok with you, I'd encourage you subscribe to the listserv and >> contact our technical team that way for the same reason. >> (Note that front-end users of LORIS typically contact their project team >> for support, rather than us.) >> Given that your lorismysql user privileges seem appropriate ('UPDATE" is >> there, I mistyped 'INSERT" before) >> -- is there any other indication why the database record is not >> updating? >> In the front-end, can your 'admin' user effect any changes in (any) Config >> setting? >> In the back-end, when you tried updating a field using your >> lorismysql credential, what happened? >> Your front end is loading ok, and you can log in there, if I understood >> correctly. >> Thanks for letting us know these details at >> [1]loris-dev at bic.mni.mcgill.ca >> Please also include what version of LORIS you are installing, and on what >> OS version. >> Best, >> Christine >> On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI Computing Support >> <[2]support-cirl at berkeley.edu> wrote: >> >> Thank you Christine, >> I'm the linux sysadmin who installed the loris database for Ioannis. >> I'm not a loris user, however, so that makes it a little awkward for >> troubleshooting via the mailing list. I'm happy to help in whatever way >> I can. >> >> Regarding the database permissions, I ran: >> >> MariaDB [(none)]> show grants for 'lorismysql'@'%'; >> +--------------------------------------------------------------------------------+ >> | Grants for lorismysql@% >> | >> +--------------------------------------------------------------------------------+ >> | GRANT USAGE ON *.* TO 'lorismysql'@'%' >> | >> | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO >> 'lorismysql'@'%' | >> +--------------------------------------------------------------------------------+ >> 2 rows in set (0.00 sec) >> >> looking at the 'tips' section in the page you referred to... >> >> | 29 | base | Base | /srv/www/loris/ | The base >> filesystem path where LORIS is installed | >> | 31 | DownloadPath | Downloads | /srv/www/loris/ | Where >> files are downloaded >> >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> | ConfigID | Name | Label | Value | >> Description | >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> | 44 | host | Host | loris.priv | >> Host | >> | 45 | url | Main LORIS URL | >> [3]http://loris.priv | Main URL where LORIS can be accessed | >> | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | >> The *new* bug/issue tracker url | >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> >> apache config: >> >> Listen 80 >> User apache >> Group apache >> DocumentRoot "/srv/www/loris/htdocs" >> >> >> AllowOverride none >> Require all denied >> >> >> >> AllowOverride All >> Options Indexes FollowSymLinks >> Require all granted >> >> >> >> Options Indexes FollowSymLinks >> AllowOverride All >> Require all granted >> >> >> file permissions: >> >> # ls -ld /srv/www/loris/smarty/templates_c >> drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 >> /srv/www/loris/smarty/templates_c/ >> >> [root at loris loris]# ls -l /srv/www/loris/smarty/templates_c >> -rw-r--r-- 1 lorisadmin lorisadmin 2444 Oct 31 09:46 >> 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 >> 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep 7 18:39 >> 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3296 Sep 7 18:35 >> 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 5901 Sep 7 21:10 >> 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep 7 18:39 >> 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 874 Sep 10 11:01 >> 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 1101 Sep 10 10:58 >> 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 >> 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3590 Sep 7 18:39 >> a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep 7 21:08 >> a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 897 Sep 7 18:35 >> a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 9210 Sep 10 11:01 >> a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 8917 Sep 10 13:21 >> ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 4811 Sep 7 18:35 >> d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3309 Sep 10 11:02 >> d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 >> e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep 7 17:42 >> fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php >> >> thanks again! >> Julie >> >> On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: >>> Hi Ioannis,? >>> Thanks for your question.? >>> Given that the URL field is not updating, I suspect it's a database >>> back-end issue.? >>> Can you verify -- Has your mysql user lorismysql? been granted the >> "INSERT" >>> privilege for the right database? If not, that would result in an >> error >>> like the kind you are seeing.? >>> Also, if you wish to check your LORIS Configuration settings in the >>> backend database such as the URL field -- to see what was actually >> stored >>> in a given database field and should display in the Config >> module:? >>> You can run the queries listed in the "Troubleshooting >> Configuration >>> settings" section of our Github-wiki Setup Guide (under Project >>> Customization) :? >>> >> [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> Lastly, this question is perfectly appropriate for the loris-dev >> community >>> support listserv -- please [2]subscribe here and then email our >> technical >>> team your next question at? [3][5]loris-dev at bic.mni.mcgill.ca >> (after checking >>> any forwarded threads for sensitive info).? >>> We prefer to answer technical questions there for the benefit of >> the >>> community and other first-time users in the same position as >> yourself.? ? >>> Thanks and cheers,? >>> Christine? >>> On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD >>> <[4][6]ioannis at berkeley.edu> wrote: >>> >>> Hi Loris support.? >>> My name is ioannis Pappas, a post-doc at the D'Esposito lab >> stroke group >>> at UC Berkeley. With the kind of help of our sys admin? Julie >> (cc'ed) we >>> have set up our loris database in our cluster (she is the sudo >> user and >>> I am the admin user). >>> If you allow me, I would like to ask you about the first >> configuration >>> steps in the front end as they are described in the tutorial. We >> can >>> login to [5][7]http://loris and the front end normally. >>> However any update that I am trying to? perform in >> Admin->Configuration >>> doesn't work (e.g. updating the study name). It just refreshes >> the same >>> page. I am just wondering if there is an issue with writing in >> the >>> configuration file. >>> Here are the permissions setup for where Loris is installed. >>> chmod 777 /var/www/loris/smarty/templates_c >>> cd /srv/www/loris >>> chown -R lorisadmin:lorisadmin . >>> chmod -c -R a+r . >>> ? ? this command gives everyone read access, and outputs what >> changes >>> were made: >>> ? ? mode of ??./project?? changed from 0770 (rwxrwx---) to 0774 >>> (rwxrwxr--) >>> ? ? mode of ??./tools/logs?? changed from 0770 (rwxrwx---) to >> 0774 >>> (rwxrwxr--) >>> find . -type d -exec chmod a+x -c {} \; >>> ? ? this command gives everyone permission to open a directory, >> and >>> outputs what changes were made: >>> ? ? mode of ??./project?? changed from 0774 (rwxrwxr--) to 0775 >>> (rwxrwxr-x) >>> ? ? mode of ??./tools/logs?? changed from 0774 (rwxrwxr--) to >> 0775 >>> (rwxrwxr-x) >>> Hopefully? you can help me with this. I also subscribed to the >> mailing >>> list but I am not sure if this too much of a basic question for >> the >>> list. >>> Best wishes, >>> Ioannis >>> On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI Computing >> Support >>> <[6][8]support-cirl at berkeley.edu> wrote: >>> >>> Hi ioannis, maybe it's best to ask the developers? You can cc >> me if >>> you'd like. >>> On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas >> <[7][9]ioannis at berkeley.edu> >>> wrote: >>> >>> That did the trick Julie. Thank you! >>> >>> I am still trying to understand how configuration works >> though. For >>> example if I just try to change the name of the >>> study from the front end, I get nowhere (it just refreshes >> the same >>> page). >>> >>> I am not sure if this requires write permissions somewhere in >> a >>> config file/folder and that???s why it doesn???t update it. >>> >>> Best wishes, >>> Ioannis >>> >>> > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI Computing >>> Support <[8][10]support-cirl at berkeley.edu> wrote: >>> > >>> > just in case you're interested, these are the permission >> changes I >>> made: >>> > >>> > chmod 777 /var/www/loris/smarty/templates_c >>> > cd /srv/www/loris >>> > chown -R lorisadmin:lorisadmin . >>> > chmod -c -R a+r . >>> >? ? this command gives everyone read access, and outputs >> what >>> changes were made: >>> >? ? mode of ??./project?? changed from 0770 (rwxrwx---) to >> 0774 >>> (rwxrwxr--) >>> >? ? mode of ??./tools/logs?? changed from 0770 (rwxrwx---) >> to 0774 >>> (rwxrwxr--) >>> > find . -type d -exec chmod a+x -c {} \; >>> >? ? this command gives everyone permission to open a >> directory, and >>> outputs what changes were made: >>> >? ? mode of ??./project?? changed from 0774 (rwxrwxr--) to >> 0775 >>> (rwxrwxr-x) >>> >? ? mode of ??./tools/logs?? changed from 0774 (rwxrwxr--) >> to 0775 >>> (rwxrwxr-x) >>> > >>> > >>> > >>> > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: >>> >> Hi Julie. >>> >> I just tried and I still don???t get anything. I also >> tried >>> private mode in Firefox in case the empty page was cached. >>> >> Sorry for this. >>> >> >>> >> Best wishes, >>> >> Ioannis >>> >> >>> >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, HWNI >> Computing >>> Support <[9][11]support-cirl at berkeley.edu> wrote: >>> >>> >>> >>> hi Ioannis, >>> >>> no worries, I changed the following directory to 777: >>> >>> >>> >>> /var/www/loris/smarty/templates_c >>> >>> >>> >>> will you please check if that works? >>> >>> >>> >>> thanks! >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas PhD wrote: >>> >>>>? Hi Julie. >>> >>>>? Apologies for bugging you with this again. We tried >> now to >>> >>>>? access?? [1][10][12]http://loris?? >>> >>>>? and we are getting a?? blank page. I think the reason >> for this >>> is that we >>> >>>>? don't have read?? permissions to read from the >> template located >>> in >>> >>>>? /var/www/loris/smarty See here bottom of the >>> >>>>? page?? >>> >> [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> >>>>? I think, in general, I am a little bit confused as to >> what the >>> permissions >>> >>>>? should be for us that are not sudos. My understanding >> is that >>> if we don't >>> >>>>? have read or write permissions then we can't access or >> write >>> to >>> >>>>? /var/www/loris, meaning that we can't access or >> configure. >>> Should >>> >>>>? everything be chmod 777 for example??? >>> >>>>? Thank you very much once again. >>> >>>>? Best wishes, >>> >>>>? Ioannis >>> >>>>? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis Pappas PhD >>> >>>>? <[3][12][14]ioannis at berkeley.edu> wrote: >>> >>>> >>> >>>>? ? Thank you very much Julie. I appreciate this and I >> will dig >>> into Loris >>> >>>>? ? given your changes. Thank you so much for your >> help. >>> >>>>? ? Best wishes, >>> >>>>? ? Ioannis >>> >>>>? ? On Thu, Oct 31, 2019 at 12:48 PM Julie Ashworth, >> HWNI >>> Computing Support >>> >>>>? ? <[4][13][15]support-cirl at berkeley.edu> wrote: >>> >>>> >>> >>>>? ? ? hi Ioannis, >>> >>>> >>> >>>>? ? ? 1. I changed the permissions of /srv/www/loris >> to be owned >>> by >>> >>>>? ? ? lorisadmin. I reivewed my installation notes, >> and I did >>> this already >>> >>>>? ? ? when >>> >>>>? ? ? I installed the server. I'm not sure why they >> changed, so >>> it's >>> >>>>? ? ? probably a >>> >>>>? ? ? good idea to keep an eye on that. >>> >>>> >>> >>>>? ? ? 2. When I installed the loris software, I also >> installed a >>> mysql >>> >>>>? ? ? database as recommended in the instructions: >>> >>>> >>> >>>>? ? ? projectname: LORIS >>> >>>>? ? ? databasename: loris_database >>> >>>>? ? ? mysqluser: lorismysql >>> >>>>? ? ? frontend: lorisweb >>> >>>> >>> >>>>? ? ? 3. A couple of weeks ago, I moved Henrik's home >> directory >>> to >>> >>>>? ? ? /home/despoA, >>> >>>>? ? ? but I forgot to update loris. This is done now. >>> >>>> >>> >>>>? ? ? best, >>> >>>>? ? ? Julie >>> >>>> >>> >>>>? ? ? On 31-10-2019 11.15 -0700, Dr. Ioannis Pappas >> PhD wrote: >>> >>>>> ??? ??? Hi Julie. >>> >>>>> ??? ??? I hope you are well. We are trying to >> configure loris >>> that you >>> >>>>? ? ? kindly set >>> >>>>> ??? ??? up for us. >>> >>>>> ??? ??? I have a couple of questions for you if you >> allow me >>> so.?? >>> >>>>> ??? ??? 1) First, although we are logging into the >> front end >>> with admin >>> >>>>? ? ? username >>> >>>>> ??? ??? (lorisweb) and password, it seems that any >> kind of >>> update of >>> >>>>? ? ? configuration >>> >>>>> ??? ??? we are trying to do fails (meaning that if >> we, say, >>> change the >>> >>>>? ? ? name of the >>> >>>>> ??? ??? study and press "submit", this doesn't do >> anything-it >>> doesn't >>> >>>>? ? ? update). >>> >>>>> ??? ??? It's almost like our lorisweb user doesn't >> have write >>> privileges >>> >>>>? ? ? in the >>> >>>>> ??? ??? /var/www/loris/project (where I think every >>> configuration should >>> >>>>? ? ? be). >>> >>>>> ??? ??? This generalizes for everything that we are >> trying to do >>> in the >>> >>>>? ? ? front end. >>> >>>>> ??? ??? Clicking any instrument/tab in the front end >> doesn't >>> really point >>> >>>>? ? ? to >>> >>>>> ??? ??? anything.?? >>> >>>>> ??? ??? 2) Loris suggest doing configurations via >> SQL. Is it >>> possible to >>> >>>>? ? ? run SQL >>> >>>>> ??? ??? scripts in the backend >>> >>>>> ??? ??? 3) For some reason typing ssh lors for Henrik >> doesn't >>> directly >>> >>>>? ? ? take him to >>> >>>>> ??? ??? loris (it requires a password that is not the >> password >>> setup for >>> >>>>? ? ? the >>> >>>>> ??? ??? lorisweb user). Will you be able to fix this >> via your >>> sudo >>> >>>>? ? ? privileges? >>> >>>>> ??? ??? Thank you very much in advance for all your >> help Julie. >>> Let us >>> >>>>? ? ? know if >>> >>>>> ??? ??? this is something that shouldn't be directed >> to you (but >>> instead >>> >>>>? ? ? to the >>> >>>>> ??? ??? loris people).?? >>> >>>>> ??? ??? Best wishes, >>> >>>>> ??? ??? Ioannis >>> >>>>> ??? ??? On Mon, Sep 9, 2019 at 6:25 PM Julie >> Ashworth, HWNI >>> Computing >>> >>>>? ? ? Support >>> >>>>> ??? ??? <[1][5][14][16]support-cirl at berkeley.edu> >> wrote: >>> >>>>> >>> >>>>> ??? ??? ??? hi Henrik and Ioannis, >>> >>>>> ??? ??? ??? the loris server is available for you to >> use. >>> >>>>> >>> >>>>> ??? ??? ??? The servername is 'loris'. I created a >> directory >>> called >>> >>>>? ? ? /data/loris for >>> >>>>> ??? ??? ??? you to store data. You may create new >> folders in >>> /data/loris to >>> >>>>? ? ? organize >>> >>>>> ??? ??? ??? your data. >>> >>>>> >>> >>>>> ??? ??? ??? 1) secure shell or secure copy: >>> >>>>> ??? ??? ??? You can log in with the 'ssh' or 'scp' >> command from >>> your remote >>> >>>>? ? ? desktop >>> >>>>> ??? ??? ??? session. You don't need to authenticate >> to log in. >>> Maybe you'll >>> >>>>? ? ? use scp >>> >>>>> ??? ??? ??? to transfer data between your cluster >> account and the >>> loris >>> >>>>? ? ? server? >>> >>>>> ??? ??? ??? Please put the data in /data/loris, so I >> can make >>> backups more >>> >>>>? ? ? easily. >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? secure shell: >>> >>>>> ??? ??? ??? ??? ??? $ ssh loris >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? secure copy (change the names >> in brackets). Let >>> me know if >>> >>>>? ? ? I can >>> >>>>> ??? ??? ??? ??? ??? help with syntax: >>> >>>>> ??? ??? ??? ??? ??? $ scp -r >> loris:/data/loris/ >>> >>>>> >>> >>>>> ??? ??? ??? 2) front-end web interface.??? Open a >> web browser in >>> your remote >>> >>>>? ? ? desktop >>> >>>>> ??? ??? ??? session and enter the hostname: >>> >>>>> ??? ??? ??? [2][6][15][17]http://loris >>> >>>>> ??? ??? ??? I created an admin user called >> 'lorisweb'. I put the >>> password >>> >>>>? ? ? in >>> >>>>> ??? ??? ??? $HOME/newuser on the cluster. To see it, >> open a >>> terminal, and >>> >>>>? ? ? run: >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? $ cat $HOME/newuser >>> >>>>> >>> >>>>> ??? ??? ??? If other people need shell access to the >> webserver, >>> please let >>> >>>>? ? ? me know >>> >>>>> ??? ??? ??? so I can create a home directory for >> them. >>> >>>>> >>> >>>>> ??? ??? ??? We should eventually discuss backups. >>> >>>>> >>> >>>>> ??? ??? ??? best, >>> >>>>> ??? ??? ??? Julie >>> >>>>> >>> >>>>> References >>> >>>>> >>> >>>>> ??? ??? Visible links >>> >>>>> ??? ??? 1. >> mailto:[7][16][18]support-cirl at berkeley.edu >>> >>>>> ??? ??? 2. [8][17][19]http://loris/ >>> >>>>? ? ? ---end quoted text--- >>> >>>> >>> >>>> References >>> >>>> >>> >>>>? Visible links >>> >>>>? 1. [18][20]http://loris/ >>> >>>>? 2. >>> >> [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> >>>>? 3. mailto:[20][22]ioannis at berkeley.edu >>> >>>>? 4. mailto:[21][23]support-cirl at berkeley.edu >>> >>>>? 5. mailto:[22][24]support-cirl at berkeley.edu >>> >>>>? 6. [23][25]http://loris/ >>> >>>>? 7. mailto:[24][26]support-cirl at berkeley.edu >>> >>>>? 8. [25][27]http://loris/ >>> >>> ---end quoted text--- >>> >> >>> > ---end quoted text--- >>> >>> -- >>> [26][28]christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> References >>> >>> Visible links >>> 1. >> [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> 2. [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> 3. mailto:[31]loris-dev at bic.mni.mcgill.ca >>> 4. mailto:[32]ioannis at berkeley.edu >>> 5. [33]http://loris/ >>> 6. mailto:[34]support-cirl at berkeley.edu >>> 7. mailto:[35]ioannis at berkeley.edu >>> 8. mailto:[36]support-cirl at berkeley.edu >>> 9. mailto:[37]support-cirl at berkeley.edu >>> 10. [38]http://xn--loris-7qa/ >>> 11. [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> 12. mailto:[40]ioannis at berkeley.edu >>> 13. mailto:[41]support-cirl at berkeley.edu >>> 14. mailto:[42]support-cirl at berkeley.edu >>> 15. [43]http://loris/ >>> 16. mailto:[44]support-cirl at berkeley.edu >>> 17. [45]http://loris/ >>> 18. [46]http://loris/ >>> 19. [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> 20. mailto:[48]ioannis at berkeley.edu >>> 21. mailto:[49]support-cirl at berkeley.edu >>> 22. mailto:[50]support-cirl at berkeley.edu >>> 23. [51]http://loris/ >>> 24. mailto:[52]support-cirl at berkeley.edu >>> 25. [53]http://loris/ >>> 26. mailto:[54]christine.rogers at mcgill.ca >> ---end quoted text--- >> >> -- >> [55]christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> References >> >> Visible links >> 1. mailto:loris-dev at bic.mni.mcgill.ca >> 2. mailto:support-cirl at berkeley.edu >> 3. http://loris.priv/ >> 4. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >> 5. mailto:loris-dev at bic.mni.mcgill.ca >> 6. mailto:ioannis at berkeley.edu >> 7. http://loris/ >> 8. mailto:support-cirl at berkeley.edu >> 9. mailto:ioannis at berkeley.edu >> 10. mailto:support-cirl at berkeley.edu >> 11. mailto:support-cirl at berkeley.edu >> 12. http://xn--loris-era/ >> 13. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 14. mailto:ioannis at berkeley.edu >> 15. mailto:support-cirl at berkeley.edu >> 16. mailto:support-cirl at berkeley.edu >> 17. http://loris/ >> 18. mailto:support-cirl at berkeley.edu >> 19. http://loris/ >> 20. http://loris/ >> 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 22. mailto:ioannis at berkeley.edu >> 23. mailto:support-cirl at berkeley.edu >> 24. mailto:support-cirl at berkeley.edu >> 25. http://loris/ >> 26. mailto:support-cirl at berkeley.edu >> 27. http://loris/ >> 28. mailto:christine.rogers at mcgill.ca >> 29. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >> 30. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> 31. mailto:loris-dev at bic.mni.mcgill.ca >> 32. mailto:ioannis at berkeley.edu >> 33. http://loris/ >> 34. mailto:support-cirl at berkeley.edu >> 35. mailto:ioannis at berkeley.edu >> 36. mailto:support-cirl at berkeley.edu >> 37. mailto:support-cirl at berkeley.edu >> 38. http://xn--loris-7qa/ >> 39. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 40. mailto:ioannis at berkeley.edu >> 41. mailto:support-cirl at berkeley.edu >> 42. mailto:support-cirl at berkeley.edu >> 43. http://loris/ >> 44. mailto:support-cirl at berkeley.edu >> 45. http://loris/ >> 46. http://loris/ >> 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 48. mailto:ioannis at berkeley.edu >> 49. mailto:support-cirl at berkeley.edu >> 50. mailto:support-cirl at berkeley.edu >> 51. http://loris/ >> 52. mailto:support-cirl at berkeley.edu >> 53. http://loris/ >> 54. mailto:christine.rogers at mcgill.ca >> 55. mailto:christine.rogers at mcgill.ca > ---end quoted text--- _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ProjectName.png Type: image/png Size: 41529 bytes Desc: ProjectName.png URL: From ioannis at berkeley.edu Fri Nov 8 17:31:23 2019 From: ioannis at berkeley.edu (Ioannis Pappas) Date: Fri, 8 Nov 2019 14:31:23 -0800 Subject: [Loris-dev] loris server In-Reply-To: References: <20191104195851.GA4052@gaia.neuro.berkeley.edu> <20191104200859.GB27438@nx6.priv> <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu> Message-ID: <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> Hi Melanie. Thank you for taking the time to reply to this. I took some to consider your comments. Unfortunately as I said to Christine we are unable to do any kind of updating to the database (either that is changing the name or changing the small html description, etc.). Based on some more digging and on some of Christine's comments I have a feeling that our lorisweb front-end, admin user cannot write anything to the database. Along these lines could it be the case the lorismysql user (the database, admin user with INSERT, UPDATE, etc privileges) is not ?talking? to the lorisweb front end user? What is the difference between the two and could it be a installation problem for them not talking to each other? As Julie said, lorismysql user is working normally with MariaDB. Thank you again for your help. Best wishes, Ioannis > On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs wrote: > > Hello, > > Changing the project name in the configuration page (https://loris.url/configuration/ ) of LORIS, only change the title of the project. To see this change, you have to log out of LORIS and then go back to the login page (https://.loris.url/ ). This is the only place you can find the project name (except from the configuration page). See ProjectName.png > > As for files permission, I would suggest a few change to improve security of you server. Some extra permissions where granted to help you but are not needed. > /srv/www/loris/smarty/templates_c/ should have ownership of lorisadmin:httpd and permission 770 (or 775) > srv/www/loris/project/ should have ownership lorisadmin:httpd and permission 770 (775) > All other files under loris should have lorisadmin:lorisadmin 755 > Reading through this change of mail, I understand that you let Apache store file in /srv/www/loris > | 31 | DownloadPath | Downloads | /srv/www/loris/ | Where > >> files are downloaded > Downloaded files should not be in the same tree as LORIS code. It should be in a separate structure where Apache will not try and do not have permission (in httpd.conf) to execute files. > > Kind regards, > > M?lanie Legault | Software developer | Faculty of Medicine | McGill University > 3801 University, Montr?al, QC H3A 2B4 > > From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Ioannis Pappas > Sent: November 7, 2019 0:18 > To: loris-dev at bic.mni.mcgill.ca > Cc: Julie Ashworth, HWNI Computing Support ; Christine Rogers, Ms. > Subject: Re: [Loris-dev] loris server > > Hi Christine and Julie. > > Yes it looks like that any attempt to configure something in the front-end results in the same page. I am sending this to the list (as you requested Christine) alongside the troubleshooting and discussion so far with Julie. > > Best wishes, > Ioannis > > > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing Support wrote: > > > > hi Christine and Ioannis, > > Ioannis, can you follow-up with Christine about using the front-end? > > > > We're using CentOS7.7 and loris-21.0.1. > > > > I confirmed that I could login as the mysql user (lorismyqsl) and change the 'url' config setting from 'http://loris.priv ' to 'http://localhost ', and back again. > > > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > | ConfigID | Name | Label | Value | Description | > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > | 44 | host | Host | loris.priv | Host | > > | 45 | url | Main LORIS URL | http://loris.priv | Main URL where LORIS can be accessed | > > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > > > MariaDB [loris_database]> UPDATE Config SET Value='http://localhost ' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > > Rows matched: 1 Changed: 1 Warnings: 0 > > > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > | ConfigID | Name | Label | Value | Description | > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > | 44 | host | Host | loris.priv | Host | > > | 45 | url | Main LORIS URL | http://localhost | Main URL where LORIS can be accessed | > > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > 3 rows in set (0.00 sec) > > > > best, > > Julie > > > > > > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: > >> Hi Julie, > >> Forgive my ambiguity - We run the community support listserv for > >> developers, project administrators and sysadmins setting up LORIS, so that > >> these users can contact our technical team for exactly such technical > >> help. > >> If it's ok with you, I'd encourage you subscribe to the listserv and > >> contact our technical team that way for the same reason. > >> (Note that front-end users of LORIS typically contact their project team > >> for support, rather than us.) > >> Given that your lorismysql user privileges seem appropriate ('UPDATE" is > >> there, I mistyped 'INSERT" before) > >> -- is there any other indication why the database record is not > >> updating? > >> In the front-end, can your 'admin' user effect any changes in (any) Config > >> setting? > >> In the back-end, when you tried updating a field using your > >> lorismysql credential, what happened? > >> Your front end is loading ok, and you can log in there, if I understood > >> correctly. > >> Thanks for letting us know these details at > >> [1]loris-dev at bic.mni.mcgill.ca > >> Please also include what version of LORIS you are installing, and on what > >> OS version. > >> Best, > >> Christine > >> On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI Computing Support > >> <[2]support-cirl at berkeley.edu> wrote: > >> > >> Thank you Christine, > >> I'm the linux sysadmin who installed the loris database for Ioannis. > >> I'm not a loris user, however, so that makes it a little awkward for > >> troubleshooting via the mailing list. I'm happy to help in whatever way > >> I can. > >> > >> Regarding the database permissions, I ran: > >> > >> MariaDB [(none)]> show grants for 'lorismysql'@'%'; > >> +--------------------------------------------------------------------------------+ > >> | Grants for lorismysql@% > >> | > >> +--------------------------------------------------------------------------------+ > >> | GRANT USAGE ON *.* TO 'lorismysql'@'%' > >> | > >> | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO > >> 'lorismysql'@'%' | > >> +--------------------------------------------------------------------------------+ > >> 2 rows in set (0.00 sec) > >> > >> looking at the 'tips' section in the page you referred to... > >> > >> | 29 | base | Base | /srv/www/loris/ | The base > >> filesystem path where LORIS is installed | > >> | 31 | DownloadPath | Downloads | /srv/www/loris/ | Where > >> files are downloaded > >> > >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> | ConfigID | Name | Label | Value | > >> Description | > >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> | 44 | host | Host | loris.priv | > >> Host | > >> | 45 | url | Main LORIS URL | > >> [3]http://loris.priv | Main URL where LORIS can be accessed | > >> | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | > >> The *new* bug/issue tracker url | > >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> > >> apache config: > >> > >> Listen 80 > >> User apache > >> Group apache > >> DocumentRoot "/srv/www/loris/htdocs" > >> > >> > >> AllowOverride none > >> Require all denied > >> > >> > >> > >> AllowOverride All > >> Options Indexes FollowSymLinks > >> Require all granted > >> > >> > >> > >> Options Indexes FollowSymLinks > >> AllowOverride All > >> Require all granted > >> > >> > >> file permissions: > >> > >> # ls -ld /srv/www/loris/smarty/templates_c > >> drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 > >> /srv/www/loris/smarty/templates_c/ > >> > >> [root at loris loris]# ls -l /srv/www/loris/smarty/templates_c > >> -rw-r--r-- 1 lorisadmin lorisadmin 2444 Oct 31 09:46 > >> 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 > >> 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep 7 18:39 > >> 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3296 Sep 7 18:35 > >> 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 5901 Sep 7 21:10 > >> 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep 7 18:39 > >> 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 874 Sep 10 11:01 > >> 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 1101 Sep 10 10:58 > >> 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 > >> 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3590 Sep 7 18:39 > >> a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep 7 21:08 > >> a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 897 Sep 7 18:35 > >> a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 9210 Sep 10 11:01 > >> a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 8917 Sep 10 13:21 > >> ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 4811 Sep 7 18:35 > >> d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3309 Sep 10 11:02 > >> d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 > >> e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep 7 17:42 > >> fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php > >> > >> thanks again! > >> Julie > >> > >> On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: > >>> Hi Ioannis,? > >>> Thanks for your question.? > >>> Given that the URL field is not updating, I suspect it's a database > >>> back-end issue.? > >>> Can you verify -- Has your mysql user lorismysql? been granted the > >> "INSERT" > >>> privilege for the right database? If not, that would result in an > >> error > >>> like the kind you are seeing.? > >>> Also, if you wish to check your LORIS Configuration settings in the > >>> backend database such as the URL field -- to see what was actually > >> stored > >>> in a given database field and should display in the Config > >> module:? > >>> You can run the queries listed in the "Troubleshooting > >> Configuration > >>> settings" section of our Github-wiki Setup Guide (under Project > >>> Customization) :? > >>> > >> [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >>> Lastly, this question is perfectly appropriate for the loris-dev > >> community > >>> support listserv -- please [2]subscribe here and then email our > >> technical > >>> team your next question at? [3][5]loris-dev at bic.mni.mcgill.ca > >> (after checking > >>> any forwarded threads for sensitive info).? > >>> We prefer to answer technical questions there for the benefit of > >> the > >>> community and other first-time users in the same position as > >> yourself.? ? > >>> Thanks and cheers,? > >>> Christine? > >>> On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD > >>> <[4][6]ioannis at berkeley.edu> wrote: > >>> > >>> Hi Loris support.? > >>> My name is ioannis Pappas, a post-doc at the D'Esposito lab > >> stroke group > >>> at UC Berkeley. With the kind of help of our sys admin? Julie > >> (cc'ed) we > >>> have set up our loris database in our cluster (she is the sudo > >> user and > >>> I am the admin user). > >>> If you allow me, I would like to ask you about the first > >> configuration > >>> steps in the front end as they are described in the tutorial. We > >> can > >>> login to [5][7]http://loris and the front end normally. > >>> However any update that I am trying to? perform in > >> Admin->Configuration > >>> doesn't work (e.g. updating the study name). It just refreshes > >> the same > >>> page. I am just wondering if there is an issue with writing in > >> the > >>> configuration file. > >>> Here are the permissions setup for where Loris is installed. > >>> chmod 777 /var/www/loris/smarty/templates_c > >>> cd /srv/www/loris > >>> chown -R lorisadmin:lorisadmin . > >>> chmod -c -R a+r . > >>> ? ? this command gives everyone read access, and outputs what > >> changes > >>> were made: > >>> ? ? mode of ??./project?? changed from 0770 (rwxrwx---) to 0774 > >>> (rwxrwxr--) > >>> ? ? mode of ??./tools/logs?? changed from 0770 (rwxrwx---) to > >> 0774 > >>> (rwxrwxr--) > >>> find . -type d -exec chmod a+x -c {} \; > >>> ? ? this command gives everyone permission to open a directory, > >> and > >>> outputs what changes were made: > >>> ? ? mode of ??./project?? changed from 0774 (rwxrwxr--) to 0775 > >>> (rwxrwxr-x) > >>> ? ? mode of ??./tools/logs?? changed from 0774 (rwxrwxr--) to > >> 0775 > >>> (rwxrwxr-x) > >>> Hopefully? you can help me with this. I also subscribed to the > >> mailing > >>> list but I am not sure if this too much of a basic question for > >> the > >>> list. > >>> Best wishes, > >>> Ioannis > >>> On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI Computing > >> Support > >>> <[6][8]support-cirl at berkeley.edu> wrote: > >>> > >>> Hi ioannis, maybe it's best to ask the developers? You can cc > >> me if > >>> you'd like. > >>> On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas > >> <[7][9]ioannis at berkeley.edu> > >>> wrote: > >>> > >>> That did the trick Julie. Thank you! > >>> > >>> I am still trying to understand how configuration works > >> though. For > >>> example if I just try to change the name of the > >>> study from the front end, I get nowhere (it just refreshes > >> the same > >>> page). > >>> > >>> I am not sure if this requires write permissions somewhere in > >> a > >>> config file/folder and that???s why it doesn???t update it. > >>> > >>> Best wishes, > >>> Ioannis > >>> > >>> > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI Computing > >>> Support <[8][10]support-cirl at berkeley.edu> wrote: > >>> > > >>> > just in case you're interested, these are the permission > >> changes I > >>> made: > >>> > > >>> > chmod 777 /var/www/loris/smarty/templates_c > >>> > cd /srv/www/loris > >>> > chown -R lorisadmin:lorisadmin . > >>> > chmod -c -R a+r . > >>> >? ? this command gives everyone read access, and outputs > >> what > >>> changes were made: > >>> >? ? mode of ??./project?? changed from 0770 (rwxrwx---) to > >> 0774 > >>> (rwxrwxr--) > >>> >? ? mode of ??./tools/logs?? changed from 0770 (rwxrwx---) > >> to 0774 > >>> (rwxrwxr--) > >>> > find . -type d -exec chmod a+x -c {} \; > >>> >? ? this command gives everyone permission to open a > >> directory, and > >>> outputs what changes were made: > >>> >? ? mode of ??./project?? changed from 0774 (rwxrwxr--) to > >> 0775 > >>> (rwxrwxr-x) > >>> >? ? mode of ??./tools/logs?? changed from 0774 (rwxrwxr--) > >> to 0775 > >>> (rwxrwxr-x) > >>> > > >>> > > >>> > > >>> > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: > >>> >> Hi Julie. > >>> >> I just tried and I still don???t get anything. I also > >> tried > >>> private mode in Firefox in case the empty page was cached. > >>> >> Sorry for this. > >>> >> > >>> >> Best wishes, > >>> >> Ioannis > >>> >> > >>> >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, HWNI > >> Computing > >>> Support <[9][11]support-cirl at berkeley.edu> wrote: > >>> >>> > >>> >>> hi Ioannis, > >>> >>> no worries, I changed the following directory to 777: > >>> >>> > >>> >>> /var/www/loris/smarty/templates_c > >>> >>> > >>> >>> will you please check if that works? > >>> >>> > >>> >>> thanks! > >>> >>> > >>> >>> > >>> >>> > >>> >>> > >>> >>> > >>> >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas PhD wrote: > >>> >>>>? Hi Julie. > >>> >>>>? Apologies for bugging you with this again. We tried > >> now to > >>> >>>>? access?? [1][10][12]http://loris?? > >>> >>>>? and we are getting a?? blank page. I think the reason > >> for this > >>> is that we > >>> >>>>? don't have read?? permissions to read from the > >> template located > >>> in > >>> >>>>? /var/www/loris/smarty See here bottom of the > >>> >>>>? page?? > >>> > >> [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> >>>>? I think, in general, I am a little bit confused as to > >> what the > >>> permissions > >>> >>>>? should be for us that are not sudos. My understanding > >> is that > >>> if we don't > >>> >>>>? have read or write permissions then we can't access or > >> write > >>> to > >>> >>>>? /var/www/loris, meaning that we can't access or > >> configure. > >>> Should > >>> >>>>? everything be chmod 777 for example??? > >>> >>>>? Thank you very much once again. > >>> >>>>? Best wishes, > >>> >>>>? Ioannis > >>> >>>>? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis Pappas PhD > >>> >>>>? <[3][12][14]ioannis at berkeley.edu> wrote: > >>> >>>> > >>> >>>>? ? Thank you very much Julie. I appreciate this and I > >> will dig > >>> into Loris > >>> >>>>? ? given your changes. Thank you so much for your > >> help. > >>> >>>>? ? Best wishes, > >>> >>>>? ? Ioannis > >>> >>>>? ? On Thu, Oct 31, 2019 at 12:48 PM Julie Ashworth, > >> HWNI > >>> Computing Support > >>> >>>>? ? <[4][13][15]support-cirl at berkeley.edu> wrote: > >>> >>>> > >>> >>>>? ? ? hi Ioannis, > >>> >>>> > >>> >>>>? ? ? 1. I changed the permissions of /srv/www/loris > >> to be owned > >>> by > >>> >>>>? ? ? lorisadmin. I reivewed my installation notes, > >> and I did > >>> this already > >>> >>>>? ? ? when > >>> >>>>? ? ? I installed the server. I'm not sure why they > >> changed, so > >>> it's > >>> >>>>? ? ? probably a > >>> >>>>? ? ? good idea to keep an eye on that. > >>> >>>> > >>> >>>>? ? ? 2. When I installed the loris software, I also > >> installed a > >>> mysql > >>> >>>>? ? ? database as recommended in the instructions: > >>> >>>> > >>> >>>>? ? ? projectname: LORIS > >>> >>>>? ? ? databasename: loris_database > >>> >>>>? ? ? mysqluser: lorismysql > >>> >>>>? ? ? frontend: lorisweb > >>> >>>> > >>> >>>>? ? ? 3. A couple of weeks ago, I moved Henrik's home > >> directory > >>> to > >>> >>>>? ? ? /home/despoA, > >>> >>>>? ? ? but I forgot to update loris. This is done now. > >>> >>>> > >>> >>>>? ? ? best, > >>> >>>>? ? ? Julie > >>> >>>> > >>> >>>>? ? ? On 31-10-2019 11.15 -0700, Dr. Ioannis Pappas > >> PhD wrote: > >>> >>>>> ??? ??? Hi Julie. > >>> >>>>> ??? ??? I hope you are well. We are trying to > >> configure loris > >>> that you > >>> >>>>? ? ? kindly set > >>> >>>>> ??? ??? up for us. > >>> >>>>> ??? ??? I have a couple of questions for you if you > >> allow me > >>> so.?? > >>> >>>>> ??? ??? 1) First, although we are logging into the > >> front end > >>> with admin > >>> >>>>? ? ? username > >>> >>>>> ??? ??? (lorisweb) and password, it seems that any > >> kind of > >>> update of > >>> >>>>? ? ? configuration > >>> >>>>> ??? ??? we are trying to do fails (meaning that if > >> we, say, > >>> change the > >>> >>>>? ? ? name of the > >>> >>>>> ??? ??? study and press "submit", this doesn't do > >> anything-it > >>> doesn't > >>> >>>>? ? ? update). > >>> >>>>> ??? ??? It's almost like our lorisweb user doesn't > >> have write > >>> privileges > >>> >>>>? ? ? in the > >>> >>>>> ??? ??? /var/www/loris/project (where I think every > >>> configuration should > >>> >>>>? ? ? be). > >>> >>>>> ??? ??? This generalizes for everything that we are > >> trying to do > >>> in the > >>> >>>>? ? ? front end. > >>> >>>>> ??? ??? Clicking any instrument/tab in the front end > >> doesn't > >>> really point > >>> >>>>? ? ? to > >>> >>>>> ??? ??? anything.?? > >>> >>>>> ??? ??? 2) Loris suggest doing configurations via > >> SQL. Is it > >>> possible to > >>> >>>>? ? ? run SQL > >>> >>>>> ??? ??? scripts in the backend > >>> >>>>> ??? ??? 3) For some reason typing ssh lors for Henrik > >> doesn't > >>> directly > >>> >>>>? ? ? take him to > >>> >>>>> ??? ??? loris (it requires a password that is not the > >> password > >>> setup for > >>> >>>>? ? ? the > >>> >>>>> ??? ??? lorisweb user). Will you be able to fix this > >> via your > >>> sudo > >>> >>>>? ? ? privileges? > >>> >>>>> ??? ??? Thank you very much in advance for all your > >> help Julie. > >>> Let us > >>> >>>>? ? ? know if > >>> >>>>> ??? ??? this is something that shouldn't be directed > >> to you (but > >>> instead > >>> >>>>? ? ? to the > >>> >>>>> ??? ??? loris people).?? > >>> >>>>> ??? ??? Best wishes, > >>> >>>>> ??? ??? Ioannis > >>> >>>>> ??? ??? On Mon, Sep 9, 2019 at 6:25 PM Julie > >> Ashworth, HWNI > >>> Computing > >>> >>>>? ? ? Support > >>> >>>>> ??? ??? <[1][5][14][16]support-cirl at berkeley.edu> > >> wrote: > >>> >>>>> > >>> >>>>> ??? ??? ??? hi Henrik and Ioannis, > >>> >>>>> ??? ??? ??? the loris server is available for you to > >> use. > >>> >>>>> > >>> >>>>> ??? ??? ??? The servername is 'loris'. I created a > >> directory > >>> called > >>> >>>>? ? ? /data/loris for > >>> >>>>> ??? ??? ??? you to store data. You may create new > >> folders in > >>> /data/loris to > >>> >>>>? ? ? organize > >>> >>>>> ??? ??? ??? your data. > >>> >>>>> > >>> >>>>> ??? ??? ??? 1) secure shell or secure copy: > >>> >>>>> ??? ??? ??? You can log in with the 'ssh' or 'scp' > >> command from > >>> your remote > >>> >>>>? ? ? desktop > >>> >>>>> ??? ??? ??? session. You don't need to authenticate > >> to log in. > >>> Maybe you'll > >>> >>>>? ? ? use scp > >>> >>>>> ??? ??? ??? to transfer data between your cluster > >> account and the > >>> loris > >>> >>>>? ? ? server? > >>> >>>>> ??? ??? ??? Please put the data in /data/loris, so I > >> can make > >>> backups more > >>> >>>>? ? ? easily. > >>> >>>>> > >>> >>>>> ??? ??? ??? ??? ??? secure shell: > >>> >>>>> ??? ??? ??? ??? ??? $ ssh loris > >>> >>>>> > >>> >>>>> ??? ??? ??? ??? ??? secure copy (change the names > >> in brackets). Let > >>> me know if > >>> >>>>? ? ? I can > >>> >>>>> ??? ??? ??? ??? ??? help with syntax: > >>> >>>>> ??? ??? ??? ??? ??? $ scp -r > >> loris:/data/loris/ > >>> >>>>> > >>> >>>>> ??? ??? ??? 2) front-end web interface.??? Open a > >> web browser in > >>> your remote > >>> >>>>? ? ? desktop > >>> >>>>> ??? ??? ??? session and enter the hostname: > >>> >>>>> ??? ??? ??? [2][6][15][17]http://loris > >>> >>>>> ??? ??? ??? I created an admin user called > >> 'lorisweb'. I put the > >>> password > >>> >>>>? ? ? in > >>> >>>>> ??? ??? ??? $HOME/newuser on the cluster. To see it, > >> open a > >>> terminal, and > >>> >>>>? ? ? run: > >>> >>>>> > >>> >>>>> ??? ??? ??? ??? ??? $ cat $HOME/newuser > >>> >>>>> > >>> >>>>> ??? ??? ??? If other people need shell access to the > >> webserver, > >>> please let > >>> >>>>? ? ? me know > >>> >>>>> ??? ??? ??? so I can create a home directory for > >> them. > >>> >>>>> > >>> >>>>> ??? ??? ??? We should eventually discuss backups. > >>> >>>>> > >>> >>>>> ??? ??? ??? best, > >>> >>>>> ??? ??? ??? Julie > >>> >>>>> > >>> >>>>> References > >>> >>>>> > >>> >>>>> ??? ??? Visible links > >>> >>>>> ??? ??? 1. > >> mailto:[7][16][18]support-cirl at berkeley.edu > >>> >>>>> ??? ??? 2. [8][17][19]http://loris/ > >>> >>>>? ? ? ---end quoted text--- > >>> >>>> > >>> >>>> References > >>> >>>> > >>> >>>>? Visible links > >>> >>>>? 1. [18][20]http://loris/ > >>> >>>>? 2. > >>> > >> [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> >>>>? 3. mailto:[20][22]ioannis at berkeley.edu > >>> >>>>? 4. mailto:[21][23]support-cirl at berkeley.edu > >>> >>>>? 5. mailto:[22][24]support-cirl at berkeley.edu > >>> >>>>? 6. [23][25]http://loris/ > >>> >>>>? 7. mailto:[24][26]support-cirl at berkeley.edu > >>> >>>>? 8. [25][27]http://loris/ > >>> >>> ---end quoted text--- > >>> >> > >>> > ---end quoted text--- > >>> > >>> -- > >>> [26][28]christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> References > >>> > >>> Visible links > >>> 1. > >> [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >>> 2. [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> 3. mailto:[31]loris-dev at bic.mni.mcgill.ca > >>> 4. mailto:[32]ioannis at berkeley.edu > >>> 5. [33]http://loris/ > >>> 6. mailto:[34]support-cirl at berkeley.edu > >>> 7. mailto:[35]ioannis at berkeley.edu > >>> 8. mailto:[36]support-cirl at berkeley.edu > >>> 9. mailto:[37]support-cirl at berkeley.edu > >>> 10. [38]http://xn--loris-7qa/ > >>> 11. [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> 12. mailto:[40]ioannis at berkeley.edu > >>> 13. mailto:[41]support-cirl at berkeley.edu > >>> 14. mailto:[42]support-cirl at berkeley.edu > >>> 15. [43]http://loris/ > >>> 16. mailto:[44]support-cirl at berkeley.edu > >>> 17. [45]http://loris/ > >>> 18. [46]http://loris/ > >>> 19. [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> 20. mailto:[48]ioannis at berkeley.edu > >>> 21. mailto:[49]support-cirl at berkeley.edu > >>> 22. mailto:[50]support-cirl at berkeley.edu > >>> 23. [51]http://loris/ > >>> 24. mailto:[52]support-cirl at berkeley.edu > >>> 25. [53]http://loris/ > >>> 26. mailto:[54]christine.rogers at mcgill.ca > >> ---end quoted text--- > >> > >> -- > >> [55]christine.rogers at mcgill.ca > >> McGill Centre for Integrative Neuroscience | MCIN.ca > >> Montreal Neurological Institute > >> McGill University | Montreal | Canada > >> > >> References > >> > >> Visible links > >> 1. mailto:loris-dev at bic.mni.mcgill.ca > >> 2. mailto:support-cirl at berkeley.edu > >> 3. http://loris.priv/ > >> 4. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >> 5. mailto:loris-dev at bic.mni.mcgill.ca > >> 6. mailto:ioannis at berkeley.edu > >> 7. http://loris/ > >> 8. mailto:support-cirl at berkeley.edu > >> 9. mailto:ioannis at berkeley.edu > >> 10. mailto:support-cirl at berkeley.edu > >> 11. mailto:support-cirl at berkeley.edu > >> 12. http://xn--loris-era/ > >> 13. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 14. mailto:ioannis at berkeley.edu > >> 15. mailto:support-cirl at berkeley.edu > >> 16. mailto:support-cirl at berkeley.edu > >> 17. http://loris/ > >> 18. mailto:support-cirl at berkeley.edu > >> 19. http://loris/ > >> 20. http://loris/ > >> 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 22. mailto:ioannis at berkeley.edu > >> 23. mailto:support-cirl at berkeley.edu > >> 24. mailto:support-cirl at berkeley.edu > >> 25. http://loris/ > >> 26. mailto:support-cirl at berkeley.edu > >> 27. http://loris/ > >> 28. mailto:christine.rogers at mcgill.ca > >> 29. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >> 30. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >> 31. mailto:loris-dev at bic.mni.mcgill.ca > >> 32. mailto:ioannis at berkeley.edu > >> 33. http://loris/ > >> 34. mailto:support-cirl at berkeley.edu > >> 35. mailto:ioannis at berkeley.edu > >> 36. mailto:support-cirl at berkeley.edu > >> 37. mailto:support-cirl at berkeley.edu > >> 38. http://xn--loris-7qa/ > >> 39. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 40. mailto:ioannis at berkeley.edu > >> 41. mailto:support-cirl at berkeley.edu > >> 42. mailto:support-cirl at berkeley.edu > >> 43. http://loris/ > >> 44. mailto:support-cirl at berkeley.edu > >> 45. http://loris/ > >> 46. http://loris/ > >> 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 48. mailto:ioannis at berkeley.edu > >> 49. mailto:support-cirl at berkeley.edu > >> 50. mailto:support-cirl at berkeley.edu > >> 51. http://loris/ > >> 52. mailto:support-cirl at berkeley.edu > >> 53. http://loris/ > >> 54. mailto:christine.rogers at mcgill.ca > >> 55. mailto:christine.rogers at mcgill.ca > > ---end quoted text--- > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Fri Nov 8 17:38:16 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sat, 9 Nov 2019 00:38:16 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Cecile, We were wondering whether Loris has a tool to check if there are problems with the dcm files, before trying to upload them. Something that could provide the same results provided in the warning_output, this is the summary from the mri_upload at the front-page. Also which attributes of the dcm header would trigger a warning? is there a dcm file header specification for Loris? Thanks Sotirios ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi, > > Yes, by parsing now() into unix_timestamp function it worked,but i thought > that something else was causing the 2nd issue. > Thanks > > On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < > xavier.lecoursboucher at mcgill.ca> wrote: > >> Hi Sotirios, >> >> The first error occurs because the QCFirstChangeTime and columns are of >> type `unsigned integer` and not `datatime`. You should be using >> UNIX_TIMESTAMP() instead of NOW(). >> >> The second error occurs because the trigger triggers a rollback of the >> insert statement in the files table. >> See mysql documentation for trigger error handling. >> >> An error during either a BEFORE or AFTER trigger results in failure of >> the entire statement that caused trigger invocation. >> >> >> Thank you for sharing that. I hope it helps. >> -- Xavier >> >> ------------------------------ >> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >> Nikoloutsopoulos >> *Sent:* October 1, 2019 8:33 AM >> *To:* Cecile Madjar >> *Cc:* loris-dev at bic.mni.mcgill.ca ; >> Christine Rogers, Ms. >> *Subject:* Re: [Loris-dev] Import mri - scripts >> >> When mincs are inserted their corresponding rows at the file table are >> inserted too >> [image: image.png] >> >> i would like to insert their rows at file_qcstatus as well, because i >> don't want manually to label them as passed throught the interface >> >> [image: image.png] >> >> >> That is the trigger i wrote >> >> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER >> INSERT ON `files` FOR EACH ROW >> BEGIN >> INSERT INTO files_qcstatus >> SET FileID = NEW.FileID, >> SeriesUID = NEW.SeriesUID, >> EchoTime = NEW.EchoTime, >> QCStatus = "Pass", >> QCFirstChangeTime = NOW(), >> QCLastChangeTime = NOW(); >> END >> >> although it contains some errors >> >> DBD::mysql::db do failed: Out of range value for column >> 'QCFirstChangeTime' at row 1 at >> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key >> constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) >> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >> >> >> >> >> >> >> >> >> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >> Hi Sotirios, >> >> In the mri_upload table, there is a TarchiveID column associated with the >> MRI upload you inserted. When this value is NULL, it means no DICOMs were >> inserted into the tarchive tables. At the end of the insertion of the >> DICOMs in the tarchive tables, this value is updated with the correct >> TarchiveID associated with the upload. >> >> Could this correspond to what you want to do? >> >> Regarding the files_qcstatus, this table is only linked to the files >> table (hence, the MINC files). You could always create a new table for >> dicom_qcstatus and link it to the tarchive table? >> >> C?cile >> >> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Hi, >> >> i would like whenever a dicom is imported to mark all their coressponding >> qc_status to "pass". I was thinking of creating a trigger for that, but >> which tables do i need to add entries to? So far from what i see i need to >> add entres at the table "files" whenever an insertion happens to >> files_qcstatus. >> >> Thanks >> >> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Oh, sorry i should have asked for StudyID, at the beginning of my email i >> sent 3 hours ago (not StudyUID). >> >> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Hi, >> >> that's the Study Instance UID, not the StudyID. So the StudyID i am >> looking for is not stored in the database? >> >> [image: image.png] >> >> Thanks. >> >> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >> Hi Sotirios, >> >> The StudyUID is stored in the DicomArchiveID field of the tarchive table. >> It can also be found in the metadata field but it is mixed with many other >> information. >> >> Hope this helps, >> >> C?cile >> >> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Hi, >> >> Is StudyUID stored somewhere at the tables? At the tarchive table, >> specifically at the AcquisitonMetadata column i found something called >> 'Unique Study ID" in its context, but that must be the Study Instance UID. >> >> Thanks >> >> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >> Hi Sotirios, >> >> Your observation is correct. A little explanation below. >> >> MINC files get inserted into the MRI violation tables if: >> >> - the scan type could not be identified (not matching an entry in the >> mri_protocol table) >> - one parameter of the scan type is out of the expected range present >> in the mri_protocol_checks (extra filtering in case you need to be stricker >> on some parameters not present in the mri_protocol table) >> - if the CandID and PSCID do not match >> >> The following cases do not get in the MRI violation tables as it happens >> before the conversion of the DICOM to MINC files and only MINC files >> violations are logged there: >> >> - "No single DICOM" (since no valid DICOM could be found to convert >> to MINC) >> - "Study already inserted" (duplicate StudyUID) since this error >> happens at the dicomTar.pl level (way before conversion into MINC files) >> >> Glad everything is working out!! >> Best, >> >> C?cile >> >> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Hi, >> >> the mri passed, for some reason it consumed 5.12GB of ram. Now about the >> mri_violations, dicoms are triggered to be inserted there only if there is >> a violation for Tr_min, Tr_max, in general for its header parameter? >> Because i don't see the cases of 'No single dicom" or with the 2 studyiuid >> to be there. >> >> Thanks >> >> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >> Hi Sotirios, >> >> Sorry to hear you are having issues with the memory. I think most of our >> VMs are set up with 4GB of RAM so with 4GB you should be fine. >> >> Hope this helps! >> >> C?cile >> >> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Hi, >> >> about that dicom that had that insertion error it's about 30mb and when >> it is being processed the ram is being drastically increased from 2gb to >> 3.28 and then the whole virtual machine is frozen. What is the recommended >> size of ram for using Loris? >> >> Thanks >> >> [image: image.png] >> >> >> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >> Hi Sotirios, >> >> Glad to see that the StudyUID problem was fixed! >> >> For the delete script issue, if you are absolutely certain that no >> processes are run for that uploadID, you can update the mri_upload table >> and set the column Inserting to 0 instead of 1 for that uploadID. It >> looks like for some reason the scripts did not update this field when it >> stopped the insertion. Not sure why that would be the case though. >> Note: only do that update if you are certain that there is no processing >> happening. >> >> Hope this helps! >> >> >> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Hi, >> >> about the Dicoms i reported that didn't have a StudyID they actually do >> >> [image: image.png] >> >> >> [image: image.png] >> >> I thought that this might be a permission because "w" was missing at the >> group. After using chmod -R 775 only 102809579 passed, but with no mnic >> files. Also now i have this error >> >> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ >> ./delete_imaging_upload.pl -uploadID 34 -ignore >> Cannot delete upload 34: the MRI pipeline is currently processing it. >> >> How can solve this? >> >> Thanks >> >> >> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Hi, >> >> Here is our auto dicom uploading python script: >> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >> >> To give you a brief idea: >> Per folder it will: >> 1) Delete all the .bak files >> 2) Locate .dcm files and update the Patient header >> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, >> TE_max parameters of T1 protocol and do an update at the mri_protocol table >> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >> For some reason some files are missing SeriesDescription/ProtocolName >> >> In total i have 7 folders >> >> [image: image.png] >> >> 3/7 passed >> >> [image: image.png] >> >> Also about the first patient with DC0000 had a violation "T1 AXIAL SE >> GADO", but my script didn't output a TE of 17 nowhere and i find that weird >> since Loris detects the SeriesDescription. >> [image: image.png] >> >> >> Now about the 4/7 that didn't passed >> >> 102327840 and 102809579 outputs "The target directory does not contain a >> single DICOM file.", therefore they are missing their StudyUID >> >> 102506134 has 2 studyuid "You can't use it with data from multiple >> studies." >> >> and 102761034 "No data could be converted into valid MINC files. >> localizer, scout will not be considered!" What is this? >> >> If i wanted to force the insertion of 102327840, 102809579 and 102506134 >> can i just pass a flag parameter to batch_uploads_imageuploader.pl? or >> modify imaging_upload_file.pl? >> >> Thank you, >> >> Sotirios >> >> PS >> >> To diagnose a folder search the name of the folder at dicom_output.txt. >> >> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios, >> Glad to hear about your progress. >> >> Yes, the script you used to delete imaging data is fully documented here >> >> -- let us know if you didn't find the answers you were looking for there. >> (Is it possible the null row in *mri_scanner* seen in your database >> management software is a visual placeholder for you as the user? I'm not >> sure why a scanner would ever be registered with ID='0' as your screenshot >> showed.) >> >> Best, >> Christine >> >> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> I fixed it with this >> >> [image: image.png] >> >> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Hi, >> >> I tried to create a new candidate using the API, is there something wrong >> with the structure? why did i receive a 500 internal error? In the >> loris-error log it state that there is something wrong with token, but i >> verfied that the type of the token is a string. >> >> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 passed >> to SinglePointLogin::JWTAuthenticate() must be of the type string, null >> given, called in /var/www/loris/php/libraries/SinglePointLogin.class.inc on >> line 169 and defined in >> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >> SinglePointLogin->authenticate()\n#2 >> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >> NDB_Client->initialize('/var/www/loris/...')\n#3 >> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >> Loris\\API\\APIBase->__construct('POST')\n#4 >> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in >> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >> >> [image: image.png] >> >> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Hi, >> >> Is there a way also to delete candidates? Just to let you know what i did >> to clear candidates, because maybe i may have missed dependencies. >> >> First i deleted all their uploads >> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit the >> backup file ? ) >> >> Afterwards i had some scanner candidates, so i deleted all the entries >> from mri_scanner except that i couldn't delete this entry with the 0 ID. >> >> [image: image.png] >> >> >> Lastly i deleted the session and then the candidate table. >> >> Thanks >> >> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios, >> >> We recommend that you use our existing tools for creating new candidates >> - either the LORIS API or if you are using a PHP script, by calling the Candidate >> class's createNew() >> function. >> These will create the necessary records for you. (It's not recommended to >> make direct modifications to mysql database tables in your script, if I >> understand you.) >> >> The CandID should be a randomized 6 digit randomized ID, and there are >> multiple reasons for this. >> You can use the PSCID for project-specific IDs and the External ID field >> in the candidate table can also be used for any values you like. >> Additionally, any number of custom IDs can be added in parallel - these >> are entered/visible in the Candidate Information module and added in the >> back-end as candidate parameters. >> >> Best, >> Christine >> >> >> >> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Hi, >> >> We are building a script that will auto insert the candidates based on >> their ExternalID. We would like to know whethere when we are creating a new >> profile in the candidate table, if we also have to insert a new record at >> another table? Furthermore is there a problem that in our case CandID won't >> be a 6digit? ( should we start it from 100000?) >> >> Thanks >> >> [image: image.png] >> >> >> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >> melanie.legault2 at mcgill.ca> ??????: >> >> That would normally be the case but the numeric part of the PSCID get >> paded with 0 on the left. >> >> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char >> with a min value of 1, the sequence would be: >> >> ABC0001 >> ABC0002 >> ... >> ABC0010 >> ... >> >> thus sorting them ascending will always get the latest value generated as >> the max value. >> >> M?lanie >> >> ------------------------------ >> *From:* Sotirios Nikoloutsopoulos >> *Sent:* September 13, 2019 10:15 >> *To:* Melanie Legault, Mrs >> *Cc:* Christine Rogers, Ms. ; >> loris-dev at bic.mni.mcgill.ca >> *Subject:* Re: [Loris-dev] Import mri - scripts >> >> I see, although the PSCID value is varchar(255), it must be stored within >> a specific length of characters. Otherwise if we were to sort strings with >> different lengths the result would not be sorted correctly ( e.x. 1,2,10,11 >> as strings would result to 1, 10, 11, 2 ). >> >> Thanks >> >> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >> melanie.legault2 at mcgill.ca> ??????: >> >> Hello Sotirios, >> >> There is no `last value` stored anywhere. >> The code simply look for the PSCID with the max value and increase that >> value by 1 in order to generate the next PSCID. >> >> Hope this info help. >> >> M?lanie Legault | Software developer | Faculty of Medicine | McGill >> University >> 3801 University, Montr?al, QC H3A 2B4 >> >> ------------------------------ >> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >> Nikoloutsopoulos >> *Sent:* September 13, 2019 9:43 >> *To:* Christine Rogers, Ms. >> *Cc:* loris-dev at bic.mni.mcgill.ca >> *Subject:* Re: [Loris-dev] Import mri - scripts >> >> Hi, >> >> how does Loris determine the next available PSCID value for a new >> candidate? https://github.com/aces/Loris/wiki/Project-Customization e.x >> in the default case the PSCID is sequential, but where do we store the last >> value for the sequential sequence? >> >> Thanks >> >> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Hi, >> >> the parameters in the mri_protocol you have assigned are global standard? >> or were assigned after trial and error? >> >> Thanks >> >> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios, >> >> Given you have done the initial setup of your tables to match your >> intended protocol/parameters according to instructions -- >> the Troubleshooting guide documentation recommends >> >> re-running the pipeline (and first deleting prior uploads). >> >> Best, >> Christine >> >> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> *if i were to change their status to resolve what would happen? >> >> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> I noticed that i can view the mnics at the brainbrowser from the >> mri_violations page ( those mnics are stored at /data/loris/data/trashbin/ >> if i were to click their issue to resolve what would happend? would they >> appear in the dicom_archive view too? ). >> >> >> >> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Hi, >> >> The defaut values of the schema exists in my local database. If i adjust >> the default values of TR_min and TE_min the mincs will be uploaded? >> >> [image: image.png] >> >> >> [image: image.png] >> >> Thanks >> >> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios, >> >> Is it possible that you haven't set up your mri_protocol table ? (and >> mri_scan_type table too, for additional types of scans) >> >> Like the psc table, this is a pre-requisite for the Imaging insertion >> setup : See the install/setup documentation : >> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >> >> To add new rows, just use MySQL insert statements. You can adapt the >> insert statements which load the default table values --> e.g. Here on >> GitHub : >> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >> (see also the mri_scan_type table) >> >> Best, >> Christine >> >> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> I see that i can edit the values but not how to insert new rows. >> >> [image: image.png] >> >> If i choose Inserted with flag then will the minc be inserted? >> >> [image: image.png] >> >> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios, >> >> Glad to hear that *dcmodify* worked correctly. >> >> For the MRI Violations module, the screenshot is enough. >> >> It says "could not identify scan type", which we knew already. Did you >> click on the link on those words? >> >> It will take you to the next page of the module, showing for each scan >> what the scan parameters were, and will also show for comparison what's >> stored in your *mri_protocol* table. >> Compare these values to find which parameter was not correct according to >> your *mri_protocol* table scan type definitions. >> >> You may end up broadening your mri_protocol value ranges (e.g. TR, TE) >> for scans. >> This can be done in the front-end, by editing the database table directly >> in the same subpage of the MRI Violations module. >> >> The MRI Violations module features are explained in more detail in the >> Help text for this module inside LORIS (click the ["?"] icon in the menu >> bar.) >> >> See also: Loris-MRI troubleshooting guide >> >> : no MINCs inserted- violated scans >> >> Best, >> Christine >> >> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Hi, >> >> looks like my previous email's attachment wasn't delivered due to >> security reasons, i uploaded my file at google drive >> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >> >> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Hi, >> >> From Dicat's view seems that dcmodify worked in both cases >> >> [image: image.png] >> >> [image: image.png] >> >> For the mri_violations i attached the .html output from webbrowser, so >> that you can check the filelds easier. >> >> [image: image.png] >> >> Thanks >> >> >> >> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios -- >> Great, sounds like more progress. >> >> About the dcmodify command -- I'm not sure why you're getting an Endian >> warning. (it's a warning not an error, correct?) >> To clarify -- Were the DICOM headers (PatientName) all successfully >> relabelled, after the command ran? >> >> You can use also our DICAT tool (https://github.com/aces/DICAT) to >> verify and/or update local DICOM headers -- though your dcmodify command is >> a great and fast solution for bulk header updates. >> >> If you're concerned about fields being changed (e.g. "(2001,105f)" from >> the warning message) - you can also dcmdump a DICOM slice before and look >> at these fields specifically. >> It's also not a bad "sanity check" to backup your DICOMS before/after >> running dcmodify, and use dcmdump on each version to diff the outputs -- >> this will pinpoint what changed. >> >> Re the protocol violation -- AcquisitionProtocol not recognized or >> unknown : this means your scans did not match what is stored in your >> mri_protocol table. >> Check the MRI Violations front-end module -- can you see why they didn't >> match? >> Send us an example, in addition to the contents of the mri_protocol >> table, if you can't find the source of the mismatch. >> >> Best, >> Christine >> >> >> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Here is the psc table >> [image: image.png] >> >> I created 2 candidates profiles through the interface >> >> [image: image.png] >> >> then runned dcmodify command to a dicom file >> >> dcmodify -ma PatientName="DCC0000_258024_V1" >> /home/lorisadmin/DICOMS/000535670/501/*.dcm >> >> and got those warning: is this okay? >> W: Found element (2001,105f) with VR UN and undefined length, reading a >> sequence with transfer syntax LittleEndianImplicit (CP-246) >> W: Found element (2005,1083) with VR UN and undefined length, reading a >> sequence with transfer syntax LittleEndianImplicit (CP-246) >> W: Found element (2005,1402) with VR UN and undefined length, reading a >> sequence with transfer syntax LittleEndianImplicit (CP-246) >> W: Found element (2005,140f) with VR UN and undefined length, reading a >> sequence with transfer syntax LittleEndianImplicit (CP-246) >> W: Found element (2001,105f) with VR UN and undefined length, reading a >> sequence with transfer syntax LittleEndianImplicit (CP-246) >> W: Found element (2005,1083) with VR UN and undefined length, reading a >> sequence with transfer syntax LittleEndianImplicit (CP-246) >> >> dcmodify at another Dicom didn't show warnings. Below you can see the >> execution for the second dicom. Mnics could not be inserted due to >> AcquisitionProtocol being unknown. >> >> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/ >> imaging_upload_file.pl -profile prod -upload_id 12 >> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >> >> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' -delete >> >> >> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >> Source: /tmp/ImagingUpload-18-36-mTrxXs >> Target: /data/loris/data/tarchive >> >> Testing for database connectivity. >> Database is available. >> >> You will archive the dir : ImagingUpload-18-36-mTrxXs >> >> You are creating a tar with the following command: >> >> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >> ImagingUpload-18-36-mTrxXs >> >> >> getting md5sums and gzipping!! >> >> * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs >> * Archive target location : >> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >> * Name of creating host : 127.0.1.1 >> * Name of host OS : Linux >> * Created by user : lorisadmin >> * Archived on : 2019-09-06 18:36:50 >> * dicomSummary version : 1 >> * dicomTar version : 1 >> * md5sum for DICOM tarball : b1dcdc8903dd2d9a5443227db2aa2814 >> ImagingUpload-18-36-mTrxXs.tar >> * md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f >> ImagingUpload-18-36-mTrxXs.tar.gz >> * md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e >> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >> >> Adding archive info into database >> >> Removing temporary files from target location >> >> >> Done adding archive info into database >> >> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation >> -profile prod >> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >> -uploadID 12 -verbose >> md5sum >> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >> PSCID is: DCC0001 >> CandID id: 602102 >> visit_label is: V1 >> PSCID is: DCC0001 >> CandID id: 602102 >> visit_label is: V1 >> candidate id 602102 >> Set centerID = 1 >> PSCID is: DCC0001 >> CandID id: 602102 >> visit_label is: V1 >> PSCID is: DCC0001 >> CandID id: 602102 >> visit_label is: V1 >> >> Number of MINC files that will be considered for inserting into the >> database: 2 >> >> log dir is /data/loris/data//logs and log file is >> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >> PSCID is: DCC0001 >> CandID id: 602102 >> visit_label is: V1 >> PSCID is: DCC0001 >> CandID id: 602102 >> visit_label is: V1 >> candidate id 602102 >> >> log dir is /data/loris/data//logs and log file is >> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >> PSCID is: DCC0001 >> CandID id: 602102 >> visit_label is: V1 >> PSCID is: DCC0001 >> CandID id: 602102 >> visit_label is: V1 >> candidate id 602102 >> >> Cleaning up temp files: rm -rf >> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >> >> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ cat >> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >> >> ==> Loading file from disk >> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >> >> --> mapping DICOM parameter for >> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >> >> ==> computing md5 hash for MINC body. >> >> --> md5: 02022dda60d9de429340fec838f50cfe >> >> ==> verifying acquisition protocol >> >> Acquisition protocol is unknown >> >> --> The minc file cannot be registered since the AcquisitionProtocol is >> unknown >> >> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios: >> >> Sure -- you can delete imaging datasets with the *delete_imaging_upload* >> script -- >> details here: >> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >> >> What's in your *psc* table? (Is it properly populated? This is a >> pre-requisite to loading imaging data. >> >> ) >> The foreign key constraint error on the candidate record is curious. >> >> There are also a few options for creating candidates when inserting >> imaging data: >> >> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline >> >> a. via the LORIS API -- Create the candidates (and visits, optionally I >> think) >> How to: >> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >> Ensure you get the DCCID/CandID assigned by LORIS. >> >> Then as a second step: >> b. Use the imaging insertion pipeline >> >> to load your DICOMs. >> You will want to first ensure that the PatientName header in the DICOMs >> as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel >> >> -- Method 2: for BIDS-format datasets: >> How to : >> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >> >> Be sure to use the *-c* and *-s* options when running the bids_import script, >> to automatically create your candidates and sessions. >> >> Best, >> Christine >> >> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> How do i delete a Study? And everytime do i have to create a new >> candidate to get DCCID and a PSCID? >> >> *First execution:* >> >> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ >> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >> log.txt >> Use of uninitialized value $_ in pattern match (m//) at ./ >> batch_uploads_imageuploader.pl line 144. >> DBD::mysql::db do failed: Cannot add or update a child row: a foreign key >> constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN >> KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at >> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >> ERROR: Failed to insert record in table mri_scanner: >> The following database commands failed: >> PREPARE s FROM 'INSERT INTO mri_scanner >> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; >> SET >> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >> Medical Systems'; >> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >> Error obtained:Cannot add or update a child row: a foreign key constraint >> fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY >> (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452) >> >> ERROR: The validation has failed. Either re-run the validation again and >> fix the problem. Or re-run tarchiveLoader.pl using -force to force the >> execution. >> >> >> The tarchiveLoader.pl insertion script has failed. >> Can't exec "mail": No such file or directory at ./ >> batch_uploads_imageuploader.pl line 249. >> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >> line 250. >> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >> line 251. >> >> >> *And second execution: * >> >> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ >> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >> log.txt >> Use of uninitialized value $_ in pattern match (m//) at ./ >> batch_uploads_imageuploader.pl line 144. >> >> PROBLEM: >> The user 'lorisadmin' has already inserted this study. >> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >> This is the information retained from the first time the study was >> inserted: >> >> * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy >> * Archive target location : >> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >> * Name of creating host : 127.0.1.1 >> * Name of host OS : Linux >> * Created by user : lorisadmin >> * Archived on : 2019-09-04 18:33:05 >> * dicomSummary version : 1 >> * dicomTar version : 1 >> * md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d >> ImagingUpload-18-33-Qq7HGy.tar >> * md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec >> ImagingUpload-18-33-Qq7HGy.tar.gz >> * md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053 >> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >> >> >> Last update of record: >> >> >> >> The dicomTar.pl execution has failed. >> Can't exec "mail": No such file or directory at ./ >> batch_uploads_imageuploader.pl line 249. >> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >> line 250. >> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >> line 251. >> >> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios, >> >> Ok, this sounds like good progress. Let us know when you next encounter >> issues as you progress through the Imaging Install/Setup docs >> . >> I'll look into how we can better handle the incoming/ directory next time. >> Best, >> Christine >> >> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >> populated correctly except its port is 'port' : ''. Also i have tested >> that i can connect to MySQL with lorisuser. >> >> I executed the script again, because the only error i had previously was >> that the /data/incoming folder didn't exist and there are no errors >> reported back except of warnings <> command line interface can be insecure>>. >> >> >> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios, >> >> It's possible -- if the script was unable to connect to the database >> during its execution (e.g. typo in the password), that would explain the >> underpopulated Image path and Loris-MRI code path you saw in the Config >> module. >> It's hard to tell without seeing the output from your script run -- Did >> you see a sign of any such error? >> The Config fields are populated by the imaging_install.sh script (starting >> at line 222 >> >> ) >> >> For example, check if the database connection information was populated >> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >> >> Best, >> Christine >> >> >> >> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> Hi Christine, >> >> If you are referring to the imaging_install.sh here is an image with the >> configurations i typed. Maybe the problem is somewhere at the last part >> which asks to configure as much as possible automatically? >> >> Thanks >> >> >> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >> Hi Sotirios, >> >> Glad to hear your LORIS core install is up and working and all the >> front-end pages are loading. >> >> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >> > and the web interface worked. >> >> Yes, it's important that project/ have 775 permissions and that >> lorisadmin be part of the sudoers group, per step 1 in the install Readme >> . >> >> > As for the Paths, LORIS-MRI code and Image should change LORIS to >> loris, right? >> >> These imaging paths will be updated during your imaging installation >> by an automated script -- you >> do not need to set them manually via the Config module. >> Please continue to follow the Setup Guide >> for detailed steps to follow. >> >> Best, >> Christine >> >> >> >> >> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >> As for the Paths, LORIS-MRI code and Image should change LORIS to loris, >> right? >> >> [image: image.png] >> >> >> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> Hi, >> >> i used >> >> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >> sudo apt-get install -y nodejs >> >> >> you had suggested in the past, make worked and now i can see all the >> contents in the web-interface, but i don't need make install? >> >> Thanks >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: warning_output Type: application/octet-stream Size: 36440 bytes Desc: not available URL: From christine.rogers at mcgill.ca Fri Nov 8 18:20:44 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Fri, 8 Nov 2019 23:20:44 +0000 Subject: [Loris-dev] loris server In-Reply-To: <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> References: <20191104195851.GA4052@gaia.neuro.berkeley.edu> <20191104200859.GB27438@nx6.priv> <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> Message-ID: Hi Ioannis, Could you open your file called config.xml (/srv/www/loris/project/config.xml) and confirm for us -- which user credential is stored there, and what's the name of the database it is connecting to? This is the mysql user which connects to the database from the front end of LORIS. If this user has insufficient privileges on your database, that would cause the errors you are seeing. I had assumed from your thread it was your lorismysql user but it sounds like this should be verified. Let us know, and we'll keep following up when we come back online after the weekend, Best, Christine On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas > wrote: Hi Melanie. Thank you for taking the time to reply to this. I took some to consider your comments. Unfortunately as I said to Christine we are unable to do any kind of updating to the database (either that is changing the name or changing the small html description, etc.). Based on some more digging and on some of Christine's comments I have a feeling that our lorisweb front-end, admin user cannot write anything to the database. Along these lines could it be the case the lorismysql user (the database, admin user with INSERT, UPDATE, etc privileges) is not ?talking? to the lorisweb front end user? What is the difference between the two and could it be a installation problem for them not talking to each other? As Julie said, lorismysql user is working normally with MariaDB. Thank you again for your help. Best wishes, Ioannis On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs > wrote: Hello, Changing the project name in the configuration page (https://loris.url/configuration/) of LORIS, only change the title of the project. To see this change, you have to log out of LORIS and then go back to the login page (https://.loris.url/). This is the only place you can find the project name (except from the configuration page). See ProjectName.png As for files permission, I would suggest a few change to improve security of you server. Some extra permissions where granted to help you but are not needed. * /srv/www/loris/smarty/templates_c/ should have ownership of lorisadmin:httpd and permission 770 (or 775) * srv/www/loris/project/ should have ownership lorisadmin:httpd and permission 770 (775) * All other files under loris should have lorisadmin:lorisadmin 755 Reading through this change of mail, I understand that you let Apache store file in /srv/www/loris | 31 | DownloadPath | Downloads | /srv/www/loris/ | Where >> files are downloaded Downloaded files should not be in the same tree as LORIS code. It should be in a separate structure where Apache will not try and do not have permission (in httpd.conf) to execute files. Kind regards, M?lanie Legault | Software developer | Faculty of Medicine | McGill University 3801 University, Montr?al, QC H3A 2B4 ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca > on behalf of Ioannis Pappas > Sent: November 7, 2019 0:18 To: loris-dev at bic.mni.mcgill.ca > Cc: Julie Ashworth, HWNI Computing Support >; Christine Rogers, Ms. > Subject: Re: [Loris-dev] loris server Hi Christine and Julie. Yes it looks like that any attempt to configure something in the front-end results in the same page. I am sending this to the list (as you requested Christine) alongside the troubleshooting and discussion so far with Julie. Best wishes, Ioannis > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing Support > wrote: > > hi Christine and Ioannis, > Ioannis, can you follow-up with Christine about using the front-end? > > We're using CentOS7.7 and loris-21.0.1. > > I confirmed that I could login as the mysql user (lorismyqsl) and change the 'url' config setting from 'http://loris.priv' to 'http://localhost', and back again. > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > | ConfigID | Name | Label | Value | Description | > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > | 44 | host | Host | loris.priv | Host | > | 45 | url | Main LORIS URL | http://loris.priv | Main URL where LORIS can be accessed | > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > MariaDB [loris_database]> UPDATE Config SET Value='http://localhost' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > Rows matched: 1 Changed: 1 Warnings: 0 > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > +----------+-------------------+-------------------+------------------+--------------------------------------+ > | ConfigID | Name | Label | Value | Description | > +----------+-------------------+-------------------+------------------+--------------------------------------+ > | 44 | host | Host | loris.priv | Host | > | 45 | url | Main LORIS URL | http://localhost | Main URL where LORIS can be accessed | > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > +----------+-------------------+-------------------+------------------+--------------------------------------+ > 3 rows in set (0.00 sec) > > best, > Julie > > > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: >> Hi Julie, >> Forgive my ambiguity - We run the community support listserv for >> developers, project administrators and sysadmins setting up LORIS, so that >> these users can contact our technical team for exactly such technical >> help. >> If it's ok with you, I'd encourage you subscribe to the listserv and >> contact our technical team that way for the same reason. >> (Note that front-end users of LORIS typically contact their project team >> for support, rather than us.) >> Given that your lorismysql user privileges seem appropriate ('UPDATE" is >> there, I mistyped 'INSERT" before) >> -- is there any other indication why the database record is not >> updating? >> In the front-end, can your 'admin' user effect any changes in (any) Config >> setting? >> In the back-end, when you tried updating a field using your >> lorismysql credential, what happened? >> Your front end is loading ok, and you can log in there, if I understood >> correctly. >> Thanks for letting us know these details at >> [1]loris-dev at bic.mni.mcgill.ca >> Please also include what version of LORIS you are installing, and on what >> OS version. >> Best, >> Christine >> On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI Computing Support >> <[2]support-cirl at berkeley.edu> wrote: >> >> Thank you Christine, >> I'm the linux sysadmin who installed the loris database for Ioannis. >> I'm not a loris user, however, so that makes it a little awkward for >> troubleshooting via the mailing list. I'm happy to help in whatever way >> I can. >> >> Regarding the database permissions, I ran: >> >> MariaDB [(none)]> show grants for 'lorismysql'@'%'; >> +--------------------------------------------------------------------------------+ >> | Grants for lorismysql@% >> | >> +--------------------------------------------------------------------------------+ >> | GRANT USAGE ON *.* TO 'lorismysql'@'%' >> | >> | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO >> 'lorismysql'@'%' | >> +--------------------------------------------------------------------------------+ >> 2 rows in set (0.00 sec) >> >> looking at the 'tips' section in the page you referred to... >> >> | 29 | base | Base | /srv/www/loris/ | The base >> filesystem path where LORIS is installed | >> | 31 | DownloadPath | Downloads | /srv/www/loris/ | Where >> files are downloaded >> >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> | ConfigID | Name | Label | Value | >> Description | >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> | 44 | host | Host | loris.priv | >> Host | >> | 45 | url | Main LORIS URL | >> [3]http://loris.priv | Main URL where LORIS can be accessed | >> | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | >> The *new* bug/issue tracker url | >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >> >> apache config: >> >> Listen 80 >> User apache >> Group apache >> DocumentRoot "/srv/www/loris/htdocs" >> >> >> AllowOverride none >> Require all denied >> >> >> >> AllowOverride All >> Options Indexes FollowSymLinks >> Require all granted >> >> >> >> Options Indexes FollowSymLinks >> AllowOverride All >> Require all granted >> >> >> file permissions: >> >> # ls -ld /srv/www/loris/smarty/templates_c >> drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 >> /srv/www/loris/smarty/templates_c/ >> >> [root at loris loris]# ls -l /srv/www/loris/smarty/templates_c >> -rw-r--r-- 1 lorisadmin lorisadmin 2444 Oct 31 09:46 >> 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 >> 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep 7 18:39 >> 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3296 Sep 7 18:35 >> 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 5901 Sep 7 21:10 >> 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep 7 18:39 >> 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 874 Sep 10 11:01 >> 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 1101 Sep 10 10:58 >> 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 >> 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3590 Sep 7 18:39 >> a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep 7 21:08 >> a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 897 Sep 7 18:35 >> a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 9210 Sep 10 11:01 >> a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 8917 Sep 10 13:21 >> ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 4811 Sep 7 18:35 >> d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 3309 Sep 10 11:02 >> d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 >> e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php >> -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep 7 17:42 >> fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php >> >> thanks again! >> Julie >> >> On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: >>> Hi Ioannis,? >>> Thanks for your question.? >>> Given that the URL field is not updating, I suspect it's a database >>> back-end issue.? >>> Can you verify -- Has your mysql user lorismysql? been granted the >> "INSERT" >>> privilege for the right database? If not, that would result in an >> error >>> like the kind you are seeing.? >>> Also, if you wish to check your LORIS Configuration settings in the >>> backend database such as the URL field -- to see what was actually >> stored >>> in a given database field and should display in the Config >> module:? >>> You can run the queries listed in the "Troubleshooting >> Configuration >>> settings" section of our Github-wiki Setup Guide (under Project >>> Customization) :? >>> >> [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> Lastly, this question is perfectly appropriate for the loris-dev >> community >>> support listserv -- please [2]subscribe here and then email our >> technical >>> team your next question at? [3][5]loris-dev at bic.mni.mcgill.ca >> (after checking >>> any forwarded threads for sensitive info).? >>> We prefer to answer technical questions there for the benefit of >> the >>> community and other first-time users in the same position as >> yourself.? ? >>> Thanks and cheers,? >>> Christine? >>> On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD >>> <[4][6]ioannis at berkeley.edu> wrote: >>> >>> Hi Loris support.? >>> My name is ioannis Pappas, a post-doc at the D'Esposito lab >> stroke group >>> at UC Berkeley. With the kind of help of our sys admin? Julie >> (cc'ed) we >>> have set up our loris database in our cluster (she is the sudo >> user and >>> I am the admin user). >>> If you allow me, I would like to ask you about the first >> configuration >>> steps in the front end as they are described in the tutorial. We >> can >>> login to [5][7]http://loris and the front end normally. >>> However any update that I am trying to? perform in >> Admin->Configuration >>> doesn't work (e.g. updating the study name). It just refreshes >> the same >>> page. I am just wondering if there is an issue with writing in >> the >>> configuration file. >>> Here are the permissions setup for where Loris is installed. >>> chmod 777 /var/www/loris/smarty/templates_c >>> cd /srv/www/loris >>> chown -R lorisadmin:lorisadmin . >>> chmod -c -R a+r . >>> ? ? this command gives everyone read access, and outputs what >> changes >>> were made: >>> ? ? mode of ??./project?? changed from 0770 (rwxrwx---) to 0774 >>> (rwxrwxr--) >>> ? ? mode of ??./tools/logs?? changed from 0770 (rwxrwx---) to >> 0774 >>> (rwxrwxr--) >>> find . -type d -exec chmod a+x -c {} \; >>> ? ? this command gives everyone permission to open a directory, >> and >>> outputs what changes were made: >>> ? ? mode of ??./project?? changed from 0774 (rwxrwxr--) to 0775 >>> (rwxrwxr-x) >>> ? ? mode of ??./tools/logs?? changed from 0774 (rwxrwxr--) to >> 0775 >>> (rwxrwxr-x) >>> Hopefully? you can help me with this. I also subscribed to the >> mailing >>> list but I am not sure if this too much of a basic question for >> the >>> list. >>> Best wishes, >>> Ioannis >>> On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI Computing >> Support >>> <[6][8]support-cirl at berkeley.edu> wrote: >>> >>> Hi ioannis, maybe it's best to ask the developers? You can cc >> me if >>> you'd like. >>> On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas >> <[7][9]ioannis at berkeley.edu> >>> wrote: >>> >>> That did the trick Julie. Thank you! >>> >>> I am still trying to understand how configuration works >> though. For >>> example if I just try to change the name of the >>> study from the front end, I get nowhere (it just refreshes >> the same >>> page). >>> >>> I am not sure if this requires write permissions somewhere in >> a >>> config file/folder and that???s why it doesn???t update it. >>> >>> Best wishes, >>> Ioannis >>> >>> > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI Computing >>> Support <[8][10]support-cirl at berkeley.edu> wrote: >>> > >>> > just in case you're interested, these are the permission >> changes I >>> made: >>> > >>> > chmod 777 /var/www/loris/smarty/templates_c >>> > cd /srv/www/loris >>> > chown -R lorisadmin:lorisadmin . >>> > chmod -c -R a+r . >>> >? ? this command gives everyone read access, and outputs >> what >>> changes were made: >>> >? ? mode of ??./project?? changed from 0770 (rwxrwx---) to >> 0774 >>> (rwxrwxr--) >>> >? ? mode of ??./tools/logs?? changed from 0770 (rwxrwx---) >> to 0774 >>> (rwxrwxr--) >>> > find . -type d -exec chmod a+x -c {} \; >>> >? ? this command gives everyone permission to open a >> directory, and >>> outputs what changes were made: >>> >? ? mode of ??./project?? changed from 0774 (rwxrwxr--) to >> 0775 >>> (rwxrwxr-x) >>> >? ? mode of ??./tools/logs?? changed from 0774 (rwxrwxr--) >> to 0775 >>> (rwxrwxr-x) >>> > >>> > >>> > >>> > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: >>> >> Hi Julie. >>> >> I just tried and I still don???t get anything. I also >> tried >>> private mode in Firefox in case the empty page was cached. >>> >> Sorry for this. >>> >> >>> >> Best wishes, >>> >> Ioannis >>> >> >>> >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, HWNI >> Computing >>> Support <[9][11]support-cirl at berkeley.edu> wrote: >>> >>> >>> >>> hi Ioannis, >>> >>> no worries, I changed the following directory to 777: >>> >>> >>> >>> /var/www/loris/smarty/templates_c >>> >>> >>> >>> will you please check if that works? >>> >>> >>> >>> thanks! >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas PhD wrote: >>> >>>>? Hi Julie. >>> >>>>? Apologies for bugging you with this again. We tried >> now to >>> >>>>? access?? [1][10][12]http://loris?? >>> >>>>? and we are getting a?? blank page. I think the reason >> for this >>> is that we >>> >>>>? don't have read?? permissions to read from the >> template located >>> in >>> >>>>? /var/www/loris/smarty See here bottom of the >>> >>>>? page?? >>> >> [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> >>>>? I think, in general, I am a little bit confused as to >> what the >>> permissions >>> >>>>? should be for us that are not sudos. My understanding >> is that >>> if we don't >>> >>>>? have read or write permissions then we can't access or >> write >>> to >>> >>>>? /var/www/loris, meaning that we can't access or >> configure. >>> Should >>> >>>>? everything be chmod 777 for example??? >>> >>>>? Thank you very much once again. >>> >>>>? Best wishes, >>> >>>>? Ioannis >>> >>>>? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis Pappas PhD >>> >>>>? <[3][12][14]ioannis at berkeley.edu> wrote: >>> >>>> >>> >>>>? ? Thank you very much Julie. I appreciate this and I >> will dig >>> into Loris >>> >>>>? ? given your changes. Thank you so much for your >> help. >>> >>>>? ? Best wishes, >>> >>>>? ? Ioannis >>> >>>>? ? On Thu, Oct 31, 2019 at 12:48 PM Julie Ashworth, >> HWNI >>> Computing Support >>> >>>>? ? <[4][13][15]support-cirl at berkeley.edu> wrote: >>> >>>> >>> >>>>? ? ? hi Ioannis, >>> >>>> >>> >>>>? ? ? 1. I changed the permissions of /srv/www/loris >> to be owned >>> by >>> >>>>? ? ? lorisadmin. I reivewed my installation notes, >> and I did >>> this already >>> >>>>? ? ? when >>> >>>>? ? ? I installed the server. I'm not sure why they >> changed, so >>> it's >>> >>>>? ? ? probably a >>> >>>>? ? ? good idea to keep an eye on that. >>> >>>> >>> >>>>? ? ? 2. When I installed the loris software, I also >> installed a >>> mysql >>> >>>>? ? ? database as recommended in the instructions: >>> >>>> >>> >>>>? ? ? projectname: LORIS >>> >>>>? ? ? databasename: loris_database >>> >>>>? ? ? mysqluser: lorismysql >>> >>>>? ? ? frontend: lorisweb >>> >>>> >>> >>>>? ? ? 3. A couple of weeks ago, I moved Henrik's home >> directory >>> to >>> >>>>? ? ? /home/despoA, >>> >>>>? ? ? but I forgot to update loris. This is done now. >>> >>>> >>> >>>>? ? ? best, >>> >>>>? ? ? Julie >>> >>>> >>> >>>>? ? ? On 31-10-2019 11.15 -0700, Dr. Ioannis Pappas >> PhD wrote: >>> >>>>> ??? ??? Hi Julie. >>> >>>>> ??? ??? I hope you are well. We are trying to >> configure loris >>> that you >>> >>>>? ? ? kindly set >>> >>>>> ??? ??? up for us. >>> >>>>> ??? ??? I have a couple of questions for you if you >> allow me >>> so.?? >>> >>>>> ??? ??? 1) First, although we are logging into the >> front end >>> with admin >>> >>>>? ? ? username >>> >>>>> ??? ??? (lorisweb) and password, it seems that any >> kind of >>> update of >>> >>>>? ? ? configuration >>> >>>>> ??? ??? we are trying to do fails (meaning that if >> we, say, >>> change the >>> >>>>? ? ? name of the >>> >>>>> ??? ??? study and press "submit", this doesn't do >> anything-it >>> doesn't >>> >>>>? ? ? update). >>> >>>>> ??? ??? It's almost like our lorisweb user doesn't >> have write >>> privileges >>> >>>>? ? ? in the >>> >>>>> ??? ??? /var/www/loris/project (where I think every >>> configuration should >>> >>>>? ? ? be). >>> >>>>> ??? ??? This generalizes for everything that we are >> trying to do >>> in the >>> >>>>? ? ? front end. >>> >>>>> ??? ??? Clicking any instrument/tab in the front end >> doesn't >>> really point >>> >>>>? ? ? to >>> >>>>> ??? ??? anything.?? >>> >>>>> ??? ??? 2) Loris suggest doing configurations via >> SQL. Is it >>> possible to >>> >>>>? ? ? run SQL >>> >>>>> ??? ??? scripts in the backend >>> >>>>> ??? ??? 3) For some reason typing ssh lors for Henrik >> doesn't >>> directly >>> >>>>? ? ? take him to >>> >>>>> ??? ??? loris (it requires a password that is not the >> password >>> setup for >>> >>>>? ? ? the >>> >>>>> ??? ??? lorisweb user). Will you be able to fix this >> via your >>> sudo >>> >>>>? ? ? privileges? >>> >>>>> ??? ??? Thank you very much in advance for all your >> help Julie. >>> Let us >>> >>>>? ? ? know if >>> >>>>> ??? ??? this is something that shouldn't be directed >> to you (but >>> instead >>> >>>>? ? ? to the >>> >>>>> ??? ??? loris people).?? >>> >>>>> ??? ??? Best wishes, >>> >>>>> ??? ??? Ioannis >>> >>>>> ??? ??? On Mon, Sep 9, 2019 at 6:25 PM Julie >> Ashworth, HWNI >>> Computing >>> >>>>? ? ? Support >>> >>>>> ??? ??? <[1][5][14][16]support-cirl at berkeley.edu> >> wrote: >>> >>>>> >>> >>>>> ??? ??? ??? hi Henrik and Ioannis, >>> >>>>> ??? ??? ??? the loris server is available for you to >> use. >>> >>>>> >>> >>>>> ??? ??? ??? The servername is 'loris'. I created a >> directory >>> called >>> >>>>? ? ? /data/loris for >>> >>>>> ??? ??? ??? you to store data. You may create new >> folders in >>> /data/loris to >>> >>>>? ? ? organize >>> >>>>> ??? ??? ??? your data. >>> >>>>> >>> >>>>> ??? ??? ??? 1) secure shell or secure copy: >>> >>>>> ??? ??? ??? You can log in with the 'ssh' or 'scp' >> command from >>> your remote >>> >>>>? ? ? desktop >>> >>>>> ??? ??? ??? session. You don't need to authenticate >> to log in. >>> Maybe you'll >>> >>>>? ? ? use scp >>> >>>>> ??? ??? ??? to transfer data between your cluster >> account and the >>> loris >>> >>>>? ? ? server? >>> >>>>> ??? ??? ??? Please put the data in /data/loris, so I >> can make >>> backups more >>> >>>>? ? ? easily. >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? secure shell: >>> >>>>> ??? ??? ??? ??? ??? $ ssh loris >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? secure copy (change the names >> in brackets). Let >>> me know if >>> >>>>? ? ? I can >>> >>>>> ??? ??? ??? ??? ??? help with syntax: >>> >>>>> ??? ??? ??? ??? ??? $ scp -r >> loris:/data/loris/ >>> >>>>> >>> >>>>> ??? ??? ??? 2) front-end web interface.??? Open a >> web browser in >>> your remote >>> >>>>? ? ? desktop >>> >>>>> ??? ??? ??? session and enter the hostname: >>> >>>>> ??? ??? ??? [2][6][15][17]http://loris >>> >>>>> ??? ??? ??? I created an admin user called >> 'lorisweb'. I put the >>> password >>> >>>>? ? ? in >>> >>>>> ??? ??? ??? $HOME/newuser on the cluster. To see it, >> open a >>> terminal, and >>> >>>>? ? ? run: >>> >>>>> >>> >>>>> ??? ??? ??? ??? ??? $ cat $HOME/newuser >>> >>>>> >>> >>>>> ??? ??? ??? If other people need shell access to the >> webserver, >>> please let >>> >>>>? ? ? me know >>> >>>>> ??? ??? ??? so I can create a home directory for >> them. >>> >>>>> >>> >>>>> ??? ??? ??? We should eventually discuss backups. >>> >>>>> >>> >>>>> ??? ??? ??? best, >>> >>>>> ??? ??? ??? Julie >>> >>>>> >>> >>>>> References >>> >>>>> >>> >>>>> ??? ??? Visible links >>> >>>>> ??? ??? 1. >> mailto:[7][16][18]support-cirl at berkeley.edu >>> >>>>> ??? ??? 2. [8][17][19]http://loris/ >>> >>>>? ? ? ---end quoted text--- >>> >>>> >>> >>>> References >>> >>>> >>> >>>>? Visible links >>> >>>>? 1. [18][20]http://loris/ >>> >>>>? 2. >>> >> [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> >>>>? 3. mailto:[20][22]ioannis at berkeley.edu >>> >>>>? 4. mailto:[21][23]support-cirl at berkeley.edu >>> >>>>? 5. mailto:[22][24]support-cirl at berkeley.edu >>> >>>>? 6. [23][25]http://loris/ >>> >>>>? 7. mailto:[24][26]support-cirl at berkeley.edu >>> >>>>? 8. [25][27]http://loris/ >>> >>> ---end quoted text--- >>> >> >>> > ---end quoted text--- >>> >>> -- >>> [26][28]christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> References >>> >>> Visible links >>> 1. >> [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> 2. [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> 3. mailto:[31]loris-dev at bic.mni.mcgill.ca >>> 4. mailto:[32]ioannis at berkeley.edu >>> 5. [33]http://loris/ >>> 6. mailto:[34]support-cirl at berkeley.edu >>> 7. mailto:[35]ioannis at berkeley.edu >>> 8. mailto:[36]support-cirl at berkeley.edu >>> 9. mailto:[37]support-cirl at berkeley.edu >>> 10. [38]http://xn--loris-7qa/ >>> 11. [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> 12. mailto:[40]ioannis at berkeley.edu >>> 13. mailto:[41]support-cirl at berkeley.edu >>> 14. mailto:[42]support-cirl at berkeley.edu >>> 15. [43]http://loris/ >>> 16. mailto:[44]support-cirl at berkeley.edu >>> 17. [45]http://loris/ >>> 18. [46]http://loris/ >>> 19. [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> 20. mailto:[48]ioannis at berkeley.edu >>> 21. mailto:[49]support-cirl at berkeley.edu >>> 22. mailto:[50]support-cirl at berkeley.edu >>> 23. [51]http://loris/ >>> 24. mailto:[52]support-cirl at berkeley.edu >>> 25. [53]http://loris/ >>> 26. mailto:[54]christine.rogers at mcgill.ca >> ---end quoted text--- >> >> -- >> [55]christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> >> References >> >> Visible links >> 1. mailto:loris-dev at bic.mni.mcgill.ca >> 2. mailto:support-cirl at berkeley.edu >> 3. http://loris.priv/ >> 4. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >> 5. mailto:loris-dev at bic.mni.mcgill.ca >> 6. mailto:ioannis at berkeley.edu >> 7. http://loris/ >> 8. mailto:support-cirl at berkeley.edu >> 9. mailto:ioannis at berkeley.edu >> 10. mailto:support-cirl at berkeley.edu >> 11. mailto:support-cirl at berkeley.edu >> 12. http://xn--loris-era/ >> 13. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 14. mailto:ioannis at berkeley.edu >> 15. mailto:support-cirl at berkeley.edu >> 16. mailto:support-cirl at berkeley.edu >> 17. http://loris/ >> 18. mailto:support-cirl at berkeley.edu >> 19. http://loris/ >> 20. http://loris/ >> 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 22. mailto:ioannis at berkeley.edu >> 23. mailto:support-cirl at berkeley.edu >> 24. mailto:support-cirl at berkeley.edu >> 25. http://loris/ >> 26. mailto:support-cirl at berkeley.edu >> 27. http://loris/ >> 28. mailto:christine.rogers at mcgill.ca >> 29. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >> 30. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> 31. mailto:loris-dev at bic.mni.mcgill.ca >> 32. mailto:ioannis at berkeley.edu >> 33. http://loris/ >> 34. mailto:support-cirl at berkeley.edu >> 35. mailto:ioannis at berkeley.edu >> 36. mailto:support-cirl at berkeley.edu >> 37. mailto:support-cirl at berkeley.edu >> 38. http://xn--loris-7qa/ >> 39. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 40. mailto:ioannis at berkeley.edu >> 41. mailto:support-cirl at berkeley.edu >> 42. mailto:support-cirl at berkeley.edu >> 43. http://loris/ >> 44. mailto:support-cirl at berkeley.edu >> 45. http://loris/ >> 46. http://loris/ >> 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 48. mailto:ioannis at berkeley.edu >> 49. mailto:support-cirl at berkeley.edu >> 50. mailto:support-cirl at berkeley.edu >> 51. http://loris/ >> 52. mailto:support-cirl at berkeley.edu >> 53. http://loris/ >> 54. mailto:christine.rogers at mcgill.ca >> 55. mailto:christine.rogers at mcgill.ca > ---end quoted text--- _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From melanie.legault2 at mcgill.ca Mon Nov 11 10:47:00 2019 From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs) Date: Mon, 11 Nov 2019 15:47:00 +0000 Subject: [Loris-dev] loris server In-Reply-To: <20191109020414.GB13279@nx6.priv> References: <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> , <20191109020414.GB13279@nx6.priv> Message-ID: Hello Julie, Could it be that your MySQL 'lorismysql' user have different permissions depending on where it is connecting to the DB? A database admin (root) can check this for you. SELECT User, Host FROM mysql.user; then for the user that match the Host (name or IP address) of your LORIS (Apache) server SHOW grants for 'lorismysql'@''; M?lanie ________________________________ From: Julie Ashworth, HWNI Computing Support Sent: November 8, 2019 21:04 To: Christine Rogers, Ms. Cc: Ioannis Pappas ; Melanie Legault, Mrs ; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] loris server thanks Christine, yes, it's the lorismysql user in the config.xml file. lorismysql loris_database lorismysql we appeciate your help troubleshooting this. best, Julie On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote: > Hi Ioannis, > Could you open your file called config.xml > (/srv/www/loris/project/config.xml) and confirm for us -- which user > credential is stored there, and what's the name of the database it is > connecting to? > This is the mysql user which connects to the database from the front end > of LORIS. > If this user has insufficient privileges on your database, that would > cause the errors you are seeing. I had assumed from your thread it was > your lorismysql user but it sounds like this should be verified. > Let us know, and we'll keep following up when we come back online after > the weekend, > Best, > Christine > On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas > wrote: > > Hi Melanie. > Thank you for taking the time to reply to this. I took some to consider > your comments. Unfortunately as I said to Christine we are unable to do > any kind of updating to the database (either that is changing the name > or changing the small html description, etc.). > Based on some more digging and on some of Christine's comments I have a > feeling that our lorisweb front-end, admin user cannot write anything to > the database. Along these lines could it be the case the lorismysql user > (the database, admin user with INSERT, UPDATE, etc privileges) is not > ???talking??? to the lorisweb front end user? What is the difference between > the two and could it be a installation problem for them not talking to > each other? As Julie said, lorismysql user is working normally with > MariaDB. > Thank you again for your help. > Best wishes, > Ioannis > > On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs > wrote: > Hello, > Changing the project name in the configuration page > (https://loris.url/configuration/) of LORIS, only change the title of > the project. To see this change, you have to log out of LORIS and then > go back to the login page (https://.loris.url/). This is the only > place you can find the project name (except from the configuration > page). See ProjectName.png > As for files permission, I would suggest a few change to improve > security of you server. Some extra permissions where granted to help > you but are not needed. > * /srv/www/loris/smarty/templates_c/ should have ownership of > lorisadmin:httpd and permission 770 (or 775) > * srv/www/loris/project/ should have ownership lorisadmin:httpd and > permission 770 (775) > * All other files under loris should have lorisadmin:lorisadmin 755 > Reading through this change of mail, I understand that you let Apache > store file in /srv/www/loris > | 31 | DownloadPath | Downloads | /srv/www/loris/ | > Where > >> files are downloaded > Downloaded files should not be in the same tree as LORIS code. It > should be in a separate structure where Apache will not try and do not > have permission (in httpd.conf) to execute files. > Kind regards, > M??lanie Legault | Software developer | Faculty of Medicine | McGill > University > 3801 University, Montr??al, QC H3A 2B4 > > ---------------------------------------------------------------------- > > From: loris-dev-bounces at bic.mni.mcgill.ca > on behalf of Ioannis Pappas > > Sent: November 7, 2019 0:18 > To: loris-dev at bic.mni.mcgill.ca > Cc: Julie Ashworth, HWNI Computing Support > ; Christine Rogers, Ms. > > Subject: Re: [Loris-dev] loris server > > Hi Christine and Julie. > > Yes it looks like that any attempt to configure something in the > front-end results in the same page. I am sending this to the list (as > you requested Christine) alongside the troubleshooting and discussion > so far with Julie. > > Best wishes, > Ioannis > > > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing Support > wrote: > > > > hi Christine and Ioannis, > > Ioannis, can you follow-up with Christine about using the front-end? > > > > We're using CentOS7.7 and loris-21.0.1. > > > > I confirmed that I could login as the mysql user (lorismyqsl) and > change the 'url' config setting from 'http://loris.priv' to > 'http://localhost', and back again. > > > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON > (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) > WHERE csp.Name = 'www'; > > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > | ConfigID | Name | Label | > Value | Description | > > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > | 44 | host | Host | > loris.priv | Host | > > | 45 | url | Main LORIS URL > | http://loris.priv | Main URL where LORIS can be accessed | > > | 46 | issue_tracker_url | Issue tracker URL | > /issue_tracker | The *new* bug/issue tracker url | > > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > > > MariaDB [loris_database]> UPDATE Config SET Value='http://localhost' > WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > > Rows matched: 1 Changed: 1 Warnings: 0 > > > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON > (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) > WHERE csp.Name = 'www'; > > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > | ConfigID | Name | Label | > Value | Description | > > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > | 44 | host | Host | > loris.priv | Host | > > | 45 | url | Main LORIS URL > | http://localhost | Main URL where LORIS can be accessed | > > | 46 | issue_tracker_url | Issue tracker URL | > /issue_tracker | The *new* bug/issue tracker url | > > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > 3 rows in set (0.00 sec) > > > > best, > > Julie > > > > > > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: > >> Hi Julie, > >> Forgive my ambiguity - We run the community support listserv for > >> developers, project administrators and sysadmins setting up > LORIS, so that > >> these users can contact our technical team for exactly such > technical > >> help. > >> If it's ok with you, I'd encourage you subscribe to the listserv > and > >> contact our technical team that way for the same reason. > >> (Note that front-end users of LORIS typically contact their > project team > >> for support, rather than us.) > >> Given that your lorismysql user privileges seem appropriate > ('UPDATE" is > >> there, I mistyped 'INSERT" before) > >> -- is there any other indication why the database record is not > >> updating? > >> In the front-end, can your 'admin' user effect any changes in > (any) Config > >> setting? > >> In the back-end, when you tried updating a field using your > >> lorismysql credential, what happened? > >> Your front end is loading ok, and you can log in there, if I > understood > >> correctly. > >> Thanks for letting us know these details at > >> [1]loris-dev at bic.mni.mcgill.ca > >> Please also include what version of LORIS you are installing, and > on what > >> OS version. > >> Best, > >> Christine > >> On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI Computing > Support > >> <[2]support-cirl at berkeley.edu> wrote: > >> > >> Thank you Christine, > >> I'm the linux sysadmin who installed the loris database for > Ioannis. > >> I'm not a loris user, however, so that makes it a little > awkward for > >> troubleshooting via the mailing list. I'm happy to help in > whatever way > >> I can. > >> > >> Regarding the database permissions, I ran: > >> > >> MariaDB [(none)]> show grants for 'lorismysql'@'%'; > >> > +--------------------------------------------------------------------------------+ > >> | Grants for lorismysql@% > >> | > >> > +--------------------------------------------------------------------------------+ > >> | GRANT USAGE ON *.* TO 'lorismysql'@'%' > >> | > >> | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO > >> 'lorismysql'@'%' | > >> > +--------------------------------------------------------------------------------+ > >> 2 rows in set (0.00 sec) > >> > >> looking at the 'tips' section in the page you referred to... > >> > >> | 29 | base | Base | /srv/www/loris/ | > The base > >> filesystem path where LORIS is > installed | > >> | 31 | DownloadPath | Downloads | /srv/www/loris/ | > Where > >> files are downloaded > >> > >> > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> | ConfigID | Name | Label | > Value | > >> Description | > >> > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> | 44 | host | Host | > loris.priv | > >> Host | > >> | 45 | url | Main LORIS URL | > >> [3]http://loris.priv | Main URL where LORIS can be accessed | > >> | 46 | issue_tracker_url | Issue tracker URL | > /issue_tracker | > >> The *new* bug/issue tracker url | > >> > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> > >> apache config: > >> > >> Listen 80 > >> User apache > >> Group apache > >> DocumentRoot "/srv/www/loris/htdocs" > >> > >> > >> AllowOverride none > >> Require all denied > >> > >> > >> > >> AllowOverride All > >> Options Indexes FollowSymLinks > >> Require all granted > >> > >> > >> > >> Options Indexes FollowSymLinks > >> AllowOverride All > >> Require all granted > >> > >> > >> file permissions: > >> > >> # ls -ld /srv/www/loris/smarty/templates_c > >> drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 > >> /srv/www/loris/smarty/templates_c/ > >> > >> [root at loris loris]# ls -l /srv/www/loris/smarty/templates_c > >> -rw-r--r-- 1 lorisadmin lorisadmin 2444 Oct 31 09:46 > >> > 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 > >> > 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep 7 18:39 > >> 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3296 Sep 7 18:35 > >> > 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 5901 Sep 7 21:10 > >> > 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep 7 18:39 > >> > 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 874 Sep 10 11:01 > >> 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 1101 Sep 10 10:58 > >> > 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 > >> > 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3590 Sep 7 18:39 > >> > a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep 7 21:08 > >> > a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 897 Sep 7 18:35 > >> a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 9210 Sep 10 11:01 > >> > a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 8917 Sep 10 13:21 > >> > ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 4811 Sep 7 18:35 > >> > d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3309 Sep 10 11:02 > >> > d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 > >> > e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep 7 17:42 > >> fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php > >> > >> thanks again! > >> Julie > >> > >> On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: > >>> Hi Ioannis,?? > >>> Thanks for your question.?? > >>> Given that the URL field is not updating, I suspect it's a > database > >>> back-end issue.?? > >>> Can you verify -- Has your mysql user lorismysql?? been granted > the > >> "INSERT" > >>> privilege for the right database? If not, that would result in > an > >> error > >>> like the kind you are seeing.?? > >>> Also, if you wish to check your LORIS Configuration settings > in the > >>> backend database such as the URL field -- to see what was > actually > >> stored > >>> in a given database field and should display in the Config > >> module:?? > >>> You can run the queries listed in the "Troubleshooting > >> Configuration > >>> settings" section of our Github-wiki Setup Guide (under > Project > >>> Customization) :?? > >>> > >> > [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >>> Lastly, this question is perfectly appropriate for the > loris-dev > >> community > >>> support listserv -- please [2]subscribe here and then email > our > >> technical > >>> team your next question at?? [3][5]loris-dev at bic.mni.mcgill.ca > >> (after checking > >>> any forwarded threads for sensitive info).?? > >>> We prefer to answer technical questions there for the benefit > of > >> the > >>> community and other first-time users in the same position as > >> yourself.?? ?? > >>> Thanks and cheers,?? > >>> Christine?? > >>> On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD > >>> <[4][6]ioannis at berkeley.edu> wrote: > >>> > >>> Hi Loris support.?? > >>> My name is ioannis Pappas, a post-doc at the D'Esposito lab > >> stroke group > >>> at UC Berkeley. With the kind of help of our sys admin?? > Julie > >> (cc'ed) we > >>> have set up our loris database in our cluster (she is the > sudo > >> user and > >>> I am the admin user). > >>> If you allow me, I would like to ask you about the first > >> configuration > >>> steps in the front end as they are described in the > tutorial. We > >> can > >>> login to [5][7]http://loris and the front end normally. > >>> However any update that I am trying to?? perform in > >> Admin->Configuration > >>> doesn't work (e.g. updating the study name). It just > refreshes > >> the same > >>> page. I am just wondering if there is an issue with writing > in > >> the > >>> configuration file. > >>> Here are the permissions setup for where Loris is installed. > >>> chmod 777 /var/www/loris/smarty/templates_c > >>> cd /srv/www/loris > >>> chown -R lorisadmin:lorisadmin . > >>> chmod -c -R a+r . > >>> ?? ?? this command gives everyone read access, and outputs > what > >> changes > >>> were made: > >>> ?? ?? mode of ????./project???? changed from 0770 (rwxrwx---) to > 0774 > >>> (rwxrwxr--) > >>> ?? ?? mode of ????./tools/logs???? changed from 0770 (rwxrwx---) > to > >> 0774 > >>> (rwxrwxr--) > >>> find . -type d -exec chmod a+x -c {} \; > >>> ?? ?? this command gives everyone permission to open a > directory, > >> and > >>> outputs what changes were made: > >>> ?? ?? mode of ????./project???? changed from 0774 (rwxrwxr--) to > 0775 > >>> (rwxrwxr-x) > >>> ?? ?? mode of ????./tools/logs???? changed from 0774 (rwxrwxr--) > to > >> 0775 > >>> (rwxrwxr-x) > >>> Hopefully?? you can help me with this. I also subscribed to > the > >> mailing > >>> list but I am not sure if this too much of a basic question > for > >> the > >>> list. > >>> Best wishes, > >>> Ioannis > >>> On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI > Computing > >> Support > >>> <[6][8]support-cirl at berkeley.edu> wrote: > >>> > >>> Hi ioannis, maybe it's best to ask the developers? You can > cc > >> me if > >>> you'd like. > >>> On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas > >> <[7][9]ioannis at berkeley.edu> > >>> wrote: > >>> > >>> That did the trick Julie. Thank you! > >>> > >>> I am still trying to understand how configuration works > >> though. For > >>> example if I just try to change the name of the > >>> study from the front end, I get nowhere (it just > refreshes > >> the same > >>> page). > >>> > >>> I am not sure if this requires write permissions > somewhere in > >> a > >>> config file/folder and that????????s why it doesn????????t update > it. > >>> > >>> Best wishes, > >>> Ioannis > >>> > >>> > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI > Computing > >>> Support <[8][10]support-cirl at berkeley.edu> wrote: > >>> > > >>> > just in case you're interested, these are the > permission > >> changes I > >>> made: > >>> > > >>> > chmod 777 /var/www/loris/smarty/templates_c > >>> > cd /srv/www/loris > >>> > chown -R lorisadmin:lorisadmin . > >>> > chmod -c -R a+r . > >>> >?? ?? this command gives everyone read access, and > outputs > >> what > >>> changes were made: > >>> >?? ?? mode of ????./project???? changed from 0770 > (rwxrwx---) to > >> 0774 > >>> (rwxrwxr--) > >>> >?? ?? mode of ????./tools/logs???? changed from 0770 > (rwxrwx---) > >> to 0774 > >>> (rwxrwxr--) > >>> > find . -type d -exec chmod a+x -c {} \; > >>> >?? ?? this command gives everyone permission to open a > >> directory, and > >>> outputs what changes were made: > >>> >?? ?? mode of ????./project???? changed from 0774 > (rwxrwxr--) to > >> 0775 > >>> (rwxrwxr-x) > >>> >?? ?? mode of ????./tools/logs???? changed from 0774 > (rwxrwxr--) > >> to 0775 > >>> (rwxrwxr-x) > >>> > > >>> > > >>> > > >>> > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: > >>> >> Hi Julie. > >>> >> I just tried and I still don???t get anything. I also > >> tried > >>> private mode in Firefox in case the empty page was > cached. > >>> >> Sorry for this. > >>> >> > >>> >> Best wishes, > >>> >> Ioannis > >>> >> > >>> >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, HWNI > >> Computing > >>> Support <[9][11]support-cirl at berkeley.edu> wrote: > >>> >>> > >>> >>> hi Ioannis, > >>> >>> no worries, I changed the following directory to > 777: > >>> >>> > >>> >>> /var/www/loris/smarty/templates_c > >>> >>> > >>> >>> will you please check if that works? > >>> >>> > >>> >>> thanks! > >>> >>> > >>> >>> > >>> >>> > >>> >>> > >>> >>> > >>> >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas PhD > wrote: > >>> >>>>?? Hi Julie. > >>> >>>>?? Apologies for bugging you with this again. We > tried > >> now to > >>> >>>>?? access????? [1][10][12]http://loris????? > >>> >>>>?? and we are getting a????? blank page. I think the > reason > >> for this > >>> is that we > >>> >>>>?? don't have read????? permissions to read from the > >> template located > >>> in > >>> >>>>?? /var/www/loris/smarty See here bottom of the > >>> >>>>?? page????? > >>> > >> > [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> >>>>?? I think, in general, I am a little bit confused > as to > >> what the > >>> permissions > >>> >>>>?? should be for us that are not sudos. My > understanding > >> is that > >>> if we don't > >>> >>>>?? have read or write permissions then we can't > access or > >> write > >>> to > >>> >>>>?? /var/www/loris, meaning that we can't access or > >> configure. > >>> Should > >>> >>>>?? everything be chmod 777 for example?????? > >>> >>>>?? Thank you very much once again. > >>> >>>>?? Best wishes, > >>> >>>>?? Ioannis > >>> >>>>?? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis > Pappas PhD > >>> >>>>?? <[3][12][14]ioannis at berkeley.edu> wrote: > >>> >>>> > >>> >>>>?? ?? Thank you very much Julie. I appreciate this > and I > >> will dig > >>> into Loris > >>> >>>>?? ?? given your changes. Thank you so much for your > >> help. > >>> >>>>?? ?? Best wishes, > >>> >>>>?? ?? Ioannis > >>> >>>>?? ?? On Thu, Oct 31, 2019 at 12:48 PM Julie > Ashworth, > >> HWNI > >>> Computing Support > >>> >>>>?? ?? <[4][13][15]support-cirl at berkeley.edu> wrote: > >>> >>>> > >>> >>>>?? ?? ?? hi Ioannis, > >>> >>>> > >>> >>>>?? ?? ?? 1. I changed the permissions of > /srv/www/loris > >> to be owned > >>> by > >>> >>>>?? ?? ?? lorisadmin. I reivewed my installation > notes, > >> and I did > >>> this already > >>> >>>>?? ?? ?? when > >>> >>>>?? ?? ?? I installed the server. I'm not sure why > they > >> changed, so > >>> it's > >>> >>>>?? ?? ?? probably a > >>> >>>>?? ?? ?? good idea to keep an eye on that. > >>> >>>> > >>> >>>>?? ?? ?? 2. When I installed the loris software, I > also > >> installed a > >>> mysql > >>> >>>>?? ?? ?? database as recommended in the > instructions: > >>> >>>> > >>> >>>>?? ?? ?? projectname: LORIS > >>> >>>>?? ?? ?? databasename: loris_database > >>> >>>>?? ?? ?? mysqluser: lorismysql > >>> >>>>?? ?? ?? frontend: lorisweb > >>> >>>> > >>> >>>>?? ?? ?? 3. A couple of weeks ago, I moved Henrik's > home > >> directory > >>> to > >>> >>>>?? ?? ?? /home/despoA, > >>> >>>>?? ?? ?? but I forgot to update loris. This is done > now. > >>> >>>> > >>> >>>>?? ?? ?? best, > >>> >>>>?? ?? ?? Julie > >>> >>>> > >>> >>>>?? ?? ?? On 31-10-2019 11.15 -0700, Dr. Ioannis > Pappas > >> PhD wrote: > >>> >>>>> ??????? ??????? Hi Julie. > >>> >>>>> ??????? ??????? I hope you are well. We are trying to > >> configure loris > >>> that you > >>> >>>>?? ?? ?? kindly set > >>> >>>>> ??????? ??????? up for us. > >>> >>>>> ??????? ??????? I have a couple of questions for you if > you > >> allow me > >>> so.????? > >>> >>>>> ??????? ??????? 1) First, although we are logging into > the > >> front end > >>> with admin > >>> >>>>?? ?? ?? username > >>> >>>>> ??????? ??????? (lorisweb) and password, it seems that > any > >> kind of > >>> update of > >>> >>>>?? ?? ?? configuration > >>> >>>>> ??????? ??????? we are trying to do fails (meaning that > if > >> we, say, > >>> change the > >>> >>>>?? ?? ?? name of the > >>> >>>>> ??????? ??????? study and press "submit", this doesn't > do > >> anything-it > >>> doesn't > >>> >>>>?? ?? ?? update). > >>> >>>>> ??????? ??????? It's almost like our lorisweb user > doesn't > >> have write > >>> privileges > >>> >>>>?? ?? ?? in the > >>> >>>>> ??????? ??????? /var/www/loris/project (where I think > every > >>> configuration should > >>> >>>>?? ?? ?? be). > >>> >>>>> ??????? ??????? This generalizes for everything that we > are > >> trying to do > >>> in the > >>> >>>>?? ?? ?? front end. > >>> >>>>> ??????? ??????? Clicking any instrument/tab in the front > end > >> doesn't > >>> really point > >>> >>>>?? ?? ?? to > >>> >>>>> ??????? ??????? anything.????? > >>> >>>>> ??????? ??????? 2) Loris suggest doing configurations > via > >> SQL. Is it > >>> possible to > >>> >>>>?? ?? ?? run SQL > >>> >>>>> ??????? ??????? scripts in the backend > >>> >>>>> ??????? ??????? 3) For some reason typing ssh lors for > Henrik > >> doesn't > >>> directly > >>> >>>>?? ?? ?? take him to > >>> >>>>> ??????? ??????? loris (it requires a password that is > not the > >> password > >>> setup for > >>> >>>>?? ?? ?? the > >>> >>>>> ??????? ??????? lorisweb user). Will you be able to fix > this > >> via your > >>> sudo > >>> >>>>?? ?? ?? privileges? > >>> >>>>> ??????? ??????? Thank you very much in advance for all > your > >> help Julie. > >>> Let us > >>> >>>>?? ?? ?? know if > >>> >>>>> ??????? ??????? this is something that shouldn't be > directed > >> to you (but > >>> instead > >>> >>>>?? ?? ?? to the > >>> >>>>> ??????? ??????? loris people).????? > >>> >>>>> ??????? ??????? Best wishes, > >>> >>>>> ??????? ??????? Ioannis > >>> >>>>> ??????? ??????? On Mon, Sep 9, 2019 at 6:25 PM Julie > >> Ashworth, HWNI > >>> Computing > >>> >>>>?? ?? ?? Support > >>> >>>>> ??????? ??????? > <[1][5][14][16]support-cirl at berkeley.edu> > >> wrote: > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? hi Henrik and Ioannis, > >>> >>>>> ??????? ??????? ??????? the loris server is available for > you to > >> use. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? The servername is 'loris'. I > created a > >> directory > >>> called > >>> >>>>?? ?? ?? /data/loris for > >>> >>>>> ??????? ??????? ??????? you to store data. You may create > new > >> folders in > >>> /data/loris to > >>> >>>>?? ?? ?? organize > >>> >>>>> ??????? ??????? ??????? your data. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? 1) secure shell or secure copy: > >>> >>>>> ??????? ??????? ??????? You can log in with the 'ssh' or > 'scp' > >> command from > >>> your remote > >>> >>>>?? ?? ?? desktop > >>> >>>>> ??????? ??????? ??????? session. You don't need to > authenticate > >> to log in. > >>> Maybe you'll > >>> >>>>?? ?? ?? use scp > >>> >>>>> ??????? ??????? ??????? to transfer data between your > cluster > >> account and the > >>> loris > >>> >>>>?? ?? ?? server? > >>> >>>>> ??????? ??????? ??????? Please put the data in /data/loris, > so I > >> can make > >>> backups more > >>> >>>>?? ?? ?? easily. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? ??????? ??????? secure shell: > >>> >>>>> ??????? ??????? ??????? ??????? ??????? $ ssh loris > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? ??????? ??????? secure copy (change the > names > >> in brackets). Let > >>> me know if > >>> >>>>?? ?? ?? I can > >>> >>>>> ??????? ??????? ??????? ??????? ??????? help with syntax: > >>> >>>>> ??????? ??????? ??????? ??????? ??????? $ scp -r > >> loris:/data/loris/ > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? 2) front-end web interface.??????? > Open a > >> web browser in > >>> your remote > >>> >>>>?? ?? ?? desktop > >>> >>>>> ??????? ??????? ??????? session and enter the hostname: > >>> >>>>> ??????? ??????? ??????? [2][6][15][17]http://loris > >>> >>>>> ??????? ??????? ??????? I created an admin user called > >> 'lorisweb'. I put the > >>> password > >>> >>>>?? ?? ?? in > >>> >>>>> ??????? ??????? ??????? $HOME/newuser on the cluster. To > see it, > >> open a > >>> terminal, and > >>> >>>>?? ?? ?? run: > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? ??????? ??????? $ cat $HOME/newuser > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? If other people need shell access > to the > >> webserver, > >>> please let > >>> >>>>?? ?? ?? me know > >>> >>>>> ??????? ??????? ??????? so I can create a home directory > for > >> them. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? We should eventually discuss > backups. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? best, > >>> >>>>> ??????? ??????? ??????? Julie > >>> >>>>> > >>> >>>>> References > >>> >>>>> > >>> >>>>> ??????? ??????? Visible links > >>> >>>>> ??????? ??????? 1. > >> mailto:[7][16][18]support-cirl at berkeley.edu > >>> >>>>> ??????? ??????? 2. [8][17][19]http://loris/ > >>> >>>>?? ?? ?? ---end quoted text--- > >>> >>>> > >>> >>>> References > >>> >>>> > >>> >>>>?? Visible links > >>> >>>>?? 1. [18][20]http://loris/ > >>> >>>>?? 2. > >>> > >> > [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> >>>>?? 3. mailto:[20][22]ioannis at berkeley.edu > >>> >>>>?? 4. mailto:[21][23]support-cirl at berkeley.edu > >>> >>>>?? 5. mailto:[22][24]support-cirl at berkeley.edu > >>> >>>>?? 6. [23][25]http://loris/ > >>> >>>>?? 7. mailto:[24][26]support-cirl at berkeley.edu > >>> >>>>?? 8. [25][27]http://loris/ > >>> >>> ---end quoted text--- > >>> >> > >>> > ---end quoted text--- > >>> > >>> -- > >>> [26][28]christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> References > >>> > >>> Visible links > >>> 1. > >> > [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >>> 2. > [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> 3. mailto:[31]loris-dev at bic.mni.mcgill.ca > >>> 4. mailto:[32]ioannis at berkeley.edu > >>> 5. [33]http://loris/ > >>> 6. mailto:[34]support-cirl at berkeley.edu > >>> 7. mailto:[35]ioannis at berkeley.edu > >>> 8. mailto:[36]support-cirl at berkeley.edu > >>> 9. mailto:[37]support-cirl at berkeley.edu > >>> 10. [38]http://xn--loris-7qa/ > >>> 11. > [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> 12. mailto:[40]ioannis at berkeley.edu > >>> 13. mailto:[41]support-cirl at berkeley.edu > >>> 14. mailto:[42]support-cirl at berkeley.edu > >>> 15. [43]http://loris/ > >>> 16. mailto:[44]support-cirl at berkeley.edu > >>> 17. [45]http://loris/ > >>> 18. [46]http://loris/ > >>> 19. > [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> 20. mailto:[48]ioannis at berkeley.edu > >>> 21. mailto:[49]support-cirl at berkeley.edu > >>> 22. mailto:[50]support-cirl at berkeley.edu > >>> 23. [51]http://loris/ > >>> 24. mailto:[52]support-cirl at berkeley.edu > >>> 25. [53]http://loris/ > >>> 26. mailto:[54]christine.rogers at mcgill.ca > >> ---end quoted text--- > >> > >> -- > >> [55]christine.rogers at mcgill.ca > >> McGill Centre for Integrative Neuroscience | MCIN.ca > >> Montreal Neurological Institute > >> McGill University | Montreal | Canada > >> > >> References > >> > >> Visible links > >> 1. mailto:loris-dev at bic.mni.mcgill.ca > >> 2. mailto:support-cirl at berkeley.edu > >> 3. http://loris.priv/ > >> > 4. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >> 5. mailto:loris-dev at bic.mni.mcgill.ca > >> 6. mailto:ioannis at berkeley.edu > >> 7. http://loris/ > >> 8. mailto:support-cirl at berkeley.edu > >> 9. mailto:ioannis at berkeley.edu > >> 10. mailto:support-cirl at berkeley.edu > >> 11. mailto:support-cirl at berkeley.edu > >> 12. http://xn--loris-era/ > >> 13. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 14. mailto:ioannis at berkeley.edu > >> 15. mailto:support-cirl at berkeley.edu > >> 16. mailto:support-cirl at berkeley.edu > >> 17. http://loris/ > >> 18. mailto:support-cirl at berkeley.edu > >> 19. http://loris/ > >> 20. http://loris/ > >> 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 22. mailto:ioannis at berkeley.edu > >> 23. mailto:support-cirl at berkeley.edu > >> 24. mailto:support-cirl at berkeley.edu > >> 25. http://loris/ > >> 26. mailto:support-cirl at berkeley.edu > >> 27. http://loris/ > >> 28. mailto:christine.rogers at mcgill.ca > >> > 29. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >> 30. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >> 31. mailto:loris-dev at bic.mni.mcgill.ca > >> 32. mailto:ioannis at berkeley.edu > >> 33. http://loris/ > >> 34. mailto:support-cirl at berkeley.edu > >> 35. mailto:ioannis at berkeley.edu > >> 36. mailto:support-cirl at berkeley.edu > >> 37. mailto:support-cirl at berkeley.edu > >> 38. http://xn--loris-7qa/ > >> 39. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 40. mailto:ioannis at berkeley.edu > >> 41. mailto:support-cirl at berkeley.edu > >> 42. mailto:support-cirl at berkeley.edu > >> 43. http://loris/ > >> 44. mailto:support-cirl at berkeley.edu > >> 45. http://loris/ > >> 46. http://loris/ > >> 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 48. mailto:ioannis at berkeley.edu > >> 49. mailto:support-cirl at berkeley.edu > >> 50. mailto:support-cirl at berkeley.edu > >> 51. http://loris/ > >> 52. mailto:support-cirl at berkeley.edu > >> 53. http://loris/ > >> 54. mailto:christine.rogers at mcgill.ca > >> 55. mailto:christine.rogers at mcgill.ca > > ---end quoted text--- > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -- > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada ---end quoted text--- -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Fri Nov 8 21:04:14 2019 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Fri, 8 Nov 2019 18:04:14 -0800 Subject: [Loris-dev] loris server In-Reply-To: References: <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> Message-ID: <20191109020414.GB13279@nx6.priv> thanks Christine, yes, it's the lorismysql user in the config.xml file. lorismysql loris_database lorismysql we appeciate your help troubleshooting this. best, Julie On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote: > Hi Ioannis, > Could you open your file called config.xml > (/srv/www/loris/project/config.xml) and confirm for us -- which user > credential is stored there, and what's the name of the database it is > connecting to? > This is the mysql user which connects to the database from the front end > of LORIS. > If this user has insufficient privileges on your database, that would > cause the errors you are seeing. I had assumed from your thread it was > your lorismysql user but it sounds like this should be verified. > Let us know, and we'll keep following up when we come back online after > the weekend, > Best, > Christine > On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas > wrote: > > Hi Melanie. > Thank you for taking the time to reply to this. I took some to consider > your comments. Unfortunately as I said to Christine we are unable to do > any kind of updating to the database (either that is changing the name > or changing the small html description, etc.). > Based on some more digging and on some of Christine's comments I have a > feeling that our lorisweb front-end, admin user cannot write anything to > the database. Along these lines could it be the case the lorismysql user > (the database, admin user with INSERT, UPDATE, etc privileges) is not > ???talking??? to the lorisweb front end user? What is the difference between > the two and could it be a installation problem for them not talking to > each other? As Julie said, lorismysql user is working normally with > MariaDB. > Thank you again for your help. > Best wishes, > Ioannis > > On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs > wrote: > Hello, > Changing the project name in the configuration page > (https://loris.url/configuration/) of LORIS, only change the title of > the project. To see this change, you have to log out of LORIS and then > go back to the login page (https://.loris.url/). This is the only > place you can find the project name (except from the configuration > page). See ProjectName.png > As for files permission, I would suggest a few change to improve > security of you server. Some extra permissions where granted to help > you but are not needed. > * /srv/www/loris/smarty/templates_c/ should have ownership of > lorisadmin:httpd and permission 770 (or 775) > * srv/www/loris/project/ should have ownership lorisadmin:httpd and > permission 770 (775) > * All other files under loris should have lorisadmin:lorisadmin 755 > Reading through this change of mail, I understand that you let Apache > store file in /srv/www/loris > | 31 | DownloadPath | Downloads | /srv/www/loris/ | > Where > >> files are downloaded > Downloaded files should not be in the same tree as LORIS code. It > should be in a separate structure where Apache will not try and do not > have permission (in httpd.conf) to execute files. > Kind regards, > M??lanie Legault | Software developer | Faculty of Medicine | McGill > University > 3801 University, Montr??al, QC H3A 2B4 > > ---------------------------------------------------------------------- > > From: loris-dev-bounces at bic.mni.mcgill.ca > on behalf of Ioannis Pappas > > Sent: November 7, 2019 0:18 > To: loris-dev at bic.mni.mcgill.ca > Cc: Julie Ashworth, HWNI Computing Support > ; Christine Rogers, Ms. > > Subject: Re: [Loris-dev] loris server > > Hi Christine and Julie. > > Yes it looks like that any attempt to configure something in the > front-end results in the same page. I am sending this to the list (as > you requested Christine) alongside the troubleshooting and discussion > so far with Julie. > > Best wishes, > Ioannis > > > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing Support > wrote: > > > > hi Christine and Ioannis, > > Ioannis, can you follow-up with Christine about using the front-end? > > > > We're using CentOS7.7 and loris-21.0.1. > > > > I confirmed that I could login as the mysql user (lorismyqsl) and > change the 'url' config setting from 'http://loris.priv' to > 'http://localhost', and back again. > > > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON > (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) > WHERE csp.Name = 'www'; > > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > | ConfigID | Name | Label | > Value | Description | > > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > | 44 | host | Host | > loris.priv | Host | > > | 45 | url | Main LORIS URL > | http://loris.priv | Main URL where LORIS can be accessed | > > | 46 | issue_tracker_url | Issue tracker URL | > /issue_tracker | The *new* bug/issue tracker url | > > > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > > > > MariaDB [loris_database]> UPDATE Config SET Value='http://localhost' > WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > > Rows matched: 1 Changed: 1 Warnings: 0 > > > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON > (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) > WHERE csp.Name = 'www'; > > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > | ConfigID | Name | Label | > Value | Description | > > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > | 44 | host | Host | > loris.priv | Host | > > | 45 | url | Main LORIS URL > | http://localhost | Main URL where LORIS can be accessed | > > | 46 | issue_tracker_url | Issue tracker URL | > /issue_tracker | The *new* bug/issue tracker url | > > > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > 3 rows in set (0.00 sec) > > > > best, > > Julie > > > > > > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: > >> Hi Julie, > >> Forgive my ambiguity - We run the community support listserv for > >> developers, project administrators and sysadmins setting up > LORIS, so that > >> these users can contact our technical team for exactly such > technical > >> help. > >> If it's ok with you, I'd encourage you subscribe to the listserv > and > >> contact our technical team that way for the same reason. > >> (Note that front-end users of LORIS typically contact their > project team > >> for support, rather than us.) > >> Given that your lorismysql user privileges seem appropriate > ('UPDATE" is > >> there, I mistyped 'INSERT" before) > >> -- is there any other indication why the database record is not > >> updating? > >> In the front-end, can your 'admin' user effect any changes in > (any) Config > >> setting? > >> In the back-end, when you tried updating a field using your > >> lorismysql credential, what happened? > >> Your front end is loading ok, and you can log in there, if I > understood > >> correctly. > >> Thanks for letting us know these details at > >> [1]loris-dev at bic.mni.mcgill.ca > >> Please also include what version of LORIS you are installing, and > on what > >> OS version. > >> Best, > >> Christine > >> On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI Computing > Support > >> <[2]support-cirl at berkeley.edu> wrote: > >> > >> Thank you Christine, > >> I'm the linux sysadmin who installed the loris database for > Ioannis. > >> I'm not a loris user, however, so that makes it a little > awkward for > >> troubleshooting via the mailing list. I'm happy to help in > whatever way > >> I can. > >> > >> Regarding the database permissions, I ran: > >> > >> MariaDB [(none)]> show grants for 'lorismysql'@'%'; > >> > +--------------------------------------------------------------------------------+ > >> | Grants for lorismysql@% > >> | > >> > +--------------------------------------------------------------------------------+ > >> | GRANT USAGE ON *.* TO 'lorismysql'@'%' > >> | > >> | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO > >> 'lorismysql'@'%' | > >> > +--------------------------------------------------------------------------------+ > >> 2 rows in set (0.00 sec) > >> > >> looking at the 'tips' section in the page you referred to... > >> > >> | 29 | base | Base | /srv/www/loris/ | > The base > >> filesystem path where LORIS is > installed | > >> | 31 | DownloadPath | Downloads | /srv/www/loris/ | > Where > >> files are downloaded > >> > >> > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> | ConfigID | Name | Label | > Value | > >> Description | > >> > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> | 44 | host | Host | > loris.priv | > >> Host | > >> | 45 | url | Main LORIS URL | > >> [3]http://loris.priv | Main URL where LORIS can be accessed | > >> | 46 | issue_tracker_url | Issue tracker URL | > /issue_tracker | > >> The *new* bug/issue tracker url | > >> > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >> > >> apache config: > >> > >> Listen 80 > >> User apache > >> Group apache > >> DocumentRoot "/srv/www/loris/htdocs" > >> > >> > >> AllowOverride none > >> Require all denied > >> > >> > >> > >> AllowOverride All > >> Options Indexes FollowSymLinks > >> Require all granted > >> > >> > >> > >> Options Indexes FollowSymLinks > >> AllowOverride All > >> Require all granted > >> > >> > >> file permissions: > >> > >> # ls -ld /srv/www/loris/smarty/templates_c > >> drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 > >> /srv/www/loris/smarty/templates_c/ > >> > >> [root at loris loris]# ls -l /srv/www/loris/smarty/templates_c > >> -rw-r--r-- 1 lorisadmin lorisadmin 2444 Oct 31 09:46 > >> > 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 > >> > 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep 7 18:39 > >> 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3296 Sep 7 18:35 > >> > 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 5901 Sep 7 21:10 > >> > 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep 7 18:39 > >> > 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 874 Sep 10 11:01 > >> 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 1101 Sep 10 10:58 > >> > 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 > >> > 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3590 Sep 7 18:39 > >> > a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep 7 21:08 > >> > a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 897 Sep 7 18:35 > >> a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 9210 Sep 10 11:01 > >> > a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 8917 Sep 10 13:21 > >> > ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 4811 Sep 7 18:35 > >> > d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 3309 Sep 10 11:02 > >> > d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 > >> > e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php > >> -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep 7 17:42 > >> fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php > >> > >> thanks again! > >> Julie > >> > >> On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: > >>> Hi Ioannis,?? > >>> Thanks for your question.?? > >>> Given that the URL field is not updating, I suspect it's a > database > >>> back-end issue.?? > >>> Can you verify -- Has your mysql user lorismysql?? been granted > the > >> "INSERT" > >>> privilege for the right database? If not, that would result in > an > >> error > >>> like the kind you are seeing.?? > >>> Also, if you wish to check your LORIS Configuration settings > in the > >>> backend database such as the URL field -- to see what was > actually > >> stored > >>> in a given database field and should display in the Config > >> module:?? > >>> You can run the queries listed in the "Troubleshooting > >> Configuration > >>> settings" section of our Github-wiki Setup Guide (under > Project > >>> Customization) :?? > >>> > >> > [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >>> Lastly, this question is perfectly appropriate for the > loris-dev > >> community > >>> support listserv -- please [2]subscribe here and then email > our > >> technical > >>> team your next question at?? [3][5]loris-dev at bic.mni.mcgill.ca > >> (after checking > >>> any forwarded threads for sensitive info).?? > >>> We prefer to answer technical questions there for the benefit > of > >> the > >>> community and other first-time users in the same position as > >> yourself.?? ?? > >>> Thanks and cheers,?? > >>> Christine?? > >>> On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD > >>> <[4][6]ioannis at berkeley.edu> wrote: > >>> > >>> Hi Loris support.?? > >>> My name is ioannis Pappas, a post-doc at the D'Esposito lab > >> stroke group > >>> at UC Berkeley. With the kind of help of our sys admin?? > Julie > >> (cc'ed) we > >>> have set up our loris database in our cluster (she is the > sudo > >> user and > >>> I am the admin user). > >>> If you allow me, I would like to ask you about the first > >> configuration > >>> steps in the front end as they are described in the > tutorial. We > >> can > >>> login to [5][7]http://loris and the front end normally. > >>> However any update that I am trying to?? perform in > >> Admin->Configuration > >>> doesn't work (e.g. updating the study name). It just > refreshes > >> the same > >>> page. I am just wondering if there is an issue with writing > in > >> the > >>> configuration file. > >>> Here are the permissions setup for where Loris is installed. > >>> chmod 777 /var/www/loris/smarty/templates_c > >>> cd /srv/www/loris > >>> chown -R lorisadmin:lorisadmin . > >>> chmod -c -R a+r . > >>> ?? ?? this command gives everyone read access, and outputs > what > >> changes > >>> were made: > >>> ?? ?? mode of ????./project???? changed from 0770 (rwxrwx---) to > 0774 > >>> (rwxrwxr--) > >>> ?? ?? mode of ????./tools/logs???? changed from 0770 (rwxrwx---) > to > >> 0774 > >>> (rwxrwxr--) > >>> find . -type d -exec chmod a+x -c {} \; > >>> ?? ?? this command gives everyone permission to open a > directory, > >> and > >>> outputs what changes were made: > >>> ?? ?? mode of ????./project???? changed from 0774 (rwxrwxr--) to > 0775 > >>> (rwxrwxr-x) > >>> ?? ?? mode of ????./tools/logs???? changed from 0774 (rwxrwxr--) > to > >> 0775 > >>> (rwxrwxr-x) > >>> Hopefully?? you can help me with this. I also subscribed to > the > >> mailing > >>> list but I am not sure if this too much of a basic question > for > >> the > >>> list. > >>> Best wishes, > >>> Ioannis > >>> On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI > Computing > >> Support > >>> <[6][8]support-cirl at berkeley.edu> wrote: > >>> > >>> Hi ioannis, maybe it's best to ask the developers? You can > cc > >> me if > >>> you'd like. > >>> On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas > >> <[7][9]ioannis at berkeley.edu> > >>> wrote: > >>> > >>> That did the trick Julie. Thank you! > >>> > >>> I am still trying to understand how configuration works > >> though. For > >>> example if I just try to change the name of the > >>> study from the front end, I get nowhere (it just > refreshes > >> the same > >>> page). > >>> > >>> I am not sure if this requires write permissions > somewhere in > >> a > >>> config file/folder and that????????s why it doesn????????t update > it. > >>> > >>> Best wishes, > >>> Ioannis > >>> > >>> > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI > Computing > >>> Support <[8][10]support-cirl at berkeley.edu> wrote: > >>> > > >>> > just in case you're interested, these are the > permission > >> changes I > >>> made: > >>> > > >>> > chmod 777 /var/www/loris/smarty/templates_c > >>> > cd /srv/www/loris > >>> > chown -R lorisadmin:lorisadmin . > >>> > chmod -c -R a+r . > >>> >?? ?? this command gives everyone read access, and > outputs > >> what > >>> changes were made: > >>> >?? ?? mode of ????./project???? changed from 0770 > (rwxrwx---) to > >> 0774 > >>> (rwxrwxr--) > >>> >?? ?? mode of ????./tools/logs???? changed from 0770 > (rwxrwx---) > >> to 0774 > >>> (rwxrwxr--) > >>> > find . -type d -exec chmod a+x -c {} \; > >>> >?? ?? this command gives everyone permission to open a > >> directory, and > >>> outputs what changes were made: > >>> >?? ?? mode of ????./project???? changed from 0774 > (rwxrwxr--) to > >> 0775 > >>> (rwxrwxr-x) > >>> >?? ?? mode of ????./tools/logs???? changed from 0774 > (rwxrwxr--) > >> to 0775 > >>> (rwxrwxr-x) > >>> > > >>> > > >>> > > >>> > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: > >>> >> Hi Julie. > >>> >> I just tried and I still don???t get anything. I also > >> tried > >>> private mode in Firefox in case the empty page was > cached. > >>> >> Sorry for this. > >>> >> > >>> >> Best wishes, > >>> >> Ioannis > >>> >> > >>> >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, HWNI > >> Computing > >>> Support <[9][11]support-cirl at berkeley.edu> wrote: > >>> >>> > >>> >>> hi Ioannis, > >>> >>> no worries, I changed the following directory to > 777: > >>> >>> > >>> >>> /var/www/loris/smarty/templates_c > >>> >>> > >>> >>> will you please check if that works? > >>> >>> > >>> >>> thanks! > >>> >>> > >>> >>> > >>> >>> > >>> >>> > >>> >>> > >>> >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas PhD > wrote: > >>> >>>>?? Hi Julie. > >>> >>>>?? Apologies for bugging you with this again. We > tried > >> now to > >>> >>>>?? access????? [1][10][12]http://loris????? > >>> >>>>?? and we are getting a????? blank page. I think the > reason > >> for this > >>> is that we > >>> >>>>?? don't have read????? permissions to read from the > >> template located > >>> in > >>> >>>>?? /var/www/loris/smarty See here bottom of the > >>> >>>>?? page????? > >>> > >> > [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> >>>>?? I think, in general, I am a little bit confused > as to > >> what the > >>> permissions > >>> >>>>?? should be for us that are not sudos. My > understanding > >> is that > >>> if we don't > >>> >>>>?? have read or write permissions then we can't > access or > >> write > >>> to > >>> >>>>?? /var/www/loris, meaning that we can't access or > >> configure. > >>> Should > >>> >>>>?? everything be chmod 777 for example?????? > >>> >>>>?? Thank you very much once again. > >>> >>>>?? Best wishes, > >>> >>>>?? Ioannis > >>> >>>>?? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis > Pappas PhD > >>> >>>>?? <[3][12][14]ioannis at berkeley.edu> wrote: > >>> >>>> > >>> >>>>?? ?? Thank you very much Julie. I appreciate this > and I > >> will dig > >>> into Loris > >>> >>>>?? ?? given your changes. Thank you so much for your > >> help. > >>> >>>>?? ?? Best wishes, > >>> >>>>?? ?? Ioannis > >>> >>>>?? ?? On Thu, Oct 31, 2019 at 12:48 PM Julie > Ashworth, > >> HWNI > >>> Computing Support > >>> >>>>?? ?? <[4][13][15]support-cirl at berkeley.edu> wrote: > >>> >>>> > >>> >>>>?? ?? ?? hi Ioannis, > >>> >>>> > >>> >>>>?? ?? ?? 1. I changed the permissions of > /srv/www/loris > >> to be owned > >>> by > >>> >>>>?? ?? ?? lorisadmin. I reivewed my installation > notes, > >> and I did > >>> this already > >>> >>>>?? ?? ?? when > >>> >>>>?? ?? ?? I installed the server. I'm not sure why > they > >> changed, so > >>> it's > >>> >>>>?? ?? ?? probably a > >>> >>>>?? ?? ?? good idea to keep an eye on that. > >>> >>>> > >>> >>>>?? ?? ?? 2. When I installed the loris software, I > also > >> installed a > >>> mysql > >>> >>>>?? ?? ?? database as recommended in the > instructions: > >>> >>>> > >>> >>>>?? ?? ?? projectname: LORIS > >>> >>>>?? ?? ?? databasename: loris_database > >>> >>>>?? ?? ?? mysqluser: lorismysql > >>> >>>>?? ?? ?? frontend: lorisweb > >>> >>>> > >>> >>>>?? ?? ?? 3. A couple of weeks ago, I moved Henrik's > home > >> directory > >>> to > >>> >>>>?? ?? ?? /home/despoA, > >>> >>>>?? ?? ?? but I forgot to update loris. This is done > now. > >>> >>>> > >>> >>>>?? ?? ?? best, > >>> >>>>?? ?? ?? Julie > >>> >>>> > >>> >>>>?? ?? ?? On 31-10-2019 11.15 -0700, Dr. Ioannis > Pappas > >> PhD wrote: > >>> >>>>> ??????? ??????? Hi Julie. > >>> >>>>> ??????? ??????? I hope you are well. We are trying to > >> configure loris > >>> that you > >>> >>>>?? ?? ?? kindly set > >>> >>>>> ??????? ??????? up for us. > >>> >>>>> ??????? ??????? I have a couple of questions for you if > you > >> allow me > >>> so.????? > >>> >>>>> ??????? ??????? 1) First, although we are logging into > the > >> front end > >>> with admin > >>> >>>>?? ?? ?? username > >>> >>>>> ??????? ??????? (lorisweb) and password, it seems that > any > >> kind of > >>> update of > >>> >>>>?? ?? ?? configuration > >>> >>>>> ??????? ??????? we are trying to do fails (meaning that > if > >> we, say, > >>> change the > >>> >>>>?? ?? ?? name of the > >>> >>>>> ??????? ??????? study and press "submit", this doesn't > do > >> anything-it > >>> doesn't > >>> >>>>?? ?? ?? update). > >>> >>>>> ??????? ??????? It's almost like our lorisweb user > doesn't > >> have write > >>> privileges > >>> >>>>?? ?? ?? in the > >>> >>>>> ??????? ??????? /var/www/loris/project (where I think > every > >>> configuration should > >>> >>>>?? ?? ?? be). > >>> >>>>> ??????? ??????? This generalizes for everything that we > are > >> trying to do > >>> in the > >>> >>>>?? ?? ?? front end. > >>> >>>>> ??????? ??????? Clicking any instrument/tab in the front > end > >> doesn't > >>> really point > >>> >>>>?? ?? ?? to > >>> >>>>> ??????? ??????? anything.????? > >>> >>>>> ??????? ??????? 2) Loris suggest doing configurations > via > >> SQL. Is it > >>> possible to > >>> >>>>?? ?? ?? run SQL > >>> >>>>> ??????? ??????? scripts in the backend > >>> >>>>> ??????? ??????? 3) For some reason typing ssh lors for > Henrik > >> doesn't > >>> directly > >>> >>>>?? ?? ?? take him to > >>> >>>>> ??????? ??????? loris (it requires a password that is > not the > >> password > >>> setup for > >>> >>>>?? ?? ?? the > >>> >>>>> ??????? ??????? lorisweb user). Will you be able to fix > this > >> via your > >>> sudo > >>> >>>>?? ?? ?? privileges? > >>> >>>>> ??????? ??????? Thank you very much in advance for all > your > >> help Julie. > >>> Let us > >>> >>>>?? ?? ?? know if > >>> >>>>> ??????? ??????? this is something that shouldn't be > directed > >> to you (but > >>> instead > >>> >>>>?? ?? ?? to the > >>> >>>>> ??????? ??????? loris people).????? > >>> >>>>> ??????? ??????? Best wishes, > >>> >>>>> ??????? ??????? Ioannis > >>> >>>>> ??????? ??????? On Mon, Sep 9, 2019 at 6:25 PM Julie > >> Ashworth, HWNI > >>> Computing > >>> >>>>?? ?? ?? Support > >>> >>>>> ??????? ??????? > <[1][5][14][16]support-cirl at berkeley.edu> > >> wrote: > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? hi Henrik and Ioannis, > >>> >>>>> ??????? ??????? ??????? the loris server is available for > you to > >> use. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? The servername is 'loris'. I > created a > >> directory > >>> called > >>> >>>>?? ?? ?? /data/loris for > >>> >>>>> ??????? ??????? ??????? you to store data. You may create > new > >> folders in > >>> /data/loris to > >>> >>>>?? ?? ?? organize > >>> >>>>> ??????? ??????? ??????? your data. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? 1) secure shell or secure copy: > >>> >>>>> ??????? ??????? ??????? You can log in with the 'ssh' or > 'scp' > >> command from > >>> your remote > >>> >>>>?? ?? ?? desktop > >>> >>>>> ??????? ??????? ??????? session. You don't need to > authenticate > >> to log in. > >>> Maybe you'll > >>> >>>>?? ?? ?? use scp > >>> >>>>> ??????? ??????? ??????? to transfer data between your > cluster > >> account and the > >>> loris > >>> >>>>?? ?? ?? server? > >>> >>>>> ??????? ??????? ??????? Please put the data in /data/loris, > so I > >> can make > >>> backups more > >>> >>>>?? ?? ?? easily. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? ??????? ??????? secure shell: > >>> >>>>> ??????? ??????? ??????? ??????? ??????? $ ssh loris > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? ??????? ??????? secure copy (change the > names > >> in brackets). Let > >>> me know if > >>> >>>>?? ?? ?? I can > >>> >>>>> ??????? ??????? ??????? ??????? ??????? help with syntax: > >>> >>>>> ??????? ??????? ??????? ??????? ??????? $ scp -r > >> loris:/data/loris/ > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? 2) front-end web interface.??????? > Open a > >> web browser in > >>> your remote > >>> >>>>?? ?? ?? desktop > >>> >>>>> ??????? ??????? ??????? session and enter the hostname: > >>> >>>>> ??????? ??????? ??????? [2][6][15][17]http://loris > >>> >>>>> ??????? ??????? ??????? I created an admin user called > >> 'lorisweb'. I put the > >>> password > >>> >>>>?? ?? ?? in > >>> >>>>> ??????? ??????? ??????? $HOME/newuser on the cluster. To > see it, > >> open a > >>> terminal, and > >>> >>>>?? ?? ?? run: > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? ??????? ??????? $ cat $HOME/newuser > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? If other people need shell access > to the > >> webserver, > >>> please let > >>> >>>>?? ?? ?? me know > >>> >>>>> ??????? ??????? ??????? so I can create a home directory > for > >> them. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? We should eventually discuss > backups. > >>> >>>>> > >>> >>>>> ??????? ??????? ??????? best, > >>> >>>>> ??????? ??????? ??????? Julie > >>> >>>>> > >>> >>>>> References > >>> >>>>> > >>> >>>>> ??????? ??????? Visible links > >>> >>>>> ??????? ??????? 1. > >> mailto:[7][16][18]support-cirl at berkeley.edu > >>> >>>>> ??????? ??????? 2. [8][17][19]http://loris/ > >>> >>>>?? ?? ?? ---end quoted text--- > >>> >>>> > >>> >>>> References > >>> >>>> > >>> >>>>?? Visible links > >>> >>>>?? 1. [18][20]http://loris/ > >>> >>>>?? 2. > >>> > >> > [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> >>>>?? 3. mailto:[20][22]ioannis at berkeley.edu > >>> >>>>?? 4. mailto:[21][23]support-cirl at berkeley.edu > >>> >>>>?? 5. mailto:[22][24]support-cirl at berkeley.edu > >>> >>>>?? 6. [23][25]http://loris/ > >>> >>>>?? 7. mailto:[24][26]support-cirl at berkeley.edu > >>> >>>>?? 8. [25][27]http://loris/ > >>> >>> ---end quoted text--- > >>> >> > >>> > ---end quoted text--- > >>> > >>> -- > >>> [26][28]christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> References > >>> > >>> Visible links > >>> 1. > >> > [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >>> 2. > [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> 3. mailto:[31]loris-dev at bic.mni.mcgill.ca > >>> 4. mailto:[32]ioannis at berkeley.edu > >>> 5. [33]http://loris/ > >>> 6. mailto:[34]support-cirl at berkeley.edu > >>> 7. mailto:[35]ioannis at berkeley.edu > >>> 8. mailto:[36]support-cirl at berkeley.edu > >>> 9. mailto:[37]support-cirl at berkeley.edu > >>> 10. [38]http://xn--loris-7qa/ > >>> 11. > [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> 12. mailto:[40]ioannis at berkeley.edu > >>> 13. mailto:[41]support-cirl at berkeley.edu > >>> 14. mailto:[42]support-cirl at berkeley.edu > >>> 15. [43]http://loris/ > >>> 16. mailto:[44]support-cirl at berkeley.edu > >>> 17. [45]http://loris/ > >>> 18. [46]http://loris/ > >>> 19. > [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >>> 20. mailto:[48]ioannis at berkeley.edu > >>> 21. mailto:[49]support-cirl at berkeley.edu > >>> 22. mailto:[50]support-cirl at berkeley.edu > >>> 23. [51]http://loris/ > >>> 24. mailto:[52]support-cirl at berkeley.edu > >>> 25. [53]http://loris/ > >>> 26. mailto:[54]christine.rogers at mcgill.ca > >> ---end quoted text--- > >> > >> -- > >> [55]christine.rogers at mcgill.ca > >> McGill Centre for Integrative Neuroscience | MCIN.ca > >> Montreal Neurological Institute > >> McGill University | Montreal | Canada > >> > >> References > >> > >> Visible links > >> 1. mailto:loris-dev at bic.mni.mcgill.ca > >> 2. mailto:support-cirl at berkeley.edu > >> 3. http://loris.priv/ > >> > 4. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >> 5. mailto:loris-dev at bic.mni.mcgill.ca > >> 6. mailto:ioannis at berkeley.edu > >> 7. http://loris/ > >> 8. mailto:support-cirl at berkeley.edu > >> 9. mailto:ioannis at berkeley.edu > >> 10. mailto:support-cirl at berkeley.edu > >> 11. mailto:support-cirl at berkeley.edu > >> 12. http://xn--loris-era/ > >> 13. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 14. mailto:ioannis at berkeley.edu > >> 15. mailto:support-cirl at berkeley.edu > >> 16. mailto:support-cirl at berkeley.edu > >> 17. http://loris/ > >> 18. mailto:support-cirl at berkeley.edu > >> 19. http://loris/ > >> 20. http://loris/ > >> 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 22. mailto:ioannis at berkeley.edu > >> 23. mailto:support-cirl at berkeley.edu > >> 24. mailto:support-cirl at berkeley.edu > >> 25. http://loris/ > >> 26. mailto:support-cirl at berkeley.edu > >> 27. http://loris/ > >> 28. mailto:christine.rogers at mcgill.ca > >> > 29. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >> 30. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >> 31. mailto:loris-dev at bic.mni.mcgill.ca > >> 32. mailto:ioannis at berkeley.edu > >> 33. http://loris/ > >> 34. mailto:support-cirl at berkeley.edu > >> 35. mailto:ioannis at berkeley.edu > >> 36. mailto:support-cirl at berkeley.edu > >> 37. mailto:support-cirl at berkeley.edu > >> 38. http://xn--loris-7qa/ > >> 39. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 40. mailto:ioannis at berkeley.edu > >> 41. mailto:support-cirl at berkeley.edu > >> 42. mailto:support-cirl at berkeley.edu > >> 43. http://loris/ > >> 44. mailto:support-cirl at berkeley.edu > >> 45. http://loris/ > >> 46. http://loris/ > >> 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >> 48. mailto:ioannis at berkeley.edu > >> 49. mailto:support-cirl at berkeley.edu > >> 50. mailto:support-cirl at berkeley.edu > >> 51. http://loris/ > >> 52. mailto:support-cirl at berkeley.edu > >> 53. http://loris/ > >> 54. mailto:christine.rogers at mcgill.ca > >> 55. mailto:christine.rogers at mcgill.ca > > ---end quoted text--- > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -- > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada ---end quoted text--- From support-cirl at berkeley.edu Mon Nov 11 12:03:42 2019 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Mon, 11 Nov 2019 09:03:42 -0800 Subject: [Loris-dev] loris server In-Reply-To: References: <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> <20191109020414.GB13279@nx6.priv> Message-ID: <20191111170342.GA4213@gaia.neuro.berkeley.edu> thanks Melanie, I'm including the output below. My understanding is that '%' matches all hostnames. Should I specifically grant permission to 'loris.priv' from user lorismysql? Or perhaps you recommend changing loris_database entries ('host' to 'localhost' and 'url' to 'http://localhost')? thanks! MariaDB [(none)]> SELECT User, Host FROM mysql.user; +------------+-----------+ | User | Host | +------------+-----------+ | lorismysql | % | | root | 127.0.0.1 | | root | ::1 | | lorismysql | localhost | | root | localhost | +------------+-----------+ 5 rows in set (0.00 sec) MariaDB [(none)]> SHOW grants for 'lorismysql'@'%'; +--------------------------------------------------------------------------------+ | Grants for lorismysql@% +--------------------------------------------------------------------------------+ | GRANT USAGE ON *.* TO 'lorismysql'@'%' | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO 'lorismysql'@'%' | +--------------------------------------------------------------------------------+ 2 rows in set (0.00 sec) On 11-11-2019 15.47 +0000, Melanie Legault, Mrs wrote: > Hello Julie, > Could it be that your MySQL 'lorismysql' user have different permissions > depending on where it is connecting to the DB? > A database admin (root) can check this for you. > SELECT User, Host FROM mysql.user; > then for the user that match the Host (name or IP address) of your LORIS > (Apache) server > SHOW grants for 'lorismysql'@''; > > M??lanie > > -------------------------------------------------------------------------- > > From: Julie Ashworth, HWNI Computing Support > Sent: November 8, 2019 21:04 > To: Christine Rogers, Ms. > Cc: Ioannis Pappas ; Melanie Legault, Mrs > ; loris-dev at bic.mni.mcgill.ca > > Subject: Re: [Loris-dev] loris server > ?? > thanks Christine, > > yes, it's the lorismysql user in the config.xml file. > ?????????????? lorismysql > ?????????????? loris_database > ?????????????? lorismysql > > we appeciate your help troubleshooting this. > best, > Julie > > On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote: > >?????? Hi Ioannis, > >?????? Could you open your file called config.xml > >?????? (/srv/www/loris/project/config.xml) and confirm for us --?? which user > >?????? credential is stored there, and what's the name of the database it is > >?????? connecting to? > >?????? This is the mysql user which connects to the database from the front > end > >?????? of LORIS.?? > >?????? If this user has insufficient privileges on your database, that would > >?????? cause the errors you are seeing.?? I had assumed from your thread it > was > >?????? your lorismysql user but it sounds like this should be verified. > >?????? Let us know, and we'll keep following up when we come back online > after > >?????? the weekend, > >?????? Best, > >?????? Christine > >?????? On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas > >?????? wrote: > > > >?????????? Hi Melanie. > >?????????? Thank you for taking the time to reply to this. I took some to > consider > >?????????? your comments. Unfortunately as I said to Christine we are unable > to do > >?????????? any kind of updating to the database (either that is changing the > name > >?????????? or changing the small html description, etc.). > >?????????? Based on some more digging and on some of Christine's comments I > have a > >?????????? feeling that our lorisweb front-end, admin user cannot write > anything to > >?????????? the database. Along these lines could it be the case the lorismysql > user > >?????????? (the database, admin user with INSERT, UPDATE, etc privileges) is > not > >?????????? ???????talking????? to the lorisweb front end user? What is the > difference between > >?????????? the two and could it be a installation problem for them not talking > to > >?????????? each other? As Julie said, lorismysql user is working normally with > >?????????? MariaDB. > >?????????? Thank you again for your help. > >?????????? Best wishes, > >?????????? Ioannis > > > >?????????????? On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs > >?????????????? wrote: > >?????????????? Hello, > >?????????????? Changing the project name in the configuration page > >?????????????? ([1]https://loris.url/configuration/) of LORIS, only change the > title of > >?????????????? the project. To see this change, you have to log out of LORIS and > then > >?????????????? go back to the login page ([2]https://.loris.url/). This is the > only > >?????????????? place you can find the project name (except from the > configuration > >?????????????? page). See ProjectName.png > >?????????????? As for files permission, I would suggest a few change to improve > >?????????????? security of you server. Some extra permissions where granted to > help > >?????????????? you but are not needed. > >?????????????????? * /srv/www/loris/smarty/templates_c/?? should have ownership of > >?????????????????????? lorisadmin:httpd and permission 770 (or 775) > >?????????????????? * srv/www/loris/project/?? should have ownership > lorisadmin:httpd and > >?????????????????????? permission 770 (775) > >?????????????????? * All other files under loris should have lorisadmin:lorisadmin > 755 > >?????????????? Reading through this change of mail, I understand that you let > Apache > >?????????????? store file in /srv/www/loris > >???????????????????? |???????????? 31 | DownloadPath???? | Downloads???? | /srv/www/loris/???? > | > >?????????????? Where > >?????????????? >>???????? files are downloaded > >?????????????? Downloaded files should not be in the same tree as LORIS code. It > >?????????????? should be in a separate structure where Apache will not try and > do not > >?????????????? have permission (in httpd.conf) to execute files. > >?????????????? Kind regards, > >?????????????? M????lanie Legault | Software developer | Faculty of Medicine | > McGill > >?????????????? University?? > >?????????????? 3801 University, Montr????al, QC H3A 2B4 > > > >?????????? > ---------------------------------------------------------------------- > > > >?????????????? From: loris-dev-bounces at bic.mni.mcgill.ca > >?????????????? on behalf of Ioannis Pappas > >?????????????? > >?????????????? Sent: November 7, 2019 0:18 > >?????????????? To: loris-dev at bic.mni.mcgill.ca > >?????????????? Cc: Julie Ashworth, HWNI Computing Support > >?????????????? ; Christine Rogers, Ms. > >?????????????? > >?????????????? Subject: Re: [Loris-dev] loris server > >???????????????? > >?????????????? Hi Christine and Julie. > > > >?????????????? Yes it looks like that any attempt to configure something in the > >?????????????? front-end results in the same page. I am sending this to the list > (as > >?????????????? you requested Christine) alongside the troubleshooting and > discussion > >?????????????? so far with Julie. > > > >?????????????? Best wishes, > >?????????????? Ioannis > > > >?????????????? > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing > Support > >?????????????? wrote: > >?????????????? > > >?????????????? > hi Christine and Ioannis, > >?????????????? > Ioannis, can you follow-up with Christine about using the > front-end? > >?????????????? > > >?????????????? > We're using CentOS7.7 and loris-21.0.1. > >?????????????? > > >?????????????? > I confirmed that I could login as the mysql user (lorismyqsl) > and > >?????????????? change the 'url' config setting from '[3]http://loris.priv' to > >?????????????? '[4]http://localhost', and back again. > >?????????????? > > >?????????????? > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > >?????????????? c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs > ON > >?????????????? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = > csp.ID) > >?????????????? WHERE csp.Name = 'www'; > >?????????????? > > >?????????????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????????????? > | ConfigID | Name?????????????????????????? | Label???????????????????????? | > >?????????????? Value???????????????????????? | Description?????????????????????????????????????????????????? | > >?????????????? > > >?????????????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????????????? > |???????????? 44 | host?????????????????????????? | Host?????????????????????????? | > >?????????????? loris.priv?????????????? | Host???????????????????????????????????????????????????????????????? | > >?????????????? > |???????????? 45 | url???????????????????????????? | Main LORIS URL???? > >?????????????? | [5]http://loris.priv | Main URL where LORIS can be accessed | > >?????????????? > |???????????? 46 | issue_tracker_url | Issue tracker URL | > >?????????????? /issue_tracker?????? | The *new* bug/issue tracker url?????????? | > >?????????????? > > >?????????????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????????????? > > >?????????????? > MariaDB [loris_database]> UPDATE Config SET > Value='[6]http://localhost' > >?????????????? WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > >?????????????? > Rows matched: 1?? Changed: 1?? Warnings: 0 > >?????????????? > > >?????????????? > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > >?????????????? c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs > ON > >?????????????? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = > csp.ID) > >?????????????? WHERE csp.Name = 'www'; > >?????????????? > > >?????????????? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >?????????????? > | ConfigID | Name?????????????????????????? | Label???????????????????????? | > >?????????????? Value?????????????????????? | Description?????????????????????????????????????????????????? | > >?????????????? > > >?????????????? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >?????????????? > |???????????? 44 | host?????????????????????????? | Host?????????????????????????? | > >?????????????? loris.priv???????????? | Host???????????????????????????????????????????????????????????????? | > >?????????????? > |???????????? 45 | url???????????????????????????? | Main LORIS URL???? > >?????????????? | [7]http://localhost | Main URL where LORIS can be accessed | > >?????????????? > |???????????? 46 | issue_tracker_url | Issue tracker URL | > >?????????????? /issue_tracker???? | The *new* bug/issue tracker url?????????? | > >?????????????? > > >?????????????? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >?????????????? > 3 rows in set (0.00 sec) > >?????????????? > > >?????????????? > best, > >?????????????? > Julie > >?????????????? > > >?????????????? > > >?????????????? > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: > >?????????????? >>???? Hi Julie, > >?????????????? >>???? Forgive my ambiguity - We run the community support listserv > for > >?????????????? >>???? developers, project administrators and sysadmins setting up > >?????????????? LORIS, so that > >?????????????? >>???? these users can contact our technical team for exactly such > >?????????????? technical > >?????????????? >>???? help.?? > >?????????????? >>???? If it's ok with you, I'd encourage you subscribe to the > listserv > >?????????????? and > >?????????????? >>???? contact our technical team that way for the same reason. > >?????????????? >>???? (Note that front-end users of LORIS typically contact their > >?????????????? project team > >?????????????? >>???? for support, rather than us.) > >?????????????? >>???? Given that your lorismysql user privileges seem appropriate > >?????????????? ('UPDATE" is > >?????????????? >>???? there, I mistyped 'INSERT" before) > >?????????????? >>???? --?? is there any other indication why the database record is > not > >?????????????? >>???? updating??? > >?????????????? >>???? In the front-end, can your 'admin' user effect any changes > in > >?????????????? (any) Config > >?????????????? >>???? setting??? > >?????????????? >>???? In the back-end, when you tried updating a field using your > >?????????????? >>???? lorismysql credential, what happened? > >?????????????? >>???? Your front end is loading ok, and you can log in there, if I > >?????????????? understood > >?????????????? >>???? correctly. > >?????????????? >>???? Thanks for letting us know these details at > >?????????????? >>???? [1]loris-dev at bic.mni.mcgill.ca > >?????????????? >>???? Please also include what version of LORIS you are > installing, and > >?????????????? on what > >?????????????? >>???? OS version. > >?????????????? >>???? Best, > >?????????????? >>???? Christine > >?????????????? >>???? On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI > Computing > >?????????????? Support > >?????????????? >>???? <[2]support-cirl at berkeley.edu> wrote: > >?????????????? >> > >?????????????? >>???????? Thank you Christine, > >?????????????? >>???????? I'm the linux sysadmin who installed the loris database > for > >?????????????? Ioannis. > >?????????????? >>???????? I'm not a loris user, however, so that makes it a little > >?????????????? awkward for > >?????????????? >>???????? troubleshooting via the mailing list. I'm happy to help in > >?????????????? whatever way > >?????????????? >>???????? I can. > >?????????????? >> > >?????????????? >>???????? Regarding the database permissions, I ran: > >?????????????? >> > >?????????????? >>???????? MariaDB [(none)]> show grants for 'lorismysql'@'%'; > >?????????????? >>?????? > >?????????????? > +--------------------------------------------------------------------------------+ > >?????????????? >>???????? | Grants for lorismysql@% > >?????????????? >>???????? | > >?????????????? >>?????? > >?????????????? > +--------------------------------------------------------------------------------+ > >?????????????? >>???????? | GRANT USAGE ON *.* TO 'lorismysql'@'%' > >?????????????? >>???????? | > >?????????????? >>???????? | GRANT SELECT, INSERT, UPDATE, DELETE ON > `loris_database`.* TO > >?????????????? >>???????? 'lorismysql'@'%' | > >?????????????? >>?????? > >?????????????? > +--------------------------------------------------------------------------------+ > >?????????????? >>???????? 2 rows in set (0.00 sec) > >?????????????? >> > >?????????????? >>???????? looking at the 'tips' section in the page you referred > to... > >?????????????? >> > >?????????????? >>???????? |???????????? 29 | base???????????????????? | Base?????????????? | > /srv/www/loris/???? | > >?????????????? The base > >?????????????? >>???????? filesystem path where LORIS is > >?????????????? installed?????????????????????????????????????????????????? | > >?????????????? >>???????? |???????????? 31 | DownloadPath???? | Downloads???? | > /srv/www/loris/???? | > >?????????????? Where > >?????????????? >>???????? files are downloaded > >?????????????? >> > >?????????????? >>?????? > >?????????????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????????????? >>???????? | ConfigID | Name?????????????????????????? | Label???????????????????????? | > >?????????????? Value???????????????????????? | > >?????????????? >>???????? Description?????????????????????????????????????????????????? | > >?????????????? >>?????? > >?????????????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????????????? >>???????? |???????????? 44 | host?????????????????????????? | Host?????????????????????????? | > >?????????????? loris.priv?????????????? | > >?????????????? >>???????? Host???????????????????????????????????????????????????????????????? | > >?????????????? >>???????? |???????????? 45 | url???????????????????????????? | Main LORIS URL?????? | > >?????????????? >>???????? [3]http://loris.priv | Main URL where LORIS can be > accessed | > >?????????????? >>???????? |???????????? 46 | issue_tracker_url | Issue tracker URL | > >?????????????? /issue_tracker?????? | > >?????????????? >>???????? The *new* bug/issue tracker url?????????? | > >?????????????? >>?????? > >?????????????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????????????? >> > >?????????????? >>???????? apache config: > >?????????????? >> > >?????????????? >>???????? Listen 80 > >?????????????? >>???????? User apache > >?????????????? >>???????? Group apache > >?????????????? >>???????? DocumentRoot "/srv/www/loris/htdocs" > >?????????????? >> > >?????????????? >>???????? > >?????????????? >>???????????????? AllowOverride none > >?????????????? >>???????????????? Require all denied > >?????????????? >>???????? > >?????????????? >> > >?????????????? >>???????? > >?????????????? >>???????????????? AllowOverride All > >?????????????? >>???????????????? Options Indexes FollowSymLinks > >?????????????? >>???????????????? Require all granted > >?????????????? >>???????? > >?????????????? >> > >?????????????? >>???????? > >?????????????? >>???????????????? Options Indexes FollowSymLinks > >?????????????? >>???????????????? AllowOverride All > >?????????????? >>???????????????? Require all granted > >?????????????? >>???????? > >?????????????? >> > >?????????????? >>???????? file permissions: > >?????????????? >> > >?????????????? >>???????? # ls -ld /srv/www/loris/smarty/templates_c > >?????????????? >>???????? drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 > >?????????????? >>???????? /srv/www/loris/smarty/templates_c/ > >?????????????? >> > >?????????????? >>???????? [root at loris loris]# ls -l > /srv/www/loris/smarty/templates_c > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 2444 Oct 31 09:46 > >?????????????? >>?????? > >?????????????? > 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 > >?????????????? >>?????? > >?????????????? > 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep?? 7 18:39 > >?????????????? >>???????? > 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 3296 Sep?? 7 18:35 > >?????????????? >>?????? > >?????????????? > 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 5901 Sep?? 7 21:10 > >?????????????? >>?????? > >?????????????? > 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep?? 7 18:39 > >?????????????? >>?????? > >?????????????? > 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin???? 874 Sep 10 11:01 > >?????????????? >>???????? > 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 1101 Sep 10 10:58 > >?????????????? >>?????? > >?????????????? > 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 > >?????????????? >>?????? > >?????????????? > 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 3590 Sep?? 7 18:39 > >?????????????? >>?????? > >?????????????? > a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep?? 7 21:08 > >?????????????? >>?????? > >?????????????? > a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin???? 897 Sep?? 7 18:35 > >?????????????? >>???????? > a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 9210 Sep 10 11:01 > >?????????????? >>?????? > >?????????????? > a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 8917 Sep 10 13:21 > >?????????????? >>?????? > >?????????????? > ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 4811 Sep?? 7 18:35 > >?????????????? >>?????? > >?????????????? > d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin?? 3309 Sep 10 11:02 > >?????????????? >>?????? > >?????????????? > d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 > >?????????????? >>?????? > >?????????????? > e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php > >?????????????? >>???????? -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep?? 7 17:42 > >?????????????? >>???????? > fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php > >?????????????? >> > >?????????????? >>???????? thanks again! > >?????????????? >>???????? Julie > >?????????????? >> > >?????????????? >>???????? On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: > >?????????????? >>>???????? Hi Ioannis,????? > >?????????????? >>>???????? Thanks for your question.????? > >?????????????? >>>???????? Given that the URL field is not updating, I suspect it's > a > >?????????????? database > >?????????????? >>>???????? back-end issue.????? > >?????????????? >>>???????? Can you verify -- Has your mysql user lorismysql????? been > granted > >?????????????? the > >?????????????? >>???????? "INSERT" > >?????????????? >>>???????? privilege for the right database? If not, that would > result in > >?????????????? an > >?????????????? >>???????? error > >?????????????? >>>???????? like the kind you are seeing.????? > >?????????????? >>>???????? Also, if you wish to check your LORIS Configuration > settings > >?????????????? in the > >?????????????? >>>???????? backend database such as the URL field -- to see what was > >?????????????? actually > >?????????????? >>???????? stored > >?????????????? >>>???????? in a given database field and should display in the > Config > >?????????????? >>???????? module:????? > >?????????????? >>>???????? You can run the queries listed in the "Troubleshooting > >?????????????? >>???????? Configuration > >?????????????? >>>???????? settings" section of our Github-wiki Setup Guide (under > >?????????????? Project > >?????????????? >>>???????? Customization) :????? > >?????????????? >>>?????? > >?????????????? >>?????? > >?????????????? > [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >?????????????? >>>???????? Lastly, this question is perfectly appropriate for the > >?????????????? loris-dev > >?????????????? >>???????? community > >?????????????? >>>???????? support listserv -- please [2]subscribe here and then > email > >?????????????? our > >?????????????? >>???????? technical > >?????????????? >>>???????? team your next question at????? > [3][5]loris-dev at bic.mni.mcgill.ca > >?????????????? >>???????? (after checking > >?????????????? >>>???????? any forwarded threads for sensitive info).????? > >?????????????? >>>???????? We prefer to answer technical questions there for the > benefit > >?????????????? of > >?????????????? >>???????? the > >?????????????? >>>???????? community and other first-time users in the same position > as > >?????????????? >>???????? yourself.????? ????? > >?????????????? >>>???????? Thanks and cheers,????? > >?????????????? >>>???????? Christine????? > >?????????????? >>>???????? On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD > >?????????????? >>>???????? <[4][6]ioannis at berkeley.edu> wrote: > >?????????????? >>> > >?????????????? >>>???????????? Hi Loris support.????? > >?????????????? >>>???????????? My name is ioannis Pappas, a post-doc at the D'Esposito > lab > >?????????????? >>???????? stroke group > >?????????????? >>>???????????? at UC Berkeley. With the kind of help of our sys > admin????? > >?????????????? Julie > >?????????????? >>???????? (cc'ed) we > >?????????????? >>>???????????? have set up our loris database in our cluster (she is > the > >?????????????? sudo > >?????????????? >>???????? user and > >?????????????? >>>???????????? I am the admin user). > >?????????????? >>>???????????? If you allow me, I would like to ask you about the > first > >?????????????? >>???????? configuration > >?????????????? >>>???????????? steps in the front end as they are described in the > >?????????????? tutorial. We > >?????????????? >>???????? can > >?????????????? >>>???????????? login to [5][7]http://loris and the front end normally. > >?????????????? >>>???????????? However any update that I am trying to????? perform in > >?????????????? >>???????? Admin->Configuration > >?????????????? >>>???????????? doesn't work (e.g. updating the study name). It just > >?????????????? refreshes > >?????????????? >>???????? the same > >?????????????? >>>???????????? page. I am just wondering if there is an issue with > writing > >?????????????? in > >?????????????? >>???????? the > >?????????????? >>>???????????? configuration file. > >?????????????? >>>???????????? Here are the permissions setup for where Loris is > installed. > >?????????????? >>>???????????? chmod 777 /var/www/loris/smarty/templates_c > >?????????????? >>>???????????? cd /srv/www/loris > >?????????????? >>>???????????? chown -R lorisadmin:lorisadmin . > >?????????????? >>>???????????? chmod -c -R a+r . > >?????????????? >>>???????????? ??????? ??????? this command gives everyone read access, and > outputs > >?????????????? what > >?????????????? >>???????? changes > >?????????????? >>>???????????? were made: > >?????????????? >>>???????????? ??????? ??????? mode of ?????????./project????????? changed from 0770 > (rwxrwx---) to > >?????????????? 0774 > >?????????????? >>>???????????? (rwxrwxr--) > >?????????????? >>>???????????? ??????? ??????? mode of ?????????./tools/logs????????? changed from 0770 > (rwxrwx---) > >?????????????? to > >?????????????? >>???????? 0774 > >?????????????? >>>???????????? (rwxrwxr--) > >?????????????? >>>???????????? find . -type d -exec chmod a+x -c {} \; > >?????????????? >>>???????????? ??????? ??????? this command gives everyone permission to open > a > >?????????????? directory, > >?????????????? >>???????? and > >?????????????? >>>???????????? outputs what changes were made: > >?????????????? >>>???????????? ??????? ??????? mode of ?????????./project????????? changed from 0774 > (rwxrwxr--) to > >?????????????? 0775 > >?????????????? >>>???????????? (rwxrwxr-x) > >?????????????? >>>???????????? ??????? ??????? mode of ?????????./tools/logs????????? changed from 0774 > (rwxrwxr--) > >?????????????? to > >?????????????? >>???????? 0775 > >?????????????? >>>???????????? (rwxrwxr-x) > >?????????????? >>>???????????? Hopefully????? you can help me with this. I also > subscribed to > >?????????????? the > >?????????????? >>???????? mailing > >?????????????? >>>???????????? list but I am not sure if this too much of a basic > question > >?????????????? for > >?????????????? >>???????? the > >?????????????? >>>???????????? list. > >?????????????? >>>???????????? Best wishes, > >?????????????? >>>???????????? Ioannis > >?????????????? >>>???????????? On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI > >?????????????? Computing > >?????????????? >>???????? Support > >?????????????? >>>???????????? <[6][8]support-cirl at berkeley.edu> wrote: > >?????????????? >>> > >?????????????? >>>???????????????? Hi ioannis, maybe it's best to ask the developers? > You can > >?????????????? cc > >?????????????? >>???????? me if > >?????????????? >>>???????????????? you'd like. > >?????????????? >>>???????????????? On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas > >?????????????? >>???????? <[7][9]ioannis at berkeley.edu> > >?????????????? >>>???????????????? wrote: > >?????????????? >>> > >?????????????? >>>???????????????????? That did the trick Julie. Thank you! > >?????????????? >>> > >?????????????? >>>???????????????????? I am still trying to understand how configuration > works > >?????????????? >>???????? though. For > >?????????????? >>>???????????????????? example if I just try to change the name of the > >?????????????? >>>???????????????????? study from the front end, I get nowhere (it just > >?????????????? refreshes > >?????????????? >>???????? the same > >?????????????? >>>???????????????????? page). > >?????????????? >>> > >?????????????? >>>???????????????????? I am not sure if this requires write permissions > >?????????????? somewhere in > >?????????????? >>???????? a > >?????????????? >>>???????????????????? config file/folder and that??????????????????s why it > doesn??????????????????t update > >?????????????? it. > >?????????????? >>> > >?????????????? >>>???????????????????? Best wishes, > >?????????????? >>>???????????????????? Ioannis > >?????????????? >>> > >?????????????? >>>???????????????????? > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI > >?????????????? Computing > >?????????????? >>>???????????????????? Support <[8][10]support-cirl at berkeley.edu> wrote: > >?????????????? >>>???????????????????? > > >?????????????? >>>???????????????????? > just in case you're interested, these are the > >?????????????? permission > >?????????????? >>???????? changes I > >?????????????? >>>???????????????????? made: > >?????????????? >>>???????????????????? > > >?????????????? >>>???????????????????? > chmod 777 /var/www/loris/smarty/templates_c > >?????????????? >>>???????????????????? > cd /srv/www/loris > >?????????????? >>>???????????????????? > chown -R lorisadmin:lorisadmin . > >?????????????? >>>???????????????????? > chmod -c -R a+r . > >?????????????? >>>???????????????????? >??????? ??????? this command gives everyone read access, > and > >?????????????? outputs > >?????????????? >>???????? what > >?????????????? >>>???????????????????? changes were made: > >?????????????? >>>???????????????????? >??????? ??????? mode of ?????????./project????????? changed from > 0770 > >?????????????? (rwxrwx---) to > >?????????????? >>???????? 0774 > >?????????????? >>>???????????????????? (rwxrwxr--) > >?????????????? >>>???????????????????? >??????? ??????? mode of ?????????./tools/logs????????? changed from > 0770 > >?????????????? (rwxrwx---) > >?????????????? >>???????? to 0774 > >?????????????? >>>???????????????????? (rwxrwxr--) > >?????????????? >>>???????????????????? > find . -type d -exec chmod a+x -c {} \; > >?????????????? >>>???????????????????? >??????? ??????? this command gives everyone permission to > open a > >?????????????? >>???????? directory, and > >?????????????? >>>???????????????????? outputs what changes were made: > >?????????????? >>>???????????????????? >??????? ??????? mode of ?????????./project????????? changed from > 0774 > >?????????????? (rwxrwxr--) to > >?????????????? >>???????? 0775 > >?????????????? >>>???????????????????? (rwxrwxr-x) > >?????????????? >>>???????????????????? >??????? ??????? mode of ?????????./tools/logs????????? changed from > 0774 > >?????????????? (rwxrwxr--) > >?????????????? >>???????? to 0775 > >?????????????? >>>???????????????????? (rwxrwxr-x) > >?????????????? >>>???????????????????? > > >?????????????? >>>???????????????????? > > >?????????????? >>>???????????????????? > > >?????????????? >>>???????????????????? > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: > >?????????????? >>>???????????????????? >> Hi Julie. > >?????????????? >>>???????????????????? >> I just tried and I still don???t get anything. I > also > >?????????????? >>???????? tried > >?????????????? >>>???????????????????? private mode in Firefox in case the empty page was > >?????????????? cached. > >?????????????? >>>???????????????????? >> Sorry for this. > >?????????????? >>>???????????????????? >> > >?????????????? >>>???????????????????? >> Best wishes, > >?????????????? >>>???????????????????? >> Ioannis > >?????????????? >>>???????????????????? >> > >?????????????? >>>???????????????????? >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, > HWNI > >?????????????? >>???????? Computing > >?????????????? >>>???????????????????? Support <[9][11]support-cirl at berkeley.edu> wrote: > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> hi Ioannis, > >?????????????? >>>???????????????????? >>> no worries, I changed the following directory > to > >?????????????? 777: > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> /var/www/loris/smarty/templates_c > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> will you please check if that works? > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> thanks! > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> > >?????????????? >>>???????????????????? >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas > PhD > >?????????????? wrote: > >?????????????? >>>???????????????????? >>>>??????? Hi Julie. > >?????????????? >>>???????????????????? >>>>??????? Apologies for bugging you with this again. > We > >?????????????? tried > >?????????????? >>???????? now to > >?????????????? >>>???????????????????? >>>>??????? access??????????? [1][10][12]http://loris??????????? > >?????????????? >>>???????????????????? >>>>??????? and we are getting a??????????? blank page. I > think the > >?????????????? reason > >?????????????? >>???????? for this > >?????????????? >>>???????????????????? is that we > >?????????????? >>>???????????????????? >>>>??????? don't have read??????????? permissions to read > from the > >?????????????? >>???????? template located > >?????????????? >>>???????????????????? in > >?????????????? >>>???????????????????? >>>>??????? /var/www/loris/smarty See here bottom of > the > >?????????????? >>>???????????????????? >>>>??????? page??????????? > >?????????????? >>>?????????????????? > >?????????????? >>?????? > >?????????????? > [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????????????? >>>???????????????????? >>>>??????? I think, in general, I am a little bit > confused > >?????????????? as to > >?????????????? >>???????? what the > >?????????????? >>>???????????????????? permissions > >?????????????? >>>???????????????????? >>>>??????? should be for us that are not sudos. My > >?????????????? understanding > >?????????????? >>???????? is that > >?????????????? >>>???????????????????? if we don't > >?????????????? >>>???????????????????? >>>>??????? have read or write permissions then we > can't > >?????????????? access or > >?????????????? >>???????? write > >?????????????? >>>???????????????????? to > >?????????????? >>>???????????????????? >>>>??????? /var/www/loris, meaning that we can't > access or > >?????????????? >>???????? configure. > >?????????????? >>>???????????????????? Should > >?????????????? >>>???????????????????? >>>>??????? everything be chmod 777 for example???????????? > >?????????????? >>>???????????????????? >>>>??????? Thank you very much once again. > >?????????????? >>>???????????????????? >>>>??????? Best wishes, > >?????????????? >>>???????????????????? >>>>??????? Ioannis > >?????????????? >>>???????????????????? >>>>??????? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis > >?????????????? Pappas PhD > >?????????????? >>>???????????????????? >>>>??????? <[3][12][14]ioannis at berkeley.edu> wrote: > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? ??????? Thank you very much Julie. I appreciate > this > >?????????????? and I > >?????????????? >>???????? will dig > >?????????????? >>>???????????????????? into Loris > >?????????????? >>>???????????????????? >>>>??????? ??????? given your changes. Thank you so much > for your > >?????????????? >>???????? help. > >?????????????? >>>???????????????????? >>>>??????? ??????? Best wishes, > >?????????????? >>>???????????????????? >>>>??????? ??????? Ioannis > >?????????????? >>>???????????????????? >>>>??????? ??????? On Thu, Oct 31, 2019 at 12:48 PM Julie > >?????????????? Ashworth, > >?????????????? >>???????? HWNI > >?????????????? >>>???????????????????? Computing Support > >?????????????? >>>???????????????????? >>>>??????? ??????? <[4][13][15]support-cirl at berkeley.edu> > wrote: > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? hi Ioannis, > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? 1. I changed the permissions of > >?????????????? /srv/www/loris > >?????????????? >>???????? to be owned > >?????????????? >>>???????????????????? by > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? lorisadmin. I reivewed my > installation > >?????????????? notes, > >?????????????? >>???????? and I did > >?????????????? >>>???????????????????? this already > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? when > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? I installed the server. I'm not > sure why > >?????????????? they > >?????????????? >>???????? changed, so > >?????????????? >>>???????????????????? it's > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? probably a > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? good idea to keep an eye on that. > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? 2. When I installed the loris > software, I > >?????????????? also > >?????????????? >>???????? installed a > >?????????????? >>>???????????????????? mysql > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? database as recommended in the > >?????????????? instructions: > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? projectname: LORIS > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? databasename: loris_database > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? mysqluser: lorismysql > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? frontend: lorisweb > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? 3. A couple of weeks ago, I moved > Henrik's > >?????????????? home > >?????????????? >>???????? directory > >?????????????? >>>???????????????????? to > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? /home/despoA, > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? but I forgot to update loris. This > is done > >?????????????? now. > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? best, > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? Julie > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? On 31-10-2019 11.15 -0700, Dr. > Ioannis > >?????????????? Pappas > >?????????????? >>???????? PhD wrote: > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? Hi Julie. > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? I hope you are well. We are > trying to > >?????????????? >>???????? configure loris > >?????????????? >>>???????????????????? that you > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? kindly set > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? up for us. > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? I have a couple of > questions for you if > >?????????????? you > >?????????????? >>???????? allow me > >?????????????? >>>???????????????????? so.??????????? > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? 1) First, although we are > logging into > >?????????????? the > >?????????????? >>???????? front end > >?????????????? >>>???????????????????? with admin > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? username > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? (lorisweb) and password, it > seems that > >?????????????? any > >?????????????? >>???????? kind of > >?????????????? >>>???????????????????? update of > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? configuration > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? we are trying to do fails > (meaning that > >?????????????? if > >?????????????? >>???????? we, say, > >?????????????? >>>???????????????????? change the > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? name of the > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? study and press "submit", > this doesn't > >?????????????? do > >?????????????? >>???????? anything-it > >?????????????? >>>???????????????????? doesn't > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? update). > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? It's almost like our > lorisweb user > >?????????????? doesn't > >?????????????? >>???????? have write > >?????????????? >>>???????????????????? privileges > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? in the > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? /var/www/loris/project > (where I think > >?????????????? every > >?????????????? >>>???????????????????? configuration should > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? be). > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? This generalizes for > everything that we > >?????????????? are > >?????????????? >>???????? trying to do > >?????????????? >>>???????????????????? in the > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? front end. > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? Clicking any instrument/tab > in the front > >?????????????? end > >?????????????? >>???????? doesn't > >?????????????? >>>???????????????????? really point > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? to > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? anything.??????????? > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? 2) Loris suggest doing > configurations > >?????????????? via > >?????????????? >>???????? SQL. Is it > >?????????????? >>>???????????????????? possible to > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? run SQL > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? scripts in the backend > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? 3) For some reason typing > ssh lors for > >?????????????? Henrik > >?????????????? >>???????? doesn't > >?????????????? >>>???????????????????? directly > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? take him to > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? loris (it requires a > password that is > >?????????????? not the > >?????????????? >>???????? password > >?????????????? >>>???????????????????? setup for > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? the > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? lorisweb user). Will you be > able to fix > >?????????????? this > >?????????????? >>???????? via your > >?????????????? >>>???????????????????? sudo > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? privileges? > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? Thank you very much in > advance for all > >?????????????? your > >?????????????? >>???????? help Julie. > >?????????????? >>>???????????????????? Let us > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? know if > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? this is something that > shouldn't be > >?????????????? directed > >?????????????? >>???????? to you (but > >?????????????? >>>???????????????????? instead > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? to the > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? loris people).??????????? > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? Best wishes, > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? Ioannis > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? On Mon, Sep 9, 2019 at 6:25 > PM Julie > >?????????????? >>???????? Ashworth, HWNI > >?????????????? >>>???????????????????? Computing > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? Support > >?????????????? >>>???????????????????? >>>>> ?????????????????? ???????????????? > >?????????????? <[1][5][14][16]support-cirl at berkeley.edu> > >?????????????? >>???????? wrote: > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? hi Henrik and > Ioannis, > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? the loris server > is available for > >?????????????? you to > >?????????????? >>???????? use. > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? The servername is > 'loris'. I > >?????????????? created a > >?????????????? >>???????? directory > >?????????????? >>>???????????????????? called > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? /data/loris for > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? you to store data. > You may create > >?????????????? new > >?????????????? >>???????? folders in > >?????????????? >>>???????????????????? /data/loris to > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? organize > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? your data. > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? 1) secure shell or > secure copy: > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? You can log in > with the 'ssh' or > >?????????????? 'scp' > >?????????????? >>???????? command from > >?????????????? >>>???????????????????? your remote > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? desktop > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? session. You don't > need to > >?????????????? authenticate > >?????????????? >>???????? to log in. > >?????????????? >>>???????????????????? Maybe you'll > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? use scp > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? to transfer data > between your > >?????????????? cluster > >?????????????? >>???????? account and the > >?????????????? >>>???????????????????? loris > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? server? > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? Please put the > data in /data/loris, > >?????????????? so I > >?????????????? >>???????? can make > >?????????????? >>>???????????????????? backups more > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? easily. > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? ?????????????????? ?????????????????? > secure shell: > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? ?????????????????? ?????????????????? > $ ssh loris > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? ?????????????????? ?????????????????? > secure copy (change the > >?????????????? names > >?????????????? >>???????? in brackets). Let > >?????????????? >>>???????????????????? me know if > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? I can > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? ?????????????????? ?????????????????? > help with syntax: > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? ?????????????????? ?????????????????? > $ scp -r > >?????????????? >>???????? loris:/data/loris/ > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? 2) front-end web > interface.???????????????? > >?????????????? Open a > >?????????????? >>???????? web browser in > >?????????????? >>>???????????????????? your remote > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? desktop > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? session and enter > the hostname: > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? > [2][6][15][17]http://loris > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? I created an admin > user called > >?????????????? >>???????? 'lorisweb'. I put the > >?????????????? >>>???????????????????? password > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? in > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? $HOME/newuser on > the cluster. To > >?????????????? see it, > >?????????????? >>???????? open a > >?????????????? >>>???????????????????? terminal, and > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? run: > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? ?????????????????? ?????????????????? > $ cat $HOME/newuser > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? If other people > need shell access > >?????????????? to the > >?????????????? >>???????? webserver, > >?????????????? >>>???????????????????? please let > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? me know > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? so I can create a > home directory > >?????????????? for > >?????????????? >>???????? them. > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? We should > eventually discuss > >?????????????? backups. > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? best, > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? ?????????????????? Julie > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> References > >?????????????? >>>???????????????????? >>>>> > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? Visible links > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? 1. > >?????????????? >>???????? mailto:[7][16][18]support-cirl at berkeley.edu > >?????????????? >>>???????????????????? >>>>> ?????????????????? ?????????????????? 2. [8][17][19]http://loris/ > >?????????????? >>>???????????????????? >>>>??????? ??????? ??????? ---end quoted text--- > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>> References > >?????????????? >>>???????????????????? >>>> > >?????????????? >>>???????????????????? >>>>??????? Visible links > >?????????????? >>>???????????????????? >>>>??????? 1. [18][20]http://loris/ > >?????????????? >>>???????????????????? >>>>??????? 2. > >?????????????? >>>?????????????????? > >?????????????? >>?????? > >?????????????? > [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????????????? >>>???????????????????? >>>>??????? 3. mailto:[20][22]ioannis at berkeley.edu > >?????????????? >>>???????????????????? >>>>??????? 4. mailto:[21][23]support-cirl at berkeley.edu > >?????????????? >>>???????????????????? >>>>??????? 5. mailto:[22][24]support-cirl at berkeley.edu > >?????????????? >>>???????????????????? >>>>??????? 6. [23][25]http://loris/ > >?????????????? >>>???????????????????? >>>>??????? 7. mailto:[24][26]support-cirl at berkeley.edu > >?????????????? >>>???????????????????? >>>>??????? 8. [25][27]http://loris/ > >?????????????? >>>???????????????????? >>> ---end quoted text--- > >?????????????? >>>???????????????????? >> > >?????????????? >>>???????????????????? > ---end quoted text--- > >?????????????? >>> > >?????????????? >>>???????? -- > >?????????????? >>>???????? [26][28]christine.rogers at mcgill.ca > >?????????????? >>>???????? McGill Centre for Integrative Neuroscience | MCIN.ca > >?????????????? >>>???????? Montreal Neurological Institute > >?????????????? >>>???????? McGill University | Montreal | Canada > >?????????????? >>> > >?????????????? >>> References > >?????????????? >>> > >?????????????? >>>???????? Visible links > >?????????????? >>>???????? 1. > >?????????????? >>?????? > >?????????????? > [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >?????????????? >>>???????? 2. > >?????????????? [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >?????????????? >>>???????? 3. mailto:[31]loris-dev at bic.mni.mcgill.ca > >?????????????? >>>???????? 4. mailto:[32]ioannis at berkeley.edu > >?????????????? >>>???????? 5. [33]http://loris/ > >?????????????? >>>???????? 6. mailto:[34]support-cirl at berkeley.edu > >?????????????? >>>???????? 7. mailto:[35]ioannis at berkeley.edu > >?????????????? >>>???????? 8. mailto:[36]support-cirl at berkeley.edu > >?????????????? >>>???????? 9. mailto:[37]support-cirl at berkeley.edu > >?????????????? >>>?????? 10. [38]http://xn--loris-7qa/ > >?????????????? >>>?????? 11. > >?????????????? [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????????????? >>>?????? 12. mailto:[40]ioannis at berkeley.edu > >?????????????? >>>?????? 13. mailto:[41]support-cirl at berkeley.edu > >?????????????? >>>?????? 14. mailto:[42]support-cirl at berkeley.edu > >?????????????? >>>?????? 15. [43]http://loris/ > >?????????????? >>>?????? 16. mailto:[44]support-cirl at berkeley.edu > >?????????????? >>>?????? 17. [45]http://loris/ > >?????????????? >>>?????? 18. [46]http://loris/ > >?????????????? >>>?????? 19. > >?????????????? [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????????????? >>>?????? 20. mailto:[48]ioannis at berkeley.edu > >?????????????? >>>?????? 21. mailto:[49]support-cirl at berkeley.edu > >?????????????? >>>?????? 22. mailto:[50]support-cirl at berkeley.edu > >?????????????? >>>?????? 23. [51]http://loris/ > >?????????????? >>>?????? 24. mailto:[52]support-cirl at berkeley.edu > >?????????????? >>>?????? 25. [53]http://loris/ > >?????????????? >>>?????? 26. mailto:[54]christine.rogers at mcgill.ca > >?????????????? >>???????? ---end quoted text--- > >?????????????? >> > >?????????????? >>???? -- > >?????????????? >>???? [55]christine.rogers at mcgill.ca > >?????????????? >>???? McGill Centre for Integrative Neuroscience | MCIN.ca > >?????????????? >>???? Montreal Neurological Institute > >?????????????? >>???? McGill University | Montreal | Canada > >?????????????? >> > >?????????????? >> References > >?????????????? >> > >?????????????? >>???? Visible links > >?????????????? >>???? 1. [8]mailto:loris-dev at bic.mni.mcgill.ca > >?????????????? >>???? 2. [9]mailto:support-cirl at berkeley.edu > >?????????????? >>???? 3. [10]http://loris.priv/ > >?????????????? >>?? > >?????????????? 4. > [11]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >?????????????? >>???? 5. [12]mailto:loris-dev at bic.mni.mcgill.ca > >?????????????? >>???? 6. [13]mailto:ioannis at berkeley.edu > >?????????????? >>???? 7. [14]http://loris/ > >?????????????? >>???? 8. [15]mailto:support-cirl at berkeley.edu > >?????????????? >>???? 9. [16]mailto:ioannis at berkeley.edu > >?????????????? >>?? 10. [17]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 11. [18]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 12. [19]http://xn--loris-era/ > >?????????????? >>?? 13. > [20]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????????????? >>?? 14. [21]mailto:ioannis at berkeley.edu > >?????????????? >>?? 15. [22]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 16. [23]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 17. [24]http://loris/ > >?????????????? >>?? 18. [25]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 19. [26]http://loris/ > >?????????????? >>?? 20. [27]http://loris/ > >?????????????? >>?? 21. > [28]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????????????? >>?? 22. [29]mailto:ioannis at berkeley.edu > >?????????????? >>?? 23. [30]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 24. [31]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 25. [32]http://loris/ > >?????????????? >>?? 26. [33]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 27. [34]http://loris/ > >?????????????? >>?? 28. [35]mailto:christine.rogers at mcgill.ca > >?????????????? >> > >?????????????? 29. > [36]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >?????????????? >>?? 30. > [37]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >?????????????? >>?? 31. [38]mailto:loris-dev at bic.mni.mcgill.ca > >?????????????? >>?? 32. [39]mailto:ioannis at berkeley.edu > >?????????????? >>?? 33. [40]http://loris/ > >?????????????? >>?? 34. [41]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 35. [42]mailto:ioannis at berkeley.edu > >?????????????? >>?? 36. [43]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 37. [44]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 38. [45]http://xn--loris-7qa/ > >?????????????? >>?? 39. > [46]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????????????? >>?? 40. [47]mailto:ioannis at berkeley.edu > >?????????????? >>?? 41. [48]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 42. [49]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 43. [50]http://loris/ > >?????????????? >>?? 44. [51]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 45. [52]http://loris/ > >?????????????? >>?? 46. [53]http://loris/ > >?????????????? >>?? 47. > [54]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????????????? >>?? 48. [55]mailto:ioannis at berkeley.edu > >?????????????? >>?? 49. [56]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 50. [57]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 51. [58]http://loris/ > >?????????????? >>?? 52. [59]mailto:support-cirl at berkeley.edu > >?????????????? >>?? 53. [60]http://loris/ > >?????????????? >>?? 54. [61]mailto:christine.rogers at mcgill.ca > >?????????????? >>?? 55. [62]mailto:christine.rogers at mcgill.ca > >?????????????? > ---end quoted text--- > > > >?????????????? _______________________________________________ > >?????????????? Loris-dev mailing list > >?????????????? Loris-dev at bic.mni.mcgill.ca > >?????????????? [63]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >?????????????? > > > >?????????? _______________________________________________ > >?????????? Loris-dev mailing list > >?????????? Loris-dev at bic.mni.mcgill.ca > >?????????? [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > >?????? -- > >?????? christine.rogers at mcgill.ca > >?????? McGill Centre for Integrative Neuroscience | MCIN.ca > >?????? Montreal Neurological Institute > >?????? McGill University | Montreal | Canada > ---end quoted text--- > > References > > Visible links > 1. https://loris.url/configuration/ > 2. https://.loris.url/ > 3. http://loris.priv/ > 4. http://localhost/ > 5. http://loris.priv/ > 6. http://localhost/ > 7. http://localhost/ > 8. mailto:loris-dev at bic.mni.mcgill.ca > 9. mailto:support-cirl at berkeley.edu > 10. http://loris.priv/ > 11. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 12. mailto:loris-dev at bic.mni.mcgill.ca > 13. mailto:ioannis at berkeley.edu > 14. http://loris/ > 15. mailto:support-cirl at berkeley.edu > 16. mailto:ioannis at berkeley.edu > 17. mailto:support-cirl at berkeley.edu > 18. mailto:support-cirl at berkeley.edu > 19. http://xn--loris-era/ > 20. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 21. mailto:ioannis at berkeley.edu > 22. mailto:support-cirl at berkeley.edu > 23. mailto:support-cirl at berkeley.edu > 24. http://loris/ > 25. mailto:support-cirl at berkeley.edu > 26. http://loris/ > 27. http://loris/ > 28. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 29. mailto:ioannis at berkeley.edu > 30. mailto:support-cirl at berkeley.edu > 31. mailto:support-cirl at berkeley.edu > 32. http://loris/ > 33. mailto:support-cirl at berkeley.edu > 34. http://loris/ > 35. mailto:christine.rogers at mcgill.ca > 36. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 37. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 38. mailto:loris-dev at bic.mni.mcgill.ca > 39. mailto:ioannis at berkeley.edu > 40. http://loris/ > 41. mailto:support-cirl at berkeley.edu > 42. mailto:ioannis at berkeley.edu > 43. mailto:support-cirl at berkeley.edu > 44. mailto:support-cirl at berkeley.edu > 45. http://xn--loris-7qa/ > 46. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 47. mailto:ioannis at berkeley.edu > 48. mailto:support-cirl at berkeley.edu > 49. mailto:support-cirl at berkeley.edu > 50. http://loris/ > 51. mailto:support-cirl at berkeley.edu > 52. http://loris/ > 53. http://loris/ > 54. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 55. mailto:ioannis at berkeley.edu > 56. mailto:support-cirl at berkeley.edu > 57. mailto:support-cirl at berkeley.edu > 58. http://loris/ > 59. mailto:support-cirl at berkeley.edu > 60. http://loris/ > 61. mailto:christine.rogers at mcgill.ca > 62. mailto:christine.rogers at mcgill.ca > 63. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 64. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ---end quoted text--- From christine.rogers at mcgill.ca Mon Nov 11 12:11:20 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Mon, 11 Nov 2019 17:11:20 +0000 Subject: [Loris-dev] loris server In-Reply-To: <20191111170342.GA4213@gaia.neuro.berkeley.edu> References: <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> <20191109020414.GB13279@nx6.priv> <20191111170342.GA4213@gaia.neuro.berkeley.edu> Message-ID: Hi Julie, perhaps you recommend changing loris_database entries ('host' to 'localhost' and 'url' to 'http://localhost')? Yes, please do try these changes to your Config table settings and let us know how it goes - (per the same Setup Guide section discussed before: https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings) I'm not sure how this would impact the current database update issue you're experiencing, however. Christine On Mon, Nov 11, 2019 at 12:04 PM Julie Ashworth, HWNI Computing Support > wrote: thanks Melanie, I'm including the output below. My understanding is that '%' matches all hostnames. Should I specifically grant permission to 'loris.priv' from user lorismysql? Or perhaps you recommend changing loris_database entries ('host' to 'localhost' and 'url' to 'http://localhost')? thanks! MariaDB [(none)]> SELECT User, Host FROM mysql.user; +------------+-----------+ | User | Host | +------------+-----------+ | lorismysql | % | | root | 127.0.0.1 | | root | ::1 | | lorismysql | localhost | | root | localhost | +------------+-----------+ 5 rows in set (0.00 sec) MariaDB [(none)]> SHOW grants for 'lorismysql'@'%'; +--------------------------------------------------------------------------------+ | Grants for lorismysql@% +--------------------------------------------------------------------------------+ | GRANT USAGE ON *.* TO 'lorismysql'@'%' | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO 'lorismysql'@'%' | +--------------------------------------------------------------------------------+ 2 rows in set (0.00 sec) On 11-11-2019 15.47 +0000, Melanie Legault, Mrs wrote: > Hello Julie, > Could it be that your MySQL 'lorismysql' user have different permissions > depending on where it is connecting to the DB? > A database admin (root) can check this for you. > SELECT User, Host FROM mysql.user; > then for the user that match the Host (name or IP address) of your LORIS > (Apache) server > SHOW grants for 'lorismysql'@''; > > M??lanie > > -------------------------------------------------------------------------- > > From: Julie Ashworth, HWNI Computing Support > > Sent: November 8, 2019 21:04 > To: Christine Rogers, Ms. > > Cc: Ioannis Pappas >; Melanie Legault, Mrs > >; loris-dev at bic.mni.mcgill.ca > > > Subject: Re: [Loris-dev] loris server > ? > thanks Christine, > > yes, it's the lorismysql user in the config.xml file. > ? ? ? ? ? ? ? lorismysql > ? ? ? ? ? ? ? loris_database > ? ? ? ? ? ? ? lorismysql > > we appeciate your help troubleshooting this. > best, > Julie > > On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote: > >? ? ? Hi Ioannis, > >? ? ? Could you open your file called config.xml > >? ? ? (/srv/www/loris/project/config.xml) and confirm for us --? which user > >? ? ? credential is stored there, and what's the name of the database it is > >? ? ? connecting to? > >? ? ? This is the mysql user which connects to the database from the front > end > >? ? ? of LORIS.? > >? ? ? If this user has insufficient privileges on your database, that would > >? ? ? cause the errors you are seeing.? I had assumed from your thread it > was > >? ? ? your lorismysql user but it sounds like this should be verified. > >? ? ? Let us know, and we'll keep following up when we come back online > after > >? ? ? the weekend, > >? ? ? Best, > >? ? ? Christine > >? ? ? On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas > > >? ? ? wrote: > > > >? ? ? ? ? Hi Melanie. > >? ? ? ? ? Thank you for taking the time to reply to this. I took some to > consider > >? ? ? ? ? your comments. Unfortunately as I said to Christine we are unable > to do > >? ? ? ? ? any kind of updating to the database (either that is changing the > name > >? ? ? ? ? or changing the small html description, etc.). > >? ? ? ? ? Based on some more digging and on some of Christine's comments I > have a > >? ? ? ? ? feeling that our lorisweb front-end, admin user cannot write > anything to > >? ? ? ? ? the database. Along these lines could it be the case the lorismysql > user > >? ? ? ? ? (the database, admin user with INSERT, UPDATE, etc privileges) is > not > >? ? ? ? ? ???????talking????? to the lorisweb front end user? What is the > difference between > >? ? ? ? ? the two and could it be a installation problem for them not talking > to > >? ? ? ? ? each other? As Julie said, lorismysql user is working normally with > >? ? ? ? ? MariaDB. > >? ? ? ? ? Thank you again for your help. > >? ? ? ? ? Best wishes, > >? ? ? ? ? Ioannis > > > >? ? ? ? ? ? ? On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs > >? ? ? ? ? ? ? > wrote: > >? ? ? ? ? ? ? Hello, > >? ? ? ? ? ? ? Changing the project name in the configuration page > >? ? ? ? ? ? ? ([1]https://loris.url/configuration/) of LORIS, only change the > title of > >? ? ? ? ? ? ? the project. To see this change, you have to log out of LORIS and > then > >? ? ? ? ? ? ? go back to the login page ([2]https://.loris.url/). This is the > only > >? ? ? ? ? ? ? place you can find the project name (except from the > configuration > >? ? ? ? ? ? ? page). See ProjectName.png > >? ? ? ? ? ? ? As for files permission, I would suggest a few change to improve > >? ? ? ? ? ? ? security of you server. Some extra permissions where granted to > help > >? ? ? ? ? ? ? you but are not needed. > >? ? ? ? ? ? ? ? ? * /srv/www/loris/smarty/templates_c/? should have ownership of > >? ? ? ? ? ? ? ? ? ? ? lorisadmin:httpd and permission 770 (or 775) > >? ? ? ? ? ? ? ? ? * srv/www/loris/project/? should have ownership > lorisadmin:httpd and > >? ? ? ? ? ? ? ? ? ? ? permission 770 (775) > >? ? ? ? ? ? ? ? ? * All other files under loris should have lorisadmin:lorisadmin > 755 > >? ? ? ? ? ? ? Reading through this change of mail, I understand that you let > Apache > >? ? ? ? ? ? ? store file in /srv/www/loris > >? ? ? ? ? ? ? ? ? ? |? ? ? ? ? ? 31 | DownloadPath? ? | Downloads? ? | /srv/www/loris/? ? > | > >? ? ? ? ? ? ? Where > >? ? ? ? ? ? ? >>? ? ? ? files are downloaded > >? ? ? ? ? ? ? Downloaded files should not be in the same tree as LORIS code. It > >? ? ? ? ? ? ? should be in a separate structure where Apache will not try and > do not > >? ? ? ? ? ? ? have permission (in httpd.conf) to execute files. > >? ? ? ? ? ? ? Kind regards, > >? ? ? ? ? ? ? M????lanie Legault | Software developer | Faculty of Medicine | > McGill > >? ? ? ? ? ? ? University? > >? ? ? ? ? ? ? 3801 University, Montr????al, QC H3A 2B4 > > > >? ? ? ? ? > ---------------------------------------------------------------------- > > > >? ? ? ? ? ? ? From: loris-dev-bounces at bic.mni.mcgill.ca > >? ? ? ? ? ? ? > on behalf of Ioannis Pappas > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? Sent: November 7, 2019 0:18 > >? ? ? ? ? ? ? To: loris-dev at bic.mni.mcgill.ca > > >? ? ? ? ? ? ? Cc: Julie Ashworth, HWNI Computing Support > >? ? ? ? ? ? ? >; Christine Rogers, Ms. > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? Subject: Re: [Loris-dev] loris server > >? ? ? ? ? ? ? ? > >? ? ? ? ? ? ? Hi Christine and Julie. > > > >? ? ? ? ? ? ? Yes it looks like that any attempt to configure something in the > >? ? ? ? ? ? ? front-end results in the same page. I am sending this to the list > (as > >? ? ? ? ? ? ? you requested Christine) alongside the troubleshooting and > discussion > >? ? ? ? ? ? ? so far with Julie. > > > >? ? ? ? ? ? ? Best wishes, > >? ? ? ? ? ? ? Ioannis > > > >? ? ? ? ? ? ? > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing > Support > >? ? ? ? ? ? ? > wrote: > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > hi Christine and Ioannis, > >? ? ? ? ? ? ? > Ioannis, can you follow-up with Christine about using the > front-end? > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > We're using CentOS7.7 and loris-21.0.1. > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > I confirmed that I could login as the mysql user (lorismyqsl) > and > >? ? ? ? ? ? ? change the 'url' config setting from '[3]http://loris.priv' to > >? ? ? ? ? ? ? '[4]http://localhost', and back again. > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > >? ? ? ? ? ? ? c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs > ON > >? ? ? ? ? ? ? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = > csp.ID) > >? ? ? ? ? ? ? WHERE csp.Name = 'www'; > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? > | ConfigID | Name? ? ? ? ? ? ? ? ? ? ? ? ? | Label? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? Value? ? ? ? ? ? ? ? ? ? ? ? | Description? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? > |? ? ? ? ? ? 44 | host? ? ? ? ? ? ? ? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? loris.priv? ? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? > |? ? ? ? ? ? 45 | url? ? ? ? ? ? ? ? ? ? ? ? ? ? | Main LORIS URL? ? > >? ? ? ? ? ? ? | [5]http://loris.priv | Main URL where LORIS can be accessed | > >? ? ? ? ? ? ? > |? ? ? ? ? ? 46 | issue_tracker_url | Issue tracker URL | > >? ? ? ? ? ? ? /issue_tracker? ? ? | The *new* bug/issue tracker url? ? ? ? ? | > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > MariaDB [loris_database]> UPDATE Config SET > Value='[6]http://localhost' > >? ? ? ? ? ? ? WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > >? ? ? ? ? ? ? > Rows matched: 1? Changed: 1? Warnings: 0 > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > >? ? ? ? ? ? ? c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs > ON > >? ? ? ? ? ? ? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = > csp.ID) > >? ? ? ? ? ? ? WHERE csp.Name = 'www'; > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? ? ? ? ? > | ConfigID | Name? ? ? ? ? ? ? ? ? ? ? ? ? | Label? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? Value? ? ? ? ? ? ? ? ? ? ? | Description? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? ? ? ? ? > |? ? ? ? ? ? 44 | host? ? ? ? ? ? ? ? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? loris.priv? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? > |? ? ? ? ? ? 45 | url? ? ? ? ? ? ? ? ? ? ? ? ? ? | Main LORIS URL? ? > >? ? ? ? ? ? ? | [7]http://localhost | Main URL where LORIS can be accessed | > >? ? ? ? ? ? ? > |? ? ? ? ? ? 46 | issue_tracker_url | Issue tracker URL | > >? ? ? ? ? ? ? /issue_tracker? ? | The *new* bug/issue tracker url? ? ? ? ? | > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? ? ? ? ? > 3 rows in set (0.00 sec) > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > best, > >? ? ? ? ? ? ? > Julie > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: > >? ? ? ? ? ? ? >>? ? Hi Julie, > >? ? ? ? ? ? ? >>? ? Forgive my ambiguity - We run the community support listserv > for > >? ? ? ? ? ? ? >>? ? developers, project administrators and sysadmins setting up > >? ? ? ? ? ? ? LORIS, so that > >? ? ? ? ? ? ? >>? ? these users can contact our technical team for exactly such > >? ? ? ? ? ? ? technical > >? ? ? ? ? ? ? >>? ? help.? > >? ? ? ? ? ? ? >>? ? If it's ok with you, I'd encourage you subscribe to the > listserv > >? ? ? ? ? ? ? and > >? ? ? ? ? ? ? >>? ? contact our technical team that way for the same reason. > >? ? ? ? ? ? ? >>? ? (Note that front-end users of LORIS typically contact their > >? ? ? ? ? ? ? project team > >? ? ? ? ? ? ? >>? ? for support, rather than us.) > >? ? ? ? ? ? ? >>? ? Given that your lorismysql user privileges seem appropriate > >? ? ? ? ? ? ? ('UPDATE" is > >? ? ? ? ? ? ? >>? ? there, I mistyped 'INSERT" before) > >? ? ? ? ? ? ? >>? ? --? is there any other indication why the database record is > not > >? ? ? ? ? ? ? >>? ? updating?? > >? ? ? ? ? ? ? >>? ? In the front-end, can your 'admin' user effect any changes > in > >? ? ? ? ? ? ? (any) Config > >? ? ? ? ? ? ? >>? ? setting?? > >? ? ? ? ? ? ? >>? ? In the back-end, when you tried updating a field using your > >? ? ? ? ? ? ? >>? ? lorismysql credential, what happened? > >? ? ? ? ? ? ? >>? ? Your front end is loading ok, and you can log in there, if I > >? ? ? ? ? ? ? understood > >? ? ? ? ? ? ? >>? ? correctly. > >? ? ? ? ? ? ? >>? ? Thanks for letting us know these details at > >? ? ? ? ? ? ? >>? ? [1]loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? ? Please also include what version of LORIS you are > installing, and > >? ? ? ? ? ? ? on what > >? ? ? ? ? ? ? >>? ? OS version. > >? ? ? ? ? ? ? >>? ? Best, > >? ? ? ? ? ? ? >>? ? Christine > >? ? ? ? ? ? ? >>? ? On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI > Computing > >? ? ? ? ? ? ? Support > >? ? ? ? ? ? ? >>? ? <[2]support-cirl at berkeley.edu> wrote: > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? Thank you Christine, > >? ? ? ? ? ? ? >>? ? ? ? I'm the linux sysadmin who installed the loris database > for > >? ? ? ? ? ? ? Ioannis. > >? ? ? ? ? ? ? >>? ? ? ? I'm not a loris user, however, so that makes it a little > >? ? ? ? ? ? ? awkward for > >? ? ? ? ? ? ? >>? ? ? ? troubleshooting via the mailing list. I'm happy to help in > >? ? ? ? ? ? ? whatever way > >? ? ? ? ? ? ? >>? ? ? ? I can. > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? Regarding the database permissions, I ran: > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? MariaDB [(none)]> show grants for 'lorismysql'@'%'; > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? | Grants for lorismysql@% > >? ? ? ? ? ? ? >>? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? | GRANT USAGE ON *.* TO 'lorismysql'@'%' > >? ? ? ? ? ? ? >>? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? | GRANT SELECT, INSERT, UPDATE, DELETE ON > `loris_database`.* TO > >? ? ? ? ? ? ? >>? ? ? ? 'lorismysql'@'%' | > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? 2 rows in set (0.00 sec) > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? looking at the 'tips' section in the page you referred > to... > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 29 | base? ? ? ? ? ? ? ? ? ? | Base? ? ? ? ? ? ? | > /srv/www/loris/? ? | > >? ? ? ? ? ? ? The base > >? ? ? ? ? ? ? >>? ? ? ? filesystem path where LORIS is > >? ? ? ? ? ? ? installed? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 31 | DownloadPath? ? | Downloads? ? | > /srv/www/loris/? ? | > >? ? ? ? ? ? ? Where > >? ? ? ? ? ? ? >>? ? ? ? files are downloaded > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? | ConfigID | Name? ? ? ? ? ? ? ? ? ? ? ? ? | Label? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? Value? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? Description? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 44 | host? ? ? ? ? ? ? ? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? loris.priv? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? Host? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 45 | url? ? ? ? ? ? ? ? ? ? ? ? ? ? | Main LORIS URL? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? [3]http://loris.priv | Main URL where LORIS can be > accessed | > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 46 | issue_tracker_url | Issue tracker URL | > >? ? ? ? ? ? ? /issue_tracker? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? The *new* bug/issue tracker url? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? apache config: > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? Listen 80 > >? ? ? ? ? ? ? >>? ? ? ? User apache > >? ? ? ? ? ? ? >>? ? ? ? Group apache > >? ? ? ? ? ? ? >>? ? ? ? DocumentRoot "/srv/www/loris/htdocs" > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? AllowOverride none > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Require all denied > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? AllowOverride All > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Options Indexes FollowSymLinks > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Require all granted > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Options Indexes FollowSymLinks > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? AllowOverride All > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Require all granted > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? file permissions: > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? # ls -ld /srv/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>? ? ? ? drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 > >? ? ? ? ? ? ? >>? ? ? ? /srv/www/loris/smarty/templates_c/ > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? [root at loris loris]# ls -l > /srv/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 2444 Oct 31 09:46 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep? 7 18:39 > >? ? ? ? ? ? ? >>? ? ? ? > 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 3296 Sep? 7 18:35 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 5901 Sep? 7 21:10 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep? 7 18:39 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? ? 874 Sep 10 11:01 > >? ? ? ? ? ? ? >>? ? ? ? > 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 1101 Sep 10 10:58 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 3590 Sep? 7 18:39 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep? 7 21:08 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? ? 897 Sep? 7 18:35 > >? ? ? ? ? ? ? >>? ? ? ? > a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 9210 Sep 10 11:01 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 8917 Sep 10 13:21 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 4811 Sep? 7 18:35 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 3309 Sep 10 11:02 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep? 7 17:42 > >? ? ? ? ? ? ? >>? ? ? ? > fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? thanks again! > >? ? ? ? ? ? ? >>? ? ? ? Julie > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: > >? ? ? ? ? ? ? >>>? ? ? ? Hi Ioannis,????? > >? ? ? ? ? ? ? >>>? ? ? ? Thanks for your question.????? > >? ? ? ? ? ? ? >>>? ? ? ? Given that the URL field is not updating, I suspect it's > a > >? ? ? ? ? ? ? database > >? ? ? ? ? ? ? >>>? ? ? ? back-end issue.????? > >? ? ? ? ? ? ? >>>? ? ? ? Can you verify -- Has your mysql user lorismysql????? been > granted > >? ? ? ? ? ? ? the > >? ? ? ? ? ? ? >>? ? ? ? "INSERT" > >? ? ? ? ? ? ? >>>? ? ? ? privilege for the right database? If not, that would > result in > >? ? ? ? ? ? ? an > >? ? ? ? ? ? ? >>? ? ? ? error > >? ? ? ? ? ? ? >>>? ? ? ? like the kind you are seeing.????? > >? ? ? ? ? ? ? >>>? ? ? ? Also, if you wish to check your LORIS Configuration > settings > >? ? ? ? ? ? ? in the > >? ? ? ? ? ? ? >>>? ? ? ? backend database such as the URL field -- to see what was > >? ? ? ? ? ? ? actually > >? ? ? ? ? ? ? >>? ? ? ? stored > >? ? ? ? ? ? ? >>>? ? ? ? in a given database field and should display in the > Config > >? ? ? ? ? ? ? >>? ? ? ? module:????? > >? ? ? ? ? ? ? >>>? ? ? ? You can run the queries listed in the "Troubleshooting > >? ? ? ? ? ? ? >>? ? ? ? Configuration > >? ? ? ? ? ? ? >>>? ? ? ? settings" section of our Github-wiki Setup Guide (under > >? ? ? ? ? ? ? Project > >? ? ? ? ? ? ? >>>? ? ? ? Customization) :????? > >? ? ? ? ? ? ? >>>? ? ? > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? ? ? ? ? >>>? ? ? ? Lastly, this question is perfectly appropriate for the > >? ? ? ? ? ? ? loris-dev > >? ? ? ? ? ? ? >>? ? ? ? community > >? ? ? ? ? ? ? >>>? ? ? ? support listserv -- please [2]subscribe here and then > email > >? ? ? ? ? ? ? our > >? ? ? ? ? ? ? >>? ? ? ? technical > >? ? ? ? ? ? ? >>>? ? ? ? team your next question at????? > [3][5]loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? ? ? ? (after checking > >? ? ? ? ? ? ? >>>? ? ? ? any forwarded threads for sensitive info).????? > >? ? ? ? ? ? ? >>>? ? ? ? We prefer to answer technical questions there for the > benefit > >? ? ? ? ? ? ? of > >? ? ? ? ? ? ? >>? ? ? ? the > >? ? ? ? ? ? ? >>>? ? ? ? community and other first-time users in the same position > as > >? ? ? ? ? ? ? >>? ? ? ? yourself.????? ????? > >? ? ? ? ? ? ? >>>? ? ? ? Thanks and cheers,????? > >? ? ? ? ? ? ? >>>? ? ? ? Christine????? > >? ? ? ? ? ? ? >>>? ? ? ? On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD > >? ? ? ? ? ? ? >>>? ? ? ? <[4][6]ioannis at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Hi Loris support.????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? My name is ioannis Pappas, a post-doc at the D'Esposito > lab > >? ? ? ? ? ? ? >>? ? ? ? stroke group > >? ? ? ? ? ? ? >>>? ? ? ? ? ? at UC Berkeley. With the kind of help of our sys > admin????? > >? ? ? ? ? ? ? Julie > >? ? ? ? ? ? ? >>? ? ? ? (cc'ed) we > >? ? ? ? ? ? ? >>>? ? ? ? ? ? have set up our loris database in our cluster (she is > the > >? ? ? ? ? ? ? sudo > >? ? ? ? ? ? ? >>? ? ? ? user and > >? ? ? ? ? ? ? >>>? ? ? ? ? ? I am the admin user). > >? ? ? ? ? ? ? >>>? ? ? ? ? ? If you allow me, I would like to ask you about the > first > >? ? ? ? ? ? ? >>? ? ? ? configuration > >? ? ? ? ? ? ? >>>? ? ? ? ? ? steps in the front end as they are described in the > >? ? ? ? ? ? ? tutorial. We > >? ? ? ? ? ? ? >>? ? ? ? can > >? ? ? ? ? ? ? >>>? ? ? ? ? ? login to [5][7]http://loris and the front end normally. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? However any update that I am trying to????? perform in > >? ? ? ? ? ? ? >>? ? ? ? Admin->Configuration > >? ? ? ? ? ? ? >>>? ? ? ? ? ? doesn't work (e.g. updating the study name). It just > >? ? ? ? ? ? ? refreshes > >? ? ? ? ? ? ? >>? ? ? ? the same > >? ? ? ? ? ? ? >>>? ? ? ? ? ? page. I am just wondering if there is an issue with > writing > >? ? ? ? ? ? ? in > >? ? ? ? ? ? ? >>? ? ? ? the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? configuration file. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Here are the permissions setup for where Loris is > installed. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? chmod 777 /var/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>>? ? ? ? ? ? cd /srv/www/loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? chown -R lorisadmin:lorisadmin . > >? ? ? ? ? ? ? >>>? ? ? ? ? ? chmod -c -R a+r . > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? this command gives everyone read access, and > outputs > >? ? ? ? ? ? ? what > >? ? ? ? ? ? ? >>? ? ? ? changes > >? ? ? ? ? ? ? >>>? ? ? ? ? ? were made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? mode of ?????????./project????????? changed from 0770 > (rwxrwx---) to > >? ? ? ? ? ? ? 0774 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? mode of ?????????./tools/logs????????? changed from 0770 > (rwxrwx---) > >? ? ? ? ? ? ? to > >? ? ? ? ? ? ? >>? ? ? ? 0774 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? find . -type d -exec chmod a+x -c {} \; > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? this command gives everyone permission to open > a > >? ? ? ? ? ? ? directory, > >? ? ? ? ? ? ? >>? ? ? ? and > >? ? ? ? ? ? ? >>>? ? ? ? ? ? outputs what changes were made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? mode of ?????????./project????????? changed from 0774 > (rwxrwxr--) to > >? ? ? ? ? ? ? 0775 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? (rwxrwxr-x) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? mode of ?????????./tools/logs????????? changed from 0774 > (rwxrwxr--) > >? ? ? ? ? ? ? to > >? ? ? ? ? ? ? >>? ? ? ? 0775 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? (rwxrwxr-x) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Hopefully????? you can help me with this. I also > subscribed to > >? ? ? ? ? ? ? the > >? ? ? ? ? ? ? >>? ? ? ? mailing > >? ? ? ? ? ? ? >>>? ? ? ? ? ? list but I am not sure if this too much of a basic > question > >? ? ? ? ? ? ? for > >? ? ? ? ? ? ? >>? ? ? ? the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? list. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI > >? ? ? ? ? ? ? Computing > >? ? ? ? ? ? ? >>? ? ? ? Support > >? ? ? ? ? ? ? >>>? ? ? ? ? ? <[6][8]support-cirl at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? Hi ioannis, maybe it's best to ask the developers? > You can > >? ? ? ? ? ? ? cc > >? ? ? ? ? ? ? >>? ? ? ? me if > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? you'd like. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas > >? ? ? ? ? ? ? >>? ? ? ? <[7][9]ioannis at berkeley.edu> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? wrote: > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? That did the trick Julie. Thank you! > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? I am still trying to understand how configuration > works > >? ? ? ? ? ? ? >>? ? ? ? though. For > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? example if I just try to change the name of the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? study from the front end, I get nowhere (it just > >? ? ? ? ? ? ? refreshes > >? ? ? ? ? ? ? >>? ? ? ? the same > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? page). > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? I am not sure if this requires write permissions > >? ? ? ? ? ? ? somewhere in > >? ? ? ? ? ? ? >>? ? ? ? a > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? config file/folder and that??????????????????s why it > doesn??????????????????t update > >? ? ? ? ? ? ? it. > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Ioannis > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI > >? ? ? ? ? ? ? Computing > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Support <[8][10]support-cirl at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > just in case you're interested, these are the > >? ? ? ? ? ? ? permission > >? ? ? ? ? ? ? >>? ? ? ? changes I > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > chmod 777 /var/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > cd /srv/www/loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > chown -R lorisadmin:lorisadmin . > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > chmod -c -R a+r . > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? this command gives everyone read access, > and > >? ? ? ? ? ? ? outputs > >? ? ? ? ? ? ? >>? ? ? ? what > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? changes were made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? mode of ?????????./project????????? changed from > 0770 > >? ? ? ? ? ? ? (rwxrwx---) to > >? ? ? ? ? ? ? >>? ? ? ? 0774 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? mode of ?????????./tools/logs????????? changed from > 0770 > >? ? ? ? ? ? ? (rwxrwx---) > >? ? ? ? ? ? ? >>? ? ? ? to 0774 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > find . -type d -exec chmod a+x -c {} \; > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? this command gives everyone permission to > open a > >? ? ? ? ? ? ? >>? ? ? ? directory, and > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? outputs what changes were made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? mode of ?????????./project????????? changed from > 0774 > >? ? ? ? ? ? ? (rwxrwxr--) to > >? ? ? ? ? ? ? >>? ? ? ? 0775 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? (rwxrwxr-x) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? mode of ?????????./tools/logs????????? changed from > 0774 > >? ? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>? ? ? ? to 0775 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? (rwxrwxr-x) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> Hi Julie. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> I just tried and I still don???t get anything. I > also > >? ? ? ? ? ? ? >>? ? ? ? tried > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? private mode in Firefox in case the empty page was > >? ? ? ? ? ? ? cached. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> Sorry for this. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, > HWNI > >? ? ? ? ? ? ? >>? ? ? ? Computing > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Support <[9][11]support-cirl at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> hi Ioannis, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> no worries, I changed the following directory > to > >? ? ? ? ? ? ? 777: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> /var/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> will you please check if that works? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> thanks! > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas > PhD > >? ? ? ? ? ? ? wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Hi Julie. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Apologies for bugging you with this again. > We > >? ? ? ? ? ? ? tried > >? ? ? ? ? ? ? >>? ? ? ? now to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? access??????????? [1][10][12]http://loris??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? and we are getting a??????????? blank page. I > think the > >? ? ? ? ? ? ? reason > >? ? ? ? ? ? ? >>? ? ? ? for this > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? is that we > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? don't have read??????????? permissions to read > from the > >? ? ? ? ? ? ? >>? ? ? ? template located > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? in > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? /var/www/loris/smarty See here bottom of > the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? page??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? I think, in general, I am a little bit > confused > >? ? ? ? ? ? ? as to > >? ? ? ? ? ? ? >>? ? ? ? what the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? permissions > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? should be for us that are not sudos. My > >? ? ? ? ? ? ? understanding > >? ? ? ? ? ? ? >>? ? ? ? is that > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? if we don't > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? have read or write permissions then we > can't > >? ? ? ? ? ? ? access or > >? ? ? ? ? ? ? >>? ? ? ? write > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? /var/www/loris, meaning that we can't > access or > >? ? ? ? ? ? ? >>? ? ? ? configure. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Should > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? everything be chmod 777 for example???????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Thank you very much once again. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis > >? ? ? ? ? ? ? Pappas PhD > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? <[3][12][14]ioannis at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? Thank you very much Julie. I appreciate > this > >? ? ? ? ? ? ? and I > >? ? ? ? ? ? ? >>? ? ? ? will dig > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? into Loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? given your changes. Thank you so much > for your > >? ? ? ? ? ? ? >>? ? ? ? help. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? On Thu, Oct 31, 2019 at 12:48 PM Julie > >? ? ? ? ? ? ? Ashworth, > >? ? ? ? ? ? ? >>? ? ? ? HWNI > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Computing Support > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? <[4][13][15]support-cirl at berkeley.edu> > wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? hi Ioannis, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? 1. I changed the permissions of > >? ? ? ? ? ? ? /srv/www/loris > >? ? ? ? ? ? ? >>? ? ? ? to be owned > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? by > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? lorisadmin. I reivewed my > installation > >? ? ? ? ? ? ? notes, > >? ? ? ? ? ? ? >>? ? ? ? and I did > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? this already > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? when > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? I installed the server. I'm not > sure why > >? ? ? ? ? ? ? they > >? ? ? ? ? ? ? >>? ? ? ? changed, so > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? it's > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? probably a > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? good idea to keep an eye on that. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? 2. When I installed the loris > software, I > >? ? ? ? ? ? ? also > >? ? ? ? ? ? ? >>? ? ? ? installed a > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? mysql > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? database as recommended in the > >? ? ? ? ? ? ? instructions: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? projectname: LORIS > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? databasename: loris_database > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? mysqluser: lorismysql > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? frontend: lorisweb > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? 3. A couple of weeks ago, I moved > Henrik's > >? ? ? ? ? ? ? home > >? ? ? ? ? ? ? >>? ? ? ? directory > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? /home/despoA, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? but I forgot to update loris. This > is done > >? ? ? ? ? ? ? now. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? best, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? Julie > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? On 31-10-2019 11.15 -0700, Dr. > Ioannis > >? ? ? ? ? ? ? Pappas > >? ? ? ? ? ? ? >>? ? ? ? PhD wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Hi Julie. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? I hope you are well. We are > trying to > >? ? ? ? ? ? ? >>? ? ? ? configure loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? that you > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? kindly set > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? up for us. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? I have a couple of > questions for you if > >? ? ? ? ? ? ? you > >? ? ? ? ? ? ? >>? ? ? ? allow me > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? so.??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 1) First, although we are > logging into > >? ? ? ? ? ? ? the > >? ? ? ? ? ? ? >>? ? ? ? front end > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? with admin > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? username > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? (lorisweb) and password, it > seems that > >? ? ? ? ? ? ? any > >? ? ? ? ? ? ? >>? ? ? ? kind of > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? update of > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? configuration > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? we are trying to do fails > (meaning that > >? ? ? ? ? ? ? if > >? ? ? ? ? ? ? >>? ? ? ? we, say, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? change the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? name of the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? study and press "submit", > this doesn't > >? ? ? ? ? ? ? do > >? ? ? ? ? ? ? >>? ? ? ? anything-it > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? doesn't > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? update). > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? It's almost like our > lorisweb user > >? ? ? ? ? ? ? doesn't > >? ? ? ? ? ? ? >>? ? ? ? have write > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? privileges > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? in the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? /var/www/loris/project > (where I think > >? ? ? ? ? ? ? every > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? configuration should > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? be). > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? This generalizes for > everything that we > >? ? ? ? ? ? ? are > >? ? ? ? ? ? ? >>? ? ? ? trying to do > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? in the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? front end. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Clicking any instrument/tab > in the front > >? ? ? ? ? ? ? end > >? ? ? ? ? ? ? >>? ? ? ? doesn't > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? really point > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? anything.??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 2) Loris suggest doing > configurations > >? ? ? ? ? ? ? via > >? ? ? ? ? ? ? >>? ? ? ? SQL. Is it > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? possible to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? run SQL > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? scripts in the backend > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 3) For some reason typing > ssh lors for > >? ? ? ? ? ? ? Henrik > >? ? ? ? ? ? ? >>? ? ? ? doesn't > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? directly > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? take him to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? loris (it requires a > password that is > >? ? ? ? ? ? ? not the > >? ? ? ? ? ? ? >>? ? ? ? password > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? setup for > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? lorisweb user). Will you be > able to fix > >? ? ? ? ? ? ? this > >? ? ? ? ? ? ? >>? ? ? ? via your > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? sudo > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? privileges? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Thank you very much in > advance for all > >? ? ? ? ? ? ? your > >? ? ? ? ? ? ? >>? ? ? ? help Julie. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Let us > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? know if > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? this is something that > shouldn't be > >? ? ? ? ? ? ? directed > >? ? ? ? ? ? ? >>? ? ? ? to you (but > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? instead > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? to the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? loris people).??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? On Mon, Sep 9, 2019 at 6:25 > PM Julie > >? ? ? ? ? ? ? >>? ? ? ? Ashworth, HWNI > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Computing > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? Support > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ???????????????? > >? ? ? ? ? ? ? <[1][5][14][16]support-cirl at berkeley.edu> > >? ? ? ? ? ? ? >>? ? ? ? wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? hi Henrik and > Ioannis, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? the loris server > is available for > >? ? ? ? ? ? ? you to > >? ? ? ? ? ? ? >>? ? ? ? use. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? The servername is > 'loris'. I > >? ? ? ? ? ? ? created a > >? ? ? ? ? ? ? >>? ? ? ? directory > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? called > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? /data/loris for > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? you to store data. > You may create > >? ? ? ? ? ? ? new > >? ? ? ? ? ? ? >>? ? ? ? folders in > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? /data/loris to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? organize > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? your data. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? 1) secure shell or > secure copy: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? You can log in > with the 'ssh' or > >? ? ? ? ? ? ? 'scp' > >? ? ? ? ? ? ? >>? ? ? ? command from > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? your remote > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? desktop > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? session. You don't > need to > >? ? ? ? ? ? ? authenticate > >? ? ? ? ? ? ? >>? ? ? ? to log in. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Maybe you'll > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? use scp > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? to transfer data > between your > >? ? ? ? ? ? ? cluster > >? ? ? ? ? ? ? >>? ? ? ? account and the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? server? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? Please put the > data in /data/loris, > >? ? ? ? ? ? ? so I > >? ? ? ? ? ? ? >>? ? ? ? can make > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? backups more > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? easily. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > secure shell: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > $ ssh loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > secure copy (change the > >? ? ? ? ? ? ? names > >? ? ? ? ? ? ? >>? ? ? ? in brackets). Let > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? me know if > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? I can > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > help with syntax: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > $ scp -r > >? ? ? ? ? ? ? >>? ? ? ? loris:/data/loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? 2) front-end web > interface.???????????????? > >? ? ? ? ? ? ? Open a > >? ? ? ? ? ? ? >>? ? ? ? web browser in > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? your remote > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? desktop > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? session and enter > the hostname: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? > [2][6][15][17]http://loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? I created an admin > user called > >? ? ? ? ? ? ? >>? ? ? ? 'lorisweb'. I put the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? password > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? in > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? $HOME/newuser on > the cluster. To > >? ? ? ? ? ? ? see it, > >? ? ? ? ? ? ? >>? ? ? ? open a > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? terminal, and > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? run: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > $ cat $HOME/newuser > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? If other people > need shell access > >? ? ? ? ? ? ? to the > >? ? ? ? ? ? ? >>? ? ? ? webserver, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? please let > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? me know > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? so I can create a > home directory > >? ? ? ? ? ? ? for > >? ? ? ? ? ? ? >>? ? ? ? them. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? We should > eventually discuss > >? ? ? ? ? ? ? backups. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? best, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? Julie > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> References > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Visible links > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 1. > >? ? ? ? ? ? ? >>? ? ? ? mailto:[7][16][18]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 2. [8][17][19]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? ---end quoted text--- > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> References > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Visible links > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 1. [18][20]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 2. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 3. mailto:[20][22]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 4. mailto:[21][23]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 5. mailto:[22][24]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 6. [23][25]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 7. mailto:[24][26]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 8. [25][27]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> ---end quoted text--- > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > ---end quoted text--- > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? -- > >? ? ? ? ? ? ? >>>? ? ? ? [26][28]christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >>>? ? ? ? McGill Centre for Integrative Neuroscience | MCIN.ca > >? ? ? ? ? ? ? >>>? ? ? ? Montreal Neurological Institute > >? ? ? ? ? ? ? >>>? ? ? ? McGill University | Montreal | Canada > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>> References > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? Visible links > >? ? ? ? ? ? ? >>>? ? ? ? 1. > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? ? ? ? ? >>>? ? ? ? 2. > >? ? ? ? ? ? ? [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? ? ? ? ? >>>? ? ? ? 3. mailto:[31]loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>>? ? ? ? 4. mailto:[32]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? 5. [33]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? 6. mailto:[34]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? 7. mailto:[35]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? 8. mailto:[36]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? 9. mailto:[37]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 10. [38]http://xn--loris-7qa/ > >? ? ? ? ? ? ? >>>? ? ? 11. > >? ? ? ? ? ? ? [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>>? ? ? 12. mailto:[40]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 13. mailto:[41]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 14. mailto:[42]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 15. [43]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 16. mailto:[44]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 17. [45]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 18. [46]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 19. > >? ? ? ? ? ? ? [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>>? ? ? 20. mailto:[48]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 21. mailto:[49]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 22. mailto:[50]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 23. [51]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 24. mailto:[52]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 25. [53]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 26. mailto:[54]christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >>? ? ? ? ---end quoted text--- > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? -- > >? ? ? ? ? ? ? >>? ? [55]christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >>? ? McGill Centre for Integrative Neuroscience | MCIN.ca > >? ? ? ? ? ? ? >>? ? Montreal Neurological Institute > >? ? ? ? ? ? ? >>? ? McGill University | Montreal | Canada > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >> References > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? Visible links > >? ? ? ? ? ? ? >>? ? 1. [8]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? ? 2. [9]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? ? 3. [10]http://loris.priv/ > >? ? ? ? ? ? ? >>? > >? ? ? ? ? ? ? 4. > [11]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? ? ? ? ? >>? ? 5. [12]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? ? 6. [13]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? ? 7. [14]http://loris/ > >? ? ? ? ? ? ? >>? ? 8. [15]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? ? 9. [16]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 10. [17]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 11. [18]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 12. [19]http://xn--loris-era/ > >? ? ? ? ? ? ? >>? 13. > [20]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>? 14. [21]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 15. [22]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 16. [23]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 17. [24]http://loris/ > >? ? ? ? ? ? ? >>? 18. [25]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 19. [26]http://loris/ > >? ? ? ? ? ? ? >>? 20. [27]http://loris/ > >? ? ? ? ? ? ? >>? 21. > [28]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>? 22. [29]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 23. [30]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 24. [31]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 25. [32]http://loris/ > >? ? ? ? ? ? ? >>? 26. [33]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 27. [34]http://loris/ > >? ? ? ? ? ? ? >>? 28. [35]mailto:christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? 29. > [36]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? ? ? ? ? >>? 30. > [37]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? ? ? ? ? >>? 31. [38]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? 32. [39]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 33. [40]http://loris/ > >? ? ? ? ? ? ? >>? 34. [41]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 35. [42]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 36. [43]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 37. [44]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 38. [45]http://xn--loris-7qa/ > >? ? ? ? ? ? ? >>? 39. > [46]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>? 40. [47]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 41. [48]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 42. [49]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 43. [50]http://loris/ > >? ? ? ? ? ? ? >>? 44. [51]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 45. [52]http://loris/ > >? ? ? ? ? ? ? >>? 46. [53]http://loris/ > >? ? ? ? ? ? ? >>? 47. > [54]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>? 48. [55]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 49. [56]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 50. [57]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 51. [58]http://loris/ > >? ? ? ? ? ? ? >>? 52. [59]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 53. [60]http://loris/ > >? ? ? ? ? ? ? >>? 54. [61]mailto:christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >>? 55. [62]mailto:christine.rogers at mcgill.ca > >? ? ? ? ? ? ? > ---end quoted text--- > > > >? ? ? ? ? ? ? _______________________________________________ > >? ? ? ? ? ? ? Loris-dev mailing list > >? ? ? ? ? ? ? Loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? [63]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? ? ? ? ? > > > >? ? ? ? ? _______________________________________________ > >? ? ? ? ? Loris-dev mailing list > >? ? ? ? ? Loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > >? ? ? -- > >? ? ? christine.rogers at mcgill.ca > >? ? ? McGill Centre for Integrative Neuroscience | MCIN.ca > >? ? ? Montreal Neurological Institute > >? ? ? McGill University | Montreal | Canada > ---end quoted text--- > > References > > Visible links > 1. https://loris.url/configuration/ > 2. https://.loris.url/ > 3. http://loris.priv/ > 4. http://localhost/ > 5. http://loris.priv/ > 6. http://localhost/ > 7. http://localhost/ > 8. mailto:loris-dev at bic.mni.mcgill.ca > 9. mailto:support-cirl at berkeley.edu > 10. http://loris.priv/ > 11. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 12. mailto:loris-dev at bic.mni.mcgill.ca > 13. mailto:ioannis at berkeley.edu > 14. http://loris/ > 15. mailto:support-cirl at berkeley.edu > 16. mailto:ioannis at berkeley.edu > 17. mailto:support-cirl at berkeley.edu > 18. mailto:support-cirl at berkeley.edu > 19. http://xn--loris-era/ > 20. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 21. mailto:ioannis at berkeley.edu > 22. mailto:support-cirl at berkeley.edu > 23. mailto:support-cirl at berkeley.edu > 24. http://loris/ > 25. mailto:support-cirl at berkeley.edu > 26. http://loris/ > 27. http://loris/ > 28. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 29. mailto:ioannis at berkeley.edu > 30. mailto:support-cirl at berkeley.edu > 31. mailto:support-cirl at berkeley.edu > 32. http://loris/ > 33. mailto:support-cirl at berkeley.edu > 34. http://loris/ > 35. mailto:christine.rogers at mcgill.ca > 36. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 37. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 38. mailto:loris-dev at bic.mni.mcgill.ca > 39. mailto:ioannis at berkeley.edu > 40. http://loris/ > 41. mailto:support-cirl at berkeley.edu > 42. mailto:ioannis at berkeley.edu > 43. mailto:support-cirl at berkeley.edu > 44. mailto:support-cirl at berkeley.edu > 45. http://xn--loris-7qa/ > 46. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 47. mailto:ioannis at berkeley.edu > 48. mailto:support-cirl at berkeley.edu > 49. mailto:support-cirl at berkeley.edu > 50. http://loris/ > 51. mailto:support-cirl at berkeley.edu > 52. http://loris/ > 53. http://loris/ > 54. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 55. mailto:ioannis at berkeley.edu > 56. mailto:support-cirl at berkeley.edu > 57. mailto:support-cirl at berkeley.edu > 58. http://loris/ > 59. mailto:support-cirl at berkeley.edu > 60. http://loris/ > 61. mailto:christine.rogers at mcgill.ca > 62. mailto:christine.rogers at mcgill.ca > 63. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 64. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ---end quoted text--- _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From melanie.legault2 at mcgill.ca Mon Nov 11 12:28:06 2019 From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs) Date: Mon, 11 Nov 2019 17:28:06 +0000 Subject: [Loris-dev] loris server In-Reply-To: <20191111170342.GA4213@gaia.neuro.berkeley.edu> References: <49264d38a0834b5d91da0d2e54c9b535@YTXPR0101MB1070.CANPRD01.PROD.OUTLOOK.COM> <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> <20191109020414.GB13279@nx6.priv> , <20191111170342.GA4213@gaia.neuro.berkeley.edu> Message-ID: Hello Julie, Yes, the '%' sign is a wildcard for 'all host'. So it should be good but I had problem with that in the past. Could you ensure the 'lorismysql'@'localhost' user proper permissions. Also, in that case, in the config.xml file, the dbHost should be 'localhost'. MySQL treat 127.0.0.1 and localhost as 2 different host. M?lanie ________________________________ From: Julie Ashworth, HWNI Computing Support Sent: November 11, 2019 12:03 To: Melanie Legault, Mrs Cc: Christine Rogers, Ms. ; Ioannis Pappas ; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] loris server thanks Melanie, I'm including the output below. My understanding is that '%' matches all hostnames. Should I specifically grant permission to 'loris.priv' from user lorismysql? Or perhaps you recommend changing loris_database entries ('host' to 'localhost' and 'url' to 'http://localhost')? thanks! MariaDB [(none)]> SELECT User, Host FROM mysql.user; +------------+-----------+ | User | Host | +------------+-----------+ | lorismysql | % | | root | 127.0.0.1 | | root | ::1 | | lorismysql | localhost | | root | localhost | +------------+-----------+ 5 rows in set (0.00 sec) MariaDB [(none)]> SHOW grants for 'lorismysql'@'%'; +--------------------------------------------------------------------------------+ | Grants for lorismysql@% +--------------------------------------------------------------------------------+ | GRANT USAGE ON *.* TO 'lorismysql'@'%' | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO 'lorismysql'@'%' | +--------------------------------------------------------------------------------+ 2 rows in set (0.00 sec) On 11-11-2019 15.47 +0000, Melanie Legault, Mrs wrote: > Hello Julie, > Could it be that your MySQL 'lorismysql' user have different permissions > depending on where it is connecting to the DB? > A database admin (root) can check this for you. > SELECT User, Host FROM mysql.user; > then for the user that match the Host (name or IP address) of your LORIS > (Apache) server > SHOW grants for 'lorismysql'@''; > > M??lanie > > -------------------------------------------------------------------------- > > From: Julie Ashworth, HWNI Computing Support > Sent: November 8, 2019 21:04 > To: Christine Rogers, Ms. > Cc: Ioannis Pappas ; Melanie Legault, Mrs > ; loris-dev at bic.mni.mcgill.ca > > Subject: Re: [Loris-dev] loris server > ? > thanks Christine, > > yes, it's the lorismysql user in the config.xml file. > ? ? ? ? ? ? ? lorismysql > ? ? ? ? ? ? ? loris_database > ? ? ? ? ? ? ? lorismysql > > we appeciate your help troubleshooting this. > best, > Julie > > On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote: > >? ? ? Hi Ioannis, > >? ? ? Could you open your file called config.xml > >? ? ? (/srv/www/loris/project/config.xml) and confirm for us --? which user > >? ? ? credential is stored there, and what's the name of the database it is > >? ? ? connecting to? > >? ? ? This is the mysql user which connects to the database from the front > end > >? ? ? of LORIS.? > >? ? ? If this user has insufficient privileges on your database, that would > >? ? ? cause the errors you are seeing.? I had assumed from your thread it > was > >? ? ? your lorismysql user but it sounds like this should be verified. > >? ? ? Let us know, and we'll keep following up when we come back online > after > >? ? ? the weekend, > >? ? ? Best, > >? ? ? Christine > >? ? ? On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas > >? ? ? wrote: > > > >? ? ? ? ? Hi Melanie. > >? ? ? ? ? Thank you for taking the time to reply to this. I took some to > consider > >? ? ? ? ? your comments. Unfortunately as I said to Christine we are unable > to do > >? ? ? ? ? any kind of updating to the database (either that is changing the > name > >? ? ? ? ? or changing the small html description, etc.). > >? ? ? ? ? Based on some more digging and on some of Christine's comments I > have a > >? ? ? ? ? feeling that our lorisweb front-end, admin user cannot write > anything to > >? ? ? ? ? the database. Along these lines could it be the case the lorismysql > user > >? ? ? ? ? (the database, admin user with INSERT, UPDATE, etc privileges) is > not > >? ? ? ? ? ???????talking????? to the lorisweb front end user? What is the > difference between > >? ? ? ? ? the two and could it be a installation problem for them not talking > to > >? ? ? ? ? each other? As Julie said, lorismysql user is working normally with > >? ? ? ? ? MariaDB. > >? ? ? ? ? Thank you again for your help. > >? ? ? ? ? Best wishes, > >? ? ? ? ? Ioannis > > > >? ? ? ? ? ? ? On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs > >? ? ? ? ? ? ? wrote: > >? ? ? ? ? ? ? Hello, > >? ? ? ? ? ? ? Changing the project name in the configuration page > >? ? ? ? ? ? ? ([1]https://loris.url/configuration/) of LORIS, only change the > title of > >? ? ? ? ? ? ? the project. To see this change, you have to log out of LORIS and > then > >? ? ? ? ? ? ? go back to the login page ([2]https://.loris.url/). This is the > only > >? ? ? ? ? ? ? place you can find the project name (except from the > configuration > >? ? ? ? ? ? ? page). See ProjectName.png > >? ? ? ? ? ? ? As for files permission, I would suggest a few change to improve > >? ? ? ? ? ? ? security of you server. Some extra permissions where granted to > help > >? ? ? ? ? ? ? you but are not needed. > >? ? ? ? ? ? ? ? ? * /srv/www/loris/smarty/templates_c/? should have ownership of > >? ? ? ? ? ? ? ? ? ? ? lorisadmin:httpd and permission 770 (or 775) > >? ? ? ? ? ? ? ? ? * srv/www/loris/project/? should have ownership > lorisadmin:httpd and > >? ? ? ? ? ? ? ? ? ? ? permission 770 (775) > >? ? ? ? ? ? ? ? ? * All other files under loris should have lorisadmin:lorisadmin > 755 > >? ? ? ? ? ? ? Reading through this change of mail, I understand that you let > Apache > >? ? ? ? ? ? ? store file in /srv/www/loris > >? ? ? ? ? ? ? ? ? ? |? ? ? ? ? ? 31 | DownloadPath? ? | Downloads? ? | /srv/www/loris/? ? > | > >? ? ? ? ? ? ? Where > >? ? ? ? ? ? ? >>? ? ? ? files are downloaded > >? ? ? ? ? ? ? Downloaded files should not be in the same tree as LORIS code. It > >? ? ? ? ? ? ? should be in a separate structure where Apache will not try and > do not > >? ? ? ? ? ? ? have permission (in httpd.conf) to execute files. > >? ? ? ? ? ? ? Kind regards, > >? ? ? ? ? ? ? M????lanie Legault | Software developer | Faculty of Medicine | > McGill > >? ? ? ? ? ? ? University? > >? ? ? ? ? ? ? 3801 University, Montr????al, QC H3A 2B4 > > > >? ? ? ? ? > ---------------------------------------------------------------------- > > > >? ? ? ? ? ? ? From: loris-dev-bounces at bic.mni.mcgill.ca > >? ? ? ? ? ? ? on behalf of Ioannis Pappas > >? ? ? ? ? ? ? > >? ? ? ? ? ? ? Sent: November 7, 2019 0:18 > >? ? ? ? ? ? ? To: loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? Cc: Julie Ashworth, HWNI Computing Support > >? ? ? ? ? ? ? ; Christine Rogers, Ms. > >? ? ? ? ? ? ? > >? ? ? ? ? ? ? Subject: Re: [Loris-dev] loris server > >? ? ? ? ? ? ? ? > >? ? ? ? ? ? ? Hi Christine and Julie. > > > >? ? ? ? ? ? ? Yes it looks like that any attempt to configure something in the > >? ? ? ? ? ? ? front-end results in the same page. I am sending this to the list > (as > >? ? ? ? ? ? ? you requested Christine) alongside the troubleshooting and > discussion > >? ? ? ? ? ? ? so far with Julie. > > > >? ? ? ? ? ? ? Best wishes, > >? ? ? ? ? ? ? Ioannis > > > >? ? ? ? ? ? ? > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI Computing > Support > >? ? ? ? ? ? ? wrote: > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > hi Christine and Ioannis, > >? ? ? ? ? ? ? > Ioannis, can you follow-up with Christine about using the > front-end? > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > We're using CentOS7.7 and loris-21.0.1. > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > I confirmed that I could login as the mysql user (lorismyqsl) > and > >? ? ? ? ? ? ? change the 'url' config setting from '[3]http://loris.priv' to > >? ? ? ? ? ? ? '[4]http://localhost', and back again. > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > >? ? ? ? ? ? ? c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs > ON > >? ? ? ? ? ? ? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = > csp.ID) > >? ? ? ? ? ? ? WHERE csp.Name = 'www'; > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? > | ConfigID | Name? ? ? ? ? ? ? ? ? ? ? ? ? | Label? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? Value? ? ? ? ? ? ? ? ? ? ? ? | Description? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? > |? ? ? ? ? ? 44 | host? ? ? ? ? ? ? ? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? loris.priv? ? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? > |? ? ? ? ? ? 45 | url? ? ? ? ? ? ? ? ? ? ? ? ? ? | Main LORIS URL? ? > >? ? ? ? ? ? ? | [5]http://loris.priv | Main URL where LORIS can be accessed | > >? ? ? ? ? ? ? > |? ? ? ? ? ? 46 | issue_tracker_url | Issue tracker URL | > >? ? ? ? ? ? ? /issue_tracker? ? ? | The *new* bug/issue tracker url? ? ? ? ? | > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > MariaDB [loris_database]> UPDATE Config SET > Value='[6]http://localhost' > >? ? ? ? ? ? ? WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='url'); > >? ? ? ? ? ? ? > Rows matched: 1? Changed: 1? Warnings: 0 > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, > >? ? ? ? ? ? ? c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs > ON > >? ? ? ? ? ? ? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = > csp.ID) > >? ? ? ? ? ? ? WHERE csp.Name = 'www'; > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? ? ? ? ? > | ConfigID | Name? ? ? ? ? ? ? ? ? ? ? ? ? | Label? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? Value? ? ? ? ? ? ? ? ? ? ? | Description? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? ? ? ? ? > |? ? ? ? ? ? 44 | host? ? ? ? ? ? ? ? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? loris.priv? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? > |? ? ? ? ? ? 45 | url? ? ? ? ? ? ? ? ? ? ? ? ? ? | Main LORIS URL? ? > >? ? ? ? ? ? ? | [7]http://localhost | Main URL where LORIS can be accessed | > >? ? ? ? ? ? ? > |? ? ? ? ? ? 46 | issue_tracker_url | Issue tracker URL | > >? ? ? ? ? ? ? /issue_tracker? ? | The *new* bug/issue tracker url? ? ? ? ? | > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? ? ? ? ? > 3 rows in set (0.00 sec) > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > best, > >? ? ? ? ? ? ? > Julie > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > > >? ? ? ? ? ? ? > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. wrote: > >? ? ? ? ? ? ? >>? ? Hi Julie, > >? ? ? ? ? ? ? >>? ? Forgive my ambiguity - We run the community support listserv > for > >? ? ? ? ? ? ? >>? ? developers, project administrators and sysadmins setting up > >? ? ? ? ? ? ? LORIS, so that > >? ? ? ? ? ? ? >>? ? these users can contact our technical team for exactly such > >? ? ? ? ? ? ? technical > >? ? ? ? ? ? ? >>? ? help.? > >? ? ? ? ? ? ? >>? ? If it's ok with you, I'd encourage you subscribe to the > listserv > >? ? ? ? ? ? ? and > >? ? ? ? ? ? ? >>? ? contact our technical team that way for the same reason. > >? ? ? ? ? ? ? >>? ? (Note that front-end users of LORIS typically contact their > >? ? ? ? ? ? ? project team > >? ? ? ? ? ? ? >>? ? for support, rather than us.) > >? ? ? ? ? ? ? >>? ? Given that your lorismysql user privileges seem appropriate > >? ? ? ? ? ? ? ('UPDATE" is > >? ? ? ? ? ? ? >>? ? there, I mistyped 'INSERT" before) > >? ? ? ? ? ? ? >>? ? --? is there any other indication why the database record is > not > >? ? ? ? ? ? ? >>? ? updating?? > >? ? ? ? ? ? ? >>? ? In the front-end, can your 'admin' user effect any changes > in > >? ? ? ? ? ? ? (any) Config > >? ? ? ? ? ? ? >>? ? setting?? > >? ? ? ? ? ? ? >>? ? In the back-end, when you tried updating a field using your > >? ? ? ? ? ? ? >>? ? lorismysql credential, what happened? > >? ? ? ? ? ? ? >>? ? Your front end is loading ok, and you can log in there, if I > >? ? ? ? ? ? ? understood > >? ? ? ? ? ? ? >>? ? correctly. > >? ? ? ? ? ? ? >>? ? Thanks for letting us know these details at > >? ? ? ? ? ? ? >>? ? [1]loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? ? Please also include what version of LORIS you are > installing, and > >? ? ? ? ? ? ? on what > >? ? ? ? ? ? ? >>? ? OS version. > >? ? ? ? ? ? ? >>? ? Best, > >? ? ? ? ? ? ? >>? ? Christine > >? ? ? ? ? ? ? >>? ? On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, HWNI > Computing > >? ? ? ? ? ? ? Support > >? ? ? ? ? ? ? >>? ? <[2]support-cirl at berkeley.edu> wrote: > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? Thank you Christine, > >? ? ? ? ? ? ? >>? ? ? ? I'm the linux sysadmin who installed the loris database > for > >? ? ? ? ? ? ? Ioannis. > >? ? ? ? ? ? ? >>? ? ? ? I'm not a loris user, however, so that makes it a little > >? ? ? ? ? ? ? awkward for > >? ? ? ? ? ? ? >>? ? ? ? troubleshooting via the mailing list. I'm happy to help in > >? ? ? ? ? ? ? whatever way > >? ? ? ? ? ? ? >>? ? ? ? I can. > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? Regarding the database permissions, I ran: > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? MariaDB [(none)]> show grants for 'lorismysql'@'%'; > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? | Grants for lorismysql@% > >? ? ? ? ? ? ? >>? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? | GRANT USAGE ON *.* TO 'lorismysql'@'%' > >? ? ? ? ? ? ? >>? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? | GRANT SELECT, INSERT, UPDATE, DELETE ON > `loris_database`.* TO > >? ? ? ? ? ? ? >>? ? ? ? 'lorismysql'@'%' | > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? 2 rows in set (0.00 sec) > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? looking at the 'tips' section in the page you referred > to... > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 29 | base? ? ? ? ? ? ? ? ? ? | Base? ? ? ? ? ? ? | > /srv/www/loris/? ? | > >? ? ? ? ? ? ? The base > >? ? ? ? ? ? ? >>? ? ? ? filesystem path where LORIS is > >? ? ? ? ? ? ? installed? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 31 | DownloadPath? ? | Downloads? ? | > /srv/www/loris/? ? | > >? ? ? ? ? ? ? Where > >? ? ? ? ? ? ? >>? ? ? ? files are downloaded > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? | ConfigID | Name? ? ? ? ? ? ? ? ? ? ? ? ? | Label? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? Value? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? Description? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 44 | host? ? ? ? ? ? ? ? ? ? ? ? ? | Host? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? loris.priv? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? Host? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 45 | url? ? ? ? ? ? ? ? ? ? ? ? ? ? | Main LORIS URL? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? [3]http://loris.priv | Main URL where LORIS can be > accessed | > >? ? ? ? ? ? ? >>? ? ? ? |? ? ? ? ? ? 46 | issue_tracker_url | Issue tracker URL | > >? ? ? ? ? ? ? /issue_tracker? ? ? | > >? ? ? ? ? ? ? >>? ? ? ? The *new* bug/issue tracker url? ? ? ? ? | > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? apache config: > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? Listen 80 > >? ? ? ? ? ? ? >>? ? ? ? User apache > >? ? ? ? ? ? ? >>? ? ? ? Group apache > >? ? ? ? ? ? ? >>? ? ? ? DocumentRoot "/srv/www/loris/htdocs" > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? AllowOverride none > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Require all denied > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? AllowOverride All > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Options Indexes FollowSymLinks > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Require all granted > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Options Indexes FollowSymLinks > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? AllowOverride All > >? ? ? ? ? ? ? >>? ? ? ? ? ? ? ? Require all granted > >? ? ? ? ? ? ? >>? ? ? ? > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? file permissions: > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? # ls -ld /srv/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>? ? ? ? drwxrwxrwx 2 lorisadmin lorisadmin 4096 Oct 31 09:46 > >? ? ? ? ? ? ? >>? ? ? ? /srv/www/loris/smarty/templates_c/ > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? [root at loris loris]# ls -l > /srv/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 2444 Oct 31 09:46 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 10490 Sep 10 10:55 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 21126 Sep? 7 18:39 > >? ? ? ? ? ? ? >>? ? ? ? > 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 3296 Sep? 7 18:35 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 5901 Sep? 7 21:10 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 23339 Sep? 7 18:39 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? ? 874 Sep 10 11:01 > >? ? ? ? ? ? ? >>? ? ? ? > 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 1101 Sep 10 10:58 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 18054 Sep 10 10:59 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 3590 Sep? 7 18:39 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 25141 Sep? 7 21:08 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? ? 897 Sep? 7 18:35 > >? ? ? ? ? ? ? >>? ? ? ? > a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 9210 Sep 10 11:01 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 8917 Sep 10 13:21 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 4811 Sep? 7 18:35 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin? 3309 Sep 10 11:02 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 10303 Sep 10 10:59 > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php > >? ? ? ? ? ? ? >>? ? ? ? -rw-r--r-- 1 lorisadmin lorisadmin 12273 Sep? 7 17:42 > >? ? ? ? ? ? ? >>? ? ? ? > fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? thanks again! > >? ? ? ? ? ? ? >>? ? ? ? Julie > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? ? ? On 06-11-2019 19.01 +0000, Christine Rogers, Ms. wrote: > >? ? ? ? ? ? ? >>>? ? ? ? Hi Ioannis,????? > >? ? ? ? ? ? ? >>>? ? ? ? Thanks for your question.????? > >? ? ? ? ? ? ? >>>? ? ? ? Given that the URL field is not updating, I suspect it's > a > >? ? ? ? ? ? ? database > >? ? ? ? ? ? ? >>>? ? ? ? back-end issue.????? > >? ? ? ? ? ? ? >>>? ? ? ? Can you verify -- Has your mysql user lorismysql????? been > granted > >? ? ? ? ? ? ? the > >? ? ? ? ? ? ? >>? ? ? ? "INSERT" > >? ? ? ? ? ? ? >>>? ? ? ? privilege for the right database? If not, that would > result in > >? ? ? ? ? ? ? an > >? ? ? ? ? ? ? >>? ? ? ? error > >? ? ? ? ? ? ? >>>? ? ? ? like the kind you are seeing.????? > >? ? ? ? ? ? ? >>>? ? ? ? Also, if you wish to check your LORIS Configuration > settings > >? ? ? ? ? ? ? in the > >? ? ? ? ? ? ? >>>? ? ? ? backend database such as the URL field -- to see what was > >? ? ? ? ? ? ? actually > >? ? ? ? ? ? ? >>? ? ? ? stored > >? ? ? ? ? ? ? >>>? ? ? ? in a given database field and should display in the > Config > >? ? ? ? ? ? ? >>? ? ? ? module:????? > >? ? ? ? ? ? ? >>>? ? ? ? You can run the queries listed in the "Troubleshooting > >? ? ? ? ? ? ? >>? ? ? ? Configuration > >? ? ? ? ? ? ? >>>? ? ? ? settings" section of our Github-wiki Setup Guide (under > >? ? ? ? ? ? ? Project > >? ? ? ? ? ? ? >>>? ? ? ? Customization) :????? > >? ? ? ? ? ? ? >>>? ? ? > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? ? ? ? ? >>>? ? ? ? Lastly, this question is perfectly appropriate for the > >? ? ? ? ? ? ? loris-dev > >? ? ? ? ? ? ? >>? ? ? ? community > >? ? ? ? ? ? ? >>>? ? ? ? support listserv -- please [2]subscribe here and then > email > >? ? ? ? ? ? ? our > >? ? ? ? ? ? ? >>? ? ? ? technical > >? ? ? ? ? ? ? >>>? ? ? ? team your next question at????? > [3][5]loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? ? ? ? (after checking > >? ? ? ? ? ? ? >>>? ? ? ? any forwarded threads for sensitive info).????? > >? ? ? ? ? ? ? >>>? ? ? ? We prefer to answer technical questions there for the > benefit > >? ? ? ? ? ? ? of > >? ? ? ? ? ? ? >>? ? ? ? the > >? ? ? ? ? ? ? >>>? ? ? ? community and other first-time users in the same position > as > >? ? ? ? ? ? ? >>? ? ? ? yourself.????? ????? > >? ? ? ? ? ? ? >>>? ? ? ? Thanks and cheers,????? > >? ? ? ? ? ? ? >>>? ? ? ? Christine????? > >? ? ? ? ? ? ? >>>? ? ? ? On Mon, Nov 4, 2019 at 5:49 PM Dr. Ioannis Pappas PhD > >? ? ? ? ? ? ? >>>? ? ? ? <[4][6]ioannis at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Hi Loris support.????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? My name is ioannis Pappas, a post-doc at the D'Esposito > lab > >? ? ? ? ? ? ? >>? ? ? ? stroke group > >? ? ? ? ? ? ? >>>? ? ? ? ? ? at UC Berkeley. With the kind of help of our sys > admin????? > >? ? ? ? ? ? ? Julie > >? ? ? ? ? ? ? >>? ? ? ? (cc'ed) we > >? ? ? ? ? ? ? >>>? ? ? ? ? ? have set up our loris database in our cluster (she is > the > >? ? ? ? ? ? ? sudo > >? ? ? ? ? ? ? >>? ? ? ? user and > >? ? ? ? ? ? ? >>>? ? ? ? ? ? I am the admin user). > >? ? ? ? ? ? ? >>>? ? ? ? ? ? If you allow me, I would like to ask you about the > first > >? ? ? ? ? ? ? >>? ? ? ? configuration > >? ? ? ? ? ? ? >>>? ? ? ? ? ? steps in the front end as they are described in the > >? ? ? ? ? ? ? tutorial. We > >? ? ? ? ? ? ? >>? ? ? ? can > >? ? ? ? ? ? ? >>>? ? ? ? ? ? login to [5][7]http://loris and the front end normally. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? However any update that I am trying to????? perform in > >? ? ? ? ? ? ? >>? ? ? ? Admin->Configuration > >? ? ? ? ? ? ? >>>? ? ? ? ? ? doesn't work (e.g. updating the study name). It just > >? ? ? ? ? ? ? refreshes > >? ? ? ? ? ? ? >>? ? ? ? the same > >? ? ? ? ? ? ? >>>? ? ? ? ? ? page. I am just wondering if there is an issue with > writing > >? ? ? ? ? ? ? in > >? ? ? ? ? ? ? >>? ? ? ? the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? configuration file. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Here are the permissions setup for where Loris is > installed. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? chmod 777 /var/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>>? ? ? ? ? ? cd /srv/www/loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? chown -R lorisadmin:lorisadmin . > >? ? ? ? ? ? ? >>>? ? ? ? ? ? chmod -c -R a+r . > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? this command gives everyone read access, and > outputs > >? ? ? ? ? ? ? what > >? ? ? ? ? ? ? >>? ? ? ? changes > >? ? ? ? ? ? ? >>>? ? ? ? ? ? were made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? mode of ?????????./project????????? changed from 0770 > (rwxrwx---) to > >? ? ? ? ? ? ? 0774 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? mode of ?????????./tools/logs????????? changed from 0770 > (rwxrwx---) > >? ? ? ? ? ? ? to > >? ? ? ? ? ? ? >>? ? ? ? 0774 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? find . -type d -exec chmod a+x -c {} \; > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? this command gives everyone permission to open > a > >? ? ? ? ? ? ? directory, > >? ? ? ? ? ? ? >>? ? ? ? and > >? ? ? ? ? ? ? >>>? ? ? ? ? ? outputs what changes were made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? mode of ?????????./project????????? changed from 0774 > (rwxrwxr--) to > >? ? ? ? ? ? ? 0775 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? (rwxrwxr-x) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ?????? ?????? mode of ?????????./tools/logs????????? changed from 0774 > (rwxrwxr--) > >? ? ? ? ? ? ? to > >? ? ? ? ? ? ? >>? ? ? ? 0775 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? (rwxrwxr-x) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Hopefully????? you can help me with this. I also > subscribed to > >? ? ? ? ? ? ? the > >? ? ? ? ? ? ? >>? ? ? ? mailing > >? ? ? ? ? ? ? >>>? ? ? ? ? ? list but I am not sure if this too much of a basic > question > >? ? ? ? ? ? ? for > >? ? ? ? ? ? ? >>? ? ? ? the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? list. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? On Mon, Nov 4, 2019 at 1:12 PM Julie Ashworth, HWNI > >? ? ? ? ? ? ? Computing > >? ? ? ? ? ? ? >>? ? ? ? Support > >? ? ? ? ? ? ? >>>? ? ? ? ? ? <[6][8]support-cirl at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? Hi ioannis, maybe it's best to ask the developers? > You can > >? ? ? ? ? ? ? cc > >? ? ? ? ? ? ? >>? ? ? ? me if > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? you'd like. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? On Mon, Nov 4, 2019, 12:37 PM Ioannis Pappas > >? ? ? ? ? ? ? >>? ? ? ? <[7][9]ioannis at berkeley.edu> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? wrote: > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? That did the trick Julie. Thank you! > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? I am still trying to understand how configuration > works > >? ? ? ? ? ? ? >>? ? ? ? though. For > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? example if I just try to change the name of the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? study from the front end, I get nowhere (it just > >? ? ? ? ? ? ? refreshes > >? ? ? ? ? ? ? >>? ? ? ? the same > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? page). > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? I am not sure if this requires write permissions > >? ? ? ? ? ? ? somewhere in > >? ? ? ? ? ? ? >>? ? ? ? a > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? config file/folder and that??????????????????s why it > doesn??????????????????t update > >? ? ? ? ? ? ? it. > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Ioannis > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > On Nov 4, 2019, at 12:08 PM, Julie Ashworth, HWNI > >? ? ? ? ? ? ? Computing > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Support <[8][10]support-cirl at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > just in case you're interested, these are the > >? ? ? ? ? ? ? permission > >? ? ? ? ? ? ? >>? ? ? ? changes I > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > chmod 777 /var/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > cd /srv/www/loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > chown -R lorisadmin:lorisadmin . > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > chmod -c -R a+r . > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? this command gives everyone read access, > and > >? ? ? ? ? ? ? outputs > >? ? ? ? ? ? ? >>? ? ? ? what > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? changes were made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? mode of ?????????./project????????? changed from > 0770 > >? ? ? ? ? ? ? (rwxrwx---) to > >? ? ? ? ? ? ? >>? ? ? ? 0774 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? mode of ?????????./tools/logs????????? changed from > 0770 > >? ? ? ? ? ? ? (rwxrwx---) > >? ? ? ? ? ? ? >>? ? ? ? to 0774 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > find . -type d -exec chmod a+x -c {} \; > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? this command gives everyone permission to > open a > >? ? ? ? ? ? ? >>? ? ? ? directory, and > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? outputs what changes were made: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? mode of ?????????./project????????? changed from > 0774 > >? ? ? ? ? ? ? (rwxrwxr--) to > >? ? ? ? ? ? ? >>? ? ? ? 0775 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? (rwxrwxr-x) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >?????? ?????? mode of ?????????./tools/logs????????? changed from > 0774 > >? ? ? ? ? ? ? (rwxrwxr--) > >? ? ? ? ? ? ? >>? ? ? ? to 0775 > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? (rwxrwxr-x) > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > On 04-11-2019 12.03 -0800, Ioannis Pappas wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> Hi Julie. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> I just tried and I still don???t get anything. I > also > >? ? ? ? ? ? ? >>? ? ? ? tried > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? private mode in Firefox in case the empty page was > >? ? ? ? ? ? ? cached. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> Sorry for this. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> On Nov 4, 2019, at 11:58 AM, Julie Ashworth, > HWNI > >? ? ? ? ? ? ? >>? ? ? ? Computing > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Support <[9][11]support-cirl at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> hi Ioannis, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> no worries, I changed the following directory > to > >? ? ? ? ? ? ? 777: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> /var/www/loris/smarty/templates_c > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> will you please check if that works? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> thanks! > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> On 04-11-2019 11.49 -0800, Dr. Ioannis Pappas > PhD > >? ? ? ? ? ? ? wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Hi Julie. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Apologies for bugging you with this again. > We > >? ? ? ? ? ? ? tried > >? ? ? ? ? ? ? >>? ? ? ? now to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? access??????????? [1][10][12]http://loris??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? and we are getting a??????????? blank page. I > think the > >? ? ? ? ? ? ? reason > >? ? ? ? ? ? ? >>? ? ? ? for this > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? is that we > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? don't have read??????????? permissions to read > from the > >? ? ? ? ? ? ? >>? ? ? ? template located > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? in > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? /var/www/loris/smarty See here bottom of > the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? page??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? I think, in general, I am a little bit > confused > >? ? ? ? ? ? ? as to > >? ? ? ? ? ? ? >>? ? ? ? what the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? permissions > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? should be for us that are not sudos. My > >? ? ? ? ? ? ? understanding > >? ? ? ? ? ? ? >>? ? ? ? is that > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? if we don't > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? have read or write permissions then we > can't > >? ? ? ? ? ? ? access or > >? ? ? ? ? ? ? >>? ? ? ? write > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? /var/www/loris, meaning that we can't > access or > >? ? ? ? ? ? ? >>? ? ? ? configure. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Should > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? everything be chmod 777 for example???????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Thank you very much once again. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? On Thu, Oct 31, 2019 at 1:56 PM Dr. Ioannis > >? ? ? ? ? ? ? Pappas PhD > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? <[3][12][14]ioannis at berkeley.edu> wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? Thank you very much Julie. I appreciate > this > >? ? ? ? ? ? ? and I > >? ? ? ? ? ? ? >>? ? ? ? will dig > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? into Loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? given your changes. Thank you so much > for your > >? ? ? ? ? ? ? >>? ? ? ? help. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? On Thu, Oct 31, 2019 at 12:48 PM Julie > >? ? ? ? ? ? ? Ashworth, > >? ? ? ? ? ? ? >>? ? ? ? HWNI > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Computing Support > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? <[4][13][15]support-cirl at berkeley.edu> > wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? hi Ioannis, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? 1. I changed the permissions of > >? ? ? ? ? ? ? /srv/www/loris > >? ? ? ? ? ? ? >>? ? ? ? to be owned > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? by > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? lorisadmin. I reivewed my > installation > >? ? ? ? ? ? ? notes, > >? ? ? ? ? ? ? >>? ? ? ? and I did > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? this already > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? when > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? I installed the server. I'm not > sure why > >? ? ? ? ? ? ? they > >? ? ? ? ? ? ? >>? ? ? ? changed, so > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? it's > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? probably a > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? good idea to keep an eye on that. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? 2. When I installed the loris > software, I > >? ? ? ? ? ? ? also > >? ? ? ? ? ? ? >>? ? ? ? installed a > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? mysql > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? database as recommended in the > >? ? ? ? ? ? ? instructions: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? projectname: LORIS > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? databasename: loris_database > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? mysqluser: lorismysql > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? frontend: lorisweb > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? 3. A couple of weeks ago, I moved > Henrik's > >? ? ? ? ? ? ? home > >? ? ? ? ? ? ? >>? ? ? ? directory > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? /home/despoA, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? but I forgot to update loris. This > is done > >? ? ? ? ? ? ? now. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? best, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? Julie > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? On 31-10-2019 11.15 -0700, Dr. > Ioannis > >? ? ? ? ? ? ? Pappas > >? ? ? ? ? ? ? >>? ? ? ? PhD wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Hi Julie. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? I hope you are well. We are > trying to > >? ? ? ? ? ? ? >>? ? ? ? configure loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? that you > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? kindly set > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? up for us. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? I have a couple of > questions for you if > >? ? ? ? ? ? ? you > >? ? ? ? ? ? ? >>? ? ? ? allow me > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? so.??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 1) First, although we are > logging into > >? ? ? ? ? ? ? the > >? ? ? ? ? ? ? >>? ? ? ? front end > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? with admin > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? username > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? (lorisweb) and password, it > seems that > >? ? ? ? ? ? ? any > >? ? ? ? ? ? ? >>? ? ? ? kind of > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? update of > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? configuration > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? we are trying to do fails > (meaning that > >? ? ? ? ? ? ? if > >? ? ? ? ? ? ? >>? ? ? ? we, say, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? change the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? name of the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? study and press "submit", > this doesn't > >? ? ? ? ? ? ? do > >? ? ? ? ? ? ? >>? ? ? ? anything-it > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? doesn't > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? update). > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? It's almost like our > lorisweb user > >? ? ? ? ? ? ? doesn't > >? ? ? ? ? ? ? >>? ? ? ? have write > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? privileges > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? in the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? /var/www/loris/project > (where I think > >? ? ? ? ? ? ? every > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? configuration should > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? be). > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? This generalizes for > everything that we > >? ? ? ? ? ? ? are > >? ? ? ? ? ? ? >>? ? ? ? trying to do > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? in the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? front end. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Clicking any instrument/tab > in the front > >? ? ? ? ? ? ? end > >? ? ? ? ? ? ? >>? ? ? ? doesn't > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? really point > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? anything.??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 2) Loris suggest doing > configurations > >? ? ? ? ? ? ? via > >? ? ? ? ? ? ? >>? ? ? ? SQL. Is it > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? possible to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? run SQL > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? scripts in the backend > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 3) For some reason typing > ssh lors for > >? ? ? ? ? ? ? Henrik > >? ? ? ? ? ? ? >>? ? ? ? doesn't > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? directly > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? take him to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? loris (it requires a > password that is > >? ? ? ? ? ? ? not the > >? ? ? ? ? ? ? >>? ? ? ? password > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? setup for > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? lorisweb user). Will you be > able to fix > >? ? ? ? ? ? ? this > >? ? ? ? ? ? ? >>? ? ? ? via your > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? sudo > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? privileges? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Thank you very much in > advance for all > >? ? ? ? ? ? ? your > >? ? ? ? ? ? ? >>? ? ? ? help Julie. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Let us > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? know if > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? this is something that > shouldn't be > >? ? ? ? ? ? ? directed > >? ? ? ? ? ? ? >>? ? ? ? to you (but > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? instead > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? to the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? loris people).??????????? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Best wishes, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Ioannis > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? On Mon, Sep 9, 2019 at 6:25 > PM Julie > >? ? ? ? ? ? ? >>? ? ? ? Ashworth, HWNI > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Computing > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? Support > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ???????????????? > >? ? ? ? ? ? ? <[1][5][14][16]support-cirl at berkeley.edu> > >? ? ? ? ? ? ? >>? ? ? ? wrote: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? hi Henrik and > Ioannis, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? the loris server > is available for > >? ? ? ? ? ? ? you to > >? ? ? ? ? ? ? >>? ? ? ? use. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? The servername is > 'loris'. I > >? ? ? ? ? ? ? created a > >? ? ? ? ? ? ? >>? ? ? ? directory > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? called > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? /data/loris for > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? you to store data. > You may create > >? ? ? ? ? ? ? new > >? ? ? ? ? ? ? >>? ? ? ? folders in > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? /data/loris to > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? organize > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? your data. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? 1) secure shell or > secure copy: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? You can log in > with the 'ssh' or > >? ? ? ? ? ? ? 'scp' > >? ? ? ? ? ? ? >>? ? ? ? command from > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? your remote > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? desktop > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? session. You don't > need to > >? ? ? ? ? ? ? authenticate > >? ? ? ? ? ? ? >>? ? ? ? to log in. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? Maybe you'll > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? use scp > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? to transfer data > between your > >? ? ? ? ? ? ? cluster > >? ? ? ? ? ? ? >>? ? ? ? account and the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? server? > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? Please put the > data in /data/loris, > >? ? ? ? ? ? ? so I > >? ? ? ? ? ? ? >>? ? ? ? can make > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? backups more > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? easily. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > secure shell: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > $ ssh loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > secure copy (change the > >? ? ? ? ? ? ? names > >? ? ? ? ? ? ? >>? ? ? ? in brackets). Let > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? me know if > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? I can > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > help with syntax: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > $ scp -r > >? ? ? ? ? ? ? >>? ? ? ? loris:/data/loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? 2) front-end web > interface.???????????????? > >? ? ? ? ? ? ? Open a > >? ? ? ? ? ? ? >>? ? ? ? web browser in > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? your remote > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? desktop > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? session and enter > the hostname: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? > [2][6][15][17]http://loris > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? I created an admin > user called > >? ? ? ? ? ? ? >>? ? ? ? 'lorisweb'. I put the > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? password > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? in > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? $HOME/newuser on > the cluster. To > >? ? ? ? ? ? ? see it, > >? ? ? ? ? ? ? >>? ? ? ? open a > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? terminal, and > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? run: > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? ????????????????? ????????????????? > $ cat $HOME/newuser > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? If other people > need shell access > >? ? ? ? ? ? ? to the > >? ? ? ? ? ? ? >>? ? ? ? webserver, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? please let > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? me know > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? so I can create a > home directory > >? ? ? ? ? ? ? for > >? ? ? ? ? ? ? >>? ? ? ? them. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? We should > eventually discuss > >? ? ? ? ? ? ? backups. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? best, > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? ????????????????? Julie > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> References > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? Visible links > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 1. > >? ? ? ? ? ? ? >>? ? ? ? mailto:[7][16][18]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>> ????????????????? ????????????????? 2. [8][17][19]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? ?????? ?????? ---end quoted text--- > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> References > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? Visible links > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 1. [18][20]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 2. > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 3. mailto:[20][22]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 4. mailto:[21][23]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 5. mailto:[22][24]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 6. [23][25]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 7. mailto:[24][26]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>>>?????? 8. [25][27]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >>> ---end quoted text--- > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>>? ? ? ? ? ? ? ? ? ? > ---end quoted text--- > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? -- > >? ? ? ? ? ? ? >>>? ? ? ? [26][28]christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >>>? ? ? ? McGill Centre for Integrative Neuroscience | MCIN.ca > >? ? ? ? ? ? ? >>>? ? ? ? Montreal Neurological Institute > >? ? ? ? ? ? ? >>>? ? ? ? McGill University | Montreal | Canada > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>> References > >? ? ? ? ? ? ? >>> > >? ? ? ? ? ? ? >>>? ? ? ? Visible links > >? ? ? ? ? ? ? >>>? ? ? ? 1. > >? ? ? ? ? ? ? >>? ? ? > >? ? ? ? ? ? ? > [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? ? ? ? ? >>>? ? ? ? 2. > >? ? ? ? ? ? ? [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? ? ? ? ? >>>? ? ? ? 3. mailto:[31]loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>>? ? ? ? 4. mailto:[32]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? 5. [33]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? ? 6. mailto:[34]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? 7. mailto:[35]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? 8. mailto:[36]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? ? 9. mailto:[37]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 10. [38]http://xn--loris-7qa/ > >? ? ? ? ? ? ? >>>? ? ? 11. > >? ? ? ? ? ? ? [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>>? ? ? 12. mailto:[40]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 13. mailto:[41]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 14. mailto:[42]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 15. [43]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 16. mailto:[44]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 17. [45]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 18. [46]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 19. > >? ? ? ? ? ? ? [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>>? ? ? 20. mailto:[48]ioannis at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 21. mailto:[49]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 22. mailto:[50]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 23. [51]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 24. mailto:[52]support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>>? ? ? 25. [53]http://loris/ > >? ? ? ? ? ? ? >>>? ? ? 26. mailto:[54]christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >>? ? ? ? ---end quoted text--- > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? -- > >? ? ? ? ? ? ? >>? ? [55]christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >>? ? McGill Centre for Integrative Neuroscience | MCIN.ca > >? ? ? ? ? ? ? >>? ? Montreal Neurological Institute > >? ? ? ? ? ? ? >>? ? McGill University | Montreal | Canada > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >> References > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? >>? ? Visible links > >? ? ? ? ? ? ? >>? ? 1. [8]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? ? 2. [9]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? ? 3. [10]http://loris.priv/ > >? ? ? ? ? ? ? >>? > >? ? ? ? ? ? ? 4. > [11]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? ? ? ? ? >>? ? 5. [12]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? ? 6. [13]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? ? 7. [14]http://loris/ > >? ? ? ? ? ? ? >>? ? 8. [15]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? ? 9. [16]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 10. [17]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 11. [18]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 12. [19]http://xn--loris-era/ > >? ? ? ? ? ? ? >>? 13. > [20]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>? 14. [21]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 15. [22]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 16. [23]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 17. [24]http://loris/ > >? ? ? ? ? ? ? >>? 18. [25]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 19. [26]http://loris/ > >? ? ? ? ? ? ? >>? 20. [27]http://loris/ > >? ? ? ? ? ? ? >>? 21. > [28]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>? 22. [29]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 23. [30]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 24. [31]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 25. [32]http://loris/ > >? ? ? ? ? ? ? >>? 26. [33]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 27. [34]http://loris/ > >? ? ? ? ? ? ? >>? 28. [35]mailto:christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >> > >? ? ? ? ? ? ? 29. > [36]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? ? ? ? ? >>? 30. > [37]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? ? ? ? ? >>? 31. [38]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? >>? 32. [39]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 33. [40]http://loris/ > >? ? ? ? ? ? ? >>? 34. [41]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 35. [42]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 36. [43]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 37. [44]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 38. [45]http://xn--loris-7qa/ > >? ? ? ? ? ? ? >>? 39. > [46]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>? 40. [47]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 41. [48]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 42. [49]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 43. [50]http://loris/ > >? ? ? ? ? ? ? >>? 44. [51]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 45. [52]http://loris/ > >? ? ? ? ? ? ? >>? 46. [53]http://loris/ > >? ? ? ? ? ? ? >>? 47. > [54]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? ? ? ? ? >>? 48. [55]mailto:ioannis at berkeley.edu > >? ? ? ? ? ? ? >>? 49. [56]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 50. [57]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 51. [58]http://loris/ > >? ? ? ? ? ? ? >>? 52. [59]mailto:support-cirl at berkeley.edu > >? ? ? ? ? ? ? >>? 53. [60]http://loris/ > >? ? ? ? ? ? ? >>? 54. [61]mailto:christine.rogers at mcgill.ca > >? ? ? ? ? ? ? >>? 55. [62]mailto:christine.rogers at mcgill.ca > >? ? ? ? ? ? ? > ---end quoted text--- > > > >? ? ? ? ? ? ? _______________________________________________ > >? ? ? ? ? ? ? Loris-dev mailing list > >? ? ? ? ? ? ? Loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? ? ? [63]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? ? ? ? ? > > > >? ? ? ? ? _______________________________________________ > >? ? ? ? ? Loris-dev mailing list > >? ? ? ? ? Loris-dev at bic.mni.mcgill.ca > >? ? ? ? ? [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > >? ? ? -- > >? ? ? christine.rogers at mcgill.ca > >? ? ? McGill Centre for Integrative Neuroscience | MCIN.ca > >? ? ? Montreal Neurological Institute > >? ? ? McGill University | Montreal | Canada > ---end quoted text--- > > References > > Visible links > 1. https://loris.url/configuration/ > 2. https://.loris.url/ > 3. http://loris.priv/ > 4. http://localhost/ > 5. http://loris.priv/ > 6. http://localhost/ > 7. http://localhost/ > 8. mailto:loris-dev at bic.mni.mcgill.ca > 9. mailto:support-cirl at berkeley.edu > 10. http://loris.priv/ > 11. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 12. mailto:loris-dev at bic.mni.mcgill.ca > 13. mailto:ioannis at berkeley.edu > 14. http://loris/ > 15. mailto:support-cirl at berkeley.edu > 16. mailto:ioannis at berkeley.edu > 17. mailto:support-cirl at berkeley.edu > 18. mailto:support-cirl at berkeley.edu > 19. http://xn--loris-era/ > 20. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 21. mailto:ioannis at berkeley.edu > 22. mailto:support-cirl at berkeley.edu > 23. mailto:support-cirl at berkeley.edu > 24. http://loris/ > 25. mailto:support-cirl at berkeley.edu > 26. http://loris/ > 27. http://loris/ > 28. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 29. mailto:ioannis at berkeley.edu > 30. mailto:support-cirl at berkeley.edu > 31. mailto:support-cirl at berkeley.edu > 32. http://loris/ > 33. mailto:support-cirl at berkeley.edu > 34. http://loris/ > 35. mailto:christine.rogers at mcgill.ca > 36. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 37. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 38. mailto:loris-dev at bic.mni.mcgill.ca > 39. mailto:ioannis at berkeley.edu > 40. http://loris/ > 41. mailto:support-cirl at berkeley.edu > 42. mailto:ioannis at berkeley.edu > 43. mailto:support-cirl at berkeley.edu > 44. mailto:support-cirl at berkeley.edu > 45. http://xn--loris-7qa/ > 46. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 47. mailto:ioannis at berkeley.edu > 48. mailto:support-cirl at berkeley.edu > 49. mailto:support-cirl at berkeley.edu > 50. http://loris/ > 51. mailto:support-cirl at berkeley.edu > 52. http://loris/ > 53. http://loris/ > 54. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 55. mailto:ioannis at berkeley.edu > 56. mailto:support-cirl at berkeley.edu > 57. mailto:support-cirl at berkeley.edu > 58. http://loris/ > 59. mailto:support-cirl at berkeley.edu > 60. http://loris/ > 61. mailto:christine.rogers at mcgill.ca > 62. mailto:christine.rogers at mcgill.ca > 63. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 64. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ---end quoted text--- -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Mon Nov 11 22:30:26 2019 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Mon, 11 Nov 2019 19:30:26 -0800 Subject: [Loris-dev] loris server In-Reply-To: References: <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> <20191109020414.GB13279@nx6.priv> <20191111170342.GA4213@gaia.neuro.berkeley.edu> Message-ID: <20191112033026.GA5955@gaia.neuro.berkeley.edu> thanks Christine and Melanie - I updated the Config table settings (see below). Ioannis, can you please test if it works now? Melanie, I couldn't find a reference to dbHost in the config.xml file. The only reference to host that I could find is: # grep -i host /srv/www/loris/project/config.xml localhost %COUCH_HOSTNAME% MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; +----------+-------------------+-------------------+------------------+--------------------------------------+ | ConfigID | Name | Label | Value | Description | +----------+-------------------+-------------------+------------------+--------------------------------------+ | 44 | host | Host | localhost | Host | | 45 | url | Main LORIS URL | http://localhost | Main URL where LORIS can be accessed | | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | +----------+-------------------+-------------------+------------------+--------------------------------------+ thanks! Julie On 11-11-2019 17.28 +0000, Melanie Legault, Mrs wrote: > Hello Julie, > Yes, the '%' sign is a wildcard for 'all host'. So it should be good but I > had problem with that in the past. > Could you ensure the 'lorismysql'@'localhost' user proper permissions. > > Also, in that case, in the config.xml file, the dbHost should be > 'localhost'. MySQL treat 127.0.0.1 and localhost as 2 different host. > > M??lanie > > -------------------------------------------------------------------------- > > From: Julie Ashworth, HWNI Computing Support > Sent: November 11, 2019 12:03 > To: Melanie Legault, Mrs > Cc: Christine Rogers, Ms. ; Ioannis Pappas > ; loris-dev at bic.mni.mcgill.ca > > Subject: Re: [Loris-dev] loris server > ?? > thanks Melanie, > I'm including the output below. My understanding is that '%' matches all > hostnames. Should I specifically grant permission to 'loris.priv' from > user lorismysql? Or perhaps you recommend changing loris_database entries > ('host' to 'localhost' and 'url' to '[1]http://localhost')? > thanks! > > MariaDB [(none)]> SELECT User, Host FROM mysql.user; > +------------+-----------+ > | User???????????? | Host?????????? | > +------------+-----------+ > | lorismysql | %???????????????? | > | root???????????? | 127.0.0.1 | > | root???????????? | ::1???????????? | > | lorismysql | localhost | > | root???????????? | localhost | > +------------+-----------+ > 5 rows in set (0.00 sec) > > MariaDB [(none)]> SHOW grants for 'lorismysql'@'%'; > +--------------------------------------------------------------------------------+ > | Grants for lorismysql@% > +--------------------------------------------------------------------------------+ > | GRANT USAGE ON *.* TO 'lorismysql'@'%' > | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO > 'lorismysql'@'%' | > +--------------------------------------------------------------------------------+ > 2 rows in set (0.00 sec) > > On 11-11-2019 15.47 +0000, Melanie Legault, Mrs wrote: > >?????? Hello Julie, > >?????? Could it be that your MySQL 'lorismysql' user have different > permissions > >?????? depending on where it is connecting to the DB? > >?????? A database admin (root) can check this for you. > >?????? SELECT User, Host FROM mysql.user; > >?????? then for the user that match the Host (name or IP address) of your > LORIS > >?????? (Apache) server > >?????? SHOW grants for 'lorismysql'@''; > > > >?????? M????lanie > > > >?????? > -------------------------------------------------------------------------- > > > >?????? From: Julie Ashworth, HWNI Computing Support > > >?????? Sent: November 8, 2019 21:04 > >?????? To: Christine Rogers, Ms. > >?????? Cc: Ioannis Pappas ; Melanie Legault, Mrs > >?????? ; loris-dev at bic.mni.mcgill.ca > >?????? > >?????? Subject: Re: [Loris-dev] loris server > >?????? ???? > >?????? thanks Christine, > > > >?????? yes, it's the lorismysql user in the config.xml file. > >?????? ???????????????????????????? lorismysql > >?????? ???????????????????????????? loris_database > >?????? ???????????????????????????? lorismysql > > > >?????? we appeciate your help troubleshooting this. > >?????? best, > >?????? Julie > > > >?????? On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote: > >?????? >???????????? Hi Ioannis, > >?????? >???????????? Could you open your file called config.xml > >?????? >???????????? (/srv/www/loris/project/config.xml) and confirm for us --???? > which user > >?????? >???????????? credential is stored there, and what's the name of the > database it is > >?????? >???????????? connecting to? > >?????? >???????????? This is the mysql user which connects to the database from > the front > >?????? end > >?????? >???????????? of LORIS.???? > >?????? >???????????? If this user has insufficient privileges on your database, > that would > >?????? >???????????? cause the errors you are seeing.???? I had assumed from your > thread it > >?????? was > >?????? >???????????? your lorismysql user but it sounds like this should be > verified. > >?????? >???????????? Let us know, and we'll keep following up when we come back > online > >?????? after > >?????? >???????????? the weekend, > >?????? >???????????? Best, > >?????? >???????????? Christine > >?????? >???????????? On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas > > >?????? >???????????? wrote: > >?????? > > >?????? >???????????????????? Hi Melanie. > >?????? >???????????????????? Thank you for taking the time to reply to this. I took > some to > >?????? consider > >?????? >???????????????????? your comments. Unfortunately as I said to Christine we > are unable > >?????? to do > >?????? >???????????????????? any kind of updating to the database (either that is > changing the > >?????? name > >?????? >???????????????????? or changing the small html description, etc.). > >?????? >???????????????????? Based on some more digging and on some of Christine's > comments I > >?????? have a > >?????? >???????????????????? feeling that our lorisweb front-end, admin user cannot > write > >?????? anything to > >?????? >???????????????????? the database. Along these lines could it be the case the > lorismysql > >?????? user > >?????? >???????????????????? (the database, admin user with INSERT, UPDATE, etc > privileges) is > >?????? not > >?????? >???????????????????? ???????????? ???talking??????????? to the lorisweb front end user? > What is the > >?????? difference between > >?????? >???????????????????? the two and could it be a installation problem for them > not talking > >?????? to > >?????? >???????????????????? each other? As Julie said, lorismysql user is working > normally with > >?????? >???????????????????? MariaDB. > >?????? >???????????????????? Thank you again for your help. > >?????? >???????????????????? Best wishes, > >?????? >???????????????????? Ioannis > >?????? > > >?????? >???????????????????????????? On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs > >?????? >???????????????????????????? wrote: > >?????? >???????????????????????????? Hello, > >?????? >???????????????????????????? Changing the project name in the configuration page > >?????? >???????????????????????????? ([1]https://loris.url/configuration/) of LORIS, only > change the > >?????? title of > >?????? >???????????????????????????? the project. To see this change, you have to log out > of LORIS and > >?????? then > >?????? >???????????????????????????? go back to the login page ([2]https://.loris.url/). > This is the > >?????? only > >?????? >???????????????????????????? place you can find the project name (except from the > >?????? configuration > >?????? >???????????????????????????? page). See ProjectName.png > >?????? >???????????????????????????? As for files permission, I would suggest a few change > to improve > >?????? >???????????????????????????? security of you server. Some extra permissions where > granted to > >?????? help > >?????? >???????????????????????????? you but are not needed. > >?????? >???????????????????????????????????? * /srv/www/loris/smarty/templates_c/???? should > have ownership of > >?????? >???????????????????????????????????????????? lorisadmin:httpd and permission 770 (or 775) > >?????? >???????????????????????????????????? * srv/www/loris/project/???? should have ownership > >?????? lorisadmin:httpd and > >?????? >???????????????????????????????????????????? permission 770 (775) > >?????? >???????????????????????????????????? * All other files under loris should have > lorisadmin:lorisadmin > >?????? 755 > >?????? >???????????????????????????? Reading through this change of mail, I understand > that you let > >?????? Apache > >?????? >???????????????????????????? store file in /srv/www/loris > >?????? >???????????????????????????????????????? |???????????????????????? 31 | DownloadPath???????? | > Downloads???????? | /srv/www/loris/???????? > >?????? | > >?????? >???????????????????????????? Where > >?????? >???????????????????????????? >>???????????????? files are downloaded > >?????? >???????????????????????????? Downloaded files should not be in the same tree as > LORIS code. It > >?????? >???????????????????????????? should be in a separate structure where Apache will > not try and > >?????? do not > >?????? >???????????????????????????? have permission (in httpd.conf) to execute files. > >?????? >???????????????????????????? Kind regards, > >?????? >???????????????????????????? M????????lanie Legault | Software developer | Faculty of > Medicine | > >?????? McGill > >?????? >???????????????????????????? University???? > >?????? >???????????????????????????? 3801 University, Montr????????al, QC H3A 2B4 > >?????? > > >?????? >???????????????????? > >?????? > ---------------------------------------------------------------------- > >?????? > > >?????? >???????????????????????????? From: loris-dev-bounces at bic.mni.mcgill.ca > >?????? >???????????????????????????? on behalf of > Ioannis Pappas > >?????? >???????????????????????????? > >?????? >???????????????????????????? Sent: November 7, 2019 0:18 > >?????? >???????????????????????????? To: loris-dev at bic.mni.mcgill.ca > > >?????? >???????????????????????????? Cc: Julie Ashworth, HWNI Computing Support > >?????? >???????????????????????????? ; Christine Rogers, Ms. > >?????? >???????????????????????????? > >?????? >???????????????????????????? Subject: Re: [Loris-dev] loris server > >?????? >???????????????????????????????? > >?????? >???????????????????????????? Hi Christine and Julie. > >?????? > > >?????? >???????????????????????????? Yes it looks like that any attempt to configure > something in the > >?????? >???????????????????????????? front-end results in the same page. I am sending this > to the list > >?????? (as > >?????? >???????????????????????????? you requested Christine) alongside the > troubleshooting and > >?????? discussion > >?????? >???????????????????????????? so far with Julie. > >?????? > > >?????? >???????????????????????????? Best wishes, > >?????? >???????????????????????????? Ioannis > >?????? > > >?????? >???????????????????????????? > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI > Computing > >?????? Support > >?????? >???????????????????????????? wrote: > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > hi Christine and Ioannis, > >?????? >???????????????????????????? > Ioannis, can you follow-up with Christine about > using the > >?????? front-end? > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > We're using CentOS7.7 and loris-21.0.1. > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > I confirmed that I could login as the mysql user > (lorismyqsl) > >?????? and > >?????? >???????????????????????????? change the 'url' config setting from > '[3]http://loris.priv' to > >?????? >???????????????????????????? '[4]http://localhost', and back again. > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > MariaDB [loris_database]> SELECT c.ConfigID, > cs.Name, cs.Label, > >?????? >???????????????????????????? c.Value, cs.Description FROM Config c LEFT JOIN > ConfigSettings cs > >?????? ON > >?????? >???????????????????????????? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON > (cs.Parent = > >?????? csp.ID) > >?????? >???????????????????????????? WHERE csp.Name = 'www'; > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????? >???????????????????????????? > | ConfigID | Name???????????????????????????????????????????????????? | > Label???????????????????????????????????????????????? | > >?????? >???????????????????????????? Value???????????????????????????????????????????????? | > Description???????????????????????????????????????????????????????????????????????????????????????????????????? | > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????? >???????????????????????????? > |???????????????????????? 44 | host???????????????????????????????????????????????????? | > Host???????????????????????????????????????????????????? | > >?????? >???????????????????????????? loris.priv???????????????????????????? | > Host???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? | > >?????? >???????????????????????????? > |???????????????????????? 45 | url???????????????????????????????????????????????????????? > | Main LORIS URL???????? > >?????? >???????????????????????????? | [5]http://loris.priv | Main URL where LORIS can be > accessed | > >?????? >???????????????????????????? > |???????????????????????? 46 | issue_tracker_url | Issue > tracker URL | > >?????? >???????????????????????????? /issue_tracker???????????? | The *new* bug/issue tracker > url???????????????????? | > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > MariaDB [loris_database]> UPDATE Config SET > >?????? Value='[6]http://localhost' > >?????? >???????????????????????????? WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE > Name='url'); > >?????? >???????????????????????????? > Rows matched: 1???? Changed: 1???? Warnings: 0 > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > MariaDB [loris_database]> SELECT c.ConfigID, > cs.Name, cs.Label, > >?????? >???????????????????????????? c.Value, cs.Description FROM Config c LEFT JOIN > ConfigSettings cs > >?????? ON > >?????? >???????????????????????????? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON > (cs.Parent = > >?????? csp.ID) > >?????? >???????????????????????????? WHERE csp.Name = 'www'; > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >?????? >???????????????????????????? > | ConfigID | Name???????????????????????????????????????????????????? | > Label???????????????????????????????????????????????? | > >?????? >???????????????????????????? Value???????????????????????????????????????????? | > Description???????????????????????????????????????????????????????????????????????????????????????????????????? | > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >?????? >???????????????????????????? > |???????????????????????? 44 | host???????????????????????????????????????????????????? | > Host???????????????????????????????????????????????????? | > >?????? >???????????????????????????? loris.priv???????????????????????? | > Host???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? | > >?????? >???????????????????????????? > |???????????????????????? 45 | url???????????????????????????????????????????????????????? > | Main LORIS URL???????? > >?????? >???????????????????????????? | [7]http://localhost | Main URL where LORIS can be > accessed | > >?????? >???????????????????????????? > |???????????????????????? 46 | issue_tracker_url | Issue > tracker URL | > >?????? >???????????????????????????? /issue_tracker???????? | The *new* bug/issue tracker > url???????????????????? | > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >?????? >???????????????????????????? > 3 rows in set (0.00 sec) > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > best, > >?????? >???????????????????????????? > Julie > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > > >?????? >???????????????????????????? > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. > wrote: > >?????? >???????????????????????????? >>???????? Hi Julie, > >?????? >???????????????????????????? >>???????? Forgive my ambiguity - We run the community > support listserv > >?????? for > >?????? >???????????????????????????? >>???????? developers, project administrators and > sysadmins setting up > >?????? >???????????????????????????? LORIS, so that > >?????? >???????????????????????????? >>???????? these users can contact our technical team for > exactly such > >?????? >???????????????????????????? technical > >?????? >???????????????????????????? >>???????? help.???? > >?????? >???????????????????????????? >>???????? If it's ok with you, I'd encourage you > subscribe to the > >?????? listserv > >?????? >???????????????????????????? and > >?????? >???????????????????????????? >>???????? contact our technical team that way for the > same reason. > >?????? >???????????????????????????? >>???????? (Note that front-end users of LORIS typically > contact their > >?????? >???????????????????????????? project team > >?????? >???????????????????????????? >>???????? for support, rather than us.) > >?????? >???????????????????????????? >>???????? Given that your lorismysql user privileges > seem appropriate > >?????? >???????????????????????????? ('UPDATE" is > >?????? >???????????????????????????? >>???????? there, I mistyped 'INSERT" before) > >?????? >???????????????????????????? >>???????? --???? is there any other indication why the > database record is > >?????? not > >?????? >???????????????????????????? >>???????? updating????? > >?????? >???????????????????????????? >>???????? In the front-end, can your 'admin' user effect > any changes > >?????? in > >?????? >???????????????????????????? (any) Config > >?????? >???????????????????????????? >>???????? setting????? > >?????? >???????????????????????????? >>???????? In the back-end, when you tried updating a > field using your > >?????? >???????????????????????????? >>???????? lorismysql credential, what happened? > >?????? >???????????????????????????? >>???????? Your front end is loading ok, and you can log > in there, if I > >?????? >???????????????????????????? understood > >?????? >???????????????????????????? >>???????? correctly. > >?????? >???????????????????????????? >>???????? Thanks for letting us know these details at > >?????? >???????????????????????????? >>???????? [1]loris-dev at bic.mni.mcgill.ca > >?????? >???????????????????????????? >>???????? Please also include what version of LORIS you > are > >?????? installing, and > >?????? >???????????????????????????? on what > >?????? >???????????????????????????? >>???????? OS version. > >?????? >???????????????????????????? >>???????? Best, > >?????? >???????????????????????????? >>???????? Christine > >?????? >???????????????????????????? >>???????? On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, > HWNI > >?????? Computing > >?????? >???????????????????????????? Support > >?????? >???????????????????????????? >>???????? <[2]support-cirl at berkeley.edu> wrote: > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? Thank you Christine, > >?????? >???????????????????????????? >>???????????????? I'm the linux sysadmin who installed the > loris database > >?????? for > >?????? >???????????????????????????? Ioannis. > >?????? >???????????????????????????? >>???????????????? I'm not a loris user, however, so that > makes it a little > >?????? >???????????????????????????? awkward for > >?????? >???????????????????????????? >>???????????????? troubleshooting via the mailing list. I'm > happy to help in > >?????? >???????????????????????????? whatever way > >?????? >???????????????????????????? >>???????????????? I can. > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? Regarding the database permissions, I ran: > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? MariaDB [(none)]> show grants for > 'lorismysql'@'%'; > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > +--------------------------------------------------------------------------------+ > >?????? >???????????????????????????? >>???????????????? | Grants for lorismysql@% > >?????? >???????????????????????????? >>???????????????? | > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > +--------------------------------------------------------------------------------+ > >?????? >???????????????????????????? >>???????????????? | GRANT USAGE ON *.* TO 'lorismysql'@'%' > >?????? >???????????????????????????? >>???????????????? | > >?????? >???????????????????????????? >>???????????????? | GRANT SELECT, INSERT, UPDATE, DELETE ON > >?????? `loris_database`.* TO > >?????? >???????????????????????????? >>???????????????? 'lorismysql'@'%' | > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > +--------------------------------------------------------------------------------+ > >?????? >???????????????????????????? >>???????????????? 2 rows in set (0.00 sec) > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? looking at the 'tips' section in the page > you referred > >?????? to... > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? |???????????????????????? 29 | > base???????????????????????????????????????? | Base???????????????????????????? | > >?????? /srv/www/loris/???????? | > >?????? >???????????????????????????? The base > >?????? >???????????????????????????? >>???????????????? filesystem path where LORIS is > >?????? >???????????????????????????? > installed???????????????????????????????????????????????????????????????????????????????????????????????????? | > >?????? >???????????????????????????? >>???????????????? |???????????????????????? 31 | DownloadPath???????? | > Downloads???????? | > >?????? /srv/www/loris/???????? | > >?????? >???????????????????????????? Where > >?????? >???????????????????????????? >>???????????????? files are downloaded > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????? >???????????????????????????? >>???????????????? | ConfigID | > Name???????????????????????????????????????????????????? | Label???????????????????????????????????????????????? | > >?????? >???????????????????????????? Value???????????????????????????????????????????????? | > >?????? >???????????????????????????? >>???????????????? > Description???????????????????????????????????????????????????????????????????????????????????????????????????? | > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????? >???????????????????????????? >>???????????????? |???????????????????????? 44 | > host???????????????????????????????????????????????????? | Host???????????????????????????????????????????????????? | > >?????? >???????????????????????????? loris.priv???????????????????????????? | > >?????? >???????????????????????????? >>???????????????? > Host???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????? | > >?????? >???????????????????????????? >>???????????????? |???????????????????????? 45 | > url???????????????????????????????????????????????????????? | Main LORIS URL???????????? | > >?????? >???????????????????????????? >>???????????????? [3]http://loris.priv | Main URL where > LORIS can be > >?????? accessed | > >?????? >???????????????????????????? >>???????????????? |???????????????????????? 46 | issue_tracker_url | > Issue tracker URL | > >?????? >???????????????????????????? /issue_tracker???????????? | > >?????? >???????????????????????????? >>???????????????? The *new* bug/issue tracker url???????????????????? > | > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? apache config: > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? Listen 80 > >?????? >???????????????????????????? >>???????????????? User apache > >?????? >???????????????????????????? >>???????????????? Group apache > >?????? >???????????????????????????? >>???????????????? DocumentRoot "/srv/www/loris/htdocs" > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? > >?????? >???????????????????????????? >>???????????????????????????????? AllowOverride none > >?????? >???????????????????????????? >>???????????????????????????????? Require all denied > >?????? >???????????????????????????? >>???????????????? > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? > >?????? >???????????????????????????? >>???????????????????????????????? AllowOverride All > >?????? >???????????????????????????? >>???????????????????????????????? Options Indexes FollowSymLinks > >?????? >???????????????????????????? >>???????????????????????????????? Require all granted > >?????? >???????????????????????????? >>???????????????? > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? > >?????? >???????????????????????????? >>???????????????????????????????? Options Indexes FollowSymLinks > >?????? >???????????????????????????? >>???????????????????????????????? AllowOverride All > >?????? >???????????????????????????? >>???????????????????????????????? Require all granted > >?????? >???????????????????????????? >>???????????????? > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? file permissions: > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? # ls -ld /srv/www/loris/smarty/templates_c > >?????? >???????????????????????????? >>???????????????? drwxrwxrwx 2 lorisadmin lorisadmin 4096 > Oct 31 09:46 > >?????? >???????????????????????????? >>???????????????? /srv/www/loris/smarty/templates_c/ > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? [root at loris loris]# ls -l > >?????? /srv/www/loris/smarty/templates_c > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 2444 > Oct 31 09:46 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin 10490 > Sep 10 10:55 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin 21126 > Sep???? 7 18:39 > >?????? >???????????????????????????? >>???????????????? > >?????? 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 3296 > Sep???? 7 18:35 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 5901 > Sep???? 7 21:10 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin 23339 > Sep???? 7 18:39 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???????? 874 > Sep 10 11:01 > >?????? >???????????????????????????? >>???????????????? > >?????? 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 1101 > Sep 10 10:58 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin 18054 > Sep 10 10:59 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 3590 > Sep???? 7 18:39 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin 25141 > Sep???? 7 21:08 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???????? 897 > Sep???? 7 18:35 > >?????? >???????????????????????????? >>???????????????? > >?????? a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 9210 > Sep 10 11:01 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 8917 > Sep 10 13:21 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 4811 > Sep???? 7 18:35 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin???? 3309 > Sep 10 11:02 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin 10303 > Sep 10 10:59 > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php > >?????? >???????????????????????????? >>???????????????? -rw-r--r-- 1 lorisadmin lorisadmin 12273 > Sep???? 7 17:42 > >?????? >???????????????????????????? >>???????????????? > >?????? fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? thanks again! > >?????? >???????????????????????????? >>???????????????? Julie > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????????????? On 06-11-2019 19.01 +0000, Christine > Rogers, Ms. wrote: > >?????? >???????????????????????????? >>>???????????????? Hi Ioannis,??????????? > >?????? >???????????????????????????? >>>???????????????? Thanks for your question.??????????? > >?????? >???????????????????????????? >>>???????????????? Given that the URL field is not updating, > I suspect it's > >?????? a > >?????? >???????????????????????????? database > >?????? >???????????????????????????? >>>???????????????? back-end issue.??????????? > >?????? >???????????????????????????? >>>???????????????? Can you verify -- Has your mysql user > lorismysql??????????? been > >?????? granted > >?????? >???????????????????????????? the > >?????? >???????????????????????????? >>???????????????? "INSERT" > >?????? >???????????????????????????? >>>???????????????? privilege for the right database? If not, > that would > >?????? result in > >?????? >???????????????????????????? an > >?????? >???????????????????????????? >>???????????????? error > >?????? >???????????????????????????? >>>???????????????? like the kind you are seeing.??????????? > >?????? >???????????????????????????? >>>???????????????? Also, if you wish to check your LORIS > Configuration > >?????? settings > >?????? >???????????????????????????? in the > >?????? >???????????????????????????? >>>???????????????? backend database such as the URL field -- > to see what was > >?????? >???????????????????????????? actually > >?????? >???????????????????????????? >>???????????????? stored > >?????? >???????????????????????????? >>>???????????????? in a given database field and should > display in the > >?????? Config > >?????? >???????????????????????????? >>???????????????? module:??????????? > >?????? >???????????????????????????? >>>???????????????? You can run the queries listed in the > "Troubleshooting > >?????? >???????????????????????????? >>???????????????? Configuration > >?????? >???????????????????????????? >>>???????????????? settings" section of our Github-wiki > Setup Guide (under > >?????? >???????????????????????????? Project > >?????? >???????????????????????????? >>>???????????????? Customization) :??????????? > >?????? >???????????????????????????? >>>???????????? > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >?????? >???????????????????????????? >>>???????????????? Lastly, this question is perfectly > appropriate for the > >?????? >???????????????????????????? loris-dev > >?????? >???????????????????????????? >>???????????????? community > >?????? >???????????????????????????? >>>???????????????? support listserv -- please [2]subscribe > here and then > >?????? email > >?????? >???????????????????????????? our > >?????? >???????????????????????????? >>???????????????? technical > >?????? >???????????????????????????? >>>???????????????? team your next question at??????????? > >?????? [3][5]loris-dev at bic.mni.mcgill.ca > >?????? >???????????????????????????? >>???????????????? (after checking > >?????? >???????????????????????????? >>>???????????????? any forwarded threads for sensitive > info).??????????? > >?????? >???????????????????????????? >>>???????????????? We prefer to answer technical questions > there for the > >?????? benefit > >?????? >???????????????????????????? of > >?????? >???????????????????????????? >>???????????????? the > >?????? >???????????????????????????? >>>???????????????? community and other first-time users in > the same position > >?????? as > >?????? >???????????????????????????? >>???????????????? yourself.??????????? ??????????? > >?????? >???????????????????????????? >>>???????????????? Thanks and cheers,??????????? > >?????? >???????????????????????????? >>>???????????????? Christine??????????? > >?????? >???????????????????????????? >>>???????????????? On Mon, Nov 4, 2019 at 5:49 PM Dr. > Ioannis Pappas PhD > >?????? >???????????????????????????? >>>???????????????? <[4][6]ioannis at berkeley.edu> wrote: > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????? Hi Loris support.??????????? > >?????? >???????????????????????????? >>>???????????????????????? My name is ioannis Pappas, a post-doc > at the D'Esposito > >?????? lab > >?????? >???????????????????????????? >>???????????????? stroke group > >?????? >???????????????????????????? >>>???????????????????????? at UC Berkeley. With the kind of help > of our sys > >?????? admin??????????? > >?????? >???????????????????????????? Julie > >?????? >???????????????????????????? >>???????????????? (cc'ed) we > >?????? >???????????????????????????? >>>???????????????????????? have set up our loris database in our > cluster (she is > >?????? the > >?????? >???????????????????????????? sudo > >?????? >???????????????????????????? >>???????????????? user and > >?????? >???????????????????????????? >>>???????????????????????? I am the admin user). > >?????? >???????????????????????????? >>>???????????????????????? If you allow me, I would like to ask > you about the > >?????? first > >?????? >???????????????????????????? >>???????????????? configuration > >?????? >???????????????????????????? >>>???????????????????????? steps in the front end as they are > described in the > >?????? >???????????????????????????? tutorial. We > >?????? >???????????????????????????? >>???????????????? can > >?????? >???????????????????????????? >>>???????????????????????? login to [5][7]http://loris and the > front end normally. > >?????? >???????????????????????????? >>>???????????????????????? However any update that I am trying > to??????????? perform in > >?????? >???????????????????????????? >>???????????????? Admin->Configuration > >?????? >???????????????????????????? >>>???????????????????????? doesn't work (e.g. updating the study > name). It just > >?????? >???????????????????????????? refreshes > >?????? >???????????????????????????? >>???????????????? the same > >?????? >???????????????????????????? >>>???????????????????????? page. I am just wondering if there is > an issue with > >?????? writing > >?????? >???????????????????????????? in > >?????? >???????????????????????????? >>???????????????? the > >?????? >???????????????????????????? >>>???????????????????????? configuration file. > >?????? >???????????????????????????? >>>???????????????????????? Here are the permissions setup for > where Loris is > >?????? installed. > >?????? >???????????????????????????? >>>???????????????????????? chmod 777 > /var/www/loris/smarty/templates_c > >?????? >???????????????????????????? >>>???????????????????????? cd /srv/www/loris > >?????? >???????????????????????????? >>>???????????????????????? chown -R lorisadmin:lorisadmin . > >?????? >???????????????????????????? >>>???????????????????????? chmod -c -R a+r . > >?????? >???????????????????????????? >>>???????????????????????? ??????????????? ??????????????? this command gives > everyone read access, and > >?????? outputs > >?????? >???????????????????????????? what > >?????? >???????????????????????????? >>???????????????? changes > >?????? >???????????????????????????? >>>???????????????????????? were made: > >?????? >???????????????????????????? >>>???????????????????????? ??????????????? ??????????????? mode of > ????????????????????./project???????????????????? changed from 0770 > >?????? (rwxrwx---) to > >?????? >???????????????????????????? 0774 > >?????? >???????????????????????????? >>>???????????????????????? (rwxrwxr--) > >?????? >???????????????????????????? >>>???????????????????????? ??????????????? ??????????????? mode of > ????????????????????./tools/logs???????????????????? changed from 0770 > >?????? (rwxrwx---) > >?????? >???????????????????????????? to > >?????? >???????????????????????????? >>???????????????? 0774 > >?????? >???????????????????????????? >>>???????????????????????? (rwxrwxr--) > >?????? >???????????????????????????? >>>???????????????????????? find . -type d -exec chmod a+x -c {} > \; > >?????? >???????????????????????????? >>>???????????????????????? ??????????????? ??????????????? this command gives > everyone permission to open > >?????? a > >?????? >???????????????????????????? directory, > >?????? >???????????????????????????? >>???????????????? and > >?????? >???????????????????????????? >>>???????????????????????? outputs what changes were made: > >?????? >???????????????????????????? >>>???????????????????????? ??????????????? ??????????????? mode of > ????????????????????./project???????????????????? changed from 0774 > >?????? (rwxrwxr--) to > >?????? >???????????????????????????? 0775 > >?????? >???????????????????????????? >>>???????????????????????? (rwxrwxr-x) > >?????? >???????????????????????????? >>>???????????????????????? ??????????????? ??????????????? mode of > ????????????????????./tools/logs???????????????????? changed from 0774 > >?????? (rwxrwxr--) > >?????? >???????????????????????????? to > >?????? >???????????????????????????? >>???????????????? 0775 > >?????? >???????????????????????????? >>>???????????????????????? (rwxrwxr-x) > >?????? >???????????????????????????? >>>???????????????????????? Hopefully??????????? you can help me with > this. I also > >?????? subscribed to > >?????? >???????????????????????????? the > >?????? >???????????????????????????? >>???????????????? mailing > >?????? >???????????????????????????? >>>???????????????????????? list but I am not sure if this too > much of a basic > >?????? question > >?????? >???????????????????????????? for > >?????? >???????????????????????????? >>???????????????? the > >?????? >???????????????????????????? >>>???????????????????????? list. > >?????? >???????????????????????????? >>>???????????????????????? Best wishes, > >?????? >???????????????????????????? >>>???????????????????????? Ioannis > >?????? >???????????????????????????? >>>???????????????????????? On Mon, Nov 4, 2019 at 1:12 PM Julie > Ashworth, HWNI > >?????? >???????????????????????????? Computing > >?????? >???????????????????????????? >>???????????????? Support > >?????? >???????????????????????????? >>>???????????????????????? <[6][8]support-cirl at berkeley.edu> > wrote: > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????? Hi ioannis, maybe it's best to > ask the developers? > >?????? You can > >?????? >???????????????????????????? cc > >?????? >???????????????????????????? >>???????????????? me if > >?????? >???????????????????????????? >>>???????????????????????????????? you'd like. > >?????? >???????????????????????????? >>>???????????????????????????????? On Mon, Nov 4, 2019, 12:37 PM > Ioannis Pappas > >?????? >???????????????????????????? >>???????????????? <[7][9]ioannis at berkeley.edu> > >?????? >???????????????????????????? >>>???????????????????????????????? wrote: > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? That did the trick Julie. > Thank you! > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? I am still trying to > understand how configuration > >?????? works > >?????? >???????????????????????????? >>???????????????? though. For > >?????? >???????????????????????????? >>>???????????????????????????????????????? example if I just try to > change the name of the > >?????? >???????????????????????????? >>>???????????????????????????????????????? study from the front end, I > get nowhere (it just > >?????? >???????????????????????????? refreshes > >?????? >???????????????????????????? >>???????????????? the same > >?????? >???????????????????????????? >>>???????????????????????????????????????? page). > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? I am not sure if this > requires write permissions > >?????? >???????????????????????????? somewhere in > >?????? >???????????????????????????? >>???????????????? a > >?????? >???????????????????????????? >>>???????????????????????????????????????? config file/folder and > that??????????????????????????????????????s why it > >?????? doesn??????????????????????????????????????t update > >?????? >???????????????????????????? it. > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? Best wishes, > >?????? >???????????????????????????? >>>???????????????????????????????????????? Ioannis > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? > On Nov 4, 2019, at 12:08 > PM, Julie Ashworth, HWNI > >?????? >???????????????????????????? Computing > >?????? >???????????????????????????? >>>???????????????????????????????????????? Support > <[8][10]support-cirl at berkeley.edu> wrote: > >?????? >???????????????????????????? >>>???????????????????????????????????????? > > >?????? >???????????????????????????? >>>???????????????????????????????????????? > just in case you're > interested, these are the > >?????? >???????????????????????????? permission > >?????? >???????????????????????????? >>???????????????? changes I > >?????? >???????????????????????????? >>>???????????????????????????????????????? made: > >?????? >???????????????????????????? >>>???????????????????????????????????????? > > >?????? >???????????????????????????? >>>???????????????????????????????????????? > chmod 777 > /var/www/loris/smarty/templates_c > >?????? >???????????????????????????? >>>???????????????????????????????????????? > cd /srv/www/loris > >?????? >???????????????????????????? >>>???????????????????????????????????????? > chown -R > lorisadmin:lorisadmin . > >?????? >???????????????????????????? >>>???????????????????????????????????????? > chmod -c -R a+r . > >?????? >???????????????????????????? >>>???????????????????????????????????????? >??????????????? ??????????????? this command > gives everyone read access, > >?????? and > >?????? >???????????????????????????? outputs > >?????? >???????????????????????????? >>???????????????? what > >?????? >???????????????????????????? >>>???????????????????????????????????????? changes were made: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >??????????????? ??????????????? mode of > ????????????????????./project???????????????????? changed from > >?????? 0770 > >?????? >???????????????????????????? (rwxrwx---) to > >?????? >???????????????????????????? >>???????????????? 0774 > >?????? >???????????????????????????? >>>???????????????????????????????????????? (rwxrwxr--) > >?????? >???????????????????????????? >>>???????????????????????????????????????? >??????????????? ??????????????? mode of > ????????????????????./tools/logs???????????????????? changed from > >?????? 0770 > >?????? >???????????????????????????? (rwxrwx---) > >?????? >???????????????????????????? >>???????????????? to 0774 > >?????? >???????????????????????????? >>>???????????????????????????????????????? (rwxrwxr--) > >?????? >???????????????????????????? >>>???????????????????????????????????????? > find . -type d -exec chmod > a+x -c {} \; > >?????? >???????????????????????????? >>>???????????????????????????????????????? >??????????????? ??????????????? this command > gives everyone permission to > >?????? open a > >?????? >???????????????????????????? >>???????????????? directory, and > >?????? >???????????????????????????? >>>???????????????????????????????????????? outputs what changes were > made: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >??????????????? ??????????????? mode of > ????????????????????./project???????????????????? changed from > >?????? 0774 > >?????? >???????????????????????????? (rwxrwxr--) to > >?????? >???????????????????????????? >>???????????????? 0775 > >?????? >???????????????????????????? >>>???????????????????????????????????????? (rwxrwxr-x) > >?????? >???????????????????????????? >>>???????????????????????????????????????? >??????????????? ??????????????? mode of > ????????????????????./tools/logs???????????????????? changed from > >?????? 0774 > >?????? >???????????????????????????? (rwxrwxr--) > >?????? >???????????????????????????? >>???????????????? to 0775 > >?????? >???????????????????????????? >>>???????????????????????????????????????? (rwxrwxr-x) > >?????? >???????????????????????????? >>>???????????????????????????????????????? > > >?????? >???????????????????????????? >>>???????????????????????????????????????? > > >?????? >???????????????????????????? >>>???????????????????????????????????????? > > >?????? >???????????????????????????? >>>???????????????????????????????????????? > On 04-11-2019 12.03 -0800, > Ioannis Pappas wrote: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >> Hi Julie. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >> I just tried and I still > don???t get anything. I > >?????? also > >?????? >???????????????????????????? >>???????????????? tried > >?????? >???????????????????????????? >>>???????????????????????????????????????? private mode in Firefox in > case the empty page was > >?????? >???????????????????????????? cached. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >> Sorry for this. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >> Best wishes, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >> Ioannis > >?????? >???????????????????????????? >>>???????????????????????????????????????? >> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> On Nov 4, 2019, at 11:58 > AM, Julie Ashworth, > >?????? HWNI > >?????? >???????????????????????????? >>???????????????? Computing > >?????? >???????????????????????????? >>>???????????????????????????????????????? Support > <[9][11]support-cirl at berkeley.edu> wrote: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> hi Ioannis, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> no worries, I changed the > following directory > >?????? to > >?????? >???????????????????????????? 777: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > /var/www/loris/smarty/templates_c > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> will you please check if > that works? > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> thanks! > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> On 04-11-2019 11.49 > -0800, Dr. Ioannis Pappas > >?????? PhD > >?????? >???????????????????????????? wrote: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? Hi Julie. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? Apologies for > bugging you with this again. > >?????? We > >?????? >???????????????????????????? tried > >?????? >???????????????????????????? >>???????????????? now to > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? access????????????????????? ?? > [1][10][12]http://loris????????????????????? ?? > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? and we are > getting a????????????????????? ?? blank page. I > >?????? think the > >?????? >???????????????????????????? reason > >?????? >???????????????????????????? >>???????????????? for this > >?????? >???????????????????????????? >>>???????????????????????????????????????? is that we > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? don't have > read????????????????????? ?? permissions to read > >?????? from the > >?????? >???????????????????????????? >>???????????????? template located > >?????? >???????????????????????????? >>>???????????????????????????????????????? in > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? > /var/www/loris/smarty See here bottom of > >?????? the > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? page????????????????????? ?? > >?????? >???????????????????????????? >>>???????????????????????????????????? > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? I think, in > general, I am a little bit > >?????? confused > >?????? >???????????????????????????? as to > >?????? >???????????????????????????? >>???????????????? what the > >?????? >???????????????????????????? >>>???????????????????????????????????????? permissions > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? should be for us > that are not sudos. My > >?????? >???????????????????????????? understanding > >?????? >???????????????????????????? >>???????????????? is that > >?????? >???????????????????????????? >>>???????????????????????????????????????? if we don't > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? have read or > write permissions then we > >?????? can't > >?????? >???????????????????????????? access or > >?????? >???????????????????????????? >>???????????????? write > >?????? >???????????????????????????? >>>???????????????????????????????????????? to > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? /var/www/loris, > meaning that we can't > >?????? access or > >?????? >???????????????????????????? >>???????????????? configure. > >?????? >???????????????????????????? >>>???????????????????????????????????????? Should > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? everything be > chmod 777 for example?????????????????????? ?? > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? Thank you very > much once again. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? Best wishes, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? Ioannis > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? On Thu, Oct 31, > 2019 at 1:56 PM Dr. Ioannis > >?????? >???????????????????????????? Pappas PhD > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? > <[3][12][14]ioannis at berkeley.edu> wrote: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? Thank you > very much Julie. I appreciate > >?????? this > >?????? >???????????????????????????? and I > >?????? >???????????????????????????? >>???????????????? will dig > >?????? >???????????????????????????? >>>???????????????????????????????????????? into Loris > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? given > your changes. Thank you so much > >?????? for your > >?????? >???????????????????????????? >>???????????????? help. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? Best > wishes, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? Ioannis > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? On Thu, > Oct 31, 2019 at 12:48 PM Julie > >?????? >???????????????????????????? Ashworth, > >?????? >???????????????????????????? >>???????????????? HWNI > >?????? >???????????????????????????? >>>???????????????????????????????????????? Computing Support > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? > <[4][13][15]support-cirl at berkeley.edu> > >?????? wrote: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > hi Ioannis, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > 1. I changed the permissions of > >?????? >???????????????????????????? /srv/www/loris > >?????? >???????????????????????????? >>???????????????? to be owned > >?????? >???????????????????????????? >>>???????????????????????????????????????? by > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > lorisadmin. I reivewed my > >?????? installation > >?????? >???????????????????????????? notes, > >?????? >???????????????????????????? >>???????????????? and I did > >?????? >???????????????????????????? >>>???????????????????????????????????????? this already > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > when > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? I > installed the server. I'm not > >?????? sure why > >?????? >???????????????????????????? they > >?????? >???????????????????????????? >>???????????????? changed, so > >?????? >???????????????????????????? >>>???????????????????????????????????????? it's > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > probably a > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > good idea to keep an eye on that. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > 2. When I installed the loris > >?????? software, I > >?????? >???????????????????????????? also > >?????? >???????????????????????????? >>???????????????? installed a > >?????? >???????????????????????????? >>>???????????????????????????????????????? mysql > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > database as recommended in the > >?????? >???????????????????????????? instructions: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > projectname: LORIS > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > databasename: loris_database > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > mysqluser: lorismysql > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > frontend: lorisweb > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > 3. A couple of weeks ago, I moved > >?????? Henrik's > >?????? >???????????????????????????? home > >?????? >???????????????????????????? >>???????????????? directory > >?????? >???????????????????????????? >>>???????????????????????????????????????? to > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > /home/despoA, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > but I forgot to update loris. This > >?????? is done > >?????? >???????????????????????????? now. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > best, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > Julie > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > On 31-10-2019 11.15 -0700, Dr. > >?????? Ioannis > >?????? >???????????????????????????? Pappas > >?????? >???????????????????????????? >>???????????????? PhD wrote: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? Hi Julie. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? I hope you are well. We are > >?????? trying to > >?????? >???????????????????????????? >>???????????????? configure loris > >?????? >???????????????????????????? >>>???????????????????????????????????????? that you > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > kindly set > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? up for us. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? I have a couple of > >?????? questions for you if > >?????? >???????????????????????????? you > >?????? >???????????????????????????? >>???????????????? allow me > >?????? >???????????????????????????? >>>???????????????????????????????????????? so.????????????????????? ?? > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? 1) First, although we are > >?????? logging into > >?????? >???????????????????????????? the > >?????? >???????????????????????????? >>???????????????? front end > >?????? >???????????????????????????? >>>???????????????????????????????????????? with admin > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > username > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? (lorisweb) and password, it > >?????? seems that > >?????? >???????????????????????????? any > >?????? >???????????????????????????? >>???????????????? kind of > >?????? >???????????????????????????? >>>???????????????????????????????????????? update of > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > configuration > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? we are trying to do fails > >?????? (meaning that > >?????? >???????????????????????????? if > >?????? >???????????????????????????? >>???????????????? we, say, > >?????? >???????????????????????????? >>>???????????????????????????????????????? change the > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > name of the > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? study and press "submit", > >?????? this doesn't > >?????? >???????????????????????????? do > >?????? >???????????????????????????? >>???????????????? anything-it > >?????? >???????????????????????????? >>>???????????????????????????????????????? doesn't > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > update). > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? It's almost like our > >?????? lorisweb user > >?????? >???????????????????????????? doesn't > >?????? >???????????????????????????? >>???????????????? have write > >?????? >???????????????????????????? >>>???????????????????????????????????????? privileges > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > in the > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? /var/www/loris/project > >?????? (where I think > >?????? >???????????????????????????? every > >?????? >???????????????????????????? >>>???????????????????????????????????????? configuration should > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > be). > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? This generalizes for > >?????? everything that we > >?????? >???????????????????????????? are > >?????? >???????????????????????????? >>???????????????? trying to do > >?????? >???????????????????????????? >>>???????????????????????????????????????? in the > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > front end. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? Clicking any instrument/tab > >?????? in the front > >?????? >???????????????????????????? end > >?????? >???????????????????????????? >>???????????????? doesn't > >?????? >???????????????????????????? >>>???????????????????????????????????????? really point > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > to > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? anything.????????????????????? ?? > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? 2) Loris suggest doing > >?????? configurations > >?????? >???????????????????????????? via > >?????? >???????????????????????????? >>???????????????? SQL. Is it > >?????? >???????????????????????????? >>>???????????????????????????????????????? possible to > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > run SQL > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? scripts in the backend > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? 3) For some reason typing > >?????? ssh lors for > >?????? >???????????????????????????? Henrik > >?????? >???????????????????????????? >>???????????????? doesn't > >?????? >???????????????????????????? >>>???????????????????????????????????????? directly > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > take him to > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? loris (it requires a > >?????? password that is > >?????? >???????????????????????????? not the > >?????? >???????????????????????????? >>???????????????? password > >?????? >???????????????????????????? >>>???????????????????????????????????????? setup for > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > the > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? lorisweb user). Will you be > >?????? able to fix > >?????? >???????????????????????????? this > >?????? >???????????????????????????? >>???????????????? via your > >?????? >???????????????????????????? >>>???????????????????????????????????????? sudo > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > privileges? > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? Thank you very much in > >?????? advance for all > >?????? >???????????????????????????? your > >?????? >???????????????????????????? >>???????????????? help Julie. > >?????? >???????????????????????????? >>>???????????????????????????????????????? Let us > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > know if > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? this is something that > >?????? shouldn't be > >?????? >???????????????????????????? directed > >?????? >???????????????????????????? >>???????????????? to you (but > >?????? >???????????????????????????? >>>???????????????????????????????????????? instead > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > to the > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? loris people).????????????????????? ?? > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? Best wishes, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? Ioannis > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? On Mon, Sep 9, 2019 at 6:25 > >?????? PM Julie > >?????? >???????????????????????????? >>???????????????? Ashworth, HWNI > >?????? >???????????????????????????? >>>???????????????????????????????????????? Computing > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > Support > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????? > >?????? >???????????????????????????? <[1][5][14][16]support-cirl at berkeley.edu> > >?????? >???????????????????????????? >>???????????????? wrote: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? hi Henrik and > >?????? Ioannis, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? the loris server > >?????? is available for > >?????? >???????????????????????????? you to > >?????? >???????????????????????????? >>???????????????? use. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? The servername is > >?????? 'loris'. I > >?????? >???????????????????????????? created a > >?????? >???????????????????????????? >>???????????????? directory > >?????? >???????????????????????????? >>>???????????????????????????????????????? called > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > /data/loris for > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? you to store data. > >?????? You may create > >?????? >???????????????????????????? new > >?????? >???????????????????????????? >>???????????????? folders in > >?????? >???????????????????????????? >>>???????????????????????????????????????? /data/loris to > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > organize > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? your data. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? 1) secure shell or > >?????? secure copy: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? You can log in > >?????? with the 'ssh' or > >?????? >???????????????????????????? 'scp' > >?????? >???????????????????????????? >>???????????????? command from > >?????? >???????????????????????????? >>>???????????????????????????????????????? your remote > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > desktop > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? session. You don't > >?????? need to > >?????? >???????????????????????????? authenticate > >?????? >???????????????????????????? >>???????????????? to log in. > >?????? >???????????????????????????? >>>???????????????????????????????????????? Maybe you'll > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > use scp > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? to transfer data > >?????? between your > >?????? >???????????????????????????? cluster > >?????? >???????????????????????????? >>???????????????? account and the > >?????? >???????????????????????????? >>>???????????????????????????????????????? loris > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > server? > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? Please put the > >?????? data in /data/loris, > >?????? >???????????????????????????? so I > >?????? >???????????????????????????? >>???????????????? can make > >?????? >???????????????????????????? >>>???????????????????????????????????????? backups more > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > easily. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? ????????????????????? ????????????????? > ????????????????????? ????????????????? > >?????? secure shell: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? ????????????????????? ????????????????? > ????????????????????? ????????????????? > >?????? $ ssh loris > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? ????????????????????? ????????????????? > ????????????????????? ????????????????? > >?????? secure copy (change the > >?????? >???????????????????????????? names > >?????? >???????????????????????????? >>???????????????? in brackets). Let > >?????? >???????????????????????????? >>>???????????????????????????????????????? me know if > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? I > can > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? ????????????????????? ????????????????? > ????????????????????? ????????????????? > >?????? help with syntax: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? ????????????????????? ????????????????? > ????????????????????? ????????????????? > >?????? $ scp -r > >?????? >???????????????????????????? >>???????????????? loris:/data/loris/ > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? 2) front-end web > >?????? interface.????????????????????? ????????????? > >?????? >???????????????????????????? Open a > >?????? >???????????????????????????? >>???????????????? web browser in > >?????? >???????????????????????????? >>>???????????????????????????????????????? your remote > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > desktop > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? session and enter > >?????? the hostname: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? > >?????? [2][6][15][17]http://loris > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? I created an admin > >?????? user called > >?????? >???????????????????????????? >>???????????????? 'lorisweb'. I put the > >?????? >???????????????????????????? >>>???????????????????????????????????????? password > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > in > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? $HOME/newuser on > >?????? the cluster. To > >?????? >???????????????????????????? see it, > >?????? >???????????????????????????? >>???????????????? open a > >?????? >???????????????????????????? >>>???????????????????????????????????????? terminal, and > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > run: > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? ????????????????????? ????????????????? > ????????????????????? ????????????????? > >?????? $ cat $HOME/newuser > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? If other people > >?????? need shell access > >?????? >???????????????????????????? to the > >?????? >???????????????????????????? >>???????????????? webserver, > >?????? >???????????????????????????? >>>???????????????????????????????????????? please let > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > me know > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? so I can create a > >?????? home directory > >?????? >???????????????????????????? for > >?????? >???????????????????????????? >>???????????????? them. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? We should > >?????? eventually discuss > >?????? >???????????????????????????? backups. > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? best, > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? ????????????????????? ????????????????? Julie > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> References > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? Visible links > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? 1. > >?????? >???????????????????????????? >>???????????????? > mailto:[7][16][18]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>> ????????????????????? ????????????????? > ????????????????????? ????????????????? 2. [8][17][19]http://loris/ > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? ??????????????? ??????????????? > ---end quoted text--- > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> References > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>> > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? Visible links > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? 1. > [18][20]http://loris/ > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? 2. > >?????? >???????????????????????????? >>>???????????????????????????????????? > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? 3. > mailto:[20][22]ioannis at berkeley.edu > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? 4. > mailto:[21][23]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? 5. > mailto:[22][24]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? 6. > [23][25]http://loris/ > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? 7. > mailto:[24][26]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>>>??????????????? 8. > [25][27]http://loris/ > >?????? >???????????????????????????? >>>???????????????????????????????????????? >>> ---end quoted text--- > >?????? >???????????????????????????? >>>???????????????????????????????????????? >> > >?????? >???????????????????????????? >>>???????????????????????????????????????? > ---end quoted text--- > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????? -- > >?????? >???????????????????????????? >>>???????????????? [26][28]christine.rogers at mcgill.ca > >?????? >???????????????????????????? >>>???????????????? McGill Centre for Integrative > Neuroscience | MCIN.ca > >?????? >???????????????????????????? >>>???????????????? Montreal Neurological Institute > >?????? >???????????????????????????? >>>???????????????? McGill University | Montreal | Canada > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>> References > >?????? >???????????????????????????? >>> > >?????? >???????????????????????????? >>>???????????????? Visible links > >?????? >???????????????????????????? >>>???????????????? 1. > >?????? >???????????????????????????? >>???????????? > >?????? >???????????????????????????? > >?????? > [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >?????? >???????????????????????????? >>>???????????????? 2. > >?????? >???????????????????????????? > [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >?????? >???????????????????????????? >>>???????????????? 3. mailto:[31]loris-dev at bic.mni.mcgill.ca > >?????? >???????????????????????????? >>>???????????????? 4. mailto:[32]ioannis at berkeley.edu > >?????? >???????????????????????????? >>>???????????????? 5. [33]http://loris/ > >?????? >???????????????????????????? >>>???????????????? 6. mailto:[34]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????????? 7. mailto:[35]ioannis at berkeley.edu > >?????? >???????????????????????????? >>>???????????????? 8. mailto:[36]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????????? 9. mailto:[37]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 10. [38]http://xn--loris-7qa/ > >?????? >???????????????????????????? >>>???????????? 11. > >?????? >???????????????????????????? > [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????? >???????????????????????????? >>>???????????? 12. mailto:[40]ioannis at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 13. mailto:[41]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 14. mailto:[42]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 15. [43]http://loris/ > >?????? >???????????????????????????? >>>???????????? 16. mailto:[44]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 17. [45]http://loris/ > >?????? >???????????????????????????? >>>???????????? 18. [46]http://loris/ > >?????? >???????????????????????????? >>>???????????? 19. > >?????? >???????????????????????????? > [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????? >???????????????????????????? >>>???????????? 20. mailto:[48]ioannis at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 21. mailto:[49]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 22. mailto:[50]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 23. [51]http://loris/ > >?????? >???????????????????????????? >>>???????????? 24. mailto:[52]support-cirl at berkeley.edu > >?????? >???????????????????????????? >>>???????????? 25. [53]http://loris/ > >?????? >???????????????????????????? >>>???????????? 26. mailto:[54]christine.rogers at mcgill.ca > >?????? >???????????????????????????? >>???????????????? ---end quoted text--- > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????? -- > >?????? >???????????????????????????? >>???????? [55]christine.rogers at mcgill.ca > >?????? >???????????????????????????? >>???????? McGill Centre for Integrative Neuroscience | > MCIN.ca > >?????? >???????????????????????????? >>???????? Montreal Neurological Institute > >?????? >???????????????????????????? >>???????? McGill University | Montreal | Canada > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >> References > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? >>???????? Visible links > >?????? >???????????????????????????? >>???????? 1. [8]mailto:loris-dev at bic.mni.mcgill.ca > >?????? >???????????????????????????? >>???????? 2. [9]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???????? 3. [10]http://loris.priv/ > >?????? >???????????????????????????? >>???? > >?????? >???????????????????????????? 4. > >?????? > [11]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >?????? >???????????????????????????? >>???????? 5. [12]mailto:loris-dev at bic.mni.mcgill.ca > >?????? >???????????????????????????? >>???????? 6. [13]mailto:ioannis at berkeley.edu > >?????? >???????????????????????????? >>???????? 7. [14]http://loris/ > >?????? >???????????????????????????? >>???????? 8. [15]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???????? 9. [16]mailto:ioannis at berkeley.edu > >?????? >???????????????????????????? >>???? 10. [17]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 11. [18]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 12. [19]http://xn--loris-era/ > >?????? >???????????????????????????? >>???? 13. > >?????? [20]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????? >???????????????????????????? >>???? 14. [21]mailto:ioannis at berkeley.edu > >?????? >???????????????????????????? >>???? 15. [22]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 16. [23]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 17. [24]http://loris/ > >?????? >???????????????????????????? >>???? 18. [25]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 19. [26]http://loris/ > >?????? >???????????????????????????? >>???? 20. [27]http://loris/ > >?????? >???????????????????????????? >>???? 21. > >?????? [28]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????? >???????????????????????????? >>???? 22. [29]mailto:ioannis at berkeley.edu > >?????? >???????????????????????????? >>???? 23. [30]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 24. [31]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 25. [32]http://loris/ > >?????? >???????????????????????????? >>???? 26. [33]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 27. [34]http://loris/ > >?????? >???????????????????????????? >>???? 28. [35]mailto:christine.rogers at mcgill.ca > >?????? >???????????????????????????? >> > >?????? >???????????????????????????? 29. > >?????? > [36]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >?????? >???????????????????????????? >>???? 30. > >?????? [37]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >?????? >???????????????????????????? >>???? 31. [38]mailto:loris-dev at bic.mni.mcgill.ca > >?????? >???????????????????????????? >>???? 32. [39]mailto:ioannis at berkeley.edu > >?????? >???????????????????????????? >>???? 33. [40]http://loris/ > >?????? >???????????????????????????? >>???? 34. [41]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 35. [42]mailto:ioannis at berkeley.edu > >?????? >???????????????????????????? >>???? 36. [43]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 37. [44]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 38. [45]http://xn--loris-7qa/ > >?????? >???????????????????????????? >>???? 39. > >?????? [46]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????? >???????????????????????????? >>???? 40. [47]mailto:ioannis at berkeley.edu > >?????? >???????????????????????????? >>???? 41. [48]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 42. [49]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 43. [50]http://loris/ > >?????? >???????????????????????????? >>???? 44. [51]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 45. [52]http://loris/ > >?????? >???????????????????????????? >>???? 46. [53]http://loris/ > >?????? >???????????????????????????? >>???? 47. > >?????? [54]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >?????? >???????????????????????????? >>???? 48. [55]mailto:ioannis at berkeley.edu > >?????? >???????????????????????????? >>???? 49. [56]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 50. [57]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 51. [58]http://loris/ > >?????? >???????????????????????????? >>???? 52. [59]mailto:support-cirl at berkeley.edu > >?????? >???????????????????????????? >>???? 53. [60]http://loris/ > >?????? >???????????????????????????? >>???? 54. [61]mailto:christine.rogers at mcgill.ca > >?????? >???????????????????????????? >>???? 55. [62]mailto:christine.rogers at mcgill.ca > >?????? >???????????????????????????? > ---end quoted text--- > >?????? > > >?????? >???????????????????????????? _______________________________________________ > >?????? >???????????????????????????? Loris-dev mailing list > >?????? >???????????????????????????? Loris-dev at bic.mni.mcgill.ca > >?????? >???????????????????????????? > [63]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >?????? >???????????????????????????? > >?????? > > >?????? >???????????????????? _______________________________________________ > >?????? >???????????????????? Loris-dev mailing list > >?????? >???????????????????? Loris-dev at bic.mni.mcgill.ca > >?????? >???????????????????? > [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >?????? > > >?????? >???????????? -- > >?????? >???????????? christine.rogers at mcgill.ca > >?????? >???????????? McGill Centre for Integrative Neuroscience | MCIN.ca > >?????? >???????????? Montreal Neurological Institute > >?????? >???????????? McGill University | Montreal | Canada > >?????? ---end quoted text--- > > > > References > > > >?????? Visible links > >?????? 1. [2]https://loris.url/configuration/ > >?????? 2. [3]https://.loris.url/ > >?????? 3. [4]http://loris.priv/ > >?????? 4. [5]http://localhost/ > >?????? 5. [6]http://loris.priv/ > >?????? 6. [7]http://localhost/ > >?????? 7. [8]http://localhost/ > >?????? 8. [9]mailto:loris-dev at bic.mni.mcgill.ca > >?????? 9. [10]mailto:support-cirl at berkeley.edu > >???? 10. [11]http://loris.priv/ > >???? 11. > [12]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >???? 12. [13]mailto:loris-dev at bic.mni.mcgill.ca > >???? 13. [14]mailto:ioannis at berkeley.edu > >???? 14. [15]http://loris/ > >???? 15. [16]mailto:support-cirl at berkeley.edu > >???? 16. [17]mailto:ioannis at berkeley.edu > >???? 17. [18]mailto:support-cirl at berkeley.edu > >???? 18. [19]mailto:support-cirl at berkeley.edu > >???? 19. [20]http://xn--loris-era/ > >???? 20. [21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >???? 21. [22]mailto:ioannis at berkeley.edu > >???? 22. [23]mailto:support-cirl at berkeley.edu > >???? 23. [24]mailto:support-cirl at berkeley.edu > >???? 24. [25]http://loris/ > >???? 25. [26]mailto:support-cirl at berkeley.edu > >???? 26. [27]http://loris/ > >???? 27. [28]http://loris/ > >???? 28. [29]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >???? 29. [30]mailto:ioannis at berkeley.edu > >???? 30. [31]mailto:support-cirl at berkeley.edu > >???? 31. [32]mailto:support-cirl at berkeley.edu > >???? 32. [33]http://loris/ > >???? 33. [34]mailto:support-cirl at berkeley.edu > >???? 34. [35]http://loris/ > >???? 35. [36]mailto:christine.rogers at mcgill.ca > >???? 36. > [37]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >???? 37. [38]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >???? 38. [39]mailto:loris-dev at bic.mni.mcgill.ca > >???? 39. [40]mailto:ioannis at berkeley.edu > >???? 40. [41]http://loris/ > >???? 41. [42]mailto:support-cirl at berkeley.edu > >???? 42. [43]mailto:ioannis at berkeley.edu > >???? 43. [44]mailto:support-cirl at berkeley.edu > >???? 44. [45]mailto:support-cirl at berkeley.edu > >???? 45. [46]http://xn--loris-7qa/ > >???? 46. [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >???? 47. [48]mailto:ioannis at berkeley.edu > >???? 48. [49]mailto:support-cirl at berkeley.edu > >???? 49. [50]mailto:support-cirl at berkeley.edu > >???? 50. [51]http://loris/ > >???? 51. [52]mailto:support-cirl at berkeley.edu > >???? 52. [53]http://loris/ > >???? 53. [54]http://loris/ > >???? 54. [55]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >???? 55. [56]mailto:ioannis at berkeley.edu > >???? 56. [57]mailto:support-cirl at berkeley.edu > >???? 57. [58]mailto:support-cirl at berkeley.edu > >???? 58. [59]http://loris/ > >???? 59. [60]mailto:support-cirl at berkeley.edu > >???? 60. [61]http://loris/ > >???? 61. [62]mailto:christine.rogers at mcgill.ca > >???? 62. [63]mailto:christine.rogers at mcgill.ca > >???? 63. [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >???? 64. [65]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > ---end quoted text--- > > References > > Visible links > 1. http://localhost/ > 2. https://loris.url/configuration/ > 3. https://.loris.url/ > 4. http://loris.priv/ > 5. http://localhost/ > 6. http://loris.priv/ > 7. http://localhost/ > 8. http://localhost/ > 9. mailto:loris-dev at bic.mni.mcgill.ca > 10. mailto:support-cirl at berkeley.edu > 11. http://loris.priv/ > 12. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 13. mailto:loris-dev at bic.mni.mcgill.ca > 14. mailto:ioannis at berkeley.edu > 15. http://loris/ > 16. mailto:support-cirl at berkeley.edu > 17. mailto:ioannis at berkeley.edu > 18. mailto:support-cirl at berkeley.edu > 19. mailto:support-cirl at berkeley.edu > 20. http://xn--loris-era/ > 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 22. mailto:ioannis at berkeley.edu > 23. mailto:support-cirl at berkeley.edu > 24. mailto:support-cirl at berkeley.edu > 25. http://loris/ > 26. mailto:support-cirl at berkeley.edu > 27. http://loris/ > 28. http://loris/ > 29. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 30. mailto:ioannis at berkeley.edu > 31. mailto:support-cirl at berkeley.edu > 32. mailto:support-cirl at berkeley.edu > 33. http://loris/ > 34. mailto:support-cirl at berkeley.edu > 35. http://loris/ > 36. mailto:christine.rogers at mcgill.ca > 37. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 38. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 39. mailto:loris-dev at bic.mni.mcgill.ca > 40. mailto:ioannis at berkeley.edu > 41. http://loris/ > 42. mailto:support-cirl at berkeley.edu > 43. mailto:ioannis at berkeley.edu > 44. mailto:support-cirl at berkeley.edu > 45. mailto:support-cirl at berkeley.edu > 46. http://xn--loris-7qa/ > 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 48. mailto:ioannis at berkeley.edu > 49. mailto:support-cirl at berkeley.edu > 50. mailto:support-cirl at berkeley.edu > 51. http://loris/ > 52. mailto:support-cirl at berkeley.edu > 53. http://loris/ > 54. http://loris/ > 55. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 56. mailto:ioannis at berkeley.edu > 57. mailto:support-cirl at berkeley.edu > 58. mailto:support-cirl at berkeley.edu > 59. http://loris/ > 60. mailto:support-cirl at berkeley.edu > 61. http://loris/ > 62. mailto:christine.rogers at mcgill.ca > 63. mailto:christine.rogers at mcgill.ca > 64. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 65. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ---end quoted text--- From ioannis at berkeley.edu Tue Nov 12 01:21:32 2019 From: ioannis at berkeley.edu (Ioannis Pappas) Date: Mon, 11 Nov 2019 22:21:32 -0800 Subject: [Loris-dev] loris server In-Reply-To: <20191112033026.GA5955@gaia.neuro.berkeley.edu> References: <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> <20191109020414.GB13279@nx6.priv> <20191111170342.GA4213@gaia.neuro.berkeley.edu> <20191112033026.GA5955@gaia.neuro.berkeley.edu> Message-ID: Hi Julie, Christine and Melanie. I am afraid I still cannot update anything. I am wondering if it has to do with the reference to the dbHost. Also would creating a new front-end user help with things? Apologies for the long thread. Best wishes, Ioannis > On Nov 11, 2019, at 7:30 PM, Julie Ashworth, HWNI Computing Support wrote: > > thanks Christine and Melanie - > I updated the Config table settings (see below). > > Ioannis, > can you please test if it works now? > > Melanie, > I couldn't find a reference to dbHost in the config.xml file. The only reference to host that I could find is: > # grep -i host /srv/www/loris/project/config.xml > localhost > %COUCH_HOSTNAME% > > > MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; > +----------+-------------------+-------------------+------------------+--------------------------------------+ > | ConfigID | Name | Label | Value | Description | > +----------+-------------------+-------------------+------------------+--------------------------------------+ > | 44 | host | Host | localhost | Host | > | 45 | url | Main LORIS URL | http://localhost | Main URL where LORIS can be accessed | > | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | > +----------+-------------------+-------------------+------------------+--------------------------------------+ > > > thanks! > Julie > > > On 11-11-2019 17.28 +0000, Melanie Legault, Mrs wrote: >> Hello Julie, >> Yes, the '%' sign is a wildcard for 'all host'. So it should be good but I >> had problem with that in the past. >> Could you ensure the 'lorismysql'@'localhost' user proper permissions. >> >> Also, in that case, in the config.xml file, the dbHost should be >> 'localhost'. MySQL treat 127.0.0.1 and localhost as 2 different host. >> >> M??lanie >> >> -------------------------------------------------------------------------- >> >> From: Julie Ashworth, HWNI Computing Support >> Sent: November 11, 2019 12:03 >> To: Melanie Legault, Mrs >> Cc: Christine Rogers, Ms. ; Ioannis Pappas >> ; loris-dev at bic.mni.mcgill.ca >> >> Subject: Re: [Loris-dev] loris server >> ? >> thanks Melanie, >> I'm including the output below. My understanding is that '%' matches all >> hostnames. Should I specifically grant permission to 'loris.priv' from >> user lorismysql? Or perhaps you recommend changing loris_database entries >> ('host' to 'localhost' and 'url' to '[1]http://localhost')? >> thanks! >> >> MariaDB [(none)]> SELECT User, Host FROM mysql.user; >> +------------+-----------+ >> | User? ? ? ? ? ? | Host? ? ? ? ? | >> +------------+-----------+ >> | lorismysql | %? ? ? ? ? ? ? ? | >> | root? ? ? ? ? ? | 127.0.0.1 | >> | root? ? ? ? ? ? | ::1? ? ? ? ? ? | >> | lorismysql | localhost | >> | root? ? ? ? ? ? | localhost | >> +------------+-----------+ >> 5 rows in set (0.00 sec) >> >> MariaDB [(none)]> SHOW grants for 'lorismysql'@'%'; >> +--------------------------------------------------------------------------------+ >> | Grants for lorismysql@% >> +--------------------------------------------------------------------------------+ >> | GRANT USAGE ON *.* TO 'lorismysql'@'%' >> | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO >> 'lorismysql'@'%' | >> +--------------------------------------------------------------------------------+ >> 2 rows in set (0.00 sec) >> >> On 11-11-2019 15.47 +0000, Melanie Legault, Mrs wrote: >>> ? ? ? Hello Julie, >>> ? ? ? Could it be that your MySQL 'lorismysql' user have different >> permissions >>> ? ? ? depending on where it is connecting to the DB? >>> ? ? ? A database admin (root) can check this for you. >>> ? ? ? SELECT User, Host FROM mysql.user; >>> ? ? ? then for the user that match the Host (name or IP address) of your >> LORIS >>> ? ? ? (Apache) server >>> ? ? ? SHOW grants for 'lorismysql'@''; >>> >>> ? ? ? M????lanie >>> >>> ? ? ? >> -------------------------------------------------------------------------- >>> >>> ? ? ? From: Julie Ashworth, HWNI Computing Support >> >>> ? ? ? Sent: November 8, 2019 21:04 >>> ? ? ? To: Christine Rogers, Ms. >>> ? ? ? Cc: Ioannis Pappas ; Melanie Legault, Mrs >>> ? ? ? ; loris-dev at bic.mni.mcgill.ca >>> ? ? ? >>> ? ? ? Subject: Re: [Loris-dev] loris server >>> ? ? ? ??? >>> ? ? ? thanks Christine, >>> >>> ? ? ? yes, it's the lorismysql user in the config.xml file. >>> ? ? ? ??? ??? ??? ??? ??? ??? ??? lorismysql >>> ? ? ? ??? ??? ??? ??? ??? ??? ??? loris_database >>> ? ? ? ??? ??? ??? ??? ??? ??? ??? lorismysql >>> >>> ? ? ? we appeciate your help troubleshooting this. >>> ? ? ? best, >>> ? ? ? Julie >>> >>> ? ? ? On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote: >>> ? ? ? >??? ??? ??? Hi Ioannis, >>> ? ? ? >??? ??? ??? Could you open your file called config.xml >>> ? ? ? >??? ??? ??? (/srv/www/loris/project/config.xml) and confirm for us --??? >> which user >>> ? ? ? >??? ??? ??? credential is stored there, and what's the name of the >> database it is >>> ? ? ? >??? ??? ??? connecting to? >>> ? ? ? >??? ??? ??? This is the mysql user which connects to the database from >> the front >>> ? ? ? end >>> ? ? ? >??? ??? ??? of LORIS.??? >>> ? ? ? >??? ??? ??? If this user has insufficient privileges on your database, >> that would >>> ? ? ? >??? ??? ??? cause the errors you are seeing.??? I had assumed from your >> thread it >>> ? ? ? was >>> ? ? ? >??? ??? ??? your lorismysql user but it sounds like this should be >> verified. >>> ? ? ? >??? ??? ??? Let us know, and we'll keep following up when we come back >> online >>> ? ? ? after >>> ? ? ? >??? ??? ??? the weekend, >>> ? ? ? >??? ??? ??? Best, >>> ? ? ? >??? ??? ??? Christine >>> ? ? ? >??? ??? ??? On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas >> >>> ? ? ? >??? ??? ??? wrote: >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? Hi Melanie. >>> ? ? ? >??? ??? ??? ??? ??? Thank you for taking the time to reply to this. I took >> some to >>> ? ? ? consider >>> ? ? ? >??? ??? ??? ??? ??? your comments. Unfortunately as I said to Christine we >> are unable >>> ? ? ? to do >>> ? ? ? >??? ??? ??? ??? ??? any kind of updating to the database (either that is >> changing the >>> ? ? ? name >>> ? ? ? >??? ??? ??? ??? ??? or changing the small html description, etc.). >>> ? ? ? >??? ??? ??? ??? ??? Based on some more digging and on some of Christine's >> comments I >>> ? ? ? have a >>> ? ? ? >??? ??? ??? ??? ??? feeling that our lorisweb front-end, admin user cannot >> write >>> ? ? ? anything to >>> ? ? ? >??? ??? ??? ??? ??? the database. Along these lines could it be the case the >> lorismysql >>> ? ? ? user >>> ? ? ? >??? ??? ??? ??? ??? (the database, admin user with INSERT, UPDATE, etc >> privileges) is >>> ? ? ? not >>> ? ? ? >??? ??? ??? ??? ??? ???????????? > ???talking??????????? to the lorisweb front end user? >> What is the >>> ? ? ? difference between >>> ? ? ? >??? ??? ??? ??? ??? the two and could it be a installation problem for them >> not talking >>> ? ? ? to >>> ? ? ? >??? ??? ??? ??? ??? each other? As Julie said, lorismysql user is working >> normally with >>> ? ? ? >??? ??? ??? ??? ??? MariaDB. >>> ? ? ? >??? ??? ??? ??? ??? Thank you again for your help. >>> ? ? ? >??? ??? ??? ??? ??? Best wishes, >>> ? ? ? >??? ??? ??? ??? ??? Ioannis >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Hello, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Changing the project name in the configuration page >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ([1]https://loris.url/configuration/) of LORIS, only >> change the >>> ? ? ? title of >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? the project. To see this change, you have to log out >> of LORIS and >>> ? ? ? then >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? go back to the login page ([2]https://.loris.url/). >> This is the >>> ? ? ? only >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? place you can find the project name (except from the >>> ? ? ? configuration >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? page). See ProjectName.png >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? As for files permission, I would suggest a few change >> to improve >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? security of you server. Some extra permissions where >> granted to >>> ? ? ? help >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? you but are not needed. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? * /srv/www/loris/smarty/templates_c/??? should >> have ownership of >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? lorisadmin:httpd and permission 770 (or 775) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? * srv/www/loris/project/??? should have ownership >>> ? ? ? lorisadmin:httpd and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? permission 770 (775) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? * All other files under loris should have >> lorisadmin:lorisadmin >>> ? ? ? 755 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Reading through this change of mail, I understand >> that you let >>> ? ? ? Apache >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? store file in /srv/www/loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 31 | DownloadPath??? ??? | >> Downloads??? ??? | /srv/www/loris/??? ??? >>> ? ? ? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Where >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? files are downloaded >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Downloaded files should not be in the same tree as >> LORIS code. It >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? should be in a separate structure where Apache will >> not try and >>> ? ? ? do not >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? have permission (in httpd.conf) to execute files. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Kind regards, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? M????????lanie Legault | Software developer | Faculty of >> Medicine | >>> ? ? ? McGill >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? University??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? 3801 University, Montr????????al, QC H3A 2B4 >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? >>> ? ? ? >> ---------------------------------------------------------------------- >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? From: loris-dev-bounces at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? on behalf of >> Ioannis Pappas >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Sent: November 7, 2019 0:18 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? To: loris-dev at bic.mni.mcgill.ca >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Cc: Julie Ashworth, HWNI Computing Support >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ; Christine Rogers, Ms. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Subject: Re: [Loris-dev] loris server >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Hi Christine and Julie. >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Yes it looks like that any attempt to configure >> something in the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? front-end results in the same page. I am sending this >> to the list >>> ? ? ? (as >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? you requested Christine) alongside the >> troubleshooting and >>> ? ? ? discussion >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? so far with Julie. >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Best wishes, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Ioannis >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI >> Computing >>> ? ? ? Support >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > hi Christine and Ioannis, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > Ioannis, can you follow-up with Christine about >> using the >>> ? ? ? front-end? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > We're using CentOS7.7 and loris-21.0.1. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > I confirmed that I could login as the mysql user >> (lorismyqsl) >>> ? ? ? and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? change the 'url' config setting from >> '[3]http://loris.priv' to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? '[4]http://localhost', and back again. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > MariaDB [loris_database]> SELECT c.ConfigID, >> cs.Name, cs.Label, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? c.Value, cs.Description FROM Config c LEFT JOIN >> ConfigSettings cs >>> ? ? ? ON >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON >> (cs.Parent = >>> ? ? ? csp.ID) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? WHERE csp.Name = 'www'; >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > | ConfigID | Name??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >> Label??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Value??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >> Description??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 44 | host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >> Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? loris.priv??? ??? ??? ??? ??? ??? ??? | >> Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 45 | url??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> | Main LORIS URL??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? | [5]http://loris.priv | Main URL where LORIS can be >> accessed | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 46 | issue_tracker_url | Issue >> tracker URL | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? /issue_tracker??? ??? ??? | The *new* bug/issue tracker >> url??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > MariaDB [loris_database]> UPDATE Config SET >>> ? ? ? Value='[6]http://localhost' >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE >> Name='url'); >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > Rows matched: 1??? Changed: 1??? Warnings: 0 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > MariaDB [loris_database]> SELECT c.ConfigID, >> cs.Name, cs.Label, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? c.Value, cs.Description FROM Config c LEFT JOIN >> ConfigSettings cs >>> ? ? ? ON >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON >> (cs.Parent = >>> ? ? ? csp.ID) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? WHERE csp.Name = 'www'; >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > | ConfigID | Name??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >> Label??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Value??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >> Description??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 44 | host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >> Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? loris.priv??? ??? ??? ??? ??? ??? | >> Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 45 | url??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> | Main LORIS URL??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? | [7]http://localhost | Main URL where LORIS can be >> accessed | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 46 | issue_tracker_url | Issue >> tracker URL | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? /issue_tracker??? ??? | The *new* bug/issue tracker >> url??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > 3 rows in set (0.00 sec) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > best, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > Julie >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. >> wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Hi Julie, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Forgive my ambiguity - We run the community >> support listserv >>> ? ? ? for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? developers, project administrators and >> sysadmins setting up >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? LORIS, so that >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? these users can contact our technical team for >> exactly such >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? technical >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? help.??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? If it's ok with you, I'd encourage you >> subscribe to the >>> ? ? ? listserv >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? contact our technical team that way for the >> same reason. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? (Note that front-end users of LORIS typically >> contact their >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? project team >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? for support, rather than us.) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Given that your lorismysql user privileges >> seem appropriate >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? ('UPDATE" is >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? there, I mistyped 'INSERT" before) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? --??? is there any other indication why the >> database record is >>> ? ? ? not >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? updating???? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? In the front-end, can your 'admin' user effect >> any changes >>> ? ? ? in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? (any) Config >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? setting???? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? In the back-end, when you tried updating a >> field using your >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? lorismysql credential, what happened? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Your front end is loading ok, and you can log >> in there, if I >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? understood >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? correctly. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Thanks for letting us know these details at >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? [1]loris-dev at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Please also include what version of LORIS you >> are >>> ? ? ? installing, and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? on what >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? OS version. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Best, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Christine >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, >> HWNI >>> ? ? ? Computing >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Support >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? <[2]support-cirl at berkeley.edu> wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Thank you Christine, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? I'm the linux sysadmin who installed the >> loris database >>> ? ? ? for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Ioannis. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? I'm not a loris user, however, so that >> makes it a little >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? awkward for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? troubleshooting via the mailing list. I'm >> happy to help in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? whatever way >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? I can. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Regarding the database permissions, I ran: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? MariaDB [(none)]> show grants for >> 'lorismysql'@'%'; >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +--------------------------------------------------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | Grants for lorismysql@% >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +--------------------------------------------------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | GRANT USAGE ON *.* TO 'lorismysql'@'%' >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | GRANT SELECT, INSERT, UPDATE, DELETE ON >>> ? ? ? `loris_database`.* TO >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 'lorismysql'@'%' | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +--------------------------------------------------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 2 rows in set (0.00 sec) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? looking at the 'tips' section in the page >> you referred >>> ? ? ? to... >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 29 | >> base??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | Base??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? /srv/www/loris/??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? The base >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? filesystem path where LORIS is >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> installed??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 31 | DownloadPath??? ??? | >> Downloads??? ??? | >>> ? ? ? /srv/www/loris/??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Where >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? files are downloaded >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | ConfigID | >> Name??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | Label??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Value??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >> Description??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 44 | >> host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? loris.priv??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >> Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 45 | >> url??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | Main LORIS URL??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? [3]http://loris.priv | Main URL where >> LORIS can be >>> ? ? ? accessed | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 46 | issue_tracker_url | >> Issue tracker URL | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? /issue_tracker??? ??? ??? | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? The *new* bug/issue tracker url??? ??? ??? ??? ??? >> | >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> +----------+-------------------+-------------------+-------------------+--------------------------------------+ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? apache config: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Listen 80 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? User apache >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Group apache >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? DocumentRoot "/srv/www/loris/htdocs" >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? AllowOverride none >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Require all denied >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? AllowOverride All >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Options Indexes FollowSymLinks >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Require all granted >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Options Indexes FollowSymLinks >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? AllowOverride All >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Require all granted >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? file permissions: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? # ls -ld /srv/www/loris/smarty/templates_c >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? drwxrwxrwx 2 lorisadmin lorisadmin 4096 >> Oct 31 09:46 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? /srv/www/loris/smarty/templates_c/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? [root at loris loris]# ls -l >>> ? ? ? /srv/www/loris/smarty/templates_c >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 2444 >> Oct 31 09:46 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 10490 >> Sep 10 10:55 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 21126 >> Sep??? 7 18:39 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 3296 >> Sep??? 7 18:35 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 5901 >> Sep??? 7 21:10 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 23339 >> Sep??? 7 18:39 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? ??? 874 >> Sep 10 11:01 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 1101 >> Sep 10 10:58 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 18054 >> Sep 10 10:59 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 3590 >> Sep??? 7 18:39 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 25141 >> Sep??? 7 21:08 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? ??? 897 >> Sep??? 7 18:35 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 9210 >> Sep 10 11:01 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 8917 >> Sep 10 13:21 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 4811 >> Sep??? 7 18:35 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 3309 >> Sep 10 11:02 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 10303 >> Sep 10 10:59 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 12273 >> Sep??? 7 17:42 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >>> ? ? ? fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? thanks again! >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Julie >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? On 06-11-2019 19.01 +0000, Christine >> Rogers, Ms. wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Hi Ioannis,??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Thanks for your question.??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Given that the URL field is not updating, >> I suspect it's >>> ? ? ? a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? database >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? back-end issue.??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Can you verify -- Has your mysql user >> lorismysql??????????? been >>> ? ? ? granted >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? "INSERT" >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? privilege for the right database? If not, >> that would >>> ? ? ? result in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? an >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? error >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? like the kind you are seeing.??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Also, if you wish to check your LORIS >> Configuration >>> ? ? ? settings >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? in the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? backend database such as the URL field -- >> to see what was >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? actually >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? stored >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? in a given database field and should >> display in the >>> ? ? ? Config >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? module:??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? You can run the queries listed in the >> "Troubleshooting >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Configuration >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? settings" section of our Github-wiki >> Setup Guide (under >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Project >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Customization) :??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Lastly, this question is perfectly >> appropriate for the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? loris-dev >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? community >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? support listserv -- please [2]subscribe >> here and then >>> ? ? ? email >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? our >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? technical >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? team your next question at??????????? >>> ? ? ? [3][5]loris-dev at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? (after checking >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? any forwarded threads for sensitive >> info).??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? We prefer to answer technical questions >> there for the >>> ? ? ? benefit >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? of >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? community and other first-time users in >> the same position >>> ? ? ? as >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? yourself.??????????? ??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Thanks and cheers,??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Christine??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? On Mon, Nov 4, 2019 at 5:49 PM Dr. >> Ioannis Pappas PhD >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? <[4][6]ioannis at berkeley.edu> wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Hi Loris support.??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? My name is ioannis Pappas, a post-doc >> at the D'Esposito >>> ? ? ? lab >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? stroke group >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? at UC Berkeley. With the kind of help >> of our sys >>> ? ? ? admin??????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Julie >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? (cc'ed) we >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? have set up our loris database in our >> cluster (she is >>> ? ? ? the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? sudo >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? user and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? I am the admin user). >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? If you allow me, I would like to ask >> you about the >>> ? ? ? first >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? configuration >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? steps in the front end as they are >> described in the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? tutorial. We >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? can >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? login to [5][7]http://loris and the >> front end normally. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? However any update that I am trying >> to??????????? perform in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Admin->Configuration >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? doesn't work (e.g. updating the study >> name). It just >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? refreshes >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the same >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? page. I am just wondering if there is >> an issue with >>> ? ? ? writing >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? configuration file. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Here are the permissions setup for >> where Loris is >>> ? ? ? installed. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? chmod 777 >> /var/www/loris/smarty/templates_c >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? cd /srv/www/loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? chown -R lorisadmin:lorisadmin . >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? chmod -c -R a+r . >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? this command gives >> everyone read access, and >>> ? ? ? outputs >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? what >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? changes >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? were made: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? mode of >> ????????????????????./project???????????????????? changed from 0770 >>> ? ? ? (rwxrwx---) to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? 0774 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? (rwxrwxr--) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? mode of >> ????????????????????./tools/logs???????????????????? changed from 0770 >>> ? ? ? (rwxrwx---) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 0774 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? (rwxrwxr--) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? find . -type d -exec chmod a+x -c {} >> \; >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? this command gives >> everyone permission to open >>> ? ? ? a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? directory, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? outputs what changes were made: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? mode of >> ????????????????????./project???????????????????? changed from 0774 >>> ? ? ? (rwxrwxr--) to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? 0775 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? (rwxrwxr-x) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? mode of >> ????????????????????./tools/logs???????????????????? changed from 0774 >>> ? ? ? (rwxrwxr--) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 0775 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? (rwxrwxr-x) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Hopefully??????????? you can help me with >> this. I also >>> ? ? ? subscribed to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? mailing >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? list but I am not sure if this too >> much of a basic >>> ? ? ? question >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? list. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Best wishes, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Ioannis >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? On Mon, Nov 4, 2019 at 1:12 PM Julie >> Ashworth, HWNI >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Computing >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Support >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? <[6][8]support-cirl at berkeley.edu> >> wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? Hi ioannis, maybe it's best to >> ask the developers? >>> ? ? ? You can >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? cc >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? me if >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? you'd like. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? On Mon, Nov 4, 2019, 12:37 PM >> Ioannis Pappas >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? <[7][9]ioannis at berkeley.edu> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? That did the trick Julie. >> Thank you! >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? I am still trying to >> understand how configuration >>> ? ? ? works >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? though. For >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? example if I just try to >> change the name of the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? study from the front end, I >> get nowhere (it just >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? refreshes >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the same >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? page). >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? I am not sure if this >> requires write permissions >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? somewhere in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? config file/folder and >> that??????????????????????????????????????s why it >>> ? ? ? doesn??????????????????????????????????????t update >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? it. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Best wishes, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Ioannis >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > On Nov 4, 2019, at 12:08 >> PM, Julie Ashworth, HWNI >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Computing >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Support >> <[8][10]support-cirl at berkeley.edu> wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > just in case you're >> interested, these are the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? permission >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? changes I >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? made: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > chmod 777 >> /var/www/loris/smarty/templates_c >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > cd /srv/www/loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > chown -R >> lorisadmin:lorisadmin . >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > chmod -c -R a+r . >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? this command >> gives everyone read access, >>> ? ? ? and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? outputs >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? what >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? changes were made: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? mode of >> ????????????????????./project???????????????????? changed from >>> ? ? ? 0770 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? (rwxrwx---) to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 0774 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? (rwxrwxr--) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? mode of >> ????????????????????./tools/logs???????????????????? changed from >>> ? ? ? 0770 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? (rwxrwx---) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to 0774 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? (rwxrwxr--) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > find . -type d -exec chmod >> a+x -c {} \; >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? this command >> gives everyone permission to >>> ? ? ? open a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? directory, and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? outputs what changes were >> made: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? mode of >> ????????????????????./project???????????????????? changed from >>> ? ? ? 0774 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? (rwxrwxr--) to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 0775 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? (rwxrwxr-x) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? mode of >> ????????????????????./tools/logs???????????????????? changed from >>> ? ? ? 0774 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? (rwxrwxr--) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to 0775 >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? (rwxrwxr-x) >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > On 04-11-2019 12.03 -0800, >> Ioannis Pappas wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> Hi Julie. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> I just tried and I still >> don???t get anything. I >>> ? ? ? also >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? tried >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? private mode in Firefox in >> case the empty page was >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? cached. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> Sorry for this. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> Best wishes, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> Ioannis >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> On Nov 4, 2019, at 11:58 >> AM, Julie Ashworth, >>> ? ? ? HWNI >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Computing >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Support >> <[9][11]support-cirl at berkeley.edu> wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> hi Ioannis, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> no worries, I changed the >> following directory >>> ? ? ? to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? 777: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >> /var/www/loris/smarty/templates_c >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> will you please check if >> that works? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> thanks! >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> On 04-11-2019 11.49 >> -0800, Dr. Ioannis Pappas >>> ? ? ? PhD >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Hi Julie. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Apologies for >> bugging you with this again. >>> ? ? ? We >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? tried >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? now to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? access????????????????????? > ?? >> [1][10][12]http://loris????????????????????? > ?? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? and we are >> getting a????????????????????? > ?? blank page. I >>> ? ? ? think the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? reason >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? for this >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? is that we >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? don't have >> read????????????????????? > ?? permissions to read >>> ? ? ? from the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? template located >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? >> /var/www/loris/smarty See here bottom of >>> ? ? ? the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? page????????????????????? > ?? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? I think, in >> general, I am a little bit >>> ? ? ? confused >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? as to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? what the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? permissions >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? should be for us >> that are not sudos. My >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? understanding >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? is that >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? if we don't >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? have read or >> write permissions then we >>> ? ? ? can't >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? access or >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? write >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? /var/www/loris, >> meaning that we can't >>> ? ? ? access or >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? configure. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Should >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? everything be >> chmod 777 for example?????????????????????? > ?? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Thank you very >> much once again. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Best wishes, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Ioannis >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? On Thu, Oct 31, >> 2019 at 1:56 PM Dr. Ioannis >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Pappas PhD >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? >> <[3][12][14]ioannis at berkeley.edu> wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? Thank you >> very much Julie. I appreciate >>> ? ? ? this >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? and I >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? will dig >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? into Loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? given >> your changes. Thank you so much >>> ? ? ? for your >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? help. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? Best >> wishes, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? Ioannis >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? On Thu, >> Oct 31, 2019 at 12:48 PM Julie >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Ashworth, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? HWNI >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Computing Support >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? >> <[4][13][15]support-cirl at berkeley.edu> >>> ? ? ? wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> hi Ioannis, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> 1. I changed the permissions of >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? /srv/www/loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to be owned >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? by >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> lorisadmin. I reivewed my >>> ? ? ? installation >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? notes, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? and I did >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? this already >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> when >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? I >> installed the server. I'm not >>> ? ? ? sure why >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? they >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? changed, so >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? it's >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> probably a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> good idea to keep an eye on that. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> 2. When I installed the loris >>> ? ? ? software, I >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? also >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? installed a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? mysql >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> database as recommended in the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? instructions: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> projectname: LORIS >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> databasename: loris_database >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> mysqluser: lorismysql >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> frontend: lorisweb >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> 3. A couple of weeks ago, I moved >>> ? ? ? Henrik's >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? home >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? directory >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> /home/despoA, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> but I forgot to update loris. This >>> ? ? ? is done >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? now. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> best, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> Julie >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> On 31-10-2019 11.15 -0700, Dr. >>> ? ? ? Ioannis >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Pappas >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? PhD wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? Hi Julie. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? I hope you are well. We are >>> ? ? ? trying to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? configure loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? that you >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> kindly set >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? up for us. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? I have a couple of >>> ? ? ? questions for you if >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? you >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? allow me >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? so.????????????????????? > ?? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? 1) First, although we are >>> ? ? ? logging into >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? front end >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? with admin >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> username >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? (lorisweb) and password, it >>> ? ? ? seems that >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? any >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? kind of >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? update of >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> configuration >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? we are trying to do fails >>> ? ? ? (meaning that >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? if >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? we, say, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? change the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> name of the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? study and press "submit", >>> ? ? ? this doesn't >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? do >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? anything-it >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? doesn't >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> update). >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? It's almost like our >>> ? ? ? lorisweb user >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? doesn't >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? have write >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? privileges >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> in the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? /var/www/loris/project >>> ? ? ? (where I think >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? every >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? configuration should >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> be). >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? This generalizes for >>> ? ? ? everything that we >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? are >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? trying to do >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? in the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> front end. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? Clicking any instrument/tab >>> ? ? ? in the front >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? end >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? doesn't >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? really point >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? anything.????????????????????? > ?? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? 2) Loris suggest doing >>> ? ? ? configurations >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? via >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? SQL. Is it >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? possible to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> run SQL >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? scripts in the backend >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? 3) For some reason typing >>> ? ? ? ssh lors for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Henrik >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? doesn't >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? directly >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> take him to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? loris (it requires a >>> ? ? ? password that is >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? not the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? password >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? setup for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? lorisweb user). Will you be >>> ? ? ? able to fix >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? this >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? via your >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? sudo >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> privileges? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? Thank you very much in >>> ? ? ? advance for all >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? your >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? help Julie. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Let us >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> know if >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? this is something that >>> ? ? ? shouldn't be >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? directed >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to you (but >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? instead >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> to the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? loris people).????????????????????? > ?? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? Best wishes, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? Ioannis >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? On Mon, Sep 9, 2019 at 6:25 >>> ? ? ? PM Julie >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Ashworth, HWNI >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Computing >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> Support >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ????????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? <[1][5][14][16]support-cirl at berkeley.edu> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? wrote: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? hi Henrik and >>> ? ? ? Ioannis, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? the loris server >>> ? ? ? is available for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? you to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? use. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? The servername is >>> ? ? ? 'loris'. I >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? created a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? directory >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? called >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> /data/loris for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? you to store data. >>> ? ? ? You may create >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? new >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? folders in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? /data/loris to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> organize >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? your data. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? 1) secure shell or >>> ? ? ? secure copy: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? You can log in >>> ? ? ? with the 'ssh' or >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? 'scp' >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? command from >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? your remote >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> desktop >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? session. You don't >>> ? ? ? need to >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? authenticate >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to log in. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Maybe you'll >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> use scp >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? to transfer data >>> ? ? ? between your >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? cluster >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? account and the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> server? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? Please put the >>> ? ? ? data in /data/loris, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? so I >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? can make >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? backups more >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> easily. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? >>> ? ? ? secure shell: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? >>> ? ? ? $ ssh loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? >>> ? ? ? secure copy (change the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? names >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? in brackets). Let >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? me know if >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? I >> can >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? >>> ? ? ? help with syntax: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? >>> ? ? ? $ scp -r >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? loris:/data/loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? 2) front-end web >>> ? ? ? interface.????????????????????? > ????????????? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Open a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? web browser in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? your remote >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> desktop >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? session and enter >>> ? ? ? the hostname: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? >>> ? ? ? [2][6][15][17]http://loris >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? I created an admin >>> ? ? ? user called >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 'lorisweb'. I put the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? password >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> in >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? $HOME/newuser on >>> ? ? ? the cluster. To >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? see it, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? open a >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? terminal, and >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> run: >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? >>> ? ? ? $ cat $HOME/newuser >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? If other people >>> ? ? ? need shell access >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? to the >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? webserver, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? please let >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> me know >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? so I can create a >>> ? ? ? home directory >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? for >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? them. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? We should >>> ? ? ? eventually discuss >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? backups. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? best, >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? ????????????????????? > ???????????????? Julie >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> References >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? Visible links >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? 1. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? >> mailto:[7][16][18]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ????????????????????? > ???????????????? >> ????????????????????? > ???????????????? 2. [8][17][19]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? >> ---end quoted text--- >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> References >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Visible links >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 1. >> [18][20]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 2. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 3. >> mailto:[20][22]ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 4. >> mailto:[21][23]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 5. >> mailto:[22][24]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 6. >> [23][25]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 7. >> mailto:[24][26]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 8. >> [25][27]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> ---end quoted text--- >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > ---end quoted text--- >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? -- >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? [26][28]christine.rogers at mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? McGill Centre for Integrative >> Neuroscience | MCIN.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Montreal Neurological Institute >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? McGill University | Montreal | Canada >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> References >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Visible links >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 1. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? >> [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 2. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 3. mailto:[31]loris-dev at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 4. mailto:[32]ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 5. [33]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 6. mailto:[34]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 7. mailto:[35]ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 8. mailto:[36]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 9. mailto:[37]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 10. [38]http://xn--loris-7qa/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 11. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 12. mailto:[40]ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 13. mailto:[41]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 14. mailto:[42]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 15. [43]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 16. mailto:[44]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 17. [45]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 18. [46]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 19. >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 20. mailto:[48]ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 21. mailto:[49]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 22. mailto:[50]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 23. [51]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 24. mailto:[52]support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 25. [53]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 26. mailto:[54]christine.rogers at mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ---end quoted text--- >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? -- >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? [55]christine.rogers at mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? McGill Centre for Integrative Neuroscience | >> MCIN.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Montreal Neurological Institute >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? McGill University | Montreal | Canada >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> References >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Visible links >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 1. [8]mailto:loris-dev at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 2. [9]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 3. [10]http://loris.priv/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? 4. >>> ? ? ? >> [11]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 5. [12]mailto:loris-dev at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 6. [13]mailto:ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 7. [14]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 8. [15]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 9. [16]mailto:ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 10. [17]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 11. [18]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 12. [19]http://xn--loris-era/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 13. >>> ? ? ? [20]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 14. [21]mailto:ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 15. [22]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 16. [23]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 17. [24]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 18. [25]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 19. [26]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 20. [27]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 21. >>> ? ? ? [28]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 22. [29]mailto:ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 23. [30]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 24. [31]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 25. [32]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 26. [33]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 27. [34]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 28. [35]mailto:christine.rogers at mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? 29. >>> ? ? ? >> [36]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 30. >>> ? ? ? [37]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 31. [38]mailto:loris-dev at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 32. [39]mailto:ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 33. [40]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 34. [41]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 35. [42]mailto:ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 36. [43]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 37. [44]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 38. [45]http://xn--loris-7qa/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 39. >>> ? ? ? [46]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 40. [47]mailto:ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 41. [48]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 42. [49]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 43. [50]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 44. [51]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 45. [52]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 46. [53]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 47. >>> ? ? ? [54]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 48. [55]mailto:ioannis at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 49. [56]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 50. [57]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 51. [58]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 52. [59]mailto:support-cirl at berkeley.edu >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 53. [60]http://loris/ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 54. [61]mailto:christine.rogers at mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 55. [62]mailto:christine.rogers at mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? > ---end quoted text--- >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? _______________________________________________ >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Loris-dev mailing list >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? Loris-dev at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >> [63]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> ? ? ? >??? ??? ??? ??? ??? ??? ??? >>> ? ? ? > >>> ? ? ? >??? ??? ??? ??? ??? _______________________________________________ >>> ? ? ? >??? ??? ??? ??? ??? Loris-dev mailing list >>> ? ? ? >??? ??? ??? ??? ??? Loris-dev at bic.mni.mcgill.ca >>> ? ? ? >??? ??? ??? ??? ??? >> [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> ? ? ? > >>> ? ? ? >??? ??? ??? -- >>> ? ? ? >??? ??? ??? christine.rogers at mcgill.ca >>> ? ? ? >??? ??? ??? McGill Centre for Integrative Neuroscience | MCIN.ca >>> ? ? ? >??? ??? ??? Montreal Neurological Institute >>> ? ? ? >??? ??? ??? McGill University | Montreal | Canada >>> ? ? ? ---end quoted text--- >>> >>> References >>> >>> ? ? ? Visible links >>> ? ? ? 1. [2]https://loris.url/configuration/ >>> ? ? ? 2. [3]https://.loris.url/ >>> ? ? ? 3. [4]http://loris.priv/ >>> ? ? ? 4. [5]http://localhost/ >>> ? ? ? 5. [6]http://loris.priv/ >>> ? ? ? 6. [7]http://localhost/ >>> ? ? ? 7. [8]http://localhost/ >>> ? ? ? 8. [9]mailto:loris-dev at bic.mni.mcgill.ca >>> ? ? ? 9. [10]mailto:support-cirl at berkeley.edu >>> ? ? 10. [11]http://loris.priv/ >>> ? ? 11. >> [12]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> ? ? 12. [13]mailto:loris-dev at bic.mni.mcgill.ca >>> ? ? 13. [14]mailto:ioannis at berkeley.edu >>> ? ? 14. [15]http://loris/ >>> ? ? 15. [16]mailto:support-cirl at berkeley.edu >>> ? ? 16. [17]mailto:ioannis at berkeley.edu >>> ? ? 17. [18]mailto:support-cirl at berkeley.edu >>> ? ? 18. [19]mailto:support-cirl at berkeley.edu >>> ? ? 19. [20]http://xn--loris-era/ >>> ? ? 20. [21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? 21. [22]mailto:ioannis at berkeley.edu >>> ? ? 22. [23]mailto:support-cirl at berkeley.edu >>> ? ? 23. [24]mailto:support-cirl at berkeley.edu >>> ? ? 24. [25]http://loris/ >>> ? ? 25. [26]mailto:support-cirl at berkeley.edu >>> ? ? 26. [27]http://loris/ >>> ? ? 27. [28]http://loris/ >>> ? ? 28. [29]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? 29. [30]mailto:ioannis at berkeley.edu >>> ? ? 30. [31]mailto:support-cirl at berkeley.edu >>> ? ? 31. [32]mailto:support-cirl at berkeley.edu >>> ? ? 32. [33]http://loris/ >>> ? ? 33. [34]mailto:support-cirl at berkeley.edu >>> ? ? 34. [35]http://loris/ >>> ? ? 35. [36]mailto:christine.rogers at mcgill.ca >>> ? ? 36. >> [37]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >>> ? ? 37. [38]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> ? ? 38. [39]mailto:loris-dev at bic.mni.mcgill.ca >>> ? ? 39. [40]mailto:ioannis at berkeley.edu >>> ? ? 40. [41]http://loris/ >>> ? ? 41. [42]mailto:support-cirl at berkeley.edu >>> ? ? 42. [43]mailto:ioannis at berkeley.edu >>> ? ? 43. [44]mailto:support-cirl at berkeley.edu >>> ? ? 44. [45]mailto:support-cirl at berkeley.edu >>> ? ? 45. [46]http://xn--loris-7qa/ >>> ? ? 46. [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? 47. [48]mailto:ioannis at berkeley.edu >>> ? ? 48. [49]mailto:support-cirl at berkeley.edu >>> ? ? 49. [50]mailto:support-cirl at berkeley.edu >>> ? ? 50. [51]http://loris/ >>> ? ? 51. [52]mailto:support-cirl at berkeley.edu >>> ? ? 52. [53]http://loris/ >>> ? ? 53. [54]http://loris/ >>> ? ? 54. [55]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >>> ? ? 55. [56]mailto:ioannis at berkeley.edu >>> ? ? 56. [57]mailto:support-cirl at berkeley.edu >>> ? ? 57. [58]mailto:support-cirl at berkeley.edu >>> ? ? 58. [59]http://loris/ >>> ? ? 59. [60]mailto:support-cirl at berkeley.edu >>> ? ? 60. [61]http://loris/ >>> ? ? 61. [62]mailto:christine.rogers at mcgill.ca >>> ? ? 62. [63]mailto:christine.rogers at mcgill.ca >>> ? ? 63. [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> ? ? 64. [65]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> ---end quoted text--- >> >> References >> >> Visible links >> 1. http://localhost/ >> 2. https://loris.url/configuration/ >> 3. https://.loris.url/ >> 4. http://loris.priv/ >> 5. http://localhost/ >> 6. http://loris.priv/ >> 7. http://localhost/ >> 8. http://localhost/ >> 9. mailto:loris-dev at bic.mni.mcgill.ca >> 10. mailto:support-cirl at berkeley.edu >> 11. http://loris.priv/ >> 12. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >> 13. mailto:loris-dev at bic.mni.mcgill.ca >> 14. mailto:ioannis at berkeley.edu >> 15. http://loris/ >> 16. mailto:support-cirl at berkeley.edu >> 17. mailto:ioannis at berkeley.edu >> 18. mailto:support-cirl at berkeley.edu >> 19. mailto:support-cirl at berkeley.edu >> 20. http://xn--loris-era/ >> 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 22. mailto:ioannis at berkeley.edu >> 23. mailto:support-cirl at berkeley.edu >> 24. mailto:support-cirl at berkeley.edu >> 25. http://loris/ >> 26. mailto:support-cirl at berkeley.edu >> 27. http://loris/ >> 28. http://loris/ >> 29. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 30. mailto:ioannis at berkeley.edu >> 31. mailto:support-cirl at berkeley.edu >> 32. mailto:support-cirl at berkeley.edu >> 33. http://loris/ >> 34. mailto:support-cirl at berkeley.edu >> 35. http://loris/ >> 36. mailto:christine.rogers at mcgill.ca >> 37. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings >> 38. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> 39. mailto:loris-dev at bic.mni.mcgill.ca >> 40. mailto:ioannis at berkeley.edu >> 41. http://loris/ >> 42. mailto:support-cirl at berkeley.edu >> 43. mailto:ioannis at berkeley.edu >> 44. mailto:support-cirl at berkeley.edu >> 45. mailto:support-cirl at berkeley.edu >> 46. http://xn--loris-7qa/ >> 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 48. mailto:ioannis at berkeley.edu >> 49. mailto:support-cirl at berkeley.edu >> 50. mailto:support-cirl at berkeley.edu >> 51. http://loris/ >> 52. mailto:support-cirl at berkeley.edu >> 53. http://loris/ >> 54. http://loris/ >> 55. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief >> 56. mailto:ioannis at berkeley.edu >> 57. mailto:support-cirl at berkeley.edu >> 58. mailto:support-cirl at berkeley.edu >> 59. http://loris/ >> 60. mailto:support-cirl at berkeley.edu >> 61. http://loris/ >> 62. mailto:christine.rogers at mcgill.ca >> 63. mailto:christine.rogers at mcgill.ca >> 64. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> 65. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > ---end quoted text--- From melanie.legault2 at mcgill.ca Tue Nov 12 07:06:51 2019 From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs) Date: Tue, 12 Nov 2019 12:06:51 +0000 Subject: [Loris-dev] loris server In-Reply-To: <20191112033026.GA5955@gaia.neuro.berkeley.edu> References: <20191107030327.GA7157@gaia.neuro.berkeley.edu> <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> <20191109020414.GB13279@nx6.priv> <20191111170342.GA4213@gaia.neuro.berkeley.edu> , <20191112033026.GA5955@gaia.neuro.berkeley.edu> Message-ID: Hello, Sorry, I didn't used the exact name of the parameter. It is . localhost lorismysql ... Also, in the config table, `url` should be `http://localhost/` with the slash at the end. Should not be the cause to the current problem. As for creating a new user, I don't think it will solve the problem. Could you ensure that in MariaDB, the user `lorismysql`@`localhost` have the update permission (select, insert, update, delete) on `loris_database`.* as well as usage on these tables. Also can you check which version of MariaDB you have? The version of MariaDB that come with CentOS 7 isn't supported for the latest versions of LORIS. We have instructions (not quite definitive yet) on how to install MariaDB 10.3 in the documentation for Release 22 that should be out soon. https://github.com/aces/Loris/blob/22.0-release/README.CentOS7.md Kind regards, M?lanie ________________________________ From: Julie Ashworth, HWNI Computing Support Sent: November 11, 2019 22:30 To: Melanie Legault, Mrs Cc: Christine Rogers, Ms. ; Ioannis Pappas ; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] loris server thanks Christine and Melanie - I updated the Config table settings (see below). Ioannis, can you please test if it works now? Melanie, I couldn't find a reference to dbHost in the config.xml file. The only reference to host that I could find is: # grep -i host /srv/www/loris/project/config.xml localhost %COUCH_HOSTNAME% MariaDB [loris_database]> SELECT c.ConfigID, cs.Name, cs.Label, c.Value, cs.Description FROM Config c LEFT JOIN ConfigSettings cs ON (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON (cs.Parent = csp.ID) WHERE csp.Name = 'www'; +----------+-------------------+-------------------+------------------+--------------------------------------+ | ConfigID | Name | Label | Value | Description | +----------+-------------------+-------------------+------------------+--------------------------------------+ | 44 | host | Host | localhost | Host | | 45 | url | Main LORIS URL | http://localhost | Main URL where LORIS can be accessed | | 46 | issue_tracker_url | Issue tracker URL | /issue_tracker | The *new* bug/issue tracker url | +----------+-------------------+-------------------+------------------+--------------------------------------+ thanks! Julie On 11-11-2019 17.28 +0000, Melanie Legault, Mrs wrote: > Hello Julie, > Yes, the '%' sign is a wildcard for 'all host'. So it should be good but I > had problem with that in the past. > Could you ensure the 'lorismysql'@'localhost' user proper permissions. > > Also, in that case, in the config.xml file, the dbHost should be > 'localhost'. MySQL treat 127.0.0.1 and localhost as 2 different host. > > M??lanie > > -------------------------------------------------------------------------- > > From: Julie Ashworth, HWNI Computing Support > Sent: November 11, 2019 12:03 > To: Melanie Legault, Mrs > Cc: Christine Rogers, Ms. ; Ioannis Pappas > ; loris-dev at bic.mni.mcgill.ca > > Subject: Re: [Loris-dev] loris server > ? > thanks Melanie, > I'm including the output below. My understanding is that '%' matches all > hostnames. Should I specifically grant permission to 'loris.priv' from > user lorismysql? Or perhaps you recommend changing loris_database entries > ('host' to 'localhost' and 'url' to '[1]http://localhost')? > thanks! > > MariaDB [(none)]> SELECT User, Host FROM mysql.user; > +------------+-----------+ > | User? ? ? ? ? ? | Host? ? ? ? ? | > +------------+-----------+ > | lorismysql | %? ? ? ? ? ? ? ? | > | root? ? ? ? ? ? | 127.0.0.1 | > | root? ? ? ? ? ? | ::1? ? ? ? ? ? | > | lorismysql | localhost | > | root? ? ? ? ? ? | localhost | > +------------+-----------+ > 5 rows in set (0.00 sec) > > MariaDB [(none)]> SHOW grants for 'lorismysql'@'%'; > +--------------------------------------------------------------------------------+ > | Grants for lorismysql@% > +--------------------------------------------------------------------------------+ > | GRANT USAGE ON *.* TO 'lorismysql'@'%' > | GRANT SELECT, INSERT, UPDATE, DELETE ON `loris_database`.* TO > 'lorismysql'@'%' | > +--------------------------------------------------------------------------------+ > 2 rows in set (0.00 sec) > > On 11-11-2019 15.47 +0000, Melanie Legault, Mrs wrote: > >? ? ? Hello Julie, > >? ? ? Could it be that your MySQL 'lorismysql' user have different > permissions > >? ? ? depending on where it is connecting to the DB? > >? ? ? A database admin (root) can check this for you. > >? ? ? SELECT User, Host FROM mysql.user; > >? ? ? then for the user that match the Host (name or IP address) of your > LORIS > >? ? ? (Apache) server > >? ? ? SHOW grants for 'lorismysql'@''; > > > >? ? ? M????lanie > > > >? ? ? > -------------------------------------------------------------------------- > > > >? ? ? From: Julie Ashworth, HWNI Computing Support > > >? ? ? Sent: November 8, 2019 21:04 > >? ? ? To: Christine Rogers, Ms. > >? ? ? Cc: Ioannis Pappas ; Melanie Legault, Mrs > >? ? ? ; loris-dev at bic.mni.mcgill.ca > >? ? ? > >? ? ? Subject: Re: [Loris-dev] loris server > >? ? ? ??? > >? ? ? thanks Christine, > > > >? ? ? yes, it's the lorismysql user in the config.xml file. > >? ? ? ??? ??? ??? ??? ??? ??? ??? lorismysql > >? ? ? ??? ??? ??? ??? ??? ??? ??? loris_database > >? ? ? ??? ??? ??? ??? ??? ??? ??? lorismysql > > > >? ? ? we appeciate your help troubleshooting this. > >? ? ? best, > >? ? ? Julie > > > >? ? ? On 08-11-2019 23.20 +0000, Christine Rogers, Ms. wrote: > >? ? ? >??? ??? ??? Hi Ioannis, > >? ? ? >??? ??? ??? Could you open your file called config.xml > >? ? ? >??? ??? ??? (/srv/www/loris/project/config.xml) and confirm for us --??? > which user > >? ? ? >??? ??? ??? credential is stored there, and what's the name of the > database it is > >? ? ? >??? ??? ??? connecting to? > >? ? ? >??? ??? ??? This is the mysql user which connects to the database from > the front > >? ? ? end > >? ? ? >??? ??? ??? of LORIS.??? > >? ? ? >??? ??? ??? If this user has insufficient privileges on your database, > that would > >? ? ? >??? ??? ??? cause the errors you are seeing.??? I had assumed from your > thread it > >? ? ? was > >? ? ? >??? ??? ??? your lorismysql user but it sounds like this should be > verified. > >? ? ? >??? ??? ??? Let us know, and we'll keep following up when we come back > online > >? ? ? after > >? ? ? >??? ??? ??? the weekend, > >? ? ? >??? ??? ??? Best, > >? ? ? >??? ??? ??? Christine > >? ? ? >??? ??? ??? On Fri, Nov 8, 2019 at 5:31 PM Ioannis Pappas > > >? ? ? >??? ??? ??? wrote: > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? Hi Melanie. > >? ? ? >??? ??? ??? ??? ??? Thank you for taking the time to reply to this. I took > some to > >? ? ? consider > >? ? ? >??? ??? ??? ??? ??? your comments. Unfortunately as I said to Christine we > are unable > >? ? ? to do > >? ? ? >??? ??? ??? ??? ??? any kind of updating to the database (either that is > changing the > >? ? ? name > >? ? ? >??? ??? ??? ??? ??? or changing the small html description, etc.). > >? ? ? >??? ??? ??? ??? ??? Based on some more digging and on some of Christine's > comments I > >? ? ? have a > >? ? ? >??? ??? ??? ??? ??? feeling that our lorisweb front-end, admin user cannot > write > >? ? ? anything to > >? ? ? >??? ??? ??? ??? ??? the database. Along these lines could it be the case the > lorismysql > >? ? ? user > >? ? ? >??? ??? ??? ??? ??? (the database, admin user with INSERT, UPDATE, etc > privileges) is > >? ? ? not > >? ? ? >??? ??? ??? ??? ??? ????????????????talking??????????? to the lorisweb front end user? > What is the > >? ? ? difference between > >? ? ? >??? ??? ??? ??? ??? the two and could it be a installation problem for them > not talking > >? ? ? to > >? ? ? >??? ??? ??? ??? ??? each other? As Julie said, lorismysql user is working > normally with > >? ? ? >??? ??? ??? ??? ??? MariaDB. > >? ? ? >??? ??? ??? ??? ??? Thank you again for your help. > >? ? ? >??? ??? ??? ??? ??? Best wishes, > >? ? ? >??? ??? ??? ??? ??? Ioannis > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? On Nov 7, 2019, at 4:33 AM, Melanie Legault, Mrs > >? ? ? >??? ??? ??? ??? ??? ??? ??? wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? Hello, > >? ? ? >??? ??? ??? ??? ??? ??? ??? Changing the project name in the configuration page > >? ? ? >??? ??? ??? ??? ??? ??? ??? ([1]https://loris.url/configuration/) of LORIS, only > change the > >? ? ? title of > >? ? ? >??? ??? ??? ??? ??? ??? ??? the project. To see this change, you have to log out > of LORIS and > >? ? ? then > >? ? ? >??? ??? ??? ??? ??? ??? ??? go back to the login page ([2]https://.loris.url/). > This is the > >? ? ? only > >? ? ? >??? ??? ??? ??? ??? ??? ??? place you can find the project name (except from the > >? ? ? configuration > >? ? ? >??? ??? ??? ??? ??? ??? ??? page). See ProjectName.png > >? ? ? >??? ??? ??? ??? ??? ??? ??? As for files permission, I would suggest a few change > to improve > >? ? ? >??? ??? ??? ??? ??? ??? ??? security of you server. Some extra permissions where > granted to > >? ? ? help > >? ? ? >??? ??? ??? ??? ??? ??? ??? you but are not needed. > >? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? * /srv/www/loris/smarty/templates_c/??? should > have ownership of > >? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? lorisadmin:httpd and permission 770 (or 775) > >? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? * srv/www/loris/project/??? should have ownership > >? ? ? lorisadmin:httpd and > >? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? permission 770 (775) > >? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? * All other files under loris should have > lorisadmin:lorisadmin > >? ? ? 755 > >? ? ? >??? ??? ??? ??? ??? ??? ??? Reading through this change of mail, I understand > that you let > >? ? ? Apache > >? ? ? >??? ??? ??? ??? ??? ??? ??? store file in /srv/www/loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 31 | DownloadPath??? ??? | > Downloads??? ??? | /srv/www/loris/??? ??? > >? ? ? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? Where > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? files are downloaded > >? ? ? >??? ??? ??? ??? ??? ??? ??? Downloaded files should not be in the same tree as > LORIS code. It > >? ? ? >??? ??? ??? ??? ??? ??? ??? should be in a separate structure where Apache will > not try and > >? ? ? do not > >? ? ? >??? ??? ??? ??? ??? ??? ??? have permission (in httpd.conf) to execute files. > >? ? ? >??? ??? ??? ??? ??? ??? ??? Kind regards, > >? ? ? >??? ??? ??? ??? ??? ??? ??? M????????lanie Legault | Software developer | Faculty of > Medicine | > >? ? ? McGill > >? ? ? >??? ??? ??? ??? ??? ??? ??? University??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? 3801 University, Montr????????al, QC H3A 2B4 > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? > >? ? ? > ---------------------------------------------------------------------- > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? From: loris-dev-bounces at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? on behalf of > Ioannis Pappas > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? Sent: November 7, 2019 0:18 > >? ? ? >??? ??? ??? ??? ??? ??? ??? To: loris-dev at bic.mni.mcgill.ca > > >? ? ? >??? ??? ??? ??? ??? ??? ??? Cc: Julie Ashworth, HWNI Computing Support > >? ? ? >??? ??? ??? ??? ??? ??? ??? ; Christine Rogers, Ms. > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? Subject: Re: [Loris-dev] loris server > >? ? ? >??? ??? ??? ??? ??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? Hi Christine and Julie. > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? Yes it looks like that any attempt to configure > something in the > >? ? ? >??? ??? ??? ??? ??? ??? ??? front-end results in the same page. I am sending this > to the list > >? ? ? (as > >? ? ? >??? ??? ??? ??? ??? ??? ??? you requested Christine) alongside the > troubleshooting and > >? ? ? discussion > >? ? ? >??? ??? ??? ??? ??? ??? ??? so far with Julie. > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? Best wishes, > >? ? ? >??? ??? ??? ??? ??? ??? ??? Ioannis > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > On Nov 6, 2019, at 7:03 PM, Julie Ashworth, HWNI > Computing > >? ? ? Support > >? ? ? >??? ??? ??? ??? ??? ??? ??? wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > hi Christine and Ioannis, > >? ? ? >??? ??? ??? ??? ??? ??? ??? > Ioannis, can you follow-up with Christine about > using the > >? ? ? front-end? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > We're using CentOS7.7 and loris-21.0.1. > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > I confirmed that I could login as the mysql user > (lorismyqsl) > >? ? ? and > >? ? ? >??? ??? ??? ??? ??? ??? ??? change the 'url' config setting from > '[3]http://loris.priv' to > >? ? ? >??? ??? ??? ??? ??? ??? ??? '[4]http://localhost', and back again. > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > MariaDB [loris_database]> SELECT c.ConfigID, > cs.Name, cs.Label, > >? ? ? >??? ??? ??? ??? ??? ??? ??? c.Value, cs.Description FROM Config c LEFT JOIN > ConfigSettings cs > >? ? ? ON > >? ? ? >??? ??? ??? ??? ??? ??? ??? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON > (cs.Parent = > >? ? ? csp.ID) > >? ? ? >??? ??? ??? ??? ??? ??? ??? WHERE csp.Name = 'www'; > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? > | ConfigID | Name??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > Label??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? Value??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > Description??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 44 | host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? loris.priv??? ??? ??? ??? ??? ??? ??? | > Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 45 | url??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > | Main LORIS URL??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? | [5]http://loris.priv | Main URL where LORIS can be > accessed | > >? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 46 | issue_tracker_url | Issue > tracker URL | > >? ? ? >??? ??? ??? ??? ??? ??? ??? /issue_tracker??? ??? ??? | The *new* bug/issue tracker > url??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > MariaDB [loris_database]> UPDATE Config SET > >? ? ? Value='[6]http://localhost' > >? ? ? >??? ??? ??? ??? ??? ??? ??? WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE > Name='url'); > >? ? ? >??? ??? ??? ??? ??? ??? ??? > Rows matched: 1??? Changed: 1??? Warnings: 0 > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > MariaDB [loris_database]> SELECT c.ConfigID, > cs.Name, cs.Label, > >? ? ? >??? ??? ??? ??? ??? ??? ??? c.Value, cs.Description FROM Config c LEFT JOIN > ConfigSettings cs > >? ? ? ON > >? ? ? >??? ??? ??? ??? ??? ??? ??? (c.ConfigID = cs.ID) JOIN ConfigSettings csp ON > (cs.Parent = > >? ? ? csp.ID) > >? ? ? >??? ??? ??? ??? ??? ??? ??? WHERE csp.Name = 'www'; > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? > | ConfigID | Name??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > Label??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? Value??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > Description??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 44 | host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? loris.priv??? ??? ??? ??? ??? ??? | > Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 45 | url??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > | Main LORIS URL??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? | [7]http://localhost | Main URL where LORIS can be > accessed | > >? ? ? >??? ??? ??? ??? ??? ??? ??? > |??? ??? ??? ??? ??? ??? 46 | issue_tracker_url | Issue > tracker URL | > >? ? ? >??? ??? ??? ??? ??? ??? ??? /issue_tracker??? ??? | The *new* bug/issue tracker > url??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? > 3 rows in set (0.00 sec) > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > best, > >? ? ? >??? ??? ??? ??? ??? ??? ??? > Julie > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? > On 06-11-2019 21.43 +0000, Christine Rogers, Ms. > wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Hi Julie, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Forgive my ambiguity - We run the community > support listserv > >? ? ? for > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? developers, project administrators and > sysadmins setting up > >? ? ? >??? ??? ??? ??? ??? ??? ??? LORIS, so that > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? these users can contact our technical team for > exactly such > >? ? ? >??? ??? ??? ??? ??? ??? ??? technical > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? help.??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? If it's ok with you, I'd encourage you > subscribe to the > >? ? ? listserv > >? ? ? >??? ??? ??? ??? ??? ??? ??? and > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? contact our technical team that way for the > same reason. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? (Note that front-end users of LORIS typically > contact their > >? ? ? >??? ??? ??? ??? ??? ??? ??? project team > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? for support, rather than us.) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Given that your lorismysql user privileges > seem appropriate > >? ? ? >??? ??? ??? ??? ??? ??? ??? ('UPDATE" is > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? there, I mistyped 'INSERT" before) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? --??? is there any other indication why the > database record is > >? ? ? not > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? updating???? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? In the front-end, can your 'admin' user effect > any changes > >? ? ? in > >? ? ? >??? ??? ??? ??? ??? ??? ??? (any) Config > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? setting???? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? In the back-end, when you tried updating a > field using your > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? lorismysql credential, what happened? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Your front end is loading ok, and you can log > in there, if I > >? ? ? >??? ??? ??? ??? ??? ??? ??? understood > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? correctly. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Thanks for letting us know these details at > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? [1]loris-dev at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Please also include what version of LORIS you > are > >? ? ? installing, and > >? ? ? >??? ??? ??? ??? ??? ??? ??? on what > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? OS version. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Best, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Christine > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? On Wed, Nov 6, 2019 at 3:31 PM Julie Ashworth, > HWNI > >? ? ? Computing > >? ? ? >??? ??? ??? ??? ??? ??? ??? Support > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? <[2]support-cirl at berkeley.edu> wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Thank you Christine, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? I'm the linux sysadmin who installed the > loris database > >? ? ? for > >? ? ? >??? ??? ??? ??? ??? ??? ??? Ioannis. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? I'm not a loris user, however, so that > makes it a little > >? ? ? >??? ??? ??? ??? ??? ??? ??? awkward for > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? troubleshooting via the mailing list. I'm > happy to help in > >? ? ? >??? ??? ??? ??? ??? ??? ??? whatever way > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? I can. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Regarding the database permissions, I ran: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? MariaDB [(none)]> show grants for > 'lorismysql'@'%'; > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | Grants for lorismysql@% > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | GRANT USAGE ON *.* TO 'lorismysql'@'%' > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | GRANT SELECT, INSERT, UPDATE, DELETE ON > >? ? ? `loris_database`.* TO > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 'lorismysql'@'%' | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +--------------------------------------------------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 2 rows in set (0.00 sec) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? looking at the 'tips' section in the page > you referred > >? ? ? to... > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 29 | > base??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | Base??? ??? ??? ??? ??? ??? ??? | > >? ? ? /srv/www/loris/??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? The base > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? filesystem path where LORIS is > >? ? ? >??? ??? ??? ??? ??? ??? ??? > installed??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 31 | DownloadPath??? ??? | > Downloads??? ??? | > >? ? ? /srv/www/loris/??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? Where > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? files are downloaded > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? | ConfigID | > Name??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | Label??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? Value??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > Description??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 44 | > host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? loris.priv??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > Host??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 45 | > url??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? ??? | Main LORIS URL??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? [3]http://loris.priv | Main URL where > LORIS can be > >? ? ? accessed | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? |??? ??? ??? ??? ??? ??? 46 | issue_tracker_url | > Issue tracker URL | > >? ? ? >??? ??? ??? ??? ??? ??? ??? /issue_tracker??? ??? ??? | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? The *new* bug/issue tracker url??? ??? ??? ??? ??? > | > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > +----------+-------------------+-------------------+-------------------+--------------------------------------+ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? apache config: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Listen 80 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? User apache > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Group apache > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? DocumentRoot "/srv/www/loris/htdocs" > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? AllowOverride none > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Require all denied > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? AllowOverride All > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Options Indexes FollowSymLinks > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Require all granted > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Options Indexes FollowSymLinks > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? AllowOverride All > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ??? ??? ??? ??? Require all granted > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? file permissions: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? # ls -ld /srv/www/loris/smarty/templates_c > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? drwxrwxrwx 2 lorisadmin lorisadmin 4096 > Oct 31 09:46 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? /srv/www/loris/smarty/templates_c/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? [root at loris loris]# ls -l > >? ? ? /srv/www/loris/smarty/templates_c > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 2444 > Oct 31 09:46 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > 0e1b94643329544102d69ebd990c8b0165d1bd0d_0.file.form_passwordexpiry.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 10490 > Sep 10 10:55 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > 195463768851669204bf65105fe4e81a03455b48_0.file.form_data_team_helper.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 21126 > Sep??? 7 18:39 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? 1ebadd1dabd19543319b9015a275a25fb3ea1271_0.file.main.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 3296 > Sep??? 7 18:35 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? 32a6e0e3cc0aee3715361b33919eac95c0bb9cdc_0.file.form_login.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 5901 > Sep??? 7 21:10 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > 5cdeb715e5ad48d381bf4ea25405f9bfe5b81533_0.file.form_my_preferences.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 23339 > Sep??? 7 18:39 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > 71d07644a1309b40189d42145f7042af6743e856_0.file.form_dashboard.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? ??? 874 > Sep 10 11:01 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? 82495f3f78d11898c2eb816f93ec7338caa5ca28_0.file.500.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 1101 > Sep 10 10:58 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > 981927c886552e58e58f493e3153d095d2fe5d66_0.file.form_instrument_builder.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 18054 > Sep 10 10:59 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > 9dc62269f6e5525550f5928a805017c5e110a582_0.file.menu_data_release.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 3590 > Sep??? 7 18:39 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? a03bc16552e4c92f220889e46134f8fe96caf2ea_0.file.progress_bar.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 25141 > Sep??? 7 21:08 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > a07d2701a4cda44e7ef7f6025b78e76f7b6e65c4_0.file.form_configuration.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? ??? 897 > Sep??? 7 18:35 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? a0b6f32d181ed65d471eea20abc4abbc40bf3469_0.file.404.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 9210 > Sep 10 11:01 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > a1c292c69532174e9aa753a48e112d4b0eb33594_0.file.menu_mri_violations.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 8917 > Sep 10 13:21 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? ae14f13d831988de3500d7174b53a47390649eb5_0.file.form_project.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 4811 > Sep??? 7 18:35 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? d1ca754a8d9c5ab253e43310722bf6504c17d6e1_0.file.public_layout.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin??? 3309 > Sep 10 11:02 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > d8ced7af9adee12c690eb2cc0d3ad5dc4ff54d10_0.file.form_statistics.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 10303 > Sep 10 10:59 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > e6424ba9933db2e98436eb3df00ea38ae63d7b18_0.file.menu_genomic_browser.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? -rw-r--r-- 1 lorisadmin lorisadmin 12273 > Sep??? 7 17:42 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > >? ? ? fb872a21af70c86930fd51b0f25275c1e0912249_0.file.install.tpl.php > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? thanks again! > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Julie > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? On 06-11-2019 19.01 +0000, Christine > Rogers, Ms. wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Hi Ioannis,??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Thanks for your question.??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Given that the URL field is not updating, > I suspect it's > >? ? ? a > >? ? ? >??? ??? ??? ??? ??? ??? ??? database > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? back-end issue.??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Can you verify -- Has your mysql user > lorismysql??????????? been > >? ? ? granted > >? ? ? >??? ??? ??? ??? ??? ??? ??? the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? "INSERT" > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? privilege for the right database? If not, > that would > >? ? ? result in > >? ? ? >??? ??? ??? ??? ??? ??? ??? an > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? error > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? like the kind you are seeing.??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Also, if you wish to check your LORIS > Configuration > >? ? ? settings > >? ? ? >??? ??? ??? ??? ??? ??? ??? in the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? backend database such as the URL field -- > to see what was > >? ? ? >??? ??? ??? ??? ??? ??? ??? actually > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? stored > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? in a given database field and should > display in the > >? ? ? Config > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? module:??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? You can run the queries listed in the > "Troubleshooting > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Configuration > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? settings" section of our Github-wiki > Setup Guide (under > >? ? ? >??? ??? ??? ??? ??? ??? ??? Project > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Customization) :??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > [1][4]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Lastly, this question is perfectly > appropriate for the > >? ? ? >??? ??? ??? ??? ??? ??? ??? loris-dev > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? community > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? support listserv -- please [2]subscribe > here and then > >? ? ? email > >? ? ? >??? ??? ??? ??? ??? ??? ??? our > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? technical > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? team your next question at??????????? > >? ? ? [3][5]loris-dev at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? (after checking > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? any forwarded threads for sensitive > info).??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? We prefer to answer technical questions > there for the > >? ? ? benefit > >? ? ? >??? ??? ??? ??? ??? ??? ??? of > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? community and other first-time users in > the same position > >? ? ? as > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? yourself.??????????? ??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Thanks and cheers,??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Christine??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? On Mon, Nov 4, 2019 at 5:49 PM Dr. > Ioannis Pappas PhD > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? <[4][6]ioannis at berkeley.edu> wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Hi Loris support.??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? My name is ioannis Pappas, a post-doc > at the D'Esposito > >? ? ? lab > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? stroke group > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? at UC Berkeley. With the kind of help > of our sys > >? ? ? admin??????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? Julie > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? (cc'ed) we > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? have set up our loris database in our > cluster (she is > >? ? ? the > >? ? ? >??? ??? ??? ??? ??? ??? ??? sudo > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? user and > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? I am the admin user). > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? If you allow me, I would like to ask > you about the > >? ? ? first > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? configuration > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? steps in the front end as they are > described in the > >? ? ? >??? ??? ??? ??? ??? ??? ??? tutorial. We > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? can > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? login to [5][7]http://loris and the > front end normally. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? However any update that I am trying > to??????????? perform in > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Admin->Configuration > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? doesn't work (e.g. updating the study > name). It just > >? ? ? >??? ??? ??? ??? ??? ??? ??? refreshes > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the same > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? page. I am just wondering if there is > an issue with > >? ? ? writing > >? ? ? >??? ??? ??? ??? ??? ??? ??? in > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? configuration file. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Here are the permissions setup for > where Loris is > >? ? ? installed. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? chmod 777 > /var/www/loris/smarty/templates_c > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? cd /srv/www/loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? chown -R lorisadmin:lorisadmin . > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? chmod -c -R a+r . > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? this command gives > everyone read access, and > >? ? ? outputs > >? ? ? >??? ??? ??? ??? ??? ??? ??? what > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? changes > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? were made: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? mode of > ????????????????????./project???????????????????? changed from 0770 > >? ? ? (rwxrwx---) to > >? ? ? >??? ??? ??? ??? ??? ??? ??? 0774 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? (rwxrwxr--) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? mode of > ????????????????????./tools/logs???????????????????? changed from 0770 > >? ? ? (rwxrwx---) > >? ? ? >??? ??? ??? ??? ??? ??? ??? to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 0774 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? (rwxrwxr--) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? find . -type d -exec chmod a+x -c {} > \; > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? this command gives > everyone permission to open > >? ? ? a > >? ? ? >??? ??? ??? ??? ??? ??? ??? directory, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? and > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? outputs what changes were made: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? mode of > ????????????????????./project???????????????????? changed from 0774 > >? ? ? (rwxrwxr--) to > >? ? ? >??? ??? ??? ??? ??? ??? ??? 0775 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? (rwxrwxr-x) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ?????????????? ?????????????? mode of > ????????????????????./tools/logs???????????????????? changed from 0774 > >? ? ? (rwxrwxr--) > >? ? ? >??? ??? ??? ??? ??? ??? ??? to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 0775 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? (rwxrwxr-x) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Hopefully??????????? you can help me with > this. I also > >? ? ? subscribed to > >? ? ? >??? ??? ??? ??? ??? ??? ??? the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? mailing > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? list but I am not sure if this too > much of a basic > >? ? ? question > >? ? ? >??? ??? ??? ??? ??? ??? ??? for > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? list. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Best wishes, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? Ioannis > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? On Mon, Nov 4, 2019 at 1:12 PM Julie > Ashworth, HWNI > >? ? ? >??? ??? ??? ??? ??? ??? ??? Computing > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Support > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? <[6][8]support-cirl at berkeley.edu> > wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? Hi ioannis, maybe it's best to > ask the developers? > >? ? ? You can > >? ? ? >??? ??? ??? ??? ??? ??? ??? cc > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? me if > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? you'd like. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? On Mon, Nov 4, 2019, 12:37 PM > Ioannis Pappas > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? <[7][9]ioannis at berkeley.edu> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? That did the trick Julie. > Thank you! > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? I am still trying to > understand how configuration > >? ? ? works > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? though. For > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? example if I just try to > change the name of the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? study from the front end, I > get nowhere (it just > >? ? ? >??? ??? ??? ??? ??? ??? ??? refreshes > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? the same > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? page). > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? I am not sure if this > requires write permissions > >? ? ? >??? ??? ??? ??? ??? ??? ??? somewhere in > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? a > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? config file/folder and > that??????????????????????????????????????s why it > >? ? ? doesn??????????????????????????????????????t update > >? ? ? >??? ??? ??? ??? ??? ??? ??? it. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Best wishes, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Ioannis > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > On Nov 4, 2019, at 12:08 > PM, Julie Ashworth, HWNI > >? ? ? >??? ??? ??? ??? ??? ??? ??? Computing > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Support > <[8][10]support-cirl at berkeley.edu> wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > just in case you're > interested, these are the > >? ? ? >??? ??? ??? ??? ??? ??? ??? permission > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? changes I > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? made: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > chmod 777 > /var/www/loris/smarty/templates_c > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > cd /srv/www/loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > chown -R > lorisadmin:lorisadmin . > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > chmod -c -R a+r . > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? this command > gives everyone read access, > >? ? ? and > >? ? ? >??? ??? ??? ??? ??? ??? ??? outputs > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? what > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? changes were made: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? mode of > ????????????????????./project???????????????????? changed from > >? ? ? 0770 > >? ? ? >??? ??? ??? ??? ??? ??? ??? (rwxrwx---) to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 0774 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? (rwxrwxr--) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? mode of > ????????????????????./tools/logs???????????????????? changed from > >? ? ? 0770 > >? ? ? >??? ??? ??? ??? ??? ??? ??? (rwxrwx---) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to 0774 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? (rwxrwxr--) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > find . -type d -exec chmod > a+x -c {} \; > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? this command > gives everyone permission to > >? ? ? open a > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? directory, and > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? outputs what changes were > made: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? mode of > ????????????????????./project???????????????????? changed from > >? ? ? 0774 > >? ? ? >??? ??? ??? ??? ??? ??? ??? (rwxrwxr--) to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 0775 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? (rwxrwxr-x) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >?????????????? ?????????????? mode of > ????????????????????./tools/logs???????????????????? changed from > >? ? ? 0774 > >? ? ? >??? ??? ??? ??? ??? ??? ??? (rwxrwxr--) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to 0775 > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? (rwxrwxr-x) > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > On 04-11-2019 12.03 -0800, > Ioannis Pappas wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> Hi Julie. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> I just tried and I still > don???t get anything. I > >? ? ? also > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? tried > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? private mode in Firefox in > case the empty page was > >? ? ? >??? ??? ??? ??? ??? ??? ??? cached. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> Sorry for this. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> Best wishes, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> Ioannis > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> On Nov 4, 2019, at 11:58 > AM, Julie Ashworth, > >? ? ? HWNI > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Computing > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Support > <[9][11]support-cirl at berkeley.edu> wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> hi Ioannis, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> no worries, I changed the > following directory > >? ? ? to > >? ? ? >??? ??? ??? ??? ??? ??? ??? 777: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > /var/www/loris/smarty/templates_c > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> will you please check if > that works? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> thanks! > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> On 04-11-2019 11.49 > -0800, Dr. Ioannis Pappas > >? ? ? PhD > >? ? ? >??? ??? ??? ??? ??? ??? ??? wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Hi Julie. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Apologies for > bugging you with this again. > >? ? ? We > >? ? ? >??? ??? ??? ??? ??? ??? ??? tried > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? now to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? access???????????????????????? > [1][10][12]http://loris???????????????????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? and we are > getting a???????????????????????? blank page. I > >? ? ? think the > >? ? ? >??? ??? ??? ??? ??? ??? ??? reason > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? for this > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? is that we > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? don't have > read???????????????????????? permissions to read > >? ? ? from the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? template located > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? in > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? > /var/www/loris/smarty See here bottom of > >? ? ? the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? page???????????????????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > [2][11][13]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? I think, in > general, I am a little bit > >? ? ? confused > >? ? ? >??? ??? ??? ??? ??? ??? ??? as to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? what the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? permissions > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? should be for us > that are not sudos. My > >? ? ? >??? ??? ??? ??? ??? ??? ??? understanding > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? is that > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? if we don't > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? have read or > write permissions then we > >? ? ? can't > >? ? ? >??? ??? ??? ??? ??? ??? ??? access or > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? write > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? /var/www/loris, > meaning that we can't > >? ? ? access or > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? configure. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Should > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? everything be > chmod 777 for example????????????????????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Thank you very > much once again. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Best wishes, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Ioannis > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? On Thu, Oct 31, > 2019 at 1:56 PM Dr. Ioannis > >? ? ? >??? ??? ??? ??? ??? ??? ??? Pappas PhD > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? > <[3][12][14]ioannis at berkeley.edu> wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? Thank you > very much Julie. I appreciate > >? ? ? this > >? ? ? >??? ??? ??? ??? ??? ??? ??? and I > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? will dig > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? into Loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? given > your changes. Thank you so much > >? ? ? for your > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? help. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? Best > wishes, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? Ioannis > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? On Thu, > Oct 31, 2019 at 12:48 PM Julie > >? ? ? >??? ??? ??? ??? ??? ??? ??? Ashworth, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? HWNI > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Computing Support > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? > <[4][13][15]support-cirl at berkeley.edu> > >? ? ? wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > hi Ioannis, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > 1. I changed the permissions of > >? ? ? >??? ??? ??? ??? ??? ??? ??? /srv/www/loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to be owned > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? by > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > lorisadmin. I reivewed my > >? ? ? installation > >? ? ? >??? ??? ??? ??? ??? ??? ??? notes, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? and I did > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? this already > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > when > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? I > installed the server. I'm not > >? ? ? sure why > >? ? ? >??? ??? ??? ??? ??? ??? ??? they > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? changed, so > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? it's > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > probably a > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > good idea to keep an eye on that. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > 2. When I installed the loris > >? ? ? software, I > >? ? ? >??? ??? ??? ??? ??? ??? ??? also > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? installed a > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? mysql > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > database as recommended in the > >? ? ? >??? ??? ??? ??? ??? ??? ??? instructions: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > projectname: LORIS > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > databasename: loris_database > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > mysqluser: lorismysql > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > frontend: lorisweb > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > 3. A couple of weeks ago, I moved > >? ? ? Henrik's > >? ? ? >??? ??? ??? ??? ??? ??? ??? home > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? directory > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > /home/despoA, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > but I forgot to update loris. This > >? ? ? is done > >? ? ? >??? ??? ??? ??? ??? ??? ??? now. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > best, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > Julie > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > On 31-10-2019 11.15 -0700, Dr. > >? ? ? Ioannis > >? ? ? >??? ??? ??? ??? ??? ??? ??? Pappas > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? PhD wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? Hi Julie. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? I hope you are well. We are > >? ? ? trying to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? configure loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? that you > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > kindly set > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? up for us. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? I have a couple of > >? ? ? questions for you if > >? ? ? >??? ??? ??? ??? ??? ??? ??? you > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? allow me > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? so.???????????????????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? 1) First, although we are > >? ? ? logging into > >? ? ? >??? ??? ??? ??? ??? ??? ??? the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? front end > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? with admin > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > username > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? (lorisweb) and password, it > >? ? ? seems that > >? ? ? >??? ??? ??? ??? ??? ??? ??? any > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? kind of > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? update of > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > configuration > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? we are trying to do fails > >? ? ? (meaning that > >? ? ? >??? ??? ??? ??? ??? ??? ??? if > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? we, say, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? change the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > name of the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? study and press "submit", > >? ? ? this doesn't > >? ? ? >??? ??? ??? ??? ??? ??? ??? do > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? anything-it > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? doesn't > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > update). > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? It's almost like our > >? ? ? lorisweb user > >? ? ? >??? ??? ??? ??? ??? ??? ??? doesn't > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? have write > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? privileges > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > in the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? /var/www/loris/project > >? ? ? (where I think > >? ? ? >??? ??? ??? ??? ??? ??? ??? every > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? configuration should > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > be). > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? This generalizes for > >? ? ? everything that we > >? ? ? >??? ??? ??? ??? ??? ??? ??? are > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? trying to do > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? in the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > front end. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? Clicking any instrument/tab > >? ? ? in the front > >? ? ? >??? ??? ??? ??? ??? ??? ??? end > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? doesn't > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? really point > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? anything.???????????????????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? 2) Loris suggest doing > >? ? ? configurations > >? ? ? >??? ??? ??? ??? ??? ??? ??? via > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? SQL. Is it > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? possible to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > run SQL > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? scripts in the backend > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? 3) For some reason typing > >? ? ? ssh lors for > >? ? ? >??? ??? ??? ??? ??? ??? ??? Henrik > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? doesn't > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? directly > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > take him to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? loris (it requires a > >? ? ? password that is > >? ? ? >??? ??? ??? ??? ??? ??? ??? not the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? password > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? setup for > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? lorisweb user). Will you be > >? ? ? able to fix > >? ? ? >??? ??? ??? ??? ??? ??? ??? this > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? via your > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? sudo > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > privileges? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? Thank you very much in > >? ? ? advance for all > >? ? ? >??? ??? ??? ??? ??? ??? ??? your > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? help Julie. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Let us > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > know if > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? this is something that > >? ? ? shouldn't be > >? ? ? >??? ??? ??? ??? ??? ??? ??? directed > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to you (but > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? instead > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > to the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? loris people).???????????????????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? Best wishes, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? Ioannis > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? On Mon, Sep 9, 2019 at 6:25 > >? ? ? PM Julie > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? Ashworth, HWNI > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Computing > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > Support > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ??????????????????????????????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? <[1][5][14][16]support-cirl at berkeley.edu> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? wrote: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? hi Henrik and > >? ? ? Ioannis, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? the loris server > >? ? ? is available for > >? ? ? >??? ??? ??? ??? ??? ??? ??? you to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? use. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? The servername is > >? ? ? 'loris'. I > >? ? ? >??? ??? ??? ??? ??? ??? ??? created a > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? directory > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? called > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > /data/loris for > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? you to store data. > >? ? ? You may create > >? ? ? >??? ??? ??? ??? ??? ??? ??? new > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? folders in > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? /data/loris to > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > organize > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? your data. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? 1) secure shell or > >? ? ? secure copy: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? You can log in > >? ? ? with the 'ssh' or > >? ? ? >??? ??? ??? ??? ??? ??? ??? 'scp' > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? command from > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? your remote > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > desktop > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? session. You don't > >? ? ? need to > >? ? ? >??? ??? ??? ??? ??? ??? ??? authenticate > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? to log in. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? Maybe you'll > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > use scp > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? to transfer data > >? ? ? between your > >? ? ? >??? ??? ??? ??? ??? ??? ??? cluster > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? account and the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > server? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? Please put the > >? ? ? data in /data/loris, > >? ? ? >??? ??? ??? ??? ??? ??? ??? so I > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? can make > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? backups more > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > easily. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? ?????????????????????????????????????? > ?????????????????????????????????????? > >? ? ? secure shell: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? ?????????????????????????????????????? > ?????????????????????????????????????? > >? ? ? $ ssh loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? ?????????????????????????????????????? > ?????????????????????????????????????? > >? ? ? secure copy (change the > >? ? ? >??? ??? ??? ??? ??? ??? ??? names > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? in brackets). Let > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? me know if > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? I > can > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? ?????????????????????????????????????? > ?????????????????????????????????????? > >? ? ? help with syntax: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? ?????????????????????????????????????? > ?????????????????????????????????????? > >? ? ? $ scp -r > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? loris:/data/loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? 2) front-end web > >? ? ? interface.??????????????????????????????????? > >? ? ? >??? ??? ??? ??? ??? ??? ??? Open a > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? web browser in > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? your remote > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > desktop > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? session and enter > >? ? ? the hostname: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? > >? ? ? [2][6][15][17]http://loris > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? I created an admin > >? ? ? user called > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? 'lorisweb'. I put the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? password > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > in > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? $HOME/newuser on > >? ? ? the cluster. To > >? ? ? >??? ??? ??? ??? ??? ??? ??? see it, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? open a > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? terminal, and > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > run: > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? ?????????????????????????????????????? > ?????????????????????????????????????? > >? ? ? $ cat $HOME/newuser > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? If other people > >? ? ? need shell access > >? ? ? >??? ??? ??? ??? ??? ??? ??? to the > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? webserver, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? please let > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > me know > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? so I can create a > >? ? ? home directory > >? ? ? >??? ??? ??? ??? ??? ??? ??? for > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? them. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? We should > >? ? ? eventually discuss > >? ? ? >??? ??? ??? ??? ??? ??? ??? backups. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? best, > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? ?????????????????????????????????????? Julie > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> References > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? Visible links > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? 1. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? > mailto:[7][16][18]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>> ?????????????????????????????????????? > ?????????????????????????????????????? 2. [8][17][19]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? ?????????????? ?????????????? > ---end quoted text--- > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> References > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? Visible links > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 1. > [18][20]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 2. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? [19][21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 3. > mailto:[20][22]ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 4. > mailto:[21][23]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 5. > mailto:[22][24]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 6. > [23][25]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 7. > mailto:[24][26]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>>>?????????????? 8. > [25][27]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >>> ---end quoted text--- > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? ??? ??? ??? ??? ??? ??? > ---end quoted text--- > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? -- > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? [26][28]christine.rogers at mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? McGill Centre for Integrative > Neuroscience | MCIN.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Montreal Neurological Institute > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? McGill University | Montreal | Canada > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> References > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? Visible links > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 1. > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > [29]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 2. > >? ? ? >??? ??? ??? ??? ??? ??? ??? > [30]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 3. mailto:[31]loris-dev at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 4. mailto:[32]ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 5. [33]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 6. mailto:[34]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 7. mailto:[35]ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 8. mailto:[36]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? ??? 9. mailto:[37]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 10. [38]http://xn--loris-7qa/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 11. > >? ? ? >??? ??? ??? ??? ??? ??? ??? > [39]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 12. mailto:[40]ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 13. mailto:[41]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 14. mailto:[42]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 15. [43]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 16. mailto:[44]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 17. [45]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 18. [46]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 19. > >? ? ? >??? ??? ??? ??? ??? ??? ??? > [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 20. mailto:[48]ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 21. mailto:[49]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 22. mailto:[50]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 23. [51]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 24. mailto:[52]support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 25. [53]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>>??? ??? ??? 26. mailto:[54]christine.rogers at mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? ??? ??? ---end quoted text--- > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? -- > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? [55]christine.rogers at mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? McGill Centre for Integrative Neuroscience | > MCIN.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Montreal Neurological Institute > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? McGill University | Montreal | Canada > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> References > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? Visible links > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 1. [8]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 2. [9]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 3. [10]http://loris.priv/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? > >? ? ? >??? ??? ??? ??? ??? ??? ??? 4. > >? ? ? > [11]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 5. [12]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 6. [13]mailto:ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 7. [14]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 8. [15]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? ??? 9. [16]mailto:ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 10. [17]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 11. [18]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 12. [19]http://xn--loris-era/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 13. > >? ? ? [20]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 14. [21]mailto:ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 15. [22]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 16. [23]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 17. [24]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 18. [25]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 19. [26]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 20. [27]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 21. > >? ? ? [28]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 22. [29]mailto:ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 23. [30]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 24. [31]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 25. [32]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 26. [33]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 27. [34]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 28. [35]mailto:christine.rogers at mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? 29. > >? ? ? > [36]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 30. > >? ? ? [37]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 31. [38]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 32. [39]mailto:ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 33. [40]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 34. [41]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 35. [42]mailto:ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 36. [43]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 37. [44]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 38. [45]http://xn--loris-7qa/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 39. > >? ? ? [46]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 40. [47]mailto:ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 41. [48]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 42. [49]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 43. [50]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 44. [51]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 45. [52]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 46. [53]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 47. > >? ? ? [54]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 48. [55]mailto:ioannis at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 49. [56]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 50. [57]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 51. [58]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 52. [59]mailto:support-cirl at berkeley.edu > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 53. [60]http://loris/ > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 54. [61]mailto:christine.rogers at mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? >>??? 55. [62]mailto:christine.rogers at mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? > ---end quoted text--- > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? ??? ??? _______________________________________________ > >? ? ? >??? ??? ??? ??? ??? ??? ??? Loris-dev mailing list > >? ? ? >??? ??? ??? ??? ??? ??? ??? Loris-dev at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? ??? ??? > [63]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? >??? ??? ??? ??? ??? ??? ??? > >? ? ? > > >? ? ? >??? ??? ??? ??? ??? _______________________________________________ > >? ? ? >??? ??? ??? ??? ??? Loris-dev mailing list > >? ? ? >??? ??? ??? ??? ??? Loris-dev at bic.mni.mcgill.ca > >? ? ? >??? ??? ??? ??? ??? > [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? ? > > >? ? ? >??? ??? ??? -- > >? ? ? >??? ??? ??? christine.rogers at mcgill.ca > >? ? ? >??? ??? ??? McGill Centre for Integrative Neuroscience | MCIN.ca > >? ? ? >??? ??? ??? Montreal Neurological Institute > >? ? ? >??? ??? ??? McGill University | Montreal | Canada > >? ? ? ---end quoted text--- > > > > References > > > >? ? ? Visible links > >? ? ? 1. [2]https://loris.url/configuration/ > >? ? ? 2. [3]https://.loris.url/ > >? ? ? 3. [4]http://loris.priv/ > >? ? ? 4. [5]http://localhost/ > >? ? ? 5. [6]http://loris.priv/ > >? ? ? 6. [7]http://localhost/ > >? ? ? 7. [8]http://localhost/ > >? ? ? 8. [9]mailto:loris-dev at bic.mni.mcgill.ca > >? ? ? 9. [10]mailto:support-cirl at berkeley.edu > >? ? 10. [11]http://loris.priv/ > >? ? 11. > [12]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? 12. [13]mailto:loris-dev at bic.mni.mcgill.ca > >? ? 13. [14]mailto:ioannis at berkeley.edu > >? ? 14. [15]http://loris/ > >? ? 15. [16]mailto:support-cirl at berkeley.edu > >? ? 16. [17]mailto:ioannis at berkeley.edu > >? ? 17. [18]mailto:support-cirl at berkeley.edu > >? ? 18. [19]mailto:support-cirl at berkeley.edu > >? ? 19. [20]http://xn--loris-era/ > >? ? 20. [21]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? 21. [22]mailto:ioannis at berkeley.edu > >? ? 22. [23]mailto:support-cirl at berkeley.edu > >? ? 23. [24]mailto:support-cirl at berkeley.edu > >? ? 24. [25]http://loris/ > >? ? 25. [26]mailto:support-cirl at berkeley.edu > >? ? 26. [27]http://loris/ > >? ? 27. [28]http://loris/ > >? ? 28. [29]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? 29. [30]mailto:ioannis at berkeley.edu > >? ? 30. [31]mailto:support-cirl at berkeley.edu > >? ? 31. [32]mailto:support-cirl at berkeley.edu > >? ? 32. [33]http://loris/ > >? ? 33. [34]mailto:support-cirl at berkeley.edu > >? ? 34. [35]http://loris/ > >? ? 35. [36]mailto:christine.rogers at mcgill.ca > >? ? 36. > [37]https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > >? ? 37. [38]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? 38. [39]mailto:loris-dev at bic.mni.mcgill.ca > >? ? 39. [40]mailto:ioannis at berkeley.edu > >? ? 40. [41]http://loris/ > >? ? 41. [42]mailto:support-cirl at berkeley.edu > >? ? 42. [43]mailto:ioannis at berkeley.edu > >? ? 43. [44]mailto:support-cirl at berkeley.edu > >? ? 44. [45]mailto:support-cirl at berkeley.edu > >? ? 45. [46]http://xn--loris-7qa/ > >? ? 46. [47]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? 47. [48]mailto:ioannis at berkeley.edu > >? ? 48. [49]mailto:support-cirl at berkeley.edu > >? ? 49. [50]mailto:support-cirl at berkeley.edu > >? ? 50. [51]http://loris/ > >? ? 51. [52]mailto:support-cirl at berkeley.edu > >? ? 52. [53]http://loris/ > >? ? 53. [54]http://loris/ > >? ? 54. [55]https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > >? ? 55. [56]mailto:ioannis at berkeley.edu > >? ? 56. [57]mailto:support-cirl at berkeley.edu > >? ? 57. [58]mailto:support-cirl at berkeley.edu > >? ? 58. [59]http://loris/ > >? ? 59. [60]mailto:support-cirl at berkeley.edu > >? ? 60. [61]http://loris/ > >? ? 61. [62]mailto:christine.rogers at mcgill.ca > >? ? 62. [63]mailto:christine.rogers at mcgill.ca > >? ? 63. [64]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >? ? 64. [65]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > ---end quoted text--- > > References > > Visible links > 1. http://localhost/ > 2. https://loris.url/configuration/ > 3. https://.loris.url/ > 4. http://loris.priv/ > 5. http://localhost/ > 6. http://loris.priv/ > 7. http://localhost/ > 8. http://localhost/ > 9. mailto:loris-dev at bic.mni.mcgill.ca > 10. mailto:support-cirl at berkeley.edu > 11. http://loris.priv/ > 12. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 13. mailto:loris-dev at bic.mni.mcgill.ca > 14. mailto:ioannis at berkeley.edu > 15. http://loris/ > 16. mailto:support-cirl at berkeley.edu > 17. mailto:ioannis at berkeley.edu > 18. mailto:support-cirl at berkeley.edu > 19. mailto:support-cirl at berkeley.edu > 20. http://xn--loris-era/ > 21. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 22. mailto:ioannis at berkeley.edu > 23. mailto:support-cirl at berkeley.edu > 24. mailto:support-cirl at berkeley.edu > 25. http://loris/ > 26. mailto:support-cirl at berkeley.edu > 27. http://loris/ > 28. http://loris/ > 29. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 30. mailto:ioannis at berkeley.edu > 31. mailto:support-cirl at berkeley.edu > 32. mailto:support-cirl at berkeley.edu > 33. http://loris/ > 34. mailto:support-cirl at berkeley.edu > 35. http://loris/ > 36. mailto:christine.rogers at mcgill.ca > 37. https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings > 38. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 39. mailto:loris-dev at bic.mni.mcgill.ca > 40. mailto:ioannis at berkeley.edu > 41. http://loris/ > 42. mailto:support-cirl at berkeley.edu > 43. mailto:ioannis at berkeley.edu > 44. mailto:support-cirl at berkeley.edu > 45. mailto:support-cirl at berkeley.edu > 46. http://xn--loris-7qa/ > 47. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 48. mailto:ioannis at berkeley.edu > 49. mailto:support-cirl at berkeley.edu > 50. mailto:support-cirl at berkeley.edu > 51. http://loris/ > 52. mailto:support-cirl at berkeley.edu > 53. http://loris/ > 54. http://loris/ > 55. https://github.com/aces/Loris/wiki/Installing-Loris-in-Brief > 56. mailto:ioannis at berkeley.edu > 57. mailto:support-cirl at berkeley.edu > 58. mailto:support-cirl at berkeley.edu > 59. http://loris/ > 60. mailto:support-cirl at berkeley.edu > 61. http://loris/ > 62. mailto:christine.rogers at mcgill.ca > 63. mailto:christine.rogers at mcgill.ca > 64. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 65. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ---end quoted text--- -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Tue Nov 12 08:28:26 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 12 Nov 2019 15:28:26 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, Could we send you a link with 10 anonymized dicom files to diagnose the warnings we get? Thanks ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi Cecile, > > We were wondering whether Loris has a tool to check if there are problems > with the dcm files, before trying to upload them. Something that could > provide the same results provided in the warning_output, this is the > summary from the mri_upload at the front-page. Also which attributes of the > dcm header would trigger a warning? is there a dcm file header > specification for Loris? > > Thanks > > Sotirios > > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi, >> >> Yes, by parsing now() into unix_timestamp function it worked,but i >> thought that something else was causing the 2nd issue. >> Thanks >> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >> xavier.lecoursboucher at mcgill.ca> wrote: >> >>> Hi Sotirios, >>> >>> The first error occurs because the QCFirstChangeTime and columns are of >>> type `unsigned integer` and not `datatime`. You should be using >>> UNIX_TIMESTAMP() instead of NOW(). >>> >>> The second error occurs because the trigger triggers a rollback of the >>> insert statement in the files table. >>> See mysql documentation for trigger error handling. >>> >>> An error during either a BEFORE or AFTER trigger results in failure of >>> the entire statement that caused trigger invocation. >>> >>> >>> Thank you for sharing that. I hope it helps. >>> -- Xavier >>> >>> ------------------------------ >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>> Nikoloutsopoulos >>> *Sent:* October 1, 2019 8:33 AM >>> *To:* Cecile Madjar >>> *Cc:* loris-dev at bic.mni.mcgill.ca ; >>> Christine Rogers, Ms. >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> When mincs are inserted their corresponding rows at the file table are >>> inserted too >>> [image: image.png] >>> >>> i would like to insert their rows at file_qcstatus as well, because i >>> don't want manually to label them as passed throught the interface >>> >>> [image: image.png] >>> >>> >>> That is the trigger i wrote >>> >>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER >>> INSERT ON `files` FOR EACH ROW >>> BEGIN >>> INSERT INTO files_qcstatus >>> SET FileID = NEW.FileID, >>> SeriesUID = NEW.SeriesUID, >>> EchoTime = NEW.EchoTime, >>> QCStatus = "Pass", >>> QCFirstChangeTime = NOW(), >>> QCLastChangeTime = NOW(); >>> END >>> >>> although it contains some errors >>> >>> DBD::mysql::db do failed: Out of range value for column >>> 'QCFirstChangeTime' at row 1 at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>> >>> >>> >>> >>> >>> >>> >>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> In the mri_upload table, there is a TarchiveID column associated with >>> the MRI upload you inserted. When this value is NULL, it means no DICOMs >>> were inserted into the tarchive tables. At the end of the insertion of the >>> DICOMs in the tarchive tables, this value is updated with the correct >>> TarchiveID associated with the upload. >>> >>> Could this correspond to what you want to do? >>> >>> Regarding the files_qcstatus, this table is only linked to the files >>> table (hence, the MINC files). You could always create a new table for >>> dicom_qcstatus and link it to the tarchive table? >>> >>> C?cile >>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> i would like whenever a dicom is imported to mark all their >>> coressponding qc_status to "pass". I was thinking of creating a trigger for >>> that, but which tables do i need to add entries to? So far from what i see >>> i need to add entres at the table "files" whenever an insertion happens to >>> files_qcstatus. >>> >>> Thanks >>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Oh, sorry i should have asked for StudyID, at the beginning of my email >>> i sent 3 hours ago (not StudyUID). >>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i am >>> looking for is not stored in the database? >>> >>> [image: image.png] >>> >>> Thanks. >>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> The StudyUID is stored in the DicomArchiveID field of the >>> tarchive table. It can also be found in the metadata field but it is mixed >>> with many other information. >>> >>> Hope this helps, >>> >>> C?cile >>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>> specifically at the AcquisitonMetadata column i found something called >>> 'Unique Study ID" in its context, but that must be the Study Instance UID. >>> >>> Thanks >>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Your observation is correct. A little explanation below. >>> >>> MINC files get inserted into the MRI violation tables if: >>> >>> - the scan type could not be identified (not matching an entry in >>> the mri_protocol table) >>> - one parameter of the scan type is out of the expected range >>> present in the mri_protocol_checks (extra filtering in case you need to be >>> stricker on some parameters not present in the mri_protocol table) >>> - if the CandID and PSCID do not match >>> >>> The following cases do not get in the MRI violation tables as it happens >>> before the conversion of the DICOM to MINC files and only MINC files >>> violations are logged there: >>> >>> - "No single DICOM" (since no valid DICOM could be found to convert >>> to MINC) >>> - "Study already inserted" (duplicate StudyUID) since this error >>> happens at the dicomTar.pl level (way before conversion into MINC files) >>> >>> Glad everything is working out!! >>> Best, >>> >>> C?cile >>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now about the >>> mri_violations, dicoms are triggered to be inserted there only if there is >>> a violation for Tr_min, Tr_max, in general for its header parameter? >>> Because i don't see the cases of 'No single dicom" or with the 2 studyiuid >>> to be there. >>> >>> Thanks >>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Sorry to hear you are having issues with the memory. I think most of our >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>> >>> Hope this helps! >>> >>> C?cile >>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> about that dicom that had that insertion error it's about 30mb and when >>> it is being processed the ram is being drastically increased from 2gb to >>> 3.28 and then the whole virtual machine is frozen. What is the recommended >>> size of ram for using Loris? >>> >>> Thanks >>> >>> [image: image.png] >>> >>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to see that the StudyUID problem was fixed! >>> >>> For the delete script issue, if you are absolutely certain that no >>> processes are run for that uploadID, you can update the mri_upload table >>> and set the column Inserting to 0 instead of 1 for that uploadID. It >>> looks like for some reason the scripts did not update this field when it >>> stopped the insertion. Not sure why that would be the case though. >>> Note: only do that update if you are certain that there is no processing >>> happening. >>> >>> Hope this helps! >>> >>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> about the Dicoms i reported that didn't have a StudyID they actually do >>> >>> [image: image.png] >>> >>> >>> [image: image.png] >>> >>> I thought that this might be a permission because "w" was missing at the >>> group. After using chmod -R 775 only 102809579 passed, but with no mnic >>> files. Also now i have this error >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>> Cannot delete upload 34: the MRI pipeline is currently processing it. >>> >>> How can solve this? >>> >>> Thanks >>> >>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> Here is our auto dicom uploading python script: >>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>> >>> To give you a brief idea: >>> Per folder it will: >>> 1) Delete all the .bak files >>> 2) Locate .dcm files and update the Patient header >>> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, >>> TE_max parameters of T1 protocol and do an update at the mri_protocol table >>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>> For some reason some files are missing SeriesDescription/ProtocolName >>> >>> In total i have 7 folders >>> >>> [image: image.png] >>> >>> 3/7 passed >>> >>> [image: image.png] >>> >>> Also about the first patient with DC0000 had a violation "T1 AXIAL SE >>> GADO", but my script didn't output a TE of 17 nowhere and i find that weird >>> since Loris detects the SeriesDescription. >>> [image: image.png] >>> >>> >>> Now about the 4/7 that didn't passed >>> >>> 102327840 and 102809579 outputs "The target directory does not contain a >>> single DICOM file.", therefore they are missing their StudyUID >>> >>> 102506134 has 2 studyuid "You can't use it with data from multiple >>> studies." >>> >>> and 102761034 "No data could be converted into valid MINC files. >>> localizer, scout will not be considered!" What is this? >>> >>> If i wanted to force the insertion of 102327840, 102809579 and 102506134 >>> can i just pass a flag parameter to batch_uploads_imageuploader.pl? or >>> modify imaging_upload_file.pl? >>> >>> Thank you, >>> >>> Sotirios >>> >>> PS >>> >>> To diagnose a folder search the name of the folder at dicom_output.txt. >>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> Glad to hear about your progress. >>> >>> Yes, the script you used to delete imaging data is fully documented here >>> >>> -- let us know if you didn't find the answers you were looking for there. >>> (Is it possible the null row in *mri_scanner* seen in your database >>> management software is a visual placeholder for you as the user? I'm not >>> sure why a scanner would ever be registered with ID='0' as your screenshot >>> showed.) >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> I fixed it with this >>> >>> [image: image.png] >>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> I tried to create a new candidate using the API, is there something >>> wrong with the structure? why did i receive a 500 internal error? In the >>> loris-error log it state that there is something wrong with token, but i >>> verfied that the type of the token is a string. >>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type string, >>> null given, called in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and >>> defined in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>> SinglePointLogin->authenticate()\n#2 >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >>> >>> [image: image.png] >>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> Is there a way also to delete candidates? Just to let you know what i >>> did to clear candidates, because maybe i may have missed dependencies. >>> >>> First i deleted all their uploads >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit >>> the backup file ? ) >>> >>> Afterwards i had some scanner candidates, so i deleted all the entries >>> from mri_scanner except that i couldn't delete this entry with the 0 ID. >>> >>> [image: image.png] >>> >>> >>> Lastly i deleted the session and then the candidate table. >>> >>> Thanks >>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> We recommend that you use our existing tools for creating new candidates >>> - either the LORIS API or if you are using a PHP script, by calling the Candidate >>> class's createNew() >>> function. >>> These will create the necessary records for you. (It's not recommended to >>> make direct modifications to mysql database tables in your script, if I >>> understand you.) >>> >>> The CandID should be a randomized 6 digit randomized ID, and there are >>> multiple reasons for this. >>> You can use the PSCID for project-specific IDs and the External ID field >>> in the candidate table can also be used for any values you like. >>> Additionally, any number of custom IDs can be added in parallel - these >>> are entered/visible in the Candidate Information module and added in the >>> back-end as candidate parameters. >>> >>> Best, >>> Christine >>> >>> >>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> We are building a script that will auto insert the candidates based on >>> their ExternalID. We would like to know whethere when we are creating a new >>> profile in the candidate table, if we also have to insert a new record at >>> another table? Furthermore is there a problem that in our case CandID won't >>> be a 6digit? ( should we start it from 100000?) >>> >>> Thanks >>> >>> [image: image.png] >>> >>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>> melanie.legault2 at mcgill.ca> ??????: >>> >>> That would normally be the case but the numeric part of the PSCID get >>> paded with 0 on the left. >>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char >>> with a min value of 1, the sequence would be: >>> >>> ABC0001 >>> ABC0002 >>> ... >>> ABC0010 >>> ... >>> >>> thus sorting them ascending will always get the latest value generated >>> as the max value. >>> >>> M?lanie >>> >>> ------------------------------ >>> *From:* Sotirios Nikoloutsopoulos >>> *Sent:* September 13, 2019 10:15 >>> *To:* Melanie Legault, Mrs >>> *Cc:* Christine Rogers, Ms. ; >>> loris-dev at bic.mni.mcgill.ca >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> I see, although the PSCID value is varchar(255), it must be stored >>> within a specific length of characters. Otherwise if we were to sort >>> strings with different lengths the result would not be sorted correctly ( >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>> >>> Thanks >>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>> melanie.legault2 at mcgill.ca> ??????: >>> >>> Hello Sotirios, >>> >>> There is no `last value` stored anywhere. >>> The code simply look for the PSCID with the max value and increase that >>> value by 1 in order to generate the next PSCID. >>> >>> Hope this info help. >>> >>> M?lanie Legault | Software developer | Faculty of Medicine | McGill >>> University >>> 3801 University, Montr?al, QC H3A 2B4 >>> >>> ------------------------------ >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>> Nikoloutsopoulos >>> *Sent:* September 13, 2019 9:43 >>> *To:* Christine Rogers, Ms. >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> Hi, >>> >>> how does Loris determine the next available PSCID value for a new >>> candidate? https://github.com/aces/Loris/wiki/Project-Customization >>> e.x in the default case the PSCID is sequential, but where do we store the >>> last value for the sequential sequence? >>> >>> Thanks >>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> the parameters in the mri_protocol you have assigned are global >>> standard? or were assigned after trial and error? >>> >>> Thanks >>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Given you have done the initial setup of your tables to match your >>> intended protocol/parameters according to instructions -- >>> the Troubleshooting guide documentation recommends >>> >>> re-running the pipeline (and first deleting prior uploads). >>> >>> Best, >>> Christine >>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> *if i were to change their status to resolve what would happen? >>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> I noticed that i can view the mnics at the brainbrowser from the >>> mri_violations page ( those mnics are stored at /data/loris/data/trashbin/ >>> if i were to click their issue to resolve what would happend? would they >>> appear in the dicom_archive view too? ). >>> >>> >>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> The defaut values of the schema exists in my local database. If i adjust >>> the default values of TR_min and TE_min the mincs will be uploaded? >>> >>> [image: image.png] >>> >>> >>> [image: image.png] >>> >>> Thanks >>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Is it possible that you haven't set up your mri_protocol table ? (and >>> mri_scan_type table too, for additional types of scans) >>> >>> Like the psc table, this is a pre-requisite for the Imaging insertion >>> setup : See the install/setup documentation : >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>> >>> To add new rows, just use MySQL insert statements. You can adapt the >>> insert statements which load the default table values --> e.g. Here on >>> GitHub : >>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>> (see also the mri_scan_type table) >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> I see that i can edit the values but not how to insert new rows. >>> >>> [image: image.png] >>> >>> If i choose Inserted with flag then will the minc be inserted? >>> >>> [image: image.png] >>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to hear that *dcmodify* worked correctly. >>> >>> For the MRI Violations module, the screenshot is enough. >>> >>> It says "could not identify scan type", which we knew already. Did you >>> click on the link on those words? >>> >>> It will take you to the next page of the module, showing for each scan >>> what the scan parameters were, and will also show for comparison what's >>> stored in your *mri_protocol* table. >>> Compare these values to find which parameter was not correct according >>> to your *mri_protocol* table scan type definitions. >>> >>> You may end up broadening your mri_protocol value ranges (e.g. TR, TE) >>> for scans. >>> This can be done in the front-end, by editing the database table >>> directly in the same subpage of the MRI Violations module. >>> >>> The MRI Violations module features are explained in more detail in the >>> Help text for this module inside LORIS (click the ["?"] icon in the menu >>> bar.) >>> >>> See also: Loris-MRI troubleshooting guide >>> >>> : no MINCs inserted- violated scans >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> looks like my previous email's attachment wasn't delivered due to >>> security reasons, i uploaded my file at google drive >>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> From Dicat's view seems that dcmodify worked in both cases >>> >>> [image: image.png] >>> >>> [image: image.png] >>> >>> For the mri_violations i attached the .html output from webbrowser, so >>> that you can check the filelds easier. >>> >>> [image: image.png] >>> >>> Thanks >>> >>> >>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios -- >>> Great, sounds like more progress. >>> >>> About the dcmodify command -- I'm not sure why you're getting an Endian >>> warning. (it's a warning not an error, correct?) >>> To clarify -- Were the DICOM headers (PatientName) all successfully >>> relabelled, after the command ran? >>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) to >>> verify and/or update local DICOM headers -- though your dcmodify command is >>> a great and fast solution for bulk header updates. >>> >>> If you're concerned about fields being changed (e.g. "(2001,105f)" from >>> the warning message) - you can also dcmdump a DICOM slice before and look >>> at these fields specifically. >>> It's also not a bad "sanity check" to backup your DICOMS before/after >>> running dcmodify, and use dcmdump on each version to diff the outputs -- >>> this will pinpoint what changed. >>> >>> Re the protocol violation -- AcquisitionProtocol not recognized or >>> unknown : this means your scans did not match what is stored in your >>> mri_protocol table. >>> Check the MRI Violations front-end module -- can you see why they didn't >>> match? >>> Send us an example, in addition to the contents of the mri_protocol >>> table, if you can't find the source of the mismatch. >>> >>> Best, >>> Christine >>> >>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Here is the psc table >>> [image: image.png] >>> >>> I created 2 candidates profiles through the interface >>> >>> [image: image.png] >>> >>> then runned dcmodify command to a dicom file >>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>> >>> and got those warning: is this okay? >>> W: Found element (2001,105f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1083) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1402) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,140f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2001,105f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1083) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> >>> dcmodify at another Dicom didn't show warnings. Below you can see the >>> execution for the second dicom. Mnics could not be inserted due to >>> AcquisitionProtocol being unknown. >>> >>> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/ >>> imaging_upload_file.pl -profile prod -upload_id 12 >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >>> -delete >>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>> Target: /data/loris/data/tarchive >>> >>> Testing for database connectivity. >>> Database is available. >>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>> >>> You are creating a tar with the following command: >>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>> ImagingUpload-18-36-mTrxXs >>> >>> >>> getting md5sums and gzipping!! >>> >>> * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs >>> * Archive target location : >>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> * Name of creating host : 127.0.1.1 >>> * Name of host OS : Linux >>> * Created by user : lorisadmin >>> * Archived on : 2019-09-06 18:36:50 >>> * dicomSummary version : 1 >>> * dicomTar version : 1 >>> * md5sum for DICOM tarball : b1dcdc8903dd2d9a5443227db2aa2814 >>> ImagingUpload-18-36-mTrxXs.tar >>> * md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f >>> ImagingUpload-18-36-mTrxXs.tar.gz >>> * md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> >>> Adding archive info into database >>> >>> Removing temporary files from target location >>> >>> >>> Done adding archive info into database >>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation >>> -profile prod >>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>> -uploadID 12 -verbose >>> md5sum >>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> Set centerID = 1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> >>> Number of MINC files that will be considered for inserting into the >>> database: 2 >>> >>> log dir is /data/loris/data//logs and log file is >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> >>> log dir is /data/loris/data//logs and log file is >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> >>> Cleaning up temp files: rm -rf >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ cat >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>> >>> ==> Loading file from disk >>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>> >>> --> mapping DICOM parameter for >>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>> >>> ==> computing md5 hash for MINC body. >>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>> >>> ==> verifying acquisition protocol >>> >>> Acquisition protocol is unknown >>> >>> --> The minc file cannot be registered since the AcquisitionProtocol >>> is unknown >>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios: >>> >>> Sure -- you can delete imaging datasets with the *delete_imaging_upload* >>> script -- >>> details here: >>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>> >>> What's in your *psc* table? (Is it properly populated? This is a >>> pre-requisite to loading imaging data. >>> >>> ) >>> The foreign key constraint error on the candidate record is curious. >>> >>> There are also a few options for creating candidates when inserting >>> imaging data: >>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline >>> >>> a. via the LORIS API -- Create the candidates (and visits, optionally I >>> think) >>> How to: >>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>> Ensure you get the DCCID/CandID assigned by LORIS. >>> >>> Then as a second step: >>> b. Use the imaging insertion pipeline >>> >>> to load your DICOMs. >>> You will want to first ensure that the PatientName header in the DICOMs >>> as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel >>> >>> -- Method 2: for BIDS-format datasets: >>> How to : >>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>> >>> Be sure to use the *-c* and *-s* options when running the bids_import script, >>> to automatically create your candidates and sessions. >>> >>> Best, >>> Christine >>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> How do i delete a Study? And everytime do i have to create a new >>> candidate to get DCCID and a PSCID? >>> >>> *First execution:* >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >>> log.txt >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>> batch_uploads_imageuploader.pl line 144. >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>> ERROR: Failed to insert record in table mri_scanner: >>> The following database commands failed: >>> PREPARE s FROM 'INSERT INTO mri_scanner >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; >>> SET >>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>> Medical Systems'; >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>> Error obtained:Cannot add or update a child row: a foreign key >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452) >>> >>> ERROR: The validation has failed. Either re-run the validation again >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to force the >>> execution. >>> >>> >>> The tarchiveLoader.pl insertion script has failed. >>> Can't exec "mail": No such file or directory at ./ >>> batch_uploads_imageuploader.pl line 249. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 250. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 251. >>> >>> >>> *And second execution: * >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >>> log.txt >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>> batch_uploads_imageuploader.pl line 144. >>> >>> PROBLEM: >>> The user 'lorisadmin' has already inserted this study. >>> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>> This is the information retained from the first time the study was >>> inserted: >>> >>> * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy >>> * Archive target location : >>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>> * Name of creating host : 127.0.1.1 >>> * Name of host OS : Linux >>> * Created by user : lorisadmin >>> * Archived on : 2019-09-04 18:33:05 >>> * dicomSummary version : 1 >>> * dicomTar version : 1 >>> * md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d >>> ImagingUpload-18-33-Qq7HGy.tar >>> * md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>> * md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053 >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>> >>> >>> Last update of record: >>> >>> >>> >>> The dicomTar.pl execution has failed. >>> Can't exec "mail": No such file or directory at ./ >>> batch_uploads_imageuploader.pl line 249. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 250. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 251. >>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Ok, this sounds like good progress. Let us know when you next encounter >>> issues as you progress through the Imaging Install/Setup docs >>> . >>> I'll look into how we can better handle the incoming/ directory next >>> time. >>> Best, >>> Christine >>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>> populated correctly except its port is 'port' : ''. Also i have tested >>> that i can connect to MySQL with lorisuser. >>> >>> I executed the script again, because the only error i had previously was >>> that the /data/incoming folder didn't exist and there are no errors >>> reported back except of warnings <>> command line interface can be insecure>>. >>> >>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> It's possible -- if the script was unable to connect to the database >>> during its execution (e.g. typo in the password), that would explain the >>> underpopulated Image path and Loris-MRI code path you saw in the Config >>> module. >>> It's hard to tell without seeing the output from your script run -- Did >>> you see a sign of any such error? >>> The Config fields are populated by the imaging_install.sh script (starting >>> at line 222 >>> >>> ) >>> >>> For example, check if the database connection information was populated >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >>> >>> Best, >>> Christine >>> >>> >>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi Christine, >>> >>> If you are referring to the imaging_install.sh here is an image with the >>> configurations i typed. Maybe the problem is somewhere at the last part >>> which asks to configure as much as possible automatically? >>> >>> Thanks >>> >>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to hear your LORIS core install is up and working and all the >>> front-end pages are loading. >>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>> > and the web interface worked. >>> >>> Yes, it's important that project/ have 775 permissions and that >>> lorisadmin be part of the sudoers group, per step 1 in the install >>> Readme . >>> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS to >>> loris, right? >>> >>> These imaging paths will be updated during your imaging installation >>> by an automated script -- >>> you do not need to set them manually via the Config module. >>> Please continue to follow the Setup Guide >>> for detailed steps to follow. >>> >>> Best, >>> Christine >>> >>> >>> >>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS to loris, >>> right? >>> >>> [image: image.png] >>> >>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> i used >>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>> sudo apt-get install -y nodejs >>> >>> >>> you had suggested in the past, make worked and now i can see all the >>> contents in the web-interface, but i don't need make install? >>> >>> Thanks >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Tue Nov 12 14:44:02 2019 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Tue, 12 Nov 2019 11:44:02 -0800 Subject: [Loris-dev] loris server In-Reply-To: References: <2A000E76-9BE1-415A-BFF6-B110A80BECCD@berkeley.edu> <20191109020414.GB13279@nx6.priv> <20191111170342.GA4213@gaia.neuro.berkeley.edu> <20191112033026.GA5955@gaia.neuro.berkeley.edu> Message-ID: <20191112194402.GA11003@gaia.neuro.berkeley.edu> Thanks Melanie, On 12-11-2019 12.06 +0000, Melanie Legault, Mrs wrote: > Hello, > Also, in the config table, `url` should be `http://localhost/` with the > slash at the end. Should not be the cause to the current problem. The 'troubleshooting' instructions state to use localhost without the slash: "ConfigSetting host value should not terminate in a slash. E.g. "http://localhost" not "http://localhost/". To fix, run: (for http) UPDATE Config SET Value='http://localhost' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='host');" https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings Will you please confirm if localhost should have a slash at the end? > As for creating a new user, I don't think it will solve the problem. > Could you ensure that in MariaDB, the user `lorismysql`@`localhost` have > the update permission (select, insert, update, delete) on > `loris_database`.* as well as?? usage on these tables. MariaDB [(none)]> SHOW grants for 'lorismysql'@'localhost'; +-------------------------------------------------------------------------------------------------------------------+ | Grants for lorismysql at localhost +-------------------------------------------------------------------------------------------------------------------+ | GRANT USAGE ON *.* TO 'lorismysql'@'localhost' IDENTIFIED BY PASSWORD xxx | GRANT SELECT, INSERT, UPDATE, DELETE, CREATE TEMPORARY TABLES ON `loris_database`.* TO 'lorismysql'@'localhost' | +-------------------------------------------------------------------------------------------------------------------+ > Also can you check which version of MariaDB you have??? The version of > MariaDB that come with CentOS 7 isn't supported for the latest versions of > LORIS. > We have instructions (not quite definitive yet) on how to install MariaDB > 10.3 in the documentation for Release 22 that should be out soon. > [1]https://github.com/aces/Loris/blob/22.0-release/README.CentOS7.md > Kind regards, > Ahh, this is probably why it isn't working. # rpm -qi mariadb Name : mariadb Epoch : 1 Version : 5.5.64 Release : 1.el7 Architecture: x86_64 Source RPM : mariadb-5.5.64-1.el7.src.rpm Build Date : Thu 08 Aug 2019 07:29:56 AM PDT Packager : CentOS BuildSystem I'll try reinstalling MariaDB. thanks, Julie From it at cnbp.ca Tue Nov 12 22:44:30 2019 From: it at cnbp.ca (Yang Ding) Date: Tue, 12 Nov 2019 22:44:30 -0500 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hey, Sotirios, Christine from the LORIS team mentioned you had some issue with DICOM. I am a fellow developer for an external project using LORIS, kind of just like you. We had to implement DICOM upload as well but more as a fully automated pipeline actually. While we were building CNBP, we had coded up some minor Python functions to check DICOM integrity (and simple validations) and you might be able to gain some inspiration from it and help you with your cause. For more comprehensive solution, PyDICOM ( https://pydicom.github.io/pydicom/stable/getting_started.html#) seems like a descent python package to help out with a lot of DICOM data checks (I was essentially just building customized wrapper calls to them). You can see some example scripts here as part of our DICOM submodule. It is pretty rough around the edges but hopefully point you in the right direcitons https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py Cheers, Yang Ding, PhD. Canadian Neonatal Brain Platform Architect On Tue, Nov 12, 2019 at 8:29 AM wrote: > Send Loris-dev mailing list submissions to > loris-dev at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > or, via email, send a message with subject or body 'help' to > loris-dev-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > loris-dev-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Loris-dev digest..." > > > Today's Topics: > > 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 12 Nov 2019 15:28:26 +0200 > From: Sotirios Nikoloutsopoulos > To: Cecile Madjar > Cc: loris-dev at bic.mni.mcgill.ca > Subject: Re: [Loris-dev] Import mri - scripts > Message-ID: > 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi, > > Could we send you a link with 10 anonymized dicom files to diagnose the > warnings we get? > > Thanks > > ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > > > Hi Cecile, > > > > We were wondering whether Loris has a tool to check if there are problems > > with the dcm files, before trying to upload them. Something that could > > provide the same results provided in the warning_output, this is the > > summary from the mri_upload at the front-page. Also which attributes of > the > > dcm header would trigger a warning? is there a dcm file header > > specification for Loris? > > > > Thanks > > > > Sotirios > > > > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos < > > sotirisnik at gmail.com> ??????: > > > >> Hi, > >> > >> Yes, by parsing now() into unix_timestamp function it worked,but i > >> thought that something else was causing the 2nd issue. > >> Thanks > >> > >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < > >> xavier.lecoursboucher at mcgill.ca> wrote: > >> > >>> Hi Sotirios, > >>> > >>> The first error occurs because the QCFirstChangeTime and columns are of > >>> type `unsigned integer` and not `datatime`. You should be using > >>> UNIX_TIMESTAMP() instead of NOW(). > >>> > >>> The second error occurs because the trigger triggers a rollback of the > >>> insert statement in the files table. > >>> See mysql documentation for trigger error handling. > >>> > >>> An error during either a BEFORE or AFTER trigger results in failure of > >>> the entire statement that caused trigger invocation. > >>> > >>> > >>> Thank you for sharing that. I hope it helps. > >>> -- Xavier > >>> > >>> ------------------------------ > >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < > >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios > >>> Nikoloutsopoulos > >>> *Sent:* October 1, 2019 8:33 AM > >>> *To:* Cecile Madjar > >>> *Cc:* loris-dev at bic.mni.mcgill.ca ; > >>> Christine Rogers, Ms. > >>> *Subject:* Re: [Loris-dev] Import mri - scripts > >>> > >>> When mincs are inserted their corresponding rows at the file table are > >>> inserted too > >>> [image: image.png] > >>> > >>> i would like to insert their rows at file_qcstatus as well, because i > >>> don't want manually to label them as passed throught the interface > >>> > >>> [image: image.png] > >>> > >>> > >>> That is the trigger i wrote > >>> > >>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` > AFTER > >>> INSERT ON `files` FOR EACH ROW > >>> BEGIN > >>> INSERT INTO files_qcstatus > >>> SET FileID = NEW.FileID, > >>> SeriesUID = NEW.SeriesUID, > >>> EchoTime = NEW.EchoTime, > >>> QCStatus = "Pass", > >>> QCFirstChangeTime = NOW(), > >>> QCLastChangeTime = NOW(); > >>> END > >>> > >>> although it contains some errors > >>> > >>> DBD::mysql::db do failed: Out of range value for column > >>> 'QCFirstChangeTime' at row 1 at > >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. > >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign > >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT > >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` > (`FileID`)) > >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> > >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < > >>> cecile.madjar at mcin.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> In the mri_upload table, there is a TarchiveID column associated with > >>> the MRI upload you inserted. When this value is NULL, it means no > DICOMs > >>> were inserted into the tarchive tables. At the end of the insertion of > the > >>> DICOMs in the tarchive tables, this value is updated with the correct > >>> TarchiveID associated with the upload. > >>> > >>> Could this correspond to what you want to do? > >>> > >>> Regarding the files_qcstatus, this table is only linked to the files > >>> table (hence, the MINC files). You could always create a new table for > >>> dicom_qcstatus and link it to the tarchive table? > >>> > >>> C?cile > >>> > >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Hi, > >>> > >>> i would like whenever a dicom is imported to mark all their > >>> coressponding qc_status to "pass". I was thinking of creating a > trigger for > >>> that, but which tables do i need to add entries to? So far from what i > see > >>> i need to add entres at the table "files" whenever an insertion > happens to > >>> files_qcstatus. > >>> > >>> Thanks > >>> > >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Oh, sorry i should have asked for StudyID, at the beginning of my email > >>> i sent 3 hours ago (not StudyUID). > >>> > >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Hi, > >>> > >>> that's the Study Instance UID, not the StudyID. So the StudyID i am > >>> looking for is not stored in the database? > >>> > >>> [image: image.png] > >>> > >>> Thanks. > >>> > >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < > >>> cecile.madjar at mcin.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> The StudyUID is stored in the DicomArchiveID field of the > >>> tarchive table. It can also be found in the metadata field but it is > mixed > >>> with many other information. > >>> > >>> Hope this helps, > >>> > >>> C?cile > >>> > >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Hi, > >>> > >>> Is StudyUID stored somewhere at the tables? At the tarchive table, > >>> specifically at the AcquisitonMetadata column i found something called > >>> 'Unique Study ID" in its context, but that must be the Study Instance > UID. > >>> > >>> Thanks > >>> > >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < > >>> cecile.madjar at mcin.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> Your observation is correct. A little explanation below. > >>> > >>> MINC files get inserted into the MRI violation tables if: > >>> > >>> - the scan type could not be identified (not matching an entry in > >>> the mri_protocol table) > >>> - one parameter of the scan type is out of the expected range > >>> present in the mri_protocol_checks (extra filtering in case you > need to be > >>> stricker on some parameters not present in the mri_protocol table) > >>> - if the CandID and PSCID do not match > >>> > >>> The following cases do not get in the MRI violation tables as it > happens > >>> before the conversion of the DICOM to MINC files and only MINC files > >>> violations are logged there: > >>> > >>> - "No single DICOM" (since no valid DICOM could be found to convert > >>> to MINC) > >>> - "Study already inserted" (duplicate StudyUID) since this error > >>> happens at the dicomTar.pl level (way before conversion into MINC > files) > >>> > >>> Glad everything is working out!! > >>> Best, > >>> > >>> C?cile > >>> > >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Hi, > >>> > >>> the mri passed, for some reason it consumed 5.12GB of ram. Now about > the > >>> mri_violations, dicoms are triggered to be inserted there only if > there is > >>> a violation for Tr_min, Tr_max, in general for its header parameter? > >>> Because i don't see the cases of 'No single dicom" or with the 2 > studyiuid > >>> to be there. > >>> > >>> Thanks > >>> > >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < > >>> cecile.madjar at mcin.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> Sorry to hear you are having issues with the memory. I think most of > our > >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. > >>> > >>> Hope this helps! > >>> > >>> C?cile > >>> > >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Hi, > >>> > >>> about that dicom that had that insertion error it's about 30mb and when > >>> it is being processed the ram is being drastically increased from 2gb > to > >>> 3.28 and then the whole virtual machine is frozen. What is the > recommended > >>> size of ram for using Loris? > >>> > >>> Thanks > >>> > >>> [image: image.png] > >>> > >>> > >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < > >>> cecile.madjar at mcin.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> Glad to see that the StudyUID problem was fixed! > >>> > >>> For the delete script issue, if you are absolutely certain that no > >>> processes are run for that uploadID, you can update the mri_upload > table > >>> and set the column Inserting to 0 instead of 1 for that uploadID. It > >>> looks like for some reason the scripts did not update this field when > it > >>> stopped the insertion. Not sure why that would be the case though. > >>> Note: only do that update if you are certain that there is no > processing > >>> happening. > >>> > >>> Hope this helps! > >>> > >>> > >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Hi, > >>> > >>> about the Dicoms i reported that didn't have a StudyID they actually do > >>> > >>> [image: image.png] > >>> > >>> > >>> [image: image.png] > >>> > >>> I thought that this might be a permission because "w" was missing at > the > >>> group. After using chmod -R 775 only 102809579 passed, but with no mnic > >>> files. Also now i have this error > >>> > >>> (loris-mri-python) lorisadmin at loris-VirtualBox > :/data/loris/bin/mri/tools$ > >>> ./delete_imaging_upload.pl -uploadID 34 -ignore > >>> Cannot delete upload 34: the MRI pipeline is currently processing it. > >>> > >>> How can solve this? > >>> > >>> Thanks > >>> > >>> > >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Hi, > >>> > >>> Here is our auto dicom uploading python script: > >>> > https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py > >>> > >>> To give you a brief idea: > >>> Per folder it will: > >>> 1) Delete all the .bak files > >>> 2) Locate .dcm files and update the Patient header > >>> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, > >>> TE_max parameters of T1 protocol and do an update at the mri_protocol > table > >>> > https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 > >>> For some reason some files are missing SeriesDescription/ProtocolName > >>> > >>> In total i have 7 folders > >>> > >>> [image: image.png] > >>> > >>> 3/7 passed > >>> > >>> [image: image.png] > >>> > >>> Also about the first patient with DC0000 had a violation "T1 AXIAL SE > >>> GADO", but my script didn't output a TE of 17 nowhere and i find that > weird > >>> since Loris detects the SeriesDescription. > >>> [image: image.png] > >>> > >>> > >>> Now about the 4/7 that didn't passed > >>> > >>> 102327840 and 102809579 outputs "The target directory does not contain > a > >>> single DICOM file.", therefore they are missing their StudyUID > >>> > >>> 102506134 has 2 studyuid "You can't use it with data from multiple > >>> studies." > >>> > >>> and 102761034 "No data could be converted into valid MINC files. > >>> localizer, scout will not be considered!" What is this? > >>> > >>> If i wanted to force the insertion of 102327840, 102809579 and > 102506134 > >>> can i just pass a flag parameter to batch_uploads_imageuploader.pl? or > >>> modify imaging_upload_file.pl? > >>> > >>> Thank you, > >>> > >>> Sotirios > >>> > >>> PS > >>> > >>> To diagnose a folder search the name of the folder at dicom_output.txt. > >>> > >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios, > >>> Glad to hear about your progress. > >>> > >>> Yes, the script you used to delete imaging data is fully documented > here > >>> < > https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md > > > >>> -- let us know if you didn't find the answers you were looking for > there. > >>> (Is it possible the null row in *mri_scanner* seen in your database > >>> management software is a visual placeholder for you as the user? I'm > not > >>> sure why a scanner would ever be registered with ID='0' as your > screenshot > >>> showed.) > >>> > >>> Best, > >>> Christine > >>> > >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> I fixed it with this > >>> > >>> [image: image.png] > >>> > >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Hi, > >>> > >>> I tried to create a new candidate using the API, is there something > >>> wrong with the structure? why did i receive a 500 internal error? In > the > >>> loris-error log it state that there is something wrong with token, but > i > >>> verfied that the type of the token is a string. > >>> > >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client > >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 > >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type > string, > >>> null given, called in > >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and > >>> defined in > >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack > >>> trace:\n#0 > /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): > >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 > >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): > >>> SinglePointLogin->authenticate()\n#2 > >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): > >>> NDB_Client->initialize('/var/www/loris/...')\n#3 > >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): > >>> Loris\\API\\APIBase->__construct('POST')\n#4 > >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): > >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n > thrown in > >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 > >>> > >>> [image: image.png] > >>> > >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Hi, > >>> > >>> Is there a way also to delete candidates? Just to let you know what i > >>> did to clear candidates, because maybe i may have missed dependencies. > >>> > >>> First i deleted all their uploads > >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit > >>> the backup file ? ) > >>> > >>> Afterwards i had some scanner candidates, so i deleted all the entries > >>> from mri_scanner except that i couldn't delete this entry with the 0 > ID. > >>> > >>> [image: image.png] > >>> > >>> > >>> Lastly i deleted the session and then the candidate table. > >>> > >>> Thanks > >>> > >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> We recommend that you use our existing tools for creating new > candidates > >>> - either the LORIS API or if you are using a PHP script, by calling > the Candidate > >>> class's createNew() > >>> < > https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 > >function. > >>> These will create the necessary records for you. (It's not > recommended to > >>> make direct modifications to mysql database tables in your script, if I > >>> understand you.) > >>> > >>> The CandID should be a randomized 6 digit randomized ID, and there are > >>> multiple reasons for this. > >>> You can use the PSCID for project-specific IDs and the External ID > field > >>> in the candidate table can also be used for any values you like. > >>> Additionally, any number of custom IDs can be added in parallel - these > >>> are entered/visible in the Candidate Information module and added in > the > >>> back-end as candidate parameters. > >>> > >>> Best, > >>> Christine > >>> > >>> > >>> > >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Hi, > >>> > >>> We are building a script that will auto insert the candidates based on > >>> their ExternalID. We would like to know whethere when we are creating > a new > >>> profile in the candidate table, if we also have to insert a new record > at > >>> another table? Furthermore is there a problem that in our case CandID > won't > >>> be a 6digit? ( should we start it from 100000?) > >>> > >>> Thanks > >>> > >>> [image: image.png] > >>> > >>> > >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < > >>> melanie.legault2 at mcgill.ca> ??????: > >>> > >>> That would normally be the case but the numeric part of the PSCID get > >>> paded with 0 on the left. > >>> > >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char > >>> with a min value of 1, the sequence would be: > >>> > >>> ABC0001 > >>> ABC0002 > >>> ... > >>> ABC0010 > >>> ... > >>> > >>> thus sorting them ascending will always get the latest value generated > >>> as the max value. > >>> > >>> M?lanie > >>> > >>> ------------------------------ > >>> *From:* Sotirios Nikoloutsopoulos > >>> *Sent:* September 13, 2019 10:15 > >>> *To:* Melanie Legault, Mrs > >>> *Cc:* Christine Rogers, Ms. ; > >>> loris-dev at bic.mni.mcgill.ca > >>> *Subject:* Re: [Loris-dev] Import mri - scripts > >>> > >>> I see, although the PSCID value is varchar(255), it must be stored > >>> within a specific length of characters. Otherwise if we were to sort > >>> strings with different lengths the result would not be sorted > correctly ( > >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). > >>> > >>> Thanks > >>> > >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < > >>> melanie.legault2 at mcgill.ca> ??????: > >>> > >>> Hello Sotirios, > >>> > >>> There is no `last value` stored anywhere. > >>> The code simply look for the PSCID with the max value and increase that > >>> value by 1 in order to generate the next PSCID. > >>> > >>> Hope this info help. > >>> > >>> M?lanie Legault | Software developer | Faculty of Medicine | McGill > >>> University > >>> 3801 University, Montr?al, QC H3A 2B4 > >>> > >>> ------------------------------ > >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < > >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios > >>> Nikoloutsopoulos > >>> *Sent:* September 13, 2019 9:43 > >>> *To:* Christine Rogers, Ms. > >>> *Cc:* loris-dev at bic.mni.mcgill.ca > >>> *Subject:* Re: [Loris-dev] Import mri - scripts > >>> > >>> Hi, > >>> > >>> how does Loris determine the next available PSCID value for a new > >>> candidate? https://github.com/aces/Loris/wiki/Project-Customization > >>> e.x in the default case the PSCID is sequential, but where do we store > the > >>> last value for the sequential sequence? > >>> > >>> Thanks > >>> > >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Hi, > >>> > >>> the parameters in the mri_protocol you have assigned are global > >>> standard? or were assigned after trial and error? > >>> > >>> Thanks > >>> > >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> Given you have done the initial setup of your tables to match your > >>> intended protocol/parameters according to instructions -- > >>> the Troubleshooting guide documentation recommends > >>> < > https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes > > > >>> re-running the pipeline (and first deleting prior uploads). > >>> > >>> Best, > >>> Christine > >>> > >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> *if i were to change their status to resolve what would happen? > >>> > >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> I noticed that i can view the mnics at the brainbrowser from the > >>> mri_violations page ( those mnics are stored at > /data/loris/data/trashbin/ > >>> if i were to click their issue to resolve what would happend? would > they > >>> appear in the dicom_archive view too? ). > >>> > >>> > >>> > >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Hi, > >>> > >>> The defaut values of the schema exists in my local database. If i > adjust > >>> the default values of TR_min and TE_min the mincs will be uploaded? > >>> > >>> [image: image.png] > >>> > >>> > >>> [image: image.png] > >>> > >>> Thanks > >>> > >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> Is it possible that you haven't set up your mri_protocol table ? (and > >>> mri_scan_type table too, for additional types of scans) > >>> > >>> Like the psc table, this is a pre-requisite for the Imaging insertion > >>> setup : See the install/setup documentation : > >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md > >>> > >>> To add new rows, just use MySQL insert statements. You can adapt the > >>> insert statements which load the default table values --> e.g. Here on > >>> GitHub : > >>> > https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 > >>> (see also the mri_scan_type table) > >>> > >>> Best, > >>> Christine > >>> > >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> I see that i can edit the values but not how to insert new rows. > >>> > >>> [image: image.png] > >>> > >>> If i choose Inserted with flag then will the minc be inserted? > >>> > >>> [image: image.png] > >>> > >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> Glad to hear that *dcmodify* worked correctly. > >>> > >>> For the MRI Violations module, the screenshot is enough. > >>> > >>> It says "could not identify scan type", which we knew already. Did you > >>> click on the link on those words? > >>> > >>> It will take you to the next page of the module, showing for each scan > >>> what the scan parameters were, and will also show for comparison what's > >>> stored in your *mri_protocol* table. > >>> Compare these values to find which parameter was not correct according > >>> to your *mri_protocol* table scan type definitions. > >>> > >>> You may end up broadening your mri_protocol value ranges (e.g. TR, TE) > >>> for scans. > >>> This can be done in the front-end, by editing the database table > >>> directly in the same subpage of the MRI Violations module. > >>> > >>> The MRI Violations module features are explained in more detail in the > >>> Help text for this module inside LORIS (click the ["?"] icon in the > menu > >>> bar.) > >>> > >>> See also: Loris-MRI troubleshooting guide > >>> < > https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md > > > >>> : no MINCs inserted- violated scans > >>> > >>> Best, > >>> Christine > >>> > >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Hi, > >>> > >>> looks like my previous email's attachment wasn't delivered due to > >>> security reasons, i uploaded my file at google drive > >>> > https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing > >>> > >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Hi, > >>> > >>> From Dicat's view seems that dcmodify worked in both cases > >>> > >>> [image: image.png] > >>> > >>> [image: image.png] > >>> > >>> For the mri_violations i attached the .html output from webbrowser, so > >>> that you can check the filelds easier. > >>> > >>> [image: image.png] > >>> > >>> Thanks > >>> > >>> > >>> > >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios -- > >>> Great, sounds like more progress. > >>> > >>> About the dcmodify command -- I'm not sure why you're getting an Endian > >>> warning. (it's a warning not an error, correct?) > >>> To clarify -- Were the DICOM headers (PatientName) all successfully > >>> relabelled, after the command ran? > >>> > >>> You can use also our DICAT tool (https://github.com/aces/DICAT) to > >>> verify and/or update local DICOM headers -- though your dcmodify > command is > >>> a great and fast solution for bulk header updates. > >>> > >>> If you're concerned about fields being changed (e.g. "(2001,105f)" from > >>> the warning message) - you can also dcmdump a DICOM slice before and > look > >>> at these fields specifically. > >>> It's also not a bad "sanity check" to backup your DICOMS before/after > >>> running dcmodify, and use dcmdump on each version to diff the outputs > -- > >>> this will pinpoint what changed. > >>> > >>> Re the protocol violation -- AcquisitionProtocol not recognized or > >>> unknown : this means your scans did not match what is stored in your > >>> mri_protocol table. > >>> Check the MRI Violations front-end module -- can you see why they > didn't > >>> match? > >>> Send us an example, in addition to the contents of the mri_protocol > >>> table, if you can't find the source of the mismatch. > >>> > >>> Best, > >>> Christine > >>> > >>> > >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Here is the psc table > >>> [image: image.png] > >>> > >>> I created 2 candidates profiles through the interface > >>> > >>> [image: image.png] > >>> > >>> then runned dcmodify command to a dicom file > >>> > >>> dcmodify -ma PatientName="DCC0000_258024_V1" > >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm > >>> > >>> and got those warning: is this okay? > >>> W: Found element (2001,105f) with VR UN and undefined length, reading a > >>> sequence with transfer syntax LittleEndianImplicit (CP-246) > >>> W: Found element (2005,1083) with VR UN and undefined length, reading a > >>> sequence with transfer syntax LittleEndianImplicit (CP-246) > >>> W: Found element (2005,1402) with VR UN and undefined length, reading a > >>> sequence with transfer syntax LittleEndianImplicit (CP-246) > >>> W: Found element (2005,140f) with VR UN and undefined length, reading a > >>> sequence with transfer syntax LittleEndianImplicit (CP-246) > >>> W: Found element (2001,105f) with VR UN and undefined length, reading a > >>> sequence with transfer syntax LittleEndianImplicit (CP-246) > >>> W: Found element (2005,1083) with VR UN and undefined length, reading a > >>> sequence with transfer syntax LittleEndianImplicit (CP-246) > >>> > >>> dcmodify at another Dicom didn't show warnings. Below you can see the > >>> execution for the second dicom. Mnics could not be inserted due to > >>> AcquisitionProtocol being unknown. > >>> > >>> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/ > >>> imaging_upload_file.pl -profile prod -upload_id 12 > >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose > >>> > >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' > >>> -delete > >>> > >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs > >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose > >>> Source: /tmp/ImagingUpload-18-36-mTrxXs > >>> Target: /data/loris/data/tarchive > >>> > >>> Testing for database connectivity. > >>> Database is available. > >>> > >>> You will archive the dir : ImagingUpload-18-36-mTrxXs > >>> > >>> You are creating a tar with the following command: > >>> > >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar > >>> ImagingUpload-18-36-mTrxXs > >>> > >>> > >>> getting md5sums and gzipping!! > >>> > >>> * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs > >>> * Archive target location : > >>> > /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar > >>> * Name of creating host : 127.0.1.1 > >>> * Name of host OS : Linux > >>> * Created by user : lorisadmin > >>> * Archived on : 2019-09-06 18:36:50 > >>> * dicomSummary version : 1 > >>> * dicomTar version : 1 > >>> * md5sum for DICOM tarball : > b1dcdc8903dd2d9a5443227db2aa2814 > >>> ImagingUpload-18-36-mTrxXs.tar > >>> * md5sum for DICOM tarball gzipped : > aeae87f20155a6805f7e0cfe5212ea5f > >>> ImagingUpload-18-36-mTrxXs.tar.gz > >>> * md5sum for complete archive : > 1d9258d1f077ebc49111ab7ba22a8d6e > >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar > >>> > >>> Adding archive info into database > >>> > >>> Removing temporary files from target location > >>> > >>> > >>> Done adding archive info into database > >>> > >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation > >>> -profile prod > >>> > \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar > >>> -uploadID 12 -verbose > >>> md5sum > >>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar > >>> PSCID is: DCC0001 > >>> CandID id: 602102 > >>> visit_label is: V1 > >>> PSCID is: DCC0001 > >>> CandID id: 602102 > >>> visit_label is: V1 > >>> candidate id 602102 > >>> Set centerID = 1 > >>> PSCID is: DCC0001 > >>> CandID id: 602102 > >>> visit_label is: V1 > >>> PSCID is: DCC0001 > >>> CandID id: 602102 > >>> visit_label is: V1 > >>> > >>> Number of MINC files that will be considered for inserting into the > >>> database: 2 > >>> > >>> log dir is /data/loris/data//logs and log file is > >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log > >>> PSCID is: DCC0001 > >>> CandID id: 602102 > >>> visit_label is: V1 > >>> PSCID is: DCC0001 > >>> CandID id: 602102 > >>> visit_label is: V1 > >>> candidate id 602102 > >>> > >>> log dir is /data/loris/data//logs and log file is > >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log > >>> PSCID is: DCC0001 > >>> CandID id: 602102 > >>> visit_label is: V1 > >>> PSCID is: DCC0001 > >>> CandID id: 602102 > >>> visit_label is: V1 > >>> candidate id 602102 > >>> > >>> Cleaning up temp files: rm -rf > >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* > >>> > >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ > cat > >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log > >>> > >>> ==> Loading file from disk > >>> > /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc > >>> > >>> --> mapping DICOM parameter for > >>> > /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc > >>> > >>> ==> computing md5 hash for MINC body. > >>> > >>> --> md5: 02022dda60d9de429340fec838f50cfe > >>> > >>> ==> verifying acquisition protocol > >>> > >>> Acquisition protocol is unknown > >>> > >>> --> The minc file cannot be registered since the AcquisitionProtocol > >>> is unknown > >>> > >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios: > >>> > >>> Sure -- you can delete imaging datasets with the > *delete_imaging_upload* > >>> script -- > >>> details here: > >>> > https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md > >>> > >>> What's in your *psc* table? (Is it properly populated? This is a > >>> pre-requisite to loading imaging data. > >>> < > https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database > > > >>> ) > >>> The foreign key constraint error on the candidate record is curious. > >>> > >>> There are also a few options for creating candidates when inserting > >>> imaging data: > >>> > >>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline > >>> > >>> a. via the LORIS API -- Create the candidates (and visits, optionally I > >>> think) > >>> How to: > >>> > https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api > >>> Ensure you get the DCCID/CandID assigned by LORIS. > >>> > >>> Then as a second step: > >>> b. Use the imaging insertion pipeline > >>> < > https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets > > > >>> to load your DICOMs. > >>> You will want to first ensure that the PatientName header in the DICOMs > >>> as well as tar package are correctly labelled with > PSCID_DCCID_VisitLabel > >>> > >>> -- Method 2: for BIDS-format datasets: > >>> How to : > >>> > https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets > >>> > >>> Be sure to use the *-c* and *-s* options when running the bids_import > script, > >>> to automatically create your candidates and sessions. > >>> > >>> Best, > >>> Christine > >>> > >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> How do i delete a Study? And everytime do i have to create a new > >>> candidate to get DCCID and a PSCID? > >>> > >>> *First execution:* > >>> > >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ > >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > > >>> log.txt > >>> Use of uninitialized value $_ in pattern match (m//) at ./ > >>> batch_uploads_imageuploader.pl line 144. > >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign > >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` > >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at > >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. > >>> ERROR: Failed to insert record in table mri_scanner: > >>> The following database commands failed: > >>> PREPARE s FROM 'INSERT INTO mri_scanner > >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; > >>> SET > >>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips > >>> Medical Systems'; > >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; > >>> Error obtained:Cannot add or update a child row: a foreign key > >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` > >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code > 1452) > >>> > >>> ERROR: The validation has failed. Either re-run the validation again > >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to force > the > >>> execution. > >>> > >>> > >>> The tarchiveLoader.pl insertion script has failed. > >>> Can't exec "mail": No such file or directory at ./ > >>> batch_uploads_imageuploader.pl line 249. > >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl > >>> line 250. > >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl > >>> line 251. > >>> > >>> > >>> *And second execution: * > >>> > >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ > >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > > >>> log.txt > >>> Use of uninitialized value $_ in pattern match (m//) at ./ > >>> batch_uploads_imageuploader.pl line 144. > >>> > >>> PROBLEM: > >>> The user 'lorisadmin' has already inserted this study. > >>> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. > >>> This is the information retained from the first time the study was > >>> inserted: > >>> > >>> * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy > >>> * Archive target location : > >>> > /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar > >>> * Name of creating host : 127.0.1.1 > >>> * Name of host OS : Linux > >>> * Created by user : lorisadmin > >>> * Archived on : 2019-09-04 18:33:05 > >>> * dicomSummary version : 1 > >>> * dicomTar version : 1 > >>> * md5sum for DICOM tarball : > 4a301b0318178b09b91e63544282364d > >>> ImagingUpload-18-33-Qq7HGy.tar > >>> * md5sum for DICOM tarball gzipped : > 9d95ea2b9111be236808bfd65d7e65ec > >>> ImagingUpload-18-33-Qq7HGy.tar.gz > >>> * md5sum for complete archive : > ab19a86357f1d4053aa3b81c8a071053 > >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar > >>> > >>> > >>> Last update of record: > >>> > >>> > >>> > >>> The dicomTar.pl execution has failed. > >>> Can't exec "mail": No such file or directory at ./ > >>> batch_uploads_imageuploader.pl line 249. > >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl > >>> line 250. > >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl > >>> line 251. > >>> > >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> Ok, this sounds like good progress. Let us know when you next > encounter > >>> issues as you progress through the Imaging Install/Setup docs > >>> . > >>> I'll look into how we can better handle the incoming/ directory next > >>> time. > >>> Best, > >>> Christine > >>> > >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is > >>> populated correctly except its port is 'port' : ''. Also i have > tested > >>> that i can connect to MySQL with lorisuser. > >>> > >>> I executed the script again, because the only error i had previously > was > >>> that the /data/incoming folder didn't exist and there are no errors > >>> reported back except of warnings < on the > >>> command line interface can be insecure>>. > >>> > >>> > >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> It's possible -- if the script was unable to connect to the database > >>> during its execution (e.g. typo in the password), that would explain > the > >>> underpopulated Image path and Loris-MRI code path you saw in the Config > >>> module. > >>> It's hard to tell without seeing the output from your script run -- Did > >>> you see a sign of any such error? > >>> The Config fields are populated by the imaging_install.sh script > (starting > >>> at line 222 > >>> < > https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222> > >>> ) > >>> > >>> For example, check if the database connection information was populated > >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py > >>> > >>> Best, > >>> Christine > >>> > >>> > >>> > >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> Hi Christine, > >>> > >>> If you are referring to the imaging_install.sh here is an image with > the > >>> configurations i typed. Maybe the problem is somewhere at the last part > >>> which asks to configure as much as possible automatically? > >>> > >>> Thanks > >>> > >>> > >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < > >>> christine.rogers at mcgill.ca> ??????: > >>> > >>> Hi Sotirios, > >>> > >>> Glad to hear your LORIS core install is up and working and all the > >>> front-end pages are loading. > >>> > >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project > >>> > and the web interface worked. > >>> > >>> Yes, it's important that project/ have 775 permissions and that > >>> lorisadmin be part of the sudoers group, per step 1 in the install > >>> Readme . > >>> > >>> > As for the Paths, LORIS-MRI code and Image should change LORIS to > >>> loris, right? > >>> > >>> These imaging paths will be updated during your imaging installation > >>> by an automated script -- > >>> you do not need to set them manually via the Config module. > >>> Please continue to follow the Setup Guide > >>> for detailed steps to > follow. > >>> > >>> Best, > >>> Christine > >>> > >>> > >>> > >>> > >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> wrote: > >>> > >>> As for the Paths, LORIS-MRI code and Image should change LORIS to > loris, > >>> right? > >>> > >>> [image: image.png] > >>> > >>> > >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos < > >>> sotirisnik at gmail.com> ??????: > >>> > >>> Hi, > >>> > >>> i used > >>> > >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - > >>> sudo apt-get install -y nodejs > >>> > >>> > >>> you had suggested in the past, make worked and now i can see all the > >>> contents in the web-interface, but i don't need make install? > >>> > >>> Thanks > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > >>> > >>> -- > >>> > >>> christine.rogers at mcgill.ca > >>> McGill Centre for Integrative Neuroscience | MCIN.ca > >>> Montreal Neurological Institute > >>> McGill University | Montreal | Canada > >>> > >>> _______________________________________________ > >>> Loris-dev mailing list > >>> Loris-dev at bic.mni.mcgill.ca > >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > >>> > >>> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html > > > > ------------------------------ > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > End of Loris-dev Digest, Vol 64, Issue 16 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Wed Nov 13 16:22:23 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 13 Nov 2019 23:22:23 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: HI Yang, We make use of pydicom library too. Now about the validate.py i see that you check if some attributes are missing such as PatientID, PatientName which all of our files contains that info. Maybe i have missed something on the setup of my other virtual machine ( although one dicom passed on the new vm successfully, the others that were inserted correctly on my old vm fails on the new one ), i think that i had asked about this error "Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/ batch_uploads_imageuploader.pl line 144." but i don't remember the solution. Thanks ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding ??????: > Hey, Sotirios, > > Christine from the LORIS team mentioned you had some issue with DICOM. I > am a fellow developer for an external project using LORIS, kind of just > like you. We had to implement DICOM upload as well but more as a fully > automated pipeline actually. > > While we were building CNBP, we had coded up some minor Python functions > to check DICOM integrity (and simple validations) and you might be able to > gain some inspiration from it and help you with your cause. For more > comprehensive solution, PyDICOM ( > https://pydicom.github.io/pydicom/stable/getting_started.html#) seems > like a descent python package to help out with a lot of DICOM data checks > (I was essentially just building customized wrapper calls to them). You can > see some example scripts here as part of our DICOM submodule. It is pretty > rough around the edges but hopefully point you in the right direcitons > https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py > > Cheers, > > Yang Ding, PhD. > Canadian Neonatal Brain Platform Architect > > On Tue, Nov 12, 2019 at 8:29 AM > wrote: > >> Send Loris-dev mailing list submissions to >> loris-dev at bic.mni.mcgill.ca >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> or, via email, send a message with subject or body 'help' to >> loris-dev-request at bic.mni.mcgill.ca >> >> You can reach the person managing the list at >> loris-dev-owner at bic.mni.mcgill.ca >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Loris-dev digest..." >> >> >> Today's Topics: >> >> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 12 Nov 2019 15:28:26 +0200 >> From: Sotirios Nikoloutsopoulos >> To: Cecile Madjar >> Cc: loris-dev at bic.mni.mcgill.ca >> Subject: Re: [Loris-dev] Import mri - scripts >> Message-ID: >> > 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi, >> >> Could we send you a link with 10 anonymized dicom files to diagnose the >> warnings we get? >> >> Thanks >> >> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >> > Hi Cecile, >> > >> > We were wondering whether Loris has a tool to check if there are >> problems >> > with the dcm files, before trying to upload them. Something that could >> > provide the same results provided in the warning_output, this is the >> > summary from the mri_upload at the front-page. Also which attributes of >> the >> > dcm header would trigger a warning? is there a dcm file header >> > specification for Loris? >> > >> > Thanks >> > >> > Sotirios >> > >> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos < >> > sotirisnik at gmail.com> ??????: >> > >> >> Hi, >> >> >> >> Yes, by parsing now() into unix_timestamp function it worked,but i >> >> thought that something else was causing the 2nd issue. >> >> Thanks >> >> >> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >> >> xavier.lecoursboucher at mcgill.ca> wrote: >> >> >> >>> Hi Sotirios, >> >>> >> >>> The first error occurs because the QCFirstChangeTime and columns are >> of >> >>> type `unsigned integer` and not `datatime`. You should be using >> >>> UNIX_TIMESTAMP() instead of NOW(). >> >>> >> >>> The second error occurs because the trigger triggers a rollback of the >> >>> insert statement in the files table. >> >>> See mysql documentation for trigger error handling. >> >>> >> >>> An error during either a BEFORE or AFTER trigger results in failure of >> >>> the entire statement that caused trigger invocation. >> >>> >> >>> >> >>> Thank you for sharing that. I hope it helps. >> >>> -- Xavier >> >>> >> >>> ------------------------------ >> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >> >>> Nikoloutsopoulos >> >>> *Sent:* October 1, 2019 8:33 AM >> >>> *To:* Cecile Madjar >> >>> *Cc:* loris-dev at bic.mni.mcgill.ca ; >> >>> Christine Rogers, Ms. >> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >> >>> >> >>> When mincs are inserted their corresponding rows at the file table are >> >>> inserted too >> >>> [image: image.png] >> >>> >> >>> i would like to insert their rows at file_qcstatus as well, because i >> >>> don't want manually to label them as passed throught the interface >> >>> >> >>> [image: image.png] >> >>> >> >>> >> >>> That is the trigger i wrote >> >>> >> >>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` >> AFTER >> >>> INSERT ON `files` FOR EACH ROW >> >>> BEGIN >> >>> INSERT INTO files_qcstatus >> >>> SET FileID = NEW.FileID, >> >>> SeriesUID = NEW.SeriesUID, >> >>> EchoTime = NEW.EchoTime, >> >>> QCStatus = "Pass", >> >>> QCFirstChangeTime = NOW(), >> >>> QCLastChangeTime = NOW(); >> >>> END >> >>> >> >>> although it contains some errors >> >>> >> >>> DBD::mysql::db do failed: Out of range value for column >> >>> 'QCFirstChangeTime' at row 1 at >> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >> >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign >> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` >> (`FileID`)) >> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> >> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >> >>> cecile.madjar at mcin.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> In the mri_upload table, there is a TarchiveID column associated with >> >>> the MRI upload you inserted. When this value is NULL, it means no >> DICOMs >> >>> were inserted into the tarchive tables. At the end of the insertion >> of the >> >>> DICOMs in the tarchive tables, this value is updated with the correct >> >>> TarchiveID associated with the upload. >> >>> >> >>> Could this correspond to what you want to do? >> >>> >> >>> Regarding the files_qcstatus, this table is only linked to the files >> >>> table (hence, the MINC files). You could always create a new table for >> >>> dicom_qcstatus and link it to the tarchive table? >> >>> >> >>> C?cile >> >>> >> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Hi, >> >>> >> >>> i would like whenever a dicom is imported to mark all their >> >>> coressponding qc_status to "pass". I was thinking of creating a >> trigger for >> >>> that, but which tables do i need to add entries to? So far from what >> i see >> >>> i need to add entres at the table "files" whenever an insertion >> happens to >> >>> files_qcstatus. >> >>> >> >>> Thanks >> >>> >> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Oh, sorry i should have asked for StudyID, at the beginning of my >> email >> >>> i sent 3 hours ago (not StudyUID). >> >>> >> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Hi, >> >>> >> >>> that's the Study Instance UID, not the StudyID. So the StudyID i am >> >>> looking for is not stored in the database? >> >>> >> >>> [image: image.png] >> >>> >> >>> Thanks. >> >>> >> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >> >>> cecile.madjar at mcin.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> The StudyUID is stored in the DicomArchiveID field of the >> >>> tarchive table. It can also be found in the metadata field but it is >> mixed >> >>> with many other information. >> >>> >> >>> Hope this helps, >> >>> >> >>> C?cile >> >>> >> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Hi, >> >>> >> >>> Is StudyUID stored somewhere at the tables? At the tarchive table, >> >>> specifically at the AcquisitonMetadata column i found something called >> >>> 'Unique Study ID" in its context, but that must be the Study Instance >> UID. >> >>> >> >>> Thanks >> >>> >> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >> >>> cecile.madjar at mcin.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> Your observation is correct. A little explanation below. >> >>> >> >>> MINC files get inserted into the MRI violation tables if: >> >>> >> >>> - the scan type could not be identified (not matching an entry in >> >>> the mri_protocol table) >> >>> - one parameter of the scan type is out of the expected range >> >>> present in the mri_protocol_checks (extra filtering in case you >> need to be >> >>> stricker on some parameters not present in the mri_protocol table) >> >>> - if the CandID and PSCID do not match >> >>> >> >>> The following cases do not get in the MRI violation tables as it >> happens >> >>> before the conversion of the DICOM to MINC files and only MINC files >> >>> violations are logged there: >> >>> >> >>> - "No single DICOM" (since no valid DICOM could be found to convert >> >>> to MINC) >> >>> - "Study already inserted" (duplicate StudyUID) since this error >> >>> happens at the dicomTar.pl level (way before conversion into MINC >> files) >> >>> >> >>> Glad everything is working out!! >> >>> Best, >> >>> >> >>> C?cile >> >>> >> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Hi, >> >>> >> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now about >> the >> >>> mri_violations, dicoms are triggered to be inserted there only if >> there is >> >>> a violation for Tr_min, Tr_max, in general for its header parameter? >> >>> Because i don't see the cases of 'No single dicom" or with the 2 >> studyiuid >> >>> to be there. >> >>> >> >>> Thanks >> >>> >> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >> >>> cecile.madjar at mcin.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> Sorry to hear you are having issues with the memory. I think most of >> our >> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >> >>> >> >>> Hope this helps! >> >>> >> >>> C?cile >> >>> >> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Hi, >> >>> >> >>> about that dicom that had that insertion error it's about 30mb and >> when >> >>> it is being processed the ram is being drastically increased from 2gb >> to >> >>> 3.28 and then the whole virtual machine is frozen. What is the >> recommended >> >>> size of ram for using Loris? >> >>> >> >>> Thanks >> >>> >> >>> [image: image.png] >> >>> >> >>> >> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >> >>> cecile.madjar at mcin.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> Glad to see that the StudyUID problem was fixed! >> >>> >> >>> For the delete script issue, if you are absolutely certain that no >> >>> processes are run for that uploadID, you can update the mri_upload >> table >> >>> and set the column Inserting to 0 instead of 1 for that uploadID. It >> >>> looks like for some reason the scripts did not update this field when >> it >> >>> stopped the insertion. Not sure why that would be the case though. >> >>> Note: only do that update if you are certain that there is no >> processing >> >>> happening. >> >>> >> >>> Hope this helps! >> >>> >> >>> >> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Hi, >> >>> >> >>> about the Dicoms i reported that didn't have a StudyID they actually >> do >> >>> >> >>> [image: image.png] >> >>> >> >>> >> >>> [image: image.png] >> >>> >> >>> I thought that this might be a permission because "w" was missing at >> the >> >>> group. After using chmod -R 775 only 102809579 passed, but with no >> mnic >> >>> files. Also now i have this error >> >>> >> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >> :/data/loris/bin/mri/tools$ >> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >> >>> Cannot delete upload 34: the MRI pipeline is currently processing it. >> >>> >> >>> How can solve this? >> >>> >> >>> Thanks >> >>> >> >>> >> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Hi, >> >>> >> >>> Here is our auto dicom uploading python script: >> >>> >> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >> >>> >> >>> To give you a brief idea: >> >>> Per folder it will: >> >>> 1) Delete all the .bak files >> >>> 2) Locate .dcm files and update the Patient header >> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, >> >>> TE_max parameters of T1 protocol and do an update at the mri_protocol >> table >> >>> >> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >> >>> For some reason some files are missing SeriesDescription/ProtocolName >> >>> >> >>> In total i have 7 folders >> >>> >> >>> [image: image.png] >> >>> >> >>> 3/7 passed >> >>> >> >>> [image: image.png] >> >>> >> >>> Also about the first patient with DC0000 had a violation "T1 AXIAL SE >> >>> GADO", but my script didn't output a TE of 17 nowhere and i find that >> weird >> >>> since Loris detects the SeriesDescription. >> >>> [image: image.png] >> >>> >> >>> >> >>> Now about the 4/7 that didn't passed >> >>> >> >>> 102327840 and 102809579 outputs "The target directory does not >> contain a >> >>> single DICOM file.", therefore they are missing their StudyUID >> >>> >> >>> 102506134 has 2 studyuid "You can't use it with data from multiple >> >>> studies." >> >>> >> >>> and 102761034 "No data could be converted into valid MINC files. >> >>> localizer, scout will not be considered!" What is this? >> >>> >> >>> If i wanted to force the insertion of 102327840, 102809579 and >> 102506134 >> >>> can i just pass a flag parameter to batch_uploads_imageuploader.pl? >> or >> >>> modify imaging_upload_file.pl? >> >>> >> >>> Thank you, >> >>> >> >>> Sotirios >> >>> >> >>> PS >> >>> >> >>> To diagnose a folder search the name of the folder at >> dicom_output.txt. >> >>> >> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> Glad to hear about your progress. >> >>> >> >>> Yes, the script you used to delete imaging data is fully documented >> here >> >>> < >> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >> > >> >>> -- let us know if you didn't find the answers you were looking for >> there. >> >>> (Is it possible the null row in *mri_scanner* seen in your database >> >>> management software is a visual placeholder for you as the user? I'm >> not >> >>> sure why a scanner would ever be registered with ID='0' as your >> screenshot >> >>> showed.) >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> I fixed it with this >> >>> >> >>> [image: image.png] >> >>> >> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Hi, >> >>> >> >>> I tried to create a new candidate using the API, is there something >> >>> wrong with the structure? why did i receive a 500 internal error? In >> the >> >>> loris-error log it state that there is something wrong with token, >> but i >> >>> verfied that the type of the token is a string. >> >>> >> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 >> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type >> string, >> >>> null given, called in >> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 >> and >> >>> defined in >> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >> >>> trace:\n#0 >> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >> >>> SinglePointLogin->authenticate()\n#2 >> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n >> thrown in >> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >> >>> >> >>> [image: image.png] >> >>> >> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Hi, >> >>> >> >>> Is there a way also to delete candidates? Just to let you know what i >> >>> did to clear candidates, because maybe i may have missed dependencies. >> >>> >> >>> First i deleted all their uploads >> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit >> >>> the backup file ? ) >> >>> >> >>> Afterwards i had some scanner candidates, so i deleted all the entries >> >>> from mri_scanner except that i couldn't delete this entry with the 0 >> ID. >> >>> >> >>> [image: image.png] >> >>> >> >>> >> >>> Lastly i deleted the session and then the candidate table. >> >>> >> >>> Thanks >> >>> >> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> We recommend that you use our existing tools for creating new >> candidates >> >>> - either the LORIS API or if you are using a PHP script, by calling >> the Candidate >> >>> class's createNew() >> >>> < >> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >> >function. >> >>> These will create the necessary records for you. (It's not >> recommended to >> >>> make direct modifications to mysql database tables in your script, if >> I >> >>> understand you.) >> >>> >> >>> The CandID should be a randomized 6 digit randomized ID, and there are >> >>> multiple reasons for this. >> >>> You can use the PSCID for project-specific IDs and the External ID >> field >> >>> in the candidate table can also be used for any values you like. >> >>> Additionally, any number of custom IDs can be added in parallel - >> these >> >>> are entered/visible in the Candidate Information module and added in >> the >> >>> back-end as candidate parameters. >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> >> >>> >> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Hi, >> >>> >> >>> We are building a script that will auto insert the candidates based on >> >>> their ExternalID. We would like to know whethere when we are creating >> a new >> >>> profile in the candidate table, if we also have to insert a new >> record at >> >>> another table? Furthermore is there a problem that in our case CandID >> won't >> >>> be a 6digit? ( should we start it from 100000?) >> >>> >> >>> Thanks >> >>> >> >>> [image: image.png] >> >>> >> >>> >> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >> >>> melanie.legault2 at mcgill.ca> ??????: >> >>> >> >>> That would normally be the case but the numeric part of the PSCID get >> >>> paded with 0 on the left. >> >>> >> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char >> >>> with a min value of 1, the sequence would be: >> >>> >> >>> ABC0001 >> >>> ABC0002 >> >>> ... >> >>> ABC0010 >> >>> ... >> >>> >> >>> thus sorting them ascending will always get the latest value generated >> >>> as the max value. >> >>> >> >>> M?lanie >> >>> >> >>> ------------------------------ >> >>> *From:* Sotirios Nikoloutsopoulos >> >>> *Sent:* September 13, 2019 10:15 >> >>> *To:* Melanie Legault, Mrs >> >>> *Cc:* Christine Rogers, Ms. ; >> >>> loris-dev at bic.mni.mcgill.ca >> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >> >>> >> >>> I see, although the PSCID value is varchar(255), it must be stored >> >>> within a specific length of characters. Otherwise if we were to sort >> >>> strings with different lengths the result would not be sorted >> correctly ( >> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >> >>> >> >>> Thanks >> >>> >> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >> >>> melanie.legault2 at mcgill.ca> ??????: >> >>> >> >>> Hello Sotirios, >> >>> >> >>> There is no `last value` stored anywhere. >> >>> The code simply look for the PSCID with the max value and increase >> that >> >>> value by 1 in order to generate the next PSCID. >> >>> >> >>> Hope this info help. >> >>> >> >>> M?lanie Legault | Software developer | Faculty of Medicine | McGill >> >>> University >> >>> 3801 University, Montr?al, QC H3A 2B4 >> >>> >> >>> ------------------------------ >> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >> >>> Nikoloutsopoulos >> >>> *Sent:* September 13, 2019 9:43 >> >>> *To:* Christine Rogers, Ms. >> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >> >>> >> >>> Hi, >> >>> >> >>> how does Loris determine the next available PSCID value for a new >> >>> candidate? https://github.com/aces/Loris/wiki/Project-Customization >> >>> e.x in the default case the PSCID is sequential, but where do we >> store the >> >>> last value for the sequential sequence? >> >>> >> >>> Thanks >> >>> >> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Hi, >> >>> >> >>> the parameters in the mri_protocol you have assigned are global >> >>> standard? or were assigned after trial and error? >> >>> >> >>> Thanks >> >>> >> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> Given you have done the initial setup of your tables to match your >> >>> intended protocol/parameters according to instructions -- >> >>> the Troubleshooting guide documentation recommends >> >>> < >> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >> > >> >>> re-running the pipeline (and first deleting prior uploads). >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> *if i were to change their status to resolve what would happen? >> >>> >> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> I noticed that i can view the mnics at the brainbrowser from the >> >>> mri_violations page ( those mnics are stored at >> /data/loris/data/trashbin/ >> >>> if i were to click their issue to resolve what would happend? would >> they >> >>> appear in the dicom_archive view too? ). >> >>> >> >>> >> >>> >> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Hi, >> >>> >> >>> The defaut values of the schema exists in my local database. If i >> adjust >> >>> the default values of TR_min and TE_min the mincs will be uploaded? >> >>> >> >>> [image: image.png] >> >>> >> >>> >> >>> [image: image.png] >> >>> >> >>> Thanks >> >>> >> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> Is it possible that you haven't set up your mri_protocol table ? >> (and >> >>> mri_scan_type table too, for additional types of scans) >> >>> >> >>> Like the psc table, this is a pre-requisite for the Imaging insertion >> >>> setup : See the install/setup documentation : >> >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >> >>> >> >>> To add new rows, just use MySQL insert statements. You can adapt the >> >>> insert statements which load the default table values --> e.g. Here on >> >>> GitHub : >> >>> >> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >> >>> (see also the mri_scan_type table) >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> I see that i can edit the values but not how to insert new rows. >> >>> >> >>> [image: image.png] >> >>> >> >>> If i choose Inserted with flag then will the minc be inserted? >> >>> >> >>> [image: image.png] >> >>> >> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> Glad to hear that *dcmodify* worked correctly. >> >>> >> >>> For the MRI Violations module, the screenshot is enough. >> >>> >> >>> It says "could not identify scan type", which we knew already. Did >> you >> >>> click on the link on those words? >> >>> >> >>> It will take you to the next page of the module, showing for each scan >> >>> what the scan parameters were, and will also show for comparison >> what's >> >>> stored in your *mri_protocol* table. >> >>> Compare these values to find which parameter was not correct according >> >>> to your *mri_protocol* table scan type definitions. >> >>> >> >>> You may end up broadening your mri_protocol value ranges (e.g. TR, TE) >> >>> for scans. >> >>> This can be done in the front-end, by editing the database table >> >>> directly in the same subpage of the MRI Violations module. >> >>> >> >>> The MRI Violations module features are explained in more detail in the >> >>> Help text for this module inside LORIS (click the ["?"] icon in the >> menu >> >>> bar.) >> >>> >> >>> See also: Loris-MRI troubleshooting guide >> >>> < >> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >> > >> >>> : no MINCs inserted- violated scans >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Hi, >> >>> >> >>> looks like my previous email's attachment wasn't delivered due to >> >>> security reasons, i uploaded my file at google drive >> >>> >> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >> >>> >> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Hi, >> >>> >> >>> From Dicat's view seems that dcmodify worked in both cases >> >>> >> >>> [image: image.png] >> >>> >> >>> [image: image.png] >> >>> >> >>> For the mri_violations i attached the .html output from webbrowser, so >> >>> that you can check the filelds easier. >> >>> >> >>> [image: image.png] >> >>> >> >>> Thanks >> >>> >> >>> >> >>> >> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios -- >> >>> Great, sounds like more progress. >> >>> >> >>> About the dcmodify command -- I'm not sure why you're getting an >> Endian >> >>> warning. (it's a warning not an error, correct?) >> >>> To clarify -- Were the DICOM headers (PatientName) all successfully >> >>> relabelled, after the command ran? >> >>> >> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) to >> >>> verify and/or update local DICOM headers -- though your dcmodify >> command is >> >>> a great and fast solution for bulk header updates. >> >>> >> >>> If you're concerned about fields being changed (e.g. "(2001,105f)" >> from >> >>> the warning message) - you can also dcmdump a DICOM slice before and >> look >> >>> at these fields specifically. >> >>> It's also not a bad "sanity check" to backup your DICOMS before/after >> >>> running dcmodify, and use dcmdump on each version to diff the outputs >> -- >> >>> this will pinpoint what changed. >> >>> >> >>> Re the protocol violation -- AcquisitionProtocol not recognized or >> >>> unknown : this means your scans did not match what is stored in your >> >>> mri_protocol table. >> >>> Check the MRI Violations front-end module -- can you see why they >> didn't >> >>> match? >> >>> Send us an example, in addition to the contents of the mri_protocol >> >>> table, if you can't find the source of the mismatch. >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> >> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Here is the psc table >> >>> [image: image.png] >> >>> >> >>> I created 2 candidates profiles through the interface >> >>> >> >>> [image: image.png] >> >>> >> >>> then runned dcmodify command to a dicom file >> >>> >> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >> >>> >> >>> and got those warning: is this okay? >> >>> W: Found element (2001,105f) with VR UN and undefined length, reading >> a >> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >> >>> W: Found element (2005,1083) with VR UN and undefined length, reading >> a >> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >> >>> W: Found element (2005,1402) with VR UN and undefined length, reading >> a >> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >> >>> W: Found element (2005,140f) with VR UN and undefined length, reading >> a >> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >> >>> W: Found element (2001,105f) with VR UN and undefined length, reading >> a >> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >> >>> W: Found element (2005,1083) with VR UN and undefined length, reading >> a >> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >> >>> >> >>> dcmodify at another Dicom didn't show warnings. Below you can see the >> >>> execution for the second dicom. Mnics could not be inserted due to >> >>> AcquisitionProtocol being unknown. >> >>> >> >>> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/ >> >>> imaging_upload_file.pl -profile prod -upload_id 12 >> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >> >>> >> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >> >>> -delete >> >>> >> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >> >>> Target: /data/loris/data/tarchive >> >>> >> >>> Testing for database connectivity. >> >>> Database is available. >> >>> >> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >> >>> >> >>> You are creating a tar with the following command: >> >>> >> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >> >>> ImagingUpload-18-36-mTrxXs >> >>> >> >>> >> >>> getting md5sums and gzipping!! >> >>> >> >>> * Taken from dir : >> /tmp/ImagingUpload-18-36-mTrxXs >> >>> * Archive target location : >> >>> >> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >> >>> * Name of creating host : 127.0.1.1 >> >>> * Name of host OS : Linux >> >>> * Created by user : lorisadmin >> >>> * Archived on : 2019-09-06 18:36:50 >> >>> * dicomSummary version : 1 >> >>> * dicomTar version : 1 >> >>> * md5sum for DICOM tarball : >> b1dcdc8903dd2d9a5443227db2aa2814 >> >>> ImagingUpload-18-36-mTrxXs.tar >> >>> * md5sum for DICOM tarball gzipped : >> aeae87f20155a6805f7e0cfe5212ea5f >> >>> ImagingUpload-18-36-mTrxXs.tar.gz >> >>> * md5sum for complete archive : >> 1d9258d1f077ebc49111ab7ba22a8d6e >> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >> >>> >> >>> Adding archive info into database >> >>> >> >>> Removing temporary files from target location >> >>> >> >>> >> >>> Done adding archive info into database >> >>> >> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >> -globLocation >> >>> -profile prod >> >>> >> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >> >>> -uploadID 12 -verbose >> >>> md5sum >> >>> >> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >> >>> PSCID is: DCC0001 >> >>> CandID id: 602102 >> >>> visit_label is: V1 >> >>> PSCID is: DCC0001 >> >>> CandID id: 602102 >> >>> visit_label is: V1 >> >>> candidate id 602102 >> >>> Set centerID = 1 >> >>> PSCID is: DCC0001 >> >>> CandID id: 602102 >> >>> visit_label is: V1 >> >>> PSCID is: DCC0001 >> >>> CandID id: 602102 >> >>> visit_label is: V1 >> >>> >> >>> Number of MINC files that will be considered for inserting into the >> >>> database: 2 >> >>> >> >>> log dir is /data/loris/data//logs and log file is >> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >> >>> PSCID is: DCC0001 >> >>> CandID id: 602102 >> >>> visit_label is: V1 >> >>> PSCID is: DCC0001 >> >>> CandID id: 602102 >> >>> visit_label is: V1 >> >>> candidate id 602102 >> >>> >> >>> log dir is /data/loris/data//logs and log file is >> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >> >>> PSCID is: DCC0001 >> >>> CandID id: 602102 >> >>> visit_label is: V1 >> >>> PSCID is: DCC0001 >> >>> CandID id: 602102 >> >>> visit_label is: V1 >> >>> candidate id 602102 >> >>> >> >>> Cleaning up temp files: rm -rf >> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >> >>> >> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >> cat >> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >> >>> >> >>> ==> Loading file from disk >> >>> >> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >> >>> >> >>> --> mapping DICOM parameter for >> >>> >> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >> >>> >> >>> ==> computing md5 hash for MINC body. >> >>> >> >>> --> md5: 02022dda60d9de429340fec838f50cfe >> >>> >> >>> ==> verifying acquisition protocol >> >>> >> >>> Acquisition protocol is unknown >> >>> >> >>> --> The minc file cannot be registered since the AcquisitionProtocol >> >>> is unknown >> >>> >> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios: >> >>> >> >>> Sure -- you can delete imaging datasets with the >> *delete_imaging_upload* >> >>> script -- >> >>> details here: >> >>> >> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >> >>> >> >>> What's in your *psc* table? (Is it properly populated? This is a >> >>> pre-requisite to loading imaging data. >> >>> < >> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >> > >> >>> ) >> >>> The foreign key constraint error on the candidate record is curious. >> >>> >> >>> There are also a few options for creating candidates when inserting >> >>> imaging data: >> >>> >> >>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline >> >>> >> >>> a. via the LORIS API -- Create the candidates (and visits, optionally >> I >> >>> think) >> >>> How to: >> >>> >> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >> >>> Ensure you get the DCCID/CandID assigned by LORIS. >> >>> >> >>> Then as a second step: >> >>> b. Use the imaging insertion pipeline >> >>> < >> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >> > >> >>> to load your DICOMs. >> >>> You will want to first ensure that the PatientName header in the >> DICOMs >> >>> as well as tar package are correctly labelled with >> PSCID_DCCID_VisitLabel >> >>> >> >>> -- Method 2: for BIDS-format datasets: >> >>> How to : >> >>> >> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >> >>> >> >>> Be sure to use the *-c* and *-s* options when running the bids_import >> script, >> >>> to automatically create your candidates and sessions. >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> How do i delete a Study? And everytime do i have to create a new >> >>> candidate to get DCCID and a PSCID? >> >>> >> >>> *First execution:* >> >>> >> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >> ./ >> >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >> >>> log.txt >> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >> >>> batch_uploads_imageuploader.pl line 144. >> >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign >> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` >> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at >> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >> >>> ERROR: Failed to insert record in table mri_scanner: >> >>> The following database commands failed: >> >>> PREPARE s FROM 'INSERT INTO mri_scanner >> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >> (?,?,?,?,?)'; >> >>> SET >> >>> >> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >> >>> Medical Systems'; >> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >> >>> Error obtained:Cannot add or update a child row: a foreign key >> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` >> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code >> 1452) >> >>> >> >>> ERROR: The validation has failed. Either re-run the validation again >> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to >> force the >> >>> execution. >> >>> >> >>> >> >>> The tarchiveLoader.pl insertion script has failed. >> >>> Can't exec "mail": No such file or directory at ./ >> >>> batch_uploads_imageuploader.pl line 249. >> >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >> >>> line 250. >> >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >> >>> line 251. >> >>> >> >>> >> >>> *And second execution: * >> >>> >> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >> ./ >> >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >> >>> log.txt >> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >> >>> batch_uploads_imageuploader.pl line 144. >> >>> >> >>> PROBLEM: >> >>> The user 'lorisadmin' has already inserted this study. >> >>> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >> >>> This is the information retained from the first time the study was >> >>> inserted: >> >>> >> >>> * Taken from dir : >> /tmp/ImagingUpload-18-33-Qq7HGy >> >>> * Archive target location : >> >>> >> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >> >>> * Name of creating host : 127.0.1.1 >> >>> * Name of host OS : Linux >> >>> * Created by user : lorisadmin >> >>> * Archived on : 2019-09-04 18:33:05 >> >>> * dicomSummary version : 1 >> >>> * dicomTar version : 1 >> >>> * md5sum for DICOM tarball : >> 4a301b0318178b09b91e63544282364d >> >>> ImagingUpload-18-33-Qq7HGy.tar >> >>> * md5sum for DICOM tarball gzipped : >> 9d95ea2b9111be236808bfd65d7e65ec >> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >> >>> * md5sum for complete archive : >> ab19a86357f1d4053aa3b81c8a071053 >> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >> >>> >> >>> >> >>> Last update of record: >> >>> >> >>> >> >>> >> >>> The dicomTar.pl execution has failed. >> >>> Can't exec "mail": No such file or directory at ./ >> >>> batch_uploads_imageuploader.pl line 249. >> >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >> >>> line 250. >> >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >> >>> line 251. >> >>> >> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> Ok, this sounds like good progress. Let us know when you next >> encounter >> >>> issues as you progress through the Imaging Install/Setup docs >> >>> . >> >>> I'll look into how we can better handle the incoming/ directory next >> >>> time. >> >>> Best, >> >>> Christine >> >>> >> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >> >>> populated correctly except its port is 'port' : ''. Also i have >> tested >> >>> that i can connect to MySQL with lorisuser. >> >>> >> >>> I executed the script again, because the only error i had previously >> was >> >>> that the /data/incoming folder didn't exist and there are no errors >> >>> reported back except of warnings <> on the >> >>> command line interface can be insecure>>. >> >>> >> >>> >> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> It's possible -- if the script was unable to connect to the database >> >>> during its execution (e.g. typo in the password), that would explain >> the >> >>> underpopulated Image path and Loris-MRI code path you saw in the >> Config >> >>> module. >> >>> It's hard to tell without seeing the output from your script run -- >> Did >> >>> you see a sign of any such error? >> >>> The Config fields are populated by the imaging_install.sh script >> (starting >> >>> at line 222 >> >>> < >> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222> >> >>> ) >> >>> >> >>> For example, check if the database connection information was >> populated >> >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> >> >>> >> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> Hi Christine, >> >>> >> >>> If you are referring to the imaging_install.sh here is an image with >> the >> >>> configurations i typed. Maybe the problem is somewhere at the last >> part >> >>> which asks to configure as much as possible automatically? >> >>> >> >>> Thanks >> >>> >> >>> >> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >> >>> christine.rogers at mcgill.ca> ??????: >> >>> >> >>> Hi Sotirios, >> >>> >> >>> Glad to hear your LORIS core install is up and working and all the >> >>> front-end pages are loading. >> >>> >> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >> >>> > and the web interface worked. >> >>> >> >>> Yes, it's important that project/ have 775 permissions and that >> >>> lorisadmin be part of the sudoers group, per step 1 in the install >> >>> Readme . >> >>> >> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS to >> >>> loris, right? >> >>> >> >>> These imaging paths will be updated during your imaging installation >> >>> by an automated script -- >> >>> you do not need to set them manually via the Config module. >> >>> Please continue to follow the Setup Guide >> >>> for detailed steps to >> follow. >> >>> >> >>> Best, >> >>> Christine >> >>> >> >>> >> >>> >> >>> >> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> wrote: >> >>> >> >>> As for the Paths, LORIS-MRI code and Image should change LORIS to >> loris, >> >>> right? >> >>> >> >>> [image: image.png] >> >>> >> >>> >> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos < >> >>> sotirisnik at gmail.com> ??????: >> >>> >> >>> Hi, >> >>> >> >>> i used >> >>> >> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >> >>> sudo apt-get install -y nodejs >> >>> >> >>> >> >>> you had suggested in the past, make worked and now i can see all the >> >>> contents in the web-interface, but i don't need make install? >> >>> >> >>> Thanks >> >>> >> >>> _______________________________________________ >> >>> Loris-dev mailing list >> >>> Loris-dev at bic.mni.mcgill.ca >> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | Canada >> >>> >> >>> _______________________________________________ >> >>> Loris-dev mailing list >> >>> Loris-dev at bic.mni.mcgill.ca >> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | Canada >> >>> >> >>> _______________________________________________ >> >>> Loris-dev mailing list >> >>> Loris-dev at bic.mni.mcgill.ca >> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | Canada >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | Canada >> >>> >> >>> _______________________________________________ >> >>> Loris-dev mailing list >> >>> Loris-dev at bic.mni.mcgill.ca >> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | Canada >> >>> >> >>> _______________________________________________ >> >>> Loris-dev mailing list >> >>> Loris-dev at bic.mni.mcgill.ca >> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | Canada >> >>> >> >>> _______________________________________________ >> >>> Loris-dev mailing list >> >>> Loris-dev at bic.mni.mcgill.ca >> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | Canada >> >>> >> >>> _______________________________________________ >> >>> Loris-dev mailing list >> >>> Loris-dev at bic.mni.mcgill.ca >> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | Canada >> >>> >> >>> _______________________________________________ >> >>> Loris-dev mailing list >> >>> Loris-dev at bic.mni.mcgill.ca >> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >>> >> >>> >> >>> >> >>> -- >> >>> >> >>> christine.rogers at mcgill.ca >> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >> >>> Montreal Neurological Institute >> >>> McGill University | Montreal | 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URL: From christine.rogers at mcgill.ca Wed Nov 13 16:45:49 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 13 Nov 2019 21:45:49 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, Can you provide us with some fresh particulars of the current issue and we'll take it from there? Yang's team has built these scripts which can definitely serve as a model for your pre-validation of your DICOM collections. cheers, Christine On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos > wrote: HI Yang, We make use of pydicom library too. Now about the validate.py i see that you check if some attributes are missing such as PatientID, PatientName which all of our files contains that info. Maybe i have missed something on the setup of my other virtual machine ( although one dicom passed on the new vm successfully, the others that were inserted correctly on my old vm fails on the new one ), i think that i had asked about this error "Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but i don't remember the solution. Thanks ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding > ??????: Hey, Sotirios, Christine from the LORIS team mentioned you had some issue with DICOM. I am a fellow developer for an external project using LORIS, kind of just like you. We had to implement DICOM upload as well but more as a fully automated pipeline actually. While we were building CNBP, we had coded up some minor Python functions to check DICOM integrity (and simple validations) and you might be able to gain some inspiration from it and help you with your cause. For more comprehensive solution, PyDICOM (https://pydicom.github.io/pydicom/stable/getting_started.html#) seems like a descent python package to help out with a lot of DICOM data checks (I was essentially just building customized wrapper calls to them). You can see some example scripts here as part of our DICOM submodule. It is pretty rough around the edges but hopefully point you in the right direcitons https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py Cheers, Yang Ding, PhD. Canadian Neonatal Brain Platform Architect On Tue, Nov 12, 2019 at 8:29 AM > wrote: Send Loris-dev mailing list submissions to loris-dev at bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev or, via email, send a message with subject or body 'help' to loris-dev-request at bic.mni.mcgill.ca You can reach the person managing the list at loris-dev-owner at bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of Loris-dev digest..." Today's Topics: 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Nov 2019 15:28:26 +0200 From: Sotirios Nikoloutsopoulos > To: Cecile Madjar > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Import mri - scripts Message-ID: > Content-Type: text/plain; charset="utf-8" Hi, Could we send you a link with 10 anonymized dicom files to diagnose the warnings we get? Thanks ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi Cecile, > > We were wondering whether Loris has a tool to check if there are problems > with the dcm files, before trying to upload them. Something that could > provide the same results provided in the warning_output, this is the > summary from the mri_upload at the front-page. Also which attributes of the > dcm header would trigger a warning? is there a dcm file header > specification for Loris? > > Thanks > > Sotirios > > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi, >> >> Yes, by parsing now() into unix_timestamp function it worked,but i >> thought that something else was causing the 2nd issue. >> Thanks >> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >> xavier.lecoursboucher at mcgill.ca> wrote: >> >>> Hi Sotirios, >>> >>> The first error occurs because the QCFirstChangeTime and columns are of >>> type `unsigned integer` and not `datatime`. You should be using >>> UNIX_TIMESTAMP() instead of NOW(). >>> >>> The second error occurs because the trigger triggers a rollback of the >>> insert statement in the files table. >>> See mysql documentation for trigger error handling. >>> >>> An error during either a BEFORE or AFTER trigger results in failure of >>> the entire statement that caused trigger invocation. >>> >>> >>> Thank you for sharing that. I hope it helps. >>> -- Xavier >>> >>> ------------------------------ >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>> Nikoloutsopoulos > >>> *Sent:* October 1, 2019 8:33 AM >>> *To:* Cecile Madjar > >>> *Cc:* loris-dev at bic.mni.mcgill.ca >; >>> Christine Rogers, Ms. > >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> When mincs are inserted their corresponding rows at the file table are >>> inserted too >>> [image: image.png] >>> >>> i would like to insert their rows at file_qcstatus as well, because i >>> don't want manually to label them as passed throught the interface >>> >>> [image: image.png] >>> >>> >>> That is the trigger i wrote >>> >>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER >>> INSERT ON `files` FOR EACH ROW >>> BEGIN >>> INSERT INTO files_qcstatus >>> SET FileID = NEW.FileID, >>> SeriesUID = NEW.SeriesUID, >>> EchoTime = NEW.EchoTime, >>> QCStatus = "Pass", >>> QCFirstChangeTime = NOW(), >>> QCLastChangeTime = NOW(); >>> END >>> >>> although it contains some errors >>> >>> DBD::mysql::db do failed: Out of range value for column >>> 'QCFirstChangeTime' at row 1 at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>> >>> >>> >>> >>> >>> >>> >>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> In the mri_upload table, there is a TarchiveID column associated with >>> the MRI upload you inserted. When this value is NULL, it means no DICOMs >>> were inserted into the tarchive tables. At the end of the insertion of the >>> DICOMs in the tarchive tables, this value is updated with the correct >>> TarchiveID associated with the upload. >>> >>> Could this correspond to what you want to do? >>> >>> Regarding the files_qcstatus, this table is only linked to the files >>> table (hence, the MINC files). You could always create a new table for >>> dicom_qcstatus and link it to the tarchive table? >>> >>> C?cile >>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> i would like whenever a dicom is imported to mark all their >>> coressponding qc_status to "pass". I was thinking of creating a trigger for >>> that, but which tables do i need to add entries to? So far from what i see >>> i need to add entres at the table "files" whenever an insertion happens to >>> files_qcstatus. >>> >>> Thanks >>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Oh, sorry i should have asked for StudyID, at the beginning of my email >>> i sent 3 hours ago (not StudyUID). >>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i am >>> looking for is not stored in the database? >>> >>> [image: image.png] >>> >>> Thanks. >>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> The StudyUID is stored in the DicomArchiveID field of the >>> tarchive table. It can also be found in the metadata field but it is mixed >>> with many other information. >>> >>> Hope this helps, >>> >>> C?cile >>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>> specifically at the AcquisitonMetadata column i found something called >>> 'Unique Study ID" in its context, but that must be the Study Instance UID. >>> >>> Thanks >>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Your observation is correct. A little explanation below. >>> >>> MINC files get inserted into the MRI violation tables if: >>> >>> - the scan type could not be identified (not matching an entry in >>> the mri_protocol table) >>> - one parameter of the scan type is out of the expected range >>> present in the mri_protocol_checks (extra filtering in case you need to be >>> stricker on some parameters not present in the mri_protocol table) >>> - if the CandID and PSCID do not match >>> >>> The following cases do not get in the MRI violation tables as it happens >>> before the conversion of the DICOM to MINC files and only MINC files >>> violations are logged there: >>> >>> - "No single DICOM" (since no valid DICOM could be found to convert >>> to MINC) >>> - "Study already inserted" (duplicate StudyUID) since this error >>> happens at the dicomTar.pl level (way before conversion into MINC files) >>> >>> Glad everything is working out!! >>> Best, >>> >>> C?cile >>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now about the >>> mri_violations, dicoms are triggered to be inserted there only if there is >>> a violation for Tr_min, Tr_max, in general for its header parameter? >>> Because i don't see the cases of 'No single dicom" or with the 2 studyiuid >>> to be there. >>> >>> Thanks >>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Sorry to hear you are having issues with the memory. I think most of our >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>> >>> Hope this helps! >>> >>> C?cile >>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> about that dicom that had that insertion error it's about 30mb and when >>> it is being processed the ram is being drastically increased from 2gb to >>> 3.28 and then the whole virtual machine is frozen. What is the recommended >>> size of ram for using Loris? >>> >>> Thanks >>> >>> [image: image.png] >>> >>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to see that the StudyUID problem was fixed! >>> >>> For the delete script issue, if you are absolutely certain that no >>> processes are run for that uploadID, you can update the mri_upload table >>> and set the column Inserting to 0 instead of 1 for that uploadID. It >>> looks like for some reason the scripts did not update this field when it >>> stopped the insertion. Not sure why that would be the case though. >>> Note: only do that update if you are certain that there is no processing >>> happening. >>> >>> Hope this helps! >>> >>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> about the Dicoms i reported that didn't have a StudyID they actually do >>> >>> [image: image.png] >>> >>> >>> [image: image.png] >>> >>> I thought that this might be a permission because "w" was missing at the >>> group. After using chmod -R 775 only 102809579 passed, but with no mnic >>> files. Also now i have this error >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>> Cannot delete upload 34: the MRI pipeline is currently processing it. >>> >>> How can solve this? >>> >>> Thanks >>> >>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> Here is our auto dicom uploading python script: >>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>> >>> To give you a brief idea: >>> Per folder it will: >>> 1) Delete all the .bak files >>> 2) Locate .dcm files and update the Patient header >>> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, >>> TE_max parameters of T1 protocol and do an update at the mri_protocol table >>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>> For some reason some files are missing SeriesDescription/ProtocolName >>> >>> In total i have 7 folders >>> >>> [image: image.png] >>> >>> 3/7 passed >>> >>> [image: image.png] >>> >>> Also about the first patient with DC0000 had a violation "T1 AXIAL SE >>> GADO", but my script didn't output a TE of 17 nowhere and i find that weird >>> since Loris detects the SeriesDescription. >>> [image: image.png] >>> >>> >>> Now about the 4/7 that didn't passed >>> >>> 102327840 and 102809579 outputs "The target directory does not contain a >>> single DICOM file.", therefore they are missing their StudyUID >>> >>> 102506134 has 2 studyuid "You can't use it with data from multiple >>> studies." >>> >>> and 102761034 "No data could be converted into valid MINC files. >>> localizer, scout will not be considered!" What is this? >>> >>> If i wanted to force the insertion of 102327840, 102809579 and 102506134 >>> can i just pass a flag parameter to batch_uploads_imageuploader.pl? or >>> modify imaging_upload_file.pl? >>> >>> Thank you, >>> >>> Sotirios >>> >>> PS >>> >>> To diagnose a folder search the name of the folder at dicom_output.txt. >>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> Glad to hear about your progress. >>> >>> Yes, the script you used to delete imaging data is fully documented here >>> >>> -- let us know if you didn't find the answers you were looking for there. >>> (Is it possible the null row in *mri_scanner* seen in your database >>> management software is a visual placeholder for you as the user? I'm not >>> sure why a scanner would ever be registered with ID='0' as your screenshot >>> showed.) >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> I fixed it with this >>> >>> [image: image.png] >>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> I tried to create a new candidate using the API, is there something >>> wrong with the structure? why did i receive a 500 internal error? In the >>> loris-error log it state that there is something wrong with token, but i >>> verfied that the type of the token is a string. >>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type string, >>> null given, called in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and >>> defined in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>> SinglePointLogin->authenticate()\n#2 >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >>> >>> [image: image.png] >>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> Is there a way also to delete candidates? Just to let you know what i >>> did to clear candidates, because maybe i may have missed dependencies. >>> >>> First i deleted all their uploads >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit >>> the backup file ? ) >>> >>> Afterwards i had some scanner candidates, so i deleted all the entries >>> from mri_scanner except that i couldn't delete this entry with the 0 ID. >>> >>> [image: image.png] >>> >>> >>> Lastly i deleted the session and then the candidate table. >>> >>> Thanks >>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> We recommend that you use our existing tools for creating new candidates >>> - either the LORIS API or if you are using a PHP script, by calling the Candidate >>> class's createNew() >>> function. >>> These will create the necessary records for you. (It's not recommended to >>> make direct modifications to mysql database tables in your script, if I >>> understand you.) >>> >>> The CandID should be a randomized 6 digit randomized ID, and there are >>> multiple reasons for this. >>> You can use the PSCID for project-specific IDs and the External ID field >>> in the candidate table can also be used for any values you like. >>> Additionally, any number of custom IDs can be added in parallel - these >>> are entered/visible in the Candidate Information module and added in the >>> back-end as candidate parameters. >>> >>> Best, >>> Christine >>> >>> >>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> We are building a script that will auto insert the candidates based on >>> their ExternalID. We would like to know whethere when we are creating a new >>> profile in the candidate table, if we also have to insert a new record at >>> another table? Furthermore is there a problem that in our case CandID won't >>> be a 6digit? ( should we start it from 100000?) >>> >>> Thanks >>> >>> [image: image.png] >>> >>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>> melanie.legault2 at mcgill.ca> ??????: >>> >>> That would normally be the case but the numeric part of the PSCID get >>> paded with 0 on the left. >>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char >>> with a min value of 1, the sequence would be: >>> >>> ABC0001 >>> ABC0002 >>> ... >>> ABC0010 >>> ... >>> >>> thus sorting them ascending will always get the latest value generated >>> as the max value. >>> >>> M?lanie >>> >>> ------------------------------ >>> *From:* Sotirios Nikoloutsopoulos > >>> *Sent:* September 13, 2019 10:15 >>> *To:* Melanie Legault, Mrs > >>> *Cc:* Christine Rogers, Ms. >; >>> loris-dev at bic.mni.mcgill.ca > >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> I see, although the PSCID value is varchar(255), it must be stored >>> within a specific length of characters. Otherwise if we were to sort >>> strings with different lengths the result would not be sorted correctly ( >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>> >>> Thanks >>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>> melanie.legault2 at mcgill.ca> ??????: >>> >>> Hello Sotirios, >>> >>> There is no `last value` stored anywhere. >>> The code simply look for the PSCID with the max value and increase that >>> value by 1 in order to generate the next PSCID. >>> >>> Hope this info help. >>> >>> M?lanie Legault | Software developer | Faculty of Medicine | McGill >>> University >>> 3801 University, Montr?al, QC H3A 2B4 >>> >>> ------------------------------ >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>> Nikoloutsopoulos > >>> *Sent:* September 13, 2019 9:43 >>> *To:* Christine Rogers, Ms. > >>> *Cc:* loris-dev at bic.mni.mcgill.ca > >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> Hi, >>> >>> how does Loris determine the next available PSCID value for a new >>> candidate? https://github.com/aces/Loris/wiki/Project-Customization >>> e.x in the default case the PSCID is sequential, but where do we store the >>> last value for the sequential sequence? >>> >>> Thanks >>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> the parameters in the mri_protocol you have assigned are global >>> standard? or were assigned after trial and error? >>> >>> Thanks >>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Given you have done the initial setup of your tables to match your >>> intended protocol/parameters according to instructions -- >>> the Troubleshooting guide documentation recommends >>> >>> re-running the pipeline (and first deleting prior uploads). >>> >>> Best, >>> Christine >>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> *if i were to change their status to resolve what would happen? >>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> I noticed that i can view the mnics at the brainbrowser from the >>> mri_violations page ( those mnics are stored at /data/loris/data/trashbin/ >>> if i were to click their issue to resolve what would happend? would they >>> appear in the dicom_archive view too? ). >>> >>> >>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> The defaut values of the schema exists in my local database. If i adjust >>> the default values of TR_min and TE_min the mincs will be uploaded? >>> >>> [image: image.png] >>> >>> >>> [image: image.png] >>> >>> Thanks >>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Is it possible that you haven't set up your mri_protocol table ? (and >>> mri_scan_type table too, for additional types of scans) >>> >>> Like the psc table, this is a pre-requisite for the Imaging insertion >>> setup : See the install/setup documentation : >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>> >>> To add new rows, just use MySQL insert statements. You can adapt the >>> insert statements which load the default table values --> e.g. Here on >>> GitHub : >>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>> (see also the mri_scan_type table) >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> I see that i can edit the values but not how to insert new rows. >>> >>> [image: image.png] >>> >>> If i choose Inserted with flag then will the minc be inserted? >>> >>> [image: image.png] >>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to hear that *dcmodify* worked correctly. >>> >>> For the MRI Violations module, the screenshot is enough. >>> >>> It says "could not identify scan type", which we knew already. Did you >>> click on the link on those words? >>> >>> It will take you to the next page of the module, showing for each scan >>> what the scan parameters were, and will also show for comparison what's >>> stored in your *mri_protocol* table. >>> Compare these values to find which parameter was not correct according >>> to your *mri_protocol* table scan type definitions. >>> >>> You may end up broadening your mri_protocol value ranges (e.g. TR, TE) >>> for scans. >>> This can be done in the front-end, by editing the database table >>> directly in the same subpage of the MRI Violations module. >>> >>> The MRI Violations module features are explained in more detail in the >>> Help text for this module inside LORIS (click the ["?"] icon in the menu >>> bar.) >>> >>> See also: Loris-MRI troubleshooting guide >>> >>> : no MINCs inserted- violated scans >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> looks like my previous email's attachment wasn't delivered due to >>> security reasons, i uploaded my file at google drive >>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> From Dicat's view seems that dcmodify worked in both cases >>> >>> [image: image.png] >>> >>> [image: image.png] >>> >>> For the mri_violations i attached the .html output from webbrowser, so >>> that you can check the filelds easier. >>> >>> [image: image.png] >>> >>> Thanks >>> >>> >>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios -- >>> Great, sounds like more progress. >>> >>> About the dcmodify command -- I'm not sure why you're getting an Endian >>> warning. (it's a warning not an error, correct?) >>> To clarify -- Were the DICOM headers (PatientName) all successfully >>> relabelled, after the command ran? >>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) to >>> verify and/or update local DICOM headers -- though your dcmodify command is >>> a great and fast solution for bulk header updates. >>> >>> If you're concerned about fields being changed (e.g. "(2001,105f)" from >>> the warning message) - you can also dcmdump a DICOM slice before and look >>> at these fields specifically. >>> It's also not a bad "sanity check" to backup your DICOMS before/after >>> running dcmodify, and use dcmdump on each version to diff the outputs -- >>> this will pinpoint what changed. >>> >>> Re the protocol violation -- AcquisitionProtocol not recognized or >>> unknown : this means your scans did not match what is stored in your >>> mri_protocol table. >>> Check the MRI Violations front-end module -- can you see why they didn't >>> match? >>> Send us an example, in addition to the contents of the mri_protocol >>> table, if you can't find the source of the mismatch. >>> >>> Best, >>> Christine >>> >>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Here is the psc table >>> [image: image.png] >>> >>> I created 2 candidates profiles through the interface >>> >>> [image: image.png] >>> >>> then runned dcmodify command to a dicom file >>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>> >>> and got those warning: is this okay? >>> W: Found element (2001,105f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1083) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1402) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,140f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2001,105f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1083) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> >>> dcmodify at another Dicom didn't show warnings. Below you can see the >>> execution for the second dicom. Mnics could not be inserted due to >>> AcquisitionProtocol being unknown. >>> >>> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/ >>> imaging_upload_file.pl -profile prod -upload_id 12 >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >>> -delete >>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>> Target: /data/loris/data/tarchive >>> >>> Testing for database connectivity. >>> Database is available. >>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>> >>> You are creating a tar with the following command: >>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>> ImagingUpload-18-36-mTrxXs >>> >>> >>> getting md5sums and gzipping!! >>> >>> * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs >>> * Archive target location : >>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> * Name of creating host : 127.0.1.1 >>> * Name of host OS : Linux >>> * Created by user : lorisadmin >>> * Archived on : 2019-09-06 18:36:50 >>> * dicomSummary version : 1 >>> * dicomTar version : 1 >>> * md5sum for DICOM tarball : b1dcdc8903dd2d9a5443227db2aa2814 >>> ImagingUpload-18-36-mTrxXs.tar >>> * md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f >>> ImagingUpload-18-36-mTrxXs.tar.gz >>> * md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> >>> Adding archive info into database >>> >>> Removing temporary files from target location >>> >>> >>> Done adding archive info into database >>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation >>> -profile prod >>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>> -uploadID 12 -verbose >>> md5sum >>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> Set centerID = 1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> >>> Number of MINC files that will be considered for inserting into the >>> database: 2 >>> >>> log dir is /data/loris/data//logs and log file is >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> >>> log dir is /data/loris/data//logs and log file is >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> >>> Cleaning up temp files: rm -rf >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ cat >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>> >>> ==> Loading file from disk >>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>> >>> --> mapping DICOM parameter for >>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>> >>> ==> computing md5 hash for MINC body. >>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>> >>> ==> verifying acquisition protocol >>> >>> Acquisition protocol is unknown >>> >>> --> The minc file cannot be registered since the AcquisitionProtocol >>> is unknown >>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios: >>> >>> Sure -- you can delete imaging datasets with the *delete_imaging_upload* >>> script -- >>> details here: >>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>> >>> What's in your *psc* table? (Is it properly populated? This is a >>> pre-requisite to loading imaging data. >>> >>> ) >>> The foreign key constraint error on the candidate record is curious. >>> >>> There are also a few options for creating candidates when inserting >>> imaging data: >>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline >>> >>> a. via the LORIS API -- Create the candidates (and visits, optionally I >>> think) >>> How to: >>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>> Ensure you get the DCCID/CandID assigned by LORIS. >>> >>> Then as a second step: >>> b. Use the imaging insertion pipeline >>> >>> to load your DICOMs. >>> You will want to first ensure that the PatientName header in the DICOMs >>> as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel >>> >>> -- Method 2: for BIDS-format datasets: >>> How to : >>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>> >>> Be sure to use the *-c* and *-s* options when running the bids_import script, >>> to automatically create your candidates and sessions. >>> >>> Best, >>> Christine >>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> How do i delete a Study? And everytime do i have to create a new >>> candidate to get DCCID and a PSCID? >>> >>> *First execution:* >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >>> log.txt >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>> batch_uploads_imageuploader.pl line 144. >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>> ERROR: Failed to insert record in table mri_scanner: >>> The following database commands failed: >>> PREPARE s FROM 'INSERT INTO mri_scanner >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; >>> SET >>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>> Medical Systems'; >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>> Error obtained:Cannot add or update a child row: a foreign key >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452) >>> >>> ERROR: The validation has failed. Either re-run the validation again >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to force the >>> execution. >>> >>> >>> The tarchiveLoader.pl insertion script has failed. >>> Can't exec "mail": No such file or directory at ./ >>> batch_uploads_imageuploader.pl line 249. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 250. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 251. >>> >>> >>> *And second execution: * >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >>> log.txt >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>> batch_uploads_imageuploader.pl line 144. >>> >>> PROBLEM: >>> The user 'lorisadmin' has already inserted this study. >>> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>> This is the information retained from the first time the study was >>> inserted: >>> >>> * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy >>> * Archive target location : >>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>> * Name of creating host : 127.0.1.1 >>> * Name of host OS : Linux >>> * Created by user : lorisadmin >>> * Archived on : 2019-09-04 18:33:05 >>> * dicomSummary version : 1 >>> * dicomTar version : 1 >>> * md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d >>> ImagingUpload-18-33-Qq7HGy.tar >>> * md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>> * md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053 >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>> >>> >>> Last update of record: >>> >>> >>> >>> The dicomTar.pl execution has failed. >>> Can't exec "mail": No such file or directory at ./ >>> batch_uploads_imageuploader.pl line 249. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 250. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 251. >>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Ok, this sounds like good progress. Let us know when you next encounter >>> issues as you progress through the Imaging Install/Setup docs >>> . >>> I'll look into how we can better handle the incoming/ directory next >>> time. >>> Best, >>> Christine >>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>> populated correctly except its port is 'port' : ''. Also i have tested >>> that i can connect to MySQL with lorisuser. >>> >>> I executed the script again, because the only error i had previously was >>> that the /data/incoming folder didn't exist and there are no errors >>> reported back except of warnings <>> command line interface can be insecure>>. >>> >>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> It's possible -- if the script was unable to connect to the database >>> during its execution (e.g. typo in the password), that would explain the >>> underpopulated Image path and Loris-MRI code path you saw in the Config >>> module. >>> It's hard to tell without seeing the output from your script run -- Did >>> you see a sign of any such error? >>> The Config fields are populated by the imaging_install.sh script (starting >>> at line 222 >>> >>> ) >>> >>> For example, check if the database connection information was populated >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >>> >>> Best, >>> Christine >>> >>> >>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi Christine, >>> >>> If you are referring to the imaging_install.sh here is an image with the >>> configurations i typed. Maybe the problem is somewhere at the last part >>> which asks to configure as much as possible automatically? >>> >>> Thanks >>> >>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to hear your LORIS core install is up and working and all the >>> front-end pages are loading. >>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>> > and the web interface worked. >>> >>> Yes, it's important that project/ have 775 permissions and that >>> lorisadmin be part of the sudoers group, per step 1 in the install >>> Readme . >>> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS to >>> loris, right? >>> >>> These imaging paths will be updated during your imaging installation >>> by an automated script -- >>> you do not need to set them manually via the Config module. >>> Please continue to follow the Setup Guide >>> for detailed steps to follow. >>> >>> Best, >>> Christine >>> >>> >>> >>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS to loris, >>> right? >>> >>> [image: image.png] >>> >>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> i used >>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>> sudo apt-get install -y nodejs >>> >>> >>> you had suggested in the past, make worked and now i can see all the >>> contents in the web-interface, but i don't need make install? >>> >>> Thanks >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... 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URL: From sotirisnik at gmail.com Wed Nov 13 17:55:20 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 14 Nov 2019 00:55:20 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Christine, In my first vm i am able to create the minc files and view them at the mri browser (except of candidate 102761034 ), meanwhile the same files gives warnings at the 2nd vm. The output of the batch upload can be seen in the file attached. Also a colleague of us has built a pre-validation tool for dicom https://github.com/aueb-wim/DataQualityControlTool/ which had found all the files that Loris gave as warning . Basically I confirmed that the total amount of files per dicom was the same amount as stated in Loris and checked some filenames given from warning to confirm that they match with our tool. But that was months ago and my colleague had changed some parameters for MIP and now our tool doesn't find all the invalid files, that's why i asked for the dicom header specification of Loris. In a discussion we had he mentioned that he doesn't check for some tags e.x. orientation. Lastly to mention that in my first vm i didn't use our tool to remove invalid dcm files. Thanks ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > Can you provide us with some fresh particulars of the current issue and > we'll take it from there? > Yang's team has built these scripts which can definitely serve as a model > for your pre-validation of your DICOM collections. > cheers, > Christine > > On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> HI Yang, >> >> We make use of pydicom library too. Now about the validate.py i see that >> you check if some attributes are missing such as PatientID, PatientName >> which all of our files contains that info. Maybe i have missed something on >> the setup of my other virtual machine ( although one dicom passed on the >> new vm successfully, the others that were inserted correctly on my old vm >> fails on the new one ), i think that i had asked about this error "Use of >> uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/ >> batch_uploads_imageuploader.pl line 144." but i don't remember the >> solution. >> >> Thanks >> >> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding ??????: >> >>> Hey, Sotirios, >>> >>> Christine from the LORIS team mentioned you had some issue with DICOM. >>> I am a fellow developer for an external project using LORIS, kind of just >>> like you. We had to implement DICOM upload as well but more as a fully >>> automated pipeline actually. >>> >>> While we were building CNBP, we had coded up some minor Python functions >>> to check DICOM integrity (and simple validations) and you might be able to >>> gain some inspiration from it and help you with your cause. For more >>> comprehensive solution, PyDICOM ( >>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>> like a descent python package to help out with a lot of DICOM data checks >>> (I was essentially just building customized wrapper calls to them). You can >>> see some example scripts here as part of our DICOM submodule. It is pretty >>> rough around the edges but hopefully point you in the right direcitons >>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>> >>> Cheers, >>> >>> Yang Ding, PhD. >>> Canadian Neonatal Brain Platform Architect >>> >>> On Tue, Nov 12, 2019 at 8:29 AM >>> wrote: >>> >>>> Send Loris-dev mailing list submissions to >>>> loris-dev at bic.mni.mcgill.ca >>>> >>>> To subscribe or unsubscribe via the World Wide Web, visit >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> or, via email, send a message with subject or body 'help' to >>>> loris-dev-request at bic.mni.mcgill.ca >>>> >>>> You can reach the person managing the list at >>>> loris-dev-owner at bic.mni.mcgill.ca >>>> >>>> When replying, please edit your Subject line so it is more specific >>>> than "Re: Contents of Loris-dev digest..." >>>> >>>> >>>> Today's Topics: >>>> >>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>> From: Sotirios Nikoloutsopoulos >>>> To: Cecile Madjar >>>> Cc: loris-dev at bic.mni.mcgill.ca >>>> Subject: Re: [Loris-dev] Import mri - scripts >>>> Message-ID: >>>> >>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hi, >>>> >>>> Could we send you a link with 10 anonymized dicom files to diagnose the >>>> warnings we get? >>>> >>>> Thanks >>>> >>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> ??????: >>>> >>>> > Hi Cecile, >>>> > >>>> > We were wondering whether Loris has a tool to check if there are >>>> problems >>>> > with the dcm files, before trying to upload them. Something that could >>>> > provide the same results provided in the warning_output, this is the >>>> > summary from the mri_upload at the front-page. Also which attributes >>>> of the >>>> > dcm header would trigger a warning? is there a dcm file header >>>> > specification for Loris? >>>> > >>>> > Thanks >>>> > >>>> > Sotirios >>>> > >>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> > sotirisnik at gmail.com> ??????: >>>> > >>>> >> Hi, >>>> >> >>>> >> Yes, by parsing now() into unix_timestamp function it worked,but i >>>> >> thought that something else was causing the 2nd issue. >>>> >> Thanks >>>> >> >>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>> >> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> The first error occurs because the QCFirstChangeTime and columns >>>> are of >>>> >>> type `unsigned integer` and not `datatime`. You should be using >>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>> >>> >>>> >>> The second error occurs because the trigger triggers a rollback of >>>> the >>>> >>> insert statement in the files table. >>>> >>> See mysql documentation for trigger error handling. >>>> >>> >>>> >>> An error during either a BEFORE or AFTER trigger results in failure >>>> of >>>> >>> the entire statement that caused trigger invocation. >>>> >>> >>>> >>> >>>> >>> Thank you for sharing that. I hope it helps. >>>> >>> -- Xavier >>>> >>> >>>> >>> ------------------------------ >>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>> >>> Nikoloutsopoulos >>>> >>> *Sent:* October 1, 2019 8:33 AM >>>> >>> *To:* Cecile Madjar >>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca ; >>>> >>> Christine Rogers, Ms. >>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>> >>> >>>> >>> When mincs are inserted their corresponding rows at the file table >>>> are >>>> >>> inserted too >>>> >>> [image: image.png] >>>> >>> >>>> >>> i would like to insert their rows at file_qcstatus as well, because >>>> i >>>> >>> don't want manually to label them as passed throught the interface >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> >>>> >>> That is the trigger i wrote >>>> >>> >>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` >>>> AFTER >>>> >>> INSERT ON `files` FOR EACH ROW >>>> >>> BEGIN >>>> >>> INSERT INTO files_qcstatus >>>> >>> SET FileID = NEW.FileID, >>>> >>> SeriesUID = NEW.SeriesUID, >>>> >>> EchoTime = NEW.EchoTime, >>>> >>> QCStatus = "Pass", >>>> >>> QCFirstChangeTime = NOW(), >>>> >>> QCLastChangeTime = NOW(); >>>> >>> END >>>> >>> >>>> >>> although it contains some errors >>>> >>> >>>> >>> DBD::mysql::db do failed: Out of range value for column >>>> >>> 'QCFirstChangeTime' at row 1 at >>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>> foreign >>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` >>>> (`FileID`)) >>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>> >>> cecile.madjar at mcin.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> In the mri_upload table, there is a TarchiveID column associated >>>> with >>>> >>> the MRI upload you inserted. When this value is NULL, it means no >>>> DICOMs >>>> >>> were inserted into the tarchive tables. At the end of the insertion >>>> of the >>>> >>> DICOMs in the tarchive tables, this value is updated with the >>>> correct >>>> >>> TarchiveID associated with the upload. >>>> >>> >>>> >>> Could this correspond to what you want to do? >>>> >>> >>>> >>> Regarding the files_qcstatus, this table is only linked to the files >>>> >>> table (hence, the MINC files). You could always create a new table >>>> for >>>> >>> dicom_qcstatus and link it to the tarchive table? >>>> >>> >>>> >>> C?cile >>>> >>> >>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> i would like whenever a dicom is imported to mark all their >>>> >>> coressponding qc_status to "pass". I was thinking of creating a >>>> trigger for >>>> >>> that, but which tables do i need to add entries to? So far from >>>> what i see >>>> >>> i need to add entres at the table "files" whenever an insertion >>>> happens to >>>> >>> files_qcstatus. >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos >>>> < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Oh, sorry i should have asked for StudyID, at the beginning of my >>>> email >>>> >>> i sent 3 hours ago (not StudyUID). >>>> >>> >>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos >>>> < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i am >>>> >>> looking for is not stored in the database? >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> Thanks. >>>> >>> >>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>> >>> cecile.madjar at mcin.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>> >>> tarchive table. It can also be found in the metadata field but it >>>> is mixed >>>> >>> with many other information. >>>> >>> >>>> >>> Hope this helps, >>>> >>> >>>> >>> C?cile >>>> >>> >>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>>> >>> specifically at the AcquisitonMetadata column i found something >>>> called >>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>> Instance UID. >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>> >>> cecile.madjar at mcin.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> Your observation is correct. A little explanation below. >>>> >>> >>>> >>> MINC files get inserted into the MRI violation tables if: >>>> >>> >>>> >>> - the scan type could not be identified (not matching an entry in >>>> >>> the mri_protocol table) >>>> >>> - one parameter of the scan type is out of the expected range >>>> >>> present in the mri_protocol_checks (extra filtering in case you >>>> need to be >>>> >>> stricker on some parameters not present in the mri_protocol >>>> table) >>>> >>> - if the CandID and PSCID do not match >>>> >>> >>>> >>> The following cases do not get in the MRI violation tables as it >>>> happens >>>> >>> before the conversion of the DICOM to MINC files and only MINC files >>>> >>> violations are logged there: >>>> >>> >>>> >>> - "No single DICOM" (since no valid DICOM could be found to >>>> convert >>>> >>> to MINC) >>>> >>> - "Study already inserted" (duplicate StudyUID) since this error >>>> >>> happens at the dicomTar.pl level (way before conversion into >>>> MINC files) >>>> >>> >>>> >>> Glad everything is working out!! >>>> >>> Best, >>>> >>> >>>> >>> C?cile >>>> >>> >>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now >>>> about the >>>> >>> mri_violations, dicoms are triggered to be inserted there only if >>>> there is >>>> >>> a violation for Tr_min, Tr_max, in general for its header parameter? >>>> >>> Because i don't see the cases of 'No single dicom" or with the 2 >>>> studyiuid >>>> >>> to be there. >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>> >>> cecile.madjar at mcin.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> Sorry to hear you are having issues with the memory. I think most >>>> of our >>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>> >>> >>>> >>> Hope this helps! >>>> >>> >>>> >>> C?cile >>>> >>> >>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> about that dicom that had that insertion error it's about 30mb and >>>> when >>>> >>> it is being processed the ram is being drastically increased from >>>> 2gb to >>>> >>> 3.28 and then the whole virtual machine is frozen. What is the >>>> recommended >>>> >>> size of ram for using Loris? >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> >>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>> >>> cecile.madjar at mcin.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> Glad to see that the StudyUID problem was fixed! >>>> >>> >>>> >>> For the delete script issue, if you are absolutely certain that no >>>> >>> processes are run for that uploadID, you can update the mri_upload >>>> table >>>> >>> and set the column Inserting to 0 instead of 1 for that uploadID. It >>>> >>> looks like for some reason the scripts did not update this field >>>> when it >>>> >>> stopped the insertion. Not sure why that would be the case though. >>>> >>> Note: only do that update if you are certain that there is no >>>> processing >>>> >>> happening. >>>> >>> >>>> >>> Hope this helps! >>>> >>> >>>> >>> >>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>> actually do >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> I thought that this might be a permission because "w" was missing >>>> at the >>>> >>> group. After using chmod -R 775 only 102809579 passed, but with no >>>> mnic >>>> >>> files. Also now i have this error >>>> >>> >>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>> :/data/loris/bin/mri/tools$ >>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>> >>> Cannot delete upload 34: the MRI pipeline is currently processing >>>> it. >>>> >>> >>>> >>> How can solve this? >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> >>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos >>>> < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> Here is our auto dicom uploading python script: >>>> >>> >>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>> >>> >>>> >>> To give you a brief idea: >>>> >>> Per folder it will: >>>> >>> 1) Delete all the .bak files >>>> >>> 2) Locate .dcm files and update the Patient header >>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, >>>> >>> TE_max parameters of T1 protocol and do an update at the >>>> mri_protocol table >>>> >>> >>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>> >>> For some reason some files are missing >>>> SeriesDescription/ProtocolName >>>> >>> >>>> >>> In total i have 7 folders >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> 3/7 passed >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> Also about the first patient with DC0000 had a violation "T1 AXIAL >>>> SE >>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i find >>>> that weird >>>> >>> since Loris detects the SeriesDescription. >>>> >>> [image: image.png] >>>> >>> >>>> >>> >>>> >>> Now about the 4/7 that didn't passed >>>> >>> >>>> >>> 102327840 and 102809579 outputs "The target directory does not >>>> contain a >>>> >>> single DICOM file.", therefore they are missing their StudyUID >>>> >>> >>>> >>> 102506134 has 2 studyuid "You can't use it with data from multiple >>>> >>> studies." >>>> >>> >>>> >>> and 102761034 "No data could be converted into valid MINC files. >>>> >>> localizer, scout will not be considered!" What is this? >>>> >>> >>>> >>> If i wanted to force the insertion of 102327840, 102809579 and >>>> 102506134 >>>> >>> can i just pass a flag parameter to batch_uploads_imageuploader.pl? >>>> or >>>> >>> modify imaging_upload_file.pl? >>>> >>> >>>> >>> Thank you, >>>> >>> >>>> >>> Sotirios >>>> >>> >>>> >>> PS >>>> >>> >>>> >>> To diagnose a folder search the name of the folder at >>>> dicom_output.txt. >>>> >>> >>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> Glad to hear about your progress. >>>> >>> >>>> >>> Yes, the script you used to delete imaging data is fully documented >>>> here >>>> >>> < >>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>> > >>>> >>> -- let us know if you didn't find the answers you were looking for >>>> there. >>>> >>> (Is it possible the null row in *mri_scanner* seen in your database >>>> >>> management software is a visual placeholder for you as the user? >>>> I'm not >>>> >>> sure why a scanner would ever be registered with ID='0' as your >>>> screenshot >>>> >>> showed.) >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> I fixed it with this >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos >>>> < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> I tried to create a new candidate using the API, is there something >>>> >>> wrong with the structure? why did i receive a 500 internal error? >>>> In the >>>> >>> loris-error log it state that there is something wrong with token, >>>> but i >>>> >>> verfied that the type of the token is a string. >>>> >>> >>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 >>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type >>>> string, >>>> >>> null given, called in >>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 >>>> and >>>> >>> defined in >>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>> >>> trace:\n#0 >>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>> >>> SinglePointLogin->authenticate()\n#2 >>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n >>>> thrown in >>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos >>>> < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> Is there a way also to delete candidates? Just to let you know what >>>> i >>>> >>> did to clear candidates, because maybe i may have missed >>>> dependencies. >>>> >>> >>>> >>> First i deleted all their uploads >>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to >>>> omit >>>> >>> the backup file ? ) >>>> >>> >>>> >>> Afterwards i had some scanner candidates, so i deleted all the >>>> entries >>>> >>> from mri_scanner except that i couldn't delete this entry with the >>>> 0 ID. >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> >>>> >>> Lastly i deleted the session and then the candidate table. >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> We recommend that you use our existing tools for creating new >>>> candidates >>>> >>> - either the LORIS API or if you are using a PHP script, by calling >>>> the Candidate >>>> >>> class's createNew() >>>> >>> < >>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>> >function. >>>> >>> These will create the necessary records for you. (It's not >>>> recommended to >>>> >>> make direct modifications to mysql database tables in your script, >>>> if I >>>> >>> understand you.) >>>> >>> >>>> >>> The CandID should be a randomized 6 digit randomized ID, and there >>>> are >>>> >>> multiple reasons for this. >>>> >>> You can use the PSCID for project-specific IDs and the External ID >>>> field >>>> >>> in the candidate table can also be used for any values you like. >>>> >>> Additionally, any number of custom IDs can be added in parallel - >>>> these >>>> >>> are entered/visible in the Candidate Information module and added >>>> in the >>>> >>> back-end as candidate parameters. >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> >>>> >>> >>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> We are building a script that will auto insert the candidates based >>>> on >>>> >>> their ExternalID. We would like to know whethere when we are >>>> creating a new >>>> >>> profile in the candidate table, if we also have to insert a new >>>> record at >>>> >>> another table? Furthermore is there a problem that in our case >>>> CandID won't >>>> >>> be a 6digit? ( should we start it from 100000?) >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> >>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>> >>> >>>> >>> That would normally be the case but the numeric part of the PSCID >>>> get >>>> >>> paded with 0 on the left. >>>> >>> >>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical >>>> char >>>> >>> with a min value of 1, the sequence would be: >>>> >>> >>>> >>> ABC0001 >>>> >>> ABC0002 >>>> >>> ... >>>> >>> ABC0010 >>>> >>> ... >>>> >>> >>>> >>> thus sorting them ascending will always get the latest value >>>> generated >>>> >>> as the max value. >>>> >>> >>>> >>> M?lanie >>>> >>> >>>> >>> ------------------------------ >>>> >>> *From:* Sotirios Nikoloutsopoulos >>>> >>> *Sent:* September 13, 2019 10:15 >>>> >>> *To:* Melanie Legault, Mrs >>>> >>> *Cc:* Christine Rogers, Ms. ; >>>> >>> loris-dev at bic.mni.mcgill.ca >>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>> >>> >>>> >>> I see, although the PSCID value is varchar(255), it must be stored >>>> >>> within a specific length of characters. Otherwise if we were to sort >>>> >>> strings with different lengths the result would not be sorted >>>> correctly ( >>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>> >>> >>>> >>> Hello Sotirios, >>>> >>> >>>> >>> There is no `last value` stored anywhere. >>>> >>> The code simply look for the PSCID with the max value and increase >>>> that >>>> >>> value by 1 in order to generate the next PSCID. >>>> >>> >>>> >>> Hope this info help. >>>> >>> >>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | McGill >>>> >>> University >>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>> >>> >>>> >>> ------------------------------ >>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>> >>> Nikoloutsopoulos >>>> >>> *Sent:* September 13, 2019 9:43 >>>> >>> *To:* Christine Rogers, Ms. >>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> how does Loris determine the next available PSCID value for a new >>>> >>> candidate? >>>> https://github.com/aces/Loris/wiki/Project-Customization >>>> >>> e.x in the default case the PSCID is sequential, but where do we >>>> store the >>>> >>> last value for the sequential sequence? >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos >>>> < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> the parameters in the mri_protocol you have assigned are global >>>> >>> standard? or were assigned after trial and error? >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> Given you have done the initial setup of your tables to match your >>>> >>> intended protocol/parameters according to instructions -- >>>> >>> the Troubleshooting guide documentation recommends >>>> >>> < >>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>> > >>>> >>> re-running the pipeline (and first deleting prior uploads). >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> *if i were to change their status to resolve what would happen? >>>> >>> >>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> I noticed that i can view the mnics at the brainbrowser from the >>>> >>> mri_violations page ( those mnics are stored at >>>> /data/loris/data/trashbin/ >>>> >>> if i were to click their issue to resolve what would happend? would >>>> they >>>> >>> appear in the dicom_archive view too? ). >>>> >>> >>>> >>> >>>> >>> >>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> The defaut values of the schema exists in my local database. If i >>>> adjust >>>> >>> the default values of TR_min and TE_min the mincs will be uploaded? >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> Is it possible that you haven't set up your mri_protocol table ? >>>> (and >>>> >>> mri_scan_type table too, for additional types of scans) >>>> >>> >>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>> insertion >>>> >>> setup : See the install/setup documentation : >>>> >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>> >>> >>>> >>> To add new rows, just use MySQL insert statements. You can adapt >>>> the >>>> >>> insert statements which load the default table values --> e.g. Here >>>> on >>>> >>> GitHub : >>>> >>> >>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>> >>> (see also the mri_scan_type table) >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> I see that i can edit the values but not how to insert new rows. >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> If i choose Inserted with flag then will the minc be inserted? >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> Glad to hear that *dcmodify* worked correctly. >>>> >>> >>>> >>> For the MRI Violations module, the screenshot is enough. >>>> >>> >>>> >>> It says "could not identify scan type", which we knew already. Did >>>> you >>>> >>> click on the link on those words? >>>> >>> >>>> >>> It will take you to the next page of the module, showing for each >>>> scan >>>> >>> what the scan parameters were, and will also show for comparison >>>> what's >>>> >>> stored in your *mri_protocol* table. >>>> >>> Compare these values to find which parameter was not correct >>>> according >>>> >>> to your *mri_protocol* table scan type definitions. >>>> >>> >>>> >>> You may end up broadening your mri_protocol value ranges (e.g. TR, >>>> TE) >>>> >>> for scans. >>>> >>> This can be done in the front-end, by editing the database table >>>> >>> directly in the same subpage of the MRI Violations module. >>>> >>> >>>> >>> The MRI Violations module features are explained in more detail in >>>> the >>>> >>> Help text for this module inside LORIS (click the ["?"] icon in >>>> the menu >>>> >>> bar.) >>>> >>> >>>> >>> See also: Loris-MRI troubleshooting guide >>>> >>> < >>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>> > >>>> >>> : no MINCs inserted- violated scans >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> looks like my previous email's attachment wasn't delivered due to >>>> >>> security reasons, i uploaded my file at google drive >>>> >>> >>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>> >>> >>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> For the mri_violations i attached the .html output from webbrowser, >>>> so >>>> >>> that you can check the filelds easier. >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> >>>> >>> >>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios -- >>>> >>> Great, sounds like more progress. >>>> >>> >>>> >>> About the dcmodify command -- I'm not sure why you're getting an >>>> Endian >>>> >>> warning. (it's a warning not an error, correct?) >>>> >>> To clarify -- Were the DICOM headers (PatientName) all successfully >>>> >>> relabelled, after the command ran? >>>> >>> >>>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) to >>>> >>> verify and/or update local DICOM headers -- though your dcmodify >>>> command is >>>> >>> a great and fast solution for bulk header updates. >>>> >>> >>>> >>> If you're concerned about fields being changed (e.g. "(2001,105f)" >>>> from >>>> >>> the warning message) - you can also dcmdump a DICOM slice before >>>> and look >>>> >>> at these fields specifically. >>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>> before/after >>>> >>> running dcmodify, and use dcmdump on each version to diff the >>>> outputs -- >>>> >>> this will pinpoint what changed. >>>> >>> >>>> >>> Re the protocol violation -- AcquisitionProtocol not recognized or >>>> >>> unknown : this means your scans did not match what is stored in >>>> your >>>> >>> mri_protocol table. >>>> >>> Check the MRI Violations front-end module -- can you see why they >>>> didn't >>>> >>> match? >>>> >>> Send us an example, in addition to the contents of the mri_protocol >>>> >>> table, if you can't find the source of the mismatch. >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> >>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Here is the psc table >>>> >>> [image: image.png] >>>> >>> >>>> >>> I created 2 candidates profiles through the interface >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> then runned dcmodify command to a dicom file >>>> >>> >>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>> >>> >>>> >>> and got those warning: is this okay? >>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>> reading a >>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>> reading a >>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>> >>> W: Found element (2005,1402) with VR UN and undefined length, >>>> reading a >>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>> >>> W: Found element (2005,140f) with VR UN and undefined length, >>>> reading a >>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>> reading a >>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>> reading a >>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>> >>> >>>> >>> dcmodify at another Dicom didn't show warnings. Below you can see >>>> the >>>> >>> execution for the second dicom. Mnics could not be inserted due to >>>> >>> AcquisitionProtocol being unknown. >>>> >>> >>>> >>> Running now the following command: >>>> /data/loris/bin/mri//uploadNeuroDB/ >>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>> >>> >>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >>>> >>> -delete >>>> >>> >>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>> >>> Target: /data/loris/data/tarchive >>>> >>> >>>> >>> Testing for database connectivity. >>>> >>> Database is available. >>>> >>> >>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>> >>> >>>> >>> You are creating a tar with the following command: >>>> >>> >>>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>> >>> ImagingUpload-18-36-mTrxXs >>>> >>> >>>> >>> >>>> >>> getting md5sums and gzipping!! >>>> >>> >>>> >>> * Taken from dir : >>>> /tmp/ImagingUpload-18-36-mTrxXs >>>> >>> * Archive target location : >>>> >>> >>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>> >>> * Name of creating host : 127.0.1.1 >>>> >>> * Name of host OS : Linux >>>> >>> * Created by user : lorisadmin >>>> >>> * Archived on : 2019-09-06 18:36:50 >>>> >>> * dicomSummary version : 1 >>>> >>> * dicomTar version : 1 >>>> >>> * md5sum for DICOM tarball : >>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>> >>> * md5sum for DICOM tarball gzipped : >>>> aeae87f20155a6805f7e0cfe5212ea5f >>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>> >>> * md5sum for complete archive : >>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>> >>> >>>> >>> Adding archive info into database >>>> >>> >>>> >>> Removing temporary files from target location >>>> >>> >>>> >>> >>>> >>> Done adding archive info into database >>>> >>> >>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>> -globLocation >>>> >>> -profile prod >>>> >>> >>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>> >>> -uploadID 12 -verbose >>>> >>> md5sum >>>> >>> >>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>> >>> PSCID is: DCC0001 >>>> >>> CandID id: 602102 >>>> >>> visit_label is: V1 >>>> >>> PSCID is: DCC0001 >>>> >>> CandID id: 602102 >>>> >>> visit_label is: V1 >>>> >>> candidate id 602102 >>>> >>> Set centerID = 1 >>>> >>> PSCID is: DCC0001 >>>> >>> CandID id: 602102 >>>> >>> visit_label is: V1 >>>> >>> PSCID is: DCC0001 >>>> >>> CandID id: 602102 >>>> >>> visit_label is: V1 >>>> >>> >>>> >>> Number of MINC files that will be considered for inserting into the >>>> >>> database: 2 >>>> >>> >>>> >>> log dir is /data/loris/data//logs and log file is >>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>> >>> PSCID is: DCC0001 >>>> >>> CandID id: 602102 >>>> >>> visit_label is: V1 >>>> >>> PSCID is: DCC0001 >>>> >>> CandID id: 602102 >>>> >>> visit_label is: V1 >>>> >>> candidate id 602102 >>>> >>> >>>> >>> log dir is /data/loris/data//logs and log file is >>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>> >>> PSCID is: DCC0001 >>>> >>> CandID id: 602102 >>>> >>> visit_label is: V1 >>>> >>> PSCID is: DCC0001 >>>> >>> CandID id: 602102 >>>> >>> visit_label is: V1 >>>> >>> candidate id 602102 >>>> >>> >>>> >>> Cleaning up temp files: rm -rf >>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>> >>> >>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>> cat >>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>> >>> >>>> >>> ==> Loading file from disk >>>> >>> >>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>> >>> >>>> >>> --> mapping DICOM parameter for >>>> >>> >>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>> >>> >>>> >>> ==> computing md5 hash for MINC body. >>>> >>> >>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>> >>> >>>> >>> ==> verifying acquisition protocol >>>> >>> >>>> >>> Acquisition protocol is unknown >>>> >>> >>>> >>> --> The minc file cannot be registered since the >>>> AcquisitionProtocol >>>> >>> is unknown >>>> >>> >>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios: >>>> >>> >>>> >>> Sure -- you can delete imaging datasets with the >>>> *delete_imaging_upload* >>>> >>> script -- >>>> >>> details here: >>>> >>> >>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>> >>> >>>> >>> What's in your *psc* table? (Is it properly populated? This is a >>>> >>> pre-requisite to loading imaging data. >>>> >>> < >>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>> > >>>> >>> ) >>>> >>> The foreign key constraint error on the candidate record is curious. >>>> >>> >>>> >>> There are also a few options for creating candidates when inserting >>>> >>> imaging data: >>>> >>> >>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline >>>> >>> >>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>> optionally I >>>> >>> think) >>>> >>> How to: >>>> >>> >>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>> >>> >>>> >>> Then as a second step: >>>> >>> b. Use the imaging insertion pipeline >>>> >>> < >>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>> > >>>> >>> to load your DICOMs. >>>> >>> You will want to first ensure that the PatientName header in the >>>> DICOMs >>>> >>> as well as tar package are correctly labelled with >>>> PSCID_DCCID_VisitLabel >>>> >>> >>>> >>> -- Method 2: for BIDS-format datasets: >>>> >>> How to : >>>> >>> >>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>> >>> >>>> >>> Be sure to use the *-c* and *-s* options when running the >>>> bids_import script, >>>> >>> to automatically create your candidates and sessions. >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> How do i delete a Study? And everytime do i have to create a new >>>> >>> candidate to get DCCID and a PSCID? >>>> >>> >>>> >>> *First execution:* >>>> >>> >>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>> ./ >>>> >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt >>>> > >>>> >>> log.txt >>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>> >>> batch_uploads_imageuploader.pl line 144. >>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>> foreign >>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>> `FK_candidate_1` >>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) >>>> at >>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>> >>> The following database commands failed: >>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>> (?,?,?,?,?)'; >>>> >>> SET >>>> >>> >>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>> >>> Medical Systems'; >>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>> >>> Error obtained:Cannot add or update a child row: a foreign key >>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>> `FK_mri_scanner_1` >>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error >>>> code 1452) >>>> >>> >>>> >>> ERROR: The validation has failed. Either re-run the validation >>>> again >>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to >>>> force the >>>> >>> execution. >>>> >>> >>>> >>> >>>> >>> The tarchiveLoader.pl insertion script has failed. >>>> >>> Can't exec "mail": No such file or directory at ./ >>>> >>> batch_uploads_imageuploader.pl line 249. >>>> >>> print() on closed filehandle MAIL at ./ >>>> batch_uploads_imageuploader.pl >>>> >>> line 250. >>>> >>> print() on closed filehandle MAIL at ./ >>>> batch_uploads_imageuploader.pl >>>> >>> line 251. >>>> >>> >>>> >>> >>>> >>> *And second execution: * >>>> >>> >>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>> ./ >>>> >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt >>>> > >>>> >>> log.txt >>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>> >>> batch_uploads_imageuploader.pl line 144. >>>> >>> >>>> >>> PROBLEM: >>>> >>> The user 'lorisadmin' has already inserted this study. >>>> >>> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>> >>> This is the information retained from the first time the study was >>>> >>> inserted: >>>> >>> >>>> >>> * Taken from dir : >>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>> >>> * Archive target location : >>>> >>> >>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>> >>> * Name of creating host : 127.0.1.1 >>>> >>> * Name of host OS : Linux >>>> >>> * Created by user : lorisadmin >>>> >>> * Archived on : 2019-09-04 18:33:05 >>>> >>> * dicomSummary version : 1 >>>> >>> * dicomTar version : 1 >>>> >>> * md5sum for DICOM tarball : >>>> 4a301b0318178b09b91e63544282364d >>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>> >>> * md5sum for DICOM tarball gzipped : >>>> 9d95ea2b9111be236808bfd65d7e65ec >>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>> >>> * md5sum for complete archive : >>>> ab19a86357f1d4053aa3b81c8a071053 >>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>> >>> >>>> >>> >>>> >>> Last update of record: >>>> >>> >>>> >>> >>>> >>> >>>> >>> The dicomTar.pl execution has failed. >>>> >>> Can't exec "mail": No such file or directory at ./ >>>> >>> batch_uploads_imageuploader.pl line 249. >>>> >>> print() on closed filehandle MAIL at ./ >>>> batch_uploads_imageuploader.pl >>>> >>> line 250. >>>> >>> print() on closed filehandle MAIL at ./ >>>> batch_uploads_imageuploader.pl >>>> >>> line 251. >>>> >>> >>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> Ok, this sounds like good progress. Let us know when you next >>>> encounter >>>> >>> issues as you progress through the Imaging Install/Setup docs >>>> >>> . >>>> >>> I'll look into how we can better handle the incoming/ directory next >>>> >>> time. >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>> >>> populated correctly except its port is 'port' : ''. Also i have >>>> tested >>>> >>> that i can connect to MySQL with lorisuser. >>>> >>> >>>> >>> I executed the script again, because the only error i had >>>> previously was >>>> >>> that the /data/incoming folder didn't exist and there are no errors >>>> >>> reported back except of warnings <>>> password on the >>>> >>> command line interface can be insecure>>. >>>> >>> >>>> >>> >>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> It's possible -- if the script was unable to connect to the database >>>> >>> during its execution (e.g. typo in the password), that would >>>> explain the >>>> >>> underpopulated Image path and Loris-MRI code path you saw in the >>>> Config >>>> >>> module. >>>> >>> It's hard to tell without seeing the output from your script run -- >>>> Did >>>> >>> you see a sign of any such error? >>>> >>> The Config fields are populated by the imaging_install.sh script >>>> (starting >>>> >>> at line 222 >>>> >>> < >>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>> > >>>> >>> ) >>>> >>> >>>> >>> For example, check if the database connection information was >>>> populated >>>> >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> >>>> >>> >>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> Hi Christine, >>>> >>> >>>> >>> If you are referring to the imaging_install.sh here is an image >>>> with the >>>> >>> configurations i typed. Maybe the problem is somewhere at the last >>>> part >>>> >>> which asks to configure as much as possible automatically? >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> >>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>>> >>> christine.rogers at mcgill.ca> ??????: >>>> >>> >>>> >>> Hi Sotirios, >>>> >>> >>>> >>> Glad to hear your LORIS core install is up and working and all the >>>> >>> front-end pages are loading. >>>> >>> >>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>>> >>> > and the web interface worked. >>>> >>> >>>> >>> Yes, it's important that project/ have 775 permissions and that >>>> >>> lorisadmin be part of the sudoers group, per step 1 in the install >>>> >>> Readme . >>>> >>> >>>> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS to >>>> >>> loris, right? >>>> >>> >>>> >>> These imaging paths will be updated during your imaging installation >>>> >>> by an automated script >>>> -- >>>> >>> you do not need to set them manually via the Config module. >>>> >>> Please continue to follow the Setup Guide >>>> >>> for detailed steps to >>>> follow. >>>> >>> >>>> >>> Best, >>>> >>> Christine >>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> wrote: >>>> >>> >>>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS to >>>> loris, >>>> >>> right? >>>> >>> >>>> >>> [image: image.png] >>>> >>> >>>> >>> >>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> >>> sotirisnik at gmail.com> ??????: >>>> >>> >>>> >>> Hi, >>>> >>> >>>> >>> i used >>>> >>> >>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>> >>> sudo apt-get install -y nodejs >>>> >>> >>>> >>> >>>> >>> you had suggested in the past, make worked and now i can see all the >>>> >>> contents in the web-interface, but i don't need make install? >>>> >>> >>>> >>> Thanks >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> >>> >>>> >>> -- >>>> >>> >>>> >>> christine.rogers at mcgill.ca >>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>> >>> Montreal Neurological Institute >>>> >>> McGill University | Montreal | Canada >>>> >>> >>>> >>> _______________________________________________ >>>> >>> Loris-dev mailing list >>>> >>> Loris-dev at bic.mni.mcgill.ca >>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>>> >>> >>>> -------------- next part -------------- >>>> An HTML attachment was scrubbed... >>>> URL: < >>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>> > >>>> >>>> ------------------------------ >>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>>> >>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>> ***************************************** >>>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- 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URL: -------------- next part -------------- (loris-mri-python) lorisadmin at hbp:~/LORIS-for-MIP$ python dicom_uploader.py ./102809579/10/1.3.12.2.1107.5.2.30.27780.2017071115494453951663644.0.0.0_0010_000010_1518429975f013.dcm 102809579 Creating candidate Update externalid Create candidate Candidate Info 465466 DCC0000 Next Visit Label 1 102809579 Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 38 /data/incoming/DCC0000_465466_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-23\-4\-mzDAXD -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-23\-4\-mzDAXD \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-23-4-mzDAXD Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. The target directory does not contain a single DICOM file. The dicomTar.pl execution has failed. Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251. 1800 ./102506134/401/1.3.46.670589.11.34037.5.0.4800.2015021615033196828_0401_000053_1517388859af29.dcm 102506134 Creating candidate Update externalid Create candidate Candidate Info 864173 DCC0001 Next Visit Label 1 102506134 Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 39 /data/incoming/DCC0001_864173_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-23\-4\-XByzUe -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-23\-4\-XByzUe \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-23-4-XByzUe Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. ERROR: This class is designed around the notion of a 'Study'. You can't use it with data from multiple studies. The following study UIDs were found: '1.3.51.0.1.1.10.49.10.222.2753369.2752207' '1.3.51.0.1.1.10.49.10.222.3332609.3331661' The dicomTar.pl execution has failed. Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251. 9.87489986419677 ./000535670/501/1.3.46.670589.11.34037.5.0.6020.2012120510342515883_0501_000009_15181073851a4d.dcm 000535670 Creating candidate Update externalid Create candidate Candidate Info 890807 DCC0002 Next Visit Label 1 000535670 Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 40 /data/incoming/DCC0002_890807_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-23\-5\-XEWlt3 -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-23\-5\-XEWlt3 \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-23-5-XEWlt3 Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-23-5-XEWlt3 You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-23-5-XEWlt3.tar ImagingUpload-23-5-XEWlt3 getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-23-5-XEWlt3 * Archive target location : /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-23-5-XEWlt3.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-11-13 23:05:01 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : ee6e8609941863466aaa4d678ee35e04 ImagingUpload-23-5-XEWlt3.tar * md5sum for DICOM tarball gzipped : f52b8bbb124f6125bb5e8be96c8b8384 ImagingUpload-23-5-XEWlt3.tar.gz * md5sum for complete archive : 98f2253565c7d1cc7c5fca7afb5be935 DCM_2012-12-05_ImagingUpload-23-5-XEWlt3.tar Adding archive info into database Removing temporary files from target location Done adding archive info into database \/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation -profile prod \/data\/loris\/data\/tarchive\/\/DCM_2012\-12\-05_ImagingUpload\-23\-5\-XEWlt3\.tar -uploadID 40 -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-23-5-XEWlt3.tar PSCID is: DCC0002 CandID id: 890807 visit_label is: V1 PSCID is: DCC0002 CandID id: 890807 visit_label is: V1 candidate id 890807 Set centerID = 1 PSCID is: DCC0002 CandID id: 890807 visit_label is: V1 PSCID is: DCC0002 CandID id: 890807 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 0 No data could be converted into valid MINC files. localizer, scout will not be considered! The tarchiveLoader.pl insertion script has failed. Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251. 9.90050029754638 ./GuyBrush_patient/18/1.3.12.2.1107.5.2.18.41694.2016041110375071672755510.0.0.0_0018_000069_15172187774ed4.dcm 102662671 Creating candidate Update externalid Create candidate Candidate Info 397410 DCC0003 Next Visit Label 1 GuyBrush_patient Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 41 /data/incoming/DCC0003_397410_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-23\-5\-6HVhcz -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-23\-5\-6HVhcz \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-23-5-6HVhcz Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-23-5-6HVhcz You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-23-5-6HVhcz.tar ImagingUpload-23-5-6HVhcz getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-23-5-6HVhcz * Archive target location : /data/loris/data/tarchive/DCM_2016-04-11_ImagingUpload-23-5-6HVhcz.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-11-13 23:05:18 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 2bb93412668127cd8e5b697862cf270a ImagingUpload-23-5-6HVhcz.tar * md5sum for DICOM tarball gzipped : 38722762e1222bc83e99b98bf774c11f ImagingUpload-23-5-6HVhcz.tar.gz * md5sum for complete archive : 8271879ea5529107fe0c3a2863b077a6 DCM_2016-04-11_ImagingUpload-23-5-6HVhcz.tar Adding archive info into database Removing temporary files from target location Done adding archive info into database \/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation -profile prod \/data\/loris\/data\/tarchive\/\/DCM_2016\-04\-11_ImagingUpload\-23\-5\-6HVhcz\.tar -uploadID 41 -verbose md5sum /data/loris/data/tarchive/DCM_2016-04-11_ImagingUpload-23-5-6HVhcz.tar PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 candidate id 397410 Set centerID = 1 PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 4 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-23-5-v9lR7q.log PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 candidate id 397410 Finished file: assembly/397410/V1/mri/native/loris_397410_V1_t1_001.mnc Creating NIfTI files found zspace at 0 0 found yspace at 1 1 found xspace at 2 2 0 2 0 1 27 6.500000 1 1 1 1 352 0.781250 2 0 2 1 512 0.781250 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-23-5-BJ3AOB.log PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 candidate id 397410 Finished file: assembly/397410/V1/mri/native/loris_397410_V1_t1_002.mnc Creating NIfTI files found zspace at 0 0 found yspace at 1 1 found xspace at 2 2 0 2 0 1 27 6.500000 1 1 1 1 352 0.781250 2 0 2 1 512 0.781250 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-23-5-TUTn0K.log PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 candidate id 397410 Finished file: assembly/397410/V1/mri/native/loris_397410_V1_t1_003.mnc Creating NIfTI files found zspace at 1 0 found yspace at 0 1 found xspace at 2 2 0 2 1 1 384 1.041667 1 1 0 1 64 1.600000 2 0 2 1 384 1.041667 Restructuring... log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-23-5-8MoSBq.log PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 PSCID is: DCC0003 CandID id: 397410 visit_label is: V1 candidate id 397410 Finished file: assembly/397410/V1/mri/native/loris_397410_V1_t1_004.mnc Creating NIfTI files found zspace at 0 0 found yspace at 1 1 found xspace at 2 2 0 2 0 1 96 1.600000 1 1 1 1 384 1.041667 2 0 2 1 384 1.041667 noise_estimate --snr /data/loris/data//assembly/397410/V1/mri/native/loris_397410_V1_t1_001.mnc SNR is: 315.565 noise_estimate --snr /data/loris/data//assembly/397410/V1/mri/native/loris_397410_V1_t1_002.mnc SNR is: 387.044 noise_estimate --snr /data/loris/data//assembly/397410/V1/mri/native/loris_397410_V1_t1_003.mnc SNR is: 60.8322 noise_estimate --snr /data/loris/data//assembly/397410/V1/mri/native/loris_397410_V1_t1_004.mnc SNR is: 72.0073 Creating Minc Pics TarchiveSource is 10 Connecting to database. FileID from mass_pic.pl is: 9 FileID from mass_pic.pl is: 10 FileID from mass_pic.pl is: 11 FileID from mass_pic.pl is: 12 Finished mass_pic.pl execution Cleaning up temp files: rm -rf /tmp/TarLoad-23-5-xhVSib/ImagingUpload-23-5-6HVhcz* find /data/loris/data/tarchive// -name *ImagingUpload-23-5-6HVhcz* rm /data/incoming/DCC0003_397410_V1.tar.gz Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251. 3.93 ./102327840/6/1.3.12.2.1107.5.2.18.41881.2015052614223027481362738.0.0.0_0006_000151_151783729799ea.dcm 102327840 Creating candidate Update externalid Create candidate Candidate Info 727195 DCC0004 Next Visit Label 1 102327840 Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 42 /data/incoming/DCC0004_727195_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-23\-6\-Qa4uJV -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-23\-6\-Qa4uJV \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-23-6-Qa4uJV Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. The target directory does not contain a single DICOM file. The dicomTar.pl execution has failed. Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251. 600 ./102761034/301/1.3.46.670589.11.34037.5.0.4664.2016120612342878292_0301_000013_151699184819f1.dcm 102761034 Creating candidate Update externalid Create candidate Candidate Info 637025 DCC0005 Next Visit Label 1 102761034 Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 43 /data/incoming/DCC0005_637025_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-23\-6\-hegVEJ -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-23\-6\-hegVEJ \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-23-6-hegVEJ Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-23-6-hegVEJ You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-23-6-hegVEJ.tar ImagingUpload-23-6-hegVEJ getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-23-6-hegVEJ * Archive target location : /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-23-6-hegVEJ.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-11-13 23:06:22 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 5fe571da9d2ae7910960d456dd812e7e ImagingUpload-23-6-hegVEJ.tar * md5sum for DICOM tarball gzipped : 68248aee5669443a4092588a04e7faf2 ImagingUpload-23-6-hegVEJ.tar.gz * md5sum for complete archive : 3f0900c926455020c22b1353f38ead2c DCM_2016-12-06_ImagingUpload-23-6-hegVEJ.tar Adding archive info into database Removing temporary files from target location Done adding archive info into database \/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation -profile prod \/data\/loris\/data\/tarchive\/\/DCM_2016\-12\-06_ImagingUpload\-23\-6\-hegVEJ\.tar -uploadID 43 -verbose md5sum /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-23-6-hegVEJ.tar PSCID is: DCC0005 CandID id: 637025 visit_label is: V1 PSCID is: DCC0005 CandID id: 637025 visit_label is: V1 candidate id 637025 Set centerID = 1 PSCID is: DCC0005 CandID id: 637025 visit_label is: V1 PSCID is: DCC0005 CandID id: 637025 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 0 No data could be converted into valid MINC files. localizer, scout will not be considered! The tarchiveLoader.pl insertion script has failed. Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251. 9.88119983673095 ./000998448/205/1.3.46.670589.11.70598.5.0.7280.2016082207333647000_0205_000005_15182175292548.dcm 000998448 Creating candidate Update externalid Create candidate Candidate Info 239975 DCC0006 Next Visit Label 1 000998448 Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 44 /data/incoming/DCC0006_239975_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-23\-6\-yv2MZz -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-23\-6\-yv2MZz \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-23-6-yv2MZz Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-23-6-yv2MZz You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-23-6-yv2MZz.tar ImagingUpload-23-6-yv2MZz getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-23-6-yv2MZz * Archive target location : /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-23-6-yv2MZz.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-11-13 23:06:37 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 44c40d7d0359347cbf18d3a4c0a363a6 ImagingUpload-23-6-yv2MZz.tar * md5sum for DICOM tarball gzipped : 4138b14ffa3ea5eb5361bde35834feed ImagingUpload-23-6-yv2MZz.tar.gz * md5sum for complete archive : 907e43ced34c119adc9c353a037ceb69 DCM_2016-08-22_ImagingUpload-23-6-yv2MZz.tar Adding archive info into database Removing temporary files from target location Done adding archive info into database \/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation -profile prod \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-23\-6\-yv2MZz\.tar -uploadID 44 -verbose md5sum /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-23-6-yv2MZz.tar PSCID is: DCC0006 CandID id: 239975 visit_label is: V1 PSCID is: DCC0006 CandID id: 239975 visit_label is: V1 candidate id 239975 Set centerID = 1 PSCID is: DCC0006 CandID id: 239975 visit_label is: V1 PSCID is: DCC0006 CandID id: 239975 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 0 No data could be converted into valid MINC files. localizer, scout will not be considered! The tarchiveLoader.pl insertion script has failed. Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251. 7.96409988403320 ./102788419/7/1.3.12.2.1107.5.2.30.27245.2015122209062920279710806.0.0.0_0007_000019_15169884050c34.dcm 102788419 Creating candidate Update externalid Create candidate Candidate Info 684908 DCC0007 Next Visit Label 1 102788419 Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 45 /data/incoming/DCC0007_684908_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-23\-6\-t3uKib -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-23\-6\-t3uKib \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-23-6-t3uKib Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. The target directory does not contain a single DICOM file. The dicomTar.pl execution has failed. Can't exec "mail": No such file or directory at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 251. From christine.rogers at mcgill.ca Wed Nov 13 18:13:27 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 13 Nov 2019 23:13:27 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: <3c83f4cc2d7f45938777a4084038e986@YTBPR01MB2895.CANPRD01.PROD.OUTLOOK.COM> References: <3c83f4cc2d7f45938777a4084038e986@YTBPR01MB2895.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi Sotirios - Thanks. Before we dive into this over the next few days, can you also let us know : Was the second machine and/or data partition cloned ? Or else, What's the difference between your two installations? If it's easy, give us the OS, mariadb version, etc. Please also confirm -- did you encounter any installation issues with dependency libraries? What steps have you taken to verify that the configurations of your pipelines, protocol setup, etc are identical in both instances? Best, Christine On Wed, Nov 13, 2019 at 5:55 PM Sotirios Nikoloutsopoulos > wrote: Hi Christine, In my first vm i am able to create the minc files and view them at the mri browser (except of candidate 102761034 ), meanwhile the same files gives warnings at the 2nd vm. The output of the batch upload can be seen in the file attached. Also a colleague of us has built a pre-validation tool for dicom https://github.com/aueb-wim/DataQualityControlTool/ which had found all the files that Loris gave as warning . Basically I confirmed that the total amount of files per dicom was the same amount as stated in Loris and checked some filenames given from warning to confirm that they match with our tool. But that was months ago and my colleague had changed some parameters for MIP and now our tool doesn't find all the invalid files, that's why i asked for the dicom header specification of Loris. In a discussion we had he mentioned that he doesn't check for some tags e.x. orientation. Lastly to mention that in my first vm i didn't use our tool to remove invalid dcm files. Thanks ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Can you provide us with some fresh particulars of the current issue and we'll take it from there? Yang's team has built these scripts which can definitely serve as a model for your pre-validation of your DICOM collections. cheers, Christine On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos > wrote: HI Yang, We make use of pydicom library too. Now about the validate.py i see that you check if some attributes are missing such as PatientID, PatientName which all of our files contains that info. Maybe i have missed something on the setup of my other virtual machine ( although one dicom passed on the new vm successfully, the others that were inserted correctly on my old vm fails on the new one ), i think that i had asked about this error "Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but i don't remember the solution. Thanks ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding > ??????: Hey, Sotirios, Christine from the LORIS team mentioned you had some issue with DICOM. I am a fellow developer for an external project using LORIS, kind of just like you. We had to implement DICOM upload as well but more as a fully automated pipeline actually. While we were building CNBP, we had coded up some minor Python functions to check DICOM integrity (and simple validations) and you might be able to gain some inspiration from it and help you with your cause. For more comprehensive solution, PyDICOM (https://pydicom.github.io/pydicom/stable/getting_started.html#) seems like a descent python package to help out with a lot of DICOM data checks (I was essentially just building customized wrapper calls to them). You can see some example scripts here as part of our DICOM submodule. It is pretty rough around the edges but hopefully point you in the right direcitons https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py Cheers, Yang Ding, PhD. Canadian Neonatal Brain Platform Architect On Tue, Nov 12, 2019 at 8:29 AM > wrote: Send Loris-dev mailing list submissions to loris-dev at bic.mni.mcgill.ca To subscribe or unsubscribe via the World Wide Web, visit https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev or, via email, send a message with subject or body 'help' to loris-dev-request at bic.mni.mcgill.ca You can reach the person managing the list at loris-dev-owner at bic.mni.mcgill.ca When replying, please edit your Subject line so it is more specific than "Re: Contents of Loris-dev digest..." Today's Topics: 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) ---------------------------------------------------------------------- Message: 1 Date: Tue, 12 Nov 2019 15:28:26 +0200 From: Sotirios Nikoloutsopoulos > To: Cecile Madjar > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Import mri - scripts Message-ID: > Content-Type: text/plain; charset="utf-8" Hi, Could we send you a link with 10 anonymized dicom files to diagnose the warnings we get? Thanks ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi Cecile, > > We were wondering whether Loris has a tool to check if there are problems > with the dcm files, before trying to upload them. Something that could > provide the same results provided in the warning_output, this is the > summary from the mri_upload at the front-page. Also which attributes of the > dcm header would trigger a warning? is there a dcm file header > specification for Loris? > > Thanks > > Sotirios > > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi, >> >> Yes, by parsing now() into unix_timestamp function it worked,but i >> thought that something else was causing the 2nd issue. >> Thanks >> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >> xavier.lecoursboucher at mcgill.ca> wrote: >> >>> Hi Sotirios, >>> >>> The first error occurs because the QCFirstChangeTime and columns are of >>> type `unsigned integer` and not `datatime`. You should be using >>> UNIX_TIMESTAMP() instead of NOW(). >>> >>> The second error occurs because the trigger triggers a rollback of the >>> insert statement in the files table. >>> See mysql documentation for trigger error handling. >>> >>> An error during either a BEFORE or AFTER trigger results in failure of >>> the entire statement that caused trigger invocation. >>> >>> >>> Thank you for sharing that. I hope it helps. >>> -- Xavier >>> >>> ------------------------------ >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>> Nikoloutsopoulos > >>> *Sent:* October 1, 2019 8:33 AM >>> *To:* Cecile Madjar > >>> *Cc:* loris-dev at bic.mni.mcgill.ca >; >>> Christine Rogers, Ms. > >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> When mincs are inserted their corresponding rows at the file table are >>> inserted too >>> [image: image.png] >>> >>> i would like to insert their rows at file_qcstatus as well, because i >>> don't want manually to label them as passed throught the interface >>> >>> [image: image.png] >>> >>> >>> That is the trigger i wrote >>> >>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` AFTER >>> INSERT ON `files` FOR EACH ROW >>> BEGIN >>> INSERT INTO files_qcstatus >>> SET FileID = NEW.FileID, >>> SeriesUID = NEW.SeriesUID, >>> EchoTime = NEW.EchoTime, >>> QCStatus = "Pass", >>> QCFirstChangeTime = NOW(), >>> QCLastChangeTime = NOW(); >>> END >>> >>> although it contains some errors >>> >>> DBD::mysql::db do failed: Out of range value for column >>> 'QCFirstChangeTime' at row 1 at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` (`FileID`)) >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>> >>> >>> >>> >>> >>> >>> >>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> In the mri_upload table, there is a TarchiveID column associated with >>> the MRI upload you inserted. When this value is NULL, it means no DICOMs >>> were inserted into the tarchive tables. At the end of the insertion of the >>> DICOMs in the tarchive tables, this value is updated with the correct >>> TarchiveID associated with the upload. >>> >>> Could this correspond to what you want to do? >>> >>> Regarding the files_qcstatus, this table is only linked to the files >>> table (hence, the MINC files). You could always create a new table for >>> dicom_qcstatus and link it to the tarchive table? >>> >>> C?cile >>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> i would like whenever a dicom is imported to mark all their >>> coressponding qc_status to "pass". I was thinking of creating a trigger for >>> that, but which tables do i need to add entries to? So far from what i see >>> i need to add entres at the table "files" whenever an insertion happens to >>> files_qcstatus. >>> >>> Thanks >>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Oh, sorry i should have asked for StudyID, at the beginning of my email >>> i sent 3 hours ago (not StudyUID). >>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i am >>> looking for is not stored in the database? >>> >>> [image: image.png] >>> >>> Thanks. >>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> The StudyUID is stored in the DicomArchiveID field of the >>> tarchive table. It can also be found in the metadata field but it is mixed >>> with many other information. >>> >>> Hope this helps, >>> >>> C?cile >>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>> specifically at the AcquisitonMetadata column i found something called >>> 'Unique Study ID" in its context, but that must be the Study Instance UID. >>> >>> Thanks >>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Your observation is correct. A little explanation below. >>> >>> MINC files get inserted into the MRI violation tables if: >>> >>> - the scan type could not be identified (not matching an entry in >>> the mri_protocol table) >>> - one parameter of the scan type is out of the expected range >>> present in the mri_protocol_checks (extra filtering in case you need to be >>> stricker on some parameters not present in the mri_protocol table) >>> - if the CandID and PSCID do not match >>> >>> The following cases do not get in the MRI violation tables as it happens >>> before the conversion of the DICOM to MINC files and only MINC files >>> violations are logged there: >>> >>> - "No single DICOM" (since no valid DICOM could be found to convert >>> to MINC) >>> - "Study already inserted" (duplicate StudyUID) since this error >>> happens at the dicomTar.pl level (way before conversion into MINC files) >>> >>> Glad everything is working out!! >>> Best, >>> >>> C?cile >>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now about the >>> mri_violations, dicoms are triggered to be inserted there only if there is >>> a violation for Tr_min, Tr_max, in general for its header parameter? >>> Because i don't see the cases of 'No single dicom" or with the 2 studyiuid >>> to be there. >>> >>> Thanks >>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Sorry to hear you are having issues with the memory. I think most of our >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>> >>> Hope this helps! >>> >>> C?cile >>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> about that dicom that had that insertion error it's about 30mb and when >>> it is being processed the ram is being drastically increased from 2gb to >>> 3.28 and then the whole virtual machine is frozen. What is the recommended >>> size of ram for using Loris? >>> >>> Thanks >>> >>> [image: image.png] >>> >>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to see that the StudyUID problem was fixed! >>> >>> For the delete script issue, if you are absolutely certain that no >>> processes are run for that uploadID, you can update the mri_upload table >>> and set the column Inserting to 0 instead of 1 for that uploadID. It >>> looks like for some reason the scripts did not update this field when it >>> stopped the insertion. Not sure why that would be the case though. >>> Note: only do that update if you are certain that there is no processing >>> happening. >>> >>> Hope this helps! >>> >>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> about the Dicoms i reported that didn't have a StudyID they actually do >>> >>> [image: image.png] >>> >>> >>> [image: image.png] >>> >>> I thought that this might be a permission because "w" was missing at the >>> group. After using chmod -R 775 only 102809579 passed, but with no mnic >>> files. Also now i have this error >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri/tools$ >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>> Cannot delete upload 34: the MRI pipeline is currently processing it. >>> >>> How can solve this? >>> >>> Thanks >>> >>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> Here is our auto dicom uploading python script: >>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>> >>> To give you a brief idea: >>> Per folder it will: >>> 1) Delete all the .bak files >>> 2) Locate .dcm files and update the Patient header >>> 3) Furthermore we are interesting in finding TR_min, TR_max, TE_min, >>> TE_max parameters of T1 protocol and do an update at the mri_protocol table >>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>> For some reason some files are missing SeriesDescription/ProtocolName >>> >>> In total i have 7 folders >>> >>> [image: image.png] >>> >>> 3/7 passed >>> >>> [image: image.png] >>> >>> Also about the first patient with DC0000 had a violation "T1 AXIAL SE >>> GADO", but my script didn't output a TE of 17 nowhere and i find that weird >>> since Loris detects the SeriesDescription. >>> [image: image.png] >>> >>> >>> Now about the 4/7 that didn't passed >>> >>> 102327840 and 102809579 outputs "The target directory does not contain a >>> single DICOM file.", therefore they are missing their StudyUID >>> >>> 102506134 has 2 studyuid "You can't use it with data from multiple >>> studies." >>> >>> and 102761034 "No data could be converted into valid MINC files. >>> localizer, scout will not be considered!" What is this? >>> >>> If i wanted to force the insertion of 102327840, 102809579 and 102506134 >>> can i just pass a flag parameter to batch_uploads_imageuploader.pl? or >>> modify imaging_upload_file.pl? >>> >>> Thank you, >>> >>> Sotirios >>> >>> PS >>> >>> To diagnose a folder search the name of the folder at dicom_output.txt. >>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> Glad to hear about your progress. >>> >>> Yes, the script you used to delete imaging data is fully documented here >>> >>> -- let us know if you didn't find the answers you were looking for there. >>> (Is it possible the null row in *mri_scanner* seen in your database >>> management software is a visual placeholder for you as the user? I'm not >>> sure why a scanner would ever be registered with ID='0' as your screenshot >>> showed.) >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> I fixed it with this >>> >>> [image: image.png] >>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> I tried to create a new candidate using the API, is there something >>> wrong with the structure? why did i receive a 500 internal error? In the >>> loris-error log it state that there is something wrong with token, but i >>> verfied that the type of the token is a string. >>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type string, >>> null given, called in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and >>> defined in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>> trace:\n#0 /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>> SinglePointLogin->authenticate()\n#2 >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n thrown in >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >>> >>> [image: image.png] >>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> Is there a way also to delete candidates? Just to let you know what i >>> did to clear candidates, because maybe i may have missed dependencies. >>> >>> First i deleted all their uploads >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to omit >>> the backup file ? ) >>> >>> Afterwards i had some scanner candidates, so i deleted all the entries >>> from mri_scanner except that i couldn't delete this entry with the 0 ID. >>> >>> [image: image.png] >>> >>> >>> Lastly i deleted the session and then the candidate table. >>> >>> Thanks >>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> We recommend that you use our existing tools for creating new candidates >>> - either the LORIS API or if you are using a PHP script, by calling the Candidate >>> class's createNew() >>> function. >>> These will create the necessary records for you. (It's not recommended to >>> make direct modifications to mysql database tables in your script, if I >>> understand you.) >>> >>> The CandID should be a randomized 6 digit randomized ID, and there are >>> multiple reasons for this. >>> You can use the PSCID for project-specific IDs and the External ID field >>> in the candidate table can also be used for any values you like. >>> Additionally, any number of custom IDs can be added in parallel - these >>> are entered/visible in the Candidate Information module and added in the >>> back-end as candidate parameters. >>> >>> Best, >>> Christine >>> >>> >>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> We are building a script that will auto insert the candidates based on >>> their ExternalID. We would like to know whethere when we are creating a new >>> profile in the candidate table, if we also have to insert a new record at >>> another table? Furthermore is there a problem that in our case CandID won't >>> be a 6digit? ( should we start it from 100000?) >>> >>> Thanks >>> >>> [image: image.png] >>> >>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>> melanie.legault2 at mcgill.ca> ??????: >>> >>> That would normally be the case but the numeric part of the PSCID get >>> paded with 0 on the left. >>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical char >>> with a min value of 1, the sequence would be: >>> >>> ABC0001 >>> ABC0002 >>> ... >>> ABC0010 >>> ... >>> >>> thus sorting them ascending will always get the latest value generated >>> as the max value. >>> >>> M?lanie >>> >>> ------------------------------ >>> *From:* Sotirios Nikoloutsopoulos > >>> *Sent:* September 13, 2019 10:15 >>> *To:* Melanie Legault, Mrs > >>> *Cc:* Christine Rogers, Ms. >; >>> loris-dev at bic.mni.mcgill.ca > >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> I see, although the PSCID value is varchar(255), it must be stored >>> within a specific length of characters. Otherwise if we were to sort >>> strings with different lengths the result would not be sorted correctly ( >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>> >>> Thanks >>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>> melanie.legault2 at mcgill.ca> ??????: >>> >>> Hello Sotirios, >>> >>> There is no `last value` stored anywhere. >>> The code simply look for the PSCID with the max value and increase that >>> value by 1 in order to generate the next PSCID. >>> >>> Hope this info help. >>> >>> M?lanie Legault | Software developer | Faculty of Medicine | McGill >>> University >>> 3801 University, Montr?al, QC H3A 2B4 >>> >>> ------------------------------ >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>> Nikoloutsopoulos > >>> *Sent:* September 13, 2019 9:43 >>> *To:* Christine Rogers, Ms. > >>> *Cc:* loris-dev at bic.mni.mcgill.ca > >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>> >>> Hi, >>> >>> how does Loris determine the next available PSCID value for a new >>> candidate? https://github.com/aces/Loris/wiki/Project-Customization >>> e.x in the default case the PSCID is sequential, but where do we store the >>> last value for the sequential sequence? >>> >>> Thanks >>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> the parameters in the mri_protocol you have assigned are global >>> standard? or were assigned after trial and error? >>> >>> Thanks >>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Given you have done the initial setup of your tables to match your >>> intended protocol/parameters according to instructions -- >>> the Troubleshooting guide documentation recommends >>> >>> re-running the pipeline (and first deleting prior uploads). >>> >>> Best, >>> Christine >>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> *if i were to change their status to resolve what would happen? >>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> I noticed that i can view the mnics at the brainbrowser from the >>> mri_violations page ( those mnics are stored at /data/loris/data/trashbin/ >>> if i were to click their issue to resolve what would happend? would they >>> appear in the dicom_archive view too? ). >>> >>> >>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> The defaut values of the schema exists in my local database. If i adjust >>> the default values of TR_min and TE_min the mincs will be uploaded? >>> >>> [image: image.png] >>> >>> >>> [image: image.png] >>> >>> Thanks >>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Is it possible that you haven't set up your mri_protocol table ? (and >>> mri_scan_type table too, for additional types of scans) >>> >>> Like the psc table, this is a pre-requisite for the Imaging insertion >>> setup : See the install/setup documentation : >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>> >>> To add new rows, just use MySQL insert statements. You can adapt the >>> insert statements which load the default table values --> e.g. Here on >>> GitHub : >>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>> (see also the mri_scan_type table) >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> I see that i can edit the values but not how to insert new rows. >>> >>> [image: image.png] >>> >>> If i choose Inserted with flag then will the minc be inserted? >>> >>> [image: image.png] >>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to hear that *dcmodify* worked correctly. >>> >>> For the MRI Violations module, the screenshot is enough. >>> >>> It says "could not identify scan type", which we knew already. Did you >>> click on the link on those words? >>> >>> It will take you to the next page of the module, showing for each scan >>> what the scan parameters were, and will also show for comparison what's >>> stored in your *mri_protocol* table. >>> Compare these values to find which parameter was not correct according >>> to your *mri_protocol* table scan type definitions. >>> >>> You may end up broadening your mri_protocol value ranges (e.g. TR, TE) >>> for scans. >>> This can be done in the front-end, by editing the database table >>> directly in the same subpage of the MRI Violations module. >>> >>> The MRI Violations module features are explained in more detail in the >>> Help text for this module inside LORIS (click the ["?"] icon in the menu >>> bar.) >>> >>> See also: Loris-MRI troubleshooting guide >>> >>> : no MINCs inserted- violated scans >>> >>> Best, >>> Christine >>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi, >>> >>> looks like my previous email's attachment wasn't delivered due to >>> security reasons, i uploaded my file at google drive >>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> From Dicat's view seems that dcmodify worked in both cases >>> >>> [image: image.png] >>> >>> [image: image.png] >>> >>> For the mri_violations i attached the .html output from webbrowser, so >>> that you can check the filelds easier. >>> >>> [image: image.png] >>> >>> Thanks >>> >>> >>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios -- >>> Great, sounds like more progress. >>> >>> About the dcmodify command -- I'm not sure why you're getting an Endian >>> warning. (it's a warning not an error, correct?) >>> To clarify -- Were the DICOM headers (PatientName) all successfully >>> relabelled, after the command ran? >>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) to >>> verify and/or update local DICOM headers -- though your dcmodify command is >>> a great and fast solution for bulk header updates. >>> >>> If you're concerned about fields being changed (e.g. "(2001,105f)" from >>> the warning message) - you can also dcmdump a DICOM slice before and look >>> at these fields specifically. >>> It's also not a bad "sanity check" to backup your DICOMS before/after >>> running dcmodify, and use dcmdump on each version to diff the outputs -- >>> this will pinpoint what changed. >>> >>> Re the protocol violation -- AcquisitionProtocol not recognized or >>> unknown : this means your scans did not match what is stored in your >>> mri_protocol table. >>> Check the MRI Violations front-end module -- can you see why they didn't >>> match? >>> Send us an example, in addition to the contents of the mri_protocol >>> table, if you can't find the source of the mismatch. >>> >>> Best, >>> Christine >>> >>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Here is the psc table >>> [image: image.png] >>> >>> I created 2 candidates profiles through the interface >>> >>> [image: image.png] >>> >>> then runned dcmodify command to a dicom file >>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>> >>> and got those warning: is this okay? >>> W: Found element (2001,105f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1083) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1402) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,140f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2001,105f) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> W: Found element (2005,1083) with VR UN and undefined length, reading a >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>> >>> dcmodify at another Dicom didn't show warnings. Below you can see the >>> execution for the second dicom. Mnics could not be inserted due to >>> AcquisitionProtocol being unknown. >>> >>> Running now the following command: /data/loris/bin/mri//uploadNeuroDB/ >>> imaging_upload_file.pl -profile prod -upload_id 12 >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >>> -delete >>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>> Target: /data/loris/data/tarchive >>> >>> Testing for database connectivity. >>> Database is available. >>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>> >>> You are creating a tar with the following command: >>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>> ImagingUpload-18-36-mTrxXs >>> >>> >>> getting md5sums and gzipping!! >>> >>> * Taken from dir : /tmp/ImagingUpload-18-36-mTrxXs >>> * Archive target location : >>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> * Name of creating host : 127.0.1.1 >>> * Name of host OS : Linux >>> * Created by user : lorisadmin >>> * Archived on : 2019-09-06 18:36:50 >>> * dicomSummary version : 1 >>> * dicomTar version : 1 >>> * md5sum for DICOM tarball : b1dcdc8903dd2d9a5443227db2aa2814 >>> ImagingUpload-18-36-mTrxXs.tar >>> * md5sum for DICOM tarball gzipped : aeae87f20155a6805f7e0cfe5212ea5f >>> ImagingUpload-18-36-mTrxXs.tar.gz >>> * md5sum for complete archive : 1d9258d1f077ebc49111ab7ba22a8d6e >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> >>> Adding archive info into database >>> >>> Removing temporary files from target location >>> >>> >>> Done adding archive info into database >>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation >>> -profile prod >>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>> -uploadID 12 -verbose >>> md5sum >>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> Set centerID = 1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> >>> Number of MINC files that will be considered for inserting into the >>> database: 2 >>> >>> log dir is /data/loris/data//logs and log file is >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> >>> log dir is /data/loris/data//logs and log file is >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> PSCID is: DCC0001 >>> CandID id: 602102 >>> visit_label is: V1 >>> candidate id 602102 >>> >>> Cleaning up temp files: rm -rf >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ cat >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>> >>> ==> Loading file from disk >>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>> >>> --> mapping DICOM parameter for >>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>> >>> ==> computing md5 hash for MINC body. >>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>> >>> ==> verifying acquisition protocol >>> >>> Acquisition protocol is unknown >>> >>> --> The minc file cannot be registered since the AcquisitionProtocol >>> is unknown >>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios: >>> >>> Sure -- you can delete imaging datasets with the *delete_imaging_upload* >>> script -- >>> details here: >>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>> >>> What's in your *psc* table? (Is it properly populated? This is a >>> pre-requisite to loading imaging data. >>> >>> ) >>> The foreign key constraint error on the candidate record is curious. >>> >>> There are also a few options for creating candidates when inserting >>> imaging data: >>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline >>> >>> a. via the LORIS API -- Create the candidates (and visits, optionally I >>> think) >>> How to: >>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>> Ensure you get the DCCID/CandID assigned by LORIS. >>> >>> Then as a second step: >>> b. Use the imaging insertion pipeline >>> >>> to load your DICOMs. >>> You will want to first ensure that the PatientName header in the DICOMs >>> as well as tar package are correctly labelled with PSCID_DCCID_VisitLabel >>> >>> -- Method 2: for BIDS-format datasets: >>> How to : >>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>> >>> Be sure to use the *-c* and *-s* options when running the bids_import script, >>> to automatically create your candidates and sessions. >>> >>> Best, >>> Christine >>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> How do i delete a Study? And everytime do i have to create a new >>> candidate to get DCCID and a PSCID? >>> >>> *First execution:* >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >>> log.txt >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>> batch_uploads_imageuploader.pl line 144. >>> DBD::mysql::db do failed: Cannot add or update a child row: a foreign >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>> ERROR: Failed to insert record in table mri_scanner: >>> The following database commands failed: >>> PREPARE s FROM 'INSERT INTO mri_scanner >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)'; >>> SET >>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>> Medical Systems'; >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>> Error obtained:Cannot add or update a child row: a foreign key >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452) >>> >>> ERROR: The validation has failed. Either re-run the validation again >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to force the >>> execution. >>> >>> >>> The tarchiveLoader.pl insertion script has failed. >>> Can't exec "mail": No such file or directory at ./ >>> batch_uploads_imageuploader.pl line 249. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 250. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 251. >>> >>> >>> *And second execution: * >>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./ >>> batch_uploads_imageuploader.pl -profile prod < ~/Desktop/input.txt > >>> log.txt >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>> batch_uploads_imageuploader.pl line 144. >>> >>> PROBLEM: >>> The user 'lorisadmin' has already inserted this study. >>> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>> This is the information retained from the first time the study was >>> inserted: >>> >>> * Taken from dir : /tmp/ImagingUpload-18-33-Qq7HGy >>> * Archive target location : >>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>> * Name of creating host : 127.0.1.1 >>> * Name of host OS : Linux >>> * Created by user : lorisadmin >>> * Archived on : 2019-09-04 18:33:05 >>> * dicomSummary version : 1 >>> * dicomTar version : 1 >>> * md5sum for DICOM tarball : 4a301b0318178b09b91e63544282364d >>> ImagingUpload-18-33-Qq7HGy.tar >>> * md5sum for DICOM tarball gzipped : 9d95ea2b9111be236808bfd65d7e65ec >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>> * md5sum for complete archive : ab19a86357f1d4053aa3b81c8a071053 >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>> >>> >>> Last update of record: >>> >>> >>> >>> The dicomTar.pl execution has failed. >>> Can't exec "mail": No such file or directory at ./ >>> batch_uploads_imageuploader.pl line 249. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 250. >>> print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl >>> line 251. >>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Ok, this sounds like good progress. Let us know when you next encounter >>> issues as you progress through the Imaging Install/Setup docs >>> . >>> I'll look into how we can better handle the incoming/ directory next >>> time. >>> Best, >>> Christine >>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>> populated correctly except its port is 'port' : ''. Also i have tested >>> that i can connect to MySQL with lorisuser. >>> >>> I executed the script again, because the only error i had previously was >>> that the /data/incoming folder didn't exist and there are no errors >>> reported back except of warnings <>> command line interface can be insecure>>. >>> >>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> It's possible -- if the script was unable to connect to the database >>> during its execution (e.g. typo in the password), that would explain the >>> underpopulated Image path and Loris-MRI code path you saw in the Config >>> module. >>> It's hard to tell without seeing the output from your script run -- Did >>> you see a sign of any such error? >>> The Config fields are populated by the imaging_install.sh script (starting >>> at line 222 >>> >>> ) >>> >>> For example, check if the database connection information was populated >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >>> >>> Best, >>> Christine >>> >>> >>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> Hi Christine, >>> >>> If you are referring to the imaging_install.sh here is an image with the >>> configurations i typed. Maybe the problem is somewhere at the last part >>> which asks to configure as much as possible automatically? >>> >>> Thanks >>> >>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>> Hi Sotirios, >>> >>> Glad to hear your LORIS core install is up and working and all the >>> front-end pages are loading. >>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>> > and the web interface worked. >>> >>> Yes, it's important that project/ have 775 permissions and that >>> lorisadmin be part of the sudoers group, per step 1 in the install >>> Readme . >>> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS to >>> loris, right? >>> >>> These imaging paths will be updated during your imaging installation >>> by an automated script -- >>> you do not need to set them manually via the Config module. >>> Please continue to follow the Setup Guide >>> for detailed steps to follow. >>> >>> Best, >>> Christine >>> >>> >>> >>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS to loris, >>> right? >>> >>> [image: image.png] >>> >>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>> Hi, >>> >>> i used >>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>> sudo apt-get install -y nodejs >>> >>> >>> you had suggested in the past, make worked and now i can see all the >>> contents in the web-interface, but i don't need make install? >>> >>> Thanks >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> -------------- next part -------------- An HTML attachment was scrubbed... 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URL: From sotirisnik at gmail.com Wed Nov 13 18:31:43 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 14 Nov 2019 01:31:43 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <3c83f4cc2d7f45938777a4084038e986@YTBPR01MB2895.CANPRD01.PROD.OUTLOOK.COM> Message-ID: It's a completely new one vm. The installations steps can be found here https://github.com/aueb-wim/LORIS-for-MIP and i didn't have installation issues. Regarding the identical part I checked in the admin panel that the configurations matched. ???? ???, 14 ??? 2019 ???? 1:13 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios - > Thanks. Before we dive into this over the next few days, can you also let > us know : > Was the second machine and/or data partition cloned ? Or else, What's the > difference between your two installations? > If it's easy, give us the OS, mariadb version, etc. > Please also confirm -- did you encounter any installation issues with > dependency libraries? > What steps have you taken to verify that the configurations of your > pipelines, protocol setup, etc are identical in both instances? > Best, > Christine > > On Wed, Nov 13, 2019 at 5:55 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Christine, >> >> In my first vm i am able to create the minc files and view them at the >> mri browser (except of candidate 102761034 ), meanwhile the same files >> gives warnings at the 2nd vm. The output of the batch upload can be seen >> in the file attached. >> Also a colleague of us has built a pre-validation tool for dicom >> https://github.com/aueb-wim/DataQualityControlTool/ which had found all >> the files that Loris gave as warning . Basically I confirmed that the total >> amount of files per dicom was the same amount as stated in Loris and >> checked some filenames given from warning to confirm that they match with >> our tool. But that was months ago and my colleague had changed some >> parameters for MIP and now our tool doesn't find all the invalid files, >> that's why i asked for the dicom header specification of Loris. In a >> discussion we had he mentioned that he doesn't check for some tags e.x. >> orientation. Lastly to mention that in my first vm i didn't use our tool to >> remove invalid dcm files. >> >> Thanks >> >> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios, >>> Can you provide us with some fresh particulars of the current issue and >>> we'll take it from there? >>> Yang's team has built these scripts which can definitely serve as a >>> model for your pre-validation of your DICOM collections. >>> cheers, >>> Christine >>> >>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> HI Yang, >>>> >>>> We make use of pydicom library too. Now about the validate.py i see >>>> that you check if some attributes are missing such as PatientID, >>>> PatientName which all of our files contains that info. Maybe i have missed >>>> something on the setup of my other virtual machine ( although one dicom >>>> passed on the new vm successfully, the others that were inserted correctly >>>> on my old vm fails on the new one ), i think that i had asked about this >>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but i >>>> don't remember the solution. >>>> >>>> Thanks >>>> >>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>> ??????: >>>> >>>>> Hey, Sotirios, >>>>> >>>>> Christine from the LORIS team mentioned you had some issue with >>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>> fully automated pipeline actually. >>>>> >>>>> While we were building CNBP, we had coded up some minor Python >>>>> functions to check DICOM integrity (and simple validations) and you might >>>>> be able to gain some inspiration from it and help you with your cause. For >>>>> more comprehensive solution, PyDICOM ( >>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>> like a descent python package to help out with a lot of DICOM data checks >>>>> (I was essentially just building customized wrapper calls to them). You can >>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>> rough around the edges but hopefully point you in the right direcitons >>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>> >>>>> Cheers, >>>>> >>>>> Yang Ding, PhD. >>>>> Canadian Neonatal Brain Platform Architect >>>>> >>>>> On Tue, Nov 12, 2019 at 8:29 AM >>>>> wrote: >>>>> >>>>>> Send Loris-dev mailing list submissions to >>>>>> loris-dev at bic.mni.mcgill.ca >>>>>> >>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> or, via email, send a message with subject or body 'help' to >>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>> >>>>>> You can reach the person managing the list at >>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>> >>>>>> When replying, please edit your Subject line so it is more specific >>>>>> than "Re: Contents of Loris-dev digest..." >>>>>> >>>>>> >>>>>> Today's Topics: >>>>>> >>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>> >>>>>> >>>>>> ---------------------------------------------------------------------- >>>>>> >>>>>> Message: 1 >>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>> From: Sotirios Nikoloutsopoulos >>>>>> To: Cecile Madjar >>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>> Message-ID: >>>>>> >>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> Hi, >>>>>> >>>>>> Could we send you a link with 10 anonymized dicom files to diagnose >>>>>> the >>>>>> warnings we get? >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>> > Hi Cecile, >>>>>> > >>>>>> > We were wondering whether Loris has a tool to check if there are >>>>>> problems >>>>>> > with the dcm files, before trying to upload them. Something that >>>>>> could >>>>>> > provide the same results provided in the warning_output, this is the >>>>>> > summary from the mri_upload at the front-page. Also which >>>>>> attributes of the >>>>>> > dcm header would trigger a warning? is there a dcm file header >>>>>> > specification for Loris? >>>>>> > >>>>>> > Thanks >>>>>> > >>>>>> > Sotirios >>>>>> > >>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>>> < >>>>>> > sotirisnik at gmail.com> ??????: >>>>>> > >>>>>> >> Hi, >>>>>> >> >>>>>> >> Yes, by parsing now() into unix_timestamp function it worked,but i >>>>>> >> thought that something else was causing the 2nd issue. >>>>>> >> Thanks >>>>>> >> >>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>> >> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> The first error occurs because the QCFirstChangeTime and columns >>>>>> are of >>>>>> >>> type `unsigned integer` and not `datatime`. You should be using >>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>> >>> >>>>>> >>> The second error occurs because the trigger triggers a rollback >>>>>> of the >>>>>> >>> insert statement in the files table. >>>>>> >>> See mysql documentation for trigger error handling. >>>>>> >>> >>>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>>> failure of >>>>>> >>> the entire statement that caused trigger invocation. >>>>>> >>> >>>>>> >>> >>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>> >>> -- Xavier >>>>>> >>> >>>>>> >>> ------------------------------ >>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>> >>> Nikoloutsopoulos >>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>> >>> *To:* Cecile Madjar >>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca ; >>>>>> >>> Christine Rogers, Ms. >>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>> >>> >>>>>> >>> When mincs are inserted their corresponding rows at the file >>>>>> table are >>>>>> >>> inserted too >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>>> because i >>>>>> >>> don't want manually to label them as passed throught the interface >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> That is the trigger i wrote >>>>>> >>> >>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>> >>> BEGIN >>>>>> >>> INSERT INTO files_qcstatus >>>>>> >>> SET FileID = NEW.FileID, >>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>> >>> EchoTime = NEW.EchoTime, >>>>>> >>> QCStatus = "Pass", >>>>>> >>> QCFirstChangeTime = NOW(), >>>>>> >>> QCLastChangeTime = NOW(); >>>>>> >>> END >>>>>> >>> >>>>>> >>> although it contains some errors >>>>>> >>> >>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>> foreign >>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` >>>>>> (`FileID`)) >>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> In the mri_upload table, there is a TarchiveID column associated >>>>>> with >>>>>> >>> the MRI upload you inserted. When this value is NULL, it means no >>>>>> DICOMs >>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>> insertion of the >>>>>> >>> DICOMs in the tarchive tables, this value is updated with the >>>>>> correct >>>>>> >>> TarchiveID associated with the upload. >>>>>> >>> >>>>>> >>> Could this correspond to what you want to do? >>>>>> >>> >>>>>> >>> Regarding the files_qcstatus, this table is only linked to the >>>>>> files >>>>>> >>> table (hence, the MINC files). You could always create a new >>>>>> table for >>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>> >>> >>>>>> >>> C?cile >>>>>> >>> >>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>> >>> coressponding qc_status to "pass". I was thinking of creating a >>>>>> trigger for >>>>>> >>> that, but which tables do i need to add entries to? So far from >>>>>> what i see >>>>>> >>> i need to add entres at the table "files" whenever an insertion >>>>>> happens to >>>>>> >>> files_qcstatus. >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning of my >>>>>> email >>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>> >>> >>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i >>>>>> am >>>>>> >>> looking for is not stored in the database? >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> Thanks. >>>>>> >>> >>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>> >>> tarchive table. It can also be found in the metadata field but it >>>>>> is mixed >>>>>> >>> with many other information. >>>>>> >>> >>>>>> >>> Hope this helps, >>>>>> >>> >>>>>> >>> C?cile >>>>>> >>> >>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>>>>> >>> specifically at the AcquisitonMetadata column i found something >>>>>> called >>>>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>>>> Instance UID. >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Your observation is correct. A little explanation below. >>>>>> >>> >>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>> >>> >>>>>> >>> - the scan type could not be identified (not matching an entry >>>>>> in >>>>>> >>> the mri_protocol table) >>>>>> >>> - one parameter of the scan type is out of the expected range >>>>>> >>> present in the mri_protocol_checks (extra filtering in case >>>>>> you need to be >>>>>> >>> stricker on some parameters not present in the mri_protocol >>>>>> table) >>>>>> >>> - if the CandID and PSCID do not match >>>>>> >>> >>>>>> >>> The following cases do not get in the MRI violation tables as it >>>>>> happens >>>>>> >>> before the conversion of the DICOM to MINC files and only MINC >>>>>> files >>>>>> >>> violations are logged there: >>>>>> >>> >>>>>> >>> - "No single DICOM" (since no valid DICOM could be found to >>>>>> convert >>>>>> >>> to MINC) >>>>>> >>> - "Study already inserted" (duplicate StudyUID) since this >>>>>> error >>>>>> >>> happens at the dicomTar.pl level (way before conversion into >>>>>> MINC files) >>>>>> >>> >>>>>> >>> Glad everything is working out!! >>>>>> >>> Best, >>>>>> >>> >>>>>> >>> C?cile >>>>>> >>> >>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now >>>>>> about the >>>>>> >>> mri_violations, dicoms are triggered to be inserted there only if >>>>>> there is >>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>> parameter? >>>>>> >>> Because i don't see the cases of 'No single dicom" or with the 2 >>>>>> studyiuid >>>>>> >>> to be there. >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Sorry to hear you are having issues with the memory. I think most >>>>>> of our >>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>> >>> >>>>>> >>> Hope this helps! >>>>>> >>> >>>>>> >>> C?cile >>>>>> >>> >>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> about that dicom that had that insertion error it's about 30mb >>>>>> and when >>>>>> >>> it is being processed the ram is being drastically increased from >>>>>> 2gb to >>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is the >>>>>> recommended >>>>>> >>> size of ram for using Loris? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>> >>> >>>>>> >>> For the delete script issue, if you are absolutely certain that no >>>>>> >>> processes are run for that uploadID, you can update the >>>>>> mri_upload table >>>>>> >>> and set the column Inserting to 0 instead of 1 for that uploadID. >>>>>> It >>>>>> >>> looks like for some reason the scripts did not update this field >>>>>> when it >>>>>> >>> stopped the insertion. Not sure why that would be the case though. >>>>>> >>> Note: only do that update if you are certain that there is no >>>>>> processing >>>>>> >>> happening. >>>>>> >>> >>>>>> >>> Hope this helps! >>>>>> >>> >>>>>> >>> >>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>>> actually do >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> I thought that this might be a permission because "w" was missing >>>>>> at the >>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but with >>>>>> no mnic >>>>>> >>> files. Also now i have this error >>>>>> >>> >>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>> :/data/loris/bin/mri/tools$ >>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently processing >>>>>> it. >>>>>> >>> >>>>>> >>> How can solve this? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> Here is our auto dicom uploading python script: >>>>>> >>> >>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>> >>> >>>>>> >>> To give you a brief idea: >>>>>> >>> Per folder it will: >>>>>> >>> 1) Delete all the .bak files >>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>> TE_min, >>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>> mri_protocol table >>>>>> >>> >>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>> >>> For some reason some files are missing >>>>>> SeriesDescription/ProtocolName >>>>>> >>> >>>>>> >>> In total i have 7 folders >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> 3/7 passed >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> Also about the first patient with DC0000 had a violation "T1 >>>>>> AXIAL SE >>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i find >>>>>> that weird >>>>>> >>> since Loris detects the SeriesDescription. >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> Now about the 4/7 that didn't passed >>>>>> >>> >>>>>> >>> 102327840 and 102809579 outputs "The target directory does not >>>>>> contain a >>>>>> >>> single DICOM file.", therefore they are missing their StudyUID >>>>>> >>> >>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from multiple >>>>>> >>> studies." >>>>>> >>> >>>>>> >>> and 102761034 "No data could be converted into valid MINC files. >>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>> >>> >>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 and >>>>>> 102506134 >>>>>> >>> can i just pass a flag parameter to >>>>>> batch_uploads_imageuploader.pl? or >>>>>> >>> modify imaging_upload_file.pl? >>>>>> >>> >>>>>> >>> Thank you, >>>>>> >>> >>>>>> >>> Sotirios >>>>>> >>> >>>>>> >>> PS >>>>>> >>> >>>>>> >>> To diagnose a folder search the name of the folder at >>>>>> dicom_output.txt. >>>>>> >>> >>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> Glad to hear about your progress. >>>>>> >>> >>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>> documented here >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>> > >>>>>> >>> -- let us know if you didn't find the answers you were looking >>>>>> for there. >>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>> database >>>>>> >>> management software is a visual placeholder for you as the user? >>>>>> I'm not >>>>>> >>> sure why a scanner would ever be registered with ID='0' as your >>>>>> screenshot >>>>>> >>> showed.) >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> I fixed it with this >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> I tried to create a new candidate using the API, is there >>>>>> something >>>>>> >>> wrong with the structure? why did i receive a 500 internal error? >>>>>> In the >>>>>> >>> loris-error log it state that there is something wrong with >>>>>> token, but i >>>>>> >>> verfied that the type of the token is a string. >>>>>> >>> >>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 >>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type >>>>>> string, >>>>>> >>> null given, called in >>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>>> 169 and >>>>>> >>> defined in >>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>> >>> trace:\n#0 >>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n >>>>>> thrown in >>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>>> 192 >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> Is there a way also to delete candidates? Just to let you know >>>>>> what i >>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>> dependencies. >>>>>> >>> >>>>>> >>> First i deleted all their uploads >>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to >>>>>> omit >>>>>> >>> the backup file ? ) >>>>>> >>> >>>>>> >>> Afterwards i had some scanner candidates, so i deleted all the >>>>>> entries >>>>>> >>> from mri_scanner except that i couldn't delete this entry with >>>>>> the 0 ID. >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> We recommend that you use our existing tools for creating new >>>>>> candidates >>>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>>> calling the Candidate >>>>>> >>> class's createNew() >>>>>> >>> < >>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>> >function. >>>>>> >>> These will create the necessary records for you. (It's not >>>>>> recommended to >>>>>> >>> make direct modifications to mysql database tables in your >>>>>> script, if I >>>>>> >>> understand you.) >>>>>> >>> >>>>>> >>> The CandID should be a randomized 6 digit randomized ID, and >>>>>> there are >>>>>> >>> multiple reasons for this. >>>>>> >>> You can use the PSCID for project-specific IDs and the External >>>>>> ID field >>>>>> >>> in the candidate table can also be used for any values you like. >>>>>> >>> Additionally, any number of custom IDs can be added in parallel - >>>>>> these >>>>>> >>> are entered/visible in the Candidate Information module and added >>>>>> in the >>>>>> >>> back-end as candidate parameters. >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> We are building a script that will auto insert the candidates >>>>>> based on >>>>>> >>> their ExternalID. We would like to know whethere when we are >>>>>> creating a new >>>>>> >>> profile in the candidate table, if we also have to insert a new >>>>>> record at >>>>>> >>> another table? Furthermore is there a problem that in our case >>>>>> CandID won't >>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> That would normally be the case but the numeric part of the PSCID >>>>>> get >>>>>> >>> paded with 0 on the left. >>>>>> >>> >>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical >>>>>> char >>>>>> >>> with a min value of 1, the sequence would be: >>>>>> >>> >>>>>> >>> ABC0001 >>>>>> >>> ABC0002 >>>>>> >>> ... >>>>>> >>> ABC0010 >>>>>> >>> ... >>>>>> >>> >>>>>> >>> thus sorting them ascending will always get the latest value >>>>>> generated >>>>>> >>> as the max value. >>>>>> >>> >>>>>> >>> M?lanie >>>>>> >>> >>>>>> >>> ------------------------------ >>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>> >>> *To:* Melanie Legault, Mrs >>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>> >>> >>>>>> >>> I see, although the PSCID value is varchar(255), it must be stored >>>>>> >>> within a specific length of characters. Otherwise if we were to >>>>>> sort >>>>>> >>> strings with different lengths the result would not be sorted >>>>>> correctly ( >>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hello Sotirios, >>>>>> >>> >>>>>> >>> There is no `last value` stored anywhere. >>>>>> >>> The code simply look for the PSCID with the max value and >>>>>> increase that >>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>> >>> >>>>>> >>> Hope this info help. >>>>>> >>> >>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | >>>>>> McGill >>>>>> >>> University >>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>> >>> >>>>>> >>> ------------------------------ >>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>> >>> Nikoloutsopoulos >>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>> >>> *To:* Christine Rogers, Ms. >>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> how does Loris determine the next available PSCID value for a new >>>>>> >>> candidate? >>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>> >>> e.x in the default case the PSCID is sequential, but where do we >>>>>> store the >>>>>> >>> last value for the sequential sequence? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> the parameters in the mri_protocol you have assigned are global >>>>>> >>> standard? or were assigned after trial and error? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Given you have done the initial setup of your tables to match your >>>>>> >>> intended protocol/parameters according to instructions -- >>>>>> >>> the Troubleshooting guide documentation recommends >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>> > >>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> *if i were to change their status to resolve what would happen? >>>>>> >>> >>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> I noticed that i can view the mnics at the brainbrowser from the >>>>>> >>> mri_violations page ( those mnics are stored at >>>>>> /data/loris/data/trashbin/ >>>>>> >>> if i were to click their issue to resolve what would happend? >>>>>> would they >>>>>> >>> appear in the dicom_archive view too? ). >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> The defaut values of the schema exists in my local database. If i >>>>>> adjust >>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>> uploaded? >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Is it possible that you haven't set up your mri_protocol table ? >>>>>> (and >>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>> >>> >>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>>> insertion >>>>>> >>> setup : See the install/setup documentation : >>>>>> >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>> >>> >>>>>> >>> To add new rows, just use MySQL insert statements. You can adapt >>>>>> the >>>>>> >>> insert statements which load the default table values --> e.g. >>>>>> Here on >>>>>> >>> GitHub : >>>>>> >>> >>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>> >>> (see also the mri_scan_type table) >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> I see that i can edit the values but not how to insert new rows. >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> If i choose Inserted with flag then will the minc be inserted? >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>> >>> >>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>> >>> >>>>>> >>> It says "could not identify scan type", which we knew already. >>>>>> Did you >>>>>> >>> click on the link on those words? >>>>>> >>> >>>>>> >>> It will take you to the next page of the module, showing for each >>>>>> scan >>>>>> >>> what the scan parameters were, and will also show for comparison >>>>>> what's >>>>>> >>> stored in your *mri_protocol* table. >>>>>> >>> Compare these values to find which parameter was not correct >>>>>> according >>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>> >>> >>>>>> >>> You may end up broadening your mri_protocol value ranges (e.g. >>>>>> TR, TE) >>>>>> >>> for scans. >>>>>> >>> This can be done in the front-end, by editing the database table >>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>> >>> >>>>>> >>> The MRI Violations module features are explained in more detail >>>>>> in the >>>>>> >>> Help text for this module inside LORIS (click the ["?"] icon in >>>>>> the menu >>>>>> >>> bar.) >>>>>> >>> >>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>> > >>>>>> >>> : no MINCs inserted- violated scans >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> looks like my previous email's attachment wasn't delivered due to >>>>>> >>> security reasons, i uploaded my file at google drive >>>>>> >>> >>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>> >>> >>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> For the mri_violations i attached the .html output from >>>>>> webbrowser, so >>>>>> >>> that you can check the filelds easier. >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios -- >>>>>> >>> Great, sounds like more progress. >>>>>> >>> >>>>>> >>> About the dcmodify command -- I'm not sure why you're getting an >>>>>> Endian >>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>> successfully >>>>>> >>> relabelled, after the command ran? >>>>>> >>> >>>>>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) >>>>>> to >>>>>> >>> verify and/or update local DICOM headers -- though your dcmodify >>>>>> command is >>>>>> >>> a great and fast solution for bulk header updates. >>>>>> >>> >>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>> "(2001,105f)" from >>>>>> >>> the warning message) - you can also dcmdump a DICOM slice before >>>>>> and look >>>>>> >>> at these fields specifically. >>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>> before/after >>>>>> >>> running dcmodify, and use dcmdump on each version to diff the >>>>>> outputs -- >>>>>> >>> this will pinpoint what changed. >>>>>> >>> >>>>>> >>> Re the protocol violation -- AcquisitionProtocol not recognized or >>>>>> >>> unknown : this means your scans did not match what is stored in >>>>>> your >>>>>> >>> mri_protocol table. >>>>>> >>> Check the MRI Violations front-end module -- can you see why they >>>>>> didn't >>>>>> >>> match? >>>>>> >>> Send us an example, in addition to the contents of the >>>>>> mri_protocol >>>>>> >>> table, if you can't find the source of the mismatch. >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> >>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Here is the psc table >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> I created 2 candidates profiles through the interface >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> then runned dcmodify command to a dicom file >>>>>> >>> >>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>> >>> >>>>>> >>> and got those warning: is this okay? >>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2005,1402) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2005,140f) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> >>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you can see >>>>>> the >>>>>> >>> execution for the second dicom. Mnics could not be inserted due to >>>>>> >>> AcquisitionProtocol being unknown. >>>>>> >>> >>>>>> >>> Running now the following command: >>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>> >>> >>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >>>>>> >>> -delete >>>>>> >>> >>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>> >>> Target: /data/loris/data/tarchive >>>>>> >>> >>>>>> >>> Testing for database connectivity. >>>>>> >>> Database is available. >>>>>> >>> >>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>> >>> >>>>>> >>> You are creating a tar with the following command: >>>>>> >>> >>>>>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>> >>> >>>>>> >>> >>>>>> >>> getting md5sums and gzipping!! >>>>>> >>> >>>>>> >>> * Taken from dir : >>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>> >>> * Archive target location : >>>>>> >>> >>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>> >>> * Name of host OS : Linux >>>>>> >>> * Created by user : lorisadmin >>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>> >>> * dicomSummary version : 1 >>>>>> >>> * dicomTar version : 1 >>>>>> >>> * md5sum for DICOM tarball : >>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>> >>> * md5sum for complete archive : >>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> >>>>>> >>> Adding archive info into database >>>>>> >>> >>>>>> >>> Removing temporary files from target location >>>>>> >>> >>>>>> >>> >>>>>> >>> Done adding archive info into database >>>>>> >>> >>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>> -globLocation >>>>>> >>> -profile prod >>>>>> >>> >>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>> >>> -uploadID 12 -verbose >>>>>> >>> md5sum >>>>>> >>> >>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> candidate id 602102 >>>>>> >>> Set centerID = 1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> >>>>>> >>> Number of MINC files that will be considered for inserting into >>>>>> the >>>>>> >>> database: 2 >>>>>> >>> >>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> candidate id 602102 >>>>>> >>> >>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> candidate id 602102 >>>>>> >>> >>>>>> >>> Cleaning up temp files: rm -rf >>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>> >>> >>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>> cat >>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>> >>> >>>>>> >>> ==> Loading file from disk >>>>>> >>> >>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>> >>> >>>>>> >>> --> mapping DICOM parameter for >>>>>> >>> >>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>> >>> >>>>>> >>> ==> computing md5 hash for MINC body. >>>>>> >>> >>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>> >>> >>>>>> >>> ==> verifying acquisition protocol >>>>>> >>> >>>>>> >>> Acquisition protocol is unknown >>>>>> >>> >>>>>> >>> --> The minc file cannot be registered since the >>>>>> AcquisitionProtocol >>>>>> >>> is unknown >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios: >>>>>> >>> >>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>> *delete_imaging_upload* >>>>>> >>> script -- >>>>>> >>> details here: >>>>>> >>> >>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>> >>> >>>>>> >>> What's in your *psc* table? (Is it properly populated? This is a >>>>>> >>> pre-requisite to loading imaging data. >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>> > >>>>>> >>> ) >>>>>> >>> The foreign key constraint error on the candidate record is >>>>>> curious. >>>>>> >>> >>>>>> >>> There are also a few options for creating candidates when >>>>>> inserting >>>>>> >>> imaging data: >>>>>> >>> >>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>> pipeline >>>>>> >>> >>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>> optionally I >>>>>> >>> think) >>>>>> >>> How to: >>>>>> >>> >>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>> >>> >>>>>> >>> Then as a second step: >>>>>> >>> b. Use the imaging insertion pipeline >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>> > >>>>>> >>> to load your DICOMs. >>>>>> >>> You will want to first ensure that the PatientName header in the >>>>>> DICOMs >>>>>> >>> as well as tar package are correctly labelled with >>>>>> PSCID_DCCID_VisitLabel >>>>>> >>> >>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>> >>> How to : >>>>>> >>> >>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>> >>> >>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>> bids_import script, >>>>>> >>> to automatically create your candidates and sessions. >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> How do i delete a Study? And everytime do i have to create a new >>>>>> >>> candidate to get DCCID and a PSCID? >>>>>> >>> >>>>>> >>> *First execution:* >>>>>> >>> >>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>> ./ >>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>> ~/Desktop/input.txt > >>>>>> >>> log.txt >>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>> foreign >>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>> `FK_candidate_1` >>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>> (`CenterID`)) at >>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>> >>> The following database commands failed: >>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>> (?,?,?,?,?)'; >>>>>> >>> SET >>>>>> >>> >>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>> >>> Medical Systems'; >>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>> >>> Error obtained:Cannot add or update a child row: a foreign key >>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>> `FK_mri_scanner_1` >>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error >>>>>> code 1452) >>>>>> >>> >>>>>> >>> ERROR: The validation has failed. Either re-run the validation >>>>>> again >>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to >>>>>> force the >>>>>> >>> execution. >>>>>> >>> >>>>>> >>> >>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>> batch_uploads_imageuploader.pl >>>>>> >>> line 250. >>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>> batch_uploads_imageuploader.pl >>>>>> >>> line 251. >>>>>> >>> >>>>>> >>> >>>>>> >>> *And second execution: * >>>>>> >>> >>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>> ./ >>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>> ~/Desktop/input.txt > >>>>>> >>> log.txt >>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>> >>> >>>>>> >>> PROBLEM: >>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>> >>> The unique study ID is >>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>> >>> This is the information retained from the first time the study was >>>>>> >>> inserted: >>>>>> >>> >>>>>> >>> * Taken from dir : >>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>> >>> * Archive target location : >>>>>> >>> >>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>> >>> * Name of host OS : Linux >>>>>> >>> * Created by user : lorisadmin >>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>> >>> * dicomSummary version : 1 >>>>>> >>> * dicomTar version : 1 >>>>>> >>> * md5sum for DICOM tarball : >>>>>> 4a301b0318178b09b91e63544282364d >>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>> >>> * md5sum for complete archive : >>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>> >>> >>>>>> >>> >>>>>> >>> Last update of record: >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> The dicomTar.pl execution has failed. >>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>> batch_uploads_imageuploader.pl >>>>>> >>> line 250. >>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>> batch_uploads_imageuploader.pl >>>>>> >>> line 251. >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Ok, this sounds like good progress. Let us know when you next >>>>>> encounter >>>>>> >>> issues as you progress through the Imaging Install/Setup docs >>>>>> >>> >>>>> >. >>>>>> >>> I'll look into how we can better handle the incoming/ directory >>>>>> next >>>>>> >>> time. >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>> >>> populated correctly except its port is 'port' : ''. Also i >>>>>> have tested >>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>> >>> >>>>>> >>> I executed the script again, because the only error i had >>>>>> previously was >>>>>> >>> that the /data/incoming folder didn't exist and there are no >>>>>> errors >>>>>> >>> reported back except of warnings <>>>>> password on the >>>>>> >>> command line interface can be insecure>>. >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> It's possible -- if the script was unable to connect to the >>>>>> database >>>>>> >>> during its execution (e.g. typo in the password), that would >>>>>> explain the >>>>>> >>> underpopulated Image path and Loris-MRI code path you saw in the >>>>>> Config >>>>>> >>> module. >>>>>> >>> It's hard to tell without seeing the output from your script run >>>>>> -- Did >>>>>> >>> you see a sign of any such error? >>>>>> >>> The Config fields are populated by the imaging_install.sh script >>>>>> (starting >>>>>> >>> at line 222 >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>> > >>>>>> >>> ) >>>>>> >>> >>>>>> >>> For example, check if the database connection information was >>>>>> populated >>>>>> >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi Christine, >>>>>> >>> >>>>>> >>> If you are referring to the imaging_install.sh here is an image >>>>>> with the >>>>>> >>> configurations i typed. Maybe the problem is somewhere at the >>>>>> last part >>>>>> >>> which asks to configure as much as possible automatically? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Glad to hear your LORIS core install is up and working and all the >>>>>> >>> front-end pages are loading. >>>>>> >>> >>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>>>>> >>> > and the web interface worked. >>>>>> >>> >>>>>> >>> Yes, it's important that project/ have 775 permissions and that >>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the install >>>>>> >>> Readme . >>>>>> >>> >>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS >>>>>> to >>>>>> >>> loris, right? >>>>>> >>> >>>>>> >>> These imaging paths will be updated during your imaging >>>>>> installation >>>>>> >>> by an automated >>>>>> script -- >>>>>> >>> you do not need to set them manually via the Config module. >>>>>> >>> Please continue to follow the Setup Guide >>>>>> >>> for detailed steps to >>>>>> follow. >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS to >>>>>> loris, >>>>>> >>> right? >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> i used >>>>>> >>> >>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>> >>> sudo apt-get install -y nodejs >>>>>> >>> >>>>>> >>> >>>>>> >>> you had suggested in the past, make worked and now i can see all >>>>>> the >>>>>> >>> contents in the web-interface, but i don't need make install? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> -------------- next part -------------- >>>>>> An HTML attachment was scrubbed... >>>>>> URL: < >>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>> > >>>>>> >>>>>> ------------------------------ >>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>>> >>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>> ***************************************** >>>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> >>> christine.rogers at mcgill.ca >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>> Montreal Neurological Institute >>> McGill University | Montreal | Canada >>> >> > > -- > > christine.rogers at mcgill.ca > McGill Centre for Integrative Neuroscience | MCIN.ca > Montreal Neurological Institute > McGill University | Montreal | Canada > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Thu Nov 14 13:30:25 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Thu, 14 Nov 2019 18:30:25 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Message-ID: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I've granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: DigitalOcean Clean Install.PNG Type: image/png Size: 193534 bytes Desc: DigitalOcean Clean Install.PNG URL: From dave.macfarlane at mcin.ca Thu Nov 14 13:33:33 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Thu, 14 Nov 2019 13:33:33 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr wrote: > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Thu Nov 14 13:39:12 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Thu, 14 Nov 2019 18:39:12 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: error.log Type: application/octet-stream Size: 1955 bytes Desc: error.log URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: loris-access.log Type: application/octet-stream Size: 1092 bytes Desc: loris-access.log URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: loris-error.log Type: application/octet-stream Size: 3560 bytes Desc: loris-error.log URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: install-2019-11-14T17_48_08.log Type: application/octet-stream Size: 1450 bytes Desc: install-2019-11-14T17_48_08.log URL: From dave.macfarlane at mcin.ca Thu Nov 14 13:56:18 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Thu, 14 Nov 2019 13:56:18 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr wrote: > Hi Dave, > > > > Certainly, my apologies for not attaching them initially. > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:34 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Do you have access to the web server's error log on Digital Ocean? It's > difficult to guess why it's generating a 500 error without seeing the error > log. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Thu Nov 14 13:59:43 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Thu, 14 Nov 2019 18:59:43 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Sorry if I was unclear. I?m not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Thu Nov 14 14:16:58 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Thu, 14 Nov 2019 14:16:58 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr wrote: > Sorry if I was unclear. I?m not upgrading. I have more than one instance > of Loris running. The v17 version will be made dormant once the latest v21 > clean install works. I would like to port a few modules from the working > v17 to the latest. Otherwise, I have 10+ point-release iterations to > updates to make. > > > > -Matthew > > > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:56 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > When upgrading, it's required to be on the latest minor release and to go > one release at a time. If you go to https://github.com/aces/Loris/releases > there should be an "Upgrade process" section for each release that you > should follow in order from 17. The error (that it can't find the autoload > file generated by composer) seems to suggest you missed step 2 of the > upgrade process to LORIS v21. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi Dave, > > > > Certainly, my apologies for not attaching them initially. > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:34 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Do you have access to the web server's error log on Digital Ocean? It's > difficult to guess why it's generating a 500 error without seeing the error > log. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Thu Nov 14 14:26:44 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Thu, 14 Nov 2019 19:26:44 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Great, thanks. Everytime I run this command I receive the following; - make: *** No targets specified and no makefile found Dependency related no doubt? Best, Matthew From: Dave MacFarlane Sent: Thursday, November 14, 2019 2:17 PM To: Matthew Sparks, Mr Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr > wrote: Sorry if I was unclear. I?m not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Thu Nov 14 14:30:57 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Thu, 14 Nov 2019 19:30:57 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Well obviously there was no file; lol sorry. How to proceed with this? root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make git describe --tags --always > VERSION fatal: not a git repository (or any of the parent directories): .git Makefile:8: recipe for target 'VERSION' failed make: *** [VERSION] Error 128 Matthew From: Matthew Sparks, Mr Sent: Thursday, November 14, 2019 2:27 PM To: Dave MacFarlane Cc: loris-dev at bic.mni.mcgill.ca Subject: RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Great, thanks. Everytime I run this command I receive the following; - make: *** No targets specified and no makefile found Dependency related no doubt? Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:17 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr > wrote: Sorry if I was unclear. I?m not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Thu Nov 14 14:35:34 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Thu, 14 Nov 2019 19:35:34 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make /var/www/loris make: Nothing to be done for '/var/www/loris'. Any other resolution? Matthew From: Matthew Sparks, Mr Sent: Thursday, November 14, 2019 2:31 PM To: Dave MacFarlane Cc: loris-dev at bic.mni.mcgill.ca Subject: RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Well obviously there was no file; lol sorry. How to proceed with this? root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make git describe --tags --always > VERSION fatal: not a git repository (or any of the parent directories): .git Makefile:8: recipe for target 'VERSION' failed make: *** [VERSION] Error 128 Matthew From: Matthew Sparks, Mr Sent: Thursday, November 14, 2019 2:27 PM To: Dave MacFarlane > Cc: loris-dev at bic.mni.mcgill.ca Subject: RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Great, thanks. Everytime I run this command I receive the following; - make: *** No targets specified and no makefile found Dependency related no doubt? Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:17 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr > wrote: Sorry if I was unclear. I?m not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Thu Nov 14 14:43:14 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 14 Nov 2019 14:43:14 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi Mattew, It seems like you are in the wrong branch. Could u check this https://github.com/aces/Loris/tree/21.0-release? There is a file named "Makefle". If you can't find it, under your loris folder, definitely you are not using 21. You need to switch to 21 branch with git . Cheers Shen On Thu, 14 Nov 2019 at 14:31, Matthew Sparks, Mr wrote: > Well obviously there was no file; lol sorry. How to proceed with this? > > > > root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make > > git describe --tags --always > VERSION > > fatal: not a git repository (or any of the parent directories): .git > > Makefile:8: recipe for target 'VERSION' failed > > make: *** [VERSION] Error 128 > > > > Matthew > > > > *From:* Matthew Sparks, Mr > *Sent:* Thursday, November 14, 2019 2:27 PM > *To:* Dave MacFarlane > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Great, thanks. Everytime I run this command I receive the following; > > - make: *** No targets specified and no makefile found > > > > Dependency related no doubt? > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:17 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > In that case. you're missing the equivalent step of the install process > (run `make` for production or `make dev` for a sandbox which invokes > composer.) > > > > There was a bug in the initial 21.0.0 release where that step wasn't > properly documented, so it's easy to have missed but it should be listed as > step 4 in the README as of v21.0.3. > > > > On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Sorry if I was unclear. I?m not upgrading. I have more than one instance > of Loris running. The v17 version will be made dormant once the latest v21 > clean install works. I would like to port a few modules from the working > v17 to the latest. Otherwise, I have 10+ point-release iterations to > updates to make. > > > > -Matthew > > > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:56 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > When upgrading, it's required to be on the latest minor release and to go > one release at a time. If you go to https://github.com/aces/Loris/releases > there should be an "Upgrade process" section for each release that you > should follow in order from 17. The error (that it can't find the autoload > file generated by composer) seems to suggest you missed step 2 of the > upgrade process to LORIS v21. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi Dave, > > > > Certainly, my apologies for not attaching them initially. > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:34 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Do you have access to the web server's error log on Digital Ocean? It's > difficult to guess why it's generating a 500 error without seeing the error > log. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Thu Nov 14 14:45:17 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Thu, 14 Nov 2019 14:45:17 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: The Makefile uses git to generate the VERSION file based on what's checked out. Since it looks like you didn't get the code via git, you can trick it into skipping that step by manually creating a file named "VERSION" in the root of the LORIS directory so that it thinks it's already up to date. Regarding your follow up email: you should run `make` with no arguments in the root of your LORIS directory. If you get the "No targets specified" error when in the correct directory try "make all" (most versions of make that I'm aware of use the first target from the Makefile if no argument is specified, but "make all" is explicit.) (You should also make sure that you have: 1. composer and 2. npm installed with a recent enough version according to the README, or the make step will likely fail.) - Dave On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr wrote: > Well obviously there was no file; lol sorry. How to proceed with this? > > > > root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make > > git describe --tags --always > VERSION > > fatal: not a git repository (or any of the parent directories): .git > > Makefile:8: recipe for target 'VERSION' failed > > make: *** [VERSION] Error 128 > > > > Matthew > > > > *From:* Matthew Sparks, Mr > *Sent:* Thursday, November 14, 2019 2:27 PM > *To:* Dave MacFarlane > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Great, thanks. Everytime I run this command I receive the following; > > - make: *** No targets specified and no makefile found > > > > Dependency related no doubt? > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:17 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > In that case. you're missing the equivalent step of the install process > (run `make` for production or `make dev` for a sandbox which invokes > composer.) > > > > There was a bug in the initial 21.0.0 release where that step wasn't > properly documented, so it's easy to have missed but it should be listed as > step 4 in the README as of v21.0.3. > > > > On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Sorry if I was unclear. I?m not upgrading. I have more than one instance > of Loris running. The v17 version will be made dormant once the latest v21 > clean install works. I would like to port a few modules from the working > v17 to the latest. Otherwise, I have 10+ point-release iterations to > updates to make. > > > > -Matthew > > > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:56 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > When upgrading, it's required to be on the latest minor release and to go > one release at a time. If you go to https://github.com/aces/Loris/releases > there should be an "Upgrade process" section for each release that you > should follow in order from 17. The error (that it can't find the autoload > file generated by composer) seems to suggest you missed step 2 of the > upgrade process to LORIS v21. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi Dave, > > > > Certainly, my apologies for not attaching them initially. > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:34 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Do you have access to the web server's error log on Digital Ocean? It's > difficult to guess why it's generating a 500 error without seeing the error > log. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Thu Nov 14 15:33:18 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Thu, 14 Nov 2019 20:33:18 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi, I was missing the npm dependency for make. However, another issue with npm ? see log; Best, Matthew From: Dave MacFarlane Sent: Thursday, November 14, 2019 2:45 PM To: Matthew Sparks, Mr Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU The Makefile uses git to generate the VERSION file based on what's checked out. Since it looks like you didn't get the code via git, you can trick it into skipping that step by manually creating a file named "VERSION" in the root of the LORIS directory so that it thinks it's already up to date. Regarding your follow up email: you should run `make` with no arguments in the root of your LORIS directory. If you get the "No targets specified" error when in the correct directory try "make all" (most versions of make that I'm aware of use the first target from the Makefile if no argument is specified, but "make all" is explicit.) (You should also make sure that you have: 1. composer and 2. npm installed with a recent enough version according to the README, or the make step will likely fail.) - Dave On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr > wrote: Well obviously there was no file; lol sorry. How to proceed with this? root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make git describe --tags --always > VERSION fatal: not a git repository (or any of the parent directories): .git Makefile:8: recipe for target 'VERSION' failed make: *** [VERSION] Error 128 Matthew From: Matthew Sparks, Mr Sent: Thursday, November 14, 2019 2:27 PM To: Dave MacFarlane > Cc: loris-dev at bic.mni.mcgill.ca Subject: RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Great, thanks. Everytime I run this command I receive the following; - make: *** No targets specified and no makefile found Dependency related no doubt? Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:17 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr > wrote: Sorry if I was unclear. I?m not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: npm-debug.log Type: application/octet-stream Size: 2335 bytes Desc: npm-debug.log URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: NPM error.png Type: image/png Size: 102903 bytes Desc: NPM error.png URL: From lingyun.ma at mcin.ca Thu Nov 14 16:18:35 2019 From: lingyun.ma at mcin.ca (Ling Ma) Date: Thu, 14 Nov 2019 16:18:35 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi Matthew, It looks most likely that you need a most recent version of nodejs and npm, as the error message indicates. Check the installation Readme. On Thu, Nov 14, 2019 at 3:33 PM Matthew Sparks, Mr wrote: > Hi, I was missing the *npm* dependency for make. *However*, another issue > with npm ? see log; > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:45 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > The Makefile uses git to generate the VERSION file based on what's checked > out. Since it looks like you didn't get the code via git, you can trick it > into skipping that step by manually creating a file named "VERSION" in the > root of the LORIS directory so that it thinks it's already up to date. > > > > Regarding your follow up email: you should run `make` with no arguments in > the root of your LORIS directory. If you get the "No targets specified" > error when in the correct directory try "make all" (most versions of make > that I'm aware of use the first target from the Makefile if no argument is > specified, but "make all" is explicit.) > > > > (You should also make sure that you have: 1. composer and 2. npm installed > with a recent enough version according to the README, or the make step will > likely fail.) > > > > - Dave > > > > On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Well obviously there was no file; lol sorry. How to proceed with this? > > > > root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make > > git describe --tags --always > VERSION > > fatal: not a git repository (or any of the parent directories): .git > > Makefile:8: recipe for target 'VERSION' failed > > make: *** [VERSION] Error 128 > > > > Matthew > > > > *From:* Matthew Sparks, Mr > *Sent:* Thursday, November 14, 2019 2:27 PM > *To:* Dave MacFarlane > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Great, thanks. Everytime I run this command I receive the following; > > - make: *** No targets specified and no makefile found > > > > Dependency related no doubt? > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:17 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > In that case. you're missing the equivalent step of the install process > (run `make` for production or `make dev` for a sandbox which invokes > composer.) > > > > There was a bug in the initial 21.0.0 release where that step wasn't > properly documented, so it's easy to have missed but it should be listed as > step 4 in the README as of v21.0.3. > > > > On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Sorry if I was unclear. I?m not upgrading. I have more than one instance > of Loris running. The v17 version will be made dormant once the latest v21 > clean install works. I would like to port a few modules from the working > v17 to the latest. Otherwise, I have 10+ point-release iterations to > updates to make. > > > > -Matthew > > > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:56 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > When upgrading, it's required to be on the latest minor release and to go > one release at a time. If you go to https://github.com/aces/Loris/releases > there should be an "Upgrade process" section for each release that you > should follow in order from 17. The error (that it can't find the autoload > file generated by composer) seems to suggest you missed step 2 of the > upgrade process to LORIS v21. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi Dave, > > > > Certainly, my apologies for not attaching them initially. > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:34 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Do you have access to the web server's error log on Digital Ocean? It's > difficult to guess why it's generating a 500 error without seeing the error > log. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Thu Nov 14 16:20:13 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Thu, 14 Nov 2019 21:20:13 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: , Message-ID: Already updated to the latest versions, as neither were installed initially. Best, Matthew ________________________________ From: Ling Ma Sent: Thursday, November 14, 2019 4:18:35 PM To: Matthew Sparks, Mr Cc: Dave MacFarlane ; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, It looks most likely that you need a most recent version of nodejs and npm, as the error message indicates. Check the installation Readme. On Thu, Nov 14, 2019 at 3:33 PM Matthew Sparks, Mr > wrote: Hi, I was missing the npm dependency for make. However, another issue with npm ? see log; Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:45 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU The Makefile uses git to generate the VERSION file based on what's checked out. Since it looks like you didn't get the code via git, you can trick it into skipping that step by manually creating a file named "VERSION" in the root of the LORIS directory so that it thinks it's already up to date. Regarding your follow up email: you should run `make` with no arguments in the root of your LORIS directory. If you get the "No targets specified" error when in the correct directory try "make all" (most versions of make that I'm aware of use the first target from the Makefile if no argument is specified, but "make all" is explicit.) (You should also make sure that you have: 1. composer and 2. npm installed with a recent enough version according to the README, or the make step will likely fail.) - Dave On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr > wrote: Well obviously there was no file; lol sorry. How to proceed with this? root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make git describe --tags --always > VERSION fatal: not a git repository (or any of the parent directories): .git Makefile:8: recipe for target 'VERSION' failed make: *** [VERSION] Error 128 Matthew From: Matthew Sparks, Mr Sent: Thursday, November 14, 2019 2:27 PM To: Dave MacFarlane > Cc: loris-dev at bic.mni.mcgill.ca Subject: RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Great, thanks. Everytime I run this command I receive the following; - make: *** No targets specified and no makefile found Dependency related no doubt? Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:17 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr > wrote: Sorry if I was unclear. I?m not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingyun.ma at mcin.ca Thu Nov 14 16:29:52 2019 From: lingyun.ma at mcin.ca (Ling Ma) Date: Thu, 14 Nov 2019 16:29:52 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi Matthew, Please indicate nodejs and npm version numbers, usually some old OS releases won't install the new versions, even if you just installed them. On Thu, Nov 14, 2019 at 4:20 PM Matthew Sparks, Mr wrote: > Already updated to the latest versions, as neither were installed > initially. > > Best, > Matthew > > ------------------------------ > *From:* Ling Ma > *Sent:* Thursday, November 14, 2019 4:18:35 PM > *To:* Matthew Sparks, Mr > *Cc:* Dave MacFarlane ; > loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > Hi Matthew, > > It looks most likely that you need a most recent version of nodejs and > npm, as the error message indicates. Check the installation Readme. > > On Thu, Nov 14, 2019 at 3:33 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi, I was missing the *npm* dependency for make. *However*, another issue > with npm ? see log; > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:45 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > The Makefile uses git to generate the VERSION file based on what's checked > out. Since it looks like you didn't get the code via git, you can trick it > into skipping that step by manually creating a file named "VERSION" in the > root of the LORIS directory so that it thinks it's already up to date. > > > > Regarding your follow up email: you should run `make` with no arguments in > the root of your LORIS directory. If you get the "No targets specified" > error when in the correct directory try "make all" (most versions of make > that I'm aware of use the first target from the Makefile if no argument is > specified, but "make all" is explicit.) > > > > (You should also make sure that you have: 1. composer and 2. npm installed > with a recent enough version according to the README, or the make step will > likely fail.) > > > > - Dave > > > > On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Well obviously there was no file; lol sorry. How to proceed with this? > > > > root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make > > git describe --tags --always > VERSION > > fatal: not a git repository (or any of the parent directories): .git > > Makefile:8: recipe for target 'VERSION' failed > > make: *** [VERSION] Error 128 > > > > Matthew > > > > *From:* Matthew Sparks, Mr > *Sent:* Thursday, November 14, 2019 2:27 PM > *To:* Dave MacFarlane > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Great, thanks. Everytime I run this command I receive the following; > > - make: *** No targets specified and no makefile found > > > > Dependency related no doubt? > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:17 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > In that case. you're missing the equivalent step of the install process > (run `make` for production or `make dev` for a sandbox which invokes > composer.) > > > > There was a bug in the initial 21.0.0 release where that step wasn't > properly documented, so it's easy to have missed but it should be listed as > step 4 in the README as of v21.0.3. > > > > On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Sorry if I was unclear. I?m not upgrading. I have more than one instance > of Loris running. The v17 version will be made dormant once the latest v21 > clean install works. I would like to port a few modules from the working > v17 to the latest. Otherwise, I have 10+ point-release iterations to > updates to make. > > > > -Matthew > > > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:56 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > When upgrading, it's required to be on the latest minor release and to go > one release at a time. If you go to https://github.com/aces/Loris/releases > there should be an "Upgrade process" section for each release that you > should follow in order from 17. The error (that it can't find the autoload > file generated by composer) seems to suggest you missed step 2 of the > upgrade process to LORIS v21. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi Dave, > > > > Certainly, my apologies for not attaching them initially. > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:34 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Do you have access to the web server's error log on Digital Ocean? It's > difficult to guess why it's generating a 500 error without seeing the error > log. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Fri Nov 15 09:57:52 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Fri, 15 Nov 2019 14:57:52 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi Installed versions of npm and nodejs; - Npm; 6.12.0 - Nodejs; 13.0.1 With these updated versions make is still failing. Best, Matthew From: Ling Ma Sent: Thursday, November 14, 2019 4:30 PM To: Matthew Sparks, Mr Cc: Dave MacFarlane ; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Please indicate nodejs and npm version numbers, usually some old OS releases won't install the new versions, even if you just installed them. On Thu, Nov 14, 2019 at 4:20 PM Matthew Sparks, Mr > wrote: Already updated to the latest versions, as neither were installed initially. Best, Matthew ________________________________ From: Ling Ma > Sent: Thursday, November 14, 2019 4:18:35 PM To: Matthew Sparks, Mr > Cc: Dave MacFarlane >; loris-dev at bic.mni.mcgill.ca > Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, It looks most likely that you need a most recent version of nodejs and npm, as the error message indicates. Check the installation Readme. On Thu, Nov 14, 2019 at 3:33 PM Matthew Sparks, Mr > wrote: Hi, I was missing the npm dependency for make. However, another issue with npm ? see log; Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:45 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU The Makefile uses git to generate the VERSION file based on what's checked out. Since it looks like you didn't get the code via git, you can trick it into skipping that step by manually creating a file named "VERSION" in the root of the LORIS directory so that it thinks it's already up to date. Regarding your follow up email: you should run `make` with no arguments in the root of your LORIS directory. If you get the "No targets specified" error when in the correct directory try "make all" (most versions of make that I'm aware of use the first target from the Makefile if no argument is specified, but "make all" is explicit.) (You should also make sure that you have: 1. composer and 2. npm installed with a recent enough version according to the README, or the make step will likely fail.) - Dave On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr > wrote: Well obviously there was no file; lol sorry. How to proceed with this? root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make git describe --tags --always > VERSION fatal: not a git repository (or any of the parent directories): .git Makefile:8: recipe for target 'VERSION' failed make: *** [VERSION] Error 128 Matthew From: Matthew Sparks, Mr Sent: Thursday, November 14, 2019 2:27 PM To: Dave MacFarlane > Cc: loris-dev at bic.mni.mcgill.ca Subject: RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Great, thanks. Everytime I run this command I receive the following; - make: *** No targets specified and no makefile found Dependency related no doubt? Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:17 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr > wrote: Sorry if I was unclear. I?m not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: log-15-11-2019.txt URL: From rida.abou-haidar at mcin.ca Fri Nov 15 10:04:58 2019 From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar) Date: Fri, 15 Nov 2019 10:04:58 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi Matthew, What's your version of composer? Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Fri, Nov 15, 2019 at 9:58 AM Matthew Sparks, Mr wrote: > Hi > > > > Installed versions of npm and nodejs; > > - Npm; 6.12.0 > > - Nodejs; 13.0.1 > > > > With these updated versions make is *still failing*. > > > > Best, > > Matthew > > > > *From:* Ling Ma > *Sent:* Thursday, November 14, 2019 4:30 PM > *To:* Matthew Sparks, Mr > *Cc:* Dave MacFarlane ; > loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Please indicate nodejs and npm version numbers, usually some old OS > releases won't install the new versions, even if you just installed them. > > > > On Thu, Nov 14, 2019 at 4:20 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Already updated to the latest versions, as neither were installed > initially. > > > > Best, > > Matthew > > > ------------------------------ > > *From:* Ling Ma > *Sent:* Thursday, November 14, 2019 4:18:35 PM > *To:* Matthew Sparks, Mr > *Cc:* Dave MacFarlane ; > loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > It looks most likely that you need a most recent version of nodejs and > npm, as the error message indicates. Check the installation Readme. > > > > On Thu, Nov 14, 2019 at 3:33 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi, I was missing the *npm* dependency for make. *However*, another issue > with npm ? see log; > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:45 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > The Makefile uses git to generate the VERSION file based on what's checked > out. Since it looks like you didn't get the code via git, you can trick it > into skipping that step by manually creating a file named "VERSION" in the > root of the LORIS directory so that it thinks it's already up to date. > > > > Regarding your follow up email: you should run `make` with no arguments in > the root of your LORIS directory. If you get the "No targets specified" > error when in the correct directory try "make all" (most versions of make > that I'm aware of use the first target from the Makefile if no argument is > specified, but "make all" is explicit.) > > > > (You should also make sure that you have: 1. composer and 2. npm installed > with a recent enough version according to the README, or the make step will > likely fail.) > > > > - Dave > > > > On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Well obviously there was no file; lol sorry. How to proceed with this? > > > > root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make > > git describe --tags --always > VERSION > > fatal: not a git repository (or any of the parent directories): .git > > Makefile:8: recipe for target 'VERSION' failed > > make: *** [VERSION] Error 128 > > > > Matthew > > > > *From:* Matthew Sparks, Mr > *Sent:* Thursday, November 14, 2019 2:27 PM > *To:* Dave MacFarlane > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Great, thanks. Everytime I run this command I receive the following; > > - make: *** No targets specified and no makefile found > > > > Dependency related no doubt? > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:17 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > In that case. you're missing the equivalent step of the install process > (run `make` for production or `make dev` for a sandbox which invokes > composer.) > > > > There was a bug in the initial 21.0.0 release where that step wasn't > properly documented, so it's easy to have missed but it should be listed as > step 4 in the README as of v21.0.3. > > > > On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Sorry if I was unclear. I?m not upgrading. I have more than one instance > of Loris running. The v17 version will be made dormant once the latest v21 > clean install works. I would like to port a few modules from the working > v17 to the latest. Otherwise, I have 10+ point-release iterations to > updates to make. > > > > -Matthew > > > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:56 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > When upgrading, it's required to be on the latest minor release and to go > one release at a time. If you go to https://github.com/aces/Loris/releases > there should be an "Upgrade process" section for each release that you > should follow in order from 17. The error (that it can't find the autoload > file generated by composer) seems to suggest you missed step 2 of the > upgrade process to LORIS v21. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi Dave, > > > > Certainly, my apologies for not attaching them initially. > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:34 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Do you have access to the web server's error log on Digital Ocean? It's > difficult to guess why it's generating a 500 error without seeing the error > log. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Fri Nov 15 15:42:10 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Fri, 15 Nov 2019 20:42:10 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Hi Rida, Thanks for this! Issue resolved - composer was outdated. Best, Matthew From: Rida Abou-Haidar Sent: Friday, November 15, 2019 10:05 AM To: Matthew Sparks, Mr Cc: Ling Ma ; Dave MacFarlane ; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, What's your version of composer? Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Fri, Nov 15, 2019 at 9:58 AM Matthew Sparks, Mr > wrote: Hi Installed versions of npm and nodejs; - Npm; 6.12.0 - Nodejs; 13.0.1 With these updated versions make is still failing. Best, Matthew From: Ling Ma > Sent: Thursday, November 14, 2019 4:30 PM To: Matthew Sparks, Mr > Cc: Dave MacFarlane >; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Please indicate nodejs and npm version numbers, usually some old OS releases won't install the new versions, even if you just installed them. On Thu, Nov 14, 2019 at 4:20 PM Matthew Sparks, Mr > wrote: Already updated to the latest versions, as neither were installed initially. Best, Matthew ________________________________ From: Ling Ma > Sent: Thursday, November 14, 2019 4:18:35 PM To: Matthew Sparks, Mr > Cc: Dave MacFarlane >; loris-dev at bic.mni.mcgill.ca > Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, It looks most likely that you need a most recent version of nodejs and npm, as the error message indicates. Check the installation Readme. On Thu, Nov 14, 2019 at 3:33 PM Matthew Sparks, Mr > wrote: Hi, I was missing the npm dependency for make. However, another issue with npm - see log; Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:45 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU The Makefile uses git to generate the VERSION file based on what's checked out. Since it looks like you didn't get the code via git, you can trick it into skipping that step by manually creating a file named "VERSION" in the root of the LORIS directory so that it thinks it's already up to date. Regarding your follow up email: you should run `make` with no arguments in the root of your LORIS directory. If you get the "No targets specified" error when in the correct directory try "make all" (most versions of make that I'm aware of use the first target from the Makefile if no argument is specified, but "make all" is explicit.) (You should also make sure that you have: 1. composer and 2. npm installed with a recent enough version according to the README, or the make step will likely fail.) - Dave On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr > wrote: Well obviously there was no file; lol sorry. How to proceed with this? root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make git describe --tags --always > VERSION fatal: not a git repository (or any of the parent directories): .git Makefile:8: recipe for target 'VERSION' failed make: *** [VERSION] Error 128 Matthew From: Matthew Sparks, Mr Sent: Thursday, November 14, 2019 2:27 PM To: Dave MacFarlane > Cc: loris-dev at bic.mni.mcgill.ca Subject: RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Great, thanks. Everytime I run this command I receive the following; - make: *** No targets specified and no makefile found Dependency related no doubt? Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:17 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr > wrote: Sorry if I was unclear. I'm not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I've granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From rida.abou-haidar at mcin.ca Fri Nov 15 15:48:39 2019 From: rida.abou-haidar at mcin.ca (Rida Abou-Haidar) Date: Fri, 15 Nov 2019 15:48:39 -0500 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: You are welcome Matthew, it was a group effort. Is loris loading now ? Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Fri., Nov. 15, 2019, 3:42 p.m. Matthew Sparks, Mr < matthew.sparks at mcgill.ca> wrote: > Hi Rida, > > > > Thanks for this! Issue resolved ? *composer* was outdated. > > > > Best, > > Matthew > > > > *From:* Rida Abou-Haidar > *Sent:* Friday, November 15, 2019 10:05 AM > *To:* Matthew Sparks, Mr > *Cc:* Ling Ma ; Dave MacFarlane < > dave.macfarlane at mcin.ca>; loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > What's your version of composer? > > > > > Rida Abou-Haidar > CCNA Software Developer > Montreal Neurological Institute > McGill University > > rida.abou-haidar at mcin.ca > > > > > > On Fri, Nov 15, 2019 at 9:58 AM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi > > > > Installed versions of npm and nodejs; > > - Npm; 6.12.0 > > - Nodejs; 13.0.1 > > > > With these updated versions make is *still failing*. > > > > Best, > > Matthew > > > > *From:* Ling Ma > *Sent:* Thursday, November 14, 2019 4:30 PM > *To:* Matthew Sparks, Mr > *Cc:* Dave MacFarlane ; > loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Please indicate nodejs and npm version numbers, usually some old OS > releases won't install the new versions, even if you just installed them. > > > > On Thu, Nov 14, 2019 at 4:20 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Already updated to the latest versions, as neither were installed > initially. > > > > Best, > > Matthew > > > ------------------------------ > > *From:* Ling Ma > *Sent:* Thursday, November 14, 2019 4:18:35 PM > *To:* Matthew Sparks, Mr > *Cc:* Dave MacFarlane ; > loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > It looks most likely that you need a most recent version of nodejs and > npm, as the error message indicates. Check the installation Readme. > > > > On Thu, Nov 14, 2019 at 3:33 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi, I was missing the *npm* dependency for make. *However*, another issue > with npm ? see log; > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:45 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > The Makefile uses git to generate the VERSION file based on what's checked > out. Since it looks like you didn't get the code via git, you can trick it > into skipping that step by manually creating a file named "VERSION" in the > root of the LORIS directory so that it thinks it's already up to date. > > > > Regarding your follow up email: you should run `make` with no arguments in > the root of your LORIS directory. If you get the "No targets specified" > error when in the correct directory try "make all" (most versions of make > that I'm aware of use the first target from the Makefile if no argument is > specified, but "make all" is explicit.) > > > > (You should also make sure that you have: 1. composer and 2. npm installed > with a recent enough version according to the README, or the make step will > likely fail.) > > > > - Dave > > > > On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Well obviously there was no file; lol sorry. How to proceed with this? > > > > root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make > > git describe --tags --always > VERSION > > fatal: not a git repository (or any of the parent directories): .git > > Makefile:8: recipe for target 'VERSION' failed > > make: *** [VERSION] Error 128 > > > > Matthew > > > > *From:* Matthew Sparks, Mr > *Sent:* Thursday, November 14, 2019 2:27 PM > *To:* Dave MacFarlane > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Great, thanks. Everytime I run this command I receive the following; > > - make: *** No targets specified and no makefile found > > > > Dependency related no doubt? > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 2:17 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > In that case. you're missing the equivalent step of the install process > (run `make` for production or `make dev` for a sandbox which invokes > composer.) > > > > There was a bug in the initial 21.0.0 release where that step wasn't > properly documented, so it's easy to have missed but it should be listed as > step 4 in the README as of v21.0.3. > > > > On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Sorry if I was unclear. I?m not upgrading. I have more than one instance > of Loris running. The v17 version will be made dormant once the latest v21 > clean install works. I would like to port a few modules from the working > v17 to the latest. Otherwise, I have 10+ point-release iterations to > updates to make. > > > > -Matthew > > > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:56 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > When upgrading, it's required to be on the latest minor release and to go > one release at a time. If you go to https://github.com/aces/Loris/releases > there should be an "Upgrade process" section for each release that you > should follow in order from 17. The error (that it can't find the autoload > file generated by composer) seems to suggest you missed step 2 of the > upgrade process to LORIS v21. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hi Dave, > > > > Certainly, my apologies for not attaching them initially. > > > > Best, > > Matthew > > > > *From:* Dave MacFarlane > *Sent:* Thursday, November 14, 2019 1:34 PM > *To:* Matthew Sparks, Mr > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU > > > > Hi Matthew, > > > > Do you have access to the web server's error log on Digital Ocean? It's > difficult to guess why it's generating a 500 error without seeing the error > log. > > > > - Dave > > > > On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr < > matthew.sparks at mcgill.ca> wrote: > > Hello Loris Devs, > > > > I have just installed a new loris instance on the DigitalOcean platform > and post-install I receive a HTTP 500 Error. > > > > Please advise and see the screenshot attached; > > - To troubleshoot; From the dev instance you can see that I?ve > granted excessive permissions beyond what is needed, and the *issue > persists*. > > > > Currently; > > - Functional Loris *v17* instance running on DO. > > - Non-functional Loris *v21.0.3 (.1-3)* instance running on DO. > > > > Nice to have; > > - DigitalOcean application for rapid reployment. > > - Up-to-date Loris install guide (e.g., deprecation of > python-properties-common etc) > > > > I can re-initialize the DO base and provide you with root credentials for > a quick install to loris v21.0.3? > > - Ultimately, we need to be able to use the *DQT*. > > > > Any suggestions to resolve the issue would be appreciated > > > > Kindest regards, > > Matthew > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew.sparks at mcgill.ca Fri Nov 15 15:53:13 2019 From: matthew.sparks at mcgill.ca (Matthew Sparks, Mr) Date: Fri, 15 Nov 2019 20:53:13 +0000 Subject: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In-Reply-To: References: Message-ID: Most definitly, thank you all. The loris team is made up of all-stars I see ? Loris now loads without issue. I will proceed to porting some modules from loris v17 into the newer loris instance. Best, Matthew From: Rida Abou-Haidar Sent: Friday, November 15, 2019 3:49 PM To: Matthew Sparks, Mr Cc: Ling Ma ; Dave MacFarlane ; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU You are welcome Matthew, it was a group effort. Is loris loading now ? Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Fri., Nov. 15, 2019, 3:42 p.m. Matthew Sparks, Mr > wrote: Hi Rida, Thanks for this! Issue resolved ? composer was outdated. Best, Matthew From: Rida Abou-Haidar > Sent: Friday, November 15, 2019 10:05 AM To: Matthew Sparks, Mr > Cc: Ling Ma >; Dave MacFarlane >; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, What's your version of composer? Rida Abou-Haidar CCNA Software Developer Montreal Neurological Institute McGill University rida.abou-haidar at mcin.ca On Fri, Nov 15, 2019 at 9:58 AM Matthew Sparks, Mr > wrote: Hi Installed versions of npm and nodejs; - Npm; 6.12.0 - Nodejs; 13.0.1 With these updated versions make is still failing. Best, Matthew From: Ling Ma > Sent: Thursday, November 14, 2019 4:30 PM To: Matthew Sparks, Mr > Cc: Dave MacFarlane >; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Please indicate nodejs and npm version numbers, usually some old OS releases won't install the new versions, even if you just installed them. On Thu, Nov 14, 2019 at 4:20 PM Matthew Sparks, Mr > wrote: Already updated to the latest versions, as neither were installed initially. Best, Matthew ________________________________ From: Ling Ma > Sent: Thursday, November 14, 2019 4:18:35 PM To: Matthew Sparks, Mr > Cc: Dave MacFarlane >; loris-dev at bic.mni.mcgill.ca > Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, It looks most likely that you need a most recent version of nodejs and npm, as the error message indicates. Check the installation Readme. On Thu, Nov 14, 2019 at 3:33 PM Matthew Sparks, Mr > wrote: Hi, I was missing the npm dependency for make. However, another issue with npm ? see log; Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:45 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU The Makefile uses git to generate the VERSION file based on what's checked out. Since it looks like you didn't get the code via git, you can trick it into skipping that step by manually creating a file named "VERSION" in the root of the LORIS directory so that it thinks it's already up to date. Regarding your follow up email: you should run `make` with no arguments in the root of your LORIS directory. If you get the "No targets specified" error when in the correct directory try "make all" (most versions of make that I'm aware of use the first target from the Makefile if no argument is specified, but "make all" is explicit.) (You should also make sure that you have: 1. composer and 2. npm installed with a recent enough version according to the README, or the make step will likely fail.) - Dave On Thu, Nov 14, 2019 at 2:30 PM Matthew Sparks, Mr > wrote: Well obviously there was no file; lol sorry. How to proceed with this? root at ubuntu-s-1vcpu-2gb-tor1-01:/var/www/loris# make git describe --tags --always > VERSION fatal: not a git repository (or any of the parent directories): .git Makefile:8: recipe for target 'VERSION' failed make: *** [VERSION] Error 128 Matthew From: Matthew Sparks, Mr Sent: Thursday, November 14, 2019 2:27 PM To: Dave MacFarlane > Cc: loris-dev at bic.mni.mcgill.ca Subject: RE: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Great, thanks. Everytime I run this command I receive the following; - make: *** No targets specified and no makefile found Dependency related no doubt? Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 2:17 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU In that case. you're missing the equivalent step of the install process (run `make` for production or `make dev` for a sandbox which invokes composer.) There was a bug in the initial 21.0.0 release where that step wasn't properly documented, so it's easy to have missed but it should be listed as step 4 in the README as of v21.0.3. On Thu, Nov 14, 2019 at 1:59 PM Matthew Sparks, Mr > wrote: Sorry if I was unclear. I?m not upgrading. I have more than one instance of Loris running. The v17 version will be made dormant once the latest v21 clean install works. I would like to port a few modules from the working v17 to the latest. Otherwise, I have 10+ point-release iterations to updates to make. -Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:56 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU When upgrading, it's required to be on the latest minor release and to go one release at a time. If you go to https://github.com/aces/Loris/releases there should be an "Upgrade process" section for each release that you should follow in order from 17. The error (that it can't find the autoload file generated by composer) seems to suggest you missed step 2 of the upgrade process to LORIS v21. - Dave On Thu, Nov 14, 2019 at 1:39 PM Matthew Sparks, Mr > wrote: Hi Dave, Certainly, my apologies for not attaching them initially. Best, Matthew From: Dave MacFarlane > Sent: Thursday, November 14, 2019 1:34 PM To: Matthew Sparks, Mr > Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] LORIS - v21.0.3 (Ubuntu Base 16.04.6) - CRU Hi Matthew, Do you have access to the web server's error log on Digital Ocean? It's difficult to guess why it's generating a 500 error without seeing the error log. - Dave On Thu, Nov 14, 2019 at 1:30 PM Matthew Sparks, Mr > wrote: Hello Loris Devs, I have just installed a new loris instance on the DigitalOcean platform and post-install I receive a HTTP 500 Error. Please advise and see the screenshot attached; - To troubleshoot; From the dev instance you can see that I?ve granted excessive permissions beyond what is needed, and the issue persists. Currently; - Functional Loris v17 instance running on DO. - Non-functional Loris v21.0.3 (.1-3) instance running on DO. Nice to have; - DigitalOcean application for rapid reployment. - Up-to-date Loris install guide (e.g., deprecation of python-properties-common etc) I can re-initialize the DO base and provide you with root credentials for a quick install to loris v21.0.3? - Ultimately, we need to be able to use the DQT. Any suggestions to resolve the issue would be appreciated Kindest regards, Matthew _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingyun.ma at mcin.ca Mon Nov 18 13:13:03 2019 From: lingyun.ma at mcin.ca (Ling Ma) Date: Mon, 18 Nov 2019 13:13:03 -0500 Subject: [Loris-dev] Fwd: LORIS - Porting (Instruments/Modules/Configuration) In-Reply-To: References: Message-ID: Hi, Does anyone know if there is a data migration guideline, or if the data structure did not change from v17 to v21? Thanks if you could answer the following questions. Ling Ma Consultant developer ---------- Forwarded message --------- From: Matthew Sparks, Mr Date: Mon, Nov 18, 2019 at 12:37 PM Subject: LORIS - Porting (Instruments/Modules/Configuration) To: Ling Ma Hello, I want to quickly port instruments/sql/modules (no patient data) from version v17 to the latest version of LORIS. Is there a general guideline to follow for this process. I could follow the loris development flow, however, it would much quicker if a guideline exists already. Please advise, Matthew -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingyun.ma at mcin.ca Mon Nov 18 13:58:22 2019 From: lingyun.ma at mcin.ca (Ling Ma) Date: Mon, 18 Nov 2019 13:58:22 -0500 Subject: [Loris-dev] LORIS - Porting (Instruments/Modules/Configuration) In-Reply-To: References: Message-ID: Hi Matthew, I don't know if there is a guideline for this task. Hope that someone in the team could help. I suggest that you create a separate installation to test the migration, then make a final port when you are satisfied with the result. By the way, it would be better to send emails to the team mail list for a better and quick response. Good luck. Ling Ma On Mon, Nov 18, 2019 at 12:37 PM Matthew Sparks, Mr < matthew.sparks at mcgill.ca> wrote: > Hello, > > > > I want to quickly port instruments/sql/modules (no patient data) from > version v17 to the latest version of LORIS. > > > > Is there a general guideline to follow for this process. I could follow > the loris development flow, however, it would much quicker if a guideline > exists already. > > > > Please advise, > > Matthew > > > -- Ling Ma Consultant developer -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue Nov 19 14:40:26 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 19 Nov 2019 14:40:26 -0500 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, I took a closer look to the batch_uploader_multiple_output.txt file you sent. It looks like there are different reasons for failure depending on the DICOM folder uploaded. - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1: it looks like there is no file of type DICOM in the folder. Have you checked to see if that is indeed the case? Maybe you can try running the following command on that folder to see what are the types of the files? If it does not return at least one DICOM medical imaging data file, then that is why you get the error message from the pipeline: - find -type f | xargs -i file {}|cut -d: -f2|sort|uniq - For 864173 DCC0001 V1: it looks like there are two different DICOM studies within the same folder. You will need to split that study in two based on the StudyUID field as the insertion pipeline does not allow for more than one StudyUID per upload. - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1: it looks like the dcm2mnc command did not produce any MINC files. Can you check in the DICOM archive what are the series present in the tarchive for that visit? Maybe only a scout or localizer was acquired for that session, hence the no valid MINC files (scout and localizer being skipped for the conversion) - For 397410 DCC0003 V1: it looks like everything went well for this one. One script that is called by our pipeline is called get_dicom_info.pl and this does all kind of checks on the DICOM files (it is being called when running the dcm2mnc conversion). You could run it independently on your folder if needed. Since one of the study got in, it does not look like you are having a problem with the setup. It seems more likely to be a problem with the data themselves. Hope this helps. C?cile On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi Christine, > > In my first vm i am able to create the minc files and view them at the mri > browser (except of candidate 102761034 ), meanwhile the same files gives > warnings at the 2nd vm. The output of the batch upload can be seen in the > file attached. > Also a colleague of us has built a pre-validation tool for dicom > https://github.com/aueb-wim/DataQualityControlTool/ which had found all > the files that Loris gave as warning . Basically I confirmed that the total > amount of files per dicom was the same amount as stated in Loris and > checked some filenames given from warning to confirm that they match with > our tool. But that was months ago and my colleague had changed some > parameters for MIP and now our tool doesn't find all the invalid files, > that's why i asked for the dicom header specification of Loris. In a > discussion we had he mentioned that he doesn't check for some tags e.x. > orientation. Lastly to mention that in my first vm i didn't use our tool to > remove invalid dcm files. > > Thanks > > ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > >> Hi Sotirios, >> Can you provide us with some fresh particulars of the current issue and >> we'll take it from there? >> Yang's team has built these scripts which can definitely serve as a model >> for your pre-validation of your DICOM collections. >> cheers, >> Christine >> >> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> HI Yang, >>> >>> We make use of pydicom library too. Now about the validate.py i see that >>> you check if some attributes are missing such as PatientID, PatientName >>> which all of our files contains that info. Maybe i have missed something on >>> the setup of my other virtual machine ( although one dicom passed on the >>> new vm successfully, the others that were inserted correctly on my old vm >>> fails on the new one ), i think that i had asked about this error "Use of >>> uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/ >>> batch_uploads_imageuploader.pl line 144." but i don't remember the >>> solution. >>> >>> Thanks >>> >>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding ??????: >>> >>>> Hey, Sotirios, >>>> >>>> Christine from the LORIS team mentioned you had some issue with DICOM. >>>> I am a fellow developer for an external project using LORIS, kind of just >>>> like you. We had to implement DICOM upload as well but more as a fully >>>> automated pipeline actually. >>>> >>>> While we were building CNBP, we had coded up some minor Python >>>> functions to check DICOM integrity (and simple validations) and you might >>>> be able to gain some inspiration from it and help you with your cause. For >>>> more comprehensive solution, PyDICOM ( >>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>> like a descent python package to help out with a lot of DICOM data checks >>>> (I was essentially just building customized wrapper calls to them). You can >>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>> rough around the edges but hopefully point you in the right direcitons >>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>> >>>> Cheers, >>>> >>>> Yang Ding, PhD. >>>> Canadian Neonatal Brain Platform Architect >>>> >>>> On Tue, Nov 12, 2019 at 8:29 AM >>>> wrote: >>>> >>>>> Send Loris-dev mailing list submissions to >>>>> loris-dev at bic.mni.mcgill.ca >>>>> >>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> or, via email, send a message with subject or body 'help' to >>>>> loris-dev-request at bic.mni.mcgill.ca >>>>> >>>>> You can reach the person managing the list at >>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>> >>>>> When replying, please edit your Subject line so it is more specific >>>>> than "Re: Contents of Loris-dev digest..." >>>>> >>>>> >>>>> Today's Topics: >>>>> >>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>> >>>>> >>>>> ---------------------------------------------------------------------- >>>>> >>>>> Message: 1 >>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>> From: Sotirios Nikoloutsopoulos >>>>> To: Cecile Madjar >>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>> Message-ID: >>>>> >>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> Hi, >>>>> >>>>> Could we send you a link with 10 anonymized dicom files to diagnose the >>>>> warnings we get? >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>> > Hi Cecile, >>>>> > >>>>> > We were wondering whether Loris has a tool to check if there are >>>>> problems >>>>> > with the dcm files, before trying to upload them. Something that >>>>> could >>>>> > provide the same results provided in the warning_output, this is the >>>>> > summary from the mri_upload at the front-page. Also which attributes >>>>> of the >>>>> > dcm header would trigger a warning? is there a dcm file header >>>>> > specification for Loris? >>>>> > >>>>> > Thanks >>>>> > >>>>> > Sotirios >>>>> > >>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> > sotirisnik at gmail.com> ??????: >>>>> > >>>>> >> Hi, >>>>> >> >>>>> >> Yes, by parsing now() into unix_timestamp function it worked,but i >>>>> >> thought that something else was causing the 2nd issue. >>>>> >> Thanks >>>>> >> >>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>> >> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> The first error occurs because the QCFirstChangeTime and columns >>>>> are of >>>>> >>> type `unsigned integer` and not `datatime`. You should be using >>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>> >>> >>>>> >>> The second error occurs because the trigger triggers a rollback of >>>>> the >>>>> >>> insert statement in the files table. >>>>> >>> See mysql documentation for trigger error handling. >>>>> >>> >>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>> failure of >>>>> >>> the entire statement that caused trigger invocation. >>>>> >>> >>>>> >>> >>>>> >>> Thank you for sharing that. I hope it helps. >>>>> >>> -- Xavier >>>>> >>> >>>>> >>> ------------------------------ >>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>> >>> Nikoloutsopoulos >>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>> >>> *To:* Cecile Madjar >>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca ; >>>>> >>> Christine Rogers, Ms. >>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>> >>> >>>>> >>> When mincs are inserted their corresponding rows at the file table >>>>> are >>>>> >>> inserted too >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>> because i >>>>> >>> don't want manually to label them as passed throught the interface >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> >>>>> >>> That is the trigger i wrote >>>>> >>> >>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER `LORIS`.`files_AFTER_INSERT` >>>>> AFTER >>>>> >>> INSERT ON `files` FOR EACH ROW >>>>> >>> BEGIN >>>>> >>> INSERT INTO files_qcstatus >>>>> >>> SET FileID = NEW.FileID, >>>>> >>> SeriesUID = NEW.SeriesUID, >>>>> >>> EchoTime = NEW.EchoTime, >>>>> >>> QCStatus = "Pass", >>>>> >>> QCFirstChangeTime = NOW(), >>>>> >>> QCLastChangeTime = NOW(); >>>>> >>> END >>>>> >>> >>>>> >>> although it contains some errors >>>>> >>> >>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>> foreign >>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` >>>>> (`FileID`)) >>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> In the mri_upload table, there is a TarchiveID column associated >>>>> with >>>>> >>> the MRI upload you inserted. When this value is NULL, it means no >>>>> DICOMs >>>>> >>> were inserted into the tarchive tables. At the end of the >>>>> insertion of the >>>>> >>> DICOMs in the tarchive tables, this value is updated with the >>>>> correct >>>>> >>> TarchiveID associated with the upload. >>>>> >>> >>>>> >>> Could this correspond to what you want to do? >>>>> >>> >>>>> >>> Regarding the files_qcstatus, this table is only linked to the >>>>> files >>>>> >>> table (hence, the MINC files). You could always create a new table >>>>> for >>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>> >>> >>>>> >>> C?cile >>>>> >>> >>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> i would like whenever a dicom is imported to mark all their >>>>> >>> coressponding qc_status to "pass". I was thinking of creating a >>>>> trigger for >>>>> >>> that, but which tables do i need to add entries to? So far from >>>>> what i see >>>>> >>> i need to add entres at the table "files" whenever an insertion >>>>> happens to >>>>> >>> files_qcstatus. >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>> Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning of my >>>>> email >>>>> >>> i sent 3 hours ago (not StudyUID). >>>>> >>> >>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>> Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i am >>>>> >>> looking for is not stored in the database? >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> Thanks. >>>>> >>> >>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>> >>> tarchive table. It can also be found in the metadata field but it >>>>> is mixed >>>>> >>> with many other information. >>>>> >>> >>>>> >>> Hope this helps, >>>>> >>> >>>>> >>> C?cile >>>>> >>> >>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>>>> >>> specifically at the AcquisitonMetadata column i found something >>>>> called >>>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>>> Instance UID. >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> Your observation is correct. A little explanation below. >>>>> >>> >>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>> >>> >>>>> >>> - the scan type could not be identified (not matching an entry >>>>> in >>>>> >>> the mri_protocol table) >>>>> >>> - one parameter of the scan type is out of the expected range >>>>> >>> present in the mri_protocol_checks (extra filtering in case you >>>>> need to be >>>>> >>> stricker on some parameters not present in the mri_protocol >>>>> table) >>>>> >>> - if the CandID and PSCID do not match >>>>> >>> >>>>> >>> The following cases do not get in the MRI violation tables as it >>>>> happens >>>>> >>> before the conversion of the DICOM to MINC files and only MINC >>>>> files >>>>> >>> violations are logged there: >>>>> >>> >>>>> >>> - "No single DICOM" (since no valid DICOM could be found to >>>>> convert >>>>> >>> to MINC) >>>>> >>> - "Study already inserted" (duplicate StudyUID) since this error >>>>> >>> happens at the dicomTar.pl level (way before conversion into >>>>> MINC files) >>>>> >>> >>>>> >>> Glad everything is working out!! >>>>> >>> Best, >>>>> >>> >>>>> >>> C?cile >>>>> >>> >>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now >>>>> about the >>>>> >>> mri_violations, dicoms are triggered to be inserted there only if >>>>> there is >>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>> parameter? >>>>> >>> Because i don't see the cases of 'No single dicom" or with the 2 >>>>> studyiuid >>>>> >>> to be there. >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> Sorry to hear you are having issues with the memory. I think most >>>>> of our >>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>> >>> >>>>> >>> Hope this helps! >>>>> >>> >>>>> >>> C?cile >>>>> >>> >>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> about that dicom that had that insertion error it's about 30mb and >>>>> when >>>>> >>> it is being processed the ram is being drastically increased from >>>>> 2gb to >>>>> >>> 3.28 and then the whole virtual machine is frozen. What is the >>>>> recommended >>>>> >>> size of ram for using Loris? >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>> >>> >>>>> >>> For the delete script issue, if you are absolutely certain that no >>>>> >>> processes are run for that uploadID, you can update the mri_upload >>>>> table >>>>> >>> and set the column Inserting to 0 instead of 1 for that uploadID. >>>>> It >>>>> >>> looks like for some reason the scripts did not update this field >>>>> when it >>>>> >>> stopped the insertion. Not sure why that would be the case though. >>>>> >>> Note: only do that update if you are certain that there is no >>>>> processing >>>>> >>> happening. >>>>> >>> >>>>> >>> Hope this helps! >>>>> >>> >>>>> >>> >>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>> actually do >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> I thought that this might be a permission because "w" was missing >>>>> at the >>>>> >>> group. After using chmod -R 775 only 102809579 passed, but with no >>>>> mnic >>>>> >>> files. Also now i have this error >>>>> >>> >>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>> :/data/loris/bin/mri/tools$ >>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>> >>> Cannot delete upload 34: the MRI pipeline is currently processing >>>>> it. >>>>> >>> >>>>> >>> How can solve this? >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>> Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> Here is our auto dicom uploading python script: >>>>> >>> >>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>> >>> >>>>> >>> To give you a brief idea: >>>>> >>> Per folder it will: >>>>> >>> 1) Delete all the .bak files >>>>> >>> 2) Locate .dcm files and update the Patient header >>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>> TE_min, >>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>> mri_protocol table >>>>> >>> >>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>> >>> For some reason some files are missing >>>>> SeriesDescription/ProtocolName >>>>> >>> >>>>> >>> In total i have 7 folders >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> 3/7 passed >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> Also about the first patient with DC0000 had a violation "T1 AXIAL >>>>> SE >>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i find >>>>> that weird >>>>> >>> since Loris detects the SeriesDescription. >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> >>>>> >>> Now about the 4/7 that didn't passed >>>>> >>> >>>>> >>> 102327840 and 102809579 outputs "The target directory does not >>>>> contain a >>>>> >>> single DICOM file.", therefore they are missing their StudyUID >>>>> >>> >>>>> >>> 102506134 has 2 studyuid "You can't use it with data from multiple >>>>> >>> studies." >>>>> >>> >>>>> >>> and 102761034 "No data could be converted into valid MINC files. >>>>> >>> localizer, scout will not be considered!" What is this? >>>>> >>> >>>>> >>> If i wanted to force the insertion of 102327840, 102809579 and >>>>> 102506134 >>>>> >>> can i just pass a flag parameter to batch_uploads_imageuploader.pl? >>>>> or >>>>> >>> modify imaging_upload_file.pl? >>>>> >>> >>>>> >>> Thank you, >>>>> >>> >>>>> >>> Sotirios >>>>> >>> >>>>> >>> PS >>>>> >>> >>>>> >>> To diagnose a folder search the name of the folder at >>>>> dicom_output.txt. >>>>> >>> >>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> Glad to hear about your progress. >>>>> >>> >>>>> >>> Yes, the script you used to delete imaging data is fully >>>>> documented here >>>>> >>> < >>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>> > >>>>> >>> -- let us know if you didn't find the answers you were looking for >>>>> there. >>>>> >>> (Is it possible the null row in *mri_scanner* seen in your database >>>>> >>> management software is a visual placeholder for you as the user? >>>>> I'm not >>>>> >>> sure why a scanner would ever be registered with ID='0' as your >>>>> screenshot >>>>> >>> showed.) >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> I fixed it with this >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>> Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> I tried to create a new candidate using the API, is there something >>>>> >>> wrong with the structure? why did i receive a 500 internal error? >>>>> In the >>>>> >>> loris-error log it state that there is something wrong with token, >>>>> but i >>>>> >>> verfied that the type of the token is a string. >>>>> >>> >>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 >>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type >>>>> string, >>>>> >>> null given, called in >>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>> 169 and >>>>> >>> defined in >>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>> >>> trace:\n#0 >>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n >>>>> thrown in >>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192 >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>> Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> Is there a way also to delete candidates? Just to let you know >>>>> what i >>>>> >>> did to clear candidates, because maybe i may have missed >>>>> dependencies. >>>>> >>> >>>>> >>> First i deleted all their uploads >>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to >>>>> omit >>>>> >>> the backup file ? ) >>>>> >>> >>>>> >>> Afterwards i had some scanner candidates, so i deleted all the >>>>> entries >>>>> >>> from mri_scanner except that i couldn't delete this entry with the >>>>> 0 ID. >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> >>>>> >>> Lastly i deleted the session and then the candidate table. >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> We recommend that you use our existing tools for creating new >>>>> candidates >>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>> calling the Candidate >>>>> >>> class's createNew() >>>>> >>> < >>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>> >function. >>>>> >>> These will create the necessary records for you. (It's not >>>>> recommended to >>>>> >>> make direct modifications to mysql database tables in your script, >>>>> if I >>>>> >>> understand you.) >>>>> >>> >>>>> >>> The CandID should be a randomized 6 digit randomized ID, and there >>>>> are >>>>> >>> multiple reasons for this. >>>>> >>> You can use the PSCID for project-specific IDs and the External ID >>>>> field >>>>> >>> in the candidate table can also be used for any values you like. >>>>> >>> Additionally, any number of custom IDs can be added in parallel - >>>>> these >>>>> >>> are entered/visible in the Candidate Information module and added >>>>> in the >>>>> >>> back-end as candidate parameters. >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> We are building a script that will auto insert the candidates >>>>> based on >>>>> >>> their ExternalID. We would like to know whethere when we are >>>>> creating a new >>>>> >>> profile in the candidate table, if we also have to insert a new >>>>> record at >>>>> >>> another table? Furthermore is there a problem that in our case >>>>> CandID won't >>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>> >>> >>>>> >>> That would normally be the case but the numeric part of the PSCID >>>>> get >>>>> >>> paded with 0 on the left. >>>>> >>> >>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical >>>>> char >>>>> >>> with a min value of 1, the sequence would be: >>>>> >>> >>>>> >>> ABC0001 >>>>> >>> ABC0002 >>>>> >>> ... >>>>> >>> ABC0010 >>>>> >>> ... >>>>> >>> >>>>> >>> thus sorting them ascending will always get the latest value >>>>> generated >>>>> >>> as the max value. >>>>> >>> >>>>> >>> M?lanie >>>>> >>> >>>>> >>> ------------------------------ >>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>> >>> *Sent:* September 13, 2019 10:15 >>>>> >>> *To:* Melanie Legault, Mrs >>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>> >>> >>>>> >>> I see, although the PSCID value is varchar(255), it must be stored >>>>> >>> within a specific length of characters. Otherwise if we were to >>>>> sort >>>>> >>> strings with different lengths the result would not be sorted >>>>> correctly ( >>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hello Sotirios, >>>>> >>> >>>>> >>> There is no `last value` stored anywhere. >>>>> >>> The code simply look for the PSCID with the max value and increase >>>>> that >>>>> >>> value by 1 in order to generate the next PSCID. >>>>> >>> >>>>> >>> Hope this info help. >>>>> >>> >>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | McGill >>>>> >>> University >>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>> >>> >>>>> >>> ------------------------------ >>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>> >>> Nikoloutsopoulos >>>>> >>> *Sent:* September 13, 2019 9:43 >>>>> >>> *To:* Christine Rogers, Ms. >>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> how does Loris determine the next available PSCID value for a new >>>>> >>> candidate? >>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>> >>> e.x in the default case the PSCID is sequential, but where do we >>>>> store the >>>>> >>> last value for the sequential sequence? >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>> Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> the parameters in the mri_protocol you have assigned are global >>>>> >>> standard? or were assigned after trial and error? >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> Given you have done the initial setup of your tables to match your >>>>> >>> intended protocol/parameters according to instructions -- >>>>> >>> the Troubleshooting guide documentation recommends >>>>> >>> < >>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>> > >>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> *if i were to change their status to resolve what would happen? >>>>> >>> >>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>> < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> I noticed that i can view the mnics at the brainbrowser from the >>>>> >>> mri_violations page ( those mnics are stored at >>>>> /data/loris/data/trashbin/ >>>>> >>> if i were to click their issue to resolve what would happend? >>>>> would they >>>>> >>> appear in the dicom_archive view too? ). >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>> < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> The defaut values of the schema exists in my local database. If i >>>>> adjust >>>>> >>> the default values of TR_min and TE_min the mincs will be uploaded? >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> Is it possible that you haven't set up your mri_protocol table ? >>>>> (and >>>>> >>> mri_scan_type table too, for additional types of scans) >>>>> >>> >>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>> insertion >>>>> >>> setup : See the install/setup documentation : >>>>> >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>> >>> >>>>> >>> To add new rows, just use MySQL insert statements. You can adapt >>>>> the >>>>> >>> insert statements which load the default table values --> e.g. >>>>> Here on >>>>> >>> GitHub : >>>>> >>> >>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>> >>> (see also the mri_scan_type table) >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> I see that i can edit the values but not how to insert new rows. >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> If i choose Inserted with flag then will the minc be inserted? >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>> >>> >>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>> >>> >>>>> >>> It says "could not identify scan type", which we knew already. >>>>> Did you >>>>> >>> click on the link on those words? >>>>> >>> >>>>> >>> It will take you to the next page of the module, showing for each >>>>> scan >>>>> >>> what the scan parameters were, and will also show for comparison >>>>> what's >>>>> >>> stored in your *mri_protocol* table. >>>>> >>> Compare these values to find which parameter was not correct >>>>> according >>>>> >>> to your *mri_protocol* table scan type definitions. >>>>> >>> >>>>> >>> You may end up broadening your mri_protocol value ranges (e.g. TR, >>>>> TE) >>>>> >>> for scans. >>>>> >>> This can be done in the front-end, by editing the database table >>>>> >>> directly in the same subpage of the MRI Violations module. >>>>> >>> >>>>> >>> The MRI Violations module features are explained in more detail in >>>>> the >>>>> >>> Help text for this module inside LORIS (click the ["?"] icon in >>>>> the menu >>>>> >>> bar.) >>>>> >>> >>>>> >>> See also: Loris-MRI troubleshooting guide >>>>> >>> < >>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>> > >>>>> >>> : no MINCs inserted- violated scans >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> looks like my previous email's attachment wasn't delivered due to >>>>> >>> security reasons, i uploaded my file at google drive >>>>> >>> >>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>> >>> >>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>> < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> For the mri_violations i attached the .html output from >>>>> webbrowser, so >>>>> >>> that you can check the filelds easier. >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios -- >>>>> >>> Great, sounds like more progress. >>>>> >>> >>>>> >>> About the dcmodify command -- I'm not sure why you're getting an >>>>> Endian >>>>> >>> warning. (it's a warning not an error, correct?) >>>>> >>> To clarify -- Were the DICOM headers (PatientName) all successfully >>>>> >>> relabelled, after the command ran? >>>>> >>> >>>>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) to >>>>> >>> verify and/or update local DICOM headers -- though your dcmodify >>>>> command is >>>>> >>> a great and fast solution for bulk header updates. >>>>> >>> >>>>> >>> If you're concerned about fields being changed (e.g. "(2001,105f)" >>>>> from >>>>> >>> the warning message) - you can also dcmdump a DICOM slice before >>>>> and look >>>>> >>> at these fields specifically. >>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>> before/after >>>>> >>> running dcmodify, and use dcmdump on each version to diff the >>>>> outputs -- >>>>> >>> this will pinpoint what changed. >>>>> >>> >>>>> >>> Re the protocol violation -- AcquisitionProtocol not recognized or >>>>> >>> unknown : this means your scans did not match what is stored in >>>>> your >>>>> >>> mri_protocol table. >>>>> >>> Check the MRI Violations front-end module -- can you see why they >>>>> didn't >>>>> >>> match? >>>>> >>> Send us an example, in addition to the contents of the mri_protocol >>>>> >>> table, if you can't find the source of the mismatch. >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> >>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Here is the psc table >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> I created 2 candidates profiles through the interface >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> then runned dcmodify command to a dicom file >>>>> >>> >>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>> >>> >>>>> >>> and got those warning: is this okay? >>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>> reading a >>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>> reading a >>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>> >>> W: Found element (2005,1402) with VR UN and undefined length, >>>>> reading a >>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>> >>> W: Found element (2005,140f) with VR UN and undefined length, >>>>> reading a >>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>> reading a >>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>> reading a >>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>> >>> >>>>> >>> dcmodify at another Dicom didn't show warnings. Below you can see >>>>> the >>>>> >>> execution for the second dicom. Mnics could not be inserted due to >>>>> >>> AcquisitionProtocol being unknown. >>>>> >>> >>>>> >>> Running now the following command: >>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>> >>> >>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >>>>> >>> -delete >>>>> >>> >>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>> >>> Target: /data/loris/data/tarchive >>>>> >>> >>>>> >>> Testing for database connectivity. >>>>> >>> Database is available. >>>>> >>> >>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>> >>> >>>>> >>> You are creating a tar with the following command: >>>>> >>> >>>>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>> >>> ImagingUpload-18-36-mTrxXs >>>>> >>> >>>>> >>> >>>>> >>> getting md5sums and gzipping!! >>>>> >>> >>>>> >>> * Taken from dir : >>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>> >>> * Archive target location : >>>>> >>> >>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>> >>> * Name of creating host : 127.0.1.1 >>>>> >>> * Name of host OS : Linux >>>>> >>> * Created by user : lorisadmin >>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>> >>> * dicomSummary version : 1 >>>>> >>> * dicomTar version : 1 >>>>> >>> * md5sum for DICOM tarball : >>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>> >>> * md5sum for DICOM tarball gzipped : >>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>> >>> * md5sum for complete archive : >>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>> >>> >>>>> >>> Adding archive info into database >>>>> >>> >>>>> >>> Removing temporary files from target location >>>>> >>> >>>>> >>> >>>>> >>> Done adding archive info into database >>>>> >>> >>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>> -globLocation >>>>> >>> -profile prod >>>>> >>> >>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>> >>> -uploadID 12 -verbose >>>>> >>> md5sum >>>>> >>> >>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>> >>> PSCID is: DCC0001 >>>>> >>> CandID id: 602102 >>>>> >>> visit_label is: V1 >>>>> >>> PSCID is: DCC0001 >>>>> >>> CandID id: 602102 >>>>> >>> visit_label is: V1 >>>>> >>> candidate id 602102 >>>>> >>> Set centerID = 1 >>>>> >>> PSCID is: DCC0001 >>>>> >>> CandID id: 602102 >>>>> >>> visit_label is: V1 >>>>> >>> PSCID is: DCC0001 >>>>> >>> CandID id: 602102 >>>>> >>> visit_label is: V1 >>>>> >>> >>>>> >>> Number of MINC files that will be considered for inserting into the >>>>> >>> database: 2 >>>>> >>> >>>>> >>> log dir is /data/loris/data//logs and log file is >>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>> >>> PSCID is: DCC0001 >>>>> >>> CandID id: 602102 >>>>> >>> visit_label is: V1 >>>>> >>> PSCID is: DCC0001 >>>>> >>> CandID id: 602102 >>>>> >>> visit_label is: V1 >>>>> >>> candidate id 602102 >>>>> >>> >>>>> >>> log dir is /data/loris/data//logs and log file is >>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>> >>> PSCID is: DCC0001 >>>>> >>> CandID id: 602102 >>>>> >>> visit_label is: V1 >>>>> >>> PSCID is: DCC0001 >>>>> >>> CandID id: 602102 >>>>> >>> visit_label is: V1 >>>>> >>> candidate id 602102 >>>>> >>> >>>>> >>> Cleaning up temp files: rm -rf >>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>> >>> >>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>> cat >>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>> >>> >>>>> >>> ==> Loading file from disk >>>>> >>> >>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>> >>> >>>>> >>> --> mapping DICOM parameter for >>>>> >>> >>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>> >>> >>>>> >>> ==> computing md5 hash for MINC body. >>>>> >>> >>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>> >>> >>>>> >>> ==> verifying acquisition protocol >>>>> >>> >>>>> >>> Acquisition protocol is unknown >>>>> >>> >>>>> >>> --> The minc file cannot be registered since the >>>>> AcquisitionProtocol >>>>> >>> is unknown >>>>> >>> >>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios: >>>>> >>> >>>>> >>> Sure -- you can delete imaging datasets with the >>>>> *delete_imaging_upload* >>>>> >>> script -- >>>>> >>> details here: >>>>> >>> >>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>> >>> >>>>> >>> What's in your *psc* table? (Is it properly populated? This is a >>>>> >>> pre-requisite to loading imaging data. >>>>> >>> < >>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>> > >>>>> >>> ) >>>>> >>> The foreign key constraint error on the candidate record is >>>>> curious. >>>>> >>> >>>>> >>> There are also a few options for creating candidates when inserting >>>>> >>> imaging data: >>>>> >>> >>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion pipeline >>>>> >>> >>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>> optionally I >>>>> >>> think) >>>>> >>> How to: >>>>> >>> >>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>> >>> >>>>> >>> Then as a second step: >>>>> >>> b. Use the imaging insertion pipeline >>>>> >>> < >>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>> > >>>>> >>> to load your DICOMs. >>>>> >>> You will want to first ensure that the PatientName header in the >>>>> DICOMs >>>>> >>> as well as tar package are correctly labelled with >>>>> PSCID_DCCID_VisitLabel >>>>> >>> >>>>> >>> -- Method 2: for BIDS-format datasets: >>>>> >>> How to : >>>>> >>> >>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>> >>> >>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>> bids_import script, >>>>> >>> to automatically create your candidates and sessions. >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> How do i delete a Study? And everytime do i have to create a new >>>>> >>> candidate to get DCCID and a PSCID? >>>>> >>> >>>>> >>> *First execution:* >>>>> >>> >>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>> ./ >>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>> ~/Desktop/input.txt > >>>>> >>> log.txt >>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>> foreign >>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>> `FK_candidate_1` >>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>> (`CenterID`)) at >>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>> >>> The following database commands failed: >>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>> (?,?,?,?,?)'; >>>>> >>> SET >>>>> >>> >>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>> >>> Medical Systems'; >>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>> >>> Error obtained:Cannot add or update a child row: a foreign key >>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>> `FK_mri_scanner_1` >>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error >>>>> code 1452) >>>>> >>> >>>>> >>> ERROR: The validation has failed. Either re-run the validation >>>>> again >>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to >>>>> force the >>>>> >>> execution. >>>>> >>> >>>>> >>> >>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>> >>> print() on closed filehandle MAIL at ./ >>>>> batch_uploads_imageuploader.pl >>>>> >>> line 250. >>>>> >>> print() on closed filehandle MAIL at ./ >>>>> batch_uploads_imageuploader.pl >>>>> >>> line 251. >>>>> >>> >>>>> >>> >>>>> >>> *And second execution: * >>>>> >>> >>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>> ./ >>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>> ~/Desktop/input.txt > >>>>> >>> log.txt >>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>> >>> >>>>> >>> PROBLEM: >>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>> >>> The unique study ID is '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>> >>> This is the information retained from the first time the study was >>>>> >>> inserted: >>>>> >>> >>>>> >>> * Taken from dir : >>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>> >>> * Archive target location : >>>>> >>> >>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>> >>> * Name of creating host : 127.0.1.1 >>>>> >>> * Name of host OS : Linux >>>>> >>> * Created by user : lorisadmin >>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>> >>> * dicomSummary version : 1 >>>>> >>> * dicomTar version : 1 >>>>> >>> * md5sum for DICOM tarball : >>>>> 4a301b0318178b09b91e63544282364d >>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>> >>> * md5sum for DICOM tarball gzipped : >>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>> >>> * md5sum for complete archive : >>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>> >>> >>>>> >>> >>>>> >>> Last update of record: >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> The dicomTar.pl execution has failed. >>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>> >>> print() on closed filehandle MAIL at ./ >>>>> batch_uploads_imageuploader.pl >>>>> >>> line 250. >>>>> >>> print() on closed filehandle MAIL at ./ >>>>> batch_uploads_imageuploader.pl >>>>> >>> line 251. >>>>> >>> >>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> Ok, this sounds like good progress. Let us know when you next >>>>> encounter >>>>> >>> issues as you progress through the Imaging Install/Setup docs >>>>> >>> . >>>>> >>> I'll look into how we can better handle the incoming/ directory >>>>> next >>>>> >>> time. >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>> >>> populated correctly except its port is 'port' : ''. Also i >>>>> have tested >>>>> >>> that i can connect to MySQL with lorisuser. >>>>> >>> >>>>> >>> I executed the script again, because the only error i had >>>>> previously was >>>>> >>> that the /data/incoming folder didn't exist and there are no errors >>>>> >>> reported back except of warnings <>>>> password on the >>>>> >>> command line interface can be insecure>>. >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> It's possible -- if the script was unable to connect to the >>>>> database >>>>> >>> during its execution (e.g. typo in the password), that would >>>>> explain the >>>>> >>> underpopulated Image path and Loris-MRI code path you saw in the >>>>> Config >>>>> >>> module. >>>>> >>> It's hard to tell without seeing the output from your script run >>>>> -- Did >>>>> >>> you see a sign of any such error? >>>>> >>> The Config fields are populated by the imaging_install.sh script >>>>> (starting >>>>> >>> at line 222 >>>>> >>> < >>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>> > >>>>> >>> ) >>>>> >>> >>>>> >>> For example, check if the database connection information was >>>>> populated >>>>> >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> Hi Christine, >>>>> >>> >>>>> >>> If you are referring to the imaging_install.sh here is an image >>>>> with the >>>>> >>> configurations i typed. Maybe the problem is somewhere at the last >>>>> part >>>>> >>> which asks to configure as much as possible automatically? >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>> >>> >>>>> >>> Hi Sotirios, >>>>> >>> >>>>> >>> Glad to hear your LORIS core install is up and working and all the >>>>> >>> front-end pages are loading. >>>>> >>> >>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>>>> >>> > and the web interface worked. >>>>> >>> >>>>> >>> Yes, it's important that project/ have 775 permissions and that >>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the install >>>>> >>> Readme . >>>>> >>> >>>>> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS to >>>>> >>> loris, right? >>>>> >>> >>>>> >>> These imaging paths will be updated during your imaging >>>>> installation >>>>> >>> by an automated script >>>>> -- >>>>> >>> you do not need to set them manually via the Config module. >>>>> >>> Please continue to follow the Setup Guide >>>>> >>> for detailed steps to >>>>> follow. >>>>> >>> >>>>> >>> Best, >>>>> >>> Christine >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>> >>> sotirisnik at gmail.com> wrote: >>>>> >>> >>>>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS to >>>>> loris, >>>>> >>> right? >>>>> >>> >>>>> >>> [image: image.png] >>>>> >>> >>>>> >>> >>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>> < >>>>> >>> sotirisnik at gmail.com> ??????: >>>>> >>> >>>>> >>> Hi, >>>>> >>> >>>>> >>> i used >>>>> >>> >>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>> >>> sudo apt-get install -y nodejs >>>>> >>> >>>>> >>> >>>>> >>> you had suggested in the past, make worked and now i can see all >>>>> the >>>>> >>> contents in the web-interface, but i don't need make install? >>>>> >>> >>>>> >>> Thanks >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> >>> >>>>> >>> -- >>>>> >>> >>>>> >>> christine.rogers at mcgill.ca >>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> >>> Montreal Neurological Institute >>>>> >>> McGill University | Montreal | Canada >>>>> >>> >>>>> >>> _______________________________________________ >>>>> >>> Loris-dev mailing list >>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>> >>>>> >>> >>>>> -------------- next part -------------- >>>>> An HTML attachment was scrubbed... >>>>> URL: < >>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>> > >>>>> >>>>> ------------------------------ >>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>>> >>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>> ***************************************** >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> >> christine.rogers at mcgill.ca >> McGill Centre for Integrative Neuroscience | MCIN.ca >> Montreal Neurological Institute >> McGill University | Montreal | Canada >> > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at gmail.com Thu Nov 21 09:55:45 2019 From: cecile.madjar at gmail.com (Cecile Madjar) Date: Thu, 21 Nov 2019 09:55:45 -0500 Subject: [Loris-dev] Error in Loris 21.0.0 In-Reply-To: References: Message-ID: Hi Iris, Unfortunately, I have no idea but I have cc'ed the loris-dev mailing list hoping someone in the team can help you with this. Best, C?cile On Thu, Nov 21, 2019 at 9:50 AM Iris Rodriguez wrote: > Hi Cecile how are you?, > > I am installing Loris 21.0.0 in a new server with Ubutnu 16.0.4, I > verified all requirement of installation, but after the run install.sh and > run make, I obtain this error: > > Makefile:4 recipe for target 'all ' failed > make:*** [all] Error 1 > I use only make for production server. > > [image: image.png] > > > An idea about this error in ubuntu server 16.04 lts, how solve this issue > please?, > > Thank you very much, > > Iris > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 124081 bytes Desc: not available URL: From lingyun.ma at mcin.ca Thu Nov 21 10:10:12 2019 From: lingyun.ma at mcin.ca (Ling Ma) Date: Thu, 21 Nov 2019 10:10:12 -0500 Subject: [Loris-dev] Error in Loris 21.0.0 In-Reply-To: References: Message-ID: Hi, I suggest you verify to make sure that you have the latest or at least recent composer and nodejs. Good luck. Ling Ma Consultant developer On Thu, Nov 21, 2019 at 9:56 AM Cecile Madjar wrote: > Hi Iris, > > Unfortunately, I have no idea but I have cc'ed the loris-dev mailing list > hoping someone in the team can help you with this. > > Best, > > C?cile > > On Thu, Nov 21, 2019 at 9:50 AM Iris Rodriguez > wrote: > >> Hi Cecile how are you?, >> >> I am installing Loris 21.0.0 in a new server with Ubutnu 16.0.4, I >> verified all requirement of installation, but after the run install.sh and >> run make, I obtain this error: >> >> Makefile:4 recipe for target 'all ' failed >> make:*** [all] Error 1 >> I use only make for production server. >> >> [image: image.png] >> >> >> An idea about this error in ubuntu server 16.04 lts, how solve this issue >> please?, >> >> Thank you very much, >> >> Iris >> >> _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 124081 bytes Desc: not available URL: From irita1909 at gmail.com Thu Nov 21 10:33:57 2019 From: irita1909 at gmail.com (Iris Rodriguez) Date: Thu, 21 Nov 2019 10:33:57 -0500 Subject: [Loris-dev] Error in Loris 21.0.0 In-Reply-To: References: Message-ID: Thanks for the tip! El jue., 21 nov. 2019 a las 10:10, Ling Ma () escribi?: > Hi, > > I suggest you verify to make sure that you have the latest or at least > recent composer and nodejs. > > Good luck. > > Ling Ma > Consultant developer > > > On Thu, Nov 21, 2019 at 9:56 AM Cecile Madjar > wrote: > >> Hi Iris, >> >> Unfortunately, I have no idea but I have cc'ed the loris-dev mailing list >> hoping someone in the team can help you with this. >> >> Best, >> >> C?cile >> >> On Thu, Nov 21, 2019 at 9:50 AM Iris Rodriguez >> wrote: >> >>> Hi Cecile how are you?, >>> >>> I am installing Loris 21.0.0 in a new server with Ubutnu 16.0.4, I >>> verified all requirement of installation, but after the run install.sh and >>> run make, I obtain this error: >>> >>> Makefile:4 recipe for target 'all ' failed >>> make:*** [all] Error 1 >>> I use only make for production server. >>> >>> [image: image.png] >>> >>> >>> An idea about this error in ubuntu server 16.04 lts, how solve this >>> issue please?, >>> >>> Thank you very much, >>> >>> Iris >>> >>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 124081 bytes Desc: not available URL: From AMORALESPINZON at bwh.harvard.edu Thu Nov 21 11:27:23 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Thu, 21 Nov 2019 16:27:23 +0000 Subject: [Loris-dev] Upgrade Loris from v21.0.0 to v21.0.4 Message-ID: <1243FD52-4A20-4225-AD9B-F207951A4510@bwh.harvard.edu> Dear LorisDev team, Are they any instructions on how to upgrade Loris from v21.0.0 to v21.0.4? I cannot find them in release notes (https://github.com/aces/Loris/releases/tag/v21.0.4). Maybe I just need to upgrade the code but I?m not sure. Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lingyun.ma at mcin.ca Thu Nov 21 11:33:37 2019 From: lingyun.ma at mcin.ca (Ling Ma) Date: Thu, 21 Nov 2019 11:33:37 -0500 Subject: [Loris-dev] Upgrade Loris from v21.0.0 to v21.0.4 In-Reply-To: <1243FD52-4A20-4225-AD9B-F207951A4510@bwh.harvard.edu> References: <1243FD52-4A20-4225-AD9B-F207951A4510@bwh.harvard.edu> Message-ID: Hi, I would suggest a migration with a separate installation, make some adjustments if necessary, then make the final upgrading when you are satisfied with the result. Best regards, Ling Ma Consultant developer On Thu, Nov 21, 2019 at 11:27 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > Are they any instructions on how to upgrade Loris from v21.0.0 to v21.0.4? > I cannot find them in release notes ( > https://github.com/aces/Loris/releases/tag/v21.0.4). Maybe I just need to > upgrade the code but I?m not sure. > > Best regards, > Alfredo. > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Sat Nov 23 19:28:08 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sun, 24 Nov 2019 02:28:08 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Cecile, i executed the find command and the output i got per folder was "DICOM medical imaging data. Maybe there is something wrong with the find command in the warning that it is unable to check if the file is a dicom file? Also when i use get_dicom_info.pl i don't get any output data. Finally i don't understand what scout or localizer is ( something like if and only if a file fails then the whole session is invalid? ). [image: image.png] Thanks Sotirios ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < cecile.madjar at mcin.ca> ??????: > Hi Sotirios, > > I took a closer look to the batch_uploader_multiple_output.txt file you > sent. It looks like there are different reasons for failure depending on > the DICOM folder uploaded. > > - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1: it > looks like there is no file of type DICOM in the folder. Have you checked > to see if that is indeed the case? Maybe you can try running the following > command on that folder to see what are the types of the files? If it does > not return at least one DICOM medical imaging data file, then that is why > you get the error message from the pipeline: > - > > find -type f | xargs -i file {}|cut -d: -f2|sort|uniq > > - For 864173 DCC0001 V1: it looks like there are two different > DICOM studies within the same folder. You will need to split that study in > two based on the StudyUID field as the insertion pipeline does not allow > for more than one StudyUID per upload. > - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1: it > looks like the dcm2mnc command did not produce any MINC files. Can you > check in the DICOM archive what are the series present in the tarchive for > that visit? Maybe only a scout or localizer was acquired for that session, > hence the no valid MINC files (scout and localizer being skipped for the > conversion) > - For 397410 DCC0003 V1: it looks like everything went well for this > one. > > One script that is called by our pipeline is called get_dicom_info.pl and > this does all kind of checks on the DICOM files (it is being called when > running the dcm2mnc conversion). You could run it independently on your > folder if needed. > > Since one of the study got in, it does not look like you are having a > problem with the setup. It seems more likely to be a problem with the data > themselves. > > Hope this helps. > > C?cile > > On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Christine, >> >> In my first vm i am able to create the minc files and view them at the >> mri browser (except of candidate 102761034 ), meanwhile the same files >> gives warnings at the 2nd vm. The output of the batch upload can be seen >> in the file attached. >> Also a colleague of us has built a pre-validation tool for dicom >> https://github.com/aueb-wim/DataQualityControlTool/ which had found all >> the files that Loris gave as warning . Basically I confirmed that the total >> amount of files per dicom was the same amount as stated in Loris and >> checked some filenames given from warning to confirm that they match with >> our tool. But that was months ago and my colleague had changed some >> parameters for MIP and now our tool doesn't find all the invalid files, >> that's why i asked for the dicom header specification of Loris. In a >> discussion we had he mentioned that he doesn't check for some tags e.x. >> orientation. Lastly to mention that in my first vm i didn't use our tool to >> remove invalid dcm files. >> >> Thanks >> >> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios, >>> Can you provide us with some fresh particulars of the current issue and >>> we'll take it from there? >>> Yang's team has built these scripts which can definitely serve as a >>> model for your pre-validation of your DICOM collections. >>> cheers, >>> Christine >>> >>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> HI Yang, >>>> >>>> We make use of pydicom library too. Now about the validate.py i see >>>> that you check if some attributes are missing such as PatientID, >>>> PatientName which all of our files contains that info. Maybe i have missed >>>> something on the setup of my other virtual machine ( although one dicom >>>> passed on the new vm successfully, the others that were inserted correctly >>>> on my old vm fails on the new one ), i think that i had asked about this >>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but i >>>> don't remember the solution. >>>> >>>> Thanks >>>> >>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>> ??????: >>>> >>>>> Hey, Sotirios, >>>>> >>>>> Christine from the LORIS team mentioned you had some issue with >>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>> fully automated pipeline actually. >>>>> >>>>> While we were building CNBP, we had coded up some minor Python >>>>> functions to check DICOM integrity (and simple validations) and you might >>>>> be able to gain some inspiration from it and help you with your cause. For >>>>> more comprehensive solution, PyDICOM ( >>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>> like a descent python package to help out with a lot of DICOM data checks >>>>> (I was essentially just building customized wrapper calls to them). You can >>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>> rough around the edges but hopefully point you in the right direcitons >>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>> >>>>> Cheers, >>>>> >>>>> Yang Ding, PhD. >>>>> Canadian Neonatal Brain Platform Architect >>>>> >>>>> On Tue, Nov 12, 2019 at 8:29 AM >>>>> wrote: >>>>> >>>>>> Send Loris-dev mailing list submissions to >>>>>> loris-dev at bic.mni.mcgill.ca >>>>>> >>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> or, via email, send a message with subject or body 'help' to >>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>> >>>>>> You can reach the person managing the list at >>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>> >>>>>> When replying, please edit your Subject line so it is more specific >>>>>> than "Re: Contents of Loris-dev digest..." >>>>>> >>>>>> >>>>>> Today's Topics: >>>>>> >>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>> >>>>>> >>>>>> ---------------------------------------------------------------------- >>>>>> >>>>>> Message: 1 >>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>> From: Sotirios Nikoloutsopoulos >>>>>> To: Cecile Madjar >>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>> Message-ID: >>>>>> >>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>> Content-Type: text/plain; charset="utf-8" >>>>>> >>>>>> Hi, >>>>>> >>>>>> Could we send you a link with 10 anonymized dicom files to diagnose >>>>>> the >>>>>> warnings we get? >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>> > Hi Cecile, >>>>>> > >>>>>> > We were wondering whether Loris has a tool to check if there are >>>>>> problems >>>>>> > with the dcm files, before trying to upload them. Something that >>>>>> could >>>>>> > provide the same results provided in the warning_output, this is the >>>>>> > summary from the mri_upload at the front-page. Also which >>>>>> attributes of the >>>>>> > dcm header would trigger a warning? is there a dcm file header >>>>>> > specification for Loris? >>>>>> > >>>>>> > Thanks >>>>>> > >>>>>> > Sotirios >>>>>> > >>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>>> < >>>>>> > sotirisnik at gmail.com> ??????: >>>>>> > >>>>>> >> Hi, >>>>>> >> >>>>>> >> Yes, by parsing now() into unix_timestamp function it worked,but i >>>>>> >> thought that something else was causing the 2nd issue. >>>>>> >> Thanks >>>>>> >> >>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>> >> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> The first error occurs because the QCFirstChangeTime and columns >>>>>> are of >>>>>> >>> type `unsigned integer` and not `datatime`. You should be using >>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>> >>> >>>>>> >>> The second error occurs because the trigger triggers a rollback >>>>>> of the >>>>>> >>> insert statement in the files table. >>>>>> >>> See mysql documentation for trigger error handling. >>>>>> >>> >>>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>>> failure of >>>>>> >>> the entire statement that caused trigger invocation. >>>>>> >>> >>>>>> >>> >>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>> >>> -- Xavier >>>>>> >>> >>>>>> >>> ------------------------------ >>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>> >>> Nikoloutsopoulos >>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>> >>> *To:* Cecile Madjar >>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca ; >>>>>> >>> Christine Rogers, Ms. >>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>> >>> >>>>>> >>> When mincs are inserted their corresponding rows at the file >>>>>> table are >>>>>> >>> inserted too >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>>> because i >>>>>> >>> don't want manually to label them as passed throught the interface >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> That is the trigger i wrote >>>>>> >>> >>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>> >>> BEGIN >>>>>> >>> INSERT INTO files_qcstatus >>>>>> >>> SET FileID = NEW.FileID, >>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>> >>> EchoTime = NEW.EchoTime, >>>>>> >>> QCStatus = "Pass", >>>>>> >>> QCFirstChangeTime = NOW(), >>>>>> >>> QCLastChangeTime = NOW(); >>>>>> >>> END >>>>>> >>> >>>>>> >>> although it contains some errors >>>>>> >>> >>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>> foreign >>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` >>>>>> (`FileID`)) >>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> In the mri_upload table, there is a TarchiveID column associated >>>>>> with >>>>>> >>> the MRI upload you inserted. When this value is NULL, it means no >>>>>> DICOMs >>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>> insertion of the >>>>>> >>> DICOMs in the tarchive tables, this value is updated with the >>>>>> correct >>>>>> >>> TarchiveID associated with the upload. >>>>>> >>> >>>>>> >>> Could this correspond to what you want to do? >>>>>> >>> >>>>>> >>> Regarding the files_qcstatus, this table is only linked to the >>>>>> files >>>>>> >>> table (hence, the MINC files). You could always create a new >>>>>> table for >>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>> >>> >>>>>> >>> C?cile >>>>>> >>> >>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>> >>> coressponding qc_status to "pass". I was thinking of creating a >>>>>> trigger for >>>>>> >>> that, but which tables do i need to add entries to? So far from >>>>>> what i see >>>>>> >>> i need to add entres at the table "files" whenever an insertion >>>>>> happens to >>>>>> >>> files_qcstatus. >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning of my >>>>>> email >>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>> >>> >>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i >>>>>> am >>>>>> >>> looking for is not stored in the database? >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> Thanks. >>>>>> >>> >>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>> >>> tarchive table. It can also be found in the metadata field but it >>>>>> is mixed >>>>>> >>> with many other information. >>>>>> >>> >>>>>> >>> Hope this helps, >>>>>> >>> >>>>>> >>> C?cile >>>>>> >>> >>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive table, >>>>>> >>> specifically at the AcquisitonMetadata column i found something >>>>>> called >>>>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>>>> Instance UID. >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Your observation is correct. A little explanation below. >>>>>> >>> >>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>> >>> >>>>>> >>> - the scan type could not be identified (not matching an entry >>>>>> in >>>>>> >>> the mri_protocol table) >>>>>> >>> - one parameter of the scan type is out of the expected range >>>>>> >>> present in the mri_protocol_checks (extra filtering in case >>>>>> you need to be >>>>>> >>> stricker on some parameters not present in the mri_protocol >>>>>> table) >>>>>> >>> - if the CandID and PSCID do not match >>>>>> >>> >>>>>> >>> The following cases do not get in the MRI violation tables as it >>>>>> happens >>>>>> >>> before the conversion of the DICOM to MINC files and only MINC >>>>>> files >>>>>> >>> violations are logged there: >>>>>> >>> >>>>>> >>> - "No single DICOM" (since no valid DICOM could be found to >>>>>> convert >>>>>> >>> to MINC) >>>>>> >>> - "Study already inserted" (duplicate StudyUID) since this >>>>>> error >>>>>> >>> happens at the dicomTar.pl level (way before conversion into >>>>>> MINC files) >>>>>> >>> >>>>>> >>> Glad everything is working out!! >>>>>> >>> Best, >>>>>> >>> >>>>>> >>> C?cile >>>>>> >>> >>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now >>>>>> about the >>>>>> >>> mri_violations, dicoms are triggered to be inserted there only if >>>>>> there is >>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>> parameter? >>>>>> >>> Because i don't see the cases of 'No single dicom" or with the 2 >>>>>> studyiuid >>>>>> >>> to be there. >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Sorry to hear you are having issues with the memory. I think most >>>>>> of our >>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>> >>> >>>>>> >>> Hope this helps! >>>>>> >>> >>>>>> >>> C?cile >>>>>> >>> >>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> about that dicom that had that insertion error it's about 30mb >>>>>> and when >>>>>> >>> it is being processed the ram is being drastically increased from >>>>>> 2gb to >>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is the >>>>>> recommended >>>>>> >>> size of ram for using Loris? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>> >>> >>>>>> >>> For the delete script issue, if you are absolutely certain that no >>>>>> >>> processes are run for that uploadID, you can update the >>>>>> mri_upload table >>>>>> >>> and set the column Inserting to 0 instead of 1 for that uploadID. >>>>>> It >>>>>> >>> looks like for some reason the scripts did not update this field >>>>>> when it >>>>>> >>> stopped the insertion. Not sure why that would be the case though. >>>>>> >>> Note: only do that update if you are certain that there is no >>>>>> processing >>>>>> >>> happening. >>>>>> >>> >>>>>> >>> Hope this helps! >>>>>> >>> >>>>>> >>> >>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>>> actually do >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> I thought that this might be a permission because "w" was missing >>>>>> at the >>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but with >>>>>> no mnic >>>>>> >>> files. Also now i have this error >>>>>> >>> >>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>> :/data/loris/bin/mri/tools$ >>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently processing >>>>>> it. >>>>>> >>> >>>>>> >>> How can solve this? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> Here is our auto dicom uploading python script: >>>>>> >>> >>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>> >>> >>>>>> >>> To give you a brief idea: >>>>>> >>> Per folder it will: >>>>>> >>> 1) Delete all the .bak files >>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>> TE_min, >>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>> mri_protocol table >>>>>> >>> >>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>> >>> For some reason some files are missing >>>>>> SeriesDescription/ProtocolName >>>>>> >>> >>>>>> >>> In total i have 7 folders >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> 3/7 passed >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> Also about the first patient with DC0000 had a violation "T1 >>>>>> AXIAL SE >>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i find >>>>>> that weird >>>>>> >>> since Loris detects the SeriesDescription. >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> Now about the 4/7 that didn't passed >>>>>> >>> >>>>>> >>> 102327840 and 102809579 outputs "The target directory does not >>>>>> contain a >>>>>> >>> single DICOM file.", therefore they are missing their StudyUID >>>>>> >>> >>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from multiple >>>>>> >>> studies." >>>>>> >>> >>>>>> >>> and 102761034 "No data could be converted into valid MINC files. >>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>> >>> >>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 and >>>>>> 102506134 >>>>>> >>> can i just pass a flag parameter to >>>>>> batch_uploads_imageuploader.pl? or >>>>>> >>> modify imaging_upload_file.pl? >>>>>> >>> >>>>>> >>> Thank you, >>>>>> >>> >>>>>> >>> Sotirios >>>>>> >>> >>>>>> >>> PS >>>>>> >>> >>>>>> >>> To diagnose a folder search the name of the folder at >>>>>> dicom_output.txt. >>>>>> >>> >>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> Glad to hear about your progress. >>>>>> >>> >>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>> documented here >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>> > >>>>>> >>> -- let us know if you didn't find the answers you were looking >>>>>> for there. >>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>> database >>>>>> >>> management software is a visual placeholder for you as the user? >>>>>> I'm not >>>>>> >>> sure why a scanner would ever be registered with ID='0' as your >>>>>> screenshot >>>>>> >>> showed.) >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> I fixed it with this >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> I tried to create a new candidate using the API, is there >>>>>> something >>>>>> >>> wrong with the structure? why did i receive a 500 internal error? >>>>>> In the >>>>>> >>> loris-error log it state that there is something wrong with >>>>>> token, but i >>>>>> >>> verfied that the type of the token is a string. >>>>>> >>> >>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument 1 >>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the type >>>>>> string, >>>>>> >>> null given, called in >>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>>> 169 and >>>>>> >>> defined in >>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>> >>> trace:\n#0 >>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n >>>>>> thrown in >>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>>> 192 >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> Is there a way also to delete candidates? Just to let you know >>>>>> what i >>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>> dependencies. >>>>>> >>> >>>>>> >>> First i deleted all their uploads >>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to >>>>>> omit >>>>>> >>> the backup file ? ) >>>>>> >>> >>>>>> >>> Afterwards i had some scanner candidates, so i deleted all the >>>>>> entries >>>>>> >>> from mri_scanner except that i couldn't delete this entry with >>>>>> the 0 ID. >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> We recommend that you use our existing tools for creating new >>>>>> candidates >>>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>>> calling the Candidate >>>>>> >>> class's createNew() >>>>>> >>> < >>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>> >function. >>>>>> >>> These will create the necessary records for you. (It's not >>>>>> recommended to >>>>>> >>> make direct modifications to mysql database tables in your >>>>>> script, if I >>>>>> >>> understand you.) >>>>>> >>> >>>>>> >>> The CandID should be a randomized 6 digit randomized ID, and >>>>>> there are >>>>>> >>> multiple reasons for this. >>>>>> >>> You can use the PSCID for project-specific IDs and the External >>>>>> ID field >>>>>> >>> in the candidate table can also be used for any values you like. >>>>>> >>> Additionally, any number of custom IDs can be added in parallel - >>>>>> these >>>>>> >>> are entered/visible in the Candidate Information module and added >>>>>> in the >>>>>> >>> back-end as candidate parameters. >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> We are building a script that will auto insert the candidates >>>>>> based on >>>>>> >>> their ExternalID. We would like to know whethere when we are >>>>>> creating a new >>>>>> >>> profile in the candidate table, if we also have to insert a new >>>>>> record at >>>>>> >>> another table? Furthermore is there a problem that in our case >>>>>> CandID won't >>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> That would normally be the case but the numeric part of the PSCID >>>>>> get >>>>>> >>> paded with 0 on the left. >>>>>> >>> >>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 numerical >>>>>> char >>>>>> >>> with a min value of 1, the sequence would be: >>>>>> >>> >>>>>> >>> ABC0001 >>>>>> >>> ABC0002 >>>>>> >>> ... >>>>>> >>> ABC0010 >>>>>> >>> ... >>>>>> >>> >>>>>> >>> thus sorting them ascending will always get the latest value >>>>>> generated >>>>>> >>> as the max value. >>>>>> >>> >>>>>> >>> M?lanie >>>>>> >>> >>>>>> >>> ------------------------------ >>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>> >>> *To:* Melanie Legault, Mrs >>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>> >>> >>>>>> >>> I see, although the PSCID value is varchar(255), it must be stored >>>>>> >>> within a specific length of characters. Otherwise if we were to >>>>>> sort >>>>>> >>> strings with different lengths the result would not be sorted >>>>>> correctly ( >>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hello Sotirios, >>>>>> >>> >>>>>> >>> There is no `last value` stored anywhere. >>>>>> >>> The code simply look for the PSCID with the max value and >>>>>> increase that >>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>> >>> >>>>>> >>> Hope this info help. >>>>>> >>> >>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | >>>>>> McGill >>>>>> >>> University >>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>> >>> >>>>>> >>> ------------------------------ >>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>> >>> Nikoloutsopoulos >>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>> >>> *To:* Christine Rogers, Ms. >>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> how does Loris determine the next available PSCID value for a new >>>>>> >>> candidate? >>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>> >>> e.x in the default case the PSCID is sequential, but where do we >>>>>> store the >>>>>> >>> last value for the sequential sequence? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> the parameters in the mri_protocol you have assigned are global >>>>>> >>> standard? or were assigned after trial and error? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Given you have done the initial setup of your tables to match your >>>>>> >>> intended protocol/parameters according to instructions -- >>>>>> >>> the Troubleshooting guide documentation recommends >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>> > >>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> *if i were to change their status to resolve what would happen? >>>>>> >>> >>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> I noticed that i can view the mnics at the brainbrowser from the >>>>>> >>> mri_violations page ( those mnics are stored at >>>>>> /data/loris/data/trashbin/ >>>>>> >>> if i were to click their issue to resolve what would happend? >>>>>> would they >>>>>> >>> appear in the dicom_archive view too? ). >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> The defaut values of the schema exists in my local database. If i >>>>>> adjust >>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>> uploaded? >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Is it possible that you haven't set up your mri_protocol table ? >>>>>> (and >>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>> >>> >>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>>> insertion >>>>>> >>> setup : See the install/setup documentation : >>>>>> >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>> >>> >>>>>> >>> To add new rows, just use MySQL insert statements. You can adapt >>>>>> the >>>>>> >>> insert statements which load the default table values --> e.g. >>>>>> Here on >>>>>> >>> GitHub : >>>>>> >>> >>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>> >>> (see also the mri_scan_type table) >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> I see that i can edit the values but not how to insert new rows. >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> If i choose Inserted with flag then will the minc be inserted? >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>> >>> >>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>> >>> >>>>>> >>> It says "could not identify scan type", which we knew already. >>>>>> Did you >>>>>> >>> click on the link on those words? >>>>>> >>> >>>>>> >>> It will take you to the next page of the module, showing for each >>>>>> scan >>>>>> >>> what the scan parameters were, and will also show for comparison >>>>>> what's >>>>>> >>> stored in your *mri_protocol* table. >>>>>> >>> Compare these values to find which parameter was not correct >>>>>> according >>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>> >>> >>>>>> >>> You may end up broadening your mri_protocol value ranges (e.g. >>>>>> TR, TE) >>>>>> >>> for scans. >>>>>> >>> This can be done in the front-end, by editing the database table >>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>> >>> >>>>>> >>> The MRI Violations module features are explained in more detail >>>>>> in the >>>>>> >>> Help text for this module inside LORIS (click the ["?"] icon in >>>>>> the menu >>>>>> >>> bar.) >>>>>> >>> >>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>> > >>>>>> >>> : no MINCs inserted- violated scans >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> looks like my previous email's attachment wasn't delivered due to >>>>>> >>> security reasons, i uploaded my file at google drive >>>>>> >>> >>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>> >>> >>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> For the mri_violations i attached the .html output from >>>>>> webbrowser, so >>>>>> >>> that you can check the filelds easier. >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios -- >>>>>> >>> Great, sounds like more progress. >>>>>> >>> >>>>>> >>> About the dcmodify command -- I'm not sure why you're getting an >>>>>> Endian >>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>> successfully >>>>>> >>> relabelled, after the command ran? >>>>>> >>> >>>>>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) >>>>>> to >>>>>> >>> verify and/or update local DICOM headers -- though your dcmodify >>>>>> command is >>>>>> >>> a great and fast solution for bulk header updates. >>>>>> >>> >>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>> "(2001,105f)" from >>>>>> >>> the warning message) - you can also dcmdump a DICOM slice before >>>>>> and look >>>>>> >>> at these fields specifically. >>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>> before/after >>>>>> >>> running dcmodify, and use dcmdump on each version to diff the >>>>>> outputs -- >>>>>> >>> this will pinpoint what changed. >>>>>> >>> >>>>>> >>> Re the protocol violation -- AcquisitionProtocol not recognized or >>>>>> >>> unknown : this means your scans did not match what is stored in >>>>>> your >>>>>> >>> mri_protocol table. >>>>>> >>> Check the MRI Violations front-end module -- can you see why they >>>>>> didn't >>>>>> >>> match? >>>>>> >>> Send us an example, in addition to the contents of the >>>>>> mri_protocol >>>>>> >>> table, if you can't find the source of the mismatch. >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> >>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Here is the psc table >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> I created 2 candidates profiles through the interface >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> then runned dcmodify command to a dicom file >>>>>> >>> >>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>> >>> >>>>>> >>> and got those warning: is this okay? >>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2005,1402) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2005,140f) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>> reading a >>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>> >>> >>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you can see >>>>>> the >>>>>> >>> execution for the second dicom. Mnics could not be inserted due to >>>>>> >>> AcquisitionProtocol being unknown. >>>>>> >>> >>>>>> >>> Running now the following command: >>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>> >>> >>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >>>>>> >>> -delete >>>>>> >>> >>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>> >>> Target: /data/loris/data/tarchive >>>>>> >>> >>>>>> >>> Testing for database connectivity. >>>>>> >>> Database is available. >>>>>> >>> >>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>> >>> >>>>>> >>> You are creating a tar with the following command: >>>>>> >>> >>>>>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>> >>> >>>>>> >>> >>>>>> >>> getting md5sums and gzipping!! >>>>>> >>> >>>>>> >>> * Taken from dir : >>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>> >>> * Archive target location : >>>>>> >>> >>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>> >>> * Name of host OS : Linux >>>>>> >>> * Created by user : lorisadmin >>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>> >>> * dicomSummary version : 1 >>>>>> >>> * dicomTar version : 1 >>>>>> >>> * md5sum for DICOM tarball : >>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>> >>> * md5sum for complete archive : >>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> >>>>>> >>> Adding archive info into database >>>>>> >>> >>>>>> >>> Removing temporary files from target location >>>>>> >>> >>>>>> >>> >>>>>> >>> Done adding archive info into database >>>>>> >>> >>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>> -globLocation >>>>>> >>> -profile prod >>>>>> >>> >>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>> >>> -uploadID 12 -verbose >>>>>> >>> md5sum >>>>>> >>> >>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> candidate id 602102 >>>>>> >>> Set centerID = 1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> >>>>>> >>> Number of MINC files that will be considered for inserting into >>>>>> the >>>>>> >>> database: 2 >>>>>> >>> >>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> candidate id 602102 >>>>>> >>> >>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> PSCID is: DCC0001 >>>>>> >>> CandID id: 602102 >>>>>> >>> visit_label is: V1 >>>>>> >>> candidate id 602102 >>>>>> >>> >>>>>> >>> Cleaning up temp files: rm -rf >>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>> >>> >>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>> cat >>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>> >>> >>>>>> >>> ==> Loading file from disk >>>>>> >>> >>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>> >>> >>>>>> >>> --> mapping DICOM parameter for >>>>>> >>> >>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>> >>> >>>>>> >>> ==> computing md5 hash for MINC body. >>>>>> >>> >>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>> >>> >>>>>> >>> ==> verifying acquisition protocol >>>>>> >>> >>>>>> >>> Acquisition protocol is unknown >>>>>> >>> >>>>>> >>> --> The minc file cannot be registered since the >>>>>> AcquisitionProtocol >>>>>> >>> is unknown >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios: >>>>>> >>> >>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>> *delete_imaging_upload* >>>>>> >>> script -- >>>>>> >>> details here: >>>>>> >>> >>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>> >>> >>>>>> >>> What's in your *psc* table? (Is it properly populated? This is a >>>>>> >>> pre-requisite to loading imaging data. >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>> > >>>>>> >>> ) >>>>>> >>> The foreign key constraint error on the candidate record is >>>>>> curious. >>>>>> >>> >>>>>> >>> There are also a few options for creating candidates when >>>>>> inserting >>>>>> >>> imaging data: >>>>>> >>> >>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>> pipeline >>>>>> >>> >>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>> optionally I >>>>>> >>> think) >>>>>> >>> How to: >>>>>> >>> >>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>> >>> >>>>>> >>> Then as a second step: >>>>>> >>> b. Use the imaging insertion pipeline >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>> > >>>>>> >>> to load your DICOMs. >>>>>> >>> You will want to first ensure that the PatientName header in the >>>>>> DICOMs >>>>>> >>> as well as tar package are correctly labelled with >>>>>> PSCID_DCCID_VisitLabel >>>>>> >>> >>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>> >>> How to : >>>>>> >>> >>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>> >>> >>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>> bids_import script, >>>>>> >>> to automatically create your candidates and sessions. >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> How do i delete a Study? And everytime do i have to create a new >>>>>> >>> candidate to get DCCID and a PSCID? >>>>>> >>> >>>>>> >>> *First execution:* >>>>>> >>> >>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>> ./ >>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>> ~/Desktop/input.txt > >>>>>> >>> log.txt >>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>> foreign >>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>> `FK_candidate_1` >>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>> (`CenterID`)) at >>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>> >>> The following database commands failed: >>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>> (?,?,?,?,?)'; >>>>>> >>> SET >>>>>> >>> >>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>> >>> Medical Systems'; >>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>> >>> Error obtained:Cannot add or update a child row: a foreign key >>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>> `FK_mri_scanner_1` >>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error >>>>>> code 1452) >>>>>> >>> >>>>>> >>> ERROR: The validation has failed. Either re-run the validation >>>>>> again >>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to >>>>>> force the >>>>>> >>> execution. >>>>>> >>> >>>>>> >>> >>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>> batch_uploads_imageuploader.pl >>>>>> >>> line 250. >>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>> batch_uploads_imageuploader.pl >>>>>> >>> line 251. >>>>>> >>> >>>>>> >>> >>>>>> >>> *And second execution: * >>>>>> >>> >>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>> ./ >>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>> ~/Desktop/input.txt > >>>>>> >>> log.txt >>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>> >>> >>>>>> >>> PROBLEM: >>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>> >>> The unique study ID is >>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>> >>> This is the information retained from the first time the study was >>>>>> >>> inserted: >>>>>> >>> >>>>>> >>> * Taken from dir : >>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>> >>> * Archive target location : >>>>>> >>> >>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>> >>> * Name of host OS : Linux >>>>>> >>> * Created by user : lorisadmin >>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>> >>> * dicomSummary version : 1 >>>>>> >>> * dicomTar version : 1 >>>>>> >>> * md5sum for DICOM tarball : >>>>>> 4a301b0318178b09b91e63544282364d >>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>> >>> * md5sum for complete archive : >>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>> >>> >>>>>> >>> >>>>>> >>> Last update of record: >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> The dicomTar.pl execution has failed. >>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>> batch_uploads_imageuploader.pl >>>>>> >>> line 250. >>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>> batch_uploads_imageuploader.pl >>>>>> >>> line 251. >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Ok, this sounds like good progress. Let us know when you next >>>>>> encounter >>>>>> >>> issues as you progress through the Imaging Install/Setup docs >>>>>> >>> >>>>> >. >>>>>> >>> I'll look into how we can better handle the incoming/ directory >>>>>> next >>>>>> >>> time. >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>> >>> populated correctly except its port is 'port' : ''. Also i >>>>>> have tested >>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>> >>> >>>>>> >>> I executed the script again, because the only error i had >>>>>> previously was >>>>>> >>> that the /data/incoming folder didn't exist and there are no >>>>>> errors >>>>>> >>> reported back except of warnings <>>>>> password on the >>>>>> >>> command line interface can be insecure>>. >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> It's possible -- if the script was unable to connect to the >>>>>> database >>>>>> >>> during its execution (e.g. typo in the password), that would >>>>>> explain the >>>>>> >>> underpopulated Image path and Loris-MRI code path you saw in the >>>>>> Config >>>>>> >>> module. >>>>>> >>> It's hard to tell without seeing the output from your script run >>>>>> -- Did >>>>>> >>> you see a sign of any such error? >>>>>> >>> The Config fields are populated by the imaging_install.sh script >>>>>> (starting >>>>>> >>> at line 222 >>>>>> >>> < >>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>> > >>>>>> >>> ) >>>>>> >>> >>>>>> >>> For example, check if the database connection information was >>>>>> populated >>>>>> >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> Hi Christine, >>>>>> >>> >>>>>> >>> If you are referring to the imaging_install.sh here is an image >>>>>> with the >>>>>> >>> configurations i typed. Maybe the problem is somewhere at the >>>>>> last part >>>>>> >>> which asks to configure as much as possible automatically? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>> >>> >>>>>> >>> Hi Sotirios, >>>>>> >>> >>>>>> >>> Glad to hear your LORIS core install is up and working and all the >>>>>> >>> front-end pages are loading. >>>>>> >>> >>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>>>>> >>> > and the web interface worked. >>>>>> >>> >>>>>> >>> Yes, it's important that project/ have 775 permissions and that >>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the install >>>>>> >>> Readme . >>>>>> >>> >>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS >>>>>> to >>>>>> >>> loris, right? >>>>>> >>> >>>>>> >>> These imaging paths will be updated during your imaging >>>>>> installation >>>>>> >>> by an automated >>>>>> script -- >>>>>> >>> you do not need to set them manually via the Config module. >>>>>> >>> Please continue to follow the Setup Guide >>>>>> >>> for detailed steps to >>>>>> follow. >>>>>> >>> >>>>>> >>> Best, >>>>>> >>> Christine >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>> >>> >>>>>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS to >>>>>> loris, >>>>>> >>> right? >>>>>> >>> >>>>>> >>> [image: image.png] >>>>>> >>> >>>>>> >>> >>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>> Nikoloutsopoulos < >>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>> >>> >>>>>> >>> Hi, >>>>>> >>> >>>>>> >>> i used >>>>>> >>> >>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>> >>> sudo apt-get install -y nodejs >>>>>> >>> >>>>>> >>> >>>>>> >>> you had suggested in the past, make worked and now i can see all >>>>>> the >>>>>> >>> contents in the web-interface, but i don't need make install? >>>>>> >>> >>>>>> >>> Thanks >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> Montreal Neurological Institute >>>>>> >>> McGill University | Montreal | Canada >>>>>> >>> >>>>>> >>> _______________________________________________ >>>>>> >>> Loris-dev mailing list >>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> -- >>>>>> >>> >>>>>> >>> christine.rogers at mcgill.ca >>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> >>> 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URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 37207 bytes Desc: not available URL: From cecile.madjar at mcin.ca Mon Nov 25 09:53:17 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 25 Nov 2019 09:53:17 -0500 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, Which version of LORIS-MRI are you using? There was a bug that got resolved in 20.2 in get_dicom_info.pl. Basically, if a DICOM did not have the (0020,0032) header, get_dicom_info.pl considered that the file was not a DICOM, which was a mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this is the issue you are encountering. About scout and localizer, they are a type of short and low resolution sequence that is used by the tech but is of no interest scientifically, which is why we tend to no insert them. Hope this helps, C?cile On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi Cecile, > > i executed the find command and the output i got per folder was "DICOM > medical imaging data. Maybe there is something wrong with the find command > in the warning that it is unable to check if the file is a dicom file? Also > when i use get_dicom_info.pl i don't get any output data. Finally i don't > understand what scout or localizer is ( something like if and only if a > file fails then the whole session is invalid? ). > > [image: image.png] > > Thanks > > Sotirios > > ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < > cecile.madjar at mcin.ca> ??????: > >> Hi Sotirios, >> >> I took a closer look to the batch_uploader_multiple_output.txt file you >> sent. It looks like there are different reasons for failure depending on >> the DICOM folder uploaded. >> >> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1: it >> looks like there is no file of type DICOM in the folder. Have you checked >> to see if that is indeed the case? Maybe you can try running the following >> command on that folder to see what are the types of the files? If it does >> not return at least one DICOM medical imaging data file, then that is why >> you get the error message from the pipeline: >> - >> >> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >> >> - For 864173 DCC0001 V1: it looks like there are two different >> DICOM studies within the same folder. You will need to split that study in >> two based on the StudyUID field as the insertion pipeline does not allow >> for more than one StudyUID per upload. >> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1: it >> looks like the dcm2mnc command did not produce any MINC files. Can you >> check in the DICOM archive what are the series present in the tarchive for >> that visit? Maybe only a scout or localizer was acquired for that session, >> hence the no valid MINC files (scout and localizer being skipped for the >> conversion) >> - For 397410 DCC0003 V1: it looks like everything went well for this >> one. >> >> One script that is called by our pipeline is called get_dicom_info.pl and >> this does all kind of checks on the DICOM files (it is being called when >> running the dcm2mnc conversion). You could run it independently on your >> folder if needed. >> >> Since one of the study got in, it does not look like you are having a >> problem with the setup. It seems more likely to be a problem with the data >> themselves. >> >> Hope this helps. >> >> C?cile >> >> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi Christine, >>> >>> In my first vm i am able to create the minc files and view them at the >>> mri browser (except of candidate 102761034 ), meanwhile the same files >>> gives warnings at the 2nd vm. The output of the batch upload can be seen >>> in the file attached. >>> Also a colleague of us has built a pre-validation tool for dicom >>> https://github.com/aueb-wim/DataQualityControlTool/ which had found all >>> the files that Loris gave as warning . Basically I confirmed that the total >>> amount of files per dicom was the same amount as stated in Loris and >>> checked some filenames given from warning to confirm that they match with >>> our tool. But that was months ago and my colleague had changed some >>> parameters for MIP and now our tool doesn't find all the invalid files, >>> that's why i asked for the dicom header specification of Loris. In a >>> discussion we had he mentioned that he doesn't check for some tags e.x. >>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>> remove invalid dcm files. >>> >>> Thanks >>> >>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotirios, >>>> Can you provide us with some fresh particulars of the current issue and >>>> we'll take it from there? >>>> Yang's team has built these scripts which can definitely serve as a >>>> model for your pre-validation of your DICOM collections. >>>> cheers, >>>> Christine >>>> >>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> HI Yang, >>>>> >>>>> We make use of pydicom library too. Now about the validate.py i see >>>>> that you check if some attributes are missing such as PatientID, >>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>> something on the setup of my other virtual machine ( although one dicom >>>>> passed on the new vm successfully, the others that were inserted correctly >>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but i >>>>> don't remember the solution. >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>> ??????: >>>>> >>>>>> Hey, Sotirios, >>>>>> >>>>>> Christine from the LORIS team mentioned you had some issue with >>>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>>> fully automated pipeline actually. >>>>>> >>>>>> While we were building CNBP, we had coded up some minor Python >>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>> more comprehensive solution, PyDICOM ( >>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>> >>>>>> Cheers, >>>>>> >>>>>> Yang Ding, PhD. >>>>>> Canadian Neonatal Brain Platform Architect >>>>>> >>>>>> On Tue, Nov 12, 2019 at 8:29 AM >>>>>> wrote: >>>>>> >>>>>>> Send Loris-dev mailing list submissions to >>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>> >>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>> >>>>>>> You can reach the person managing the list at >>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>> >>>>>>> When replying, please edit your Subject line so it is more specific >>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>> >>>>>>> >>>>>>> Today's Topics: >>>>>>> >>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>> >>>>>>> >>>>>>> >>>>>>> ---------------------------------------------------------------------- >>>>>>> >>>>>>> Message: 1 >>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>> To: Cecile Madjar >>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>> Message-ID: >>>>>>> >>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Could we send you a link with 10 anonymized dicom files to diagnose >>>>>>> the >>>>>>> warnings we get? >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> ??????: >>>>>>> >>>>>>> > Hi Cecile, >>>>>>> > >>>>>>> > We were wondering whether Loris has a tool to check if there are >>>>>>> problems >>>>>>> > with the dcm files, before trying to upload them. Something that >>>>>>> could >>>>>>> > provide the same results provided in the warning_output, this is >>>>>>> the >>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>> attributes of the >>>>>>> > dcm header would trigger a warning? is there a dcm file header >>>>>>> > specification for Loris? >>>>>>> > >>>>>>> > Thanks >>>>>>> > >>>>>>> > Sotirios >>>>>>> > >>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>> > >>>>>>> >> Hi, >>>>>>> >> >>>>>>> >> Yes, by parsing now() into unix_timestamp function it worked,but i >>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>> >> Thanks >>>>>>> >> >>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>> >> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> The first error occurs because the QCFirstChangeTime and columns >>>>>>> are of >>>>>>> >>> type `unsigned integer` and not `datatime`. You should be using >>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>> >>> >>>>>>> >>> The second error occurs because the trigger triggers a rollback >>>>>>> of the >>>>>>> >>> insert statement in the files table. >>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>> >>> >>>>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>>>> failure of >>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>> >>> -- Xavier >>>>>>> >>> >>>>>>> >>> ------------------------------ >>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>> >>> Nikoloutsopoulos >>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>> >>> *To:* Cecile Madjar >>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca ; >>>>>>> >>> Christine Rogers, Ms. >>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>> >>> >>>>>>> >>> When mincs are inserted their corresponding rows at the file >>>>>>> table are >>>>>>> >>> inserted too >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>>>> because i >>>>>>> >>> don't want manually to label them as passed throught the >>>>>>> interface >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> That is the trigger i wrote >>>>>>> >>> >>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>> >>> BEGIN >>>>>>> >>> INSERT INTO files_qcstatus >>>>>>> >>> SET FileID = NEW.FileID, >>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>> >>> QCStatus = "Pass", >>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>> >>> END >>>>>>> >>> >>>>>>> >>> although it contains some errors >>>>>>> >>> >>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>>> foreign >>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` >>>>>>> (`FileID`)) >>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> In the mri_upload table, there is a TarchiveID column associated >>>>>>> with >>>>>>> >>> the MRI upload you inserted. When this value is NULL, it means >>>>>>> no DICOMs >>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>> insertion of the >>>>>>> >>> DICOMs in the tarchive tables, this value is updated with the >>>>>>> correct >>>>>>> >>> TarchiveID associated with the upload. >>>>>>> >>> >>>>>>> >>> Could this correspond to what you want to do? >>>>>>> >>> >>>>>>> >>> Regarding the files_qcstatus, this table is only linked to the >>>>>>> files >>>>>>> >>> table (hence, the MINC files). You could always create a new >>>>>>> table for >>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>> >>> >>>>>>> >>> C?cile >>>>>>> >>> >>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>>> >>> coressponding qc_status to "pass". I was thinking of creating a >>>>>>> trigger for >>>>>>> >>> that, but which tables do i need to add entries to? So far from >>>>>>> what i see >>>>>>> >>> i need to add entres at the table "files" whenever an insertion >>>>>>> happens to >>>>>>> >>> files_qcstatus. >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning of >>>>>>> my email >>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>> >>> >>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> that's the Study Instance UID, not the StudyID. So the StudyID i >>>>>>> am >>>>>>> >>> looking for is not stored in the database? >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> Thanks. >>>>>>> >>> >>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>> >>> tarchive table. It can also be found in the metadata field but >>>>>>> it is mixed >>>>>>> >>> with many other information. >>>>>>> >>> >>>>>>> >>> Hope this helps, >>>>>>> >>> >>>>>>> >>> C?cile >>>>>>> >>> >>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive >>>>>>> table, >>>>>>> >>> specifically at the AcquisitonMetadata column i found something >>>>>>> called >>>>>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>>>>> Instance UID. >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>> >>> >>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>> >>> >>>>>>> >>> - the scan type could not be identified (not matching an >>>>>>> entry in >>>>>>> >>> the mri_protocol table) >>>>>>> >>> - one parameter of the scan type is out of the expected range >>>>>>> >>> present in the mri_protocol_checks (extra filtering in case >>>>>>> you need to be >>>>>>> >>> stricker on some parameters not present in the mri_protocol >>>>>>> table) >>>>>>> >>> - if the CandID and PSCID do not match >>>>>>> >>> >>>>>>> >>> The following cases do not get in the MRI violation tables as it >>>>>>> happens >>>>>>> >>> before the conversion of the DICOM to MINC files and only MINC >>>>>>> files >>>>>>> >>> violations are logged there: >>>>>>> >>> >>>>>>> >>> - "No single DICOM" (since no valid DICOM could be found to >>>>>>> convert >>>>>>> >>> to MINC) >>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since this >>>>>>> error >>>>>>> >>> happens at the dicomTar.pl level (way before conversion into >>>>>>> MINC files) >>>>>>> >>> >>>>>>> >>> Glad everything is working out!! >>>>>>> >>> Best, >>>>>>> >>> >>>>>>> >>> C?cile >>>>>>> >>> >>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now >>>>>>> about the >>>>>>> >>> mri_violations, dicoms are triggered to be inserted there only >>>>>>> if there is >>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>> parameter? >>>>>>> >>> Because i don't see the cases of 'No single dicom" or with the 2 >>>>>>> studyiuid >>>>>>> >>> to be there. >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> Sorry to hear you are having issues with the memory. I think >>>>>>> most of our >>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>>> >>> >>>>>>> >>> Hope this helps! >>>>>>> >>> >>>>>>> >>> C?cile >>>>>>> >>> >>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> about that dicom that had that insertion error it's about 30mb >>>>>>> and when >>>>>>> >>> it is being processed the ram is being drastically increased >>>>>>> from 2gb to >>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is the >>>>>>> recommended >>>>>>> >>> size of ram for using Loris? >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>> >>> >>>>>>> >>> For the delete script issue, if you are absolutely certain that >>>>>>> no >>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>> mri_upload table >>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>> uploadID. It >>>>>>> >>> looks like for some reason the scripts did not update this field >>>>>>> when it >>>>>>> >>> stopped the insertion. Not sure why that would be the case >>>>>>> though. >>>>>>> >>> Note: only do that update if you are certain that there is no >>>>>>> processing >>>>>>> >>> happening. >>>>>>> >>> >>>>>>> >>> Hope this helps! >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>>>> actually do >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>> missing at the >>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but with >>>>>>> no mnic >>>>>>> >>> files. Also now i have this error >>>>>>> >>> >>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>> :/data/loris/bin/mri/tools$ >>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>> processing it. >>>>>>> >>> >>>>>>> >>> How can solve this? >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>> >>> >>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>> >>> >>>>>>> >>> To give you a brief idea: >>>>>>> >>> Per folder it will: >>>>>>> >>> 1) Delete all the .bak files >>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>>> TE_min, >>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>> mri_protocol table >>>>>>> >>> >>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>> >>> For some reason some files are missing >>>>>>> SeriesDescription/ProtocolName >>>>>>> >>> >>>>>>> >>> In total i have 7 folders >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> 3/7 passed >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> Also about the first patient with DC0000 had a violation "T1 >>>>>>> AXIAL SE >>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i find >>>>>>> that weird >>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>> >>> >>>>>>> >>> 102327840 and 102809579 outputs "The target directory does not >>>>>>> contain a >>>>>>> >>> single DICOM file.", therefore they are missing their StudyUID >>>>>>> >>> >>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>> multiple >>>>>>> >>> studies." >>>>>>> >>> >>>>>>> >>> and 102761034 "No data could be converted into valid MINC files. >>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>> >>> >>>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 and >>>>>>> 102506134 >>>>>>> >>> can i just pass a flag parameter to >>>>>>> batch_uploads_imageuploader.pl? or >>>>>>> >>> modify imaging_upload_file.pl? >>>>>>> >>> >>>>>>> >>> Thank you, >>>>>>> >>> >>>>>>> >>> Sotirios >>>>>>> >>> >>>>>>> >>> PS >>>>>>> >>> >>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>> dicom_output.txt. >>>>>>> >>> >>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> Glad to hear about your progress. >>>>>>> >>> >>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>> documented here >>>>>>> >>> < >>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>> > >>>>>>> >>> -- let us know if you didn't find the answers you were looking >>>>>>> for there. >>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>> database >>>>>>> >>> management software is a visual placeholder for you as the >>>>>>> user? I'm not >>>>>>> >>> sure why a scanner would ever be registered with ID='0' as your >>>>>>> screenshot >>>>>>> >>> showed.) >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> I fixed it with this >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>> something >>>>>>> >>> wrong with the structure? why did i receive a 500 internal >>>>>>> error? In the >>>>>>> >>> loris-error log it state that there is something wrong with >>>>>>> token, but i >>>>>>> >>> verfied that the type of the token is a string. >>>>>>> >>> >>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] [client >>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: Argument >>>>>>> 1 >>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the >>>>>>> type string, >>>>>>> >>> null given, called in >>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>>>> 169 and >>>>>>> >>> defined in >>>>>>> >>> >>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>> >>> trace:\n#0 >>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n >>>>>>> thrown in >>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>>>> 192 >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> Is there a way also to delete candidates? Just to let you know >>>>>>> what i >>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>> dependencies. >>>>>>> >>> >>>>>>> >>> First i deleted all their uploads >>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way to >>>>>>> omit >>>>>>> >>> the backup file ? ) >>>>>>> >>> >>>>>>> >>> Afterwards i had some scanner candidates, so i deleted all the >>>>>>> entries >>>>>>> >>> from mri_scanner except that i couldn't delete this entry with >>>>>>> the 0 ID. >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> We recommend that you use our existing tools for creating new >>>>>>> candidates >>>>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>>>> calling the Candidate >>>>>>> >>> class's createNew() >>>>>>> >>> < >>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>> >function. >>>>>>> >>> These will create the necessary records for you. (It's not >>>>>>> recommended to >>>>>>> >>> make direct modifications to mysql database tables in your >>>>>>> script, if I >>>>>>> >>> understand you.) >>>>>>> >>> >>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, and >>>>>>> there are >>>>>>> >>> multiple reasons for this. >>>>>>> >>> You can use the PSCID for project-specific IDs and the External >>>>>>> ID field >>>>>>> >>> in the candidate table can also be used for any values you like. >>>>>>> >>> Additionally, any number of custom IDs can be added in parallel >>>>>>> - these >>>>>>> >>> are entered/visible in the Candidate Information module and >>>>>>> added in the >>>>>>> >>> back-end as candidate parameters. >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> We are building a script that will auto insert the candidates >>>>>>> based on >>>>>>> >>> their ExternalID. We would like to know whethere when we are >>>>>>> creating a new >>>>>>> >>> profile in the candidate table, if we also have to insert a new >>>>>>> record at >>>>>>> >>> another table? Furthermore is there a problem that in our case >>>>>>> CandID won't >>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> That would normally be the case but the numeric part of the >>>>>>> PSCID get >>>>>>> >>> paded with 0 on the left. >>>>>>> >>> >>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>> numerical char >>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>> >>> >>>>>>> >>> ABC0001 >>>>>>> >>> ABC0002 >>>>>>> >>> ... >>>>>>> >>> ABC0010 >>>>>>> >>> ... >>>>>>> >>> >>>>>>> >>> thus sorting them ascending will always get the latest value >>>>>>> generated >>>>>>> >>> as the max value. >>>>>>> >>> >>>>>>> >>> M?lanie >>>>>>> >>> >>>>>>> >>> ------------------------------ >>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>> >>> >>>>>>> >>> I see, although the PSCID value is varchar(255), it must be >>>>>>> stored >>>>>>> >>> within a specific length of characters. Otherwise if we were to >>>>>>> sort >>>>>>> >>> strings with different lengths the result would not be sorted >>>>>>> correctly ( >>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hello Sotirios, >>>>>>> >>> >>>>>>> >>> There is no `last value` stored anywhere. >>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>> increase that >>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>> >>> >>>>>>> >>> Hope this info help. >>>>>>> >>> >>>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | >>>>>>> McGill >>>>>>> >>> University >>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>> >>> >>>>>>> >>> ------------------------------ >>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>> >>> Nikoloutsopoulos >>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> how does Loris determine the next available PSCID value for a new >>>>>>> >>> candidate? >>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>> >>> e.x in the default case the PSCID is sequential, but where do we >>>>>>> store the >>>>>>> >>> last value for the sequential sequence? >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> the parameters in the mri_protocol you have assigned are global >>>>>>> >>> standard? or were assigned after trial and error? >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> Given you have done the initial setup of your tables to match >>>>>>> your >>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>> >>> < >>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>> > >>>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> *if i were to change their status to resolve what would happen? >>>>>>> >>> >>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> I noticed that i can view the mnics at the brainbrowser from the >>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>> /data/loris/data/trashbin/ >>>>>>> >>> if i were to click their issue to resolve what would happend? >>>>>>> would they >>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> The defaut values of the schema exists in my local database. If >>>>>>> i adjust >>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>> uploaded? >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> Is it possible that you haven't set up your mri_protocol table >>>>>>> ? (and >>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>> >>> >>>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>>>> insertion >>>>>>> >>> setup : See the install/setup documentation : >>>>>>> >>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>> >>> >>>>>>> >>> To add new rows, just use MySQL insert statements. You can >>>>>>> adapt the >>>>>>> >>> insert statements which load the default table values --> e.g. >>>>>>> Here on >>>>>>> >>> GitHub : >>>>>>> >>> >>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>> >>> (see also the mri_scan_type table) >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> I see that i can edit the values but not how to insert new rows. >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> If i choose Inserted with flag then will the minc be inserted? >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>> >>> >>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>> >>> >>>>>>> >>> It says "could not identify scan type", which we knew already. >>>>>>> Did you >>>>>>> >>> click on the link on those words? >>>>>>> >>> >>>>>>> >>> It will take you to the next page of the module, showing for >>>>>>> each scan >>>>>>> >>> what the scan parameters were, and will also show for comparison >>>>>>> what's >>>>>>> >>> stored in your *mri_protocol* table. >>>>>>> >>> Compare these values to find which parameter was not correct >>>>>>> according >>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>> >>> >>>>>>> >>> You may end up broadening your mri_protocol value ranges (e.g. >>>>>>> TR, TE) >>>>>>> >>> for scans. >>>>>>> >>> This can be done in the front-end, by editing the database table >>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>> >>> >>>>>>> >>> The MRI Violations module features are explained in more detail >>>>>>> in the >>>>>>> >>> Help text for this module inside LORIS (click the ["?"] icon in >>>>>>> the menu >>>>>>> >>> bar.) >>>>>>> >>> >>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>> >>> < >>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>> > >>>>>>> >>> : no MINCs inserted- violated scans >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> looks like my previous email's attachment wasn't delivered due to >>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>> >>> >>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>> >>> >>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>> webbrowser, so >>>>>>> >>> that you can check the filelds easier. >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios -- >>>>>>> >>> Great, sounds like more progress. >>>>>>> >>> >>>>>>> >>> About the dcmodify command -- I'm not sure why you're getting an >>>>>>> Endian >>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>> successfully >>>>>>> >>> relabelled, after the command ran? >>>>>>> >>> >>>>>>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) >>>>>>> to >>>>>>> >>> verify and/or update local DICOM headers -- though your dcmodify >>>>>>> command is >>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>> >>> >>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>> "(2001,105f)" from >>>>>>> >>> the warning message) - you can also dcmdump a DICOM slice >>>>>>> before and look >>>>>>> >>> at these fields specifically. >>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>> before/after >>>>>>> >>> running dcmodify, and use dcmdump on each version to diff the >>>>>>> outputs -- >>>>>>> >>> this will pinpoint what changed. >>>>>>> >>> >>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not recognized >>>>>>> or >>>>>>> >>> unknown : this means your scans did not match what is stored >>>>>>> in your >>>>>>> >>> mri_protocol table. >>>>>>> >>> Check the MRI Violations front-end module -- can you see why >>>>>>> they didn't >>>>>>> >>> match? >>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>> mri_protocol >>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Here is the psc table >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>> >>> >>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>> >>> >>>>>>> >>> and got those warning: is this okay? >>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>>> reading a >>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>>> reading a >>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined length, >>>>>>> reading a >>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined length, >>>>>>> reading a >>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>>> reading a >>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>>> reading a >>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>> >>> >>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you can >>>>>>> see the >>>>>>> >>> execution for the second dicom. Mnics could not be inserted due >>>>>>> to >>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>> >>> >>>>>>> >>> Running now the following command: >>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>> >>> >>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX' >>>>>>> >>> -delete >>>>>>> >>> >>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>> >>> >>>>>>> >>> Testing for database connectivity. >>>>>>> >>> Database is available. >>>>>>> >>> >>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>> >>> >>>>>>> >>> You are creating a tar with the following command: >>>>>>> >>> >>>>>>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> getting md5sums and gzipping!! >>>>>>> >>> >>>>>>> >>> * Taken from dir : >>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>> >>> * Archive target location : >>>>>>> >>> >>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>> >>> * Name of host OS : Linux >>>>>>> >>> * Created by user : lorisadmin >>>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>>> >>> * dicomSummary version : 1 >>>>>>> >>> * dicomTar version : 1 >>>>>>> >>> * md5sum for DICOM tarball : >>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>> >>> * md5sum for complete archive : >>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>> >>> >>>>>>> >>> Adding archive info into database >>>>>>> >>> >>>>>>> >>> Removing temporary files from target location >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> Done adding archive info into database >>>>>>> >>> >>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>> -globLocation >>>>>>> >>> -profile prod >>>>>>> >>> >>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>> >>> -uploadID 12 -verbose >>>>>>> >>> md5sum >>>>>>> >>> >>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>> >>> PSCID is: DCC0001 >>>>>>> >>> CandID id: 602102 >>>>>>> >>> visit_label is: V1 >>>>>>> >>> PSCID is: DCC0001 >>>>>>> >>> CandID id: 602102 >>>>>>> >>> visit_label is: V1 >>>>>>> >>> candidate id 602102 >>>>>>> >>> Set centerID = 1 >>>>>>> >>> PSCID is: DCC0001 >>>>>>> >>> CandID id: 602102 >>>>>>> >>> visit_label is: V1 >>>>>>> >>> PSCID is: DCC0001 >>>>>>> >>> CandID id: 602102 >>>>>>> >>> visit_label is: V1 >>>>>>> >>> >>>>>>> >>> Number of MINC files that will be considered for inserting into >>>>>>> the >>>>>>> >>> database: 2 >>>>>>> >>> >>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>> >>> PSCID is: DCC0001 >>>>>>> >>> CandID id: 602102 >>>>>>> >>> visit_label is: V1 >>>>>>> >>> PSCID is: DCC0001 >>>>>>> >>> CandID id: 602102 >>>>>>> >>> visit_label is: V1 >>>>>>> >>> candidate id 602102 >>>>>>> >>> >>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>> >>> PSCID is: DCC0001 >>>>>>> >>> CandID id: 602102 >>>>>>> >>> visit_label is: V1 >>>>>>> >>> PSCID is: DCC0001 >>>>>>> >>> CandID id: 602102 >>>>>>> >>> visit_label is: V1 >>>>>>> >>> candidate id 602102 >>>>>>> >>> >>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>> >>> >>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>> cat >>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>> >>> >>>>>>> >>> ==> Loading file from disk >>>>>>> >>> >>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>> >>> >>>>>>> >>> --> mapping DICOM parameter for >>>>>>> >>> >>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>> >>> >>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>> >>> >>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>> >>> >>>>>>> >>> ==> verifying acquisition protocol >>>>>>> >>> >>>>>>> >>> Acquisition protocol is unknown >>>>>>> >>> >>>>>>> >>> --> The minc file cannot be registered since the >>>>>>> AcquisitionProtocol >>>>>>> >>> is unknown >>>>>>> >>> >>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios: >>>>>>> >>> >>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>> *delete_imaging_upload* >>>>>>> >>> script -- >>>>>>> >>> details here: >>>>>>> >>> >>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>> >>> >>>>>>> >>> What's in your *psc* table? (Is it properly populated? This is a >>>>>>> >>> pre-requisite to loading imaging data. >>>>>>> >>> < >>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>> > >>>>>>> >>> ) >>>>>>> >>> The foreign key constraint error on the candidate record is >>>>>>> curious. >>>>>>> >>> >>>>>>> >>> There are also a few options for creating candidates when >>>>>>> inserting >>>>>>> >>> imaging data: >>>>>>> >>> >>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>>> pipeline >>>>>>> >>> >>>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>>> optionally I >>>>>>> >>> think) >>>>>>> >>> How to: >>>>>>> >>> >>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>> >>> >>>>>>> >>> Then as a second step: >>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>> >>> < >>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>> > >>>>>>> >>> to load your DICOMs. >>>>>>> >>> You will want to first ensure that the PatientName header in the >>>>>>> DICOMs >>>>>>> >>> as well as tar package are correctly labelled with >>>>>>> PSCID_DCCID_VisitLabel >>>>>>> >>> >>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>> >>> How to : >>>>>>> >>> >>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>> >>> >>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>> bids_import script, >>>>>>> >>> to automatically create your candidates and sessions. >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> How do i delete a Study? And everytime do i have to create a new >>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>> >>> >>>>>>> >>> *First execution:* >>>>>>> >>> >>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>> ./ >>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>> ~/Desktop/input.txt > >>>>>>> >>> log.txt >>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>>> foreign >>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>> `FK_candidate_1` >>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>> (`CenterID`)) at >>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>> >>> The following database commands failed: >>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>> (?,?,?,?,?)'; >>>>>>> >>> SET >>>>>>> >>> >>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>> >>> Medical Systems'; >>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>> >>> Error obtained:Cannot add or update a child row: a foreign key >>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>> `FK_mri_scanner_1` >>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error >>>>>>> code 1452) >>>>>>> >>> >>>>>>> >>> ERROR: The validation has failed. Either re-run the validation >>>>>>> again >>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force to >>>>>>> force the >>>>>>> >>> execution. >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>> batch_uploads_imageuploader.pl >>>>>>> >>> line 250. >>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>> batch_uploads_imageuploader.pl >>>>>>> >>> line 251. >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> *And second execution: * >>>>>>> >>> >>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>> ./ >>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>> ~/Desktop/input.txt > >>>>>>> >>> log.txt >>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>> >>> >>>>>>> >>> PROBLEM: >>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>> >>> The unique study ID is >>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>> >>> This is the information retained from the first time the study >>>>>>> was >>>>>>> >>> inserted: >>>>>>> >>> >>>>>>> >>> * Taken from dir : >>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>> >>> * Archive target location : >>>>>>> >>> >>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>> >>> * Name of host OS : Linux >>>>>>> >>> * Created by user : lorisadmin >>>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>>> >>> * dicomSummary version : 1 >>>>>>> >>> * dicomTar version : 1 >>>>>>> >>> * md5sum for DICOM tarball : >>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>> >>> * md5sum for complete archive : >>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> Last update of record: >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>> batch_uploads_imageuploader.pl >>>>>>> >>> line 250. >>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>> batch_uploads_imageuploader.pl >>>>>>> >>> line 251. >>>>>>> >>> >>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> Ok, this sounds like good progress. Let us know when you next >>>>>>> encounter >>>>>>> >>> issues as you progress through the Imaging Install/Setup docs >>>>>>> >>> >>>>>> >. >>>>>>> >>> I'll look into how we can better handle the incoming/ directory >>>>>>> next >>>>>>> >>> time. >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py >>>>>>> is >>>>>>> >>> populated correctly except its port is 'port' : ''. Also i >>>>>>> have tested >>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>> >>> >>>>>>> >>> I executed the script again, because the only error i had >>>>>>> previously was >>>>>>> >>> that the /data/incoming folder didn't exist and there are no >>>>>>> errors >>>>>>> >>> reported back except of warnings <>>>>>> password on the >>>>>>> >>> command line interface can be insecure>>. >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> It's possible -- if the script was unable to connect to the >>>>>>> database >>>>>>> >>> during its execution (e.g. typo in the password), that would >>>>>>> explain the >>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw in the >>>>>>> Config >>>>>>> >>> module. >>>>>>> >>> It's hard to tell without seeing the output from your script run >>>>>>> -- Did >>>>>>> >>> you see a sign of any such error? >>>>>>> >>> The Config fields are populated by the imaging_install.sh script >>>>>>> (starting >>>>>>> >>> at line 222 >>>>>>> >>> < >>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>> > >>>>>>> >>> ) >>>>>>> >>> >>>>>>> >>> For example, check if the database connection information was >>>>>>> populated >>>>>>> >>> accurately in $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> Hi Christine, >>>>>>> >>> >>>>>>> >>> If you are referring to the imaging_install.sh here is an image >>>>>>> with the >>>>>>> >>> configurations i typed. Maybe the problem is somewhere at the >>>>>>> last part >>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>> >>>>>>> >>> Hi Sotirios, >>>>>>> >>> >>>>>>> >>> Glad to hear your LORIS core install is up and working and all >>>>>>> the >>>>>>> >>> front-end pages are loading. >>>>>>> >>> >>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>>>>>> >>> > and the web interface worked. >>>>>>> >>> >>>>>>> >>> Yes, it's important that project/ have 775 permissions and that >>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the >>>>>>> install >>>>>>> >>> Readme . >>>>>>> >>> >>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change LORIS >>>>>>> to >>>>>>> >>> loris, right? >>>>>>> >>> >>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>> installation >>>>>>> >>> by an automated >>>>>>> script -- >>>>>>> >>> you do not need to set them manually via the Config module. >>>>>>> >>> Please continue to follow the Setup Guide >>>>>>> >>> for detailed steps >>>>>>> to follow. >>>>>>> >>> >>>>>>> >>> Best, >>>>>>> >>> Christine >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>> >>> >>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS >>>>>>> to loris, >>>>>>> >>> right? >>>>>>> >>> >>>>>>> >>> [image: image.png] >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>> Nikoloutsopoulos < >>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>> >>> >>>>>>> >>> Hi, >>>>>>> >>> >>>>>>> >>> i used >>>>>>> >>> >>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>> >>> sudo apt-get install -y nodejs >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> you had suggested in the past, make worked and now i can see all >>>>>>> the >>>>>>> >>> contents in the web-interface, but i don't need make install? >>>>>>> >>> >>>>>>> >>> Thanks >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> >>>>>>> >>> -- >>>>>>> >>> >>>>>>> >>> christine.rogers at mcgill.ca >>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> >>> Montreal Neurological Institute >>>>>>> >>> McGill University | Montreal | Canada >>>>>>> >>> >>>>>>> >>> _______________________________________________ >>>>>>> >>> Loris-dev mailing list >>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>> >>>>>>> >>> >>>>>>> -------------- next part -------------- >>>>>>> An HTML attachment was scrubbed... >>>>>>> URL: < >>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>>> > >>>>>>> >>>>>>> ------------------------------ >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>>> >>>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>>> ***************************************** >>>>>>> >>>>>> 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URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 37207 bytes Desc: not available URL: From sotirisnik at gmail.com Mon Nov 25 09:58:04 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 25 Nov 2019 16:58:04 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Cecile, We are using this version https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to insert low resolution now? Thanks On Mon, 25 Nov 2019, 16:53 Cecile Madjar, wrote: > Hi Sotirios, > > Which version of LORIS-MRI are you using? > > There was a bug that got resolved in 20.2 in get_dicom_info.pl. > Basically, if a DICOM did not have the (0020,0032) header, > get_dicom_info.pl considered that the file was not a DICOM, which was a > mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this is the > issue you are encountering. > > About scout and localizer, they are a type of short and low resolution > sequence that is used by the tech but is of no interest scientifically, > which is why we tend to no insert them. > > Hope this helps, > > C?cile > > > On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Cecile, >> >> i executed the find command and the output i got per folder was "DICOM >> medical imaging data. Maybe there is something wrong with the find command >> in the warning that it is unable to check if the file is a dicom file? Also >> when i use get_dicom_info.pl i don't get any output data. Finally i >> don't understand what scout or localizer is ( something like if and only if >> a file fails then the whole session is invalid? ). >> >> [image: image.png] >> >> Thanks >> >> Sotirios >> >> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >>> Hi Sotirios, >>> >>> I took a closer look to the batch_uploader_multiple_output.txt file you >>> sent. It looks like there are different reasons for failure depending on >>> the DICOM folder uploaded. >>> >>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1: it >>> looks like there is no file of type DICOM in the folder. Have you checked >>> to see if that is indeed the case? Maybe you can try running the following >>> command on that folder to see what are the types of the files? If it does >>> not return at least one DICOM medical imaging data file, then that is why >>> you get the error message from the pipeline: >>> - >>> >>> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >>> >>> - For 864173 DCC0001 V1: it looks like there are two different >>> DICOM studies within the same folder. You will need to split that study in >>> two based on the StudyUID field as the insertion pipeline does not allow >>> for more than one StudyUID per upload. >>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1: it >>> looks like the dcm2mnc command did not produce any MINC files. Can you >>> check in the DICOM archive what are the series present in the tarchive for >>> that visit? Maybe only a scout or localizer was acquired for that session, >>> hence the no valid MINC files (scout and localizer being skipped for the >>> conversion) >>> - For 397410 DCC0003 V1: it looks like everything went well for this >>> one. >>> >>> One script that is called by our pipeline is called get_dicom_info.pl and >>> this does all kind of checks on the DICOM files (it is being called when >>> running the dcm2mnc conversion). You could run it independently on your >>> folder if needed. >>> >>> Since one of the study got in, it does not look like you are having a >>> problem with the setup. It seems more likely to be a problem with the data >>> themselves. >>> >>> Hope this helps. >>> >>> C?cile >>> >>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi Christine, >>>> >>>> In my first vm i am able to create the minc files and view them at the >>>> mri browser (except of candidate 102761034 ), meanwhile the same files >>>> gives warnings at the 2nd vm. The output of the batch upload can be seen >>>> in the file attached. >>>> Also a colleague of us has built a pre-validation tool for dicom >>>> https://github.com/aueb-wim/DataQualityControlTool/ which had found >>>> all the files that Loris gave as warning . Basically I confirmed that the >>>> total amount of files per dicom was the same amount as stated in Loris and >>>> checked some filenames given from warning to confirm that they match with >>>> our tool. But that was months ago and my colleague had changed some >>>> parameters for MIP and now our tool doesn't find all the invalid files, >>>> that's why i asked for the dicom header specification of Loris. In a >>>> discussion we had he mentioned that he doesn't check for some tags e.x. >>>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>>> remove invalid dcm files. >>>> >>>> Thanks >>>> >>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> Can you provide us with some fresh particulars of the current issue >>>>> and we'll take it from there? >>>>> Yang's team has built these scripts which can definitely serve as a >>>>> model for your pre-validation of your DICOM collections. >>>>> cheers, >>>>> Christine >>>>> >>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> HI Yang, >>>>>> >>>>>> We make use of pydicom library too. Now about the validate.py i see >>>>>> that you check if some attributes are missing such as PatientID, >>>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>>> something on the setup of my other virtual machine ( although one dicom >>>>>> passed on the new vm successfully, the others that were inserted correctly >>>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but i >>>>>> don't remember the solution. >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>>> ??????: >>>>>> >>>>>>> Hey, Sotirios, >>>>>>> >>>>>>> Christine from the LORIS team mentioned you had some issue with >>>>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>>>> fully automated pipeline actually. >>>>>>> >>>>>>> While we were building CNBP, we had coded up some minor Python >>>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>>> more comprehensive solution, PyDICOM ( >>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>>> >>>>>>> Cheers, >>>>>>> >>>>>>> Yang Ding, PhD. >>>>>>> Canadian Neonatal Brain Platform Architect >>>>>>> >>>>>>> On Tue, Nov 12, 2019 at 8:29 AM >>>>>>> wrote: >>>>>>> >>>>>>>> Send Loris-dev mailing list submissions to >>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>> >>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>>> >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>>> >>>>>>>> You can reach the person managing the list at >>>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>>> >>>>>>>> When replying, please edit your Subject line so it is more specific >>>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>>> >>>>>>>> >>>>>>>> Today's Topics: >>>>>>>> >>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> ---------------------------------------------------------------------- >>>>>>>> >>>>>>>> Message: 1 >>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>>> To: Cecile Madjar >>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>>> Message-ID: >>>>>>>> >>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>>> >>>>>>>> Hi, >>>>>>>> >>>>>>>> Could we send you a link with 10 anonymized dicom files to diagnose >>>>>>>> the >>>>>>>> warnings we get? >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios Nikoloutsopoulos >>>>>>>> < >>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>> >>>>>>>> > Hi Cecile, >>>>>>>> > >>>>>>>> > We were wondering whether Loris has a tool to check if there are >>>>>>>> problems >>>>>>>> > with the dcm files, before trying to upload them. Something that >>>>>>>> could >>>>>>>> > provide the same results provided in the warning_output, this is >>>>>>>> the >>>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>>> attributes of the >>>>>>>> > dcm header would trigger a warning? is there a dcm file header >>>>>>>> > specification for Loris? >>>>>>>> > >>>>>>>> > Thanks >>>>>>>> > >>>>>>>> > Sotirios >>>>>>>> > >>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>>> > >>>>>>>> >> Hi, >>>>>>>> >> >>>>>>>> >> Yes, by parsing now() into unix_timestamp function it worked,but >>>>>>>> i >>>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>>> >> Thanks >>>>>>>> >> >>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>>> >> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> The first error occurs because the QCFirstChangeTime and >>>>>>>> columns are of >>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be using >>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>>> >>> >>>>>>>> >>> The second error occurs because the trigger triggers a rollback >>>>>>>> of the >>>>>>>> >>> insert statement in the files table. >>>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>>> >>> >>>>>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>>>>> failure of >>>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>>> >>> -- Xavier >>>>>>>> >>> >>>>>>>> >>> ------------------------------ >>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>> >>> Nikoloutsopoulos >>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>>> >>> *To:* Cecile Madjar >>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>>>>> >; >>>>>>>> >>> Christine Rogers, Ms. >>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>> >>> >>>>>>>> >>> When mincs are inserted their corresponding rows at the file >>>>>>>> table are >>>>>>>> >>> inserted too >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>>>>> because i >>>>>>>> >>> don't want manually to label them as passed throught the >>>>>>>> interface >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> That is the trigger i wrote >>>>>>>> >>> >>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>>> >>> BEGIN >>>>>>>> >>> INSERT INTO files_qcstatus >>>>>>>> >>> SET FileID = NEW.FileID, >>>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>>> >>> QCStatus = "Pass", >>>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>>> >>> END >>>>>>>> >>> >>>>>>>> >>> although it contains some errors >>>>>>>> >>> >>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>>>> foreign >>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES `files` >>>>>>>> (`FileID`)) >>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> In the mri_upload table, there is a TarchiveID column >>>>>>>> associated with >>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it means >>>>>>>> no DICOMs >>>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>>> insertion of the >>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with the >>>>>>>> correct >>>>>>>> >>> TarchiveID associated with the upload. >>>>>>>> >>> >>>>>>>> >>> Could this correspond to what you want to do? >>>>>>>> >>> >>>>>>>> >>> Regarding the files_qcstatus, this table is only linked to the >>>>>>>> files >>>>>>>> >>> table (hence, the MINC files). You could always create a new >>>>>>>> table for >>>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>>> >>> >>>>>>>> >>> C?cile >>>>>>>> >>> >>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>>>> >>> coressponding qc_status to "pass". I was thinking of creating a >>>>>>>> trigger for >>>>>>>> >>> that, but which tables do i need to add entries to? So far from >>>>>>>> what i see >>>>>>>> >>> i need to add entres at the table "files" whenever an >>>>>>>> insertion happens to >>>>>>>> >>> files_qcstatus. >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning of >>>>>>>> my email >>>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>>> >>> >>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the StudyID >>>>>>>> i am >>>>>>>> >>> looking for is not stored in the database? >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> Thanks. >>>>>>>> >>> >>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>>> >>> tarchive table. It can also be found in the metadata field but >>>>>>>> it is mixed >>>>>>>> >>> with many other information. >>>>>>>> >>> >>>>>>>> >>> Hope this helps, >>>>>>>> >>> >>>>>>>> >>> C?cile >>>>>>>> >>> >>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive >>>>>>>> table, >>>>>>>> >>> specifically at the AcquisitonMetadata column i found something >>>>>>>> called >>>>>>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>>>>>> Instance UID. >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>>> >>> >>>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>>> >>> >>>>>>>> >>> - the scan type could not be identified (not matching an >>>>>>>> entry in >>>>>>>> >>> the mri_protocol table) >>>>>>>> >>> - one parameter of the scan type is out of the expected range >>>>>>>> >>> present in the mri_protocol_checks (extra filtering in case >>>>>>>> you need to be >>>>>>>> >>> stricker on some parameters not present in the mri_protocol >>>>>>>> table) >>>>>>>> >>> - if the CandID and PSCID do not match >>>>>>>> >>> >>>>>>>> >>> The following cases do not get in the MRI violation tables as >>>>>>>> it happens >>>>>>>> >>> before the conversion of the DICOM to MINC files and only MINC >>>>>>>> files >>>>>>>> >>> violations are logged there: >>>>>>>> >>> >>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be found to >>>>>>>> convert >>>>>>>> >>> to MINC) >>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since this >>>>>>>> error >>>>>>>> >>> happens at the dicomTar.pl level (way before conversion into >>>>>>>> MINC files) >>>>>>>> >>> >>>>>>>> >>> Glad everything is working out!! >>>>>>>> >>> Best, >>>>>>>> >>> >>>>>>>> >>> C?cile >>>>>>>> >>> >>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now >>>>>>>> about the >>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there only >>>>>>>> if there is >>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>>> parameter? >>>>>>>> >>> Because i don't see the cases of 'No single dicom" or with the >>>>>>>> 2 studyiuid >>>>>>>> >>> to be there. >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> Sorry to hear you are having issues with the memory. I think >>>>>>>> most of our >>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>>>> >>> >>>>>>>> >>> Hope this helps! >>>>>>>> >>> >>>>>>>> >>> C?cile >>>>>>>> >>> >>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> about that dicom that had that insertion error it's about 30mb >>>>>>>> and when >>>>>>>> >>> it is being processed the ram is being drastically increased >>>>>>>> from 2gb to >>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is the >>>>>>>> recommended >>>>>>>> >>> size of ram for using Loris? >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>>> >>> >>>>>>>> >>> For the delete script issue, if you are absolutely certain that >>>>>>>> no >>>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>>> mri_upload table >>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>>> uploadID. It >>>>>>>> >>> looks like for some reason the scripts did not update this >>>>>>>> field when it >>>>>>>> >>> stopped the insertion. Not sure why that would be the case >>>>>>>> though. >>>>>>>> >>> Note: only do that update if you are certain that there is no >>>>>>>> processing >>>>>>>> >>> happening. >>>>>>>> >>> >>>>>>>> >>> Hope this helps! >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>>>>> actually do >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>>> missing at the >>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but with >>>>>>>> no mnic >>>>>>>> >>> files. Also now i have this error >>>>>>>> >>> >>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>>> :/data/loris/bin/mri/tools$ >>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>> processing it. >>>>>>>> >>> >>>>>>>> >>> How can solve this? >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>>> >>> >>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>> >>> >>>>>>>> >>> To give you a brief idea: >>>>>>>> >>> Per folder it will: >>>>>>>> >>> 1) Delete all the .bak files >>>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>>>> TE_min, >>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>>> mri_protocol table >>>>>>>> >>> >>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>> >>> For some reason some files are missing >>>>>>>> SeriesDescription/ProtocolName >>>>>>>> >>> >>>>>>>> >>> In total i have 7 folders >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> 3/7 passed >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> Also about the first patient with DC0000 had a violation "T1 >>>>>>>> AXIAL SE >>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i >>>>>>>> find that weird >>>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>>> >>> >>>>>>>> >>> 102327840 and 102809579 outputs "The target directory does not >>>>>>>> contain a >>>>>>>> >>> single DICOM file.", therefore they are missing their StudyUID >>>>>>>> >>> >>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>> multiple >>>>>>>> >>> studies." >>>>>>>> >>> >>>>>>>> >>> and 102761034 "No data could be converted into valid MINC files. >>>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>>> >>> >>>>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 and >>>>>>>> 102506134 >>>>>>>> >>> can i just pass a flag parameter to >>>>>>>> batch_uploads_imageuploader.pl? or >>>>>>>> >>> modify imaging_upload_file.pl? >>>>>>>> >>> >>>>>>>> >>> Thank you, >>>>>>>> >>> >>>>>>>> >>> Sotirios >>>>>>>> >>> >>>>>>>> >>> PS >>>>>>>> >>> >>>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>>> dicom_output.txt. >>>>>>>> >>> >>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, Ms. >>>>>>>> < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> Glad to hear about your progress. >>>>>>>> >>> >>>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>>> documented here >>>>>>>> >>> < >>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>>> > >>>>>>>> >>> -- let us know if you didn't find the answers you were looking >>>>>>>> for there. >>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>> database >>>>>>>> >>> management software is a visual placeholder for you as the >>>>>>>> user? I'm not >>>>>>>> >>> sure why a scanner would ever be registered with ID='0' as your >>>>>>>> screenshot >>>>>>>> >>> showed.) >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> I fixed it with this >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>>> something >>>>>>>> >>> wrong with the structure? why did i receive a 500 internal >>>>>>>> error? In the >>>>>>>> >>> loris-error log it state that there is something wrong with >>>>>>>> token, but i >>>>>>>> >>> verfied that the type of the token is a string. >>>>>>>> >>> >>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>> [client >>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: >>>>>>>> Argument 1 >>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the >>>>>>>> type string, >>>>>>>> >>> null given, called in >>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>>>>> 169 and >>>>>>>> >>> defined in >>>>>>>> >>> >>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>> >>> trace:\n#0 >>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 >>>>>>>> {main}\n thrown in >>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line >>>>>>>> 192 >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> Is there a way also to delete candidates? Just to let you know >>>>>>>> what i >>>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>>> dependencies. >>>>>>>> >>> >>>>>>>> >>> First i deleted all their uploads >>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way >>>>>>>> to omit >>>>>>>> >>> the backup file ? ) >>>>>>>> >>> >>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted all the >>>>>>>> entries >>>>>>>> >>> from mri_scanner except that i couldn't delete this entry with >>>>>>>> the 0 ID. >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. >>>>>>>> < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> We recommend that you use our existing tools for creating new >>>>>>>> candidates >>>>>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>>>>> calling the Candidate >>>>>>>> >>> class's createNew() >>>>>>>> >>> < >>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>>> >function. >>>>>>>> >>> These will create the necessary records for you. (It's not >>>>>>>> recommended to >>>>>>>> >>> make direct modifications to mysql database tables in your >>>>>>>> script, if I >>>>>>>> >>> understand you.) >>>>>>>> >>> >>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, and >>>>>>>> there are >>>>>>>> >>> multiple reasons for this. >>>>>>>> >>> You can use the PSCID for project-specific IDs and the External >>>>>>>> ID field >>>>>>>> >>> in the candidate table can also be used for any values you like. >>>>>>>> >>> Additionally, any number of custom IDs can be added in parallel >>>>>>>> - these >>>>>>>> >>> are entered/visible in the Candidate Information module and >>>>>>>> added in the >>>>>>>> >>> back-end as candidate parameters. >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> We are building a script that will auto insert the candidates >>>>>>>> based on >>>>>>>> >>> their ExternalID. We would like to know whethere when we are >>>>>>>> creating a new >>>>>>>> >>> profile in the candidate table, if we also have to insert a new >>>>>>>> record at >>>>>>>> >>> another table? Furthermore is there a problem that in our case >>>>>>>> CandID won't >>>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs < >>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> That would normally be the case but the numeric part of the >>>>>>>> PSCID get >>>>>>>> >>> paded with 0 on the left. >>>>>>>> >>> >>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>> numerical char >>>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>>> >>> >>>>>>>> >>> ABC0001 >>>>>>>> >>> ABC0002 >>>>>>>> >>> ... >>>>>>>> >>> ABC0010 >>>>>>>> >>> ... >>>>>>>> >>> >>>>>>>> >>> thus sorting them ascending will always get the latest value >>>>>>>> generated >>>>>>>> >>> as the max value. >>>>>>>> >>> >>>>>>>> >>> M?lanie >>>>>>>> >>> >>>>>>>> >>> ------------------------------ >>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>> >>> >>>>>>>> >>> I see, although the PSCID value is varchar(255), it must be >>>>>>>> stored >>>>>>>> >>> within a specific length of characters. Otherwise if we were to >>>>>>>> sort >>>>>>>> >>> strings with different lengths the result would not be sorted >>>>>>>> correctly ( >>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs < >>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hello Sotirios, >>>>>>>> >>> >>>>>>>> >>> There is no `last value` stored anywhere. >>>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>>> increase that >>>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>>> >>> >>>>>>>> >>> Hope this info help. >>>>>>>> >>> >>>>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | >>>>>>>> McGill >>>>>>>> >>> University >>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>> >>> >>>>>>>> >>> ------------------------------ >>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>> >>> Nikoloutsopoulos >>>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> how does Loris determine the next available PSCID value for a >>>>>>>> new >>>>>>>> >>> candidate? >>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>> >>> e.x in the default case the PSCID is sequential, but where do >>>>>>>> we store the >>>>>>>> >>> last value for the sequential sequence? >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> the parameters in the mri_protocol you have assigned are global >>>>>>>> >>> standard? or were assigned after trial and error? >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, Ms. >>>>>>>> < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> Given you have done the initial setup of your tables to match >>>>>>>> your >>>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>>> >>> < >>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>>> > >>>>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> *if i were to change their status to resolve what would happen? >>>>>>>> >>> >>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser from the >>>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>>> /data/loris/data/trashbin/ >>>>>>>> >>> if i were to click their issue to resolve what would happend? >>>>>>>> would they >>>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> The defaut values of the schema exists in my local database. If >>>>>>>> i adjust >>>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>>> uploaded? >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> Is it possible that you haven't set up your mri_protocol table >>>>>>>> ? (and >>>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>>> >>> >>>>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>>>>> insertion >>>>>>>> >>> setup : See the install/setup documentation : >>>>>>>> >>> >>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>> >>> >>>>>>>> >>> To add new rows, just use MySQL insert statements. You can >>>>>>>> adapt the >>>>>>>> >>> insert statements which load the default table values --> e.g. >>>>>>>> Here on >>>>>>>> >>> GitHub : >>>>>>>> >>> >>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>> >>> (see also the mri_scan_type table) >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> I see that i can edit the values but not how to insert new rows. >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> If i choose Inserted with flag then will the minc be inserted? >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>>> >>> >>>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>>> >>> >>>>>>>> >>> It says "could not identify scan type", which we knew already. >>>>>>>> Did you >>>>>>>> >>> click on the link on those words? >>>>>>>> >>> >>>>>>>> >>> It will take you to the next page of the module, showing for >>>>>>>> each scan >>>>>>>> >>> what the scan parameters were, and will also show for >>>>>>>> comparison what's >>>>>>>> >>> stored in your *mri_protocol* table. >>>>>>>> >>> Compare these values to find which parameter was not correct >>>>>>>> according >>>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>>> >>> >>>>>>>> >>> You may end up broadening your mri_protocol value ranges (e.g. >>>>>>>> TR, TE) >>>>>>>> >>> for scans. >>>>>>>> >>> This can be done in the front-end, by editing the database table >>>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>>> >>> >>>>>>>> >>> The MRI Violations module features are explained in more detail >>>>>>>> in the >>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] icon >>>>>>>> in the menu >>>>>>>> >>> bar.) >>>>>>>> >>> >>>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>>> >>> < >>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>> > >>>>>>>> >>> : no MINCs inserted- violated scans >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> looks like my previous email's attachment wasn't delivered due >>>>>>>> to >>>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>>> >>> >>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>> >>> >>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>>> webbrowser, so >>>>>>>> >>> that you can check the filelds easier. >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios -- >>>>>>>> >>> Great, sounds like more progress. >>>>>>>> >>> >>>>>>>> >>> About the dcmodify command -- I'm not sure why you're getting >>>>>>>> an Endian >>>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>> successfully >>>>>>>> >>> relabelled, after the command ran? >>>>>>>> >>> >>>>>>>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) >>>>>>>> to >>>>>>>> >>> verify and/or update local DICOM headers -- though your >>>>>>>> dcmodify command is >>>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>>> >>> >>>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>>> "(2001,105f)" from >>>>>>>> >>> the warning message) - you can also dcmdump a DICOM slice >>>>>>>> before and look >>>>>>>> >>> at these fields specifically. >>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>> before/after >>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff the >>>>>>>> outputs -- >>>>>>>> >>> this will pinpoint what changed. >>>>>>>> >>> >>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not recognized >>>>>>>> or >>>>>>>> >>> unknown : this means your scans did not match what is stored >>>>>>>> in your >>>>>>>> >>> mri_protocol table. >>>>>>>> >>> Check the MRI Violations front-end module -- can you see why >>>>>>>> they didn't >>>>>>>> >>> match? >>>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>>> mri_protocol >>>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Here is the psc table >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>>> >>> >>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>> >>> >>>>>>>> >>> and got those warning: is this okay? >>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>>>> reading a >>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>>>> reading a >>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined length, >>>>>>>> reading a >>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined length, >>>>>>>> reading a >>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>>>> reading a >>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>>>> reading a >>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>> >>> >>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you can >>>>>>>> see the >>>>>>>> >>> execution for the second dicom. Mnics could not be inserted due >>>>>>>> to >>>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>>> >>> >>>>>>>> >>> Running now the following command: >>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>> >>> >>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>> '__MACOSX' >>>>>>>> >>> -delete >>>>>>>> >>> >>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose >>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>>> >>> >>>>>>>> >>> Testing for database connectivity. >>>>>>>> >>> Database is available. >>>>>>>> >>> >>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>> >>> >>>>>>>> >>> You are creating a tar with the following command: >>>>>>>> >>> >>>>>>>> >>> tar -cf /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> getting md5sums and gzipping!! >>>>>>>> >>> >>>>>>>> >>> * Taken from dir : >>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>> >>> * Archive target location : >>>>>>>> >>> >>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>> >>> * Name of host OS : Linux >>>>>>>> >>> * Created by user : lorisadmin >>>>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>>>> >>> * dicomSummary version : 1 >>>>>>>> >>> * dicomTar version : 1 >>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>> >>> * md5sum for complete archive : >>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>> >>> >>>>>>>> >>> Adding archive info into database >>>>>>>> >>> >>>>>>>> >>> Removing temporary files from target location >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> Done adding archive info into database >>>>>>>> >>> >>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>> -globLocation >>>>>>>> >>> -profile prod >>>>>>>> >>> >>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>> >>> -uploadID 12 -verbose >>>>>>>> >>> md5sum >>>>>>>> >>> >>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>> >>> PSCID is: DCC0001 >>>>>>>> >>> CandID id: 602102 >>>>>>>> >>> visit_label is: V1 >>>>>>>> >>> PSCID is: DCC0001 >>>>>>>> >>> CandID id: 602102 >>>>>>>> >>> visit_label is: V1 >>>>>>>> >>> candidate id 602102 >>>>>>>> >>> Set centerID = 1 >>>>>>>> >>> PSCID is: DCC0001 >>>>>>>> >>> CandID id: 602102 >>>>>>>> >>> visit_label is: V1 >>>>>>>> >>> PSCID is: DCC0001 >>>>>>>> >>> CandID id: 602102 >>>>>>>> >>> visit_label is: V1 >>>>>>>> >>> >>>>>>>> >>> Number of MINC files that will be considered for inserting into >>>>>>>> the >>>>>>>> >>> database: 2 >>>>>>>> >>> >>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>> >>> PSCID is: DCC0001 >>>>>>>> >>> CandID id: 602102 >>>>>>>> >>> visit_label is: V1 >>>>>>>> >>> PSCID is: DCC0001 >>>>>>>> >>> CandID id: 602102 >>>>>>>> >>> visit_label is: V1 >>>>>>>> >>> candidate id 602102 >>>>>>>> >>> >>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>> >>> PSCID is: DCC0001 >>>>>>>> >>> CandID id: 602102 >>>>>>>> >>> visit_label is: V1 >>>>>>>> >>> PSCID is: DCC0001 >>>>>>>> >>> CandID id: 602102 >>>>>>>> >>> visit_label is: V1 >>>>>>>> >>> candidate id 602102 >>>>>>>> >>> >>>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>> >>> >>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>> cat >>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>> >>> >>>>>>>> >>> ==> Loading file from disk >>>>>>>> >>> >>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>> >>> >>>>>>>> >>> --> mapping DICOM parameter for >>>>>>>> >>> >>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>> >>> >>>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>>> >>> >>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>> >>> >>>>>>>> >>> ==> verifying acquisition protocol >>>>>>>> >>> >>>>>>>> >>> Acquisition protocol is unknown >>>>>>>> >>> >>>>>>>> >>> --> The minc file cannot be registered since the >>>>>>>> AcquisitionProtocol >>>>>>>> >>> is unknown >>>>>>>> >>> >>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, Ms. >>>>>>>> < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios: >>>>>>>> >>> >>>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>>> *delete_imaging_upload* >>>>>>>> >>> script -- >>>>>>>> >>> details here: >>>>>>>> >>> >>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>> >>> >>>>>>>> >>> What's in your *psc* table? (Is it properly populated? This is >>>>>>>> a >>>>>>>> >>> pre-requisite to loading imaging data. >>>>>>>> >>> < >>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>>> > >>>>>>>> >>> ) >>>>>>>> >>> The foreign key constraint error on the candidate record is >>>>>>>> curious. >>>>>>>> >>> >>>>>>>> >>> There are also a few options for creating candidates when >>>>>>>> inserting >>>>>>>> >>> imaging data: >>>>>>>> >>> >>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>>>> pipeline >>>>>>>> >>> >>>>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>>>> optionally I >>>>>>>> >>> think) >>>>>>>> >>> How to: >>>>>>>> >>> >>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>> >>> >>>>>>>> >>> Then as a second step: >>>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>>> >>> < >>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>>> > >>>>>>>> >>> to load your DICOMs. >>>>>>>> >>> You will want to first ensure that the PatientName header in >>>>>>>> the DICOMs >>>>>>>> >>> as well as tar package are correctly labelled with >>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>> >>> >>>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>>> >>> How to : >>>>>>>> >>> >>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>> >>> >>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>>> bids_import script, >>>>>>>> >>> to automatically create your candidates and sessions. >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> How do i delete a Study? And everytime do i have to create a new >>>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>>> >>> >>>>>>>> >>> *First execution:* >>>>>>>> >>> >>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>> ./ >>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>> ~/Desktop/input.txt > >>>>>>>> >>> log.txt >>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>>>> foreign >>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>> `FK_candidate_1` >>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>> (`CenterID`)) at >>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>> >>> The following database commands failed: >>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>>> (?,?,?,?,?)'; >>>>>>>> >>> SET >>>>>>>> >>> >>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>> >>> Medical Systems'; >>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>> >>> Error obtained:Cannot add or update a child row: a foreign key >>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>> `FK_mri_scanner_1` >>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) >>>>>>>> (error code 1452) >>>>>>>> >>> >>>>>>>> >>> ERROR: The validation has failed. Either re-run the validation >>>>>>>> again >>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force >>>>>>>> to force the >>>>>>>> >>> execution. >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>> batch_uploads_imageuploader.pl >>>>>>>> >>> line 250. >>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>> batch_uploads_imageuploader.pl >>>>>>>> >>> line 251. >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> *And second execution: * >>>>>>>> >>> >>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>> ./ >>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>> ~/Desktop/input.txt > >>>>>>>> >>> log.txt >>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>> >>> >>>>>>>> >>> PROBLEM: >>>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>>> >>> The unique study ID is >>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>> >>> This is the information retained from the first time the study >>>>>>>> was >>>>>>>> >>> inserted: >>>>>>>> >>> >>>>>>>> >>> * Taken from dir : >>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>> >>> * Archive target location : >>>>>>>> >>> >>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>> >>> * Name of host OS : Linux >>>>>>>> >>> * Created by user : lorisadmin >>>>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>>>> >>> * dicomSummary version : 1 >>>>>>>> >>> * dicomTar version : 1 >>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>> >>> * md5sum for complete archive : >>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> Last update of record: >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>> batch_uploads_imageuploader.pl >>>>>>>> >>> line 250. >>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>> batch_uploads_imageuploader.pl >>>>>>>> >>> line 251. >>>>>>>> >>> >>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> Ok, this sounds like good progress. Let us know when you next >>>>>>>> encounter >>>>>>>> >>> issues as you progress through the Imaging Install/Setup docs >>>>>>>> >>> < >>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>. >>>>>>>> >>> I'll look into how we can better handle the incoming/ directory >>>>>>>> next >>>>>>>> >>> time. >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py >>>>>>>> is >>>>>>>> >>> populated correctly except its port is 'port' : ''. Also i >>>>>>>> have tested >>>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>>> >>> >>>>>>>> >>> I executed the script again, because the only error i had >>>>>>>> previously was >>>>>>>> >>> that the /data/incoming folder didn't exist and there are no >>>>>>>> errors >>>>>>>> >>> reported back except of warnings <>>>>>>> password on the >>>>>>>> >>> command line interface can be insecure>>. >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> It's possible -- if the script was unable to connect to the >>>>>>>> database >>>>>>>> >>> during its execution (e.g. typo in the password), that would >>>>>>>> explain the >>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw in >>>>>>>> the Config >>>>>>>> >>> module. >>>>>>>> >>> It's hard to tell without seeing the output from your script >>>>>>>> run -- Did >>>>>>>> >>> you see a sign of any such error? >>>>>>>> >>> The Config fields are populated by the imaging_install.sh >>>>>>>> script (starting >>>>>>>> >>> at line 222 >>>>>>>> >>> < >>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>>> > >>>>>>>> >>> ) >>>>>>>> >>> >>>>>>>> >>> For example, check if the database connection information was >>>>>>>> populated >>>>>>>> >>> accurately in >>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> Hi Christine, >>>>>>>> >>> >>>>>>>> >>> If you are referring to the imaging_install.sh here is an image >>>>>>>> with the >>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at the >>>>>>>> last part >>>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi Sotirios, >>>>>>>> >>> >>>>>>>> >>> Glad to hear your LORIS core install is up and working and all >>>>>>>> the >>>>>>>> >>> front-end pages are loading. >>>>>>>> >>> >>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project >>>>>>>> >>> > and the web interface worked. >>>>>>>> >>> >>>>>>>> >>> Yes, it's important that project/ have 775 permissions and that >>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the >>>>>>>> install >>>>>>>> >>> Readme . >>>>>>>> >>> >>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change >>>>>>>> LORIS to >>>>>>>> >>> loris, right? >>>>>>>> >>> >>>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>>> installation >>>>>>>> >>> by an automated >>>>>>>> script -- >>>>>>>> >>> you do not need to set them manually via the Config module. >>>>>>>> >>> Please continue to follow the Setup Guide >>>>>>>> >>> for detailed steps >>>>>>>> to follow. >>>>>>>> >>> >>>>>>>> >>> Best, >>>>>>>> >>> Christine >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>> >>> >>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS >>>>>>>> to loris, >>>>>>>> >>> right? >>>>>>>> >>> >>>>>>>> >>> [image: image.png] >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>> Nikoloutsopoulos < >>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>> >>> >>>>>>>> >>> Hi, >>>>>>>> >>> >>>>>>>> >>> i used >>>>>>>> >>> >>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>> >>> sudo apt-get install -y nodejs >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> you had suggested in the past, make worked and now i can see >>>>>>>> all the >>>>>>>> >>> contents in the web-interface, but i don't need make install? >>>>>>>> >>> >>>>>>>> >>> Thanks >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> >>> -- >>>>>>>> >>> >>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>> >>> Montreal Neurological Institute >>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>> >>> >>>>>>>> >>> _______________________________________________ >>>>>>>> >>> Loris-dev mailing list >>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>> >>>>>>>> >>> >>>>>>>> -------------- next part -------------- >>>>>>>> An HTML attachment was scrubbed... >>>>>>>> URL: < >>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>>>> > >>>>>>>> >>>>>>>> ------------------------------ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>>> >>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>>>> ***************************************** >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> >>>>> christine.rogers at mcgill.ca >>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>> Montreal Neurological Institute >>>>> McGill University | Montreal | Canada >>>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> 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URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 37207 bytes Desc: not available URL: From AMORALESPINZON at bwh.harvard.edu Mon Nov 25 10:02:32 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Mon, 25 Nov 2019 15:02:32 +0000 Subject: [Loris-dev] LORIS Error: The target directory does not contain a single DICOM file. Message-ID: <4A0C0CF2-B5BC-47F1-84F9-287D4BD9B547@bwh.harvard.edu> Dear LorisDev team, I am batch uploading images to imaging visits using the script batch_uploads_imageuploader but for some images I get the following error: The target directory does not contain a single DICOM file. I had seen this error previously due to missing dicom fields like StudyID (0020,0010) and ImagePositionPatient (0020,0032). However, after checking these particular dicom fields and setting StudyID it to '0' I am still getting the same error. What other dicom fields should I check? Is there a log where I can exactly find the error? Does the "StudyInstanceUID" need to have a value? I'm pasting the dcmdump of a dicom at the end of this email in case this might help figuring out what is the issue. I am using LORIS v at 20.1.1. Thank you in advance for your help. Best regards, Alfredo. -------------------------------------------------------------------------------------- # Dicom-File-Format # Dicom-Meta-Information-Header # Used TransferSyntax: Little Endian Explicit (0002,0000) UL 230 # 4, 1 FileMetaInformationGroupLength (0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion (0002,0002) UI =MRImageStorage # 26, 1 MediaStorageSOPClassUID (0002,0003) UI [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] # 64, 1 MediaStorageSOPInstanceUID (0002,0010) UI =LittleEndianImplicit # 18, 1 TransferSyntaxUID (0002,0012) UI [1.2.276.0.7230010.3.0.3.6.0] # 28, 1 ImplementationClassUID (0002,0013) SH [OFFIS_DCMTK_360] # 16, 1 ImplementationVersionName (0002,0016) AE [GDCM/ITK 3.17.0] # 16, 1 SourceApplicationEntityTitle # Dicom-Data-Set # Used TransferSyntax: Little Endian Implicit (0008,0008) CS [DERIVED\SECONDARY] # 18, 2 ImageType (0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID (0008,0018) UI [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] # 64, 1 SOPInstanceUID (0008,0020) DA [20000101] # 8, 1 StudyDate (0008,0021) DA [20000101] # 8, 1 SeriesDate (0008,0022) DA [20000101] # 8, 1 AcquisitionDate (0008,0030) TM (no value available) # 0, 0 StudyTime (0008,0031) TM [085517] # 6, 1 SeriesTime (0008,0032) TM [085517] # 6, 1 AcquisitionTime (0008,0060) CS [MR] # 2, 1 Modality (0008,0070) LO [AAABBBCCC] # 6, 1 Manufacturer (0008,0104) LO [Anonymized] # 10, 1 CodeMeaning (0008,103e) LO [t1c] # 4, 1 SeriesDescription (0008,1090) LO [nifti2dicom] # 12, 1 ManufacturerModelName (0010,0010) PN [10041] # 6, 1 PatientName (0010,0020) LO [10041] # 6, 1 PatientID (0010,0021) LO [Anonymized] # 10, 1 IssuerOfPatientID (0010,0030) DA [19650101] # 8, 1 PatientBirthDate (0010,0040) CS [Anonymized] # 10, 1 PatientSex (0010,1010) AS [Anonymized] # 10, 1 PatientAge (0010,1030) DS (no value available) # 0, 0 PatientWeight (0010,2150) LO [Anonymized] # 10, 1 CountryOfResidence (0010,2152) LO [Anonymized] # 10, 1 RegionOfResidence (0010,21f0) LO [Anonymized] # 10, 1 PatientReligiousPreference (0012,0050) LO [baseline] # 8, 1 ClinicalTrialTimePointID (0012,0062) CS [Yes] # 4, 1 PatientIdentityRemoved (0012,0063) LO [Genentech] # 10, 1 DeidentificationMethod (0018,0050) DS [3] # 2, 1 SliceThickness (0018,0088) DS [3] # 2, 1 SpacingBetweenSlices (0020,000d) UI (no value available) # 0, 0 StudyInstanceUID (0020,000e) UI [1.2.826.0.1.3680043.2.1143.2737712182581015462892759360372011946] # 64, 1 SeriesInstanceUID (0020,0010) SH [0] # 2, 1 StudyID (0020,0011) IS [901] # 4, 1 SeriesNumber (0020,0012) IS [1] # 2, 1 AcquisitionNumber (0020,0013) IS [1] # 2, 1 InstanceNumber (0020,0020) CS [L\R] # 4, 2 PatientOrientation (0020,0032) DS [-116.48152160645\-118.93698120117\-275.82513427734] # 50, 3 ImagePositionPatient (0020,0037) DS [1\0\0\0\1\0] # 12, 6 ImageOrientationPatient (0020,0052) UI [1.2.826.0.1.3680043.2.1143.263896814292546686535778822643473818] # 64, 1 FrameOfReferenceUID (0028,0002) US 1 # 2, 1 SamplesPerPixel (0028,0004) CS [MONOCHROME2] # 12, 1 PhotometricInterpretation (0028,0010) US 256 # 2, 1 Rows (0028,0011) US 256 # 2, 1 Columns (0028,0030) DS [1\1] # 4, 2 PixelSpacing (0028,0100) US 16 # 2, 1 BitsAllocated (0028,0101) US 16 # 2, 1 BitsStored (0028,0102) US 15 # 2, 1 HighBit (0028,0103) US 1 # 2, 1 PixelRepresentation (0032,1033) LO [Anonymized] # 10, 1 RequestingService (0040,0280) ST [Anonymized] # 10, 1 CommentsOnThePerformedProcedureStep (0400,0563) LO [Anonymized] # 10, 1 ModifyingSystem (0400,0564) LO [Anonymized] # 10, 1 SourceOfPreviousValues (0400,0565) CS [Anonymized] # 10, 1 ReasonForTheAttributeModification (1110,21b0) ?? 0a\00 # 2, 1 Unknown Tag & Data (7fe0,0010) OW 0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000... # 131072, 1 PixelData The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Mon Nov 25 10:06:08 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 25 Nov 2019 10:06:08 -0500 Subject: [Loris-dev] LORIS Error: The target directory does not contain a single DICOM file. In-Reply-To: <4A0C0CF2-B5BC-47F1-84F9-287D4BD9B547@bwh.harvard.edu> References: <4A0C0CF2-B5BC-47F1-84F9-287D4BD9B547@bwh.harvard.edu> Message-ID: Hi Alfredo, Indeed, the StudyInstanceUID needs to have a value for the insertion pipeline to work so that could explain the no DICOM found error. FYI - StudyInstanceUID also needs to be unique for each uploaded study otherwise insertion in the tarchive tables would fail with the error: "the study has already been uploaded" Hope this helps, C?cile On Mon, Nov 25, 2019 at 10:02 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > I am batch uploading images to imaging visits using the script > batch_uploads_imageuploader but for some images I get the following error: > > *The target directory does not contain a single DICOM file.* > > I had seen this error previously due to missing dicom fields like StudyID > (0020,0010) and ImagePositionPatient (0020,0032). However, after checking > these particular dicom fields and setting StudyID it to '0' I am still > getting the same error. What other dicom fields should I check? > > Is there a log where I can exactly find the error? Does the > "StudyInstanceUID" need to have a value? > > I'm pasting the dcmdump of a dicom at the end of this email in case this > might help figuring out what is the issue. > > I am using LORIS v at 20.1.1. > > Thank you in advance for your help. > > Best regards, > Alfredo. > > > -------------------------------------------------------------------------------------- > > # Dicom-File-Format > > # Dicom-Meta-Information-Header > # Used TransferSyntax: Little Endian Explicit > (0002,0000) UL 230 # 4, 1 > FileMetaInformationGroupLength > (0002,0001) OB 00\01 # 2, 1 > FileMetaInformationVersion > (0002,0002) UI =MRImageStorage # 26, 1 > MediaStorageSOPClassUID > (0002,0003) UI > [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] # 64, 1 > MediaStorageSOPInstanceUID > (0002,0010) UI =LittleEndianImplicit # 18, 1 > TransferSyntaxUID > (0002,0012) UI [1.2.276.0.7230010.3.0.3.6.0] # 28, 1 > ImplementationClassUID > (0002,0013) SH [OFFIS_DCMTK_360] # 16, 1 > ImplementationVersionName > (0002,0016) AE [GDCM/ITK 3.17.0] # 16, 1 > SourceApplicationEntityTitle > > # Dicom-Data-Set > # Used TransferSyntax: Little Endian Implicit > (0008,0008) CS [DERIVED\SECONDARY] # 18, 2 ImageType > (0008,0016) UI =MRImageStorage # 26, 1 > SOPClassUID > (0008,0018) UI > [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] # 64, 1 > SOPInstanceUID > (0008,0020) DA [20000101] # 8, 1 StudyDate > (0008,0021) DA [20000101] # 8, 1 SeriesDate > (0008,0022) DA [20000101] # 8, 1 > AcquisitionDate > (0008,0030) TM (no value available) # 0, 0 StudyTime > (0008,0031) TM [085517] # 6, 1 SeriesTime > (0008,0032) TM [085517] # 6, 1 > AcquisitionTime > (0008,0060) CS [MR] # 2, 1 Modality > (0008,0070) LO [AAABBBCCC] # 6, 1 > Manufacturer > (0008,0104) LO [Anonymized] # 10, 1 > CodeMeaning > (0008,103e) LO [t1c] # 4, 1 > SeriesDescription > (0008,1090) LO [nifti2dicom] # 12, 1 > ManufacturerModelName > (0010,0010) PN [10041] # 6, 1 > PatientName > (0010,0020) LO [10041] # 6, 1 PatientID > (0010,0021) LO [Anonymized] # 10, 1 > IssuerOfPatientID > (0010,0030) DA [19650101] # 8, 1 > PatientBirthDate > (0010,0040) CS [Anonymized] # 10, 1 PatientSex > (0010,1010) AS [Anonymized] # 10, 1 PatientAge > (0010,1030) DS (no value available) # 0, 0 > PatientWeight > (0010,2150) LO [Anonymized] # 10, 1 > CountryOfResidence > (0010,2152) LO [Anonymized] # 10, 1 > RegionOfResidence > (0010,21f0) LO [Anonymized] # 10, 1 > PatientReligiousPreference > (0012,0050) LO [baseline] # 8, 1 > ClinicalTrialTimePointID > (0012,0062) CS [Yes] # 4, 1 > PatientIdentityRemoved > (0012,0063) LO [Genentech] # 10, 1 > DeidentificationMethod > (0018,0050) DS [3] # 2, 1 > SliceThickness > (0018,0088) DS [3] # 2, 1 > SpacingBetweenSlices > (0020,000d) UI (no value available) # 0, 0 > StudyInstanceUID > (0020,000e) UI > [1.2.826.0.1.3680043.2.1143.2737712182581015462892759360372011946] # 64, 1 > SeriesInstanceUID > *(0020,0010) SH [0] # 2, 1 StudyID* > (0020,0011) IS [901] # 4, 1 > SeriesNumber > (0020,0012) IS [1] # 2, 1 > AcquisitionNumber > (0020,0013) IS [1] # 2, 1 > InstanceNumber > (0020,0020) CS [L\R] # 4, 2 > PatientOrientation > (0020,0032) DS [-116.48152160645\-118.93698120117\-275.82513427734] # 50, > 3 ImagePositionPatient > (0020,0037) DS [1\0\0\0\1\0] # 12, 6 > ImageOrientationPatient > (0020,0052) UI > [1.2.826.0.1.3680043.2.1143.263896814292546686535778822643473818] # 64, 1 > FrameOfReferenceUID > (0028,0002) US 1 # 2, 1 > SamplesPerPixel > (0028,0004) CS [MONOCHROME2] # 12, 1 > PhotometricInterpretation > (0028,0010) US 256 # 2, 1 Rows > (0028,0011) US 256 # 2, 1 Columns > (0028,0030) DS [1\1] # 4, 2 > PixelSpacing > (0028,0100) US 16 # 2, 1 > BitsAllocated > (0028,0101) US 16 # 2, 1 BitsStored > (0028,0102) US 15 # 2, 1 HighBit > (0028,0103) US 1 # 2, 1 > PixelRepresentation > (0032,1033) LO [Anonymized] # 10, 1 > RequestingService > (0040,0280) ST [Anonymized] # 10, 1 > CommentsOnThePerformedProcedureStep > (0400,0563) LO [Anonymized] # 10, 1 > ModifyingSystem > (0400,0564) LO [Anonymized] # 10, 1 > SourceOfPreviousValues > (0400,0565) CS [Anonymized] # 10, 1 > ReasonForTheAttributeModification > (1110,21b0) ?? 0a\00 # 2, 1 Unknown > Tag & Data > (7fe0,0010) OW > 0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000... # > 131072, 1 PixelData > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Mon Nov 25 10:22:26 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 25 Nov 2019 10:22:26 -0500 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, OK. So the issue I mentioned should not be a problem for you. Is the StudyInstanceUID DICOM header set in your images? If it is not set, then you would end up with the error message "The target directory does not contain a single DICOM file". So maybe this is the issue you are having with those datasets? Regarding not excluding series descriptions, you can configure that in the Config module under the Imaging Pipeline section. Simply remove all entries for the "Series description to exclude from imaging insertion" setting. C?cile On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi Cecile, > > We are using this version > https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to > insert low resolution now? > > Thanks > > On Mon, 25 Nov 2019, 16:53 Cecile Madjar, wrote: > >> Hi Sotirios, >> >> Which version of LORIS-MRI are you using? >> >> There was a bug that got resolved in 20.2 in get_dicom_info.pl. >> Basically, if a DICOM did not have the (0020,0032) header, >> get_dicom_info.pl considered that the file was not a DICOM, which was a >> mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this is the >> issue you are encountering. >> >> About scout and localizer, they are a type of short and low resolution >> sequence that is used by the tech but is of no interest scientifically, >> which is why we tend to no insert them. >> >> Hope this helps, >> >> C?cile >> >> >> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi Cecile, >>> >>> i executed the find command and the output i got per folder was "DICOM >>> medical imaging data. Maybe there is something wrong with the find command >>> in the warning that it is unable to check if the file is a dicom file? Also >>> when i use get_dicom_info.pl i don't get any output data. Finally i >>> don't understand what scout or localizer is ( something like if and only if >>> a file fails then the whole session is invalid? ). >>> >>> [image: image.png] >>> >>> Thanks >>> >>> Sotirios >>> >>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>>> Hi Sotirios, >>>> >>>> I took a closer look to the batch_uploader_multiple_output.txt file you >>>> sent. It looks like there are different reasons for failure depending on >>>> the DICOM folder uploaded. >>>> >>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1: >>>> it looks like there is no file of type DICOM in the folder. Have you >>>> checked to see if that is indeed the case? Maybe you can try running the >>>> following command on that folder to see what are the types of the files? If >>>> it does not return at least one DICOM medical imaging data file, then that >>>> is why you get the error message from the pipeline: >>>> - >>>> >>>> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >>>> >>>> - For 864173 DCC0001 V1: it looks like there are two different >>>> DICOM studies within the same folder. You will need to split that study in >>>> two based on the StudyUID field as the insertion pipeline does not allow >>>> for more than one StudyUID per upload. >>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1: >>>> it looks like the dcm2mnc command did not produce any MINC files. Can you >>>> check in the DICOM archive what are the series present in the tarchive for >>>> that visit? Maybe only a scout or localizer was acquired for that session, >>>> hence the no valid MINC files (scout and localizer being skipped for the >>>> conversion) >>>> - For 397410 DCC0003 V1: it looks like everything went well for >>>> this one. >>>> >>>> One script that is called by our pipeline is called get_dicom_info.pl and >>>> this does all kind of checks on the DICOM files (it is being called when >>>> running the dcm2mnc conversion). You could run it independently on your >>>> folder if needed. >>>> >>>> Since one of the study got in, it does not look like you are having a >>>> problem with the setup. It seems more likely to be a problem with the data >>>> themselves. >>>> >>>> Hope this helps. >>>> >>>> C?cile >>>> >>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi Christine, >>>>> >>>>> In my first vm i am able to create the minc files and view them at the >>>>> mri browser (except of candidate 102761034 ), meanwhile the same files >>>>> gives warnings at the 2nd vm. The output of the batch upload can be seen >>>>> in the file attached. >>>>> Also a colleague of us has built a pre-validation tool for dicom >>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had found >>>>> all the files that Loris gave as warning . Basically I confirmed that the >>>>> total amount of files per dicom was the same amount as stated in Loris and >>>>> checked some filenames given from warning to confirm that they match with >>>>> our tool. But that was months ago and my colleague had changed some >>>>> parameters for MIP and now our tool doesn't find all the invalid files, >>>>> that's why i asked for the dicom header specification of Loris. In a >>>>> discussion we had he mentioned that he doesn't check for some tags e.x. >>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>>>> remove invalid dcm files. >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>>>> christine.rogers at mcgill.ca> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> Can you provide us with some fresh particulars of the current issue >>>>>> and we'll take it from there? >>>>>> Yang's team has built these scripts which can definitely serve as a >>>>>> model for your pre-validation of your DICOM collections. >>>>>> cheers, >>>>>> Christine >>>>>> >>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> HI Yang, >>>>>>> >>>>>>> We make use of pydicom library too. Now about the validate.py i see >>>>>>> that you check if some attributes are missing such as PatientID, >>>>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>>>> something on the setup of my other virtual machine ( although one dicom >>>>>>> passed on the new vm successfully, the others that were inserted correctly >>>>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but i >>>>>>> don't remember the solution. >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>>>> ??????: >>>>>>> >>>>>>>> Hey, Sotirios, >>>>>>>> >>>>>>>> Christine from the LORIS team mentioned you had some issue with >>>>>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>>>>> fully automated pipeline actually. >>>>>>>> >>>>>>>> While we were building CNBP, we had coded up some minor Python >>>>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>>>> more comprehensive solution, PyDICOM ( >>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>>>> >>>>>>>> Cheers, >>>>>>>> >>>>>>>> Yang Ding, PhD. >>>>>>>> Canadian Neonatal Brain Platform Architect >>>>>>>> >>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM < >>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote: >>>>>>>> >>>>>>>>> Send Loris-dev mailing list submissions to >>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>>>> >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>>>> >>>>>>>>> You can reach the person managing the list at >>>>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>>>> >>>>>>>>> When replying, please edit your Subject line so it is more specific >>>>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>>>> >>>>>>>>> >>>>>>>>> Today's Topics: >>>>>>>>> >>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> ---------------------------------------------------------------------- >>>>>>>>> >>>>>>>>> Message: 1 >>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>>>> To: Cecile Madjar >>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>>>> Message-ID: >>>>>>>>> >>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>>>> >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Could we send you a link with 10 anonymized dicom files to >>>>>>>>> diagnose the >>>>>>>>> warnings we get? >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>>>>>>>> > Hi Cecile, >>>>>>>>> > >>>>>>>>> > We were wondering whether Loris has a tool to check if there are >>>>>>>>> problems >>>>>>>>> > with the dcm files, before trying to upload them. Something that >>>>>>>>> could >>>>>>>>> > provide the same results provided in the warning_output, this is >>>>>>>>> the >>>>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>>>> attributes of the >>>>>>>>> > dcm header would trigger a warning? is there a dcm file header >>>>>>>>> > specification for Loris? >>>>>>>>> > >>>>>>>>> > Thanks >>>>>>>>> > >>>>>>>>> > Sotirios >>>>>>>>> > >>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>>>> > >>>>>>>>> >> Hi, >>>>>>>>> >> >>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it >>>>>>>>> worked,but i >>>>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>>>> >> Thanks >>>>>>>>> >> >>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>>>> >> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and >>>>>>>>> columns are of >>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be using >>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>>>> >>> >>>>>>>>> >>> The second error occurs because the trigger triggers a >>>>>>>>> rollback of the >>>>>>>>> >>> insert statement in the files table. >>>>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>>>> >>> >>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>>>>>> failure of >>>>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>>>> >>> -- Xavier >>>>>>>>> >>> >>>>>>>>> >>> ------------------------------ >>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>>>> >>> *To:* Cecile Madjar >>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>>>>>> >; >>>>>>>>> >>> Christine Rogers, Ms. >>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>> >>> >>>>>>>>> >>> When mincs are inserted their corresponding rows at the file >>>>>>>>> table are >>>>>>>>> >>> inserted too >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>>>>>> because i >>>>>>>>> >>> don't want manually to label them as passed throught the >>>>>>>>> interface >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> That is the trigger i wrote >>>>>>>>> >>> >>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>>>> >>> BEGIN >>>>>>>>> >>> INSERT INTO files_qcstatus >>>>>>>>> >>> SET FileID = NEW.FileID, >>>>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>>>> >>> QCStatus = "Pass", >>>>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>>>> >>> END >>>>>>>>> >>> >>>>>>>>> >>> although it contains some errors >>>>>>>>> >>> >>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>>>>> foreign >>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES >>>>>>>>> `files` (`FileID`)) >>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column >>>>>>>>> associated with >>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it means >>>>>>>>> no DICOMs >>>>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>>>> insertion of the >>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with the >>>>>>>>> correct >>>>>>>>> >>> TarchiveID associated with the upload. >>>>>>>>> >>> >>>>>>>>> >>> Could this correspond to what you want to do? >>>>>>>>> >>> >>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked to the >>>>>>>>> files >>>>>>>>> >>> table (hence, the MINC files). You could always create a new >>>>>>>>> table for >>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>>>> >>> >>>>>>>>> >>> C?cile >>>>>>>>> >>> >>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of creating >>>>>>>>> a trigger for >>>>>>>>> >>> that, but which tables do i need to add entries to? So far >>>>>>>>> from what i see >>>>>>>>> >>> i need to add entres at the table "files" whenever an >>>>>>>>> insertion happens to >>>>>>>>> >>> files_qcstatus. >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning of >>>>>>>>> my email >>>>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the StudyID >>>>>>>>> i am >>>>>>>>> >>> looking for is not stored in the database? >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> Thanks. >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>>>> >>> tarchive table. It can also be found in the metadata field but >>>>>>>>> it is mixed >>>>>>>>> >>> with many other information. >>>>>>>>> >>> >>>>>>>>> >>> Hope this helps, >>>>>>>>> >>> >>>>>>>>> >>> C?cile >>>>>>>>> >>> >>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive >>>>>>>>> table, >>>>>>>>> >>> specifically at the AcquisitonMetadata column i found >>>>>>>>> something called >>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>>>>>>> Instance UID. >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>>>> >>> >>>>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>>>> >>> >>>>>>>>> >>> - the scan type could not be identified (not matching an >>>>>>>>> entry in >>>>>>>>> >>> the mri_protocol table) >>>>>>>>> >>> - one parameter of the scan type is out of the expected >>>>>>>>> range >>>>>>>>> >>> present in the mri_protocol_checks (extra filtering in case >>>>>>>>> you need to be >>>>>>>>> >>> stricker on some parameters not present in the mri_protocol >>>>>>>>> table) >>>>>>>>> >>> - if the CandID and PSCID do not match >>>>>>>>> >>> >>>>>>>>> >>> The following cases do not get in the MRI violation tables as >>>>>>>>> it happens >>>>>>>>> >>> before the conversion of the DICOM to MINC files and only MINC >>>>>>>>> files >>>>>>>>> >>> violations are logged there: >>>>>>>>> >>> >>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be found to >>>>>>>>> convert >>>>>>>>> >>> to MINC) >>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since this >>>>>>>>> error >>>>>>>>> >>> happens at the dicomTar.pl level (way before conversion >>>>>>>>> into MINC files) >>>>>>>>> >>> >>>>>>>>> >>> Glad everything is working out!! >>>>>>>>> >>> Best, >>>>>>>>> >>> >>>>>>>>> >>> C?cile >>>>>>>>> >>> >>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. Now >>>>>>>>> about the >>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there only >>>>>>>>> if there is >>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>>>> parameter? >>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or with the >>>>>>>>> 2 studyiuid >>>>>>>>> >>> to be there. >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> Sorry to hear you are having issues with the memory. I think >>>>>>>>> most of our >>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>>>>> >>> >>>>>>>>> >>> Hope this helps! >>>>>>>>> >>> >>>>>>>>> >>> C?cile >>>>>>>>> >>> >>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> about that dicom that had that insertion error it's about 30mb >>>>>>>>> and when >>>>>>>>> >>> it is being processed the ram is being drastically increased >>>>>>>>> from 2gb to >>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is the >>>>>>>>> recommended >>>>>>>>> >>> size of ram for using Loris? >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>>>> >>> >>>>>>>>> >>> For the delete script issue, if you are absolutely certain >>>>>>>>> that no >>>>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>>>> mri_upload table >>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>> uploadID. It >>>>>>>>> >>> looks like for some reason the scripts did not update this >>>>>>>>> field when it >>>>>>>>> >>> stopped the insertion. Not sure why that would be the case >>>>>>>>> though. >>>>>>>>> >>> Note: only do that update if you are certain that there is no >>>>>>>>> processing >>>>>>>>> >>> happening. >>>>>>>>> >>> >>>>>>>>> >>> Hope this helps! >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>>>>>> actually do >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>>>> missing at the >>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but >>>>>>>>> with no mnic >>>>>>>>> >>> files. Also now i have this error >>>>>>>>> >>> >>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>>>> :/data/loris/bin/mri/tools$ >>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>> processing it. >>>>>>>>> >>> >>>>>>>>> >>> How can solve this? >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>>>> >>> >>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>> >>> >>>>>>>>> >>> To give you a brief idea: >>>>>>>>> >>> Per folder it will: >>>>>>>>> >>> 1) Delete all the .bak files >>>>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>>>>> TE_min, >>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>>>> mri_protocol table >>>>>>>>> >>> >>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>> >>> For some reason some files are missing >>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>> >>> >>>>>>>>> >>> In total i have 7 folders >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> 3/7 passed >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> Also about the first patient with DC0000 had a violation "T1 >>>>>>>>> AXIAL SE >>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i >>>>>>>>> find that weird >>>>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>>>> >>> >>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory does not >>>>>>>>> contain a >>>>>>>>> >>> single DICOM file.", therefore they are missing their StudyUID >>>>>>>>> >>> >>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>> multiple >>>>>>>>> >>> studies." >>>>>>>>> >>> >>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC >>>>>>>>> files. >>>>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>>>> >>> >>>>>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 and >>>>>>>>> 102506134 >>>>>>>>> >>> can i just pass a flag parameter to >>>>>>>>> batch_uploads_imageuploader.pl? or >>>>>>>>> >>> modify imaging_upload_file.pl? >>>>>>>>> >>> >>>>>>>>> >>> Thank you, >>>>>>>>> >>> >>>>>>>>> >>> Sotirios >>>>>>>>> >>> >>>>>>>>> >>> PS >>>>>>>>> >>> >>>>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>>>> dicom_output.txt. >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, >>>>>>>>> Ms. < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> Glad to hear about your progress. >>>>>>>>> >>> >>>>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>>>> documented here >>>>>>>>> >>> < >>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>>>> > >>>>>>>>> >>> -- let us know if you didn't find the answers you were looking >>>>>>>>> for there. >>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>>> database >>>>>>>>> >>> management software is a visual placeholder for you as the >>>>>>>>> user? I'm not >>>>>>>>> >>> sure why a scanner would ever be registered with ID='0' as >>>>>>>>> your screenshot >>>>>>>>> >>> showed.) >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> I fixed it with this >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>>>> something >>>>>>>>> >>> wrong with the structure? why did i receive a 500 internal >>>>>>>>> error? In the >>>>>>>>> >>> loris-error log it state that there is something wrong with >>>>>>>>> token, but i >>>>>>>>> >>> verfied that the type of the token is a string. >>>>>>>>> >>> >>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>> [client >>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: >>>>>>>>> Argument 1 >>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the >>>>>>>>> type string, >>>>>>>>> >>> null given, called in >>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>> line 169 and >>>>>>>>> >>> defined in >>>>>>>>> >>> >>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>> >>> trace:\n#0 >>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 >>>>>>>>> {main}\n thrown in >>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>> line 192 >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> Is there a way also to delete candidates? Just to let you know >>>>>>>>> what i >>>>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>>>> dependencies. >>>>>>>>> >>> >>>>>>>>> >>> First i deleted all their uploads >>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way >>>>>>>>> to omit >>>>>>>>> >>> the backup file ? ) >>>>>>>>> >>> >>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted all the >>>>>>>>> entries >>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry with >>>>>>>>> the 0 ID. >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, >>>>>>>>> Ms. < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> We recommend that you use our existing tools for creating new >>>>>>>>> candidates >>>>>>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>>>>>> calling the Candidate >>>>>>>>> >>> class's createNew() >>>>>>>>> >>> < >>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>>>> >function. >>>>>>>>> >>> These will create the necessary records for you. (It's not >>>>>>>>> recommended to >>>>>>>>> >>> make direct modifications to mysql database tables in your >>>>>>>>> script, if I >>>>>>>>> >>> understand you.) >>>>>>>>> >>> >>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, and >>>>>>>>> there are >>>>>>>>> >>> multiple reasons for this. >>>>>>>>> >>> You can use the PSCID for project-specific IDs and the >>>>>>>>> External ID field >>>>>>>>> >>> in the candidate table can also be used for any values you >>>>>>>>> like. >>>>>>>>> >>> Additionally, any number of custom IDs can be added in >>>>>>>>> parallel - these >>>>>>>>> >>> are entered/visible in the Candidate Information module and >>>>>>>>> added in the >>>>>>>>> >>> back-end as candidate parameters. >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> We are building a script that will auto insert the candidates >>>>>>>>> based on >>>>>>>>> >>> their ExternalID. We would like to know whethere when we are >>>>>>>>> creating a new >>>>>>>>> >>> profile in the candidate table, if we also have to insert a >>>>>>>>> new record at >>>>>>>>> >>> another table? Furthermore is there a problem that in our case >>>>>>>>> CandID won't >>>>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs >>>>>>>>> < >>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> That would normally be the case but the numeric part of the >>>>>>>>> PSCID get >>>>>>>>> >>> paded with 0 on the left. >>>>>>>>> >>> >>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>> numerical char >>>>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>>>> >>> >>>>>>>>> >>> ABC0001 >>>>>>>>> >>> ABC0002 >>>>>>>>> >>> ... >>>>>>>>> >>> ABC0010 >>>>>>>>> >>> ... >>>>>>>>> >>> >>>>>>>>> >>> thus sorting them ascending will always get the latest value >>>>>>>>> generated >>>>>>>>> >>> as the max value. >>>>>>>>> >>> >>>>>>>>> >>> M?lanie >>>>>>>>> >>> >>>>>>>>> >>> ------------------------------ >>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>> >>> >>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must be >>>>>>>>> stored >>>>>>>>> >>> within a specific length of characters. Otherwise if we were >>>>>>>>> to sort >>>>>>>>> >>> strings with different lengths the result would not be sorted >>>>>>>>> correctly ( >>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, Mrs >>>>>>>>> < >>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hello Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> There is no `last value` stored anywhere. >>>>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>>>> increase that >>>>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>>>> >>> >>>>>>>>> >>> Hope this info help. >>>>>>>>> >>> >>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | >>>>>>>>> McGill >>>>>>>>> >>> University >>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>> >>> >>>>>>>>> >>> ------------------------------ >>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca >>>>>>>> > >>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> how does Loris determine the next available PSCID value for a >>>>>>>>> new >>>>>>>>> >>> candidate? >>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>> >>> e.x in the default case the PSCID is sequential, but where do >>>>>>>>> we store the >>>>>>>>> >>> last value for the sequential sequence? >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> the parameters in the mri_protocol you have assigned are global >>>>>>>>> >>> standard? or were assigned after trial and error? >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, >>>>>>>>> Ms. < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> Given you have done the initial setup of your tables to match >>>>>>>>> your >>>>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>>>> >>> < >>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>>>> > >>>>>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> *if i were to change their status to resolve what would happen? >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser from >>>>>>>>> the >>>>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>>>> /data/loris/data/trashbin/ >>>>>>>>> >>> if i were to click their issue to resolve what would happend? >>>>>>>>> would they >>>>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> The defaut values of the schema exists in my local database. >>>>>>>>> If i adjust >>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>>>> uploaded? >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>> < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol table >>>>>>>>> ? (and >>>>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>>>> >>> >>>>>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>>>>>> insertion >>>>>>>>> >>> setup : See the install/setup documentation : >>>>>>>>> >>> >>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>> >>> >>>>>>>>> >>> To add new rows, just use MySQL insert statements. You can >>>>>>>>> adapt the >>>>>>>>> >>> insert statements which load the default table values --> e.g. >>>>>>>>> Here on >>>>>>>>> >>> GitHub : >>>>>>>>> >>> >>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>> >>> (see also the mri_scan_type table) >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> I see that i can edit the values but not how to insert new >>>>>>>>> rows. >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> If i choose Inserted with flag then will the minc be inserted? >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>> < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>> >>> >>>>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>>>> >>> >>>>>>>>> >>> It says "could not identify scan type", which we knew >>>>>>>>> already. Did you >>>>>>>>> >>> click on the link on those words? >>>>>>>>> >>> >>>>>>>>> >>> It will take you to the next page of the module, showing for >>>>>>>>> each scan >>>>>>>>> >>> what the scan parameters were, and will also show for >>>>>>>>> comparison what's >>>>>>>>> >>> stored in your *mri_protocol* table. >>>>>>>>> >>> Compare these values to find which parameter was not correct >>>>>>>>> according >>>>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>>>> >>> >>>>>>>>> >>> You may end up broadening your mri_protocol value ranges (e.g. >>>>>>>>> TR, TE) >>>>>>>>> >>> for scans. >>>>>>>>> >>> This can be done in the front-end, by editing the database >>>>>>>>> table >>>>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>>>> >>> >>>>>>>>> >>> The MRI Violations module features are explained in more >>>>>>>>> detail in the >>>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] icon >>>>>>>>> in the menu >>>>>>>>> >>> bar.) >>>>>>>>> >>> >>>>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>>>> >>> < >>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>> > >>>>>>>>> >>> : no MINCs inserted- violated scans >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> looks like my previous email's attachment wasn't delivered due >>>>>>>>> to >>>>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>>>> >>> >>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>>>> webbrowser, so >>>>>>>>> >>> that you can check the filelds easier. >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>> < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios -- >>>>>>>>> >>> Great, sounds like more progress. >>>>>>>>> >>> >>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're getting >>>>>>>>> an Endian >>>>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>> successfully >>>>>>>>> >>> relabelled, after the command ran? >>>>>>>>> >>> >>>>>>>>> >>> You can use also our DICAT tool (https://github.com/aces/DICAT) >>>>>>>>> to >>>>>>>>> >>> verify and/or update local DICOM headers -- though your >>>>>>>>> dcmodify command is >>>>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>>>> >>> >>>>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>>>> "(2001,105f)" from >>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM slice >>>>>>>>> before and look >>>>>>>>> >>> at these fields specifically. >>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>> before/after >>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff the >>>>>>>>> outputs -- >>>>>>>>> >>> this will pinpoint what changed. >>>>>>>>> >>> >>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>> recognized or >>>>>>>>> >>> unknown : this means your scans did not match what is stored >>>>>>>>> in your >>>>>>>>> >>> mri_protocol table. >>>>>>>>> >>> Check the MRI Violations front-end module -- can you see why >>>>>>>>> they didn't >>>>>>>>> >>> match? >>>>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>>>> mri_protocol >>>>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Here is the psc table >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>>>> >>> >>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>> >>> >>>>>>>>> >>> and got those warning: is this okay? >>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>>>>> reading a >>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>>>>> reading a >>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined length, >>>>>>>>> reading a >>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined length, >>>>>>>>> reading a >>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>>>>> reading a >>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>>>>> reading a >>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>> >>> >>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you can >>>>>>>>> see the >>>>>>>>> >>> execution for the second dicom. Mnics could not be inserted >>>>>>>>> due to >>>>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>>>> >>> >>>>>>>>> >>> Running now the following command: >>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>> >>> >>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>> '__MACOSX' >>>>>>>>> >>> -delete >>>>>>>>> >>> >>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod >>>>>>>>> -verbose >>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>>>> >>> >>>>>>>>> >>> Testing for database connectivity. >>>>>>>>> >>> Database is available. >>>>>>>>> >>> >>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>> >>> >>>>>>>>> >>> You are creating a tar with the following command: >>>>>>>>> >>> >>>>>>>>> >>> tar -cf >>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> getting md5sums and gzipping!! >>>>>>>>> >>> >>>>>>>>> >>> * Taken from dir : >>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>> >>> * Archive target location : >>>>>>>>> >>> >>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>> >>> >>>>>>>>> >>> Adding archive info into database >>>>>>>>> >>> >>>>>>>>> >>> Removing temporary files from target location >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> Done adding archive info into database >>>>>>>>> >>> >>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>> -globLocation >>>>>>>>> >>> -profile prod >>>>>>>>> >>> >>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>> >>> -uploadID 12 -verbose >>>>>>>>> >>> md5sum >>>>>>>>> >>> >>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>> >>> CandID id: 602102 >>>>>>>>> >>> visit_label is: V1 >>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>> >>> CandID id: 602102 >>>>>>>>> >>> visit_label is: V1 >>>>>>>>> >>> candidate id 602102 >>>>>>>>> >>> Set centerID = 1 >>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>> >>> CandID id: 602102 >>>>>>>>> >>> visit_label is: V1 >>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>> >>> CandID id: 602102 >>>>>>>>> >>> visit_label is: V1 >>>>>>>>> >>> >>>>>>>>> >>> Number of MINC files that will be considered for inserting >>>>>>>>> into the >>>>>>>>> >>> database: 2 >>>>>>>>> >>> >>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>> >>> CandID id: 602102 >>>>>>>>> >>> visit_label is: V1 >>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>> >>> CandID id: 602102 >>>>>>>>> >>> visit_label is: V1 >>>>>>>>> >>> candidate id 602102 >>>>>>>>> >>> >>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>> >>> CandID id: 602102 >>>>>>>>> >>> visit_label is: V1 >>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>> >>> CandID id: 602102 >>>>>>>>> >>> visit_label is: V1 >>>>>>>>> >>> candidate id 602102 >>>>>>>>> >>> >>>>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>> >>> >>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>> cat >>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>> >>> >>>>>>>>> >>> ==> Loading file from disk >>>>>>>>> >>> >>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>> >>> >>>>>>>>> >>> --> mapping DICOM parameter for >>>>>>>>> >>> >>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>> >>> >>>>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>>>> >>> >>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>> >>> >>>>>>>>> >>> ==> verifying acquisition protocol >>>>>>>>> >>> >>>>>>>>> >>> Acquisition protocol is unknown >>>>>>>>> >>> >>>>>>>>> >>> --> The minc file cannot be registered since the >>>>>>>>> AcquisitionProtocol >>>>>>>>> >>> is unknown >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, >>>>>>>>> Ms. < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios: >>>>>>>>> >>> >>>>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>>>> *delete_imaging_upload* >>>>>>>>> >>> script -- >>>>>>>>> >>> details here: >>>>>>>>> >>> >>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>> >>> >>>>>>>>> >>> What's in your *psc* table? (Is it properly populated? This >>>>>>>>> is a >>>>>>>>> >>> pre-requisite to loading imaging data. >>>>>>>>> >>> < >>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>>>> > >>>>>>>>> >>> ) >>>>>>>>> >>> The foreign key constraint error on the candidate record is >>>>>>>>> curious. >>>>>>>>> >>> >>>>>>>>> >>> There are also a few options for creating candidates when >>>>>>>>> inserting >>>>>>>>> >>> imaging data: >>>>>>>>> >>> >>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>>>>> pipeline >>>>>>>>> >>> >>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>>>>> optionally I >>>>>>>>> >>> think) >>>>>>>>> >>> How to: >>>>>>>>> >>> >>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>> >>> >>>>>>>>> >>> Then as a second step: >>>>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>>>> >>> < >>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>>>> > >>>>>>>>> >>> to load your DICOMs. >>>>>>>>> >>> You will want to first ensure that the PatientName header in >>>>>>>>> the DICOMs >>>>>>>>> >>> as well as tar package are correctly labelled with >>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>> >>> >>>>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>>>> >>> How to : >>>>>>>>> >>> >>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>> >>> >>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>>>> bids_import script, >>>>>>>>> >>> to automatically create your candidates and sessions. >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> How do i delete a Study? And everytime do i have to create a >>>>>>>>> new >>>>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>>>> >>> >>>>>>>>> >>> *First execution:* >>>>>>>>> >>> >>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>> ./ >>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>> ~/Desktop/input.txt > >>>>>>>>> >>> log.txt >>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>>>>> foreign >>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>> `FK_candidate_1` >>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>> (`CenterID`)) at >>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>> >>> The following database commands failed: >>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>>>> (?,?,?,?,?)'; >>>>>>>>> >>> SET >>>>>>>>> >>> >>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>> >>> Medical Systems'; >>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>> >>> Error obtained:Cannot add or update a child row: a foreign key >>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>> `FK_mri_scanner_1` >>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) >>>>>>>>> (error code 1452) >>>>>>>>> >>> >>>>>>>>> >>> ERROR: The validation has failed. Either re-run the >>>>>>>>> validation again >>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force >>>>>>>>> to force the >>>>>>>>> >>> execution. >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>> >>> line 250. >>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>> >>> line 251. >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> *And second execution: * >>>>>>>>> >>> >>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>> ./ >>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>> ~/Desktop/input.txt > >>>>>>>>> >>> log.txt >>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>> >>> >>>>>>>>> >>> PROBLEM: >>>>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>>>> >>> The unique study ID is >>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>> >>> This is the information retained from the first time the study >>>>>>>>> was >>>>>>>>> >>> inserted: >>>>>>>>> >>> >>>>>>>>> >>> * Taken from dir : >>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>> >>> * Archive target location : >>>>>>>>> >>> >>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> Last update of record: >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>> >>> line 250. >>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>> >>> line 251. >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>> < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> Ok, this sounds like good progress. Let us know when you next >>>>>>>>> encounter >>>>>>>>> >>> issues as you progress through the Imaging Install/Setup docs >>>>>>>>> >>> < >>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>. >>>>>>>>> >>> I'll look into how we can better handle the incoming/ >>>>>>>>> directory next >>>>>>>>> >>> time. >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>>>>> >>> populated correctly except its port is 'port' : ''. Also i >>>>>>>>> have tested >>>>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>>>> >>> >>>>>>>>> >>> I executed the script again, because the only error i had >>>>>>>>> previously was >>>>>>>>> >>> that the /data/incoming folder didn't exist and there are no >>>>>>>>> errors >>>>>>>>> >>> reported back except of warnings <>>>>>>>> password on the >>>>>>>>> >>> command line interface can be insecure>>. >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>> < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> It's possible -- if the script was unable to connect to the >>>>>>>>> database >>>>>>>>> >>> during its execution (e.g. typo in the password), that would >>>>>>>>> explain the >>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw in >>>>>>>>> the Config >>>>>>>>> >>> module. >>>>>>>>> >>> It's hard to tell without seeing the output from your script >>>>>>>>> run -- Did >>>>>>>>> >>> you see a sign of any such error? >>>>>>>>> >>> The Config fields are populated by the imaging_install.sh >>>>>>>>> script (starting >>>>>>>>> >>> at line 222 >>>>>>>>> >>> < >>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>>>> > >>>>>>>>> >>> ) >>>>>>>>> >>> >>>>>>>>> >>> For example, check if the database connection information was >>>>>>>>> populated >>>>>>>>> >>> accurately in >>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> Hi Christine, >>>>>>>>> >>> >>>>>>>>> >>> If you are referring to the imaging_install.sh here is an >>>>>>>>> image with the >>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at the >>>>>>>>> last part >>>>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>> < >>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi Sotirios, >>>>>>>>> >>> >>>>>>>>> >>> Glad to hear your LORIS core install is up and working and all >>>>>>>>> the >>>>>>>>> >>> front-end pages are loading. >>>>>>>>> >>> >>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>> project >>>>>>>>> >>> > and the web interface worked. >>>>>>>>> >>> >>>>>>>>> >>> Yes, it's important that project/ have 775 permissions and that >>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the >>>>>>>>> install >>>>>>>>> >>> Readme . >>>>>>>>> >>> >>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change >>>>>>>>> LORIS to >>>>>>>>> >>> loris, right? >>>>>>>>> >>> >>>>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>>>> installation >>>>>>>>> >>> by an automated >>>>>>>>> script -- >>>>>>>>> >>> you do not need to set them manually via the Config module. >>>>>>>>> >>> Please continue to follow the Setup Guide >>>>>>>>> >>> for detailed steps >>>>>>>>> to follow. >>>>>>>>> >>> >>>>>>>>> >>> Best, >>>>>>>>> >>> Christine >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>> >>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change LORIS >>>>>>>>> to loris, >>>>>>>>> >>> right? >>>>>>>>> >>> >>>>>>>>> >>> [image: image.png] >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>> Nikoloutsopoulos < >>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>> >>> >>>>>>>>> >>> Hi, >>>>>>>>> >>> >>>>>>>>> >>> i used >>>>>>>>> >>> >>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash - >>>>>>>>> >>> sudo apt-get install -y nodejs >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> you had suggested in the past, make worked and now i can see >>>>>>>>> all the >>>>>>>>> >>> contents in the web-interface, but i don't need make install? >>>>>>>>> >>> >>>>>>>>> >>> Thanks >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> >>> -- >>>>>>>>> >>> >>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>> >>> >>>>>>>>> >>> _______________________________________________ >>>>>>>>> >>> Loris-dev mailing list >>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>> >>>>>>>>> >>> >>>>>>>>> -------------- next part -------------- >>>>>>>>> An HTML attachment was scrubbed... >>>>>>>>> URL: < >>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>>>>> > >>>>>>>>> >>>>>>>>> ------------------------------ >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>>> >>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>>>>> ***************************************** >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> >>>>>> christine.rogers at mcgill.ca >>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>> Montreal Neurological Institute >>>>>> McGill University | Montreal | Canada >>>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 37207 bytes Desc: not available URL: From AMORALESPINZON at bwh.harvard.edu Mon Nov 25 10:25:09 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Mon, 25 Nov 2019 15:25:09 +0000 Subject: [Loris-dev] LORIS Error: The target directory does not contain a single DICOM file. In-Reply-To: References: <4A0C0CF2-B5BC-47F1-84F9-287D4BD9B547@bwh.harvard.edu> Message-ID: <88DDA28F-928E-4923-99AE-81FF0E63B622@bwh.harvard.edu> Hi C?cile, Thank you for your prompt response. We will make the changes, try again, and report back to this thread. Best regards, Alfredo. On Nov 25, 2019, at 10:06 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Indeed, the StudyInstanceUID needs to have a value for the insertion pipeline to work so that could explain the no DICOM found error. FYI - StudyInstanceUID also needs to be unique for each uploaded study otherwise insertion in the tarchive tables would fail with the error: "the study has already been uploaded" Hope this helps, C?cile On Mon, Nov 25, 2019 at 10:02 AM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, I am batch uploading images to imaging visits using the script batch_uploads_imageuploader but for some images I get the following error: The target directory does not contain a single DICOM file. I had seen this error previously due to missing dicom fields like StudyID (0020,0010) and ImagePositionPatient (0020,0032). However, after checking these particular dicom fields and setting StudyID it to '0' I am still getting the same error. What other dicom fields should I check? Is there a log where I can exactly find the error? Does the "StudyInstanceUID" need to have a value? I'm pasting the dcmdump of a dicom at the end of this email in case this might help figuring out what is the issue. I am using LORIS v at 20.1.1. Thank you in advance for your help. Best regards, Alfredo. -------------------------------------------------------------------------------------- # Dicom-File-Format # Dicom-Meta-Information-Header # Used TransferSyntax: Little Endian Explicit (0002,0000) UL 230 # 4, 1 FileMetaInformationGroupLength (0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion (0002,0002) UI =MRImageStorage # 26, 1 MediaStorageSOPClassUID (0002,0003) UI [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] # 64, 1 MediaStorageSOPInstanceUID (0002,0010) UI =LittleEndianImplicit # 18, 1 TransferSyntaxUID (0002,0012) UI [1.2.276.0.7230010.3.0.3.6.0] # 28, 1 ImplementationClassUID (0002,0013) SH [OFFIS_DCMTK_360] # 16, 1 ImplementationVersionName (0002,0016) AE [GDCM/ITK 3.17.0] # 16, 1 SourceApplicationEntityTitle # Dicom-Data-Set # Used TransferSyntax: Little Endian Implicit (0008,0008) CS [DERIVED\SECONDARY] # 18, 2 ImageType (0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID (0008,0018) UI [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] # 64, 1 SOPInstanceUID (0008,0020) DA [20000101] # 8, 1 StudyDate (0008,0021) DA [20000101] # 8, 1 SeriesDate (0008,0022) DA [20000101] # 8, 1 AcquisitionDate (0008,0030) TM (no value available) # 0, 0 StudyTime (0008,0031) TM [085517] # 6, 1 SeriesTime (0008,0032) TM [085517] # 6, 1 AcquisitionTime (0008,0060) CS [MR] # 2, 1 Modality (0008,0070) LO [AAABBBCCC] # 6, 1 Manufacturer (0008,0104) LO [Anonymized] # 10, 1 CodeMeaning (0008,103e) LO [t1c] # 4, 1 SeriesDescription (0008,1090) LO [nifti2dicom] # 12, 1 ManufacturerModelName (0010,0010) PN [10041] # 6, 1 PatientName (0010,0020) LO [10041] # 6, 1 PatientID (0010,0021) LO [Anonymized] # 10, 1 IssuerOfPatientID (0010,0030) DA [19650101] # 8, 1 PatientBirthDate (0010,0040) CS [Anonymized] # 10, 1 PatientSex (0010,1010) AS [Anonymized] # 10, 1 PatientAge (0010,1030) DS (no value available) # 0, 0 PatientWeight (0010,2150) LO [Anonymized] # 10, 1 CountryOfResidence (0010,2152) LO [Anonymized] # 10, 1 RegionOfResidence (0010,21f0) LO [Anonymized] # 10, 1 PatientReligiousPreference (0012,0050) LO [baseline] # 8, 1 ClinicalTrialTimePointID (0012,0062) CS [Yes] # 4, 1 PatientIdentityRemoved (0012,0063) LO [Genentech] # 10, 1 DeidentificationMethod (0018,0050) DS [3] # 2, 1 SliceThickness (0018,0088) DS [3] # 2, 1 SpacingBetweenSlices (0020,000d) UI (no value available) # 0, 0 StudyInstanceUID (0020,000e) UI [1.2.826.0.1.3680043.2.1143.2737712182581015462892759360372011946] # 64, 1 SeriesInstanceUID (0020,0010) SH [0] # 2, 1 StudyID (0020,0011) IS [901] # 4, 1 SeriesNumber (0020,0012) IS [1] # 2, 1 AcquisitionNumber (0020,0013) IS [1] # 2, 1 InstanceNumber (0020,0020) CS [L\R] # 4, 2 PatientOrientation (0020,0032) DS [-116.48152160645\-118.93698120117\-275.82513427734] # 50, 3 ImagePositionPatient (0020,0037) DS [1\0\0\0\1\0] # 12, 6 ImageOrientationPatient (0020,0052) UI [1.2.826.0.1.3680043.2.1143.263896814292546686535778822643473818] # 64, 1 FrameOfReferenceUID (0028,0002) US 1 # 2, 1 SamplesPerPixel (0028,0004) CS [MONOCHROME2] # 12, 1 PhotometricInterpretation (0028,0010) US 256 # 2, 1 Rows (0028,0011) US 256 # 2, 1 Columns (0028,0030) DS [1\1] # 4, 2 PixelSpacing (0028,0100) US 16 # 2, 1 BitsAllocated (0028,0101) US 16 # 2, 1 BitsStored (0028,0102) US 15 # 2, 1 HighBit (0028,0103) US 1 # 2, 1 PixelRepresentation (0032,1033) LO [Anonymized] # 10, 1 RequestingService (0040,0280) ST [Anonymized] # 10, 1 CommentsOnThePerformedProcedureStep (0400,0563) LO [Anonymized] # 10, 1 ModifyingSystem (0400,0564) LO [Anonymized] # 10, 1 SourceOfPreviousValues (0400,0565) CS [Anonymized] # 10, 1 ReasonForTheAttributeModification (1110,21b0) ?? 0a\00 # 2, 1 Unknown Tag & Data (7fe0,0010) OW 0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000... # 131072, 1 PixelData The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at bwh.harvard.edu Mon Nov 25 12:46:53 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Mon, 25 Nov 2019 17:46:53 +0000 Subject: [Loris-dev] Error dcm2mnc: UNKNOWN DICOM TRANSFER SYNTAX Message-ID: Dear LorisDev team, I am having the following error when converting dcm2mnc: ---------------------------------------------------------------------------- $ dcm2mnc -verbose 094901-00003-Dicom-pdw/ . Expanding directory '094901-00003-Dicom-pdw/' Checking file types... File 094901-00003-Dicom-pdw/0000100012.dcm appears to be DICOM (CD/Export). UNKNOWN DICOM TRANSFER SYNTAX: 1.2.840.10008.1.2.4.57 ---------------------------------------------------------------------------- Do you know why this might be happening? You may find the dcmdump of one dicom file at the end of this email. Thank you in advance. Alfredo. ---------------------------------------------------------------------------- # Dicom-File-Format # Dicom-Meta-Information-Header # Used TransferSyntax: Little Endian Explicit (0002,0000) UL 202 # 4, 1 FileMetaInformationGroupLength (0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion (0002,0002) UI =MRImageStorage # 26, 1 MediaStorageSOPClassUID (0002,0003) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] # 56, 1 MediaStorageSOPInstanceUID (0002,0010) UI =JPEGLossless:Non-hierarchical:Process14 # 22, 1 TransferSyntaxUID (0002,0012) UI [1.2.276.0.7230010.3.0.3.6.1] # 28, 1 ImplementationClassUID (0002,0013) SH [OFFIS_DCMTK_361] # 16, 1 ImplementationVersionName # Dicom-Data-Set # Used TransferSyntax: JPEG Lossless, Non-hierarchical, Process 14 (0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet (0008,0008) CS [ORIGINAL\PRIMARY\OTHER] # 22, 3 ImageType (0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID (0008,0018) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] # 56, 1 SOPInstanceUID (0008,0020) DA [20000101] # 8, 1 StudyDate (0008,0021) DA [20000101] # 8, 1 SeriesDate (0008,0022) DA [20000101] # 8, 1 AcquisitionDate (0008,0030) TM [094647] # 6, 1 StudyTime (0008,0031) TM [094901] # 6, 1 SeriesTime (0008,0032) TM [094901] # 6, 1 AcquisitionTime (0008,0033) TM [094901] # 6, 1 ContentTime (0008,0060) CS [MR] # 2, 1 Modality (0008,0070) LO [AAABBBCCC] # 18, 1 Manufacturer (0008,0082) SQ (Sequence with explicit length #=0) # 0, 1 InstitutionCodeSequence (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0008,0104) LO [Anonymized] # 10, 1 CodeMeaning (0008,1032) SQ (Sequence with explicit length #=0) # 0, 1 ProcedureCodeSequence (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0008,103e) LO [pdw] # 4, 1 SeriesDescription (0008,1090) LO [Signa HDxt] # 10, 1 ManufacturerModelName (0008,1110) SQ (Sequence with explicit length #=1) # 104, 1 ReferencedStudySequence (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item (0008,1150) UI =RETIRED_DetachedStudyManagementSOPClass # 24, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.341] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0008,1111) SQ (Sequence with explicit length #=1) # 104, 1 ReferencedPerformedProcedureStepSequence (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item (0008,1150) UI =ModalityPerformedProcedureStepSOPClass # 24, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.340] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0008,1140) SQ (Sequence with explicit length #=3) # 318, 1 ReferencedImageSequence (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.285] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.286] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.287] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0010,0010) PN [AAABBBCCC] # 24, 1 PatientName (0010,0020) LO [11111] # 6, 1 PatientID (0010,0021) LO [Anonymized] # 10, 1 IssuerOfPatientID (0010,0030) DA [19000101] # 8, 1 PatientBirthDate (0010,0040) CS [Anonymized] # 10, 1 PatientSex (0010,1010) AS [Anonymized] # 10, 1 PatientAge (0010,1030) DS [10] # 2, 1 PatientWeight (0010,2150) LO [Anonymized] # 10, 1 CountryOfResidence (0010,2152) LO [Anonymized] # 10, 1 RegionOfResidence (0012,0050) LO [AAABBBCCC] # 8, 1 ClinicalTrialTimePointID (0012,0062) CS [Yes] # 4, 1 PatientIdentityRemoved (0012,0063) LO [Genentech] # 10, 1 DeidentificationMethod (0018,0020) CS [SE] # 2, 1 ScanningSequence (0018,0021) CS [SK] # 2, 1 SequenceVariant (0018,0022) CS [FAST_GEMS\EDR_GEMS\TRF_GEMS] # 28, 3 ScanOptions (0018,0023) CS [2D] # 2, 1 MRAcquisitionType (0018,0025) CS [N] # 2, 1 AngioFlag (0018,0050) DS [3] # 2, 1 SliceThickness (0018,0080) DS [2900] # 4, 1 RepetitionTime (0018,0081) DS [9.424] # 6, 1 EchoTime (0018,0082) DS [0] # 2, 1 InversionTime (0018,0083) DS [1] # 2, 1 NumberOfAverages (0018,0084) DS [127.723758] # 10, 1 ImagingFrequency (0018,0085) SH [1H] # 2, 1 ImagedNucleus (0018,0086) IS [1] # 2, 1 EchoNumbers (0018,0087) DS [3] # 2, 1 MagneticFieldStrength (0018,0088) DS [3] # 2, 1 SpacingBetweenSlices (0018,0091) IS [3] # 2, 1 EchoTrainLength (0018,0093) DS [100] # 4, 1 PercentSampling (0018,0094) DS [100] # 4, 1 PercentPhaseFieldOfView (0018,0095) DS [177.578] # 8, 1 PixelBandwidth (0018,1000) LO [056MRE3TH2565370] # 16, 1 DeviceSerialNumber (0018,1020) LO [15\LX\MR Software release:15.0_M4_0910.a] # 40, 3 SoftwareVersions (0018,1088) IS [0] # 2, 1 HeartRate (0018,1090) IS [0] # 2, 1 CardiacNumberOfImages (0018,1094) IS [0] # 2, 1 TriggerWindow (0018,1100) DS [250] # 4, 1 ReconstructionDiameter (0018,1250) SH [AAABBBBRAIN] # 8, 1 ReceiveCoilName (0018,1310) US 0\256\256\0 # 8, 4 AcquisitionMatrix (0018,1312) CS [ROW] # 4, 1 InPlanePhaseEncodingDirection (0018,1314) DS [90] # 2, 1 FlipAngle (0018,1315) CS [N] # 2, 1 VariableFlipAngleFlag (0018,1316) DS [1.3561] # 6, 1 SAR (0018,5100) CS [HFS] # 4, 1 PatientPosition (0020,000d) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.344] # 56, 1 StudyInstanceUID (0020,000e) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.349] # 56, 1 SeriesInstanceUID (0020,0010) SH [35313] # 6, 1 StudyID (0020,0011) IS [3] # 2, 1 SeriesNumber (0020,0012) IS [1] # 2, 1 AcquisitionNumber (0020,0013) IS [1] # 2, 1 InstanceNumber (0020,0032) DS [-130.858\-141.195\94.3036] # 26, 3 ImagePositionPatient (0020,0037) DS [0.999785\-0.0207525\0\0.0207528\0.999767\0.00598169] # 52, 6 ImageOrientationPatient (0020,0052) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.343] # 56, 1 FrameOfReferenceUID (0020,0060) CS (no value available) # 0, 0 Laterality (0020,1002) IS [55] # 2, 1 ImagesInAcquisition (0020,1040) LO (no value available) # 0, 0 PositionReferenceIndicator (0020,1041) DS [95.04837036] # 12, 1 SliceLocation (0020,9056) SH [1] # 2, 1 StackID (0020,9057) UL 1 # 4, 1 InStackPositionNumber (0028,0002) US 1 # 2, 1 SamplesPerPixel (0028,0004) CS [MONOCHROME2] # 12, 1 PhotometricInterpretation (0028,0010) US 256 # 2, 1 Rows (0028,0011) US 256 # 2, 1 Columns (0028,0030) DS [0.9766\0.9766] # 14, 2 PixelSpacing (0028,0100) US 16 # 2, 1 BitsAllocated (0028,0101) US 16 # 2, 1 BitsStored (0028,0102) US 15 # 2, 1 HighBit (0028,0103) US 1 # 2, 1 PixelRepresentation (0028,0106) SS 0 # 2, 1 SmallestImagePixelValue (0028,0107) SS 133 # 2, 1 LargestImagePixelValue (0028,1050) DS [66] # 2, 1 WindowCenter (0028,1051) DS [133] # 4, 1 WindowWidth (0032,1033) LO [Anonymized] # 10, 1 RequestingService (0040,0253) SH [MR1354787338] # 12, 1 PerformedProcedureStepID (0040,0260) SQ (Sequence with explicit length #=0) # 0, 1 PerformedProtocolCodeSequence (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0040,0280) ST [Anonymized] # 10, 1 CommentsOnThePerformedProcedureStep (1110,21b0) UN 0a\00 # 2, 1 Unknown Tag & Data (7fe0,0010) OB (PixelSequence #=2) # u/l, 1 PixelData (fffe,e000) pi 00\00\00\00 # 4, 1 Item (fffe,e000) pi ff\d8\ff\fe\00\26\43\6f\6d\70\72\65\73\73\65\64\20\62\79\20\44\69... # 50160, 1 Item (fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From iris.rodriguez at cneuro.edu.cu Mon Nov 25 13:15:24 2019 From: iris.rodriguez at cneuro.edu.cu (=?iso-8859-1?Q?Iris_Rodr=EDguez_Gil?=) Date: Mon, 25 Nov 2019 13:15:24 -0500 Subject: [Loris-dev] Bids Insertion Message-ID: Hi, Where I can get a general guideline for the insertion in Bids Format? I have a server Loris with version 21.0.0 and Ubuntu 16. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Mon Nov 25 13:24:19 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 25 Nov 2019 13:24:19 -0500 Subject: [Loris-dev] Bids Insertion In-Reply-To: References: Message-ID: Hi Iris, Are you inserting only EEG data organized according to BIDS in LORIS? If your data includes also MRI datasets organized according to BIDS, then you would need to use release 22.0 of LORIS (which should get out this week). Documentation on how to do run the BIDS insertion script can be found here . Hope this helps, C?cile On Mon, Nov 25, 2019 at 1:16 PM Iris Rodr?guez Gil < iris.rodriguez at cneuro.edu.cu> wrote: > Hi, > > > > Where I can get a general guideline for the insertion in Bids Format? > > I have a server Loris with version 21.0.0 and Ubuntu 16. > > > > Thanks > > > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicolasbrossard.mni at gmail.com Tue Nov 26 07:14:06 2019 From: nicolasbrossard.mni at gmail.com (Nicolas Brossard) Date: Tue, 26 Nov 2019 07:14:06 -0500 Subject: [Loris-dev] Error dcm2mnc: UNKNOWN DICOM TRANSFER SYNTAX In-Reply-To: References: Message-ID: Hi Alfredo, As you can see from the dcmdump output you provided, your file's TransferSyntaxUID is JPEGLossless and it looks like dcm2mnc does not like that. You can try converting your DICOM file so that it has a TransferSyntaxUID set to LittleEndianExplicit, like this: dcmdjpeg Dcm2mnc on the new converted file will most likely succeed then. If you have a lot of DICOM files located in a given directory, you can convert them all with one command: find -type f | xargs -i dcmdjpeg {} {} Let me know how it goes! Cheers, Nicolas On Mon, Nov 25, 2019 at 12:47 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > I am having the following error when converting dcm2mnc: > > > ---------------------------------------------------------------------------- > $ dcm2mnc -verbose 094901-00003-Dicom-pdw/ . > > Expanding directory '094901-00003-Dicom-pdw/' > Checking file types... > File 094901-00003-Dicom-pdw/0000100012.dcm appears to be DICOM (CD/Export). > UNKNOWN DICOM TRANSFER SYNTAX: 1.2.840.10008.1.2.4.57 > > ---------------------------------------------------------------------------- > > Do you know why this might be happening? You may find the dcmdump of one > dicom file at the end of this email. > > Thank you in advance. > > Alfredo. > > > ---------------------------------------------------------------------------- > > # Dicom-File-Format > > # Dicom-Meta-Information-Header > # Used TransferSyntax: Little Endian Explicit > (0002,0000) UL 202 # 4, 1 > FileMetaInformationGroupLength > (0002,0001) OB 00\01 # 2, 1 > FileMetaInformationVersion > (0002,0002) UI =MRImageStorage # 26, 1 > MediaStorageSOPClassUID > (0002,0003) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] # > 56, 1 MediaStorageSOPInstanceUID > (0002,0010) UI =JPEGLossless:Non-hierarchical:Process14 # 22, 1 > TransferSyntaxUID > (0002,0012) UI [1.2.276.0.7230010.3.0.3.6.1] # 28, 1 > ImplementationClassUID > (0002,0013) SH [OFFIS_DCMTK_361] # 16, 1 > ImplementationVersionName > > # Dicom-Data-Set > # Used TransferSyntax: JPEG Lossless, Non-hierarchical, Process 14 > (0008,0005) CS [ISO_IR 100] # 10, 1 > SpecificCharacterSet > (0008,0008) CS [ORIGINAL\PRIMARY\OTHER] # 22, 3 ImageType > (0008,0016) UI =MRImageStorage # 26, 1 > SOPClassUID > (0008,0018) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] # > 56, 1 SOPInstanceUID > (0008,0020) DA [20000101] # 8, 1 StudyDate > (0008,0021) DA [20000101] # 8, 1 SeriesDate > (0008,0022) DA [20000101] # 8, 1 > AcquisitionDate > (0008,0030) TM [094647] # 6, 1 StudyTime > (0008,0031) TM [094901] # 6, 1 SeriesTime > (0008,0032) TM [094901] # 6, 1 > AcquisitionTime > (0008,0033) TM [094901] # 6, 1 > ContentTime > (0008,0060) CS [MR] # 2, 1 Modality > (0008,0070) LO [AAABBBCCC] # 18, 1 Manufacturer > (0008,0082) SQ (Sequence with explicit length #=0) # 0, 1 > InstitutionCodeSequence > (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 > SequenceDelimitationItem > (0008,0104) LO [Anonymized] # 10, 1 > CodeMeaning > (0008,1032) SQ (Sequence with explicit length #=0) # 0, 1 > ProcedureCodeSequence > (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 > SequenceDelimitationItem > (0008,103e) LO [pdw] # 4, 1 > SeriesDescription > (0008,1090) LO [Signa HDxt] # 10, 1 > ManufacturerModelName > (0008,1110) SQ (Sequence with explicit length #=1) # 104, 1 > ReferencedStudySequence > (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item > (0008,1150) UI =RETIRED_DetachedStudyManagementSOPClass # 24, 1 > ReferencedSOPClassUID > (0008,1155) UI > [1.2.840.113619.2.244.3596.11861676.21950.1354710592.341] # 56, 1 > ReferencedSOPInstanceUID > (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 > ItemDelimitationItem > (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 > SequenceDelimitationItem > (0008,1111) SQ (Sequence with explicit length #=1) # 104, 1 > ReferencedPerformedProcedureStepSequence > (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item > (0008,1150) UI =ModalityPerformedProcedureStepSOPClass # 24, 1 > ReferencedSOPClassUID > (0008,1155) UI > [1.2.840.113619.2.244.3596.11861676.21950.1354710592.340] # 56, 1 > ReferencedSOPInstanceUID > (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 > ItemDelimitationItem > (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 > SequenceDelimitationItem > (0008,1140) SQ (Sequence with explicit length #=3) # 318, 1 > ReferencedImageSequence > (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item > (0008,1150) UI =MRImageStorage # 26, 1 > ReferencedSOPClassUID > (0008,1155) UI > [1.2.840.113619.2.244.3596.11861676.21355.1354711179.285] # 56, 1 > ReferencedSOPInstanceUID > (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 > ItemDelimitationItem > (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item > (0008,1150) UI =MRImageStorage # 26, 1 > ReferencedSOPClassUID > (0008,1155) UI > [1.2.840.113619.2.244.3596.11861676.21355.1354711179.286] # 56, 1 > ReferencedSOPInstanceUID > (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 > ItemDelimitationItem > (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item > (0008,1150) UI =MRImageStorage # 26, 1 > ReferencedSOPClassUID > (0008,1155) UI > [1.2.840.113619.2.244.3596.11861676.21355.1354711179.287] # 56, 1 > ReferencedSOPInstanceUID > (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 > ItemDelimitationItem > (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 > SequenceDelimitationItem > (0010,0010) PN [AAABBBCCC] # 24, 1 PatientName > (0010,0020) LO [11111] # 6, 1 PatientID > (0010,0021) LO [Anonymized] # 10, 1 > IssuerOfPatientID > (0010,0030) DA [19000101] # 8, 1 > PatientBirthDate > (0010,0040) CS [Anonymized] # 10, 1 PatientSex > (0010,1010) AS [Anonymized] # 10, 1 PatientAge > (0010,1030) DS [10] # 2, 1 > PatientWeight > (0010,2150) LO [Anonymized] # 10, 1 > CountryOfResidence > (0010,2152) LO [Anonymized] # 10, 1 > RegionOfResidence > (0012,0050) LO [AAABBBCCC] # 8, 1 > ClinicalTrialTimePointID > (0012,0062) CS [Yes] # 4, 1 > PatientIdentityRemoved > (0012,0063) LO [Genentech] # 10, 1 > DeidentificationMethod > (0018,0020) CS [SE] # 2, 1 > ScanningSequence > (0018,0021) CS [SK] # 2, 1 > SequenceVariant > (0018,0022) CS [FAST_GEMS\EDR_GEMS\TRF_GEMS] # 28, 3 > ScanOptions > (0018,0023) CS [2D] # 2, 1 > MRAcquisitionType > (0018,0025) CS [N] # 2, 1 AngioFlag > (0018,0050) DS [3] # 2, 1 > SliceThickness > (0018,0080) DS [2900] # 4, 1 > RepetitionTime > (0018,0081) DS [9.424] # 6, 1 EchoTime > (0018,0082) DS [0] # 2, 1 > InversionTime > (0018,0083) DS [1] # 2, 1 > NumberOfAverages > (0018,0084) DS [127.723758] # 10, 1 > ImagingFrequency > (0018,0085) SH [1H] # 2, 1 > ImagedNucleus > (0018,0086) IS [1] # 2, 1 > EchoNumbers > (0018,0087) DS [3] # 2, 1 > MagneticFieldStrength > (0018,0088) DS [3] # 2, 1 > SpacingBetweenSlices > (0018,0091) IS [3] # 2, 1 > EchoTrainLength > (0018,0093) DS [100] # 4, 1 > PercentSampling > (0018,0094) DS [100] # 4, 1 > PercentPhaseFieldOfView > (0018,0095) DS [177.578] # 8, 1 > PixelBandwidth > (0018,1000) LO [056MRE3TH2565370] # 16, 1 > DeviceSerialNumber > (0018,1020) LO [15\LX\MR Software release:15.0_M4_0910.a] # 40, 3 > SoftwareVersions > (0018,1088) IS [0] # 2, 1 HeartRate > (0018,1090) IS [0] # 2, 1 > CardiacNumberOfImages > (0018,1094) IS [0] # 2, 1 > TriggerWindow > (0018,1100) DS [250] # 4, 1 > ReconstructionDiameter > (0018,1250) SH [AAABBBBRAIN] # 8, 1 > ReceiveCoilName > (0018,1310) US 0\256\256\0 # 8, 4 > AcquisitionMatrix > (0018,1312) CS [ROW] # 4, 1 > InPlanePhaseEncodingDirection > (0018,1314) DS [90] # 2, 1 FlipAngle > (0018,1315) CS [N] # 2, 1 > VariableFlipAngleFlag > (0018,1316) DS [1.3561] # 6, 1 SAR > (0018,5100) CS [HFS] # 4, 1 > PatientPosition > (0020,000d) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.344] # > 56, 1 StudyInstanceUID > (0020,000e) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.349] # > 56, 1 SeriesInstanceUID > (0020,0010) SH [35313] # 6, 1 StudyID > (0020,0011) IS [3] # 2, 1 > SeriesNumber > (0020,0012) IS [1] # 2, 1 > AcquisitionNumber > (0020,0013) IS [1] # 2, 1 > InstanceNumber > (0020,0032) DS [-130.858\-141.195\94.3036] # 26, 3 > ImagePositionPatient > (0020,0037) DS [0.999785\-0.0207525\0\0.0207528\0.999767\0.00598169] # > 52, 6 ImageOrientationPatient > (0020,0052) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.343] # > 56, 1 FrameOfReferenceUID > (0020,0060) CS (no value available) # 0, 0 Laterality > (0020,1002) IS [55] # 2, 1 > ImagesInAcquisition > (0020,1040) LO (no value available) # 0, 0 > PositionReferenceIndicator > (0020,1041) DS [95.04837036] # 12, 1 > SliceLocation > (0020,9056) SH [1] # 2, 1 StackID > (0020,9057) UL 1 # 4, 1 > InStackPositionNumber > (0028,0002) US 1 # 2, 1 > SamplesPerPixel > (0028,0004) CS [MONOCHROME2] # 12, 1 > PhotometricInterpretation > (0028,0010) US 256 # 2, 1 Rows > (0028,0011) US 256 # 2, 1 Columns > (0028,0030) DS [0.9766\0.9766] # 14, 2 > PixelSpacing > (0028,0100) US 16 # 2, 1 > BitsAllocated > (0028,0101) US 16 # 2, 1 BitsStored > (0028,0102) US 15 # 2, 1 HighBit > (0028,0103) US 1 # 2, 1 > PixelRepresentation > (0028,0106) SS 0 # 2, 1 > SmallestImagePixelValue > (0028,0107) SS 133 # 2, 1 > LargestImagePixelValue > (0028,1050) DS [66] # 2, 1 > WindowCenter > (0028,1051) DS [133] # 4, 1 > WindowWidth > (0032,1033) LO [Anonymized] # 10, 1 > RequestingService > (0040,0253) SH [MR1354787338] # 12, 1 > PerformedProcedureStepID > (0040,0260) SQ (Sequence with explicit length #=0) # 0, 1 > PerformedProtocolCodeSequence > (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 > SequenceDelimitationItem > (0040,0280) ST [Anonymized] # 10, 1 > CommentsOnThePerformedProcedureStep > (1110,21b0) UN 0a\00 # 2, 1 Unknown > Tag & Data > (7fe0,0010) OB (PixelSequence #=2) # u/l, 1 PixelData > (fffe,e000) pi 00\00\00\00 # 4, 1 Item > (fffe,e000) pi > ff\d8\ff\fe\00\26\43\6f\6d\70\72\65\73\73\65\64\20\62\79\20\44\69... # > 50160, 1 Item > (fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 > SequenceDelimitationItem > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Tue Nov 26 10:12:37 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 26 Nov 2019 17:12:37 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Cecile, I checked for the StudyInstacueUID at the files with "The target directory does not contain a single DICOM file"" and their attribute has a value. Regarding the scouter and localizer, i modified the settings in the imaging pipeline and now i don't get that error message, but still it doesn't create the mnics. The errors i am getting are ( uninitialized value $_ is not important? because i haven't got comments about that ) Use of uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/ batch_uploads_imageuploader.pl line 144. Running now the following command: /data/loris/data//uploadNeuroDB/ imaging_upload_file.pl -profile prod -upload_id 134 /data/incoming/DCC0025_118008_V1.tar.gz -verbose and Number of MINC files that will be considered for inserting into the database: 0 No data could be converted into valid MINC files. The tarchiveLoader.pl insertion script has failed. Use of uninitialized value $mail_user in concatenation (.) or string at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. Can't exec "mail": No such file or directory at /data/loris/bin/mri/ batch_uploads_imageuploader.pl line 249. print() on closed filehandle MAIL at /data/loris/bin/mri/ batch_uploads_imageuploader.pl line 250. print() on closed filehandle MAIL at /data/loris/bin/mri/ batch_uploads_imageuploader.pl line 251. Thanks Sotirios ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar < cecile.madjar at mcin.ca> ??????: > Hi Sotirios, > > OK. So the issue I mentioned should not be a problem for you. > > Is the StudyInstanceUID DICOM header set in your images? If it is not set, > then you would end up with the error message "The target directory does not > contain a single DICOM file". So maybe this is the issue you are having > with those datasets? > > Regarding not excluding series descriptions, you can configure that in the > Config module under the Imaging Pipeline section. Simply remove all entries > for the "Series description to exclude from imaging insertion" setting. > > C?cile > > On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Cecile, >> >> We are using this version >> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to >> insert low resolution now? >> >> Thanks >> >> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, wrote: >> >>> Hi Sotirios, >>> >>> Which version of LORIS-MRI are you using? >>> >>> There was a bug that got resolved in 20.2 in get_dicom_info.pl. >>> Basically, if a DICOM did not have the (0020,0032) header, >>> get_dicom_info.pl considered that the file was not a DICOM, which was a >>> mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this is the >>> issue you are encountering. >>> >>> About scout and localizer, they are a type of short and low resolution >>> sequence that is used by the tech but is of no interest scientifically, >>> which is why we tend to no insert them. >>> >>> Hope this helps, >>> >>> C?cile >>> >>> >>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi Cecile, >>>> >>>> i executed the find command and the output i got per folder was "DICOM >>>> medical imaging data. Maybe there is something wrong with the find command >>>> in the warning that it is unable to check if the file is a dicom file? Also >>>> when i use get_dicom_info.pl i don't get any output data. Finally i >>>> don't understand what scout or localizer is ( something like if and only if >>>> a file fails then the whole session is invalid? ). >>>> >>>> [image: image.png] >>>> >>>> Thanks >>>> >>>> Sotirios >>>> >>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < >>>> cecile.madjar at mcin.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> I took a closer look to the batch_uploader_multiple_output.txt file >>>>> you sent. It looks like there are different reasons for failure depending >>>>> on the DICOM folder uploaded. >>>>> >>>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1: >>>>> it looks like there is no file of type DICOM in the folder. Have you >>>>> checked to see if that is indeed the case? Maybe you can try running the >>>>> following command on that folder to see what are the types of the files? If >>>>> it does not return at least one DICOM medical imaging data file, then that >>>>> is why you get the error message from the pipeline: >>>>> - >>>>> >>>>> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >>>>> >>>>> - For 864173 DCC0001 V1: it looks like there are two different >>>>> DICOM studies within the same folder. You will need to split that study in >>>>> two based on the StudyUID field as the insertion pipeline does not allow >>>>> for more than one StudyUID per upload. >>>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1: >>>>> it looks like the dcm2mnc command did not produce any MINC files. Can you >>>>> check in the DICOM archive what are the series present in the tarchive for >>>>> that visit? Maybe only a scout or localizer was acquired for that session, >>>>> hence the no valid MINC files (scout and localizer being skipped for the >>>>> conversion) >>>>> - For 397410 DCC0003 V1: it looks like everything went well for >>>>> this one. >>>>> >>>>> One script that is called by our pipeline is called get_dicom_info.pl and >>>>> this does all kind of checks on the DICOM files (it is being called when >>>>> running the dcm2mnc conversion). You could run it independently on your >>>>> folder if needed. >>>>> >>>>> Since one of the study got in, it does not look like you are having a >>>>> problem with the setup. It seems more likely to be a problem with the data >>>>> themselves. >>>>> >>>>> Hope this helps. >>>>> >>>>> C?cile >>>>> >>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi Christine, >>>>>> >>>>>> In my first vm i am able to create the minc files and view them at >>>>>> the mri browser (except of candidate 102761034 ), meanwhile the same files >>>>>> gives warnings at the 2nd vm. The output of the batch upload can be seen >>>>>> in the file attached. >>>>>> Also a colleague of us has built a pre-validation tool for dicom >>>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had found >>>>>> all the files that Loris gave as warning . Basically I confirmed that the >>>>>> total amount of files per dicom was the same amount as stated in Loris and >>>>>> checked some filenames given from warning to confirm that they match with >>>>>> our tool. But that was months ago and my colleague had changed some >>>>>> parameters for MIP and now our tool doesn't find all the invalid files, >>>>>> that's why i asked for the dicom header specification of Loris. In a >>>>>> discussion we had he mentioned that he doesn't check for some tags e.x. >>>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>>>>> remove invalid dcm files. >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>>>>> christine.rogers at mcgill.ca> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> Can you provide us with some fresh particulars of the current issue >>>>>>> and we'll take it from there? >>>>>>> Yang's team has built these scripts which can definitely serve as a >>>>>>> model for your pre-validation of your DICOM collections. >>>>>>> cheers, >>>>>>> Christine >>>>>>> >>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> HI Yang, >>>>>>>> >>>>>>>> We make use of pydicom library too. Now about the validate.py i see >>>>>>>> that you check if some attributes are missing such as PatientID, >>>>>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>>>>> something on the setup of my other virtual machine ( although one dicom >>>>>>>> passed on the new vm successfully, the others that were inserted correctly >>>>>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but >>>>>>>> i don't remember the solution. >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>>>>> ??????: >>>>>>>> >>>>>>>>> Hey, Sotirios, >>>>>>>>> >>>>>>>>> Christine from the LORIS team mentioned you had some issue with >>>>>>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>>>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>>>>>> fully automated pipeline actually. >>>>>>>>> >>>>>>>>> While we were building CNBP, we had coded up some minor Python >>>>>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>>>>> more comprehensive solution, PyDICOM ( >>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>>>>> >>>>>>>>> Cheers, >>>>>>>>> >>>>>>>>> Yang Ding, PhD. >>>>>>>>> Canadian Neonatal Brain Platform Architect >>>>>>>>> >>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM < >>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote: >>>>>>>>> >>>>>>>>>> Send Loris-dev mailing list submissions to >>>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>>>>> >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>>>>> >>>>>>>>>> You can reach the person managing the list at >>>>>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>>>>> >>>>>>>>>> When replying, please edit your Subject line so it is more >>>>>>>>>> specific >>>>>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> Today's Topics: >>>>>>>>>> >>>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ---------------------------------------------------------------------- >>>>>>>>>> >>>>>>>>>> Message: 1 >>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>>>>> To: Cecile Madjar >>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>>>>> Message-ID: >>>>>>>>>> >>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>>>>> >>>>>>>>>> Hi, >>>>>>>>>> >>>>>>>>>> Could we send you a link with 10 anonymized dicom files to >>>>>>>>>> diagnose the >>>>>>>>>> warnings we get? >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>>>>>>>>> > Hi Cecile, >>>>>>>>>> > >>>>>>>>>> > We were wondering whether Loris has a tool to check if there >>>>>>>>>> are problems >>>>>>>>>> > with the dcm files, before trying to upload them. Something >>>>>>>>>> that could >>>>>>>>>> > provide the same results provided in the warning_output, this >>>>>>>>>> is the >>>>>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>>>>> attributes of the >>>>>>>>>> > dcm header would trigger a warning? is there a dcm file header >>>>>>>>>> > specification for Loris? >>>>>>>>>> > >>>>>>>>>> > Thanks >>>>>>>>>> > >>>>>>>>>> > Sotirios >>>>>>>>>> > >>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>>>>> > >>>>>>>>>> >> Hi, >>>>>>>>>> >> >>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it >>>>>>>>>> worked,but i >>>>>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>>>>> >> Thanks >>>>>>>>>> >> >>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>>>>> >> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and >>>>>>>>>> columns are of >>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be >>>>>>>>>> using >>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>>>>> >>> >>>>>>>>>> >>> The second error occurs because the trigger triggers a >>>>>>>>>> rollback of the >>>>>>>>>> >>> insert statement in the files table. >>>>>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>>>>> >>> >>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>>>>>>> failure of >>>>>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>>>>> >>> -- Xavier >>>>>>>>>> >>> >>>>>>>>>> >>> ------------------------------ >>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>>>>> >>> *To:* Cecile Madjar >>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>> loris-dev at bic.mni.mcgill.ca>; >>>>>>>>>> >>> Christine Rogers, Ms. >>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>> >>> >>>>>>>>>> >>> When mincs are inserted their corresponding rows at the file >>>>>>>>>> table are >>>>>>>>>> >>> inserted too >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>>>>>>> because i >>>>>>>>>> >>> don't want manually to label them as passed throught the >>>>>>>>>> interface >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> That is the trigger i wrote >>>>>>>>>> >>> >>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>>>>> >>> BEGIN >>>>>>>>>> >>> INSERT INTO files_qcstatus >>>>>>>>>> >>> SET FileID = NEW.FileID, >>>>>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>>>>> >>> QCStatus = "Pass", >>>>>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>>>>> >>> END >>>>>>>>>> >>> >>>>>>>>>> >>> although it contains some errors >>>>>>>>>> >>> >>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>>>>>> foreign >>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES >>>>>>>>>> `files` (`FileID`)) >>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column >>>>>>>>>> associated with >>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it >>>>>>>>>> means no DICOMs >>>>>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>>>>> insertion of the >>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with the >>>>>>>>>> correct >>>>>>>>>> >>> TarchiveID associated with the upload. >>>>>>>>>> >>> >>>>>>>>>> >>> Could this correspond to what you want to do? >>>>>>>>>> >>> >>>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked to >>>>>>>>>> the files >>>>>>>>>> >>> table (hence, the MINC files). You could always create a new >>>>>>>>>> table for >>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>>>>> >>> >>>>>>>>>> >>> C?cile >>>>>>>>>> >>> >>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of creating >>>>>>>>>> a trigger for >>>>>>>>>> >>> that, but which tables do i need to add entries to? So far >>>>>>>>>> from what i see >>>>>>>>>> >>> i need to add entres at the table "files" whenever an >>>>>>>>>> insertion happens to >>>>>>>>>> >>> files_qcstatus. >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning >>>>>>>>>> of my email >>>>>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the >>>>>>>>>> StudyID i am >>>>>>>>>> >>> looking for is not stored in the database? >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks. >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>>>>> >>> tarchive table. It can also be found in the metadata field >>>>>>>>>> but it is mixed >>>>>>>>>> >>> with many other information. >>>>>>>>>> >>> >>>>>>>>>> >>> Hope this helps, >>>>>>>>>> >>> >>>>>>>>>> >>> C?cile >>>>>>>>>> >>> >>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive >>>>>>>>>> table, >>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found >>>>>>>>>> something called >>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>>>>>>>> Instance UID. >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>>>>> >>> >>>>>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>>>>> >>> >>>>>>>>>> >>> - the scan type could not be identified (not matching an >>>>>>>>>> entry in >>>>>>>>>> >>> the mri_protocol table) >>>>>>>>>> >>> - one parameter of the scan type is out of the expected >>>>>>>>>> range >>>>>>>>>> >>> present in the mri_protocol_checks (extra filtering in >>>>>>>>>> case you need to be >>>>>>>>>> >>> stricker on some parameters not present in the >>>>>>>>>> mri_protocol table) >>>>>>>>>> >>> - if the CandID and PSCID do not match >>>>>>>>>> >>> >>>>>>>>>> >>> The following cases do not get in the MRI violation tables as >>>>>>>>>> it happens >>>>>>>>>> >>> before the conversion of the DICOM to MINC files and only >>>>>>>>>> MINC files >>>>>>>>>> >>> violations are logged there: >>>>>>>>>> >>> >>>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be found >>>>>>>>>> to convert >>>>>>>>>> >>> to MINC) >>>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since this >>>>>>>>>> error >>>>>>>>>> >>> happens at the dicomTar.pl level (way before conversion >>>>>>>>>> into MINC files) >>>>>>>>>> >>> >>>>>>>>>> >>> Glad everything is working out!! >>>>>>>>>> >>> Best, >>>>>>>>>> >>> >>>>>>>>>> >>> C?cile >>>>>>>>>> >>> >>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. >>>>>>>>>> Now about the >>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there >>>>>>>>>> only if there is >>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>>>>> parameter? >>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or with >>>>>>>>>> the 2 studyiuid >>>>>>>>>> >>> to be there. >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> Sorry to hear you are having issues with the memory. I think >>>>>>>>>> most of our >>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be fine. >>>>>>>>>> >>> >>>>>>>>>> >>> Hope this helps! >>>>>>>>>> >>> >>>>>>>>>> >>> C?cile >>>>>>>>>> >>> >>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> about that dicom that had that insertion error it's about >>>>>>>>>> 30mb and when >>>>>>>>>> >>> it is being processed the ram is being drastically increased >>>>>>>>>> from 2gb to >>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is >>>>>>>>>> the recommended >>>>>>>>>> >>> size of ram for using Loris? >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>>>>> >>> >>>>>>>>>> >>> For the delete script issue, if you are absolutely certain >>>>>>>>>> that no >>>>>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>>>>> mri_upload table >>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>>> uploadID. It >>>>>>>>>> >>> looks like for some reason the scripts did not update this >>>>>>>>>> field when it >>>>>>>>>> >>> stopped the insertion. Not sure why that would be the case >>>>>>>>>> though. >>>>>>>>>> >>> Note: only do that update if you are certain that there is no >>>>>>>>>> processing >>>>>>>>>> >>> happening. >>>>>>>>>> >>> >>>>>>>>>> >>> Hope this helps! >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>>>>>>> actually do >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>>>>> missing at the >>>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but >>>>>>>>>> with no mnic >>>>>>>>>> >>> files. Also now i have this error >>>>>>>>>> >>> >>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>>>>> :/data/loris/bin/mri/tools$ >>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>>> processing it. >>>>>>>>>> >>> >>>>>>>>>> >>> How can solve this? >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>>>>> >>> >>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>> >>> >>>>>>>>>> >>> To give you a brief idea: >>>>>>>>>> >>> Per folder it will: >>>>>>>>>> >>> 1) Delete all the .bak files >>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>>>>>> TE_min, >>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>>>>> mri_protocol table >>>>>>>>>> >>> >>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>> >>> For some reason some files are missing >>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>> >>> >>>>>>>>>> >>> In total i have 7 folders >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> 3/7 passed >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> Also about the first patient with DC0000 had a violation "T1 >>>>>>>>>> AXIAL SE >>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i >>>>>>>>>> find that weird >>>>>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>>>>> >>> >>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory does >>>>>>>>>> not contain a >>>>>>>>>> >>> single DICOM file.", therefore they are missing their StudyUID >>>>>>>>>> >>> >>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>> multiple >>>>>>>>>> >>> studies." >>>>>>>>>> >>> >>>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC >>>>>>>>>> files. >>>>>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>>>>> >>> >>>>>>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 >>>>>>>>>> and 102506134 >>>>>>>>>> >>> can i just pass a flag parameter to >>>>>>>>>> batch_uploads_imageuploader.pl? or >>>>>>>>>> >>> modify imaging_upload_file.pl? >>>>>>>>>> >>> >>>>>>>>>> >>> Thank you, >>>>>>>>>> >>> >>>>>>>>>> >>> Sotirios >>>>>>>>>> >>> >>>>>>>>>> >>> PS >>>>>>>>>> >>> >>>>>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>>>>> dicom_output.txt. >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> Glad to hear about your progress. >>>>>>>>>> >>> >>>>>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>>>>> documented here >>>>>>>>>> >>> < >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>> > >>>>>>>>>> >>> -- let us know if you didn't find the answers you were >>>>>>>>>> looking for there. >>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>>>> database >>>>>>>>>> >>> management software is a visual placeholder for you as the >>>>>>>>>> user? I'm not >>>>>>>>>> >>> sure why a scanner would ever be registered with ID='0' as >>>>>>>>>> your screenshot >>>>>>>>>> >>> showed.) >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> I fixed it with this >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>>>>> something >>>>>>>>>> >>> wrong with the structure? why did i receive a 500 internal >>>>>>>>>> error? In the >>>>>>>>>> >>> loris-error log it state that there is something wrong with >>>>>>>>>> token, but i >>>>>>>>>> >>> verfied that the type of the token is a string. >>>>>>>>>> >>> >>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>> [client >>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: >>>>>>>>>> Argument 1 >>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the >>>>>>>>>> type string, >>>>>>>>>> >>> null given, called in >>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>>> line 169 and >>>>>>>>>> >>> defined in >>>>>>>>>> >>> >>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>> >>> trace:\n#0 >>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 >>>>>>>>>> {main}\n thrown in >>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>>> line 192 >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> Is there a way also to delete candidates? Just to let you >>>>>>>>>> know what i >>>>>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>>>>> dependencies. >>>>>>>>>> >>> >>>>>>>>>> >>> First i deleted all their uploads >>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a way >>>>>>>>>> to omit >>>>>>>>>> >>> the backup file ? ) >>>>>>>>>> >>> >>>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted all >>>>>>>>>> the entries >>>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry >>>>>>>>>> with the 0 ID. >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> We recommend that you use our existing tools for creating new >>>>>>>>>> candidates >>>>>>>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>>>>>>> calling the Candidate >>>>>>>>>> >>> class's createNew() >>>>>>>>>> >>> < >>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>>>>> >function. >>>>>>>>>> >>> These will create the necessary records for you. (It's not >>>>>>>>>> recommended to >>>>>>>>>> >>> make direct modifications to mysql database tables in your >>>>>>>>>> script, if I >>>>>>>>>> >>> understand you.) >>>>>>>>>> >>> >>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, and >>>>>>>>>> there are >>>>>>>>>> >>> multiple reasons for this. >>>>>>>>>> >>> You can use the PSCID for project-specific IDs and the >>>>>>>>>> External ID field >>>>>>>>>> >>> in the candidate table can also be used for any values you >>>>>>>>>> like. >>>>>>>>>> >>> Additionally, any number of custom IDs can be added in >>>>>>>>>> parallel - these >>>>>>>>>> >>> are entered/visible in the Candidate Information module and >>>>>>>>>> added in the >>>>>>>>>> >>> back-end as candidate parameters. >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> We are building a script that will auto insert the candidates >>>>>>>>>> based on >>>>>>>>>> >>> their ExternalID. We would like to know whethere when we are >>>>>>>>>> creating a new >>>>>>>>>> >>> profile in the candidate table, if we also have to insert a >>>>>>>>>> new record at >>>>>>>>>> >>> another table? Furthermore is there a problem that in our >>>>>>>>>> case CandID won't >>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, >>>>>>>>>> Mrs < >>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> That would normally be the case but the numeric part of the >>>>>>>>>> PSCID get >>>>>>>>>> >>> paded with 0 on the left. >>>>>>>>>> >>> >>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>> numerical char >>>>>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>>>>> >>> >>>>>>>>>> >>> ABC0001 >>>>>>>>>> >>> ABC0002 >>>>>>>>>> >>> ... >>>>>>>>>> >>> ABC0010 >>>>>>>>>> >>> ... >>>>>>>>>> >>> >>>>>>>>>> >>> thus sorting them ascending will always get the latest value >>>>>>>>>> generated >>>>>>>>>> >>> as the max value. >>>>>>>>>> >>> >>>>>>>>>> >>> M?lanie >>>>>>>>>> >>> >>>>>>>>>> >>> ------------------------------ >>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>> >>> >>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must be >>>>>>>>>> stored >>>>>>>>>> >>> within a specific length of characters. Otherwise if we were >>>>>>>>>> to sort >>>>>>>>>> >>> strings with different lengths the result would not be sorted >>>>>>>>>> correctly ( >>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, >>>>>>>>>> Mrs < >>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hello Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> There is no `last value` stored anywhere. >>>>>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>>>>> increase that >>>>>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>>>>> >>> >>>>>>>>>> >>> Hope this info help. >>>>>>>>>> >>> >>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | >>>>>>>>>> McGill >>>>>>>>>> >>> University >>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>> >>> >>>>>>>>>> >>> ------------------------------ >>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> how does Loris determine the next available PSCID value for a >>>>>>>>>> new >>>>>>>>>> >>> candidate? >>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but where do >>>>>>>>>> we store the >>>>>>>>>> >>> last value for the sequential sequence? >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> the parameters in the mri_protocol you have assigned are >>>>>>>>>> global >>>>>>>>>> >>> standard? or were assigned after trial and error? >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> Given you have done the initial setup of your tables to match >>>>>>>>>> your >>>>>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>>>>> >>> < >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>>>>> > >>>>>>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> *if i were to change their status to resolve what would >>>>>>>>>> happen? >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser from >>>>>>>>>> the >>>>>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>>>>> /data/loris/data/trashbin/ >>>>>>>>>> >>> if i were to click their issue to resolve what would happend? >>>>>>>>>> would they >>>>>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> The defaut values of the schema exists in my local database. >>>>>>>>>> If i adjust >>>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>>>>> uploaded? >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol >>>>>>>>>> table ? (and >>>>>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>>>>> >>> >>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>>>>>>> insertion >>>>>>>>>> >>> setup : See the install/setup documentation : >>>>>>>>>> >>> >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>> >>> >>>>>>>>>> >>> To add new rows, just use MySQL insert statements. You can >>>>>>>>>> adapt the >>>>>>>>>> >>> insert statements which load the default table values --> >>>>>>>>>> e.g. Here on >>>>>>>>>> >>> GitHub : >>>>>>>>>> >>> >>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>> >>> (see also the mri_scan_type table) >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> I see that i can edit the values but not how to insert new >>>>>>>>>> rows. >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> If i choose Inserted with flag then will the minc be inserted? >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>> >>> >>>>>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>>>>> >>> >>>>>>>>>> >>> It says "could not identify scan type", which we knew >>>>>>>>>> already. Did you >>>>>>>>>> >>> click on the link on those words? >>>>>>>>>> >>> >>>>>>>>>> >>> It will take you to the next page of the module, showing for >>>>>>>>>> each scan >>>>>>>>>> >>> what the scan parameters were, and will also show for >>>>>>>>>> comparison what's >>>>>>>>>> >>> stored in your *mri_protocol* table. >>>>>>>>>> >>> Compare these values to find which parameter was not correct >>>>>>>>>> according >>>>>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>>>>> >>> >>>>>>>>>> >>> You may end up broadening your mri_protocol value ranges >>>>>>>>>> (e.g. TR, TE) >>>>>>>>>> >>> for scans. >>>>>>>>>> >>> This can be done in the front-end, by editing the database >>>>>>>>>> table >>>>>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>>>>> >>> >>>>>>>>>> >>> The MRI Violations module features are explained in more >>>>>>>>>> detail in the >>>>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] icon >>>>>>>>>> in the menu >>>>>>>>>> >>> bar.) >>>>>>>>>> >>> >>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>>>>> >>> < >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>> > >>>>>>>>>> >>> : no MINCs inserted- violated scans >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> looks like my previous email's attachment wasn't delivered >>>>>>>>>> due to >>>>>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>>>>> >>> >>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>>>>> webbrowser, so >>>>>>>>>> >>> that you can check the filelds easier. >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios -- >>>>>>>>>> >>> Great, sounds like more progress. >>>>>>>>>> >>> >>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're getting >>>>>>>>>> an Endian >>>>>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>> successfully >>>>>>>>>> >>> relabelled, after the command ran? >>>>>>>>>> >>> >>>>>>>>>> >>> You can use also our DICAT tool ( >>>>>>>>>> https://github.com/aces/DICAT) to >>>>>>>>>> >>> verify and/or update local DICOM headers -- though your >>>>>>>>>> dcmodify command is >>>>>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>>>>> >>> >>>>>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>>>>> "(2001,105f)" from >>>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM slice >>>>>>>>>> before and look >>>>>>>>>> >>> at these fields specifically. >>>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>>> before/after >>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff the >>>>>>>>>> outputs -- >>>>>>>>>> >>> this will pinpoint what changed. >>>>>>>>>> >>> >>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>> recognized or >>>>>>>>>> >>> unknown : this means your scans did not match what is >>>>>>>>>> stored in your >>>>>>>>>> >>> mri_protocol table. >>>>>>>>>> >>> Check the MRI Violations front-end module -- can you see why >>>>>>>>>> they didn't >>>>>>>>>> >>> match? >>>>>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>>>>> mri_protocol >>>>>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Here is the psc table >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>>>>> >>> >>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>> >>> >>>>>>>>>> >>> and got those warning: is this okay? >>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>>>>>> reading a >>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>>>>>> reading a >>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined length, >>>>>>>>>> reading a >>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined length, >>>>>>>>>> reading a >>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined length, >>>>>>>>>> reading a >>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined length, >>>>>>>>>> reading a >>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>> >>> >>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you can >>>>>>>>>> see the >>>>>>>>>> >>> execution for the second dicom. Mnics could not be inserted >>>>>>>>>> due to >>>>>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>>>>> >>> >>>>>>>>>> >>> Running now the following command: >>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>> >>> >>>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>> '__MACOSX' >>>>>>>>>> >>> -delete >>>>>>>>>> >>> >>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod >>>>>>>>>> -verbose >>>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>>>>> >>> >>>>>>>>>> >>> Testing for database connectivity. >>>>>>>>>> >>> Database is available. >>>>>>>>>> >>> >>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>> >>> >>>>>>>>>> >>> You are creating a tar with the following command: >>>>>>>>>> >>> >>>>>>>>>> >>> tar -cf >>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> getting md5sums and gzipping!! >>>>>>>>>> >>> >>>>>>>>>> >>> * Taken from dir : >>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>> >>> * Archive target location : >>>>>>>>>> >>> >>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>> >>> >>>>>>>>>> >>> Adding archive info into database >>>>>>>>>> >>> >>>>>>>>>> >>> Removing temporary files from target location >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> Done adding archive info into database >>>>>>>>>> >>> >>>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>> -globLocation >>>>>>>>>> >>> -profile prod >>>>>>>>>> >>> >>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>> >>> -uploadID 12 -verbose >>>>>>>>>> >>> md5sum >>>>>>>>>> >>> >>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>> >>> candidate id 602102 >>>>>>>>>> >>> Set centerID = 1 >>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>> >>> >>>>>>>>>> >>> Number of MINC files that will be considered for inserting >>>>>>>>>> into the >>>>>>>>>> >>> database: 2 >>>>>>>>>> >>> >>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>> >>> candidate id 602102 >>>>>>>>>> >>> >>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>> >>> candidate id 602102 >>>>>>>>>> >>> >>>>>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>> >>> >>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>> cat >>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>> >>> >>>>>>>>>> >>> ==> Loading file from disk >>>>>>>>>> >>> >>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>> >>> >>>>>>>>>> >>> --> mapping DICOM parameter for >>>>>>>>>> >>> >>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>> >>> >>>>>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>>>>> >>> >>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>> >>> >>>>>>>>>> >>> ==> verifying acquisition protocol >>>>>>>>>> >>> >>>>>>>>>> >>> Acquisition protocol is unknown >>>>>>>>>> >>> >>>>>>>>>> >>> --> The minc file cannot be registered since the >>>>>>>>>> AcquisitionProtocol >>>>>>>>>> >>> is unknown >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios: >>>>>>>>>> >>> >>>>>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>>>>> *delete_imaging_upload* >>>>>>>>>> >>> script -- >>>>>>>>>> >>> details here: >>>>>>>>>> >>> >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>> >>> >>>>>>>>>> >>> What's in your *psc* table? (Is it properly populated? This >>>>>>>>>> is a >>>>>>>>>> >>> pre-requisite to loading imaging data. >>>>>>>>>> >>> < >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>>>>> > >>>>>>>>>> >>> ) >>>>>>>>>> >>> The foreign key constraint error on the candidate record is >>>>>>>>>> curious. >>>>>>>>>> >>> >>>>>>>>>> >>> There are also a few options for creating candidates when >>>>>>>>>> inserting >>>>>>>>>> >>> imaging data: >>>>>>>>>> >>> >>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>>>>>> pipeline >>>>>>>>>> >>> >>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>>>>>> optionally I >>>>>>>>>> >>> think) >>>>>>>>>> >>> How to: >>>>>>>>>> >>> >>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>> >>> >>>>>>>>>> >>> Then as a second step: >>>>>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>>>>> >>> < >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>>>>> > >>>>>>>>>> >>> to load your DICOMs. >>>>>>>>>> >>> You will want to first ensure that the PatientName header in >>>>>>>>>> the DICOMs >>>>>>>>>> >>> as well as tar package are correctly labelled with >>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>> >>> >>>>>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>>>>> >>> How to : >>>>>>>>>> >>> >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>> >>> >>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>>>>> bids_import script, >>>>>>>>>> >>> to automatically create your candidates and sessions. >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> How do i delete a Study? And everytime do i have to create a >>>>>>>>>> new >>>>>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>>>>> >>> >>>>>>>>>> >>> *First execution:* >>>>>>>>>> >>> >>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>> ./ >>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>> >>> log.txt >>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: a >>>>>>>>>> foreign >>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>> `FK_candidate_1` >>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>> (`CenterID`)) at >>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>> >>> The following database commands failed: >>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>>>>> (?,?,?,?,?)'; >>>>>>>>>> >>> SET >>>>>>>>>> >>> >>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>> >>> Medical Systems'; >>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a foreign key >>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>> `FK_mri_scanner_1` >>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) >>>>>>>>>> (error code 1452) >>>>>>>>>> >>> >>>>>>>>>> >>> ERROR: The validation has failed. Either re-run the >>>>>>>>>> validation again >>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using -force >>>>>>>>>> to force the >>>>>>>>>> >>> execution. >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>> >>> line 250. >>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>> >>> line 251. >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> *And second execution: * >>>>>>>>>> >>> >>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>> ./ >>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>> >>> log.txt >>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>> >>> >>>>>>>>>> >>> PROBLEM: >>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>> >>> The unique study ID is >>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>> >>> This is the information retained from the first time the >>>>>>>>>> study was >>>>>>>>>> >>> inserted: >>>>>>>>>> >>> >>>>>>>>>> >>> * Taken from dir : >>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>> >>> * Archive target location : >>>>>>>>>> >>> >>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> Last update of record: >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>> >>> line 250. >>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>> >>> line 251. >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> Ok, this sounds like good progress. Let us know when you >>>>>>>>>> next encounter >>>>>>>>>> >>> issues as you progress through the Imaging Install/Setup docs >>>>>>>>>> >>> < >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md>. >>>>>>>>>> >>> I'll look into how we can better handle the incoming/ >>>>>>>>>> directory next >>>>>>>>>> >>> time. >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>>>>>> >>> populated correctly except its port is 'port' : ''. Also >>>>>>>>>> i have tested >>>>>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>>>>> >>> >>>>>>>>>> >>> I executed the script again, because the only error i had >>>>>>>>>> previously was >>>>>>>>>> >>> that the /data/incoming folder didn't exist and there are no >>>>>>>>>> errors >>>>>>>>>> >>> reported back except of warnings <>>>>>>>>> password on the >>>>>>>>>> >>> command line interface can be insecure>>. >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> It's possible -- if the script was unable to connect to the >>>>>>>>>> database >>>>>>>>>> >>> during its execution (e.g. typo in the password), that would >>>>>>>>>> explain the >>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw in >>>>>>>>>> the Config >>>>>>>>>> >>> module. >>>>>>>>>> >>> It's hard to tell without seeing the output from your script >>>>>>>>>> run -- Did >>>>>>>>>> >>> you see a sign of any such error? >>>>>>>>>> >>> The Config fields are populated by the imaging_install.sh >>>>>>>>>> script (starting >>>>>>>>>> >>> at line 222 >>>>>>>>>> >>> < >>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>>>>> > >>>>>>>>>> >>> ) >>>>>>>>>> >>> >>>>>>>>>> >>> For example, check if the database connection information was >>>>>>>>>> populated >>>>>>>>>> >>> accurately in >>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Christine, >>>>>>>>>> >>> >>>>>>>>>> >>> If you are referring to the imaging_install.sh here is an >>>>>>>>>> image with the >>>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at the >>>>>>>>>> last part >>>>>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>> Ms. < >>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>> >>> >>>>>>>>>> >>> Glad to hear your LORIS core install is up and working and >>>>>>>>>> all the >>>>>>>>>> >>> front-end pages are loading. >>>>>>>>>> >>> >>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>>> project >>>>>>>>>> >>> > and the web interface worked. >>>>>>>>>> >>> >>>>>>>>>> >>> Yes, it's important that project/ have 775 permissions and >>>>>>>>>> that >>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the >>>>>>>>>> install >>>>>>>>>> >>> Readme . >>>>>>>>>> >>> >>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>> LORIS to >>>>>>>>>> >>> loris, right? >>>>>>>>>> >>> >>>>>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>>>>> installation >>>>>>>>>> >>> by an automated >>>>>>>>>> script -- >>>>>>>>>> >>> you do not need to set them manually via the Config module. >>>>>>>>>> >>> Please continue to follow the Setup Guide >>>>>>>>>> >>> for detailed >>>>>>>>>> steps to follow. >>>>>>>>>> >>> >>>>>>>>>> >>> Best, >>>>>>>>>> >>> Christine >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>> >>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>> LORIS to loris, >>>>>>>>>> >>> right? >>>>>>>>>> >>> >>>>>>>>>> >>> [image: image.png] >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>> >>> >>>>>>>>>> >>> Hi, >>>>>>>>>> >>> >>>>>>>>>> >>> i used >>>>>>>>>> >>> >>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E bash >>>>>>>>>> - >>>>>>>>>> >>> sudo apt-get install -y nodejs >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> you had suggested in the past, make worked and now i can see >>>>>>>>>> all the >>>>>>>>>> >>> contents in the web-interface, but i don't need make install? >>>>>>>>>> >>> >>>>>>>>>> >>> Thanks >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> >>> -- >>>>>>>>>> >>> >>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>> >>> >>>>>>>>>> >>> _______________________________________________ >>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>> >>>>>>>>>> >>> >>>>>>>>>> -------------- next part -------------- >>>>>>>>>> An HTML attachment was scrubbed... >>>>>>>>>> URL: < >>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>>>>>> > >>>>>>>>>> >>>>>>>>>> ------------------------------ >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>>>>>> ***************************************** >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> christine.rogers at mcgill.ca >>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>> Montreal Neurological Institute >>>>>>> McGill University | Montreal | Canada >>>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 37207 bytes Desc: not available URL: From AMORALESPINZON at bwh.harvard.edu Tue Nov 26 14:25:50 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 26 Nov 2019 19:25:50 +0000 Subject: [Loris-dev] Error dcm2mnc: UNKNOWN DICOM TRANSFER SYNTAX In-Reply-To: References: Message-ID: Hi Nicolas, Thank you for your answer and suggestion. We will try the conversion and report the results. Best, Alfredo. On Nov 26, 2019, at 7:14 AM, Nicolas Brossard > wrote: External Email - Use Caution Hi Alfredo, As you can see from the dcmdump output you provided, your file's TransferSyntaxUID is JPEGLossless and it looks like dcm2mnc does not like that. You can try converting your DICOM file so that it has a TransferSyntaxUID set to LittleEndianExplicit, like this: dcmdjpeg Dcm2mnc on the new converted file will most likely succeed then. If you have a lot of DICOM files located in a given directory, you can convert them all with one command: find -type f | xargs -i dcmdjpeg {} {} Let me know how it goes! Cheers, Nicolas On Mon, Nov 25, 2019 at 12:47 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, I am having the following error when converting dcm2mnc: ---------------------------------------------------------------------------- $ dcm2mnc -verbose 094901-00003-Dicom-pdw/ . Expanding directory '094901-00003-Dicom-pdw/' Checking file types... File 094901-00003-Dicom-pdw/0000100012.dcm appears to be DICOM (CD/Export). UNKNOWN DICOM TRANSFER SYNTAX: 1.2.840.10008.1.2.4.57 ---------------------------------------------------------------------------- Do you know why this might be happening? You may find the dcmdump of one dicom file at the end of this email. Thank you in advance. Alfredo. ---------------------------------------------------------------------------- # Dicom-File-Format # Dicom-Meta-Information-Header # Used TransferSyntax: Little Endian Explicit (0002,0000) UL 202 # 4, 1 FileMetaInformationGroupLength (0002,0001) OB 00\01 # 2, 1 FileMetaInformationVersion (0002,0002) UI =MRImageStorage # 26, 1 MediaStorageSOPClassUID (0002,0003) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] # 56, 1 MediaStorageSOPInstanceUID (0002,0010) UI =JPEGLossless:Non-hierarchical:Process14 # 22, 1 TransferSyntaxUID (0002,0012) UI [1.2.276.0.7230010.3.0.3.6.1] # 28, 1 ImplementationClassUID (0002,0013) SH [OFFIS_DCMTK_361] # 16, 1 ImplementationVersionName # Dicom-Data-Set # Used TransferSyntax: JPEG Lossless, Non-hierarchical, Process 14 (0008,0005) CS [ISO_IR 100] # 10, 1 SpecificCharacterSet (0008,0008) CS [ORIGINAL\PRIMARY\OTHER] # 22, 3 ImageType (0008,0016) UI =MRImageStorage # 26, 1 SOPClassUID (0008,0018) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.590] # 56, 1 SOPInstanceUID (0008,0020) DA [20000101] # 8, 1 StudyDate (0008,0021) DA [20000101] # 8, 1 SeriesDate (0008,0022) DA [20000101] # 8, 1 AcquisitionDate (0008,0030) TM [094647] # 6, 1 StudyTime (0008,0031) TM [094901] # 6, 1 SeriesTime (0008,0032) TM [094901] # 6, 1 AcquisitionTime (0008,0033) TM [094901] # 6, 1 ContentTime (0008,0060) CS [MR] # 2, 1 Modality (0008,0070) LO [AAABBBCCC] # 18, 1 Manufacturer (0008,0082) SQ (Sequence with explicit length #=0) # 0, 1 InstitutionCodeSequence (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0008,0104) LO [Anonymized] # 10, 1 CodeMeaning (0008,1032) SQ (Sequence with explicit length #=0) # 0, 1 ProcedureCodeSequence (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0008,103e) LO [pdw] # 4, 1 SeriesDescription (0008,1090) LO [Signa HDxt] # 10, 1 ManufacturerModelName (0008,1110) SQ (Sequence with explicit length #=1) # 104, 1 ReferencedStudySequence (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item (0008,1150) UI =RETIRED_DetachedStudyManagementSOPClass # 24, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.341] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0008,1111) SQ (Sequence with explicit length #=1) # 104, 1 ReferencedPerformedProcedureStepSequence (fffe,e000) na (Item with explicit length #=2) # 96, 1 Item (0008,1150) UI =ModalityPerformedProcedureStepSOPClass # 24, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.340] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0008,1140) SQ (Sequence with explicit length #=3) # 318, 1 ReferencedImageSequence (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.285] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.286] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e000) na (Item with explicit length #=2) # 98, 1 Item (0008,1150) UI =MRImageStorage # 26, 1 ReferencedSOPClassUID (0008,1155) UI [1.2.840.113619.2.244.3596.11861676.21355.1354711179.287] # 56, 1 ReferencedSOPInstanceUID (fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem (fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem (0010,0010) PN [AAABBBCCC] # 24, 1 PatientName (0010,0020) LO [11111] # 6, 1 PatientID (0010,0021) LO [Anonymized] # 10, 1 IssuerOfPatientID (0010,0030) DA [19000101] # 8, 1 PatientBirthDate (0010,0040) CS [Anonymized] # 10, 1 PatientSex (0010,1010) AS [Anonymized] # 10, 1 PatientAge (0010,1030) DS [10] # 2, 1 PatientWeight (0010,2150) LO [Anonymized] # 10, 1 CountryOfResidence (0010,2152) LO [Anonymized] # 10, 1 RegionOfResidence (0012,0050) LO [AAABBBCCC] # 8, 1 ClinicalTrialTimePointID (0012,0062) CS [Yes] # 4, 1 PatientIdentityRemoved (0012,0063) LO [Genentech] # 10, 1 DeidentificationMethod (0018,0020) CS [SE] # 2, 1 ScanningSequence (0018,0021) CS [SK] # 2, 1 SequenceVariant (0018,0022) CS [FAST_GEMS\EDR_GEMS\TRF_GEMS] # 28, 3 ScanOptions (0018,0023) CS [2D] # 2, 1 MRAcquisitionType (0018,0025) CS [N] # 2, 1 AngioFlag (0018,0050) DS [3] # 2, 1 SliceThickness (0018,0080) DS [2900] # 4, 1 RepetitionTime (0018,0081) DS [9.424] # 6, 1 EchoTime (0018,0082) DS [0] # 2, 1 InversionTime (0018,0083) DS [1] # 2, 1 NumberOfAverages (0018,0084) DS [127.723758] # 10, 1 ImagingFrequency (0018,0085) SH [1H] # 2, 1 ImagedNucleus (0018,0086) IS [1] # 2, 1 EchoNumbers (0018,0087) DS [3] # 2, 1 MagneticFieldStrength (0018,0088) DS [3] # 2, 1 SpacingBetweenSlices (0018,0091) IS [3] # 2, 1 EchoTrainLength (0018,0093) DS [100] # 4, 1 PercentSampling (0018,0094) DS [100] # 4, 1 PercentPhaseFieldOfView (0018,0095) DS [177.578] # 8, 1 PixelBandwidth (0018,1000) LO [056MRE3TH2565370] # 16, 1 DeviceSerialNumber (0018,1020) LO [15\LX\MR Software release:15.0_M4_0910.a] # 40, 3 SoftwareVersions (0018,1088) IS [0] # 2, 1 HeartRate (0018,1090) IS [0] # 2, 1 CardiacNumberOfImages (0018,1094) IS [0] # 2, 1 TriggerWindow (0018,1100) DS [250] # 4, 1 ReconstructionDiameter (0018,1250) SH [AAABBBBRAIN] # 8, 1 ReceiveCoilName (0018,1310) US 0\256\256\0 # 8, 4 AcquisitionMatrix (0018,1312) CS [ROW] # 4, 1 InPlanePhaseEncodingDirection (0018,1314) DS [90] # 2, 1 FlipAngle (0018,1315) CS [N] # 2, 1 VariableFlipAngleFlag (0018,1316) DS [1.3561] # 6, 1 SAR (0018,5100) CS [HFS] # 4, 1 PatientPosition (0020,000d) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.344] # 56, 1 StudyInstanceUID (0020,000e) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.349] # 56, 1 SeriesInstanceUID (0020,0010) SH [35313] # 6, 1 StudyID (0020,0011) IS [3] # 2, 1 SeriesNumber (0020,0012) IS [1] # 2, 1 AcquisitionNumber (0020,0013) IS [1] # 2, 1 InstanceNumber (0020,0032) DS [-130.858\-141.195\94.3036] # 26, 3 ImagePositionPatient (0020,0037) DS [0.999785\-0.0207525\0\0.0207528\0.999767\0.00598169] # 52, 6 ImageOrientationPatient (0020,0052) UI [1.2.840.113619.2.244.3596.11861676.21950.1354710592.343] # 56, 1 FrameOfReferenceUID (0020,0060) CS (no value available) # 0, 0 Laterality (0020,1002) IS [55] # 2, 1 ImagesInAcquisition (0020,1040) LO (no value available) # 0, 0 PositionReferenceIndicator (0020,1041) DS [95.04837036] # 12, 1 SliceLocation (0020,9056) SH [1] # 2, 1 StackID (0020,9057) UL 1 # 4, 1 InStackPositionNumber (0028,0002) US 1 # 2, 1 SamplesPerPixel (0028,0004) CS [MONOCHROME2] # 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50160, 1 Item (fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue Nov 26 16:34:00 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 26 Nov 2019 16:34:00 -0500 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, that is puzzling... A few additional questions: - what is the bash variable TMPDIR set to on the environment file? - could you try running separately dcm2mnc on the DICOM folder to see if that works? - could you send us the detailed log from the notification spool table (SELECT * FROM notification_spool WHERE UploadID=) and send it back to us? Maybe there are some additional clues that could help figuring out what is going on. Thank you! C?cile On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi Cecile, > > I checked for the StudyInstacueUID at the files with "The target directory > does not contain a single DICOM file"" and their attribute has a value. > > Regarding the scouter and localizer, i modified the settings in the > imaging pipeline and now i don't get that error message, but still it > doesn't create the mnics. > > The errors i am getting are ( uninitialized value $_ is not important? > because i haven't got comments about that ) > > Use of uninitialized value $_ in pattern match (m//) at > /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. > Running now the following command: /data/loris/data//uploadNeuroDB/ > imaging_upload_file.pl -profile prod -upload_id 134 > /data/incoming/DCC0025_118008_V1.tar.gz -verbose > > and > > Number of MINC files that will be considered for inserting into the > database: 0 > > No data could be converted into valid MINC files. > > The tarchiveLoader.pl insertion script has failed. > Use of uninitialized value $mail_user in concatenation (.) or string at > /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. > Can't exec "mail": No such file or directory at /data/loris/bin/mri/ > batch_uploads_imageuploader.pl line 249. > print() on closed filehandle MAIL at /data/loris/bin/mri/ > batch_uploads_imageuploader.pl line 250. > print() on closed filehandle MAIL at /data/loris/bin/mri/ > batch_uploads_imageuploader.pl line 251. > > Thanks > > Sotirios > > ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar < > cecile.madjar at mcin.ca> ??????: > >> Hi Sotirios, >> >> OK. So the issue I mentioned should not be a problem for you. >> >> Is the StudyInstanceUID DICOM header set in your images? If it is not >> set, then you would end up with the error message "The target directory >> does not contain a single DICOM file". So maybe this is the issue you are >> having with those datasets? >> >> Regarding not excluding series descriptions, you can configure that in >> the Config module under the Imaging Pipeline section. Simply remove all >> entries for the "Series description to exclude from imaging insertion" >> setting. >> >> C?cile >> >> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi Cecile, >>> >>> We are using this version >>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to >>> insert low resolution now? >>> >>> Thanks >>> >>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, wrote: >>> >>>> Hi Sotirios, >>>> >>>> Which version of LORIS-MRI are you using? >>>> >>>> There was a bug that got resolved in 20.2 in get_dicom_info.pl. >>>> Basically, if a DICOM did not have the (0020,0032) header, >>>> get_dicom_info.pl considered that the file was not a DICOM, which was >>>> a mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this is >>>> the issue you are encountering. >>>> >>>> About scout and localizer, they are a type of short and low resolution >>>> sequence that is used by the tech but is of no interest scientifically, >>>> which is why we tend to no insert them. >>>> >>>> Hope this helps, >>>> >>>> C?cile >>>> >>>> >>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi Cecile, >>>>> >>>>> i executed the find command and the output i got per folder was "DICOM >>>>> medical imaging data. Maybe there is something wrong with the find command >>>>> in the warning that it is unable to check if the file is a dicom file? Also >>>>> when i use get_dicom_info.pl i don't get any output data. Finally i >>>>> don't understand what scout or localizer is ( something like if and only if >>>>> a file fails then the whole session is invalid? ). >>>>> >>>>> [image: image.png] >>>>> >>>>> Thanks >>>>> >>>>> Sotirios >>>>> >>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < >>>>> cecile.madjar at mcin.ca> ??????: >>>>> >>>>>> Hi Sotirios, >>>>>> >>>>>> I took a closer look to the batch_uploader_multiple_output.txt file >>>>>> you sent. It looks like there are different reasons for failure depending >>>>>> on the DICOM folder uploaded. >>>>>> >>>>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 V1: >>>>>> it looks like there is no file of type DICOM in the folder. Have you >>>>>> checked to see if that is indeed the case? Maybe you can try running the >>>>>> following command on that folder to see what are the types of the files? If >>>>>> it does not return at least one DICOM medical imaging data file, then that >>>>>> is why you get the error message from the pipeline: >>>>>> - >>>>>> >>>>>> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >>>>>> >>>>>> - For 864173 DCC0001 V1: it looks like there are two different >>>>>> DICOM studies within the same folder. You will need to split that study in >>>>>> two based on the StudyUID field as the insertion pipeline does not allow >>>>>> for more than one StudyUID per upload. >>>>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 V1: >>>>>> it looks like the dcm2mnc command did not produce any MINC files. Can you >>>>>> check in the DICOM archive what are the series present in the tarchive for >>>>>> that visit? Maybe only a scout or localizer was acquired for that session, >>>>>> hence the no valid MINC files (scout and localizer being skipped for the >>>>>> conversion) >>>>>> - For 397410 DCC0003 V1: it looks like everything went well for >>>>>> this one. >>>>>> >>>>>> One script that is called by our pipeline is called get_dicom_info.pl and >>>>>> this does all kind of checks on the DICOM files (it is being called when >>>>>> running the dcm2mnc conversion). You could run it independently on your >>>>>> folder if needed. >>>>>> >>>>>> Since one of the study got in, it does not look like you are having a >>>>>> problem with the setup. It seems more likely to be a problem with the data >>>>>> themselves. >>>>>> >>>>>> Hope this helps. >>>>>> >>>>>> C?cile >>>>>> >>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi Christine, >>>>>>> >>>>>>> In my first vm i am able to create the minc files and view them at >>>>>>> the mri browser (except of candidate 102761034 ), meanwhile the same files >>>>>>> gives warnings at the 2nd vm. The output of the batch upload can be seen >>>>>>> in the file attached. >>>>>>> Also a colleague of us has built a pre-validation tool for dicom >>>>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had found >>>>>>> all the files that Loris gave as warning . Basically I confirmed that the >>>>>>> total amount of files per dicom was the same amount as stated in Loris and >>>>>>> checked some filenames given from warning to confirm that they match with >>>>>>> our tool. But that was months ago and my colleague had changed some >>>>>>> parameters for MIP and now our tool doesn't find all the invalid files, >>>>>>> that's why i asked for the dicom header specification of Loris. In a >>>>>>> discussion we had he mentioned that he doesn't check for some tags e.x. >>>>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>>>>>> remove invalid dcm files. >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> Can you provide us with some fresh particulars of the current issue >>>>>>>> and we'll take it from there? >>>>>>>> Yang's team has built these scripts which can definitely serve as a >>>>>>>> model for your pre-validation of your DICOM collections. >>>>>>>> cheers, >>>>>>>> Christine >>>>>>>> >>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> HI Yang, >>>>>>>>> >>>>>>>>> We make use of pydicom library too. Now about the validate.py i >>>>>>>>> see that you check if some attributes are missing such as PatientID, >>>>>>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>>>>>> something on the setup of my other virtual machine ( although one dicom >>>>>>>>> passed on the new vm successfully, the others that were inserted correctly >>>>>>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." but >>>>>>>>> i don't remember the solution. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>>>>>> ??????: >>>>>>>>> >>>>>>>>>> Hey, Sotirios, >>>>>>>>>> >>>>>>>>>> Christine from the LORIS team mentioned you had some issue with >>>>>>>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>>>>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>>>>>>> fully automated pipeline actually. >>>>>>>>>> >>>>>>>>>> While we were building CNBP, we had coded up some minor Python >>>>>>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>>>>>> more comprehensive solution, PyDICOM ( >>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>>>>>> >>>>>>>>>> Cheers, >>>>>>>>>> >>>>>>>>>> Yang Ding, PhD. >>>>>>>>>> Canadian Neonatal Brain Platform Architect >>>>>>>>>> >>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM < >>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote: >>>>>>>>>> >>>>>>>>>>> Send Loris-dev mailing list submissions to >>>>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>>>>>> >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>>>>>> >>>>>>>>>>> You can reach the person managing the list at >>>>>>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>>>>>> >>>>>>>>>>> When replying, please edit your Subject line so it is more >>>>>>>>>>> specific >>>>>>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Today's Topics: >>>>>>>>>>> >>>>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> ---------------------------------------------------------------------- >>>>>>>>>>> >>>>>>>>>>> Message: 1 >>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>>>>>> To: Cecile Madjar >>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>>>>>> Message-ID: >>>>>>>>>>> >>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>>>>>> >>>>>>>>>>> Hi, >>>>>>>>>>> >>>>>>>>>>> Could we send you a link with 10 anonymized dicom files to >>>>>>>>>>> diagnose the >>>>>>>>>>> warnings we get? >>>>>>>>>>> >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>>>>>>>>>> > Hi Cecile, >>>>>>>>>>> > >>>>>>>>>>> > We were wondering whether Loris has a tool to check if there >>>>>>>>>>> are problems >>>>>>>>>>> > with the dcm files, before trying to upload them. Something >>>>>>>>>>> that could >>>>>>>>>>> > provide the same results provided in the warning_output, this >>>>>>>>>>> is the >>>>>>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>>>>>> attributes of the >>>>>>>>>>> > dcm header would trigger a warning? is there a dcm file header >>>>>>>>>>> > specification for Loris? >>>>>>>>>>> > >>>>>>>>>>> > Thanks >>>>>>>>>>> > >>>>>>>>>>> > Sotirios >>>>>>>>>>> > >>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>>>>>> > >>>>>>>>>>> >> Hi, >>>>>>>>>>> >> >>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it >>>>>>>>>>> worked,but i >>>>>>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>>>>>> >> Thanks >>>>>>>>>>> >> >>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>>>>>> >> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and >>>>>>>>>>> columns are of >>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be >>>>>>>>>>> using >>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>>>>>> >>> >>>>>>>>>>> >>> The second error occurs because the trigger triggers a >>>>>>>>>>> rollback of the >>>>>>>>>>> >>> insert statement in the files table. >>>>>>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>>>>>> >>> >>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>>>>>>>> failure of >>>>>>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>>>>>> >>> -- Xavier >>>>>>>>>>> >>> >>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>>>>>> >>> *To:* Cecile Madjar >>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>; >>>>>>>>>>> >>> Christine Rogers, Ms. >>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>> >>> >>>>>>>>>>> >>> When mincs are inserted their corresponding rows at the file >>>>>>>>>>> table are >>>>>>>>>>> >>> inserted too >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>>>>>>>> because i >>>>>>>>>>> >>> don't want manually to label them as passed throught the >>>>>>>>>>> interface >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> That is the trigger i wrote >>>>>>>>>>> >>> >>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>>>>>> >>> BEGIN >>>>>>>>>>> >>> INSERT INTO files_qcstatus >>>>>>>>>>> >>> SET FileID = NEW.FileID, >>>>>>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>>>>>> >>> QCStatus = "Pass", >>>>>>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>>>>>> >>> END >>>>>>>>>>> >>> >>>>>>>>>>> >>> although it contains some errors >>>>>>>>>>> >>> >>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: >>>>>>>>>>> a foreign >>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES >>>>>>>>>>> `files` (`FileID`)) >>>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848. >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column >>>>>>>>>>> associated with >>>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it >>>>>>>>>>> means no DICOMs >>>>>>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>>>>>> insertion of the >>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with >>>>>>>>>>> the correct >>>>>>>>>>> >>> TarchiveID associated with the upload. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Could this correspond to what you want to do? >>>>>>>>>>> >>> >>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked to >>>>>>>>>>> the files >>>>>>>>>>> >>> table (hence, the MINC files). You could always create a new >>>>>>>>>>> table for >>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>>>>>> >>> >>>>>>>>>>> >>> C?cile >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of >>>>>>>>>>> creating a trigger for >>>>>>>>>>> >>> that, but which tables do i need to add entries to? So far >>>>>>>>>>> from what i see >>>>>>>>>>> >>> i need to add entres at the table "files" whenever an >>>>>>>>>>> insertion happens to >>>>>>>>>>> >>> files_qcstatus. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning >>>>>>>>>>> of my email >>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the >>>>>>>>>>> StudyID i am >>>>>>>>>>> >>> looking for is not stored in the database? >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks. >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>>>>>> >>> tarchive table. It can also be found in the metadata field >>>>>>>>>>> but it is mixed >>>>>>>>>>> >>> with many other information. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hope this helps, >>>>>>>>>>> >>> >>>>>>>>>>> >>> C?cile >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive >>>>>>>>>>> table, >>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found >>>>>>>>>>> something called >>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the Study >>>>>>>>>>> Instance UID. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>>>>>> >>> >>>>>>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>>>>>> >>> >>>>>>>>>>> >>> - the scan type could not be identified (not matching an >>>>>>>>>>> entry in >>>>>>>>>>> >>> the mri_protocol table) >>>>>>>>>>> >>> - one parameter of the scan type is out of the expected >>>>>>>>>>> range >>>>>>>>>>> >>> present in the mri_protocol_checks (extra filtering in >>>>>>>>>>> case you need to be >>>>>>>>>>> >>> stricker on some parameters not present in the >>>>>>>>>>> mri_protocol table) >>>>>>>>>>> >>> - if the CandID and PSCID do not match >>>>>>>>>>> >>> >>>>>>>>>>> >>> The following cases do not get in the MRI violation tables >>>>>>>>>>> as it happens >>>>>>>>>>> >>> before the conversion of the DICOM to MINC files and only >>>>>>>>>>> MINC files >>>>>>>>>>> >>> violations are logged there: >>>>>>>>>>> >>> >>>>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be found >>>>>>>>>>> to convert >>>>>>>>>>> >>> to MINC) >>>>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since >>>>>>>>>>> this error >>>>>>>>>>> >>> happens at the dicomTar.pl level (way before conversion >>>>>>>>>>> into MINC files) >>>>>>>>>>> >>> >>>>>>>>>>> >>> Glad everything is working out!! >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> >>>>>>>>>>> >>> C?cile >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. >>>>>>>>>>> Now about the >>>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there >>>>>>>>>>> only if there is >>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>>>>>> parameter? >>>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or with >>>>>>>>>>> the 2 studyiuid >>>>>>>>>>> >>> to be there. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Sorry to hear you are having issues with the memory. I think >>>>>>>>>>> most of our >>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be >>>>>>>>>>> fine. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>> >>> >>>>>>>>>>> >>> C?cile >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> about that dicom that had that insertion error it's about >>>>>>>>>>> 30mb and when >>>>>>>>>>> >>> it is being processed the ram is being drastically increased >>>>>>>>>>> from 2gb to >>>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is >>>>>>>>>>> the recommended >>>>>>>>>>> >>> size of ram for using Loris? >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>>>>>> >>> >>>>>>>>>>> >>> For the delete script issue, if you are absolutely certain >>>>>>>>>>> that no >>>>>>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>>>>>> mri_upload table >>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>>>> uploadID. It >>>>>>>>>>> >>> looks like for some reason the scripts did not update this >>>>>>>>>>> field when it >>>>>>>>>>> >>> stopped the insertion. Not sure why that would be the case >>>>>>>>>>> though. >>>>>>>>>>> >>> Note: only do that update if you are certain that there is >>>>>>>>>>> no processing >>>>>>>>>>> >>> happening. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>>>>>>>> actually do >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>>>>>> missing at the >>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but >>>>>>>>>>> with no mnic >>>>>>>>>>> >>> files. Also now i have this error >>>>>>>>>>> >>> >>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>>>>>> :/data/loris/bin/mri/tools$ >>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>>>> processing it. >>>>>>>>>>> >>> >>>>>>>>>>> >>> How can solve this? >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>>>>>> >>> >>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>>> >>> >>>>>>>>>>> >>> To give you a brief idea: >>>>>>>>>>> >>> Per folder it will: >>>>>>>>>>> >>> 1) Delete all the .bak files >>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, TR_max, >>>>>>>>>>> TE_min, >>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>>>>>> mri_protocol table >>>>>>>>>>> >>> >>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>>> >>> For some reason some files are missing >>>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>>> >>> >>>>>>>>>>> >>> In total i have 7 folders >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> 3/7 passed >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> Also about the first patient with DC0000 had a violation "T1 >>>>>>>>>>> AXIAL SE >>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i >>>>>>>>>>> find that weird >>>>>>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>>>>>> >>> >>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory does >>>>>>>>>>> not contain a >>>>>>>>>>> >>> single DICOM file.", therefore they are missing their >>>>>>>>>>> StudyUID >>>>>>>>>>> >>> >>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>>> multiple >>>>>>>>>>> >>> studies." >>>>>>>>>>> >>> >>>>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC >>>>>>>>>>> files. >>>>>>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>>>>>> >>> >>>>>>>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 >>>>>>>>>>> and 102506134 >>>>>>>>>>> >>> can i just pass a flag parameter to >>>>>>>>>>> batch_uploads_imageuploader.pl? or >>>>>>>>>>> >>> modify imaging_upload_file.pl? >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thank you, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Sotirios >>>>>>>>>>> >>> >>>>>>>>>>> >>> PS >>>>>>>>>>> >>> >>>>>>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>>>>>> dicom_output.txt. >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> Glad to hear about your progress. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>>>>>> documented here >>>>>>>>>>> >>> < >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>> > >>>>>>>>>>> >>> -- let us know if you didn't find the answers you were >>>>>>>>>>> looking for there. >>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>>>>> database >>>>>>>>>>> >>> management software is a visual placeholder for you as the >>>>>>>>>>> user? I'm not >>>>>>>>>>> >>> sure why a scanner would ever be registered with ID='0' as >>>>>>>>>>> your screenshot >>>>>>>>>>> >>> showed.) >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I fixed it with this >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>>>>>> something >>>>>>>>>>> >>> wrong with the structure? why did i receive a 500 internal >>>>>>>>>>> error? In the >>>>>>>>>>> >>> loris-error log it state that there is something wrong with >>>>>>>>>>> token, but i >>>>>>>>>>> >>> verfied that the type of the token is a string. >>>>>>>>>>> >>> >>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>>> [client >>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: >>>>>>>>>>> Argument 1 >>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of the >>>>>>>>>>> type string, >>>>>>>>>>> >>> null given, called in >>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>>>> line 169 and >>>>>>>>>>> >>> defined in >>>>>>>>>>> >>> >>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>>> >>> trace:\n#0 >>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 >>>>>>>>>>> {main}\n thrown in >>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>>>> line 192 >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Is there a way also to delete candidates? Just to let you >>>>>>>>>>> know what i >>>>>>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>>>>>> dependencies. >>>>>>>>>>> >>> >>>>>>>>>>> >>> First i deleted all their uploads >>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a >>>>>>>>>>> way to omit >>>>>>>>>>> >>> the backup file ? ) >>>>>>>>>>> >>> >>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted all >>>>>>>>>>> the entries >>>>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry >>>>>>>>>>> with the 0 ID. >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> We recommend that you use our existing tools for creating >>>>>>>>>>> new candidates >>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>>>>>>>> calling the Candidate >>>>>>>>>>> >>> class's createNew() >>>>>>>>>>> >>> < >>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>>>>>> >function. >>>>>>>>>>> >>> These will create the necessary records for you. (It's not >>>>>>>>>>> recommended to >>>>>>>>>>> >>> make direct modifications to mysql database tables in your >>>>>>>>>>> script, if I >>>>>>>>>>> >>> understand you.) >>>>>>>>>>> >>> >>>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, and >>>>>>>>>>> there are >>>>>>>>>>> >>> multiple reasons for this. >>>>>>>>>>> >>> You can use the PSCID for project-specific IDs and the >>>>>>>>>>> External ID field >>>>>>>>>>> >>> in the candidate table can also be used for any values you >>>>>>>>>>> like. >>>>>>>>>>> >>> Additionally, any number of custom IDs can be added in >>>>>>>>>>> parallel - these >>>>>>>>>>> >>> are entered/visible in the Candidate Information module and >>>>>>>>>>> added in the >>>>>>>>>>> >>> back-end as candidate parameters. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> We are building a script that will auto insert the >>>>>>>>>>> candidates based on >>>>>>>>>>> >>> their ExternalID. We would like to know whethere when we are >>>>>>>>>>> creating a new >>>>>>>>>>> >>> profile in the candidate table, if we also have to insert a >>>>>>>>>>> new record at >>>>>>>>>>> >>> another table? Furthermore is there a problem that in our >>>>>>>>>>> case CandID won't >>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, >>>>>>>>>>> Mrs < >>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> That would normally be the case but the numeric part of the >>>>>>>>>>> PSCID get >>>>>>>>>>> >>> paded with 0 on the left. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>>> numerical char >>>>>>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>>>>>> >>> >>>>>>>>>>> >>> ABC0001 >>>>>>>>>>> >>> ABC0002 >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> ABC0010 >>>>>>>>>>> >>> ... >>>>>>>>>>> >>> >>>>>>>>>>> >>> thus sorting them ascending will always get the latest value >>>>>>>>>>> generated >>>>>>>>>>> >>> as the max value. >>>>>>>>>>> >>> >>>>>>>>>>> >>> M?lanie >>>>>>>>>>> >>> >>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>> >>> >>>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must be >>>>>>>>>>> stored >>>>>>>>>>> >>> within a specific length of characters. Otherwise if we were >>>>>>>>>>> to sort >>>>>>>>>>> >>> strings with different lengths the result would not be >>>>>>>>>>> sorted correctly ( >>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, >>>>>>>>>>> Mrs < >>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hello Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> There is no `last value` stored anywhere. >>>>>>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>>>>>> increase that >>>>>>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hope this info help. >>>>>>>>>>> >>> >>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine | >>>>>>>>>>> McGill >>>>>>>>>>> >>> University >>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>>> >>> >>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> how does Loris determine the next available PSCID value for >>>>>>>>>>> a new >>>>>>>>>>> >>> candidate? >>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but where >>>>>>>>>>> do we store the >>>>>>>>>>> >>> last value for the sequential sequence? >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> the parameters in the mri_protocol you have assigned are >>>>>>>>>>> global >>>>>>>>>>> >>> standard? or were assigned after trial and error? >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Given you have done the initial setup of your tables to >>>>>>>>>>> match your >>>>>>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>>>>>> >>> < >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>>>>>> > >>>>>>>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> *if i were to change their status to resolve what would >>>>>>>>>>> happen? >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser from >>>>>>>>>>> the >>>>>>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>>>>>> /data/loris/data/trashbin/ >>>>>>>>>>> >>> if i were to click their issue to resolve what would >>>>>>>>>>> happend? would they >>>>>>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> The defaut values of the schema exists in my local database. >>>>>>>>>>> If i adjust >>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>>>>>> uploaded? >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol >>>>>>>>>>> table ? (and >>>>>>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>>>>>> >>> >>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>>>>>>>> insertion >>>>>>>>>>> >>> setup : See the install/setup documentation : >>>>>>>>>>> >>> >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>>> >>> >>>>>>>>>>> >>> To add new rows, just use MySQL insert statements. You can >>>>>>>>>>> adapt the >>>>>>>>>>> >>> insert statements which load the default table values --> >>>>>>>>>>> e.g. Here on >>>>>>>>>>> >>> GitHub : >>>>>>>>>>> >>> >>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>>> >>> (see also the mri_scan_type table) >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> I see that i can edit the values but not how to insert new >>>>>>>>>>> rows. >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> If i choose Inserted with flag then will the minc be >>>>>>>>>>> inserted? >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>>> >>> >>>>>>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>>>>>> >>> >>>>>>>>>>> >>> It says "could not identify scan type", which we knew >>>>>>>>>>> already. Did you >>>>>>>>>>> >>> click on the link on those words? >>>>>>>>>>> >>> >>>>>>>>>>> >>> It will take you to the next page of the module, showing for >>>>>>>>>>> each scan >>>>>>>>>>> >>> what the scan parameters were, and will also show for >>>>>>>>>>> comparison what's >>>>>>>>>>> >>> stored in your *mri_protocol* table. >>>>>>>>>>> >>> Compare these values to find which parameter was not correct >>>>>>>>>>> according >>>>>>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>>>>>> >>> >>>>>>>>>>> >>> You may end up broadening your mri_protocol value ranges >>>>>>>>>>> (e.g. TR, TE) >>>>>>>>>>> >>> for scans. >>>>>>>>>>> >>> This can be done in the front-end, by editing the database >>>>>>>>>>> table >>>>>>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>>>>>> >>> >>>>>>>>>>> >>> The MRI Violations module features are explained in more >>>>>>>>>>> detail in the >>>>>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] >>>>>>>>>>> icon in the menu >>>>>>>>>>> >>> bar.) >>>>>>>>>>> >>> >>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>>>>>> >>> < >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>> > >>>>>>>>>>> >>> : no MINCs inserted- violated scans >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> looks like my previous email's attachment wasn't delivered >>>>>>>>>>> due to >>>>>>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>>>>>> >>> >>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>>>>>> webbrowser, so >>>>>>>>>>> >>> that you can check the filelds easier. >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios -- >>>>>>>>>>> >>> Great, sounds like more progress. >>>>>>>>>>> >>> >>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're >>>>>>>>>>> getting an Endian >>>>>>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>>> successfully >>>>>>>>>>> >>> relabelled, after the command ran? >>>>>>>>>>> >>> >>>>>>>>>>> >>> You can use also our DICAT tool ( >>>>>>>>>>> https://github.com/aces/DICAT) to >>>>>>>>>>> >>> verify and/or update local DICOM headers -- though your >>>>>>>>>>> dcmodify command is >>>>>>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>>>>>> >>> >>>>>>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>>>>>> "(2001,105f)" from >>>>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM slice >>>>>>>>>>> before and look >>>>>>>>>>> >>> at these fields specifically. >>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>>>> before/after >>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff >>>>>>>>>>> the outputs -- >>>>>>>>>>> >>> this will pinpoint what changed. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>>> recognized or >>>>>>>>>>> >>> unknown : this means your scans did not match what is >>>>>>>>>>> stored in your >>>>>>>>>>> >>> mri_protocol table. >>>>>>>>>>> >>> Check the MRI Violations front-end module -- can you see why >>>>>>>>>>> they didn't >>>>>>>>>>> >>> match? >>>>>>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>>>>>> mri_protocol >>>>>>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Here is the psc table >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>>>>>> >>> >>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>>> >>> >>>>>>>>>>> >>> and got those warning: is this okay? >>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>> length, reading a >>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>> length, reading a >>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined >>>>>>>>>>> length, reading a >>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined >>>>>>>>>>> length, reading a >>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>> length, reading a >>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>> length, reading a >>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>> >>> >>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you >>>>>>>>>>> can see the >>>>>>>>>>> >>> execution for the second dicom. Mnics could not be inserted >>>>>>>>>>> due to >>>>>>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Running now the following command: >>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>>> >>> >>>>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>>> '__MACOSX' >>>>>>>>>>> >>> -delete >>>>>>>>>>> >>> >>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod >>>>>>>>>>> -verbose >>>>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>>>>>> >>> >>>>>>>>>>> >>> Testing for database connectivity. >>>>>>>>>>> >>> Database is available. >>>>>>>>>>> >>> >>>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>>> >>> >>>>>>>>>>> >>> You are creating a tar with the following command: >>>>>>>>>>> >>> >>>>>>>>>>> >>> tar -cf >>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> getting md5sums and gzipping!! >>>>>>>>>>> >>> >>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>> >>> >>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>> >>> >>>>>>>>>>> >>> Adding archive info into database >>>>>>>>>>> >>> >>>>>>>>>>> >>> Removing temporary files from target location >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> Done adding archive info into database >>>>>>>>>>> >>> >>>>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>>> -globLocation >>>>>>>>>>> >>> -profile prod >>>>>>>>>>> >>> >>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>>> >>> -uploadID 12 -verbose >>>>>>>>>>> >>> md5sum >>>>>>>>>>> >>> >>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>> >>> Set centerID = 1 >>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>> >>> >>>>>>>>>>> >>> Number of MINC files that will be considered for inserting >>>>>>>>>>> into the >>>>>>>>>>> >>> database: 2 >>>>>>>>>>> >>> >>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>> >>> >>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>> >>> >>>>>>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>>> >>> >>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>> cat >>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>> >>> >>>>>>>>>>> >>> ==> Loading file from disk >>>>>>>>>>> >>> >>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>> >>> >>>>>>>>>>> >>> --> mapping DICOM parameter for >>>>>>>>>>> >>> >>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>> >>> >>>>>>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>>>>>> >>> >>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>>> >>> >>>>>>>>>>> >>> ==> verifying acquisition protocol >>>>>>>>>>> >>> >>>>>>>>>>> >>> Acquisition protocol is unknown >>>>>>>>>>> >>> >>>>>>>>>>> >>> --> The minc file cannot be registered since the >>>>>>>>>>> AcquisitionProtocol >>>>>>>>>>> >>> is unknown >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>>>>>> *delete_imaging_upload* >>>>>>>>>>> >>> script -- >>>>>>>>>>> >>> details here: >>>>>>>>>>> >>> >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>> >>> >>>>>>>>>>> >>> What's in your *psc* table? (Is it properly populated? This >>>>>>>>>>> is a >>>>>>>>>>> >>> pre-requisite to loading imaging data. >>>>>>>>>>> >>> < >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>>>>>> > >>>>>>>>>>> >>> ) >>>>>>>>>>> >>> The foreign key constraint error on the candidate record is >>>>>>>>>>> curious. >>>>>>>>>>> >>> >>>>>>>>>>> >>> There are also a few options for creating candidates when >>>>>>>>>>> inserting >>>>>>>>>>> >>> imaging data: >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>>>>>>> pipeline >>>>>>>>>>> >>> >>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>>>>>>> optionally I >>>>>>>>>>> >>> think) >>>>>>>>>>> >>> How to: >>>>>>>>>>> >>> >>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Then as a second step: >>>>>>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>>>>>> >>> < >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>>>>>> > >>>>>>>>>>> >>> to load your DICOMs. >>>>>>>>>>> >>> You will want to first ensure that the PatientName header in >>>>>>>>>>> the DICOMs >>>>>>>>>>> >>> as well as tar package are correctly labelled with >>>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>>>>>> >>> How to : >>>>>>>>>>> >>> >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>>> >>> >>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>>>>>> bids_import script, >>>>>>>>>>> >>> to automatically create your candidates and sessions. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> How do i delete a Study? And everytime do i have to create a >>>>>>>>>>> new >>>>>>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>>>>>> >>> >>>>>>>>>>> >>> *First execution:* >>>>>>>>>>> >>> >>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>> ./ >>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>> >>> log.txt >>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: >>>>>>>>>>> a foreign >>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>>> `FK_candidate_1` >>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>>> (`CenterID`)) at >>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>>> >>> The following database commands failed: >>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>>>>>> (?,?,?,?,?)'; >>>>>>>>>>> >>> SET >>>>>>>>>>> >>> >>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>>> >>> Medical Systems'; >>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a foreign >>>>>>>>>>> key >>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>>> `FK_mri_scanner_1` >>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) >>>>>>>>>>> (error code 1452) >>>>>>>>>>> >>> >>>>>>>>>>> >>> ERROR: The validation has failed. Either re-run the >>>>>>>>>>> validation again >>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using >>>>>>>>>>> -force to force the >>>>>>>>>>> >>> execution. >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>> >>> line 250. >>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>> >>> line 251. >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> *And second execution: * >>>>>>>>>>> >>> >>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>> ./ >>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>> >>> log.txt >>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>> >>> >>>>>>>>>>> >>> PROBLEM: >>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>>> >>> The unique study ID is >>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>>> >>> This is the information retained from the first time the >>>>>>>>>>> study was >>>>>>>>>>> >>> inserted: >>>>>>>>>>> >>> >>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>> >>> >>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> Last update of record: >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>> >>> line 250. >>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>> >>> line 251. >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Ok, this sounds like good progress. Let us know when you >>>>>>>>>>> next encounter >>>>>>>>>>> >>> issues as you progress through the Imaging Install/Setup docs >>>>>>>>>>> >>> < >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md >>>>>>>>>>> >. >>>>>>>>>>> >>> I'll look into how we can better handle the incoming/ >>>>>>>>>>> directory next >>>>>>>>>>> >>> time. >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>>>>>>> >>> populated correctly except its port is 'port' : ''. Also >>>>>>>>>>> i have tested >>>>>>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>>>>>> >>> >>>>>>>>>>> >>> I executed the script again, because the only error i had >>>>>>>>>>> previously was >>>>>>>>>>> >>> that the /data/incoming folder didn't exist and there are no >>>>>>>>>>> errors >>>>>>>>>>> >>> reported back except of warnings <>>>>>>>>>> password on the >>>>>>>>>>> >>> command line interface can be insecure>>. >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> It's possible -- if the script was unable to connect to the >>>>>>>>>>> database >>>>>>>>>>> >>> during its execution (e.g. typo in the password), that would >>>>>>>>>>> explain the >>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw in >>>>>>>>>>> the Config >>>>>>>>>>> >>> module. >>>>>>>>>>> >>> It's hard to tell without seeing the output from your script >>>>>>>>>>> run -- Did >>>>>>>>>>> >>> you see a sign of any such error? >>>>>>>>>>> >>> The Config fields are populated by the imaging_install.sh >>>>>>>>>>> script (starting >>>>>>>>>>> >>> at line 222 >>>>>>>>>>> >>> < >>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>>>>>> > >>>>>>>>>>> >>> ) >>>>>>>>>>> >>> >>>>>>>>>>> >>> For example, check if the database connection information >>>>>>>>>>> was populated >>>>>>>>>>> >>> accurately in >>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Christine, >>>>>>>>>>> >>> >>>>>>>>>>> >>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>> image with the >>>>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>> the last part >>>>>>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>> Ms. < >>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>> >>> >>>>>>>>>>> >>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>> all the >>>>>>>>>>> >>> front-end pages are loading. >>>>>>>>>>> >>> >>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>>>> project >>>>>>>>>>> >>> > and the web interface worked. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Yes, it's important that project/ have 775 permissions and >>>>>>>>>>> that >>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the >>>>>>>>>>> install >>>>>>>>>>> >>> Readme . >>>>>>>>>>> >>> >>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>> LORIS to >>>>>>>>>>> >>> loris, right? >>>>>>>>>>> >>> >>>>>>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>>>>>> installation >>>>>>>>>>> >>> by an automated >>>>>>>>>>> script -- >>>>>>>>>>> >>> you do not need to set them manually via the Config module. >>>>>>>>>>> >>> Please continue to follow the Setup Guide >>>>>>>>>>> >>> for detailed >>>>>>>>>>> steps to follow. >>>>>>>>>>> >>> >>>>>>>>>>> >>> Best, >>>>>>>>>>> >>> Christine >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>> >>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>> LORIS to loris, >>>>>>>>>>> >>> right? >>>>>>>>>>> >>> >>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>> >>> >>>>>>>>>>> >>> Hi, >>>>>>>>>>> >>> >>>>>>>>>>> >>> i used >>>>>>>>>>> >>> >>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E >>>>>>>>>>> bash - >>>>>>>>>>> >>> sudo apt-get install -y nodejs >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> you had suggested in the past, make worked and now i can see >>>>>>>>>>> all the >>>>>>>>>>> >>> contents in the web-interface, but i don't need make install? >>>>>>>>>>> >>> >>>>>>>>>>> >>> Thanks >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> >>>>>>>>>>> >>> -- >>>>>>>>>>> >>> >>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>> >>> >>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> >>> 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URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 37207 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Nov 26 17:17:08 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 27 Nov 2019 00:17:08 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Cecile, In both my virtual machines export TMPDIR=/tmp In both vm also with dcm2mnc i get this output. Just to verify that this passed in my 1st vm and produced mincs. I attached the spool as a csv. [image: image.png] And also one difference i found was this in the Loris-mri code ( left 1st workable vm, right 2nd vm that has to be fixed, although i changed it seems to be independent of the uninitialized value $_ ) [image: image.png] Thanks, Sotirios ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar < cecile.madjar at mcin.ca> ??????: > Hi Sotirios, > > that is puzzling... A few additional questions: > > - what is the bash variable TMPDIR set to on the environment file? > - could you try running separately dcm2mnc on the DICOM folder to see > if that works? > - could you send us the detailed log from the notification spool table > (SELECT * FROM notification_spool WHERE UploadID=) and send > it back to us? Maybe there are some additional clues that could help > figuring out what is going on. > > Thank you! > > C?cile > > On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Cecile, >> >> I checked for the StudyInstacueUID at the files with "The target >> directory does not contain a single DICOM file"" and their attribute has a >> value. >> >> Regarding the scouter and localizer, i modified the settings in the >> imaging pipeline and now i don't get that error message, but still it >> doesn't create the mnics. >> >> The errors i am getting are ( uninitialized value $_ is not important? >> because i haven't got comments about that ) >> >> Use of uninitialized value $_ in pattern match (m//) at >> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. >> Running now the following command: /data/loris/data//uploadNeuroDB/ >> imaging_upload_file.pl -profile prod -upload_id 134 >> /data/incoming/DCC0025_118008_V1.tar.gz -verbose >> >> and >> >> Number of MINC files that will be considered for inserting into the >> database: 0 >> >> No data could be converted into valid MINC files. >> >> The tarchiveLoader.pl insertion script has failed. >> Use of uninitialized value $mail_user in concatenation (.) or string at >> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. >> Can't exec "mail": No such file or directory at /data/loris/bin/mri/ >> batch_uploads_imageuploader.pl line 249. >> print() on closed filehandle MAIL at /data/loris/bin/mri/ >> batch_uploads_imageuploader.pl line 250. >> print() on closed filehandle MAIL at /data/loris/bin/mri/ >> batch_uploads_imageuploader.pl line 251. >> >> Thanks >> >> Sotirios >> >> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >>> Hi Sotirios, >>> >>> OK. So the issue I mentioned should not be a problem for you. >>> >>> Is the StudyInstanceUID DICOM header set in your images? If it is not >>> set, then you would end up with the error message "The target directory >>> does not contain a single DICOM file". So maybe this is the issue you are >>> having with those datasets? >>> >>> Regarding not excluding series descriptions, you can configure that in >>> the Config module under the Imaging Pipeline section. Simply remove all >>> entries for the "Series description to exclude from imaging insertion" >>> setting. >>> >>> C?cile >>> >>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi Cecile, >>>> >>>> We are using this version >>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to >>>> insert low resolution now? >>>> >>>> Thanks >>>> >>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, >>>> wrote: >>>> >>>>> Hi Sotirios, >>>>> >>>>> Which version of LORIS-MRI are you using? >>>>> >>>>> There was a bug that got resolved in 20.2 in get_dicom_info.pl. >>>>> Basically, if a DICOM did not have the (0020,0032) header, >>>>> get_dicom_info.pl considered that the file was not a DICOM, which was >>>>> a mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this is >>>>> the issue you are encountering. >>>>> >>>>> About scout and localizer, they are a type of short and low resolution >>>>> sequence that is used by the tech but is of no interest scientifically, >>>>> which is why we tend to no insert them. >>>>> >>>>> Hope this helps, >>>>> >>>>> C?cile >>>>> >>>>> >>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi Cecile, >>>>>> >>>>>> i executed the find command and the output i got per folder was >>>>>> "DICOM medical imaging data. Maybe there is something wrong with the find >>>>>> command in the warning that it is unable to check if the file is a dicom >>>>>> file? Also when i use get_dicom_info.pl i don't get any output data. >>>>>> Finally i don't understand what scout or localizer is ( something like if >>>>>> and only if a file fails then the whole session is invalid? ). >>>>>> >>>>>> [image: image.png] >>>>>> >>>>>> Thanks >>>>>> >>>>>> Sotirios >>>>>> >>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < >>>>>> cecile.madjar at mcin.ca> ??????: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> I took a closer look to the batch_uploader_multiple_output.txt file >>>>>>> you sent. It looks like there are different reasons for failure depending >>>>>>> on the DICOM folder uploaded. >>>>>>> >>>>>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 >>>>>>> V1: it looks like there is no file of type DICOM in the folder. Have you >>>>>>> checked to see if that is indeed the case? Maybe you can try running the >>>>>>> following command on that folder to see what are the types of the files? If >>>>>>> it does not return at least one DICOM medical imaging data file, then that >>>>>>> is why you get the error message from the pipeline: >>>>>>> - >>>>>>> >>>>>>> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >>>>>>> >>>>>>> - For 864173 DCC0001 V1: it looks like there are two >>>>>>> different DICOM studies within the same folder. You will need to split that >>>>>>> study in two based on the StudyUID field as the insertion pipeline does not >>>>>>> allow for more than one StudyUID per upload. >>>>>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 >>>>>>> V1: it looks like the dcm2mnc command did not produce any MINC files. Can >>>>>>> you check in the DICOM archive what are the series present in the tarchive >>>>>>> for that visit? Maybe only a scout or localizer was acquired for that >>>>>>> session, hence the no valid MINC files (scout and localizer being skipped >>>>>>> for the conversion) >>>>>>> - For 397410 DCC0003 V1: it looks like everything went well for >>>>>>> this one. >>>>>>> >>>>>>> One script that is called by our pipeline is called >>>>>>> get_dicom_info.pl and this does all kind of checks on the DICOM >>>>>>> files (it is being called when running the dcm2mnc conversion). You could >>>>>>> run it independently on your folder if needed. >>>>>>> >>>>>>> Since one of the study got in, it does not look like you are having >>>>>>> a problem with the setup. It seems more likely to be a problem with the >>>>>>> data themselves. >>>>>>> >>>>>>> Hope this helps. >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi Christine, >>>>>>>> >>>>>>>> In my first vm i am able to create the minc files and view them at >>>>>>>> the mri browser (except of candidate 102761034 ), meanwhile the same files >>>>>>>> gives warnings at the 2nd vm. The output of the batch upload can be seen >>>>>>>> in the file attached. >>>>>>>> Also a colleague of us has built a pre-validation tool for dicom >>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had >>>>>>>> found all the files that Loris gave as warning . Basically I confirmed that >>>>>>>> the total amount of files per dicom was the same amount as stated in Loris >>>>>>>> and checked some filenames given from warning to confirm that they match >>>>>>>> with our tool. But that was months ago and my colleague had changed some >>>>>>>> parameters for MIP and now our tool doesn't find all the invalid files, >>>>>>>> that's why i asked for the dicom header specification of Loris. In a >>>>>>>> discussion we had he mentioned that he doesn't check for some tags e.x. >>>>>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>>>>>>> remove invalid dcm files. >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> Can you provide us with some fresh particulars of the >>>>>>>>> current issue and we'll take it from there? >>>>>>>>> Yang's team has built these scripts which can definitely serve as >>>>>>>>> a model for your pre-validation of your DICOM collections. >>>>>>>>> cheers, >>>>>>>>> Christine >>>>>>>>> >>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> HI Yang, >>>>>>>>>> >>>>>>>>>> We make use of pydicom library too. Now about the validate.py i >>>>>>>>>> see that you check if some attributes are missing such as PatientID, >>>>>>>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>>>>>>> something on the setup of my other virtual machine ( although one dicom >>>>>>>>>> passed on the new vm successfully, the others that were inserted correctly >>>>>>>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." >>>>>>>>>> but i don't remember the solution. >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>>>>>>> ??????: >>>>>>>>>> >>>>>>>>>>> Hey, Sotirios, >>>>>>>>>>> >>>>>>>>>>> Christine from the LORIS team mentioned you had some issue with >>>>>>>>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>>>>>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>>>>>>>> fully automated pipeline actually. >>>>>>>>>>> >>>>>>>>>>> While we were building CNBP, we had coded up some minor Python >>>>>>>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>>>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>>>>>>> more comprehensive solution, PyDICOM ( >>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>>>>>>> >>>>>>>>>>> Cheers, >>>>>>>>>>> >>>>>>>>>>> Yang Ding, PhD. >>>>>>>>>>> Canadian Neonatal Brain Platform Architect >>>>>>>>>>> >>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM < >>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote: >>>>>>>>>>> >>>>>>>>>>>> Send Loris-dev mailing list submissions to >>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>>>>>>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>>>>>>> >>>>>>>>>>>> You can reach the person managing the list at >>>>>>>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>>>>>>> >>>>>>>>>>>> When replying, please edit your Subject line so it is more >>>>>>>>>>>> specific >>>>>>>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> Today's Topics: >>>>>>>>>>>> >>>>>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> ---------------------------------------------------------------------- >>>>>>>>>>>> >>>>>>>>>>>> Message: 1 >>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>>>>>>> To: Cecile Madjar >>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>> Message-ID: >>>>>>>>>>>> >>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>>>>>>> >>>>>>>>>>>> Hi, >>>>>>>>>>>> >>>>>>>>>>>> Could we send you a link with 10 anonymized dicom files to >>>>>>>>>>>> diagnose the >>>>>>>>>>>> warnings we get? >>>>>>>>>>>> >>>>>>>>>>>> Thanks >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>>>>>>>>>>> > Hi Cecile, >>>>>>>>>>>> > >>>>>>>>>>>> > We were wondering whether Loris has a tool to check if there >>>>>>>>>>>> are problems >>>>>>>>>>>> > with the dcm files, before trying to upload them. Something >>>>>>>>>>>> that could >>>>>>>>>>>> > provide the same results provided in the warning_output, this >>>>>>>>>>>> is the >>>>>>>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>>>>>>> attributes of the >>>>>>>>>>>> > dcm header would trigger a warning? is there a dcm file header >>>>>>>>>>>> > specification for Loris? >>>>>>>>>>>> > >>>>>>>>>>>> > Thanks >>>>>>>>>>>> > >>>>>>>>>>>> > Sotirios >>>>>>>>>>>> > >>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>>>>>>> > >>>>>>>>>>>> >> Hi, >>>>>>>>>>>> >> >>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it >>>>>>>>>>>> worked,but i >>>>>>>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>>>>>>> >> Thanks >>>>>>>>>>>> >> >>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>>>>>>> >> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and >>>>>>>>>>>> columns are of >>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be >>>>>>>>>>>> using >>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The second error occurs because the trigger triggers a >>>>>>>>>>>> rollback of the >>>>>>>>>>>> >>> insert statement in the files table. >>>>>>>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results in >>>>>>>>>>>> failure of >>>>>>>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>>>>>>> >>> -- Xavier >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>>>>>>> >>> *To:* Cecile Madjar >>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>; >>>>>>>>>>>> >>> Christine Rogers, Ms. >>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> When mincs are inserted their corresponding rows at the >>>>>>>>>>>> file table are >>>>>>>>>>>> >>> inserted too >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as well, >>>>>>>>>>>> because i >>>>>>>>>>>> >>> don't want manually to label them as passed throught the >>>>>>>>>>>> interface >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> That is the trigger i wrote >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>>>>>>> >>> BEGIN >>>>>>>>>>>> >>> INSERT INTO files_qcstatus >>>>>>>>>>>> >>> SET FileID = NEW.FileID, >>>>>>>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>>>>>>> >>> QCStatus = "Pass", >>>>>>>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>>>>>>> >>> END >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> although it contains some errors >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: >>>>>>>>>>>> a foreign >>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES >>>>>>>>>>>> `files` (`FileID`)) >>>>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>> 848. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column >>>>>>>>>>>> associated with >>>>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it >>>>>>>>>>>> means no DICOMs >>>>>>>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>>>>>>> insertion of the >>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with >>>>>>>>>>>> the correct >>>>>>>>>>>> >>> TarchiveID associated with the upload. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Could this correspond to what you want to do? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked to >>>>>>>>>>>> the files >>>>>>>>>>>> >>> table (hence, the MINC files). You could always create a >>>>>>>>>>>> new table for >>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> C?cile >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of >>>>>>>>>>>> creating a trigger for >>>>>>>>>>>> >>> that, but which tables do i need to add entries to? So far >>>>>>>>>>>> from what i see >>>>>>>>>>>> >>> i need to add entres at the table "files" whenever an >>>>>>>>>>>> insertion happens to >>>>>>>>>>>> >>> files_qcstatus. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the beginning >>>>>>>>>>>> of my email >>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the >>>>>>>>>>>> StudyID i am >>>>>>>>>>>> >>> looking for is not stored in the database? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>>>>>>> >>> tarchive table. It can also be found in the metadata field >>>>>>>>>>>> but it is mixed >>>>>>>>>>>> >>> with many other information. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hope this helps, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> C?cile >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the tarchive >>>>>>>>>>>> table, >>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found >>>>>>>>>>>> something called >>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the >>>>>>>>>>>> Study Instance UID. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> - the scan type could not be identified (not matching an >>>>>>>>>>>> entry in >>>>>>>>>>>> >>> the mri_protocol table) >>>>>>>>>>>> >>> - one parameter of the scan type is out of the expected >>>>>>>>>>>> range >>>>>>>>>>>> >>> present in the mri_protocol_checks (extra filtering in >>>>>>>>>>>> case you need to be >>>>>>>>>>>> >>> stricker on some parameters not present in the >>>>>>>>>>>> mri_protocol table) >>>>>>>>>>>> >>> - if the CandID and PSCID do not match >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The following cases do not get in the MRI violation tables >>>>>>>>>>>> as it happens >>>>>>>>>>>> >>> before the conversion of the DICOM to MINC files and only >>>>>>>>>>>> MINC files >>>>>>>>>>>> >>> violations are logged there: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be found >>>>>>>>>>>> to convert >>>>>>>>>>>> >>> to MINC) >>>>>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since >>>>>>>>>>>> this error >>>>>>>>>>>> >>> happens at the dicomTar.pl level (way before conversion >>>>>>>>>>>> into MINC files) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Glad everything is working out!! >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> C?cile >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. >>>>>>>>>>>> Now about the >>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there >>>>>>>>>>>> only if there is >>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>>>>>>> parameter? >>>>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or with >>>>>>>>>>>> the 2 studyiuid >>>>>>>>>>>> >>> to be there. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Sorry to hear you are having issues with the memory. I >>>>>>>>>>>> think most of our >>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be >>>>>>>>>>>> fine. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> C?cile >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> about that dicom that had that insertion error it's about >>>>>>>>>>>> 30mb and when >>>>>>>>>>>> >>> it is being processed the ram is being drastically >>>>>>>>>>>> increased from 2gb to >>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is >>>>>>>>>>>> the recommended >>>>>>>>>>>> >>> size of ram for using Loris? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> For the delete script issue, if you are absolutely certain >>>>>>>>>>>> that no >>>>>>>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>>>>>>> mri_upload table >>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>>>>> uploadID. It >>>>>>>>>>>> >>> looks like for some reason the scripts did not update this >>>>>>>>>>>> field when it >>>>>>>>>>>> >>> stopped the insertion. Not sure why that would be the case >>>>>>>>>>>> though. >>>>>>>>>>>> >>> Note: only do that update if you are certain that there is >>>>>>>>>>>> no processing >>>>>>>>>>>> >>> happening. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID they >>>>>>>>>>>> actually do >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>>>>>>> missing at the >>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but >>>>>>>>>>>> with no mnic >>>>>>>>>>>> >>> files. Also now i have this error >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>>>>>>> :/data/loris/bin/mri/tools$ >>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>>>>> processing it. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> How can solve this? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>>>>>>> >>> >>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> To give you a brief idea: >>>>>>>>>>>> >>> Per folder it will: >>>>>>>>>>>> >>> 1) Delete all the .bak files >>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, >>>>>>>>>>>> TR_max, TE_min, >>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>>>>>>> mri_protocol table >>>>>>>>>>>> >>> >>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>>>> >>> For some reason some files are missing >>>>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> In total i have 7 folders >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> 3/7 passed >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Also about the first patient with DC0000 had a violation >>>>>>>>>>>> "T1 AXIAL SE >>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and i >>>>>>>>>>>> find that weird >>>>>>>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory does >>>>>>>>>>>> not contain a >>>>>>>>>>>> >>> single DICOM file.", therefore they are missing their >>>>>>>>>>>> StudyUID >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>>>> multiple >>>>>>>>>>>> >>> studies." >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC >>>>>>>>>>>> files. >>>>>>>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 >>>>>>>>>>>> and 102506134 >>>>>>>>>>>> >>> can i just pass a flag parameter to >>>>>>>>>>>> batch_uploads_imageuploader.pl? or >>>>>>>>>>>> >>> modify imaging_upload_file.pl? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thank you, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Sotirios >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> PS >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>>>>>>> dicom_output.txt. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> Glad to hear about your progress. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>>>>>>> documented here >>>>>>>>>>>> >>> < >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>> > >>>>>>>>>>>> >>> -- let us know if you didn't find the answers you were >>>>>>>>>>>> looking for there. >>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>>>>>> database >>>>>>>>>>>> >>> management software is a visual placeholder for you as the >>>>>>>>>>>> user? I'm not >>>>>>>>>>>> >>> sure why a scanner would ever be registered with ID='0' as >>>>>>>>>>>> your screenshot >>>>>>>>>>>> >>> showed.) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> I fixed it with this >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>>>>>>> something >>>>>>>>>>>> >>> wrong with the structure? why did i receive a 500 internal >>>>>>>>>>>> error? In the >>>>>>>>>>>> >>> loris-error log it state that there is something wrong with >>>>>>>>>>>> token, but i >>>>>>>>>>>> >>> verfied that the type of the token is a string. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>>>> [client >>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: >>>>>>>>>>>> Argument 1 >>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of >>>>>>>>>>>> the type string, >>>>>>>>>>>> >>> null given, called in >>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>>>>> line 169 and >>>>>>>>>>>> >>> defined in >>>>>>>>>>>> >>> >>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>>>> >>> trace:\n#0 >>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 >>>>>>>>>>>> {main}\n thrown in >>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>>>>> line 192 >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Is there a way also to delete candidates? Just to let you >>>>>>>>>>>> know what i >>>>>>>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>>>>>>> dependencies. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> First i deleted all their uploads >>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a >>>>>>>>>>>> way to omit >>>>>>>>>>>> >>> the backup file ? ) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted all >>>>>>>>>>>> the entries >>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry >>>>>>>>>>>> with the 0 ID. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> We recommend that you use our existing tools for creating >>>>>>>>>>>> new candidates >>>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP script, by >>>>>>>>>>>> calling the Candidate >>>>>>>>>>>> >>> class's createNew() >>>>>>>>>>>> >>> < >>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>>>>>>> >function. >>>>>>>>>>>> >>> These will create the necessary records for you. (It's not >>>>>>>>>>>> recommended to >>>>>>>>>>>> >>> make direct modifications to mysql database tables in your >>>>>>>>>>>> script, if I >>>>>>>>>>>> >>> understand you.) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, >>>>>>>>>>>> and there are >>>>>>>>>>>> >>> multiple reasons for this. >>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs and the >>>>>>>>>>>> External ID field >>>>>>>>>>>> >>> in the candidate table can also be used for any values you >>>>>>>>>>>> like. >>>>>>>>>>>> >>> Additionally, any number of custom IDs can be added in >>>>>>>>>>>> parallel - these >>>>>>>>>>>> >>> are entered/visible in the Candidate Information module and >>>>>>>>>>>> added in the >>>>>>>>>>>> >>> back-end as candidate parameters. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> We are building a script that will auto insert the >>>>>>>>>>>> candidates based on >>>>>>>>>>>> >>> their ExternalID. We would like to know whethere when we >>>>>>>>>>>> are creating a new >>>>>>>>>>>> >>> profile in the candidate table, if we also have to insert a >>>>>>>>>>>> new record at >>>>>>>>>>>> >>> another table? Furthermore is there a problem that in our >>>>>>>>>>>> case CandID won't >>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, >>>>>>>>>>>> Mrs < >>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> That would normally be the case but the numeric part of the >>>>>>>>>>>> PSCID get >>>>>>>>>>>> >>> paded with 0 on the left. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>>>> numerical char >>>>>>>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ABC0001 >>>>>>>>>>>> >>> ABC0002 >>>>>>>>>>>> >>> ... >>>>>>>>>>>> >>> ABC0010 >>>>>>>>>>>> >>> ... >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> thus sorting them ascending will always get the latest >>>>>>>>>>>> value generated >>>>>>>>>>>> >>> as the max value. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> M?lanie >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must be >>>>>>>>>>>> stored >>>>>>>>>>>> >>> within a specific length of characters. Otherwise if we >>>>>>>>>>>> were to sort >>>>>>>>>>>> >>> strings with different lengths the result would not be >>>>>>>>>>>> sorted correctly ( >>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, >>>>>>>>>>>> Mrs < >>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hello Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> There is no `last value` stored anywhere. >>>>>>>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>>>>>>> increase that >>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hope this info help. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine >>>>>>>>>>>> | McGill >>>>>>>>>>>> >>> University >>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> how does Loris determine the next available PSCID value for >>>>>>>>>>>> a new >>>>>>>>>>>> >>> candidate? >>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but where >>>>>>>>>>>> do we store the >>>>>>>>>>>> >>> last value for the sequential sequence? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> the parameters in the mri_protocol you have assigned are >>>>>>>>>>>> global >>>>>>>>>>>> >>> standard? or were assigned after trial and error? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Given you have done the initial setup of your tables to >>>>>>>>>>>> match your >>>>>>>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>>>>>>> >>> < >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>>>>>>> > >>>>>>>>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> *if i were to change their status to resolve what would >>>>>>>>>>>> happen? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser >>>>>>>>>>>> from the >>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>>>>>>> /data/loris/data/trashbin/ >>>>>>>>>>>> >>> if i were to click their issue to resolve what would >>>>>>>>>>>> happend? would they >>>>>>>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The defaut values of the schema exists in my local >>>>>>>>>>>> database. If i adjust >>>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>>>>>>> uploaded? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol >>>>>>>>>>>> table ? (and >>>>>>>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the Imaging >>>>>>>>>>>> insertion >>>>>>>>>>>> >>> setup : See the install/setup documentation : >>>>>>>>>>>> >>> >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> To add new rows, just use MySQL insert statements. You can >>>>>>>>>>>> adapt the >>>>>>>>>>>> >>> insert statements which load the default table values --> >>>>>>>>>>>> e.g. Here on >>>>>>>>>>>> >>> GitHub : >>>>>>>>>>>> >>> >>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>>>> >>> (see also the mri_scan_type table) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> I see that i can edit the values but not how to insert new >>>>>>>>>>>> rows. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> If i choose Inserted with flag then will the minc be >>>>>>>>>>>> inserted? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> It says "could not identify scan type", which we knew >>>>>>>>>>>> already. Did you >>>>>>>>>>>> >>> click on the link on those words? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> It will take you to the next page of the module, showing >>>>>>>>>>>> for each scan >>>>>>>>>>>> >>> what the scan parameters were, and will also show for >>>>>>>>>>>> comparison what's >>>>>>>>>>>> >>> stored in your *mri_protocol* table. >>>>>>>>>>>> >>> Compare these values to find which parameter was not >>>>>>>>>>>> correct according >>>>>>>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> You may end up broadening your mri_protocol value ranges >>>>>>>>>>>> (e.g. TR, TE) >>>>>>>>>>>> >>> for scans. >>>>>>>>>>>> >>> This can be done in the front-end, by editing the database >>>>>>>>>>>> table >>>>>>>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The MRI Violations module features are explained in more >>>>>>>>>>>> detail in the >>>>>>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] >>>>>>>>>>>> icon in the menu >>>>>>>>>>>> >>> bar.) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>>>>>>> >>> < >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>> > >>>>>>>>>>>> >>> : no MINCs inserted- violated scans >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> looks like my previous email's attachment wasn't delivered >>>>>>>>>>>> due to >>>>>>>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>>>>>>> >>> >>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>>>>>>> webbrowser, so >>>>>>>>>>>> >>> that you can check the filelds easier. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios -- >>>>>>>>>>>> >>> Great, sounds like more progress. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're >>>>>>>>>>>> getting an Endian >>>>>>>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>>>> successfully >>>>>>>>>>>> >>> relabelled, after the command ran? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> You can use also our DICAT tool ( >>>>>>>>>>>> https://github.com/aces/DICAT) to >>>>>>>>>>>> >>> verify and/or update local DICOM headers -- though your >>>>>>>>>>>> dcmodify command is >>>>>>>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>>>>>>> "(2001,105f)" from >>>>>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM slice >>>>>>>>>>>> before and look >>>>>>>>>>>> >>> at these fields specifically. >>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>>>>> before/after >>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff >>>>>>>>>>>> the outputs -- >>>>>>>>>>>> >>> this will pinpoint what changed. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>>>> recognized or >>>>>>>>>>>> >>> unknown : this means your scans did not match what is >>>>>>>>>>>> stored in your >>>>>>>>>>>> >>> mri_protocol table. >>>>>>>>>>>> >>> Check the MRI Violations front-end module -- can you see >>>>>>>>>>>> why they didn't >>>>>>>>>>>> >>> match? >>>>>>>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>>>>>>> mri_protocol >>>>>>>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Here is the psc table >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> and got those warning: is this okay? >>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>> length, reading a >>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>> length, reading a >>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined >>>>>>>>>>>> length, reading a >>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined >>>>>>>>>>>> length, reading a >>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>> length, reading a >>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>> length, reading a >>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you >>>>>>>>>>>> can see the >>>>>>>>>>>> >>> execution for the second dicom. Mnics could not be inserted >>>>>>>>>>>> due to >>>>>>>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Running now the following command: >>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>>>> '__MACOSX' >>>>>>>>>>>> >>> -delete >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod >>>>>>>>>>>> -verbose >>>>>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Testing for database connectivity. >>>>>>>>>>>> >>> Database is available. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> You are creating a tar with the following command: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> tar -cf >>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> getting md5sums and gzipping!! >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>>> >>> >>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Adding archive info into database >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Removing temporary files from target location >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Done adding archive info into database >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>>>> -globLocation >>>>>>>>>>>> >>> -profile prod >>>>>>>>>>>> >>> >>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>>>> >>> -uploadID 12 -verbose >>>>>>>>>>>> >>> md5sum >>>>>>>>>>>> >>> >>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>> >>> Set centerID = 1 >>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Number of MINC files that will be considered for inserting >>>>>>>>>>>> into the >>>>>>>>>>>> >>> database: 2 >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>> cat >>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ==> Loading file from disk >>>>>>>>>>>> >>> >>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> --> mapping DICOM parameter for >>>>>>>>>>>> >>> >>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ==> verifying acquisition protocol >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Acquisition protocol is unknown >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> --> The minc file cannot be registered since the >>>>>>>>>>>> AcquisitionProtocol >>>>>>>>>>>> >>> is unknown >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>>>>>>> *delete_imaging_upload* >>>>>>>>>>>> >>> script -- >>>>>>>>>>>> >>> details here: >>>>>>>>>>>> >>> >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> What's in your *psc* table? (Is it properly populated? >>>>>>>>>>>> This is a >>>>>>>>>>>> >>> pre-requisite to loading imaging data. >>>>>>>>>>>> >>> < >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>>>>>>> > >>>>>>>>>>>> >>> ) >>>>>>>>>>>> >>> The foreign key constraint error on the candidate record is >>>>>>>>>>>> curious. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> There are also a few options for creating candidates when >>>>>>>>>>>> inserting >>>>>>>>>>>> >>> imaging data: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>>>>>>>> pipeline >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>>>>>>>> optionally I >>>>>>>>>>>> >>> think) >>>>>>>>>>>> >>> How to: >>>>>>>>>>>> >>> >>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Then as a second step: >>>>>>>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>>>>>>> >>> < >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>>>>>>> > >>>>>>>>>>>> >>> to load your DICOMs. >>>>>>>>>>>> >>> You will want to first ensure that the PatientName header >>>>>>>>>>>> in the DICOMs >>>>>>>>>>>> >>> as well as tar package are correctly labelled with >>>>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>>>>>>> >>> How to : >>>>>>>>>>>> >>> >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>>>>>>> bids_import script, >>>>>>>>>>>> >>> to automatically create your candidates and sessions. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> How do i delete a Study? And everytime do i have to create >>>>>>>>>>>> a new >>>>>>>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> *First execution:* >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>> ./ >>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>>> >>> log.txt >>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child row: >>>>>>>>>>>> a foreign >>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>>>> `FK_candidate_1` >>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>>>> (`CenterID`)) at >>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>>>> >>> The following database commands failed: >>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>>>>>>> (?,?,?,?,?)'; >>>>>>>>>>>> >>> SET >>>>>>>>>>>> >>> >>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>>>> >>> Medical Systems'; >>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a foreign >>>>>>>>>>>> key >>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>>>> `FK_mri_scanner_1` >>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) >>>>>>>>>>>> (error code 1452) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ERROR: The validation has failed. Either re-run the >>>>>>>>>>>> validation again >>>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using >>>>>>>>>>>> -force to force the >>>>>>>>>>>> >>> execution. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>> >>> line 250. >>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>> >>> line 251. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> *And second execution: * >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>> ./ >>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>>> >>> log.txt >>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> PROBLEM: >>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>>>> >>> The unique study ID is >>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>>>> >>> This is the information retained from the first time the >>>>>>>>>>>> study was >>>>>>>>>>>> >>> inserted: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>>> >>> >>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Last update of record: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>> >>> line 250. >>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>> >>> line 251. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Ok, this sounds like good progress. Let us know when you >>>>>>>>>>>> next encounter >>>>>>>>>>>> >>> issues as you progress through the Imaging Install/Setup >>>>>>>>>>>> docs >>>>>>>>>>>> >>> < >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md >>>>>>>>>>>> >. >>>>>>>>>>>> >>> I'll look into how we can better handle the incoming/ >>>>>>>>>>>> directory next >>>>>>>>>>>> >>> time. >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>>>>>>>> >>> populated correctly except its port is 'port' : ''. >>>>>>>>>>>> Also i have tested >>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> I executed the script again, because the only error i had >>>>>>>>>>>> previously was >>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and there are >>>>>>>>>>>> no errors >>>>>>>>>>>> >>> reported back except of warnings <>>>>>>>>>>> password on the >>>>>>>>>>>> >>> command line interface can be insecure>>. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> It's possible -- if the script was unable to connect to the >>>>>>>>>>>> database >>>>>>>>>>>> >>> during its execution (e.g. typo in the password), that >>>>>>>>>>>> would explain the >>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw >>>>>>>>>>>> in the Config >>>>>>>>>>>> >>> module. >>>>>>>>>>>> >>> It's hard to tell without seeing the output from your >>>>>>>>>>>> script run -- Did >>>>>>>>>>>> >>> you see a sign of any such error? >>>>>>>>>>>> >>> The Config fields are populated by the imaging_install.sh >>>>>>>>>>>> script (starting >>>>>>>>>>>> >>> at line 222 >>>>>>>>>>>> >>> < >>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>>>>>>> > >>>>>>>>>>>> >>> ) >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> For example, check if the database connection information >>>>>>>>>>>> was populated >>>>>>>>>>>> >>> accurately in >>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Christine, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>> image with the >>>>>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>> the last part >>>>>>>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>> Ms. < >>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>> all the >>>>>>>>>>>> >>> front-end pages are loading. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>>>>> project >>>>>>>>>>>> >>> > and the web interface worked. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Yes, it's important that project/ have 775 permissions and >>>>>>>>>>>> that >>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the >>>>>>>>>>>> install >>>>>>>>>>>> >>> Readme . >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>>> LORIS to >>>>>>>>>>>> >>> loris, right? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>>>>>>> installation >>>>>>>>>>>> >>> by an automated >>>>>>>>>>>> script -- >>>>>>>>>>>> >>> you do not need to set them manually via the Config module. >>>>>>>>>>>> >>> Please continue to follow the Setup Guide >>>>>>>>>>>> >>> for detailed >>>>>>>>>>>> steps to follow. >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Best, >>>>>>>>>>>> >>> Christine >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>>> LORIS to loris, >>>>>>>>>>>> >>> right? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Hi, >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> i used >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E >>>>>>>>>>>> bash - >>>>>>>>>>>> >>> sudo apt-get install -y nodejs >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> you had suggested in the past, make worked and now i can >>>>>>>>>>>> see all the >>>>>>>>>>>> >>> contents in the web-interface, but i don't need make >>>>>>>>>>>> install? >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> Thanks >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> -- >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> >>> >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>> >>>>>>>>>>>> >>> >>>>>>>>>>>> -------------- next part -------------- >>>>>>>>>>>> An HTML attachment was scrubbed... >>>>>>>>>>>> URL: < >>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>>>>>>>> > >>>>>>>>>>>> >>>>>>>>>>>> ------------------------------ >>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>>>>>>>> ***************************************** >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> >>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University | Montreal | Canada >>>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> 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URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 37207 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 92124 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 62956 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: outputcsv.csv Type: text/csv Size: 44958 bytes Desc: not available URL: From cecile.madjar at mcin.ca Wed Nov 27 09:29:26 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Wed, 27 Nov 2019 09:29:26 -0500 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, Thank you for the details! A few things to try: - modify the TMPDIR to be on your /data directory where there might be more space to do processing (could create a /data/tmp where the temporary files would be created) - how many files are there for that upload in tarchive_files? Are they different from the ones showing the warning message? - FYI: query to get that: SELECT tf.* FROM tarchive_files tf JOIN mri_upload USING (TarchiveID) WHERE UploadID= (the output of that query would be very useful if you can provide it) - how many series are there for that upload in tarchive_series? - FYI: query to get that: SELECT ts.* FROM tarchive_series ts JOIN mri_upload USING (TarchiveID) WHERE UploadID= (the output of that query would be very useful if you can provide it) - things are failing when the scripts try running the following command: find /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f | /data/loris/bin/mri/dicom-archive/get_dicom_info.pl -studyuid -series -echo -image -file -attvalue 0018 0024 -series_descr -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4 | cut -f 5 | dcm2mnc -dname '' -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa - clearly the problems come from get_dicom_info.pl but I cannot pinpoint the error yet. I will ask around and get back to you If I cannot figure it out remotely, is there a way to have a call using zoom? This way you could share your screen with me and run the debugger on that script and hopefully we can figure out what is going on with those datasets? Thanks! C?cile On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi Cecile, > > In both my virtual machines > export TMPDIR=/tmp > > In both vm also with dcm2mnc i get this output. Just to verify that this > passed in my 1st vm and produced mincs. > > I attached the spool as a csv. > > [image: image.png] > > And also one difference i found was this in the Loris-mri code ( left 1st > workable vm, right 2nd vm that has to be fixed, although i changed it seems > to be independent of the uninitialized value $_ ) > > > [image: image.png] > > Thanks, > > Sotirios > > > > > ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar < > cecile.madjar at mcin.ca> ??????: > >> Hi Sotirios, >> >> that is puzzling... A few additional questions: >> >> - what is the bash variable TMPDIR set to on the environment file? >> - could you try running separately dcm2mnc on the DICOM folder to see >> if that works? >> - could you send us the detailed log from the notification spool >> table (SELECT * FROM notification_spool WHERE UploadID=) and >> send it back to us? Maybe there are some additional clues that could help >> figuring out what is going on. >> >> Thank you! >> >> C?cile >> >> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi Cecile, >>> >>> I checked for the StudyInstacueUID at the files with "The target >>> directory does not contain a single DICOM file"" and their attribute has a >>> value. >>> >>> Regarding the scouter and localizer, i modified the settings in the >>> imaging pipeline and now i don't get that error message, but still it >>> doesn't create the mnics. >>> >>> The errors i am getting are ( uninitialized value $_ is not important? >>> because i haven't got comments about that ) >>> >>> Use of uninitialized value $_ in pattern match (m//) at >>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. >>> Running now the following command: /data/loris/data//uploadNeuroDB/ >>> imaging_upload_file.pl -profile prod -upload_id 134 >>> /data/incoming/DCC0025_118008_V1.tar.gz -verbose >>> >>> and >>> >>> Number of MINC files that will be considered for inserting into the >>> database: 0 >>> >>> No data could be converted into valid MINC files. >>> >>> The tarchiveLoader.pl insertion script has failed. >>> Use of uninitialized value $mail_user in concatenation (.) or string at >>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. >>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/ >>> batch_uploads_imageuploader.pl line 249. >>> print() on closed filehandle MAIL at /data/loris/bin/mri/ >>> batch_uploads_imageuploader.pl line 250. >>> print() on closed filehandle MAIL at /data/loris/bin/mri/ >>> batch_uploads_imageuploader.pl line 251. >>> >>> Thanks >>> >>> Sotirios >>> >>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar < >>> cecile.madjar at mcin.ca> ??????: >>> >>>> Hi Sotirios, >>>> >>>> OK. So the issue I mentioned should not be a problem for you. >>>> >>>> Is the StudyInstanceUID DICOM header set in your images? If it is not >>>> set, then you would end up with the error message "The target directory >>>> does not contain a single DICOM file". So maybe this is the issue you are >>>> having with those datasets? >>>> >>>> Regarding not excluding series descriptions, you can configure that in >>>> the Config module under the Imaging Pipeline section. Simply remove all >>>> entries for the "Series description to exclude from imaging insertion" >>>> setting. >>>> >>>> C?cile >>>> >>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi Cecile, >>>>> >>>>> We are using this version >>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to >>>>> insert low resolution now? >>>>> >>>>> Thanks >>>>> >>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, >>>>> wrote: >>>>> >>>>>> Hi Sotirios, >>>>>> >>>>>> Which version of LORIS-MRI are you using? >>>>>> >>>>>> There was a bug that got resolved in 20.2 in get_dicom_info.pl. >>>>>> Basically, if a DICOM did not have the (0020,0032) header, >>>>>> get_dicom_info.pl considered that the file was not a DICOM, which >>>>>> was a mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this >>>>>> is the issue you are encountering. >>>>>> >>>>>> About scout and localizer, they are a type of short and low >>>>>> resolution sequence that is used by the tech but is of no interest >>>>>> scientifically, which is why we tend to no insert them. >>>>>> >>>>>> Hope this helps, >>>>>> >>>>>> C?cile >>>>>> >>>>>> >>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> wrote: >>>>>> >>>>>>> Hi Cecile, >>>>>>> >>>>>>> i executed the find command and the output i got per folder was >>>>>>> "DICOM medical imaging data. Maybe there is something wrong with the find >>>>>>> command in the warning that it is unable to check if the file is a dicom >>>>>>> file? Also when i use get_dicom_info.pl i don't get any output >>>>>>> data. Finally i don't understand what scout or localizer is ( something >>>>>>> like if and only if a file fails then the whole session is invalid? ). >>>>>>> >>>>>>> [image: image.png] >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> Sotirios >>>>>>> >>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < >>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>> >>>>>>>> Hi Sotirios, >>>>>>>> >>>>>>>> I took a closer look to the batch_uploader_multiple_output.txt file >>>>>>>> you sent. It looks like there are different reasons for failure depending >>>>>>>> on the DICOM folder uploaded. >>>>>>>> >>>>>>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 >>>>>>>> V1: it looks like there is no file of type DICOM in the folder. Have you >>>>>>>> checked to see if that is indeed the case? Maybe you can try running the >>>>>>>> following command on that folder to see what are the types of the files? If >>>>>>>> it does not return at least one DICOM medical imaging data file, then that >>>>>>>> is why you get the error message from the pipeline: >>>>>>>> - >>>>>>>> >>>>>>>> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >>>>>>>> >>>>>>>> - For 864173 DCC0001 V1: it looks like there are two >>>>>>>> different DICOM studies within the same folder. You will need to split that >>>>>>>> study in two based on the StudyUID field as the insertion pipeline does not >>>>>>>> allow for more than one StudyUID per upload. >>>>>>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 >>>>>>>> V1: it looks like the dcm2mnc command did not produce any MINC files. Can >>>>>>>> you check in the DICOM archive what are the series present in the tarchive >>>>>>>> for that visit? Maybe only a scout or localizer was acquired for that >>>>>>>> session, hence the no valid MINC files (scout and localizer being skipped >>>>>>>> for the conversion) >>>>>>>> - For 397410 DCC0003 V1: it looks like everything went well for >>>>>>>> this one. >>>>>>>> >>>>>>>> One script that is called by our pipeline is called >>>>>>>> get_dicom_info.pl and this does all kind of checks on the DICOM >>>>>>>> files (it is being called when running the dcm2mnc conversion). You could >>>>>>>> run it independently on your folder if needed. >>>>>>>> >>>>>>>> Since one of the study got in, it does not look like you are having >>>>>>>> a problem with the setup. It seems more likely to be a problem with the >>>>>>>> data themselves. >>>>>>>> >>>>>>>> Hope this helps. >>>>>>>> >>>>>>>> C?cile >>>>>>>> >>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>> >>>>>>>>> Hi Christine, >>>>>>>>> >>>>>>>>> In my first vm i am able to create the minc files and view them at >>>>>>>>> the mri browser (except of candidate 102761034 ), meanwhile the same files >>>>>>>>> gives warnings at the 2nd vm. The output of the batch upload can be seen >>>>>>>>> in the file attached. >>>>>>>>> Also a colleague of us has built a pre-validation tool for dicom >>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had >>>>>>>>> found all the files that Loris gave as warning . Basically I confirmed that >>>>>>>>> the total amount of files per dicom was the same amount as stated in Loris >>>>>>>>> and checked some filenames given from warning to confirm that they match >>>>>>>>> with our tool. But that was months ago and my colleague had changed some >>>>>>>>> parameters for MIP and now our tool doesn't find all the invalid files, >>>>>>>>> that's why i asked for the dicom header specification of Loris. In a >>>>>>>>> discussion we had he mentioned that he doesn't check for some tags e.x. >>>>>>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>>>>>>>> remove invalid dcm files. >>>>>>>>> >>>>>>>>> Thanks >>>>>>>>> >>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>> >>>>>>>>>> Hi Sotirios, >>>>>>>>>> Can you provide us with some fresh particulars of the >>>>>>>>>> current issue and we'll take it from there? >>>>>>>>>> Yang's team has built these scripts which can definitely serve as >>>>>>>>>> a model for your pre-validation of your DICOM collections. >>>>>>>>>> cheers, >>>>>>>>>> Christine >>>>>>>>>> >>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>> >>>>>>>>>>> HI Yang, >>>>>>>>>>> >>>>>>>>>>> We make use of pydicom library too. Now about the validate.py i >>>>>>>>>>> see that you check if some attributes are missing such as PatientID, >>>>>>>>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>>>>>>>> something on the setup of my other virtual machine ( although one dicom >>>>>>>>>>> passed on the new vm successfully, the others that were inserted correctly >>>>>>>>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>>>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." >>>>>>>>>>> but i don't remember the solution. >>>>>>>>>>> >>>>>>>>>>> Thanks >>>>>>>>>>> >>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>>>>>>>> ??????: >>>>>>>>>>> >>>>>>>>>>>> Hey, Sotirios, >>>>>>>>>>>> >>>>>>>>>>>> Christine from the LORIS team mentioned you had some issue with >>>>>>>>>>>> DICOM. I am a fellow developer for an external project using LORIS, kind >>>>>>>>>>>> of just like you. We had to implement DICOM upload as well but more as a >>>>>>>>>>>> fully automated pipeline actually. >>>>>>>>>>>> >>>>>>>>>>>> While we were building CNBP, we had coded up some minor Python >>>>>>>>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>>>>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>>>>>>>> more comprehensive solution, PyDICOM ( >>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>>>>>>>> >>>>>>>>>>>> Cheers, >>>>>>>>>>>> >>>>>>>>>>>> Yang Ding, PhD. >>>>>>>>>>>> Canadian Neonatal Brain Platform Architect >>>>>>>>>>>> >>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM < >>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Send Loris-dev mailing list submissions to >>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>>>>>>>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>>>>>>>> >>>>>>>>>>>>> You can reach the person managing the list at >>>>>>>>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>>>>>>>> >>>>>>>>>>>>> When replying, please edit your Subject line so it is more >>>>>>>>>>>>> specific >>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> Today's Topics: >>>>>>>>>>>>> >>>>>>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ---------------------------------------------------------------------- >>>>>>>>>>>>> >>>>>>>>>>>>> Message: 1 >>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>>>>>>>> To: Cecile Madjar >>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>> Message-ID: >>>>>>>>>>>>> >>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>>>>>>>> >>>>>>>>>>>>> Hi, >>>>>>>>>>>>> >>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom files to >>>>>>>>>>>>> diagnose the >>>>>>>>>>>>> warnings we get? >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> > Hi Cecile, >>>>>>>>>>>>> > >>>>>>>>>>>>> > We were wondering whether Loris has a tool to check if there >>>>>>>>>>>>> are problems >>>>>>>>>>>>> > with the dcm files, before trying to upload them. Something >>>>>>>>>>>>> that could >>>>>>>>>>>>> > provide the same results provided in the warning_output, >>>>>>>>>>>>> this is the >>>>>>>>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>>>>>>>> attributes of the >>>>>>>>>>>>> > dcm header would trigger a warning? is there a dcm file >>>>>>>>>>>>> header >>>>>>>>>>>>> > specification for Loris? >>>>>>>>>>>>> > >>>>>>>>>>>>> > Thanks >>>>>>>>>>>>> > >>>>>>>>>>>>> > Sotirios >>>>>>>>>>>>> > >>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> > >>>>>>>>>>>>> >> Hi, >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it >>>>>>>>>>>>> worked,but i >>>>>>>>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>>>>>>>> >> Thanks >>>>>>>>>>>>> >> >>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>>>>>>>> >> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and >>>>>>>>>>>>> columns are of >>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be >>>>>>>>>>>>> using >>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The second error occurs because the trigger triggers a >>>>>>>>>>>>> rollback of the >>>>>>>>>>>>> >>> insert statement in the files table. >>>>>>>>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results >>>>>>>>>>>>> in failure of >>>>>>>>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>>>>>>>> >>> -- Xavier >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>>>>>>>> >>> *To:* Cecile Madjar >>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>; >>>>>>>>>>>>> >>> Christine Rogers, Ms. >>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> When mincs are inserted their corresponding rows at the >>>>>>>>>>>>> file table are >>>>>>>>>>>>> >>> inserted too >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as >>>>>>>>>>>>> well, because i >>>>>>>>>>>>> >>> don't want manually to label them as passed throught the >>>>>>>>>>>>> interface >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> That is the trigger i wrote >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>>>>>>>> >>> BEGIN >>>>>>>>>>>>> >>> INSERT INTO files_qcstatus >>>>>>>>>>>>> >>> SET FileID = NEW.FileID, >>>>>>>>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>>>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>>>>>>>> >>> QCStatus = "Pass", >>>>>>>>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>>>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>>>>>>>> >>> END >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> although it contains some errors >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>> row: a foreign >>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES >>>>>>>>>>>>> `files` (`FileID`)) >>>>>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>> 848. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column >>>>>>>>>>>>> associated with >>>>>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it >>>>>>>>>>>>> means no DICOMs >>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>>>>>>>> insertion of the >>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with >>>>>>>>>>>>> the correct >>>>>>>>>>>>> >>> TarchiveID associated with the upload. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Could this correspond to what you want to do? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked to >>>>>>>>>>>>> the files >>>>>>>>>>>>> >>> table (hence, the MINC files). You could always create a >>>>>>>>>>>>> new table for >>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> i would like whenever a dicom is imported to mark all their >>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of >>>>>>>>>>>>> creating a trigger for >>>>>>>>>>>>> >>> that, but which tables do i need to add entries to? So far >>>>>>>>>>>>> from what i see >>>>>>>>>>>>> >>> i need to add entres at the table "files" whenever an >>>>>>>>>>>>> insertion happens to >>>>>>>>>>>>> >>> files_qcstatus. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the >>>>>>>>>>>>> beginning of my email >>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the >>>>>>>>>>>>> StudyID i am >>>>>>>>>>>>> >>> looking for is not stored in the database? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>>>>>>>> >>> tarchive table. It can also be found in the metadata field >>>>>>>>>>>>> but it is mixed >>>>>>>>>>>>> >>> with many other information. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hope this helps, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the >>>>>>>>>>>>> tarchive table, >>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found >>>>>>>>>>>>> something called >>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the >>>>>>>>>>>>> Study Instance UID. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> - the scan type could not be identified (not matching >>>>>>>>>>>>> an entry in >>>>>>>>>>>>> >>> the mri_protocol table) >>>>>>>>>>>>> >>> - one parameter of the scan type is out of the expected >>>>>>>>>>>>> range >>>>>>>>>>>>> >>> present in the mri_protocol_checks (extra filtering in >>>>>>>>>>>>> case you need to be >>>>>>>>>>>>> >>> stricker on some parameters not present in the >>>>>>>>>>>>> mri_protocol table) >>>>>>>>>>>>> >>> - if the CandID and PSCID do not match >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The following cases do not get in the MRI violation tables >>>>>>>>>>>>> as it happens >>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC files and only >>>>>>>>>>>>> MINC files >>>>>>>>>>>>> >>> violations are logged there: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be >>>>>>>>>>>>> found to convert >>>>>>>>>>>>> >>> to MINC) >>>>>>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since >>>>>>>>>>>>> this error >>>>>>>>>>>>> >>> happens at the dicomTar.pl level (way before conversion >>>>>>>>>>>>> into MINC files) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Glad everything is working out!! >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of ram. >>>>>>>>>>>>> Now about the >>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there >>>>>>>>>>>>> only if there is >>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>>>>>>>> parameter? >>>>>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or with >>>>>>>>>>>>> the 2 studyiuid >>>>>>>>>>>>> >>> to be there. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Sorry to hear you are having issues with the memory. I >>>>>>>>>>>>> think most of our >>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be >>>>>>>>>>>>> fine. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> about that dicom that had that insertion error it's about >>>>>>>>>>>>> 30mb and when >>>>>>>>>>>>> >>> it is being processed the ram is being drastically >>>>>>>>>>>>> increased from 2gb to >>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What is >>>>>>>>>>>>> the recommended >>>>>>>>>>>>> >>> size of ram for using Loris? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> For the delete script issue, if you are absolutely certain >>>>>>>>>>>>> that no >>>>>>>>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>>>>>>>> mri_upload table >>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>>>>>> uploadID. It >>>>>>>>>>>>> >>> looks like for some reason the scripts did not update this >>>>>>>>>>>>> field when it >>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would be the case >>>>>>>>>>>>> though. >>>>>>>>>>>>> >>> Note: only do that update if you are certain that there is >>>>>>>>>>>>> no processing >>>>>>>>>>>>> >>> happening. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>> < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID >>>>>>>>>>>>> they actually do >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>>>>>>>> missing at the >>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, but >>>>>>>>>>>>> with no mnic >>>>>>>>>>>>> >>> files. Also now i have this error >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>>>>>>>> :/data/loris/bin/mri/tools$ >>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>>>>>> processing it. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> How can solve this? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> To give you a brief idea: >>>>>>>>>>>>> >>> Per folder it will: >>>>>>>>>>>>> >>> 1) Delete all the .bak files >>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, >>>>>>>>>>>>> TR_max, TE_min, >>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>>>>>>>> mri_protocol table >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>>>>> >>> For some reason some files are missing >>>>>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> In total i have 7 folders >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> 3/7 passed >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a violation >>>>>>>>>>>>> "T1 AXIAL SE >>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and >>>>>>>>>>>>> i find that weird >>>>>>>>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory does >>>>>>>>>>>>> not contain a >>>>>>>>>>>>> >>> single DICOM file.", therefore they are missing their >>>>>>>>>>>>> StudyUID >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>>>>> multiple >>>>>>>>>>>>> >>> studies." >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC >>>>>>>>>>>>> files. >>>>>>>>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> If i wanted to force the insertion of 102327840, 102809579 >>>>>>>>>>>>> and 102506134 >>>>>>>>>>>>> >>> can i just pass a flag parameter to >>>>>>>>>>>>> batch_uploads_imageuploader.pl? or >>>>>>>>>>>>> >>> modify imaging_upload_file.pl? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thank you, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Sotirios >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> PS >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>>>>>>>> dicom_output.txt. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine >>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> Glad to hear about your progress. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>>>>>>>> documented here >>>>>>>>>>>>> >>> < >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>> > >>>>>>>>>>>>> >>> -- let us know if you didn't find the answers you were >>>>>>>>>>>>> looking for there. >>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in your >>>>>>>>>>>>> database >>>>>>>>>>>>> >>> management software is a visual placeholder for you as the >>>>>>>>>>>>> user? I'm not >>>>>>>>>>>>> >>> sure why a scanner would ever be registered with ID='0' as >>>>>>>>>>>>> your screenshot >>>>>>>>>>>>> >>> showed.) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> I fixed it with this >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>>>>>>>> something >>>>>>>>>>>>> >>> wrong with the structure? why did i receive a 500 internal >>>>>>>>>>>>> error? In the >>>>>>>>>>>>> >>> loris-error log it state that there is something wrong >>>>>>>>>>>>> with token, but i >>>>>>>>>>>>> >>> verfied that the type of the token is a string. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>>>>> [client >>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: >>>>>>>>>>>>> Argument 1 >>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of >>>>>>>>>>>>> the type string, >>>>>>>>>>>>> >>> null given, called in >>>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>>>>>> line 169 and >>>>>>>>>>>>> >>> defined in >>>>>>>>>>>>> >>> >>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>>>>> >>> trace:\n#0 >>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 >>>>>>>>>>>>> {main}\n thrown in >>>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on >>>>>>>>>>>>> line 192 >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just to let you >>>>>>>>>>>>> know what i >>>>>>>>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>>>>>>>> dependencies. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> First i deleted all their uploads >>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a >>>>>>>>>>>>> way to omit >>>>>>>>>>>>> >>> the backup file ? ) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted all >>>>>>>>>>>>> the entries >>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry >>>>>>>>>>>>> with the 0 ID. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine >>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> We recommend that you use our existing tools for creating >>>>>>>>>>>>> new candidates >>>>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP script, >>>>>>>>>>>>> by calling the Candidate >>>>>>>>>>>>> >>> class's createNew() >>>>>>>>>>>>> >>> < >>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>>>>>>>> >function. >>>>>>>>>>>>> >>> These will create the necessary records for you. (It's >>>>>>>>>>>>> not recommended to >>>>>>>>>>>>> >>> make direct modifications to mysql database tables in your >>>>>>>>>>>>> script, if I >>>>>>>>>>>>> >>> understand you.) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, >>>>>>>>>>>>> and there are >>>>>>>>>>>>> >>> multiple reasons for this. >>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs and the >>>>>>>>>>>>> External ID field >>>>>>>>>>>>> >>> in the candidate table can also be used for any values you >>>>>>>>>>>>> like. >>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be added in >>>>>>>>>>>>> parallel - these >>>>>>>>>>>>> >>> are entered/visible in the Candidate Information module >>>>>>>>>>>>> and added in the >>>>>>>>>>>>> >>> back-end as candidate parameters. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> We are building a script that will auto insert the >>>>>>>>>>>>> candidates based on >>>>>>>>>>>>> >>> their ExternalID. We would like to know whethere when we >>>>>>>>>>>>> are creating a new >>>>>>>>>>>>> >>> profile in the candidate table, if we also have to insert >>>>>>>>>>>>> a new record at >>>>>>>>>>>>> >>> another table? Furthermore is there a problem that in our >>>>>>>>>>>>> case CandID won't >>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, >>>>>>>>>>>>> Mrs < >>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> That would normally be the case but the numeric part of >>>>>>>>>>>>> the PSCID get >>>>>>>>>>>>> >>> paded with 0 on the left. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>>>>> numerical char >>>>>>>>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ABC0001 >>>>>>>>>>>>> >>> ABC0002 >>>>>>>>>>>>> >>> ... >>>>>>>>>>>>> >>> ABC0010 >>>>>>>>>>>>> >>> ... >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> thus sorting them ascending will always get the latest >>>>>>>>>>>>> value generated >>>>>>>>>>>>> >>> as the max value. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> M?lanie >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must >>>>>>>>>>>>> be stored >>>>>>>>>>>>> >>> within a specific length of characters. Otherwise if we >>>>>>>>>>>>> were to sort >>>>>>>>>>>>> >>> strings with different lengths the result would not be >>>>>>>>>>>>> sorted correctly ( >>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie Legault, >>>>>>>>>>>>> Mrs < >>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hello Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> There is no `last value` stored anywhere. >>>>>>>>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>>>>>>>> increase that >>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hope this info help. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of Medicine >>>>>>>>>>>>> | McGill >>>>>>>>>>>>> >>> University >>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of Sotirios >>>>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> how does Loris determine the next available PSCID value >>>>>>>>>>>>> for a new >>>>>>>>>>>>> >>> candidate? >>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but where >>>>>>>>>>>>> do we store the >>>>>>>>>>>>> >>> last value for the sequential sequence? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> the parameters in the mri_protocol you have assigned are >>>>>>>>>>>>> global >>>>>>>>>>>>> >>> standard? or were assigned after trial and error? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine >>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Given you have done the initial setup of your tables to >>>>>>>>>>>>> match your >>>>>>>>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>>>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>>>>>>>> >>> < >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>>>>>>>> > >>>>>>>>>>>>> >>> re-running the pipeline (and first deleting prior uploads). >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> *if i were to change their status to resolve what would >>>>>>>>>>>>> happen? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser >>>>>>>>>>>>> from the >>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>>>>>>>> /data/loris/data/trashbin/ >>>>>>>>>>>>> >>> if i were to click their issue to resolve what would >>>>>>>>>>>>> happend? would they >>>>>>>>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The defaut values of the schema exists in my local >>>>>>>>>>>>> database. If i adjust >>>>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>>>>>>>> uploaded? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol >>>>>>>>>>>>> table ? (and >>>>>>>>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the >>>>>>>>>>>>> Imaging insertion >>>>>>>>>>>>> >>> setup : See the install/setup documentation : >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> To add new rows, just use MySQL insert statements. You >>>>>>>>>>>>> can adapt the >>>>>>>>>>>>> >>> insert statements which load the default table values --> >>>>>>>>>>>>> e.g. Here on >>>>>>>>>>>>> >>> GitHub : >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>>>>> >>> (see also the mri_scan_type table) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> I see that i can edit the values but not how to insert new >>>>>>>>>>>>> rows. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> If i choose Inserted with flag then will the minc be >>>>>>>>>>>>> inserted? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> It says "could not identify scan type", which we knew >>>>>>>>>>>>> already. Did you >>>>>>>>>>>>> >>> click on the link on those words? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> It will take you to the next page of the module, showing >>>>>>>>>>>>> for each scan >>>>>>>>>>>>> >>> what the scan parameters were, and will also show for >>>>>>>>>>>>> comparison what's >>>>>>>>>>>>> >>> stored in your *mri_protocol* table. >>>>>>>>>>>>> >>> Compare these values to find which parameter was not >>>>>>>>>>>>> correct according >>>>>>>>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> You may end up broadening your mri_protocol value ranges >>>>>>>>>>>>> (e.g. TR, TE) >>>>>>>>>>>>> >>> for scans. >>>>>>>>>>>>> >>> This can be done in the front-end, by editing the database >>>>>>>>>>>>> table >>>>>>>>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The MRI Violations module features are explained in more >>>>>>>>>>>>> detail in the >>>>>>>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] >>>>>>>>>>>>> icon in the menu >>>>>>>>>>>>> >>> bar.) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>>>>>>>> >>> < >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>> > >>>>>>>>>>>>> >>> : no MINCs inserted- violated scans >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> looks like my previous email's attachment wasn't delivered >>>>>>>>>>>>> due to >>>>>>>>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>>>>>>>> webbrowser, so >>>>>>>>>>>>> >>> that you can check the filelds easier. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios -- >>>>>>>>>>>>> >>> Great, sounds like more progress. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're >>>>>>>>>>>>> getting an Endian >>>>>>>>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>>>>> successfully >>>>>>>>>>>>> >>> relabelled, after the command ran? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> You can use also our DICAT tool ( >>>>>>>>>>>>> https://github.com/aces/DICAT) to >>>>>>>>>>>>> >>> verify and/or update local DICOM headers -- though your >>>>>>>>>>>>> dcmodify command is >>>>>>>>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>>>>>>>> "(2001,105f)" from >>>>>>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM slice >>>>>>>>>>>>> before and look >>>>>>>>>>>>> >>> at these fields specifically. >>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>>>>>> before/after >>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff >>>>>>>>>>>>> the outputs -- >>>>>>>>>>>>> >>> this will pinpoint what changed. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>>>>> recognized or >>>>>>>>>>>>> >>> unknown : this means your scans did not match what is >>>>>>>>>>>>> stored in your >>>>>>>>>>>>> >>> mri_protocol table. >>>>>>>>>>>>> >>> Check the MRI Violations front-end module -- can you see >>>>>>>>>>>>> why they didn't >>>>>>>>>>>>> >>> match? >>>>>>>>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>>>>>>>> mri_protocol >>>>>>>>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Here is the psc table >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> and got those warning: is this okay? >>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>> length, reading a >>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>> length, reading a >>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined >>>>>>>>>>>>> length, reading a >>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined >>>>>>>>>>>>> length, reading a >>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>> length, reading a >>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>> length, reading a >>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit (CP-246) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you >>>>>>>>>>>>> can see the >>>>>>>>>>>>> >>> execution for the second dicom. Mnics could not be >>>>>>>>>>>>> inserted due to >>>>>>>>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Running now the following command: >>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>>>>> '__MACOSX' >>>>>>>>>>>>> >>> -delete >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod >>>>>>>>>>>>> -verbose >>>>>>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Testing for database connectivity. >>>>>>>>>>>>> >>> Database is available. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> You are creating a tar with the following command: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> tar -cf >>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> getting md5sums and gzipping!! >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>>>> >>> >>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>>>> >>> * Archived on : 2019-09-06 18:36:50 >>>>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Adding archive info into database >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Removing temporary files from target location >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Done adding archive info into database >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>>>>> -globLocation >>>>>>>>>>>>> >>> -profile prod >>>>>>>>>>>>> >>> >>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>>>>> >>> -uploadID 12 -verbose >>>>>>>>>>>>> >>> md5sum >>>>>>>>>>>>> >>> >>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>> >>> Set centerID = 1 >>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Number of MINC files that will be considered for inserting >>>>>>>>>>>>> into the >>>>>>>>>>>>> >>> database: 2 >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>> cat >>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ==> Loading file from disk >>>>>>>>>>>>> >>> >>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> --> mapping DICOM parameter for >>>>>>>>>>>>> >>> >>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ==> verifying acquisition protocol >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Acquisition protocol is unknown >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> --> The minc file cannot be registered since the >>>>>>>>>>>>> AcquisitionProtocol >>>>>>>>>>>>> >>> is unknown >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine >>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>>>>>>>> *delete_imaging_upload* >>>>>>>>>>>>> >>> script -- >>>>>>>>>>>>> >>> details here: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> What's in your *psc* table? (Is it properly populated? >>>>>>>>>>>>> This is a >>>>>>>>>>>>> >>> pre-requisite to loading imaging data. >>>>>>>>>>>>> >>> < >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>>>>>>>> > >>>>>>>>>>>>> >>> ) >>>>>>>>>>>>> >>> The foreign key constraint error on the candidate record >>>>>>>>>>>>> is curious. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> There are also a few options for creating candidates when >>>>>>>>>>>>> inserting >>>>>>>>>>>>> >>> imaging data: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM insertion >>>>>>>>>>>>> pipeline >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and visits, >>>>>>>>>>>>> optionally I >>>>>>>>>>>>> >>> think) >>>>>>>>>>>>> >>> How to: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Then as a second step: >>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>>>>>>>> >>> < >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>>>>>>>> > >>>>>>>>>>>>> >>> to load your DICOMs. >>>>>>>>>>>>> >>> You will want to first ensure that the PatientName header >>>>>>>>>>>>> in the DICOMs >>>>>>>>>>>>> >>> as well as tar package are correctly labelled with >>>>>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>>>>>>>> >>> How to : >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>>>>>>>> bids_import script, >>>>>>>>>>>>> >>> to automatically create your candidates and sessions. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i have to create >>>>>>>>>>>>> a new >>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> *First execution:* >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>> ./ >>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>>>> >>> log.txt >>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>> row: a foreign >>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>>>>> `FK_candidate_1` >>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>>>>> (`CenterID`)) at >>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060. >>>>>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>>>>> >>> The following database commands failed: >>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>>>>>>>> (?,?,?,?,?)'; >>>>>>>>>>>>> >>> SET >>>>>>>>>>>>> >>> >>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>>>>> >>> Medical Systems'; >>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a foreign >>>>>>>>>>>>> key >>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>>>>> `FK_mri_scanner_1` >>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) >>>>>>>>>>>>> (error code 1452) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ERROR: The validation has failed. Either re-run the >>>>>>>>>>>>> validation again >>>>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using >>>>>>>>>>>>> -force to force the >>>>>>>>>>>>> >>> execution. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>> >>> line 250. >>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>> >>> line 251. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> *And second execution: * >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>> ./ >>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>>>> >>> log.txt >>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> PROBLEM: >>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>>>>> >>> The unique study ID is >>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>>>>> >>> This is the information retained from the first time the >>>>>>>>>>>>> study was >>>>>>>>>>>>> >>> inserted: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>>>> >>> >>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>>>> >>> * Archived on : 2019-09-04 18:33:05 >>>>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Last update of record: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>> >>> line 250. >>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>> >>> line 251. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Ok, this sounds like good progress. Let us know when you >>>>>>>>>>>>> next encounter >>>>>>>>>>>>> >>> issues as you progress through the Imaging Install/Setup >>>>>>>>>>>>> docs >>>>>>>>>>>>> >>> < >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md >>>>>>>>>>>>> >. >>>>>>>>>>>>> >>> I'll look into how we can better handle the incoming/ >>>>>>>>>>>>> directory next >>>>>>>>>>>>> >>> time. >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>>>>>>>>> >>> populated correctly except its port is 'port' : ''. >>>>>>>>>>>>> Also i have tested >>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> I executed the script again, because the only error i had >>>>>>>>>>>>> previously was >>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and there are >>>>>>>>>>>>> no errors >>>>>>>>>>>>> >>> reported back except of warnings <>>>>>>>>>>>> a password on the >>>>>>>>>>>>> >>> command line interface can be insecure>>. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> It's possible -- if the script was unable to connect to >>>>>>>>>>>>> the database >>>>>>>>>>>>> >>> during its execution (e.g. typo in the password), that >>>>>>>>>>>>> would explain the >>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw >>>>>>>>>>>>> in the Config >>>>>>>>>>>>> >>> module. >>>>>>>>>>>>> >>> It's hard to tell without seeing the output from your >>>>>>>>>>>>> script run -- Did >>>>>>>>>>>>> >>> you see a sign of any such error? >>>>>>>>>>>>> >>> The Config fields are populated by the imaging_install.sh >>>>>>>>>>>>> script (starting >>>>>>>>>>>>> >>> at line 222 >>>>>>>>>>>>> >>> < >>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>>>>>>>> > >>>>>>>>>>>>> >>> ) >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> For example, check if the database connection information >>>>>>>>>>>>> was populated >>>>>>>>>>>>> >>> accurately in >>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Christine, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>> image with the >>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>> the last part >>>>>>>>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>> Ms. < >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>> all the >>>>>>>>>>>>> >>> front-end pages are loading. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>>>>>> project >>>>>>>>>>>>> >>> > and the web interface worked. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Yes, it's important that project/ have 775 permissions and >>>>>>>>>>>>> that >>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in the >>>>>>>>>>>>> install >>>>>>>>>>>>> >>> Readme . >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>>>> LORIS to >>>>>>>>>>>>> >>> loris, right? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>>>>>>>> installation >>>>>>>>>>>>> >>> by an >>>>>>>>>>>>> automated script -- >>>>>>>>>>>>> >>> you do not need to set them manually via the Config module. >>>>>>>>>>>>> >>> Please continue to follow the Setup Guide >>>>>>>>>>>>> >>> for detailed >>>>>>>>>>>>> steps to follow. >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>>>> LORIS to loris, >>>>>>>>>>>>> >>> right? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> i used >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E >>>>>>>>>>>>> bash - >>>>>>>>>>>>> >>> sudo apt-get install -y nodejs >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> you had suggested in the past, make worked and now i can >>>>>>>>>>>>> see all the >>>>>>>>>>>>> >>> contents in the web-interface, but i don't need make >>>>>>>>>>>>> install? >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> -- >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> >>> >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>> >>>>>>>>>>>>> >>> >>>>>>>>>>>>> -------------- next part -------------- >>>>>>>>>>>>> An HTML attachment was scrubbed... >>>>>>>>>>>>> URL: < >>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>>>>>>>>> > >>>>>>>>>>>>> >>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>>>>>>>>> ***************************************** >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 37207 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 92124 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 62956 bytes Desc: not available URL: From nicolasbrossard.mni at gmail.com Wed Nov 27 10:57:25 2019 From: nicolasbrossard.mni at gmail.com (Nicolas Brossard) Date: Wed, 27 Nov 2019 10:57:25 -0500 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, My name is Nicolas and I am part of the LORIS team. I was told by Cecile that you were having a problem with the imaging pipeline. Would you be willing to share your problematic DICOM archive with me? I could set up an account for you on one of our sftp server and you could upload your data there. I know patient scans are sensitive data but this would greatly simplify the debugging process. Thanks Nicolas On Wed, Nov 27, 2019 at 9:30 AM Cecile Madjar wrote: > Hi Sotirios, > > Thank you for the details! > > A few things to try: > > - modify the TMPDIR to be on your /data directory where there might be > more space to do processing (could create a /data/tmp where the temporary > files would be created) > - how many files are there for that upload in tarchive_files? Are they > different from the ones showing the warning message? > - FYI: query to get that: SELECT tf.* FROM tarchive_files tf JOIN > mri_upload USING (TarchiveID) WHERE UploadID= (the > output of that query would be very useful if you can provide it) > - how many series are there for that upload in tarchive_series? > - FYI: query to get that: SELECT ts.* FROM tarchive_series ts JOIN > mri_upload USING (TarchiveID) WHERE UploadID= (the > output of that query would be very useful if you can provide it) > - things are failing when the scripts try running the following > command: find /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO > -type f | /data/loris/bin/mri/dicom-archive/get_dicom_info.pl > -studyuid -series -echo -image -file -attvalue 0018 0024 -series_descr > -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4 | cut -f 5 | dcm2mnc -dname '' > -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa > - clearly the problems come from get_dicom_info.pl but I cannot > pinpoint the error yet. I will ask around and get back to you > > If I cannot figure it out remotely, is there a way to have a call using > zoom? This way you could share your screen with me and run the debugger on > that script and hopefully we can figure out what is going on with those > datasets? > > Thanks! > > C?cile > > On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Cecile, >> >> In both my virtual machines >> export TMPDIR=/tmp >> >> In both vm also with dcm2mnc i get this output. Just to verify that this >> passed in my 1st vm and produced mincs. >> >> I attached the spool as a csv. >> >> [image: image.png] >> >> And also one difference i found was this in the Loris-mri code ( left 1st >> workable vm, right 2nd vm that has to be fixed, although i changed it seems >> to be independent of the uninitialized value $_ ) >> >> >> [image: image.png] >> >> Thanks, >> >> Sotirios >> >> >> >> >> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >>> Hi Sotirios, >>> >>> that is puzzling... A few additional questions: >>> >>> - what is the bash variable TMPDIR set to on the environment file? >>> - could you try running separately dcm2mnc on the DICOM folder to >>> see if that works? >>> - could you send us the detailed log from the notification spool >>> table (SELECT * FROM notification_spool WHERE UploadID=) and >>> send it back to us? Maybe there are some additional clues that could help >>> figuring out what is going on. >>> >>> Thank you! >>> >>> C?cile >>> >>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi Cecile, >>>> >>>> I checked for the StudyInstacueUID at the files with "The target >>>> directory does not contain a single DICOM file"" and their attribute has a >>>> value. >>>> >>>> Regarding the scouter and localizer, i modified the settings in the >>>> imaging pipeline and now i don't get that error message, but still it >>>> doesn't create the mnics. >>>> >>>> The errors i am getting are ( uninitialized value $_ is not important? >>>> because i haven't got comments about that ) >>>> >>>> Use of uninitialized value $_ in pattern match (m//) at >>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. >>>> Running now the following command: /data/loris/data//uploadNeuroDB/ >>>> imaging_upload_file.pl -profile prod -upload_id 134 >>>> /data/incoming/DCC0025_118008_V1.tar.gz -verbose >>>> >>>> and >>>> >>>> Number of MINC files that will be considered for inserting into the >>>> database: 0 >>>> >>>> No data could be converted into valid MINC files. >>>> >>>> The tarchiveLoader.pl insertion script has failed. >>>> Use of uninitialized value $mail_user in concatenation (.) or string at >>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. >>>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/ >>>> batch_uploads_imageuploader.pl line 249. >>>> print() on closed filehandle MAIL at /data/loris/bin/mri/ >>>> batch_uploads_imageuploader.pl line 250. >>>> print() on closed filehandle MAIL at /data/loris/bin/mri/ >>>> batch_uploads_imageuploader.pl line 251. >>>> >>>> Thanks >>>> >>>> Sotirios >>>> >>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar < >>>> cecile.madjar at mcin.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> OK. So the issue I mentioned should not be a problem for you. >>>>> >>>>> Is the StudyInstanceUID DICOM header set in your images? If it is not >>>>> set, then you would end up with the error message "The target directory >>>>> does not contain a single DICOM file". So maybe this is the issue you are >>>>> having with those datasets? >>>>> >>>>> Regarding not excluding series descriptions, you can configure that in >>>>> the Config module under the Imaging Pipeline section. Simply remove all >>>>> entries for the "Series description to exclude from imaging insertion" >>>>> setting. >>>>> >>>>> C?cile >>>>> >>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi Cecile, >>>>>> >>>>>> We are using this version >>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to >>>>>> insert low resolution now? >>>>>> >>>>>> Thanks >>>>>> >>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, >>>>>> wrote: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> Which version of LORIS-MRI are you using? >>>>>>> >>>>>>> There was a bug that got resolved in 20.2 in get_dicom_info.pl. >>>>>>> Basically, if a DICOM did not have the (0020,0032) header, >>>>>>> get_dicom_info.pl considered that the file was not a DICOM, which >>>>>>> was a mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this >>>>>>> is the issue you are encountering. >>>>>>> >>>>>>> About scout and localizer, they are a type of short and low >>>>>>> resolution sequence that is used by the tech but is of no interest >>>>>>> scientifically, which is why we tend to no insert them. >>>>>>> >>>>>>> Hope this helps, >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> >>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi Cecile, >>>>>>>> >>>>>>>> i executed the find command and the output i got per folder was >>>>>>>> "DICOM medical imaging data. Maybe there is something wrong with the find >>>>>>>> command in the warning that it is unable to check if the file is a dicom >>>>>>>> file? Also when i use get_dicom_info.pl i don't get any output >>>>>>>> data. Finally i don't understand what scout or localizer is ( something >>>>>>>> like if and only if a file fails then the whole session is invalid? ). >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> Sotirios >>>>>>>> >>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < >>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> >>>>>>>>> I took a closer look to the batch_uploader_multiple_output.txt >>>>>>>>> file you sent. It looks like there are different reasons for failure >>>>>>>>> depending on the DICOM folder uploaded. >>>>>>>>> >>>>>>>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 >>>>>>>>> V1: it looks like there is no file of type DICOM in the folder. Have you >>>>>>>>> checked to see if that is indeed the case? Maybe you can try running the >>>>>>>>> following command on that folder to see what are the types of the files? If >>>>>>>>> it does not return at least one DICOM medical imaging data file, then that >>>>>>>>> is why you get the error message from the pipeline: >>>>>>>>> - >>>>>>>>> >>>>>>>>> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >>>>>>>>> >>>>>>>>> - For 864173 DCC0001 V1: it looks like there are two >>>>>>>>> different DICOM studies within the same folder. You will need to split that >>>>>>>>> study in two based on the StudyUID field as the insertion pipeline does not >>>>>>>>> allow for more than one StudyUID per upload. >>>>>>>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 >>>>>>>>> V1: it looks like the dcm2mnc command did not produce any MINC files. Can >>>>>>>>> you check in the DICOM archive what are the series present in the tarchive >>>>>>>>> for that visit? Maybe only a scout or localizer was acquired for that >>>>>>>>> session, hence the no valid MINC files (scout and localizer being skipped >>>>>>>>> for the conversion) >>>>>>>>> - For 397410 DCC0003 V1: it looks like everything went well >>>>>>>>> for this one. >>>>>>>>> >>>>>>>>> One script that is called by our pipeline is called >>>>>>>>> get_dicom_info.pl and this does all kind of checks on the DICOM >>>>>>>>> files (it is being called when running the dcm2mnc conversion). You could >>>>>>>>> run it independently on your folder if needed. >>>>>>>>> >>>>>>>>> Since one of the study got in, it does not look like you are >>>>>>>>> having a problem with the setup. It seems more likely to be a problem with >>>>>>>>> the data themselves. >>>>>>>>> >>>>>>>>> Hope this helps. >>>>>>>>> >>>>>>>>> C?cile >>>>>>>>> >>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi Christine, >>>>>>>>>> >>>>>>>>>> In my first vm i am able to create the minc files and view them >>>>>>>>>> at the mri browser (except of candidate 102761034 ), meanwhile the same >>>>>>>>>> files gives warnings at the 2nd vm. The output of the batch upload can be >>>>>>>>>> seen in the file attached. >>>>>>>>>> Also a colleague of us has built a pre-validation tool for dicom >>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had >>>>>>>>>> found all the files that Loris gave as warning . Basically I confirmed that >>>>>>>>>> the total amount of files per dicom was the same amount as stated in Loris >>>>>>>>>> and checked some filenames given from warning to confirm that they match >>>>>>>>>> with our tool. But that was months ago and my colleague had changed some >>>>>>>>>> parameters for MIP and now our tool doesn't find all the invalid files, >>>>>>>>>> that's why i asked for the dicom header specification of Loris. In a >>>>>>>>>> discussion we had he mentioned that he doesn't check for some tags e.x. >>>>>>>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>>>>>>>>> remove invalid dcm files. >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> Can you provide us with some fresh particulars of the >>>>>>>>>>> current issue and we'll take it from there? >>>>>>>>>>> Yang's team has built these scripts which can definitely serve >>>>>>>>>>> as a model for your pre-validation of your DICOM collections. >>>>>>>>>>> cheers, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> HI Yang, >>>>>>>>>>>> >>>>>>>>>>>> We make use of pydicom library too. Now about the validate.py i >>>>>>>>>>>> see that you check if some attributes are missing such as PatientID, >>>>>>>>>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>>>>>>>>> something on the setup of my other virtual machine ( although one dicom >>>>>>>>>>>> passed on the new vm successfully, the others that were inserted correctly >>>>>>>>>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>>>>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." >>>>>>>>>>>> but i don't remember the solution. >>>>>>>>>>>> >>>>>>>>>>>> Thanks >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>>>>>>>>> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hey, Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> Christine from the LORIS team mentioned you had some issue >>>>>>>>>>>>> with DICOM. I am a fellow developer for an external project using LORIS, >>>>>>>>>>>>> kind of just like you. We had to implement DICOM upload as well but more as >>>>>>>>>>>>> a fully automated pipeline actually. >>>>>>>>>>>>> >>>>>>>>>>>>> While we were building CNBP, we had coded up some minor Python >>>>>>>>>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>>>>>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>>>>>>>>> more comprehensive solution, PyDICOM ( >>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>>>>>>>>> >>>>>>>>>>>>> Cheers, >>>>>>>>>>>>> >>>>>>>>>>>>> Yang Ding, PhD. >>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM < >>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Send Loris-dev mailing list submissions to >>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>>>>>>>>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>>>>>>>>>>>>> You can reach the person managing the list at >>>>>>>>>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>>>>>>>>>>>>> When replying, please edit your Subject line so it is more >>>>>>>>>>>>>> specific >>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Today's Topics: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> ---------------------------------------------------------------------- >>>>>>>>>>>>>> >>>>>>>>>>>>>> Message: 1 >>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> To: Cecile Madjar >>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>> Message-ID: >>>>>>>>>>>>>> >>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom files to >>>>>>>>>>>>>> diagnose the >>>>>>>>>>>>>> warnings we get? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> > Hi Cecile, >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > We were wondering whether Loris has a tool to check if >>>>>>>>>>>>>> there are problems >>>>>>>>>>>>>> > with the dcm files, before trying to upload them. Something >>>>>>>>>>>>>> that could >>>>>>>>>>>>>> > provide the same results provided in the warning_output, >>>>>>>>>>>>>> this is the >>>>>>>>>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>>>>>>>>> attributes of the >>>>>>>>>>>>>> > dcm header would trigger a warning? is there a dcm file >>>>>>>>>>>>>> header >>>>>>>>>>>>>> > specification for Loris? >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > Thanks >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > Sotirios >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >> Hi, >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it >>>>>>>>>>>>>> worked,but i >>>>>>>>>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>>>>>>>>> >> Thanks >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and >>>>>>>>>>>>>> columns are of >>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be >>>>>>>>>>>>>> using >>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The second error occurs because the trigger triggers a >>>>>>>>>>>>>> rollback of the >>>>>>>>>>>>>> >>> insert statement in the files table. >>>>>>>>>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results >>>>>>>>>>>>>> in failure of >>>>>>>>>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>>>>>>>>> >>> -- Xavier >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>>>>>>>>> >>> *To:* Cecile Madjar >>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>; >>>>>>>>>>>>>> >>> Christine Rogers, Ms. >>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> When mincs are inserted their corresponding rows at the >>>>>>>>>>>>>> file table are >>>>>>>>>>>>>> >>> inserted too >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as >>>>>>>>>>>>>> well, because i >>>>>>>>>>>>>> >>> don't want manually to label them as passed throught the >>>>>>>>>>>>>> interface >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> That is the trigger i wrote >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>>>>>>>>> >>> BEGIN >>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus >>>>>>>>>>>>>> >>> SET FileID = NEW.FileID, >>>>>>>>>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>>>>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>>>>>>>>> >>> QCStatus = "Pass", >>>>>>>>>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>>>>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>>>>>>>>> >>> END >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> although it contains some errors >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>>> row: a foreign >>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES >>>>>>>>>>>>>> `files` (`FileID`)) >>>>>>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>>> 848. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column >>>>>>>>>>>>>> associated with >>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it >>>>>>>>>>>>>> means no DICOMs >>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>>>>>>>>> insertion of the >>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with >>>>>>>>>>>>>> the correct >>>>>>>>>>>>>> >>> TarchiveID associated with the upload. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Could this correspond to what you want to do? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked >>>>>>>>>>>>>> to the files >>>>>>>>>>>>>> >>> table (hence, the MINC files). You could always create a >>>>>>>>>>>>>> new table for >>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to mark all >>>>>>>>>>>>>> their >>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of >>>>>>>>>>>>>> creating a trigger for >>>>>>>>>>>>>> >>> that, but which tables do i need to add entries to? So >>>>>>>>>>>>>> far from what i see >>>>>>>>>>>>>> >>> i need to add entres at the table "files" whenever an >>>>>>>>>>>>>> insertion happens to >>>>>>>>>>>>>> >>> files_qcstatus. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the >>>>>>>>>>>>>> beginning of my email >>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the >>>>>>>>>>>>>> StudyID i am >>>>>>>>>>>>>> >>> looking for is not stored in the database? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>>>>>>>>> >>> tarchive table. It can also be found in the metadata >>>>>>>>>>>>>> field but it is mixed >>>>>>>>>>>>>> >>> with many other information. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hope this helps, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the >>>>>>>>>>>>>> tarchive table, >>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found >>>>>>>>>>>>>> something called >>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the >>>>>>>>>>>>>> Study Instance UID. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> - the scan type could not be identified (not matching >>>>>>>>>>>>>> an entry in >>>>>>>>>>>>>> >>> the mri_protocol table) >>>>>>>>>>>>>> >>> - one parameter of the scan type is out of the >>>>>>>>>>>>>> expected range >>>>>>>>>>>>>> >>> present in the mri_protocol_checks (extra filtering in >>>>>>>>>>>>>> case you need to be >>>>>>>>>>>>>> >>> stricker on some parameters not present in the >>>>>>>>>>>>>> mri_protocol table) >>>>>>>>>>>>>> >>> - if the CandID and PSCID do not match >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The following cases do not get in the MRI violation >>>>>>>>>>>>>> tables as it happens >>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC files and only >>>>>>>>>>>>>> MINC files >>>>>>>>>>>>>> >>> violations are logged there: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be >>>>>>>>>>>>>> found to convert >>>>>>>>>>>>>> >>> to MINC) >>>>>>>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since >>>>>>>>>>>>>> this error >>>>>>>>>>>>>> >>> happens at the dicomTar.pl level (way before >>>>>>>>>>>>>> conversion into MINC files) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Glad everything is working out!! >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of >>>>>>>>>>>>>> ram. Now about the >>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there >>>>>>>>>>>>>> only if there is >>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>>>>>>>>> parameter? >>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or >>>>>>>>>>>>>> with the 2 studyiuid >>>>>>>>>>>>>> >>> to be there. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the memory. I >>>>>>>>>>>>>> think most of our >>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be >>>>>>>>>>>>>> fine. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> about that dicom that had that insertion error it's about >>>>>>>>>>>>>> 30mb and when >>>>>>>>>>>>>> >>> it is being processed the ram is being drastically >>>>>>>>>>>>>> increased from 2gb to >>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What >>>>>>>>>>>>>> is the recommended >>>>>>>>>>>>>> >>> size of ram for using Loris? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> For the delete script issue, if you are absolutely >>>>>>>>>>>>>> certain that no >>>>>>>>>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>>>>>>>>> mri_upload table >>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>>>>>>> uploadID. It >>>>>>>>>>>>>> >>> looks like for some reason the scripts did not update >>>>>>>>>>>>>> this field when it >>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would be the >>>>>>>>>>>>>> case though. >>>>>>>>>>>>>> >>> Note: only do that update if you are certain that there >>>>>>>>>>>>>> is no processing >>>>>>>>>>>>>> >>> happening. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID >>>>>>>>>>>>>> they actually do >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>>>>>>>>> missing at the >>>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, >>>>>>>>>>>>>> but with no mnic >>>>>>>>>>>>>> >>> files. Also now i have this error >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>>>>>>>>> :/data/loris/bin/mri/tools$ >>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>>>>>>> processing it. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> How can solve this? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> To give you a brief idea: >>>>>>>>>>>>>> >>> Per folder it will: >>>>>>>>>>>>>> >>> 1) Delete all the .bak files >>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, >>>>>>>>>>>>>> TR_max, TE_min, >>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>>>>>>>>> mri_protocol table >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>>>>>> >>> For some reason some files are missing >>>>>>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> In total i have 7 folders >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> 3/7 passed >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a violation >>>>>>>>>>>>>> "T1 AXIAL SE >>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and >>>>>>>>>>>>>> i find that weird >>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory >>>>>>>>>>>>>> does not contain a >>>>>>>>>>>>>> >>> single DICOM file.", therefore they are missing their >>>>>>>>>>>>>> StudyUID >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>>>>>> multiple >>>>>>>>>>>>>> >>> studies." >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC >>>>>>>>>>>>>> files. >>>>>>>>>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> If i wanted to force the insertion of 102327840, >>>>>>>>>>>>>> 102809579 and 102506134 >>>>>>>>>>>>>> >>> can i just pass a flag parameter to >>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or >>>>>>>>>>>>>> >>> modify imaging_upload_file.pl? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thank you, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Sotirios >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> PS >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>>>>>>>>> dicom_output.txt. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> Glad to hear about your progress. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>>>>>>>>> documented here >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers you were >>>>>>>>>>>>>> looking for there. >>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in >>>>>>>>>>>>>> your database >>>>>>>>>>>>>> >>> management software is a visual placeholder for you as >>>>>>>>>>>>>> the user? I'm not >>>>>>>>>>>>>> >>> sure why a scanner would ever be registered with ID='0' >>>>>>>>>>>>>> as your screenshot >>>>>>>>>>>>>> >>> showed.) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I fixed it with this >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>>>>>>>>> something >>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a 500 >>>>>>>>>>>>>> internal error? In the >>>>>>>>>>>>>> >>> loris-error log it state that there is something wrong >>>>>>>>>>>>>> with token, but i >>>>>>>>>>>>>> >>> verfied that the type of the token is a string. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>>>>>> [client >>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: >>>>>>>>>>>>>> Argument 1 >>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of >>>>>>>>>>>>>> the type string, >>>>>>>>>>>>>> >>> null given, called in >>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc >>>>>>>>>>>>>> on line 169 and >>>>>>>>>>>>>> >>> defined in >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>>>>>> >>> trace:\n#0 >>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 >>>>>>>>>>>>>> {main}\n thrown in >>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc >>>>>>>>>>>>>> on line 192 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just to let you >>>>>>>>>>>>>> know what i >>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>>>>>>>>> dependencies. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> First i deleted all their uploads >>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a >>>>>>>>>>>>>> way to omit >>>>>>>>>>>>>> >>> the backup file ? ) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted >>>>>>>>>>>>>> all the entries >>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry >>>>>>>>>>>>>> with the 0 ID. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> We recommend that you use our existing tools for creating >>>>>>>>>>>>>> new candidates >>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP script, >>>>>>>>>>>>>> by calling the Candidate >>>>>>>>>>>>>> >>> class's createNew() >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>>>>>>>>> >function. >>>>>>>>>>>>>> >>> These will create the necessary records for you. (It's >>>>>>>>>>>>>> not recommended to >>>>>>>>>>>>>> >>> make direct modifications to mysql database tables in >>>>>>>>>>>>>> your script, if I >>>>>>>>>>>>>> >>> understand you.) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, >>>>>>>>>>>>>> and there are >>>>>>>>>>>>>> >>> multiple reasons for this. >>>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs and the >>>>>>>>>>>>>> External ID field >>>>>>>>>>>>>> >>> in the candidate table can also be used for any values >>>>>>>>>>>>>> you like. >>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be added in >>>>>>>>>>>>>> parallel - these >>>>>>>>>>>>>> >>> are entered/visible in the Candidate Information module >>>>>>>>>>>>>> and added in the >>>>>>>>>>>>>> >>> back-end as candidate parameters. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> We are building a script that will auto insert the >>>>>>>>>>>>>> candidates based on >>>>>>>>>>>>>> >>> their ExternalID. We would like to know whethere when we >>>>>>>>>>>>>> are creating a new >>>>>>>>>>>>>> >>> profile in the candidate table, if we also have to insert >>>>>>>>>>>>>> a new record at >>>>>>>>>>>>>> >>> another table? Furthermore is there a problem that in our >>>>>>>>>>>>>> case CandID won't >>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie >>>>>>>>>>>>>> Legault, Mrs < >>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> That would normally be the case but the numeric part of >>>>>>>>>>>>>> the PSCID get >>>>>>>>>>>>>> >>> paded with 0 on the left. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>>>>>> numerical char >>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ABC0001 >>>>>>>>>>>>>> >>> ABC0002 >>>>>>>>>>>>>> >>> ... >>>>>>>>>>>>>> >>> ABC0010 >>>>>>>>>>>>>> >>> ... >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> thus sorting them ascending will always get the latest >>>>>>>>>>>>>> value generated >>>>>>>>>>>>>> >>> as the max value. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> M?lanie >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must >>>>>>>>>>>>>> be stored >>>>>>>>>>>>>> >>> within a specific length of characters. Otherwise if we >>>>>>>>>>>>>> were to sort >>>>>>>>>>>>>> >>> strings with different lengths the result would not be >>>>>>>>>>>>>> sorted correctly ( >>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie >>>>>>>>>>>>>> Legault, Mrs < >>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hello Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> There is no `last value` stored anywhere. >>>>>>>>>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>>>>>>>>> increase that >>>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hope this info help. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of >>>>>>>>>>>>>> Medicine | McGill >>>>>>>>>>>>>> >>> University >>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> how does Loris determine the next available PSCID value >>>>>>>>>>>>>> for a new >>>>>>>>>>>>>> >>> candidate? >>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but >>>>>>>>>>>>>> where do we store the >>>>>>>>>>>>>> >>> last value for the sequential sequence? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have assigned are >>>>>>>>>>>>>> global >>>>>>>>>>>>>> >>> standard? or were assigned after trial and error? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Given you have done the initial setup of your tables to >>>>>>>>>>>>>> match your >>>>>>>>>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>>>>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting prior >>>>>>>>>>>>>> uploads). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> *if i were to change their status to resolve what would >>>>>>>>>>>>>> happen? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser >>>>>>>>>>>>>> from the >>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>>>>>>>>> /data/loris/data/trashbin/ >>>>>>>>>>>>>> >>> if i were to click their issue to resolve what would >>>>>>>>>>>>>> happend? would they >>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The defaut values of the schema exists in my local >>>>>>>>>>>>>> database. If i adjust >>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>>>>>>>>> uploaded? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol >>>>>>>>>>>>>> table ? (and >>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the >>>>>>>>>>>>>> Imaging insertion >>>>>>>>>>>>>> >>> setup : See the install/setup documentation : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert statements. You >>>>>>>>>>>>>> can adapt the >>>>>>>>>>>>>> >>> insert statements which load the default table values --> >>>>>>>>>>>>>> e.g. Here on >>>>>>>>>>>>>> >>> GitHub : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>>>>>> >>> (see also the mri_scan_type table) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I see that i can edit the values but not how to insert >>>>>>>>>>>>>> new rows. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the minc be >>>>>>>>>>>>>> inserted? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> It says "could not identify scan type", which we knew >>>>>>>>>>>>>> already. Did you >>>>>>>>>>>>>> >>> click on the link on those words? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> It will take you to the next page of the module, showing >>>>>>>>>>>>>> for each scan >>>>>>>>>>>>>> >>> what the scan parameters were, and will also show for >>>>>>>>>>>>>> comparison what's >>>>>>>>>>>>>> >>> stored in your *mri_protocol* table. >>>>>>>>>>>>>> >>> Compare these values to find which parameter was not >>>>>>>>>>>>>> correct according >>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol value ranges >>>>>>>>>>>>>> (e.g. TR, TE) >>>>>>>>>>>>>> >>> for scans. >>>>>>>>>>>>>> >>> This can be done in the front-end, by editing the >>>>>>>>>>>>>> database table >>>>>>>>>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The MRI Violations module features are explained in more >>>>>>>>>>>>>> detail in the >>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] >>>>>>>>>>>>>> icon in the menu >>>>>>>>>>>>>> >>> bar.) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> : no MINCs inserted- violated scans >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> looks like my previous email's attachment wasn't >>>>>>>>>>>>>> delivered due to >>>>>>>>>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>>>>>>>>> webbrowser, so >>>>>>>>>>>>>> >>> that you can check the filelds easier. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios -- >>>>>>>>>>>>>> >>> Great, sounds like more progress. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're >>>>>>>>>>>>>> getting an Endian >>>>>>>>>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>>>>>> successfully >>>>>>>>>>>>>> >>> relabelled, after the command ran? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> You can use also our DICAT tool ( >>>>>>>>>>>>>> https://github.com/aces/DICAT) to >>>>>>>>>>>>>> >>> verify and/or update local DICOM headers -- though your >>>>>>>>>>>>>> dcmodify command is >>>>>>>>>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>>>>>>>>> "(2001,105f)" from >>>>>>>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM >>>>>>>>>>>>>> slice before and look >>>>>>>>>>>>>> >>> at these fields specifically. >>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>>>>>>> before/after >>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff >>>>>>>>>>>>>> the outputs -- >>>>>>>>>>>>>> >>> this will pinpoint what changed. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>>>>>> recognized or >>>>>>>>>>>>>> >>> unknown : this means your scans did not match what is >>>>>>>>>>>>>> stored in your >>>>>>>>>>>>>> >>> mri_protocol table. >>>>>>>>>>>>>> >>> Check the MRI Violations front-end module -- can you see >>>>>>>>>>>>>> why they didn't >>>>>>>>>>>>>> >>> match? >>>>>>>>>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>>>>>>>>> mri_protocol >>>>>>>>>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Here is the psc table >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> and got those warning: is this okay? >>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you >>>>>>>>>>>>>> can see the >>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could not be >>>>>>>>>>>>>> inserted due to >>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Running now the following command: >>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>>>>>> '__MACOSX' >>>>>>>>>>>>>> >>> -delete >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod >>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Testing for database connectivity. >>>>>>>>>>>>>> >>> Database is available. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> You are creating a tar with the following command: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> tar -cf >>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> getting md5sums and gzipping!! >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>>>>> >>> * Archived on : 2019-09-06 >>>>>>>>>>>>>> 18:36:50 >>>>>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Adding archive info into database >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Removing temporary files from target location >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Done adding archive info into database >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>>>>>> -globLocation >>>>>>>>>>>>>> >>> -profile prod >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>>>>>> >>> -uploadID 12 -verbose >>>>>>>>>>>>>> >>> md5sum >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>>> >>> Set centerID = 1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Number of MINC files that will be considered for >>>>>>>>>>>>>> inserting into the >>>>>>>>>>>>>> >>> database: 2 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>> cat >>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ==> Loading file from disk >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> --> mapping DICOM parameter for >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ==> verifying acquisition protocol >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Acquisition protocol is unknown >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> --> The minc file cannot be registered since the >>>>>>>>>>>>>> AcquisitionProtocol >>>>>>>>>>>>>> >>> is unknown >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>>>>>>>>> *delete_imaging_upload* >>>>>>>>>>>>>> >>> script -- >>>>>>>>>>>>>> >>> details here: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> What's in your *psc* table? (Is it properly populated? >>>>>>>>>>>>>> This is a >>>>>>>>>>>>>> >>> pre-requisite to loading imaging data. >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> ) >>>>>>>>>>>>>> >>> The foreign key constraint error on the candidate record >>>>>>>>>>>>>> is curious. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> There are also a few options for creating candidates when >>>>>>>>>>>>>> inserting >>>>>>>>>>>>>> >>> imaging data: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM >>>>>>>>>>>>>> insertion pipeline >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and >>>>>>>>>>>>>> visits, optionally I >>>>>>>>>>>>>> >>> think) >>>>>>>>>>>>>> >>> How to: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Then as a second step: >>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> to load your DICOMs. >>>>>>>>>>>>>> >>> You will want to first ensure that the PatientName header >>>>>>>>>>>>>> in the DICOMs >>>>>>>>>>>>>> >>> as well as tar package are correctly labelled with >>>>>>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>>>>>>>>> >>> How to : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>>>>>>>>> bids_import script, >>>>>>>>>>>>>> >>> to automatically create your candidates and sessions. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i have to >>>>>>>>>>>>>> create a new >>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> *First execution:* >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>> ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>>>>> >>> log.txt >>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>>> row: a foreign >>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>>>>>> `FK_candidate_1` >>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>>>>>> (`CenterID`)) at >>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>>> 1060. >>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>>>>>> >>> The following database commands failed: >>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>>>>>>>>> (?,?,?,?,?)'; >>>>>>>>>>>>>> >>> SET >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>>>>>> >>> Medical Systems'; >>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a >>>>>>>>>>>>>> foreign key >>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>>>>>> `FK_mri_scanner_1` >>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) >>>>>>>>>>>>>> (error code 1452) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ERROR: The validation has failed. Either re-run the >>>>>>>>>>>>>> validation again >>>>>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using >>>>>>>>>>>>>> -force to force the >>>>>>>>>>>>>> >>> execution. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>>> >>> line 250. >>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>>> >>> line 251. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> *And second execution: * >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>> ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>>>>> >>> log.txt >>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> PROBLEM: >>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>>>>>> >>> The unique study ID is >>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>>>>>> >>> This is the information retained from the first time the >>>>>>>>>>>>>> study was >>>>>>>>>>>>>> >>> inserted: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>>>>> >>> * Archived on : 2019-09-04 >>>>>>>>>>>>>> 18:33:05 >>>>>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Last update of record: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>>> >>> line 250. >>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>>> >>> line 251. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Ok, this sounds like good progress. Let us know when you >>>>>>>>>>>>>> next encounter >>>>>>>>>>>>>> >>> issues as you progress through the Imaging Install/Setup >>>>>>>>>>>>>> docs >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md >>>>>>>>>>>>>> >. >>>>>>>>>>>>>> >>> I'll look into how we can better handle the incoming/ >>>>>>>>>>>>>> directory next >>>>>>>>>>>>>> >>> time. >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>>>>>>>>>> >>> populated correctly except its port is 'port' : ''. >>>>>>>>>>>>>> Also i have tested >>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I executed the script again, because the only error i had >>>>>>>>>>>>>> previously was >>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and there are >>>>>>>>>>>>>> no errors >>>>>>>>>>>>>> >>> reported back except of warnings <>>>>>>>>>>>>> a password on the >>>>>>>>>>>>>> >>> command line interface can be insecure>>. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> It's possible -- if the script was unable to connect to >>>>>>>>>>>>>> the database >>>>>>>>>>>>>> >>> during its execution (e.g. typo in the password), that >>>>>>>>>>>>>> would explain the >>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw >>>>>>>>>>>>>> in the Config >>>>>>>>>>>>>> >>> module. >>>>>>>>>>>>>> >>> It's hard to tell without seeing the output from your >>>>>>>>>>>>>> script run -- Did >>>>>>>>>>>>>> >>> you see a sign of any such error? >>>>>>>>>>>>>> >>> The Config fields are populated by the imaging_install.sh >>>>>>>>>>>>>> script (starting >>>>>>>>>>>>>> >>> at line 222 >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> ) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> For example, check if the database connection information >>>>>>>>>>>>>> was populated >>>>>>>>>>>>>> >>> accurately in >>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Christine, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>> image with the >>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>> the last part >>>>>>>>>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and working >>>>>>>>>>>>>> and all the >>>>>>>>>>>>>> >>> front-end pages are loading. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>>>>>>> project >>>>>>>>>>>>>> >>> > and the web interface worked. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775 permissions >>>>>>>>>>>>>> and that >>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in >>>>>>>>>>>>>> the install >>>>>>>>>>>>>> >>> Readme . >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should >>>>>>>>>>>>>> change LORIS to >>>>>>>>>>>>>> >>> loris, right? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>>>>>>>>> installation >>>>>>>>>>>>>> >>> by an >>>>>>>>>>>>>> automated script -- >>>>>>>>>>>>>> >>> you do not need to set them manually via the Config >>>>>>>>>>>>>> module. >>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide >>>>>>>>>>>>>> >>> for detailed >>>>>>>>>>>>>> steps to follow. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>>>>> LORIS to loris, >>>>>>>>>>>>>> >>> right? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> i used >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E >>>>>>>>>>>>>> bash - >>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> you had suggested in the past, make worked and now i can >>>>>>>>>>>>>> see all the >>>>>>>>>>>>>> >>> contents in the web-interface, but i don't need make >>>>>>>>>>>>>> install? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> -------------- next part -------------- >>>>>>>>>>>>>> An HTML attachment was scrubbed... >>>>>>>>>>>>>> URL: < >>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>>>>>>>>>> ***************************************** >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 62956 bytes Desc: not available URL: From iris.rodriguez at cneuro.edu.cu Thu Nov 28 16:06:37 2019 From: iris.rodriguez at cneuro.edu.cu (=?utf-8?B?SXJpcyBSb2Ryw61ndWV6IEdpbA==?=) Date: Thu, 28 Nov 2019 16:06:37 -0500 Subject: [Loris-dev] RV: Uncaught bounce notification In-Reply-To: References: Message-ID: De: Christine Rogers, Ms. [mailto:christine.rogers at mcgill.ca] Enviado el: Thursday, November 28, 2019 2:19 PM Para: Iris Rodr?guez Gil Asunto: Fwd: Uncaught bounce notification Hi Iris, Could you please re-send this email, to the correct address for our listserv? the address is loris-dev at bic.mni.mcgill.ca Thanks! Christine ---------- Forwarded message --------- From: > Date: Thu, Nov 28, 2019 at 12:28 PM Subject: Uncaught bounce notification To: > The attached message was received as a bounce, but either the bounce format was not recognized, or no member addresses could be extracted from it. This mailing list has been configured to send all unrecognized bounce messages to the list administrator(s). For more information see: https://mailman.bic.mni.mcgill.ca/mailman/admin/loris-dev/bounce ---------- Forwarded message ---------- From: "Iris Rodr?guez Gil" > To: "loris-dev-bounces at bic.mni.mcgill.ca" > Cc: Bcc: Date: Thu, 28 Nov 2019 12:27:41 -0500 Subject: Inserting BIDS Hi all, I testing de bids import.py pipeline in loris 22.0 with a small dataset and obtain error. I attached the file with the error, Any idea for solve this problem?. Thanks, Iris -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: error.txt URL: From sotirisnik at gmail.com Fri Nov 29 20:06:03 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sat, 30 Nov 2019 03:06:03 +0200 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Cecile, Thanks to Nicholas i was able to create all the mincs images. The problem was that the files were in Little-Endian-Implicit transfer syntax and i had to convert them Little-Endian-Explicit transfer syntax with this command find -type f | xargs -i dcmconv --write-xfer-little {} {} Looking back at our mails i saw that Little-Endian error had occurred when i used dcmodify, but i switcthed to using pydicom instead. [image: image.png] In the output i see an error sometimes about "gsl: bessel_I0.c:216: ERROR: overflow". Is this okay? Restructuring... gsl: bessel_I0.c:216: ERROR: overflow Default GSL error handler invoked. noise_estimate --snr /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc SNR is: gsl: bessel_I0.c:216: ERROR: overflow Default GSL error handler invoked. Thanks, Sotirios ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar < cecile.madjar at mcin.ca> ??????: > Hi Sotirios, > > Thank you for the details! > > A few things to try: > > - modify the TMPDIR to be on your /data directory where there might be > more space to do processing (could create a /data/tmp where the temporary > files would be created) > - how many files are there for that upload in tarchive_files? Are they > different from the ones showing the warning message? > - FYI: query to get that: SELECT tf.* FROM tarchive_files tf JOIN > mri_upload USING (TarchiveID) WHERE UploadID= (the > output of that query would be very useful if you can provide it) > - how many series are there for that upload in tarchive_series? > - FYI: query to get that: SELECT ts.* FROM tarchive_series ts JOIN > mri_upload USING (TarchiveID) WHERE UploadID= (the > output of that query would be very useful if you can provide it) > - things are failing when the scripts try running the following > command: find /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO > -type f | /data/loris/bin/mri/dicom-archive/get_dicom_info.pl > -studyuid -series -echo -image -file -attvalue 0018 0024 -series_descr > -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4 | cut -f 5 | dcm2mnc -dname '' > -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa > - clearly the problems come from get_dicom_info.pl but I cannot > pinpoint the error yet. I will ask around and get back to you > > If I cannot figure it out remotely, is there a way to have a call using > zoom? This way you could share your screen with me and run the debugger on > that script and hopefully we can figure out what is going on with those > datasets? > > Thanks! > > C?cile > > On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi Cecile, >> >> In both my virtual machines >> export TMPDIR=/tmp >> >> In both vm also with dcm2mnc i get this output. Just to verify that this >> passed in my 1st vm and produced mincs. >> >> I attached the spool as a csv. >> >> [image: image.png] >> >> And also one difference i found was this in the Loris-mri code ( left 1st >> workable vm, right 2nd vm that has to be fixed, although i changed it seems >> to be independent of the uninitialized value $_ ) >> >> >> [image: image.png] >> >> Thanks, >> >> Sotirios >> >> >> >> >> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar < >> cecile.madjar at mcin.ca> ??????: >> >>> Hi Sotirios, >>> >>> that is puzzling... A few additional questions: >>> >>> - what is the bash variable TMPDIR set to on the environment file? >>> - could you try running separately dcm2mnc on the DICOM folder to >>> see if that works? >>> - could you send us the detailed log from the notification spool >>> table (SELECT * FROM notification_spool WHERE UploadID=) and >>> send it back to us? Maybe there are some additional clues that could help >>> figuring out what is going on. >>> >>> Thank you! >>> >>> C?cile >>> >>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi Cecile, >>>> >>>> I checked for the StudyInstacueUID at the files with "The target >>>> directory does not contain a single DICOM file"" and their attribute has a >>>> value. >>>> >>>> Regarding the scouter and localizer, i modified the settings in the >>>> imaging pipeline and now i don't get that error message, but still it >>>> doesn't create the mnics. >>>> >>>> The errors i am getting are ( uninitialized value $_ is not important? >>>> because i haven't got comments about that ) >>>> >>>> Use of uninitialized value $_ in pattern match (m//) at >>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144. >>>> Running now the following command: /data/loris/data//uploadNeuroDB/ >>>> imaging_upload_file.pl -profile prod -upload_id 134 >>>> /data/incoming/DCC0025_118008_V1.tar.gz -verbose >>>> >>>> and >>>> >>>> Number of MINC files that will be considered for inserting into the >>>> database: 0 >>>> >>>> No data could be converted into valid MINC files. >>>> >>>> The tarchiveLoader.pl insertion script has failed. >>>> Use of uninitialized value $mail_user in concatenation (.) or string at >>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249. >>>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/ >>>> batch_uploads_imageuploader.pl line 249. >>>> print() on closed filehandle MAIL at /data/loris/bin/mri/ >>>> batch_uploads_imageuploader.pl line 250. >>>> print() on closed filehandle MAIL at /data/loris/bin/mri/ >>>> batch_uploads_imageuploader.pl line 251. >>>> >>>> Thanks >>>> >>>> Sotirios >>>> >>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar < >>>> cecile.madjar at mcin.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> >>>>> OK. So the issue I mentioned should not be a problem for you. >>>>> >>>>> Is the StudyInstanceUID DICOM header set in your images? If it is not >>>>> set, then you would end up with the error message "The target directory >>>>> does not contain a single DICOM file". So maybe this is the issue you are >>>>> having with those datasets? >>>>> >>>>> Regarding not excluding series descriptions, you can configure that in >>>>> the Config module under the Imaging Pipeline section. Simply remove all >>>>> entries for the "Series description to exclude from imaging insertion" >>>>> setting. >>>>> >>>>> C?cile >>>>> >>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi Cecile, >>>>>> >>>>>> We are using this version >>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to >>>>>> insert low resolution now? >>>>>> >>>>>> Thanks >>>>>> >>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, >>>>>> wrote: >>>>>> >>>>>>> Hi Sotirios, >>>>>>> >>>>>>> Which version of LORIS-MRI are you using? >>>>>>> >>>>>>> There was a bug that got resolved in 20.2 in get_dicom_info.pl. >>>>>>> Basically, if a DICOM did not have the (0020,0032) header, >>>>>>> get_dicom_info.pl considered that the file was not a DICOM, which >>>>>>> was a mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this >>>>>>> is the issue you are encountering. >>>>>>> >>>>>>> About scout and localizer, they are a type of short and low >>>>>>> resolution sequence that is used by the tech but is of no interest >>>>>>> scientifically, which is why we tend to no insert them. >>>>>>> >>>>>>> Hope this helps, >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> >>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> wrote: >>>>>>> >>>>>>>> Hi Cecile, >>>>>>>> >>>>>>>> i executed the find command and the output i got per folder was >>>>>>>> "DICOM medical imaging data. Maybe there is something wrong with the find >>>>>>>> command in the warning that it is unable to check if the file is a dicom >>>>>>>> file? Also when i use get_dicom_info.pl i don't get any output >>>>>>>> data. Finally i don't understand what scout or localizer is ( something >>>>>>>> like if and only if a file fails then the whole session is invalid? ). >>>>>>>> >>>>>>>> [image: image.png] >>>>>>>> >>>>>>>> Thanks >>>>>>>> >>>>>>>> Sotirios >>>>>>>> >>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar < >>>>>>>> cecile.madjar at mcin.ca> ??????: >>>>>>>> >>>>>>>>> Hi Sotirios, >>>>>>>>> >>>>>>>>> I took a closer look to the batch_uploader_multiple_output.txt >>>>>>>>> file you sent. It looks like there are different reasons for failure >>>>>>>>> depending on the DICOM folder uploaded. >>>>>>>>> >>>>>>>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007 >>>>>>>>> V1: it looks like there is no file of type DICOM in the folder. Have you >>>>>>>>> checked to see if that is indeed the case? Maybe you can try running the >>>>>>>>> following command on that folder to see what are the types of the files? If >>>>>>>>> it does not return at least one DICOM medical imaging data file, then that >>>>>>>>> is why you get the error message from the pipeline: >>>>>>>>> - >>>>>>>>> >>>>>>>>> find -type f | xargs -i file {}|cut -d: -f2|sort|uniq >>>>>>>>> >>>>>>>>> - For 864173 DCC0001 V1: it looks like there are two >>>>>>>>> different DICOM studies within the same folder. You will need to split that >>>>>>>>> study in two based on the StudyUID field as the insertion pipeline does not >>>>>>>>> allow for more than one StudyUID per upload. >>>>>>>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006 >>>>>>>>> V1: it looks like the dcm2mnc command did not produce any MINC files. Can >>>>>>>>> you check in the DICOM archive what are the series present in the tarchive >>>>>>>>> for that visit? Maybe only a scout or localizer was acquired for that >>>>>>>>> session, hence the no valid MINC files (scout and localizer being skipped >>>>>>>>> for the conversion) >>>>>>>>> - For 397410 DCC0003 V1: it looks like everything went well >>>>>>>>> for this one. >>>>>>>>> >>>>>>>>> One script that is called by our pipeline is called >>>>>>>>> get_dicom_info.pl and this does all kind of checks on the DICOM >>>>>>>>> files (it is being called when running the dcm2mnc conversion). You could >>>>>>>>> run it independently on your folder if needed. >>>>>>>>> >>>>>>>>> Since one of the study got in, it does not look like you are >>>>>>>>> having a problem with the setup. It seems more likely to be a problem with >>>>>>>>> the data themselves. >>>>>>>>> >>>>>>>>> Hope this helps. >>>>>>>>> >>>>>>>>> C?cile >>>>>>>>> >>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos < >>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> Hi Christine, >>>>>>>>>> >>>>>>>>>> In my first vm i am able to create the minc files and view them >>>>>>>>>> at the mri browser (except of candidate 102761034 ), meanwhile the same >>>>>>>>>> files gives warnings at the 2nd vm. The output of the batch upload can be >>>>>>>>>> seen in the file attached. >>>>>>>>>> Also a colleague of us has built a pre-validation tool for dicom >>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had >>>>>>>>>> found all the files that Loris gave as warning . Basically I confirmed that >>>>>>>>>> the total amount of files per dicom was the same amount as stated in Loris >>>>>>>>>> and checked some filenames given from warning to confirm that they match >>>>>>>>>> with our tool. But that was months ago and my colleague had changed some >>>>>>>>>> parameters for MIP and now our tool doesn't find all the invalid files, >>>>>>>>>> that's why i asked for the dicom header specification of Loris. In a >>>>>>>>>> discussion we had he mentioned that he doesn't check for some tags e.x. >>>>>>>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to >>>>>>>>>> remove invalid dcm files. >>>>>>>>>> >>>>>>>>>> Thanks >>>>>>>>>> >>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms. < >>>>>>>>>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>> >>>>>>>>>>> Hi Sotirios, >>>>>>>>>>> Can you provide us with some fresh particulars of the >>>>>>>>>>> current issue and we'll take it from there? >>>>>>>>>>> Yang's team has built these scripts which can definitely serve >>>>>>>>>>> as a model for your pre-validation of your DICOM collections. >>>>>>>>>>> cheers, >>>>>>>>>>> Christine >>>>>>>>>>> >>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> HI Yang, >>>>>>>>>>>> >>>>>>>>>>>> We make use of pydicom library too. Now about the validate.py i >>>>>>>>>>>> see that you check if some attributes are missing such as PatientID, >>>>>>>>>>>> PatientName which all of our files contains that info. Maybe i have missed >>>>>>>>>>>> something on the setup of my other virtual machine ( although one dicom >>>>>>>>>>>> passed on the new vm successfully, the others that were inserted correctly >>>>>>>>>>>> on my old vm fails on the new one ), i think that i had asked about this >>>>>>>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at >>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144." >>>>>>>>>>>> but i don't remember the solution. >>>>>>>>>>>> >>>>>>>>>>>> Thanks >>>>>>>>>>>> >>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding >>>>>>>>>>>> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> Hey, Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> Christine from the LORIS team mentioned you had some issue >>>>>>>>>>>>> with DICOM. I am a fellow developer for an external project using LORIS, >>>>>>>>>>>>> kind of just like you. We had to implement DICOM upload as well but more as >>>>>>>>>>>>> a fully automated pipeline actually. >>>>>>>>>>>>> >>>>>>>>>>>>> While we were building CNBP, we had coded up some minor Python >>>>>>>>>>>>> functions to check DICOM integrity (and simple validations) and you might >>>>>>>>>>>>> be able to gain some inspiration from it and help you with your cause. For >>>>>>>>>>>>> more comprehensive solution, PyDICOM ( >>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems >>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks >>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can >>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty >>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons >>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py >>>>>>>>>>>>> >>>>>>>>>>>>> Cheers, >>>>>>>>>>>>> >>>>>>>>>>>>> Yang Ding, PhD. >>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect >>>>>>>>>>>>> >>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM < >>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Send Loris-dev mailing list submissions to >>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit >>>>>>>>>>>>>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> or, via email, send a message with subject or body 'help' to >>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>>>>>>>>>>>>> You can reach the person managing the list at >>>>>>>>>>>>>> loris-dev-owner at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>>>>>>>>>>>>> When replying, please edit your Subject line so it is more >>>>>>>>>>>>>> specific >>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..." >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> Today's Topics: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos) >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> ---------------------------------------------------------------------- >>>>>>>>>>>>>> >>>>>>>>>>>>>> Message: 1 >>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200 >>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> To: Cecile Madjar >>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>> Message-ID: >>>>>>>>>>>>>> >>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com> >>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8" >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom files to >>>>>>>>>>>>>> diagnose the >>>>>>>>>>>>>> warnings we get? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> > Hi Cecile, >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > We were wondering whether Loris has a tool to check if >>>>>>>>>>>>>> there are problems >>>>>>>>>>>>>> > with the dcm files, before trying to upload them. Something >>>>>>>>>>>>>> that could >>>>>>>>>>>>>> > provide the same results provided in the warning_output, >>>>>>>>>>>>>> this is the >>>>>>>>>>>>>> > summary from the mri_upload at the front-page. Also which >>>>>>>>>>>>>> attributes of the >>>>>>>>>>>>>> > dcm header would trigger a warning? is there a dcm file >>>>>>>>>>>>>> header >>>>>>>>>>>>>> > specification for Loris? >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > Thanks >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > Sotirios >>>>>>>>>>>>>> > >>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >> Hi, >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it >>>>>>>>>>>>>> worked,but i >>>>>>>>>>>>>> >> thought that something else was causing the 2nd issue. >>>>>>>>>>>>>> >> Thanks >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, < >>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote: >>>>>>>>>>>>>> >> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and >>>>>>>>>>>>>> columns are of >>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be >>>>>>>>>>>>>> using >>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW(). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The second error occurs because the trigger triggers a >>>>>>>>>>>>>> rollback of the >>>>>>>>>>>>>> >>> insert statement in the files table. >>>>>>>>>>>>>> >>> See mysql documentation for trigger error handling. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results >>>>>>>>>>>>>> in failure of >>>>>>>>>>>>>> >>> the entire statement that caused trigger invocation. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps. >>>>>>>>>>>>>> >>> -- Xavier >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM >>>>>>>>>>>>>> >>> *To:* Cecile Madjar >>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>; >>>>>>>>>>>>>> >>> Christine Rogers, Ms. >>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> When mincs are inserted their corresponding rows at the >>>>>>>>>>>>>> file table are >>>>>>>>>>>>>> >>> inserted too >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as >>>>>>>>>>>>>> well, because i >>>>>>>>>>>>>> >>> don't want manually to label them as passed throught the >>>>>>>>>>>>>> interface >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> That is the trigger i wrote >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER >>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER >>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW >>>>>>>>>>>>>> >>> BEGIN >>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus >>>>>>>>>>>>>> >>> SET FileID = NEW.FileID, >>>>>>>>>>>>>> >>> SeriesUID = NEW.SeriesUID, >>>>>>>>>>>>>> >>> EchoTime = NEW.EchoTime, >>>>>>>>>>>>>> >>> QCStatus = "Pass", >>>>>>>>>>>>>> >>> QCFirstChangeTime = NOW(), >>>>>>>>>>>>>> >>> QCLastChangeTime = NOW(); >>>>>>>>>>>>>> >>> END >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> although it contains some errors >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column >>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at >>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823. >>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>>> row: a foreign >>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT >>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES >>>>>>>>>>>>>> `files` (`FileID`)) >>>>>>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>>> 848. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column >>>>>>>>>>>>>> associated with >>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it >>>>>>>>>>>>>> means no DICOMs >>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the end of the >>>>>>>>>>>>>> insertion of the >>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with >>>>>>>>>>>>>> the correct >>>>>>>>>>>>>> >>> TarchiveID associated with the upload. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Could this correspond to what you want to do? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked >>>>>>>>>>>>>> to the files >>>>>>>>>>>>>> >>> table (hence, the MINC files). You could always create a >>>>>>>>>>>>>> new table for >>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to mark all >>>>>>>>>>>>>> their >>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of >>>>>>>>>>>>>> creating a trigger for >>>>>>>>>>>>>> >>> that, but which tables do i need to add entries to? So >>>>>>>>>>>>>> far from what i see >>>>>>>>>>>>>> >>> i need to add entres at the table "files" whenever an >>>>>>>>>>>>>> insertion happens to >>>>>>>>>>>>>> >>> files_qcstatus. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the >>>>>>>>>>>>>> beginning of my email >>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the >>>>>>>>>>>>>> StudyID i am >>>>>>>>>>>>>> >>> looking for is not stored in the database? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the >>>>>>>>>>>>>> >>> tarchive table. It can also be found in the metadata >>>>>>>>>>>>>> field but it is mixed >>>>>>>>>>>>>> >>> with many other information. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hope this helps, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the >>>>>>>>>>>>>> tarchive table, >>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found >>>>>>>>>>>>>> something called >>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the >>>>>>>>>>>>>> Study Instance UID. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Your observation is correct. A little explanation below. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation tables if: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> - the scan type could not be identified (not matching >>>>>>>>>>>>>> an entry in >>>>>>>>>>>>>> >>> the mri_protocol table) >>>>>>>>>>>>>> >>> - one parameter of the scan type is out of the >>>>>>>>>>>>>> expected range >>>>>>>>>>>>>> >>> present in the mri_protocol_checks (extra filtering in >>>>>>>>>>>>>> case you need to be >>>>>>>>>>>>>> >>> stricker on some parameters not present in the >>>>>>>>>>>>>> mri_protocol table) >>>>>>>>>>>>>> >>> - if the CandID and PSCID do not match >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The following cases do not get in the MRI violation >>>>>>>>>>>>>> tables as it happens >>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC files and only >>>>>>>>>>>>>> MINC files >>>>>>>>>>>>>> >>> violations are logged there: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be >>>>>>>>>>>>>> found to convert >>>>>>>>>>>>>> >>> to MINC) >>>>>>>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID) since >>>>>>>>>>>>>> this error >>>>>>>>>>>>>> >>> happens at the dicomTar.pl level (way before >>>>>>>>>>>>>> conversion into MINC files) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Glad everything is working out!! >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of >>>>>>>>>>>>>> ram. Now about the >>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there >>>>>>>>>>>>>> only if there is >>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header >>>>>>>>>>>>>> parameter? >>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or >>>>>>>>>>>>>> with the 2 studyiuid >>>>>>>>>>>>>> >>> to be there. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the memory. I >>>>>>>>>>>>>> think most of our >>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be >>>>>>>>>>>>>> fine. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> C?cile >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> about that dicom that had that insertion error it's about >>>>>>>>>>>>>> 30mb and when >>>>>>>>>>>>>> >>> it is being processed the ram is being drastically >>>>>>>>>>>>>> increased from 2gb to >>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What >>>>>>>>>>>>>> is the recommended >>>>>>>>>>>>>> >>> size of ram for using Loris? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar < >>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed! >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> For the delete script issue, if you are absolutely >>>>>>>>>>>>>> certain that no >>>>>>>>>>>>>> >>> processes are run for that uploadID, you can update the >>>>>>>>>>>>>> mri_upload table >>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that >>>>>>>>>>>>>> uploadID. It >>>>>>>>>>>>>> >>> looks like for some reason the scripts did not update >>>>>>>>>>>>>> this field when it >>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would be the >>>>>>>>>>>>>> case though. >>>>>>>>>>>>>> >>> Note: only do that update if you are certain that there >>>>>>>>>>>>>> is no processing >>>>>>>>>>>>>> >>> happening. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hope this helps! >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID >>>>>>>>>>>>>> they actually do >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I thought that this might be a permission because "w" was >>>>>>>>>>>>>> missing at the >>>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed, >>>>>>>>>>>>>> but with no mnic >>>>>>>>>>>>>> >>> files. Also now i have this error >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox >>>>>>>>>>>>>> :/data/loris/bin/mri/tools$ >>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore >>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently >>>>>>>>>>>>>> processing it. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> How can solve this? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Here is our auto dicom uploading python script: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> To give you a brief idea: >>>>>>>>>>>>>> >>> Per folder it will: >>>>>>>>>>>>>> >>> 1) Delete all the .bak files >>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header >>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min, >>>>>>>>>>>>>> TR_max, TE_min, >>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the >>>>>>>>>>>>>> mri_protocol table >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205 >>>>>>>>>>>>>> >>> For some reason some files are missing >>>>>>>>>>>>>> SeriesDescription/ProtocolName >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> In total i have 7 folders >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> 3/7 passed >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a violation >>>>>>>>>>>>>> "T1 AXIAL SE >>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and >>>>>>>>>>>>>> i find that weird >>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription. >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory >>>>>>>>>>>>>> does not contain a >>>>>>>>>>>>>> >>> single DICOM file.", therefore they are missing their >>>>>>>>>>>>>> StudyUID >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from >>>>>>>>>>>>>> multiple >>>>>>>>>>>>>> >>> studies." >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC >>>>>>>>>>>>>> files. >>>>>>>>>>>>>> >>> localizer, scout will not be considered!" What is this? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> If i wanted to force the insertion of 102327840, >>>>>>>>>>>>>> 102809579 and 102506134 >>>>>>>>>>>>>> >>> can i just pass a flag parameter to >>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or >>>>>>>>>>>>>> >>> modify imaging_upload_file.pl? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thank you, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Sotirios >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> PS >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> To diagnose a folder search the name of the folder at >>>>>>>>>>>>>> dicom_output.txt. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> Glad to hear about your progress. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging data is fully >>>>>>>>>>>>>> documented here >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers you were >>>>>>>>>>>>>> looking for there. >>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in >>>>>>>>>>>>>> your database >>>>>>>>>>>>>> >>> management software is a visual placeholder for you as >>>>>>>>>>>>>> the user? I'm not >>>>>>>>>>>>>> >>> sure why a scanner would ever be registered with ID='0' >>>>>>>>>>>>>> as your screenshot >>>>>>>>>>>>>> >>> showed.) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I fixed it with this >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I tried to create a new candidate using the API, is there >>>>>>>>>>>>>> something >>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a 500 >>>>>>>>>>>>>> internal error? In the >>>>>>>>>>>>>> >>> loris-error log it state that there is something wrong >>>>>>>>>>>>>> with token, but i >>>>>>>>>>>>>> >>> verfied that the type of the token is a string. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535] >>>>>>>>>>>>>> [client >>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught TypeError: >>>>>>>>>>>>>> Argument 1 >>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of >>>>>>>>>>>>>> the type string, >>>>>>>>>>>>>> >>> null given, called in >>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc >>>>>>>>>>>>>> on line 169 and >>>>>>>>>>>>>> >>> defined in >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack >>>>>>>>>>>>>> >>> trace:\n#0 >>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169): >>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1 >>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171): >>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2 >>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73): >>>>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3 >>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44): >>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4 >>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244): >>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 >>>>>>>>>>>>>> {main}\n thrown in >>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc >>>>>>>>>>>>>> on line 192 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just to let you >>>>>>>>>>>>>> know what i >>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may have missed >>>>>>>>>>>>>> dependencies. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> First i deleted all their uploads >>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a >>>>>>>>>>>>>> way to omit >>>>>>>>>>>>>> >>> the backup file ? ) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted >>>>>>>>>>>>>> all the entries >>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry >>>>>>>>>>>>>> with the 0 ID. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Lastly i deleted the session and then the candidate table. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> We recommend that you use our existing tools for creating >>>>>>>>>>>>>> new candidates >>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP script, >>>>>>>>>>>>>> by calling the Candidate >>>>>>>>>>>>>> >>> class's createNew() >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200 >>>>>>>>>>>>>> >function. >>>>>>>>>>>>>> >>> These will create the necessary records for you. (It's >>>>>>>>>>>>>> not recommended to >>>>>>>>>>>>>> >>> make direct modifications to mysql database tables in >>>>>>>>>>>>>> your script, if I >>>>>>>>>>>>>> >>> understand you.) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID, >>>>>>>>>>>>>> and there are >>>>>>>>>>>>>> >>> multiple reasons for this. >>>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs and the >>>>>>>>>>>>>> External ID field >>>>>>>>>>>>>> >>> in the candidate table can also be used for any values >>>>>>>>>>>>>> you like. >>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be added in >>>>>>>>>>>>>> parallel - these >>>>>>>>>>>>>> >>> are entered/visible in the Candidate Information module >>>>>>>>>>>>>> and added in the >>>>>>>>>>>>>> >>> back-end as candidate parameters. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> We are building a script that will auto insert the >>>>>>>>>>>>>> candidates based on >>>>>>>>>>>>>> >>> their ExternalID. We would like to know whethere when we >>>>>>>>>>>>>> are creating a new >>>>>>>>>>>>>> >>> profile in the candidate table, if we also have to insert >>>>>>>>>>>>>> a new record at >>>>>>>>>>>>>> >>> another table? Furthermore is there a problem that in our >>>>>>>>>>>>>> case CandID won't >>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie >>>>>>>>>>>>>> Legault, Mrs < >>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> That would normally be the case but the numeric part of >>>>>>>>>>>>>> the PSCID get >>>>>>>>>>>>>> >>> paded with 0 on the left. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4 >>>>>>>>>>>>>> numerical char >>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ABC0001 >>>>>>>>>>>>>> >>> ABC0002 >>>>>>>>>>>>>> >>> ... >>>>>>>>>>>>>> >>> ABC0010 >>>>>>>>>>>>>> >>> ... >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> thus sorting them ascending will always get the latest >>>>>>>>>>>>>> value generated >>>>>>>>>>>>>> >>> as the max value. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> M?lanie >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15 >>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs >>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. ; >>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must >>>>>>>>>>>>>> be stored >>>>>>>>>>>>>> >>> within a specific length of characters. Otherwise if we >>>>>>>>>>>>>> were to sort >>>>>>>>>>>>>> >>> strings with different lengths the result would not be >>>>>>>>>>>>>> sorted correctly ( >>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie >>>>>>>>>>>>>> Legault, Mrs < >>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hello Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> There is no `last value` stored anywhere. >>>>>>>>>>>>>> >>> The code simply look for the PSCID with the max value and >>>>>>>>>>>>>> increase that >>>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hope this info help. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of >>>>>>>>>>>>>> Medicine | McGill >>>>>>>>>>>>>> >>> University >>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ------------------------------ >>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca < >>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of >>>>>>>>>>>>>> Sotirios >>>>>>>>>>>>>> >>> Nikoloutsopoulos >>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43 >>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. >>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca < >>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca> >>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> how does Loris determine the next available PSCID value >>>>>>>>>>>>>> for a new >>>>>>>>>>>>>> >>> candidate? >>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization >>>>>>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but >>>>>>>>>>>>>> where do we store the >>>>>>>>>>>>>> >>> last value for the sequential sequence? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have assigned are >>>>>>>>>>>>>> global >>>>>>>>>>>>>> >>> standard? or were assigned after trial and error? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Given you have done the initial setup of your tables to >>>>>>>>>>>>>> match your >>>>>>>>>>>>>> >>> intended protocol/parameters according to instructions -- >>>>>>>>>>>>>> >>> the Troubleshooting guide documentation recommends >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting prior >>>>>>>>>>>>>> uploads). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> *if i were to change their status to resolve what would >>>>>>>>>>>>>> happen? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser >>>>>>>>>>>>>> from the >>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at >>>>>>>>>>>>>> /data/loris/data/trashbin/ >>>>>>>>>>>>>> >>> if i were to click their issue to resolve what would >>>>>>>>>>>>>> happend? would they >>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ). >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The defaut values of the schema exists in my local >>>>>>>>>>>>>> database. If i adjust >>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be >>>>>>>>>>>>>> uploaded? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol >>>>>>>>>>>>>> table ? (and >>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types of scans) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the >>>>>>>>>>>>>> Imaging insertion >>>>>>>>>>>>>> >>> setup : See the install/setup documentation : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert statements. You >>>>>>>>>>>>>> can adapt the >>>>>>>>>>>>>> >>> insert statements which load the default table values --> >>>>>>>>>>>>>> e.g. Here on >>>>>>>>>>>>>> >>> GitHub : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718 >>>>>>>>>>>>>> >>> (see also the mri_scan_type table) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I see that i can edit the values but not how to insert >>>>>>>>>>>>>> new rows. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the minc be >>>>>>>>>>>>>> inserted? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot is enough. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> It says "could not identify scan type", which we knew >>>>>>>>>>>>>> already. Did you >>>>>>>>>>>>>> >>> click on the link on those words? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> It will take you to the next page of the module, showing >>>>>>>>>>>>>> for each scan >>>>>>>>>>>>>> >>> what the scan parameters were, and will also show for >>>>>>>>>>>>>> comparison what's >>>>>>>>>>>>>> >>> stored in your *mri_protocol* table. >>>>>>>>>>>>>> >>> Compare these values to find which parameter was not >>>>>>>>>>>>>> correct according >>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type definitions. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol value ranges >>>>>>>>>>>>>> (e.g. TR, TE) >>>>>>>>>>>>>> >>> for scans. >>>>>>>>>>>>>> >>> This can be done in the front-end, by editing the >>>>>>>>>>>>>> database table >>>>>>>>>>>>>> >>> directly in the same subpage of the MRI Violations module. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The MRI Violations module features are explained in more >>>>>>>>>>>>>> detail in the >>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click the ["?"] >>>>>>>>>>>>>> icon in the menu >>>>>>>>>>>>>> >>> bar.) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> : no MINCs inserted- violated scans >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> looks like my previous email's attachment wasn't >>>>>>>>>>>>>> delivered due to >>>>>>>>>>>>>> >>> security reasons, i uploaded my file at google drive >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> For the mri_violations i attached the .html output from >>>>>>>>>>>>>> webbrowser, so >>>>>>>>>>>>>> >>> that you can check the filelds easier. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios -- >>>>>>>>>>>>>> >>> Great, sounds like more progress. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're >>>>>>>>>>>>>> getting an Endian >>>>>>>>>>>>>> >>> warning. (it's a warning not an error, correct?) >>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all >>>>>>>>>>>>>> successfully >>>>>>>>>>>>>> >>> relabelled, after the command ran? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> You can use also our DICAT tool ( >>>>>>>>>>>>>> https://github.com/aces/DICAT) to >>>>>>>>>>>>>> >>> verify and/or update local DICOM headers -- though your >>>>>>>>>>>>>> dcmodify command is >>>>>>>>>>>>>> >>> a great and fast solution for bulk header updates. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> If you're concerned about fields being changed (e.g. >>>>>>>>>>>>>> "(2001,105f)" from >>>>>>>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM >>>>>>>>>>>>>> slice before and look >>>>>>>>>>>>>> >>> at these fields specifically. >>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS >>>>>>>>>>>>>> before/after >>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff >>>>>>>>>>>>>> the outputs -- >>>>>>>>>>>>>> >>> this will pinpoint what changed. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not >>>>>>>>>>>>>> recognized or >>>>>>>>>>>>>> >>> unknown : this means your scans did not match what is >>>>>>>>>>>>>> stored in your >>>>>>>>>>>>>> >>> mri_protocol table. >>>>>>>>>>>>>> >>> Check the MRI Violations front-end module -- can you see >>>>>>>>>>>>>> why they didn't >>>>>>>>>>>>>> >>> match? >>>>>>>>>>>>>> >>> Send us an example, in addition to the contents of the >>>>>>>>>>>>>> mri_protocol >>>>>>>>>>>>>> >>> table, if you can't find the source of the mismatch. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Here is the psc table >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I created 2 candidates profiles through the interface >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1" >>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> and got those warning: is this okay? >>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined >>>>>>>>>>>>>> length, reading a >>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit >>>>>>>>>>>>>> (CP-246) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you >>>>>>>>>>>>>> can see the >>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could not be >>>>>>>>>>>>>> inserted due to >>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Running now the following command: >>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/ >>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12 >>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name >>>>>>>>>>>>>> '__MACOSX' >>>>>>>>>>>>>> >>> -delete >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs >>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod >>>>>>>>>>>>>> -verbose >>>>>>>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Testing for database connectivity. >>>>>>>>>>>>>> >>> Database is available. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> You are creating a tar with the following command: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> tar -cf >>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> getting md5sums and gzipping!! >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs >>>>>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>>>>> >>> * Archived on : 2019-09-06 >>>>>>>>>>>>>> 18:36:50 >>>>>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814 >>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f >>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz >>>>>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e >>>>>>>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Adding archive info into database >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Removing temporary files from target location >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Done adding archive info into database >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl >>>>>>>>>>>>>> -globLocation >>>>>>>>>>>>>> >>> -profile prod >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar >>>>>>>>>>>>>> >>> -uploadID 12 -verbose >>>>>>>>>>>>>> >>> md5sum >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>>> >>> Set centerID = 1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Number of MINC files that will be considered for >>>>>>>>>>>>>> inserting into the >>>>>>>>>>>>>> >>> database: 2 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is >>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> PSCID is: DCC0001 >>>>>>>>>>>>>> >>> CandID id: 602102 >>>>>>>>>>>>>> >>> visit_label is: V1 >>>>>>>>>>>>>> >>> candidate id 602102 >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf >>>>>>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs* >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>> cat >>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ==> Loading file from disk >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> --> mapping DICOM parameter for >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ==> verifying acquisition protocol >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Acquisition protocol is unknown >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> --> The minc file cannot be registered since the >>>>>>>>>>>>>> AcquisitionProtocol >>>>>>>>>>>>>> >>> is unknown >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the >>>>>>>>>>>>>> *delete_imaging_upload* >>>>>>>>>>>>>> >>> script -- >>>>>>>>>>>>>> >>> details here: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> What's in your *psc* table? (Is it properly populated? >>>>>>>>>>>>>> This is a >>>>>>>>>>>>>> >>> pre-requisite to loading imaging data. >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> ) >>>>>>>>>>>>>> >>> The foreign key constraint error on the candidate record >>>>>>>>>>>>>> is curious. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> There are also a few options for creating candidates when >>>>>>>>>>>>>> inserting >>>>>>>>>>>>>> >>> imaging data: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM >>>>>>>>>>>>>> insertion pipeline >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and >>>>>>>>>>>>>> visits, optionally I >>>>>>>>>>>>>> >>> think) >>>>>>>>>>>>>> >>> How to: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api >>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Then as a second step: >>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> to load your DICOMs. >>>>>>>>>>>>>> >>> You will want to first ensure that the PatientName header >>>>>>>>>>>>>> in the DICOMs >>>>>>>>>>>>>> >>> as well as tar package are correctly labelled with >>>>>>>>>>>>>> PSCID_DCCID_VisitLabel >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets: >>>>>>>>>>>>>> >>> How to : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the >>>>>>>>>>>>>> bids_import script, >>>>>>>>>>>>>> >>> to automatically create your candidates and sessions. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i have to >>>>>>>>>>>>>> create a new >>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> *First execution:* >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>> ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>>>>> >>> log.txt >>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child >>>>>>>>>>>>>> row: a foreign >>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT >>>>>>>>>>>>>> `FK_candidate_1` >>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` >>>>>>>>>>>>>> (`CenterID`)) at >>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line >>>>>>>>>>>>>> 1060. >>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner: >>>>>>>>>>>>>> >>> The following database commands failed: >>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner >>>>>>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES >>>>>>>>>>>>>> (?,?,?,?,?)'; >>>>>>>>>>>>>> >>> SET >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips >>>>>>>>>>>>>> >>> Medical Systems'; >>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5; >>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a >>>>>>>>>>>>>> foreign key >>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT >>>>>>>>>>>>>> `FK_mri_scanner_1` >>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) >>>>>>>>>>>>>> (error code 1452) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ERROR: The validation has failed. Either re-run the >>>>>>>>>>>>>> validation again >>>>>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using >>>>>>>>>>>>>> -force to force the >>>>>>>>>>>>>> >>> execution. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed. >>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>>> >>> line 250. >>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>>> >>> line 251. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> *And second execution: * >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ >>>>>>>>>>>>>> ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod < >>>>>>>>>>>>>> ~/Desktop/input.txt > >>>>>>>>>>>>>> >>> log.txt >>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> PROBLEM: >>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study. >>>>>>>>>>>>>> >>> The unique study ID is >>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'. >>>>>>>>>>>>>> >>> This is the information retained from the first time the >>>>>>>>>>>>>> study was >>>>>>>>>>>>>> >>> inserted: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> * Taken from dir : >>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy >>>>>>>>>>>>>> >>> * Archive target location : >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1 >>>>>>>>>>>>>> >>> * Name of host OS : Linux >>>>>>>>>>>>>> >>> * Created by user : lorisadmin >>>>>>>>>>>>>> >>> * Archived on : 2019-09-04 >>>>>>>>>>>>>> 18:33:05 >>>>>>>>>>>>>> >>> * dicomSummary version : 1 >>>>>>>>>>>>>> >>> * dicomTar version : 1 >>>>>>>>>>>>>> >>> * md5sum for DICOM tarball : >>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d >>>>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped : >>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec >>>>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz >>>>>>>>>>>>>> >>> * md5sum for complete archive : >>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053 >>>>>>>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Last update of record: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed. >>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./ >>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249. >>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>>> >>> line 250. >>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./ >>>>>>>>>>>>>> batch_uploads_imageuploader.pl >>>>>>>>>>>>>> >>> line 251. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Ok, this sounds like good progress. Let us know when you >>>>>>>>>>>>>> next encounter >>>>>>>>>>>>>> >>> issues as you progress through the Imaging Install/Setup >>>>>>>>>>>>>> docs >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md >>>>>>>>>>>>>> >. >>>>>>>>>>>>>> >>> I'll look into how we can better handle the incoming/ >>>>>>>>>>>>>> directory next >>>>>>>>>>>>>> >>> time. >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos >>>>>>>>>>>>>> < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is >>>>>>>>>>>>>> >>> populated correctly except its port is 'port' : ''. >>>>>>>>>>>>>> Also i have tested >>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> I executed the script again, because the only error i had >>>>>>>>>>>>>> previously was >>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and there are >>>>>>>>>>>>>> no errors >>>>>>>>>>>>>> >>> reported back except of warnings <>>>>>>>>>>>>> a password on the >>>>>>>>>>>>>> >>> command line interface can be insecure>>. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> It's possible -- if the script was unable to connect to >>>>>>>>>>>>>> the database >>>>>>>>>>>>>> >>> during its execution (e.g. typo in the password), that >>>>>>>>>>>>>> would explain the >>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw >>>>>>>>>>>>>> in the Config >>>>>>>>>>>>>> >>> module. >>>>>>>>>>>>>> >>> It's hard to tell without seeing the output from your >>>>>>>>>>>>>> script run -- Did >>>>>>>>>>>>>> >>> you see a sign of any such error? >>>>>>>>>>>>>> >>> The Config fields are populated by the imaging_install.sh >>>>>>>>>>>>>> script (starting >>>>>>>>>>>>>> >>> at line 222 >>>>>>>>>>>>>> >>> < >>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222 >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>> ) >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> For example, check if the database connection information >>>>>>>>>>>>>> was populated >>>>>>>>>>>>>> >>> accurately in >>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Christine, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>> image with the >>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>> the last part >>>>>>>>>>>>>> >>> which asks to configure as much as possible automatically? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine >>>>>>>>>>>>>> Rogers, Ms. < >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi Sotirios, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and working >>>>>>>>>>>>>> and all the >>>>>>>>>>>>>> >>> front-end pages are loading. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 >>>>>>>>>>>>>> project >>>>>>>>>>>>>> >>> > and the web interface worked. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775 permissions >>>>>>>>>>>>>> and that >>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in >>>>>>>>>>>>>> the install >>>>>>>>>>>>>> >>> Readme . >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should >>>>>>>>>>>>>> change LORIS to >>>>>>>>>>>>>> >>> loris, right? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> These imaging paths will be updated during your imaging >>>>>>>>>>>>>> installation >>>>>>>>>>>>>> >>> by an >>>>>>>>>>>>>> automated script -- >>>>>>>>>>>>>> >>> you do not need to set them manually via the Config >>>>>>>>>>>>>> module. >>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide >>>>>>>>>>>>>> >>> for detailed >>>>>>>>>>>>>> steps to follow. >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Best, >>>>>>>>>>>>>> >>> Christine >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change >>>>>>>>>>>>>> LORIS to loris, >>>>>>>>>>>>>> >>> right? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> [image: image.png] >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios >>>>>>>>>>>>>> Nikoloutsopoulos < >>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????: >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Hi, >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> i used >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E >>>>>>>>>>>>>> bash - >>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> you had suggested in the past, make worked and now i can >>>>>>>>>>>>>> see all the >>>>>>>>>>>>>> >>> contents in the web-interface, but i don't need make >>>>>>>>>>>>>> install? >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> Thanks >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> -- >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca >>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>>>>> >>> Montreal Neurological Institute >>>>>>>>>>>>>> >>> McGill University | Montreal | Canada >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> _______________________________________________ >>>>>>>>>>>>>> >>> Loris-dev mailing list >>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> >>> >>>>>>>>>>>>>> -------------- next part -------------- >>>>>>>>>>>>>> An HTML attachment was scrubbed... >>>>>>>>>>>>>> URL: < >>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html >>>>>>>>>>>>>> > >>>>>>>>>>>>>> >>>>>>>>>>>>>> ------------------------------ >>>>>>>>>>>>>> >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16 >>>>>>>>>>>>>> ***************************************** >>>>>>>>>>>>>> >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> >>>>>>>>>>> christine.rogers at mcgill.ca >>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University | Montreal | Canada >>>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... 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