From sotirisnik at gmail.com Sun Sep 1 15:19:41 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sun, 1 Sep 2019 22:19:41 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 i installed composer 1.9 with these following commands. curl -sS https://getcomposer.org/installer -o composer-setup.php php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer And afterwards composer install worked and the only warning i got at the end of the installation was <> And from the loris-error.log [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Mon Sep 2 15:16:11 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 2 Sep 2019 22:16:11 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, it there a solution for this? https://github.com/aces/Loris/issues/3313 I need to meet a deadline about Loris by the end of September. Thanks ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi, > based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 > > i installed composer 1.9 with these following commands. > > > curl -sS https://getcomposer.org/installer -o composer-setup.php > > php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" > sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer > > And afterwards composer install worked and the only warning i got at the end of the installation was > > < Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested. > Package phpunit/dbunit is abandoned, you should avoid using it. No replacement was suggested.>> > > And from the loris-error.log > > [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon Sep 2 19:47:06 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Mon, 2 Sep 2019 23:47:06 +0000 Subject: [Loris-dev] Questions regarding querying LORIS In-Reply-To: References: Message-ID: Hi Remya, Thanks for your inquiry -- 1. If we have data stored on several instruments within LORIS, is it possible to query, filter and export specific data that we need into a CSV file (or any spreadsheet) using the LORIS interface? If not, is this a feature currently being developed? Yes, the Data Querying Tool (DQT) module is designed for precisely that purpose. Try it out at demo.loris.ca -- you'll find this module under the "Tools" menu. The Data Querying Tool allows users to design, save and share custom queries, and to download the results as a CSV file, though the LORIS front-end. Users can query and filter specific data fields or whole instruments across timepoints, including metadata, demographic data, and imaging data. The DQT is also extensible for genomic data. For example, a user can filter for only female subjects that have a T1 scan completed, and have an IQ score above a certain threshold, etc. 2. Currently we understand the way to do mass uploads of data into a LORIS instrument is via the database directly. Is there any way to upload data into an instrument directly from a CSV instead (or any spreadsheet format file)? A module to load instrument data via the front-end is in our Roadmap for development; for the present we recommend a simple script to load instruments fields from a CSV into the corresponding database table field. Storing files in LORIS attached to a participant-timepoint (without processing the data contents), can also be done via the Media Module. Best, Christine The LORIS team On Fri, Aug 30, 2019 at 5:44 PM Remya Nair > wrote: Hi, We have a couple of questions that we were hoping the LORIS developers might be able to help with. Apologies if this has been answered previously on this forum. 1. If we have data stored on several instruments within LORIS, is it possible to query, filter and export specific data that we need into a CSV file (or any spreadsheet) using the LORIS interface? If not, is this a feature currently being developed? 2. Currently we understand the way to do mass uploads of data into a LORIS instrument is via the database directly. Is there any way to upload data into an instrument directly from a CSV instead (or any spreadsheet format file)? Your take on the above questions would be greatly appreciated. Thank you in advance for your help. Best, Remya -- _______________________________________________ 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 sotirisnik at gmail.com Tue Sep 3 08:08:44 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 3 Sep 2019 15:08:44 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, i didn't remember that config.xml was being created during the execution of installdb.php. Now am i getting white content on the pages only because fontawesome is missing? Was that part of the composer install? because i hadn't such error. Thanks [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/ [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_browser/ [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_uploader/ [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/examiner/ [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/conflict_resolver/ [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_browser/ [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/dicom_archive/ [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_uploader/ ???? ???, 2 ??? 2019 ???? 10:16 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Hi, > > it there a solution for this? > https://github.com/aces/Loris/issues/3313 > > I need to meet a deadline about Loris by the end of September. > > Thanks > > ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> Hi, >> based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 >> >> i installed composer 1.9 with these following commands. >> >> >> curl -sS https://getcomposer.org/installer -o composer-setup.php >> >> php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" >> sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer >> >> And afterwards composer install worked and the only warning i got at the end of the installation was >> >> <> Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested. >> Package phpunit/dbunit is abandoned, you should avoid using it. No replacement was suggested.>> >> >> And from the loris-error.log >> >> [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Tue Sep 3 08:48:29 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 3 Sep 2019 12:48:29 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi Sotirios, You've got your LORIS up and running, and are running into font library issues? great. The symlink under htdocs/ for fontawesome is supposed to point to: ./../node_modules/@fortawesome/fontawesome-free/ (see: https://github.com/aces/Loris/blob/21.0-release/htdocs/fontawesome ) This sounds like it may be a permissions issue, or with your node modules. Can you give us more specifics on the permissions in your htdocs directory and if any other links or packages look funny? You have run composer commands but not the makefile, is that correct? Note we have an even newer stable release out already: 21.0.1 Best, Christine On Tue, Sep 3, 2019 at 8:09 AM Sotirios Nikoloutsopoulos > wrote: Hi, i didn't remember that config.xml was being created during the execution of installdb.php. Now am i getting white content on the pages only because fontawesome is missing? Was that part of the composer install? because i hadn't such error. Thanks [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/ [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_browser/ [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_uploader/ [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/examiner/ [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/conflict_resolver/ [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_browser/ [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/dicom_archive/ [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_uploader/ ???? ???, 2 ??? 2019 ???? 10:16 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, it there a solution for this? https://github.com/aces/Loris/issues/3313 I need to meet a deadline about Loris by the end of September. Thanks ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 i installed composer 1.9 with these following commands. curl -sS https://getcomposer.org/installer -o composer-setup.php php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer And afterwards composer install worked and the only warning i got at the end of the installation was <> And from the loris-error.log [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 _______________________________________________ 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 sotirisnik at gmail.com Tue Sep 3 09:20:58 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 3 Sep 2019 16:20:58 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: It seems that the links's point is correct. And yes i only runned composer not the makefile. lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ ls -l total 116 drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 acknowledgements -rw-r--r-- 1 lorisadmin lorisadmin 3217 ???? 23 20:37 AjaxHelper.php drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 api drwxr-xr-x 5 lorisadmin lorisadmin 4096 ???? 23 20:37 bootstrap drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 css -rw-r--r-- 1 lorisadmin lorisadmin 7730 ???? 23 20:37 direct.css -rw-r--r-- 1 lorisadmin lorisadmin 5361 ???? 23 20:37 feedback_mri_popup.php lrwxrwxrwx 1 lorisadmin lorisadmin 48 ??? 31 02:17 fontawesome -> ./../node_modules/@fortawesome/fontawesome-free/ drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 images -rw-r--r-- 1 lorisadmin lorisadmin 2040 ???? 23 20:37 index.php -rw-r--r-- 1 lorisadmin lorisadmin 8311 ???? 23 20:37 installdb.php drwxr-xr-x 11 lorisadmin lorisadmin 4096 ???? 23 20:37 js -rw-r--r-- 1 lorisadmin lorisadmin 12640 ???? 23 20:37 main.css -rw-r--r-- 1 lorisadmin lorisadmin 9189 ???? 23 20:37 main.php drwxr-xr-x 3 lorisadmin lorisadmin 4096 ???? 23 20:37 mri -rw-r--r-- 1 lorisadmin lorisadmin 2532 ???? 23 20:37 postdeploy.php -rw-r--r-- 1 lorisadmin lorisadmin 2293 ???? 23 20:37 router.php -rw-r--r-- 1 lorisadmin lorisadmin 12131 ???? 23 20:37 survey.php drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 vendor ???? ???, 3 ??? 2019 ???? 3:48 ?.?., ?/? Christine Rogers, Ms. < christine.rogers at mcgill.ca> ??????: > Hi Sotirios, > You've got your LORIS up and running, and are running into font library > issues? great. > > The symlink under htdocs/ for fontawesome is supposed to point to: > ./../node_modules/@fortawesome/fontawesome-free/ > (see: https://github.com/aces/Loris/blob/21.0-release/htdocs/fontawesome > ) > This sounds like it may be a permissions issue, or with your node modules. > Can you give us more specifics on the permissions in your htdocs directory > and if any other links or packages look funny? > > You have run composer commands but not the makefile, is that correct? > > Note we have an even newer stable release out already: 21.0.1 > > > Best, > Christine > > On Tue, Sep 3, 2019 at 8:09 AM Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> wrote: > >> Hi, >> >> i didn't remember that config.xml was being created during the execution >> of installdb.php. Now am i getting white content on the pages only because >> fontawesome is missing? Was that part of the composer install? because i >> hadn't such error. >> >> Thanks >> >> [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client >> 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target not >> accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/ >> [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client >> 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target not >> accessible: /var/www/loris/htdocs/fontawesome, referer: >> http://localhost/imaging_browser/ >> [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client >> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >> accessible: /var/www/loris/htdocs/fontawesome, referer: >> http://localhost/imaging_uploader/ >> [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client >> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >> accessible: /var/www/loris/htdocs/fontawesome, referer: >> http://localhost/examiner/ >> [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client >> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >> accessible: /var/www/loris/htdocs/fontawesome, referer: >> http://localhost/conflict_resolver/ >> [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client >> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >> accessible: /var/www/loris/htdocs/fontawesome, referer: >> http://localhost/imaging_browser/ >> [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client >> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >> accessible: /var/www/loris/htdocs/fontawesome, referer: >> http://localhost/dicom_archive/ >> [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client >> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >> accessible: /var/www/loris/htdocs/fontawesome, referer: >> http://localhost/imaging_uploader/ >> >> ???? ???, 2 ??? 2019 ???? 10:16 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> Hi, >>> >>> it there a solution for this? >>> https://github.com/aces/Loris/issues/3313 >>> >>> I need to meet a deadline about Loris by the end of September. >>> >>> Thanks >>> >>> ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> Hi, >>>> based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 >>>> >>>> i installed composer 1.9 with these following commands. >>>> >>>> >>>> curl -sS https://getcomposer.org/installer -o composer-setup.php >>>> >>>> php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" >>>> sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer >>>> >>>> And afterwards composer install worked and the only warning i got at the end of the installation was >>>> >>>> <>>> Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested. >>>> Package phpunit/dbunit is abandoned, you should avoid using it. No replacement was suggested.>> >>>> >>>> And from the loris-error.log >>>> >>>> [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 >>>> >>>> _______________________________________________ >> 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 sotirisnik at gmail.com Tue Sep 3 14:39:18 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 3 Sep 2019 21:39:18 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: I tried to change the permissions but afterwards i got the previous error again that was reporting that could not find the the config.xml, although now the config.xml exists ... I also execute * sudo chown -**R **lorisadmin.lorisadmin /var/www/**l**oris* *to reverse what i did but it didn't work.* [Tue Sep 03 21:32:56.993915 2019] [php7:error] [pid 5819] [client 127.0.0.1:40460] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 [image: image.png] Lastly i tried to re-create the config.xml using the installdb.php but now it couldn't write to the directory. [image: image.png] ???? ???, 3 ??? 2019 ???? 4:20 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > It seems that the links's point is correct. And yes i only runned composer > not the makefile. > > lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ ls -l > total 116 > drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 acknowledgements > -rw-r--r-- 1 lorisadmin lorisadmin 3217 ???? 23 20:37 AjaxHelper.php > drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 api > drwxr-xr-x 5 lorisadmin lorisadmin 4096 ???? 23 20:37 bootstrap > drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 css > -rw-r--r-- 1 lorisadmin lorisadmin 7730 ???? 23 20:37 direct.css > -rw-r--r-- 1 lorisadmin lorisadmin 5361 ???? 23 20:37 > feedback_mri_popup.php > lrwxrwxrwx 1 lorisadmin lorisadmin 48 ??? 31 02:17 fontawesome -> > ./../node_modules/@fortawesome/fontawesome-free/ > drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 images > -rw-r--r-- 1 lorisadmin lorisadmin 2040 ???? 23 20:37 index.php > -rw-r--r-- 1 lorisadmin lorisadmin 8311 ???? 23 20:37 installdb.php > drwxr-xr-x 11 lorisadmin lorisadmin 4096 ???? 23 20:37 js > -rw-r--r-- 1 lorisadmin lorisadmin 12640 ???? 23 20:37 main.css > -rw-r--r-- 1 lorisadmin lorisadmin 9189 ???? 23 20:37 main.php > drwxr-xr-x 3 lorisadmin lorisadmin 4096 ???? 23 20:37 mri > -rw-r--r-- 1 lorisadmin lorisadmin 2532 ???? 23 20:37 postdeploy.php > -rw-r--r-- 1 lorisadmin lorisadmin 2293 ???? 23 20:37 router.php > -rw-r--r-- 1 lorisadmin lorisadmin 12131 ???? 23 20:37 survey.php > drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 vendor > > ???? ???, 3 ??? 2019 ???? 3:48 ?.?., ?/? Christine Rogers, Ms. < > christine.rogers at mcgill.ca> ??????: > >> Hi Sotirios, >> You've got your LORIS up and running, and are running into font library >> issues? great. >> >> The symlink under htdocs/ for fontawesome is supposed to point to: >> ./../node_modules/@fortawesome/fontawesome-free/ >> (see: https://github.com/aces/Loris/blob/21.0-release/htdocs/fontawesome >> ) >> This sounds like it may be a permissions issue, or with your node >> modules. >> Can you give us more specifics on the permissions in your htdocs >> directory and if any other links or packages look funny? >> >> You have run composer commands but not the makefile, is that correct? >> >> Note we have an even newer stable release out already: 21.0.1 >> >> >> Best, >> Christine >> >> On Tue, Sep 3, 2019 at 8:09 AM Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> wrote: >> >>> Hi, >>> >>> i didn't remember that config.xml was being created during the execution >>> of installdb.php. Now am i getting white content on the pages only because >>> fontawesome is missing? Was that part of the composer install? because i >>> hadn't such error. >>> >>> Thanks >>> >>> [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client >>> 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target not >>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>> http://localhost/ >>> [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client >>> 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target not >>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>> http://localhost/imaging_browser/ >>> [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client >>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>> http://localhost/imaging_uploader/ >>> [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client >>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>> http://localhost/examiner/ >>> [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client >>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>> http://localhost/conflict_resolver/ >>> [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client >>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>> http://localhost/imaging_browser/ >>> [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client >>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>> http://localhost/dicom_archive/ >>> [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client >>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>> http://localhost/imaging_uploader/ >>> >>> ???? ???, 2 ??? 2019 ???? 10:16 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> Hi, >>>> >>>> it there a solution for this? >>>> https://github.com/aces/Loris/issues/3313 >>>> >>>> I need to meet a deadline about Loris by the end of September. >>>> >>>> Thanks >>>> >>>> ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> ??????: >>>> >>>>> Hi, >>>>> based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 >>>>> >>>>> i installed composer 1.9 with these following commands. >>>>> >>>>> >>>>> curl -sS https://getcomposer.org/installer -o composer-setup.php >>>>> >>>>> php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" >>>>> sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer >>>>> >>>>> And afterwards composer install worked and the only warning i got at the end of the installation was >>>>> >>>>> <>>>> Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested. >>>>> Package phpunit/dbunit is abandoned, you should avoid using it. No replacement was suggested.>> >>>>> >>>>> And from the loris-error.log >>>>> >>>>> [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 >>>>> >>>>> _______________________________________________ >>> 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 292458 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 74697 bytes Desc: not available URL: From christine.rogers at mcgill.ca Tue Sep 3 14:49:23 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 3 Sep 2019 18:49:23 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Thanks Sotirios, those details help. Try the following and let us know what happens: cd /var/www/loris make sudo vi /var/www/loris/project/config.xml --> copy-paste the content shown in your installdb.php screen. make sure the file saves sudo chown -R lorisadmin:lorisadmin ./ sudo service apache2 restart let us know -- Christine On Tue, Sep 3, 2019 at 2:39 PM Sotirios Nikoloutsopoulos > wrote: I tried to change the permissions but afterwards i got the previous error again that was reporting that could not find the the config.xml, although now the config.xml exists ... I also execute sudo chown -R lorisadmin.lorisadmin /var/www/loris to reverse what i did but it didn't work. [Tue Sep 03 21:32:56.993915 2019] [php7:error] [pid 5819] [client 127.0.0.1:40460] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 [image.png] Lastly i tried to re-create the config.xml using the installdb.php but now it couldn't write to the directory. [image.png] ???? ???, 3 ??? 2019 ???? 4:20 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: It seems that the links's point is correct. And yes i only runned composer not the makefile. lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ ls -l total 116 drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 acknowledgements -rw-r--r-- 1 lorisadmin lorisadmin 3217 ???? 23 20:37 AjaxHelper.php drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 api drwxr-xr-x 5 lorisadmin lorisadmin 4096 ???? 23 20:37 bootstrap drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 css -rw-r--r-- 1 lorisadmin lorisadmin 7730 ???? 23 20:37 direct.css -rw-r--r-- 1 lorisadmin lorisadmin 5361 ???? 23 20:37 feedback_mri_popup.php lrwxrwxrwx 1 lorisadmin lorisadmin 48 ??? 31 02:17 fontawesome -> ./../node_modules/@fortawesome/fontawesome-free/ drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 images -rw-r--r-- 1 lorisadmin lorisadmin 2040 ???? 23 20:37 index.php -rw-r--r-- 1 lorisadmin lorisadmin 8311 ???? 23 20:37 installdb.php drwxr-xr-x 11 lorisadmin lorisadmin 4096 ???? 23 20:37 js -rw-r--r-- 1 lorisadmin lorisadmin 12640 ???? 23 20:37 main.css -rw-r--r-- 1 lorisadmin lorisadmin 9189 ???? 23 20:37 main.php drwxr-xr-x 3 lorisadmin lorisadmin 4096 ???? 23 20:37 mri -rw-r--r-- 1 lorisadmin lorisadmin 2532 ???? 23 20:37 postdeploy.php -rw-r--r-- 1 lorisadmin lorisadmin 2293 ???? 23 20:37 router.php -rw-r--r-- 1 lorisadmin lorisadmin 12131 ???? 23 20:37 survey.php drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 vendor ???? ???, 3 ??? 2019 ???? 3:48 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, You've got your LORIS up and running, and are running into font library issues? great. The symlink under htdocs/ for fontawesome is supposed to point to: ./../node_modules/@fortawesome/fontawesome-free/ (see: https://github.com/aces/Loris/blob/21.0-release/htdocs/fontawesome ) This sounds like it may be a permissions issue, or with your node modules. Can you give us more specifics on the permissions in your htdocs directory and if any other links or packages look funny? You have run composer commands but not the makefile, is that correct? Note we have an even newer stable release out already: 21.0.1 Best, Christine On Tue, Sep 3, 2019 at 8:09 AM Sotirios Nikoloutsopoulos > wrote: Hi, i didn't remember that config.xml was being created during the execution of installdb.php. Now am i getting white content on the pages only because fontawesome is missing? Was that part of the composer install? because i hadn't such error. Thanks [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/ [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_browser/ [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_uploader/ [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/examiner/ [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/conflict_resolver/ [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_browser/ [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/dicom_archive/ [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not accessible: /var/www/loris/htdocs/fontawesome, referer: http://localhost/imaging_uploader/ ???? ???, 2 ??? 2019 ???? 10:16 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, it there a solution for this? https://github.com/aces/Loris/issues/3313 I need to meet a deadline about Loris by the end of September. Thanks ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: Hi, based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 i installed composer 1.9 with these following commands. curl -sS https://getcomposer.org/installer -o composer-setup.php php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer And afterwards composer install worked and the only warning i got at the end of the installation was <> And from the loris-error.log [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 292458 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 74697 bytes Desc: image.png URL: From wangshen.mcin at gmail.com Tue Sep 3 14:57:33 2019 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 3 Sep 2019 14:57:33 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Hi, you need to make a config.xml manually. Step 1: go to project folder. cd /var/www/loris/project; Step 2: touch config.xml; Step 3: paste all the xml content to config.xml file. then reload the localhost page. It should work. Sotirios Nikoloutsopoulos ?2019?9?3? ????2:39??? > I tried to change the permissions but afterwards i got the previous error > again that was reporting that could not find the the config.xml, although > now the config.xml exists ... I also execute > * sudo chown -**R **lorisadmin.lorisadmin /var/www/**l**oris* > > > *to reverse what i did but it didn't work.* > > [Tue Sep 03 21:32:56.993915 2019] [php7:error] [pid 5819] [client > 127.0.0.1:40460] PHP Fatal error: Uncaught ConfigurationException: > Config file config.xml does not exist in the defined locations. in > /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 > /var/www/loris/php/libraries/NDB_Config.class.inc(66): > NDB_Config->configFilePath()\n#1 > /var/www/loris/php/libraries/NDB_Factory.class.inc(118): > NDB_Config::singleton(NULL)\n#2 > /var/www/loris/php/libraries/NDB_Client.class.inc(54): > NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): > NDB_Client->initialize()\n#4 {main}\n thrown in > /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 > > [image: image.png] > > Lastly i tried to re-create the config.xml using the installdb.php but now > it couldn't write to the directory. > > [image: image.png] > > > ???? ???, 3 ??? 2019 ???? 4:20 ?.?., ?/? Sotirios Nikoloutsopoulos < > sotirisnik at gmail.com> ??????: > >> It seems that the links's point is correct. And yes i only runned >> composer not the makefile. >> >> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ ls -l >> total 116 >> drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 acknowledgements >> -rw-r--r-- 1 lorisadmin lorisadmin 3217 ???? 23 20:37 AjaxHelper.php >> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 api >> drwxr-xr-x 5 lorisadmin lorisadmin 4096 ???? 23 20:37 bootstrap >> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 css >> -rw-r--r-- 1 lorisadmin lorisadmin 7730 ???? 23 20:37 direct.css >> -rw-r--r-- 1 lorisadmin lorisadmin 5361 ???? 23 20:37 >> feedback_mri_popup.php >> lrwxrwxrwx 1 lorisadmin lorisadmin 48 ??? 31 02:17 fontawesome -> >> ./../node_modules/@fortawesome/fontawesome-free/ >> drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 images >> -rw-r--r-- 1 lorisadmin lorisadmin 2040 ???? 23 20:37 index.php >> -rw-r--r-- 1 lorisadmin lorisadmin 8311 ???? 23 20:37 installdb.php >> drwxr-xr-x 11 lorisadmin lorisadmin 4096 ???? 23 20:37 js >> -rw-r--r-- 1 lorisadmin lorisadmin 12640 ???? 23 20:37 main.css >> -rw-r--r-- 1 lorisadmin lorisadmin 9189 ???? 23 20:37 main.php >> drwxr-xr-x 3 lorisadmin lorisadmin 4096 ???? 23 20:37 mri >> -rw-r--r-- 1 lorisadmin lorisadmin 2532 ???? 23 20:37 postdeploy.php >> -rw-r--r-- 1 lorisadmin lorisadmin 2293 ???? 23 20:37 router.php >> -rw-r--r-- 1 lorisadmin lorisadmin 12131 ???? 23 20:37 survey.php >> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 vendor >> >> ???? ???, 3 ??? 2019 ???? 3:48 ?.?., ?/? Christine Rogers, Ms. < >> christine.rogers at mcgill.ca> ??????: >> >>> Hi Sotirios, >>> You've got your LORIS up and running, and are running into font library >>> issues? great. >>> >>> The symlink under htdocs/ for fontawesome is supposed to point to: >>> ./../node_modules/@fortawesome/fontawesome-free/ >>> (see: >>> https://github.com/aces/Loris/blob/21.0-release/htdocs/fontawesome ) >>> This sounds like it may be a permissions issue, or with your node >>> modules. >>> Can you give us more specifics on the permissions in your htdocs >>> directory and if any other links or packages look funny? >>> >>> You have run composer commands but not the makefile, is that correct? >>> >>> Note we have an even newer stable release out already: 21.0.1 >>> >>> >>> Best, >>> Christine >>> >>> On Tue, Sep 3, 2019 at 8:09 AM Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> wrote: >>> >>>> Hi, >>>> >>>> i didn't remember that config.xml was being created during the >>>> execution of installdb.php. Now am i getting white content on the pages >>>> only because fontawesome is missing? Was that part of the composer install? >>>> because i hadn't such error. >>>> >>>> Thanks >>>> >>>> [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client >>>> 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target not >>>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>>> http://localhost/ >>>> [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client >>>> 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target not >>>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>>> http://localhost/imaging_browser/ >>>> [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client >>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>>> http://localhost/imaging_uploader/ >>>> [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client >>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>>> http://localhost/examiner/ >>>> [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client >>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>>> http://localhost/conflict_resolver/ >>>> [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client >>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>>> http://localhost/imaging_browser/ >>>> [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client >>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>>> http://localhost/dicom_archive/ >>>> [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client >>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target not >>>> accessible: /var/www/loris/htdocs/fontawesome, referer: >>>> http://localhost/imaging_uploader/ >>>> >>>> ???? ???, 2 ??? 2019 ???? 10:16 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> ??????: >>>> >>>>> Hi, >>>>> >>>>> it there a solution for this? >>>>> https://github.com/aces/Loris/issues/3313 >>>>> >>>>> I need to meet a deadline about Loris by the end of September. >>>>> >>>>> Thanks >>>>> >>>>> ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>>> Hi, >>>>>> based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 >>>>>> >>>>>> i installed composer 1.9 with these following commands. >>>>>> >>>>>> >>>>>> curl -sS https://getcomposer.org/installer -o composer-setup.php >>>>>> >>>>>> php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" >>>>>> sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer >>>>>> >>>>>> And afterwards composer install worked and the only warning i got at the end of the installation was >>>>>> >>>>>> <>>>>> Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested. >>>>>> Package phpunit/dbunit is abandoned, you should avoid using it. No replacement was suggested.>> >>>>>> >>>>>> And from the loris-error.log >>>>>> >>>>>> [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 >>>>>> >>>>>> _______________________________________________ >>>> 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 74697 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 292458 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Sep 3 15:02:05 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 3 Sep 2019 22:02:05 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Actually the current config.xml is the one from the output of the browser. On Tue, 3 Sep 2019, 21:57 Shen Wang, wrote: > Hi, > you need to make a config.xml manually. > Step 1: go to project folder. cd /var/www/loris/project; > Step 2: touch config.xml; > Step 3: paste all the xml content to config.xml file. > then reload the localhost page. > It should work. > > Sotirios Nikoloutsopoulos ?2019?9?3? ????2:39??? > >> I tried to change the permissions but afterwards i got the previous error >> again that was reporting that could not find the the config.xml, although >> now the config.xml exists ... I also execute >> * sudo chown -**R **lorisadmin.lorisadmin /var/www/**l**oris* >> >> >> *to reverse what i did but it didn't work.* >> >> [Tue Sep 03 21:32:56.993915 2019] [php7:error] [pid 5819] [client >> 127.0.0.1:40460] PHP Fatal error: Uncaught ConfigurationException: >> Config file config.xml does not exist in the defined locations. in >> /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 >> /var/www/loris/php/libraries/NDB_Config.class.inc(66): >> NDB_Config->configFilePath()\n#1 >> /var/www/loris/php/libraries/NDB_Factory.class.inc(118): >> NDB_Config::singleton(NULL)\n#2 >> /var/www/loris/php/libraries/NDB_Client.class.inc(54): >> NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): >> NDB_Client->initialize()\n#4 {main}\n thrown in >> /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 >> >> [image: image.png] >> >> Lastly i tried to re-create the config.xml using the installdb.php but >> now it couldn't write to the directory. >> >> [image: image.png] >> >> >> ???? ???, 3 ??? 2019 ???? 4:20 ?.?., ?/? Sotirios Nikoloutsopoulos < >> sotirisnik at gmail.com> ??????: >> >>> It seems that the links's point is correct. And yes i only runned >>> composer not the makefile. >>> >>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ ls -l >>> total 116 >>> drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 acknowledgements >>> -rw-r--r-- 1 lorisadmin lorisadmin 3217 ???? 23 20:37 AjaxHelper.php >>> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 api >>> drwxr-xr-x 5 lorisadmin lorisadmin 4096 ???? 23 20:37 bootstrap >>> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 css >>> -rw-r--r-- 1 lorisadmin lorisadmin 7730 ???? 23 20:37 direct.css >>> -rw-r--r-- 1 lorisadmin lorisadmin 5361 ???? 23 20:37 >>> feedback_mri_popup.php >>> lrwxrwxrwx 1 lorisadmin lorisadmin 48 ??? 31 02:17 fontawesome -> >>> ./../node_modules/@fortawesome/fontawesome-free/ >>> drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 images >>> -rw-r--r-- 1 lorisadmin lorisadmin 2040 ???? 23 20:37 index.php >>> -rw-r--r-- 1 lorisadmin lorisadmin 8311 ???? 23 20:37 installdb.php >>> drwxr-xr-x 11 lorisadmin lorisadmin 4096 ???? 23 20:37 js >>> -rw-r--r-- 1 lorisadmin lorisadmin 12640 ???? 23 20:37 main.css >>> -rw-r--r-- 1 lorisadmin lorisadmin 9189 ???? 23 20:37 main.php >>> drwxr-xr-x 3 lorisadmin lorisadmin 4096 ???? 23 20:37 mri >>> -rw-r--r-- 1 lorisadmin lorisadmin 2532 ???? 23 20:37 postdeploy.php >>> -rw-r--r-- 1 lorisadmin lorisadmin 2293 ???? 23 20:37 router.php >>> -rw-r--r-- 1 lorisadmin lorisadmin 12131 ???? 23 20:37 survey.php >>> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 vendor >>> >>> ???? ???, 3 ??? 2019 ???? 3:48 ?.?., ?/? Christine Rogers, Ms. < >>> christine.rogers at mcgill.ca> ??????: >>> >>>> Hi Sotirios, >>>> You've got your LORIS up and running, and are running into font library >>>> issues? great. >>>> >>>> The symlink under htdocs/ for fontawesome is supposed to point to: >>>> ./../node_modules/@fortawesome/fontawesome-free/ >>>> (see: >>>> https://github.com/aces/Loris/blob/21.0-release/htdocs/fontawesome ) >>>> This sounds like it may be a permissions issue, or with your node >>>> modules. >>>> Can you give us more specifics on the permissions in your htdocs >>>> directory and if any other links or packages look funny? >>>> >>>> You have run composer commands but not the makefile, is that correct? >>>> >>>> Note we have an even newer stable release out already: 21.0.1 >>>> >>>> >>>> Best, >>>> Christine >>>> >>>> On Tue, Sep 3, 2019 at 8:09 AM Sotirios Nikoloutsopoulos < >>>> sotirisnik at gmail.com> wrote: >>>> >>>>> Hi, >>>>> >>>>> i didn't remember that config.xml was being created during the >>>>> execution of installdb.php. Now am i getting white content on the pages >>>>> only because fontawesome is missing? Was that part of the composer install? >>>>> because i hadn't such error. >>>>> >>>>> Thanks >>>>> >>>>> [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client >>>>> 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target >>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>> http://localhost/ >>>>> [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client >>>>> 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target >>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>> http://localhost/imaging_browser/ >>>>> [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client >>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>> http://localhost/imaging_uploader/ >>>>> [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client >>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>> http://localhost/examiner/ >>>>> [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client >>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>> http://localhost/conflict_resolver/ >>>>> [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client >>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>> http://localhost/imaging_browser/ >>>>> [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client >>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>> http://localhost/dicom_archive/ >>>>> [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client >>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>> http://localhost/imaging_uploader/ >>>>> >>>>> ???? ???, 2 ??? 2019 ???? 10:16 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> ??????: >>>>> >>>>>> Hi, >>>>>> >>>>>> it there a solution for this? >>>>>> https://github.com/aces/Loris/issues/3313 >>>>>> >>>>>> I need to meet a deadline about Loris by the end of September. >>>>>> >>>>>> Thanks >>>>>> >>>>>> ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Hi, >>>>>>> based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 >>>>>>> >>>>>>> i installed composer 1.9 with these following commands. >>>>>>> >>>>>>> >>>>>>> curl -sS https://getcomposer.org/installer -o composer-setup.php >>>>>>> >>>>>>> php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" >>>>>>> sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer >>>>>>> >>>>>>> And afterwards composer install worked and the only warning i got at the end of the installation was >>>>>>> >>>>>>> <>>>>>> Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested. >>>>>>> Package phpunit/dbunit is abandoned, you should avoid using it. No replacement was suggested.>> >>>>>>> >>>>>>> And from the loris-error.log >>>>>>> >>>>>>> [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 >>>>>>> >>>>>>> _______________________________________________ >>>>> 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: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 292458 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 74697 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Sep 3 20:49:05 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 4 Sep 2019 03:49:05 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: About << PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139>> i checked that the variable $file outputs a valid path and that file_exists was failing for some reason. The permissions of the project folder were drwxrwx---and since there was no permissions for the other group and that must be the reasion why file_exists failed. [image: image.png] I changed the permissions to lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775 project and the web interface worked. As for the execution of make i attached the npm-debug and i am getting 404 errors for the js's components. 127.0.0.1 - - [04/Sep/2019:03:41:20 +0300] "GET /js/components/Form.js HTTP/1.1" 404 30317 "http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:20 +0300] "GET /js/components/Markdown.js HTTP/1.1" 404 30317 "http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:20 +0300] "GET /js/components/StaticDataTable.js HTTP/1.1" 404 30317 " http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:20 +0300] "GET /js/components/DynamicDataTable.js HTTP/1.1" 404 30317 " http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:21 +0300] "GET /dicom_archive/js/dicom_archive.js HTTP/1.1" 404 31039 " http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:21 +0300] "GET /js/components/Form.js HTTP/1.1" 404 30317 "http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:21 +0300] "GET /js/components/Markdown.js HTTP/1.1" 404 30317 "http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:21 +0300] "GET /js/components/PaginationLinks.js HTTP/1.1" 404 30317 " http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:21 +0300] "GET /js/components/StaticDataTable.js HTTP/1.1" 404 30317 " http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:21 +0300] "GET /js/components/DynamicDataTable.js HTTP/1.1" 404 30317 " http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:21 +0300] "GET /dicom_archive/js/dicom_archive.js HTTP/1.1" 404 31039 " http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:22 +0300] "GET /imaging_browser/ HTTP/1.1" 200 4010 "http://localhost/dicom_archive/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:22 +0300] "GET /js/components/Breadcrumbs.js HTTP/1.1" 404 30317 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:22 +0300] "GET /js/components/Form.js HTTP/1.1" 404 30317 "http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:22 +0300] "GET /js/components/PaginationLinks.js HTTP/1.1" 404 30317 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:22 +0300] "GET /js/components/Markdown.js HTTP/1.1" 404 30317 "http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:22 +0300] "GET /js/components/DynamicDataTable.js HTTP/1.1" 404 30317 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:22 +0300] "GET /js/components/StaticDataTable.js HTTP/1.1" 404 30317 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:22 +0300] "GET /imaging_browser/js/imagingBrowserIndex.js HTTP/1.1" 404 31053 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:23 +0300] "GET /imaging_browser/css/imaging_browser.css HTTP/1.1" 200 1147 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:23 +0300] "GET /js/components/Form.js HTTP/1.1" 404 30317 "http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:23 +0300] "GET /js/components/Markdown.js HTTP/1.1" 404 30317 "http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:23 +0300] "GET /js/components/PaginationLinks.js HTTP/1.1" 404 30317 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:23 +0300] "GET /js/components/StaticDataTable.js HTTP/1.1" 404 30317 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:23 +0300] "GET /js/components/DynamicDataTable.js HTTP/1.1" 404 30317 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" 127.0.0.1 - - [04/Sep/2019:03:41:23 +0300] "GET /imaging_browser/js/imagingBrowserIndex.js HTTP/1.1" 404 31053 " http://localhost/imaging_browser/" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:68.0) Gecko/20100101 Firefox/68.0" ::1 - - [04/Sep/2019:03:41:29 +0300] "OPTIONS * HTTP/1.0" 200 126 "-" "Apache/2.4.18 (Ubuntu) (internal dummy connection)" ???? ???, 3 ??? 2019 ???? 10:02 ?.?., ?/? Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> ??????: > Actually the current config.xml is the one from the output of the browser. > > On Tue, 3 Sep 2019, 21:57 Shen Wang, wrote: > >> Hi, >> you need to make a config.xml manually. >> Step 1: go to project folder. cd /var/www/loris/project; >> Step 2: touch config.xml; >> Step 3: paste all the xml content to config.xml file. >> then reload the localhost page. >> It should work. >> >> Sotirios Nikoloutsopoulos ?2019?9?3? ????2:39??? >> >>> I tried to change the permissions but afterwards i got the previous >>> error again that was reporting that could not find the the config.xml, >>> although now the config.xml exists ... I also execute >>> * sudo chown -**R **lorisadmin.lorisadmin /var/www/**l**oris* >>> >>> >>> *to reverse what i did but it didn't work.* >>> >>> [Tue Sep 03 21:32:56.993915 2019] [php7:error] [pid 5819] [client >>> 127.0.0.1:40460] PHP Fatal error: Uncaught ConfigurationException: >>> Config file config.xml does not exist in the defined locations. in >>> /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 >>> /var/www/loris/php/libraries/NDB_Config.class.inc(66): >>> NDB_Config->configFilePath()\n#1 >>> /var/www/loris/php/libraries/NDB_Factory.class.inc(118): >>> NDB_Config::singleton(NULL)\n#2 >>> /var/www/loris/php/libraries/NDB_Client.class.inc(54): >>> NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): >>> NDB_Client->initialize()\n#4 {main}\n thrown in >>> /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 >>> >>> [image: image.png] >>> >>> Lastly i tried to re-create the config.xml using the installdb.php but >>> now it couldn't write to the directory. >>> >>> [image: image.png] >>> >>> >>> ???? ???, 3 ??? 2019 ???? 4:20 ?.?., ?/? Sotirios Nikoloutsopoulos < >>> sotirisnik at gmail.com> ??????: >>> >>>> It seems that the links's point is correct. And yes i only runned >>>> composer not the makefile. >>>> >>>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ ls -l >>>> total 116 >>>> drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 acknowledgements >>>> -rw-r--r-- 1 lorisadmin lorisadmin 3217 ???? 23 20:37 AjaxHelper.php >>>> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 api >>>> drwxr-xr-x 5 lorisadmin lorisadmin 4096 ???? 23 20:37 bootstrap >>>> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 css >>>> -rw-r--r-- 1 lorisadmin lorisadmin 7730 ???? 23 20:37 direct.css >>>> -rw-r--r-- 1 lorisadmin lorisadmin 5361 ???? 23 20:37 >>>> feedback_mri_popup.php >>>> lrwxrwxrwx 1 lorisadmin lorisadmin 48 ??? 31 02:17 fontawesome -> >>>> ./../node_modules/@fortawesome/fontawesome-free/ >>>> drwxr-xr-x 2 lorisadmin lorisadmin 4096 ???? 23 20:37 images >>>> -rw-r--r-- 1 lorisadmin lorisadmin 2040 ???? 23 20:37 index.php >>>> -rw-r--r-- 1 lorisadmin lorisadmin 8311 ???? 23 20:37 installdb.php >>>> drwxr-xr-x 11 lorisadmin lorisadmin 4096 ???? 23 20:37 js >>>> -rw-r--r-- 1 lorisadmin lorisadmin 12640 ???? 23 20:37 main.css >>>> -rw-r--r-- 1 lorisadmin lorisadmin 9189 ???? 23 20:37 main.php >>>> drwxr-xr-x 3 lorisadmin lorisadmin 4096 ???? 23 20:37 mri >>>> -rw-r--r-- 1 lorisadmin lorisadmin 2532 ???? 23 20:37 postdeploy.php >>>> -rw-r--r-- 1 lorisadmin lorisadmin 2293 ???? 23 20:37 router.php >>>> -rw-r--r-- 1 lorisadmin lorisadmin 12131 ???? 23 20:37 survey.php >>>> drwxr-xr-x 4 lorisadmin lorisadmin 4096 ???? 23 20:37 vendor >>>> >>>> ???? ???, 3 ??? 2019 ???? 3:48 ?.?., ?/? Christine Rogers, Ms. < >>>> christine.rogers at mcgill.ca> ??????: >>>> >>>>> Hi Sotirios, >>>>> You've got your LORIS up and running, and are running into font >>>>> library issues? great. >>>>> >>>>> The symlink under htdocs/ for fontawesome is supposed to point to: >>>>> ./../node_modules/@fortawesome/fontawesome-free/ >>>>> (see: >>>>> https://github.com/aces/Loris/blob/21.0-release/htdocs/fontawesome ) >>>>> This sounds like it may be a permissions issue, or with your node >>>>> modules. >>>>> Can you give us more specifics on the permissions in your htdocs >>>>> directory and if any other links or packages look funny? >>>>> >>>>> You have run composer commands but not the makefile, is that correct? >>>>> >>>>> Note we have an even newer stable release out already: 21.0.1 >>>>> >>>>> >>>>> Best, >>>>> Christine >>>>> >>>>> On Tue, Sep 3, 2019 at 8:09 AM Sotirios Nikoloutsopoulos < >>>>> sotirisnik at gmail.com> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> i didn't remember that config.xml was being created during the >>>>>> execution of installdb.php. Now am i getting white content on the pages >>>>>> only because fontawesome is missing? Was that part of the composer install? >>>>>> because i hadn't such error. >>>>>> >>>>>> Thanks >>>>>> >>>>>> [Tue Sep 03 15:01:35.265016 2019] [core:error] [pid 32545] [client >>>>>> 127.0.0.1:44206] AH00037: Symbolic link not allowed or link target >>>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>>> http://localhost/ >>>>>> [Tue Sep 03 15:01:43.036540 2019] [core:error] [pid 32674] [client >>>>>> 127.0.0.1:44218] AH00037: Symbolic link not allowed or link target >>>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>>> http://localhost/imaging_browser/ >>>>>> [Tue Sep 03 15:01:45.528635 2019] [core:error] [pid 405] [client >>>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>>> http://localhost/imaging_uploader/ >>>>>> [Tue Sep 03 15:01:50.143756 2019] [core:error] [pid 405] [client >>>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>>> http://localhost/examiner/ >>>>>> [Tue Sep 03 15:01:52.938614 2019] [core:error] [pid 405] [client >>>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>>> http://localhost/conflict_resolver/ >>>>>> [Tue Sep 03 15:01:57.802263 2019] [core:error] [pid 405] [client >>>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>>> http://localhost/imaging_browser/ >>>>>> [Tue Sep 03 15:02:00.203105 2019] [core:error] [pid 405] [client >>>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>>> http://localhost/dicom_archive/ >>>>>> [Tue Sep 03 15:02:03.390223 2019] [core:error] [pid 405] [client >>>>>> 127.0.0.1:44224] AH00037: Symbolic link not allowed or link target >>>>>> not accessible: /var/www/loris/htdocs/fontawesome, referer: >>>>>> http://localhost/imaging_uploader/ >>>>>> >>>>>> ???? ???, 2 ??? 2019 ???? 10:16 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>> sotirisnik at gmail.com> ??????: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> it there a solution for this? >>>>>>> https://github.com/aces/Loris/issues/3313 >>>>>>> >>>>>>> I need to meet a deadline about Loris by the end of September. >>>>>>> >>>>>>> Thanks >>>>>>> >>>>>>> ???? ???, 1 ??? 2019 ???? 10:19 ?.?., ?/? Sotirios Nikoloutsopoulos < >>>>>>> sotirisnik at gmail.com> ??????: >>>>>>> >>>>>>>> Hi, >>>>>>>> based on this link https://www.digitalocean.com/community/tutorials/how-to-install-and-use-composer-on-ubuntu-16-04 >>>>>>>> >>>>>>>> i installed composer 1.9 with these following commands. >>>>>>>> >>>>>>>> >>>>>>>> curl -sS https://getcomposer.org/installer -o composer-setup.php >>>>>>>> >>>>>>>> php -r "if (hash_file('SHA384', 'composer-setup.php') === 'a5c698ffe4b8e849a443b120cd5ba38043260d5c4023dbf93e1558871f1f07f58274fc6f4c93bcfd858c6bd0775cd8d1') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;" >>>>>>>> sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer >>>>>>>> >>>>>>>> And afterwards composer install worked and the only warning i got at the end of the installation was >>>>>>>> >>>>>>>> <>>>>>>> Package phpunit/phpunit-mock-objects is abandoned, you should avoid using it. No replacement was suggested. >>>>>>>> Package phpunit/dbunit is abandoned, you should avoid using it. No replacement was suggested.>> >>>>>>>> >>>>>>>> And from the loris-error.log >>>>>>>> >>>>>>>> [Sun Sep 01 22:18:03.479956 2019] [php7:error] [pid 15737] [client 127.0.0.1:43560] PHP Fatal error: Uncaught ConfigurationException: Config file config.xml does not exist in the defined locations. in /var/www/loris/php/libraries/NDB_Config.class.inc:139\nStack trace:\n#0 /var/www/loris/php/libraries/NDB_Config.class.inc(66): NDB_Config->configFilePath()\n#1 /var/www/loris/php/libraries/NDB_Factory.class.inc(118): NDB_Config::singleton(NULL)\n#2 /var/www/loris/php/libraries/NDB_Client.class.inc(54): NDB_Factory->config(NULL)\n#3 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#4 {main}\n thrown in /var/www/loris/php/libraries/NDB_Config.class.inc on line 139 >>>>>>>> >>>>>>>> _______________________________________________ >>>>>> 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... 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Name: image.png Type: image/png Size: 157606 bytes Desc: not available URL: -------------- next part -------------- lorisadmin at loris-VirtualBox:/var/www/loris$ sudo cat /var/www/loris/npm-debug.log 0 info it worked if it ends with ok 1 verbose cli [ '/usr/bin/nodejs', '/usr/bin/npm', 'run', 'compile' ] 2 info using npm at 3.5.2 3 info using node at v4.2.6 4 verbose run-script [ 'precompile', 'compile', 'postcompile' ] 5 info lifecycle loris at 1.0.0~precompile: loris at 1.0.0 6 silly lifecycle loris at 1.0.0~precompile: no script for precompile, continuing 7 info lifecycle loris at 1.0.0~compile: loris at 1.0.0 8 verbose lifecycle loris at 1.0.0~compile: unsafe-perm in lifecycle true 9 verbose lifecycle loris at 1.0.0~compile: PATH: /usr/share/npm/bin/node-gyp-bin:/var/www/loris/node_modules/.bin:/home/lorisadmin/bin:/home/lorisadmin/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin 10 verbose lifecycle loris at 1.0.0~compile: CWD: /var/www/loris 11 silly lifecycle loris at 1.0.0~compile: Args: [ '-c', 'webpack' ] 12 info lifecycle loris at 1.0.0~compile: Failed to exec compile script 13 verbose stack Error: loris at 1.0.0 compile: `webpack` 13 verbose stack spawn ENOENT 13 verbose stack at ChildProcess. (/usr/share/npm/lib/utils/spawn.js:17:16) 13 verbose stack at emitTwo (events.js:87:13) 13 verbose stack at ChildProcess.emit (events.js:172:7) 13 verbose stack at maybeClose (internal/child_process.js:821:16) 13 verbose stack at Process.ChildProcess._handle.onexit (internal/child_process.js:211:5) 14 verbose pkgid loris at 1.0.0 15 verbose cwd /var/www/loris 16 error Linux 4.15.0-58-generic 17 error argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile" 18 error node v4.2.6 19 error npm v3.5.2 20 error file sh 21 error code ELIFECYCLE 22 error errno ENOENT 23 error syscall spawn 24 error loris at 1.0.0 compile: `webpack` 24 error spawn ENOENT 25 error Failed at the loris at 1.0.0 compile script 'webpack'. 25 error Make sure you have the latest version of node.js and npm installed. 25 error If you do, this is most likely a problem with the loris package, 25 error not with npm itself. 25 error Tell the author that this fails on your system: 25 error webpack 25 error You can get information on how to open an issue for this project with: 25 error npm bugs loris 25 error Or if that isn't available, you can get their info via: 25 error npm owner ls loris 25 error There is likely additional logging output above. 26 verbose exit [ 1, true ] lorisadmin at loris-VirtualBox:/var/www/loris$ From sotirisnik at gmail.com Wed Sep 4 07:28:29 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 4 Sep 2019 14:28:29 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Wed Sep 4 08:05:05 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 4 Sep 2019 15:05:05 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: not available URL: From christine.rogers at mcgill.ca Wed Sep 4 09:16:35 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 4 Sep 2019 13:16:35 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: image.png URL: From sotirisnik at gmail.com Wed Sep 4 09:33:48 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 4 Sep 2019 16:33:48 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: not available URL: From christine.rogers at mcgill.ca Wed Sep 4 09:38:32 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 4 Sep 2019 13:38:32 +0000 Subject: [Loris-dev] Questions regarding querying LORIS In-Reply-To: <859bbc79fad0471b832e9fd7e0012c0f@YT1PR01MB3307.CANPRD01.PROD.OUTLOOK.COM> References: <859bbc79fad0471b832e9fd7e0012c0f@YT1PR01MB3307.CANPRD01.PROD.OUTLOOK.COM> Message-ID: Hi Remya, Thanks for your comments and followup -- I have a setup where all my imaging data is already stored in an XNAT database and if I now store my behavioral data and other subject metadata in LORIS and want to use the DQT (or some tool) for querying the LORIS DB and well as the xnat database, is this possible currently? Yes, this is definitely possible, since the current LORIS API can be used to load imaging data for existing subjects/visits (and many other tasks). LORIS' API (documentation here) can be used to insert imaging data into the main LORIS database from XNAT, depending on the appropriate level of anonymization and labelling (e.g. with LORIS-recognizable IDs and visit labels). If you have specific questions on what the API can do, please don't hesitate. To do this, you'd want to create custom scripts to load images and their metadata either into LORIS via API, or just into the DQT via a custom PHP script. The imaging data from XNAT may need to be scrubbed, relabelled and/or re-packaged for insertion, and the IDs would need to match those stored in LORIS for each subject. For example, LORIS uses 2 subject IDs with a visit label to identify incoming DICOM packages. In additions to the scans, you'd also want to import any Quality Control information and metadata (like provenance and DICOM header fields). If you have detailed parameterized QC (e.g. to annotate the quality of scans), this can be loaded in LORIS as well. In the bigger picture -- if your data collection is still growing, and still undergoing curation and/or QC -- you'd want to set up syncing between the two repositories, to refresh LORIS as soon as any data is updated in XNAT. This should be done very regularly (and automated) if data collection or curation is ongoing, for example. In our experience the challenge of working with two systems simultaneously to maintain this sync requires careful planning and skilled execution, particularly to maintain the integrity of the linked datasets in the long term. Let me know if we can help further -- Best, Christine On Tue, Sep 3, 2019 at 3:13 PM Remya Nair > wrote: Hi Christine, Thank you for your replies. They are very helpful and I will test out the DQT shortly. I have one more follow up question for you : I have a setup where all my imaging data is already stored in an XNAT database and if I now store my behavioral data and other subject metadata in LORIS and want to use the DQT (or some tool) for querying the LORIS DB and well as the xnat database, is this possible currently? In short, is there any way to interface between XNAT and LORIS that you would know about or perhaps such a feature (or an API) is being developed? Please advise. Thank you again for your help. Best wishes, Remya ----------------- Staff Scientist Emotion and Social Cognition Lab & Caltech Center for Brain Imaging emotion.caltech.edu | accinfantstudy.com On Mon, Sep 2, 2019 at 4:47 PM Christine Rogers, Ms. > wrote: Hi Remya, Thanks for your inquiry -- 1. If we have data stored on several instruments within LORIS, is it possible to query, filter and export specific data that we need into a CSV file (or any spreadsheet) using the LORIS interface? If not, is this a feature currently being developed? Yes, the Data Querying Tool (DQT) module is designed for precisely that purpose. Try it out at demo.loris.ca -- you'll find this module under the "Tools" menu. The Data Querying Tool allows users to design, save and share custom queries, and to download the results as a CSV file, though the LORIS front-end. Users can query and filter specific data fields or whole instruments across timepoints, including metadata, demographic data, and imaging data. The DQT is also extensible for genomic data. For example, a user can filter for only female subjects that have a T1 scan completed, and have an IQ score above a certain threshold, etc. 2. Currently we understand the way to do mass uploads of data into a LORIS instrument is via the database directly. Is there any way to upload data into an instrument directly from a CSV instead (or any spreadsheet format file)? A module to load instrument data via the front-end is in our Roadmap for development; for the present we recommend a simple script to load instruments fields from a CSV into the corresponding database table field. Storing files in LORIS attached to a participant-timepoint (without processing the data contents), can also be done via the Media Module. Best, Christine The LORIS team On Fri, Aug 30, 2019 at 5:44 PM Remya Nair > wrote: Hi, We have a couple of questions that we were hoping the LORIS developers might be able to help with. Apologies if this has been answered previously on this forum. 1. If we have data stored on several instruments within LORIS, is it possible to query, filter and export specific data that we need into a CSV file (or any spreadsheet) using the LORIS interface? If not, is this a feature currently being developed? 2. Currently we understand the way to do mass uploads of data into a LORIS instrument is via the database directly. Is there any way to upload data into an instrument directly from a CSV instead (or any spreadsheet format file)? Your take on the above questions would be greatly appreciated. Thank you in advance for your help. Best, Remya -- _______________________________________________ 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 christine.rogers at mcgill.ca Wed Sep 4 09:53:05 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 4 Sep 2019 13:53:05 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: image.png URL: From sotirisnik at gmail.com Wed Sep 4 10:22:57 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 4 Sep 2019 17:22:57 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: /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 <>. ???? ???, 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: not available URL: From christine.rogers at mcgill.ca Wed Sep 4 10:35:56 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 4 Sep 2019 14:35:56 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: image.png URL: From sotirisnik at gmail.com Wed Sep 4 11:42:48 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 4 Sep 2019 18:42:48 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: not available URL: From christine.rogers at mcgill.ca Wed Sep 4 15:46:19 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Wed, 4 Sep 2019 19:46:19 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: <42a221bce9f645d78a93cd0dba39b78f@YTBPR01MB3309.CANPRD01.PROD.OUTLOOK.COM> References: <42a221bce9f645d78a93cd0dba39b78f@YTBPR01MB3309.CANPRD01.PROD.OUTLOOK.COM> Message-ID: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: image.png URL: From sotirisnik at gmail.com Fri Sep 6 12:03:39 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 6 Sep 2019 19:03:39 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <42a221bce9f645d78a93cd0dba39b78f@YTBPR01MB3309.CANPRD01.PROD.OUTLOOK.COM> Message-ID: 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42220 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 29279 bytes Desc: not available URL: From christine.rogers at mcgill.ca Fri Sep 6 12:49:03 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Fri, 6 Sep 2019 16:49:03 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <42a221bce9f645d78a93cd0dba39b78f@YTBPR01MB3309.CANPRD01.PROD.OUTLOOK.COM> Message-ID: 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 > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [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. > ??????: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 29279 bytes Desc: image.png URL: From sotirisnik at gmail.com Fri Sep 6 20:10:54 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sat, 7 Sep 2019 03:10:54 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: <42a221bce9f645d78a93cd0dba39b78f@YTBPR01MB3309.CANPRD01.PROD.OUTLOOK.COM> Message-ID: 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 ??????: >>>>>>>>>>> >>>>>>>>>>>> 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 >> > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 5819 bytes Desc: not available URL: From christine.rogers at mcgill.ca Fri Sep 6 20:21:47 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Sat, 7 Sep 2019 00:21:47 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: Message-ID: 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 > 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 > ??????: Hi, From Dicat's view seems that dcmodify worked in both cases [image.png] [image.png] For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier. [image.png] Thanks ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [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. > ??????: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 5819 bytes Desc: image.png URL: From sotirisnik at gmail.com Fri Sep 6 20:32:17 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sat, 7 Sep 2019 03:32:17 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 <>>>>>>>> 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 >>>>>>>>>> >>>>>>>>>> ) >>>>>>>>>> >>>>>>>>>> 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 ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: not available URL: From christine.rogers at mcgill.ca Sat Sep 7 10:48:53 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Sat, 7 Sep 2019 14:48:53 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > wrote: I see that i can edit the values but not how to insert new rows. [image.png] If i choose Inserted with flag then will the minc be inserted? [image.png] ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > 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 > ??????: Hi, From Dicat's view seems that dcmodify worked in both cases [image.png] [image.png] For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier. [image.png] Thanks ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [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. > ??????: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: image.png URL: From sotirisnik at gmail.com Sun Sep 8 09:17:08 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sun, 8 Sep 2019 16:17:08 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 <>>>>>>>>>> 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 >>>>>>>>>>>> >>>>>>>>>>>> ) >>>>>>>>>>>> >>>>>>>>>>>> For example, check if the database connection information was >>>>>>>>>>>> populated accurately in $mridir >>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>> >>>>>>>>>>>> Best, >>>>>>>>>>>> Christine >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>> >>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>>> all the front-end pages are loading. >>>>>>>>>>>>>> >>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 84052 bytes Desc: not available URL: From sotirisnik at gmail.com Sun Sep 8 10:12:14 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sun, 8 Sep 2019 17:12:14 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 <>>>>>>>>>>> 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 >>>>>>>>>>>>> >>>>>>>>>>>>> ) >>>>>>>>>>>>> >>>>>>>>>>>>> For example, check if the database connection information was >>>>>>>>>>>>> populated accurately in $mridir >>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>> >>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>>>> all the front-end pages are loading. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 >> > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44301 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 84052 bytes Desc: not available URL: From sotirisnik at gmail.com Sun Sep 8 10:12:52 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Sun, 8 Sep 2019 17:12:52 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: *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 <>>>>>>>>>>>> on the command line interface can be insecure>>. >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>>>>> all the front-end pages are loading. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> 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 >>> >> -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 84052 bytes Desc: not available URL: From christine.rogers at mcgill.ca Sun Sep 8 15:11:01 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Sun, 8 Sep 2019 19:11:01 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > wrote: *if i were to change their status to resolve what would happen? ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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? ). [https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y] ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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.png] [image.png] Thanks ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: I see that i can edit the values but not how to insert new rows. [image.png] If i choose Inserted with flag then will the minc be inserted? [image.png] ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > 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 > ??????: Hi, From Dicat's view seems that dcmodify worked in both cases [image.png] [image.png] For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier. [image.png] Thanks ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [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. > ??????: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44301 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 84052 bytes Desc: image.png URL: From sotirisnik at gmail.com Mon Sep 9 21:00:42 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 10 Sep 2019 04:00:42 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working >>>>>>>>>>>>>>>>>> and all the front-end pages are loading. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44301 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 84052 bytes Desc: not available URL: From sotirisnik at gmail.com Tue Sep 10 10:09:05 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 10 Sep 2019 17:09:05 +0300 Subject: [Loris-dev] Data query tool Message-ID: Hi, is there a way to run automated queries and download the csv files? Like the one in the managed saved queries named Sotiris_test_q https://demo.loris.ca/dataquery/ Thank you Sotirios -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue Sep 10 11:59:12 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 10 Sep 2019 11:59:12 -0400 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: Message-ID: Hi Alfredo, Sorry, I just came back from vacation. I don't know if you still have issues inserting the data. Just in case and to let you know, the MD5SUM is computed on the MINC files based on the following list of MINC headers: - patient:full_name - study:start_time - patient:identification - patient:sex - patient:age - patient:birthdate - study_instance_uid - series_description - processing:intergradient_rejected The code with the list of headers to use to create an MD5sum is in the MRI.pm library (function called compute_hash ). When I had to develop the insertion of processed DWI images into the database, most of the headers used were identical to the native image which resulted in the duplicate error message you got. To bypass that, I created a new MINC header (under a processing category) in the processed images that I wanted to insert with some parameters specific to that processed image and modified the code in the compute_hash function to include that new header when computing the MD5sum. You would just need to add an additional if statement like in line 1198 of MRI.pm . Let me know if you have questions or if something is not clear. Best, C?cile On Fri, Aug 30, 2019 at 3:35 PM Christine Rogers, Ms. < christine.rogers at mcgill.ca> wrote: > Hi Alfredo, > > Great, this is helpful to know. If I understand you - the filename is the > same for all the packages of processed data you are trying to upload, for > various subject-visits. > e.g. you may have organized them in subdirectories like: > $subject/$visit/processed_data.gz > > One solution could be to make a copy with a different name before >> uploading. > > > Instead of making a copy (or renaming) -- try a unique soft-link for each > package. I should think that would work (though can't confirm right now). > e.g. Use a simple bash command to execute for each package: > > ln -s $subject/$visit/processed_data.gz > ./$subject_$visit_processed_data.gz > (then tell the pipeline to load each $subject_$visit_processed_data.gz ) > > Again, this no-duplicate check exists to help ensure duplicate data isn't > inserted, which is a protection we try to preserve as much as possible. > Since all the code is customizable, this check could be manually bypassed, > but ideally this workaround will help keep the error-proofing intact. > > Let us know how this goes - > We'll be offline for Labour day weekend but back in the office next > Tuesday. > Best, > Christine > > > On Fri, Aug 30, 2019 at 12:53 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi Christine, >> >> Thank you for your answer. >> >> Here are the answers to your questions: >> >> Can you use distinct filenames ? >> We could but we already have all the images, thousands, with a >> pre-defined convention. One solution could be to make a copy with a >> different name before uploading. >> >> Are you are trying to load additional data for a participant session >> (i.e. same IDs and visit label) ? >> Yes, we are uploading the result of a couple of pipelines for each >> participant for each label. >> >> Let me know if you can find a workaround, in the mean time I will check >> with Pisti if we can make a copy of the files with a different name before >> uploading. >> >> Best, >> Alfredo. >> >> ------------------------------ >> *From:* Christine Rogers, Ms. >> *Sent:* Friday, August 30, 2019 11:17 AM >> *To:* Morales Pinzon, Alfredo >> *Cc:* loris-dev at bic.mni.mcgill.ca ; Cecile >> Madjar ; Sridar Narayanan, Dr. < >> sridar.narayanan at mcgill.ca>; Rozie Arnaoutelis, Ms. < >> rozie.arnaoutelis at mcgill.ca>; Douglas Arnold, Dr. < >> douglas.arnold at mcgill.ca>; Guttmann, Charles,M.D. < >> guttmann at bwh.harvard.edu> >> *Subject:* Re: [Loris-dev] Error "not a unique file" inserting >> segmentation files in LORIS >> >> >> External Email - Use Caution >> >> Hi Alfredo, >> >> Could you please help me inserting those files which are different in >> size and md5 from previous uploaded files? >> >> >> >> The only similarity between the previous uploaded files and the ones that >> could not be uploaded is the filename. >> >> >> To provide a quick answer (since most of our imaging team is on vacation >> this week) : >> >> Yes the MD5hash seems to require a unique filename (* below). >> Can you use distinct filenames ? i.e. Are you are trying to load >> additional data for a participant session (i.e. same IDs and visit label) >> ? >> Or, are you trying to load more than one participant/session at a time? >> >> (*) This line in the actual MRIProcessingUtility library >> : >> (around Line 617) >> >> $md5hash = &NeuroDB::MRI::compute_hash(\$file); >> >> and >> >> my $unique = &NeuroDB::MRI::is_unique_hash(\$file); >> >> >> >> I'll check with other imaging devs to see if we have a workaround while >> our senior devs are away -- I think there must be some solution... >> Meanwhile, the MD5hash for imaging files is documented here (per this >> script documentation >> ) >> : >> >> computeMd5Hash($file, $upload_id) >> Computes the MD5 hash of a file and makes sure it is unique. >> INPUTS: >> >> - $file : file to use to compute the MD5 hash >> >> >> - $upload_id: upload ID of the study >> >> RETURNS: 1 if the file is unique, 0 otherwise >> >> >> >> Best, >> Christine >> >> >> >> On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >> Dear DevLoris Team, >> >> I started the uploading process of processed files, segmentations and >> transformations, using the file "register_processed_data.pl" but some >> files are not being uploaded. The error reported in >> "data/logs/registerProcessed" show the following log for one of the files >> that could not be inserted: >> >> >> ------------------------------------------------------------------------------- >> ==> Successfully connected to database >> Log file, 2019-08-29_19:08:17 >> >> >> ==>Mapped DICOM parameters >> -> using user-defined filterParameters for >> /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz >> >> ==> Verifying acquisition center >> - Center Name : UNKN >> - CenterID : 0 >> -> Set ScannerID to 0. >> >> ==> Data found for candidate : 123456 - Visit: w024 >> -> Set SessionID to 28269. >> -> Set SourceFileID to 49598. >> -> Set AcquisitionProtocolID to 1013. >> -> Set CoordinateSpace to stx152lsq6. >> -> Set SourcePipeline to ConsensusGd. >> -> Set PipelineDate to 2019-08-29. >> -> Set OutputType to gvf. >> -> Set md5hash to *b877648ed0ef9a7458ad4931f4dbfd11*. >> >> ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be >> added to database. >> >> ------------------------------------------------------------------------------- >> >> I checked the md5hash for a previous uploaded file, which is different >> from the previous, but the same "md5hash" was calculated. See the following >> log: >> >> >> ------------------------------------------------------------------------------- >> >> ==> Successfully connected to database >> Log file, 2019-08-19_10:11:53 >> >> >> ==>Mapped DICOM parameters >> -> using user-defined filterParameters for >> >> ==> Verifying acquisition center >> - Center Name : UNKN >> - CenterID : 0 >> -> Set ScannerID to 0. >> >> ==> Data found for candidate : 123456 - Visit: baseline >> -> Set SessionID to 28268. >> -> Set SourceFileID to 49593. >> -> Set AcquisitionProtocolID to 1013. >> -> Set CoordinateSpace to stx152lsq6. >> -> Set SourcePipeline to T2Vol. >> -> Set PipelineDate to 2019-08-19. >> -> Set OutputType to gvf. >> -> Set md5hash to *b877648ed0ef9a7458ad4931f4dbfd11*. >> File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz >> moved to: >> >> /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz >> >> ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! >> >> Making JIV >> >> ==> Registered >> /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz >> in database, given FileID: 112945 >> >> ------------------------------------------------------------------------------- >> >> Here are the corresponding md5 for each file calculated using the command >> md5sum: >> /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c >> /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 >> >> Could you please help me inserting those files which are different in >> size and md5 from previous uploaded files? The only similarity between the >> previous uploaded files and the ones that could not be uploaded is the >> filename. >> >> Let me know if you need more information. >> >> 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 >> >> >> >> -- >> >> 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 dave.macfarlane at mcin.ca Tue Sep 10 12:38:14 2019 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Tue, 10 Sep 2019 12:38:14 -0400 Subject: [Loris-dev] Data query tool In-Reply-To: References: Message-ID: The DQT does not provide an API, and the logic of and/or'ing the different filters, or converting the data to CSV is done via javascript on the front end, so there is no way to automatically do that. You would need to save a query and manually run/save it. - Dave On Tue, Sep 10, 2019 at 10:09 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > Hi, > > is there a way to run automated queries and download the csv files? Like > the one in the managed saved queries named Sotiris_test_q > https://demo.loris.ca/dataquery/ > > Thank you > > Sotirios > _______________________________________________ > 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 Wed Sep 11 11:39:58 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Wed, 11 Sep 2019 11:39:58 -0400 Subject: [Loris-dev] Questions about LORIS/CBRAIN images database In-Reply-To: References: Message-ID: Hello Yichao, Thank you very much for reaching out! I took the liberty to cc the LORIS dev mailing list in my reply so they can complement my answers. I personally don't have any experience with MongoDB. However, we are developing a system called LORIS that is a web-based data and project management software for neuroimaging research studies. LORIS is a flexible, customizable and OPEN SOURCE neuroimaging database suitable for multiple types of projects. The backend database used by LORIS can be MySQL or MariaDB. Unfortunately, LORIS does not work on MongoDB. Here is the link to our website where you can find additional information about LORIS and a link to our demo database where you can play a bit with LORIS and see if that would work for your project. Feel free to contact us via loris-dev at bic.mni.mcgill.ca if you have any questions. We will be happy to help you out. Best regards, C?cile On Wed, Sep 11, 2019 at 11:27 AM Yichao Liang wrote: > Hi, > > I am Yichao. I am hired by Dr. Sultan Darvesh to do the brain images > database development. My colleague Nirav (cc above) and I wonder it is > practical to store brain images in MongoDB or there is any other database > that we can use and link images with data. Thank you. > > > > Best Regards, > > Yichao > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sotirisnik at gmail.com Fri Sep 13 09:43:21 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 13 Sep 2019 16:43:21 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 >>>>>>>>> ??????: >>>>>>>>> >>>>>>>>>> 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. >>>>>>>>>>>> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine >>>>>>>>>>>>>>>>>> Rogers, Ms. ??????: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working >>>>>>>>>>>>>>>>>>> and all the front-end pages are loading. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 >>>>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> 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 >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 61107 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42220 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 29279 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 78077 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 5647 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 5819 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 135445 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44301 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 84052 bytes Desc: not available URL: From melanie.legault2 at mcgill.ca Fri Sep 13 09:52:31 2019 From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs) Date: Fri, 13 Sep 2019 13:52:31 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: , Message-ID: 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. Melanie Legault | Software developer | Faculty of Medicine | McGill University 3801 University, Montreal, QC H3A 2B4 ________________________________ From: 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 > ??????: 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. > ??????: 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 > wrote: *if i were to change their status to resolve what would happen? ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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? ). [https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y] ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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.png] [image.png] Thanks ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: I see that i can edit the values but not how to insert new rows. [image.png] If i choose Inserted with flag then will the minc be inserted? [image.png] ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > 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 > ??????: Hi, >From Dicat's view seems that dcmodify worked in both cases [image.png] [image.png] For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier. [image.png] Thanks ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [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. > ??????: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44301 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 84052 bytes Desc: image.png URL: From sotirisnik at gmail.com Fri Sep 13 10:15:51 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 13 Sep 2019 17:15:51 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44301 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 84052 bytes Desc: not available URL: From melanie.legault2 at mcgill.ca Fri Sep 13 10:38:14 2019 From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs) Date: Fri, 13 Sep 2019 14:38:14 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: , Message-ID: 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 > ??????: 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 > 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 > ??????: 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. > ??????: 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 > wrote: *if i were to change their status to resolve what would happen? ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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? ). [https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y] ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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.png] [image.png] Thanks ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: I see that i can edit the values but not how to insert new rows. [image.png] If i choose Inserted with flag then will the minc be inserted? [image.png] ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > 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 > ??????: Hi, From Dicat's view seems that dcmodify worked in both cases [image.png] [image.png] For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier. [image.png] Thanks ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [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. > ??????: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44301 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 84052 bytes Desc: image.png URL: From AMORALESPINZON at bwh.harvard.edu Tue Sep 17 08:07:10 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Tue, 17 Sep 2019 12:07:10 +0000 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: , Message-ID: Hi C?cile, I tried your solution but it didn't work as the mnc headers do not contain any information about patient nor "processing". The headers only have information about the spacing and intensity of the image and are almost similar among them. Attached I'm sending the header for two different mnc files. Is there another way to make the images have different hash? Or maybe bypass the hash check? Best, Alfredo. ________________________________ From: Cecile Madjar Sent: Tuesday, September 10, 2019 11:59 AM To: Christine Rogers, Ms. Cc: Morales Pinzon, Alfredo ; loris-dev at bic.mni.mcgill.ca ; Rozie Arnaoutelis, Ms. ; Sridar Narayanan, Dr. ; Douglas Arnold, Dr. ; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, Sorry, I just came back from vacation. I don't know if you still have issues inserting the data. Just in case and to let you know, the MD5SUM is computed on the MINC files based on the following list of MINC headers: * patient:full_name * study:start_time * patient:identification * patient:sex * patient:age * patient:birthdate * study_instance_uid * series_description * processing:intergradient_rejected The code with the list of headers to use to create an MD5sum is in the MRI.pm library (function called compute_hash). When I had to develop the insertion of processed DWI images into the database, most of the headers used were identical to the native image which resulted in the duplicate error message you got. To bypass that, I created a new MINC header (under a processing category) in the processed images that I wanted to insert with some parameters specific to that processed image and modified the code in the compute_hash function to include that new header when computing the MD5sum. You would just need to add an additional if statement like in line 1198 of MRI.pm. Let me know if you have questions or if something is not clear. Best, C?cile On Fri, Aug 30, 2019 at 3:35 PM Christine Rogers, Ms. > wrote: Hi Alfredo, Great, this is helpful to know. If I understand you - the filename is the same for all the packages of processed data you are trying to upload, for various subject-visits. e.g. you may have organized them in subdirectories like: $subject/$visit/processed_data.gz One solution could be to make a copy with a different name before uploading. Instead of making a copy (or renaming) -- try a unique soft-link for each package. I should think that would work (though can't confirm right now). e.g. Use a simple bash command to execute for each package: > ln -s $subject/$visit/processed_data.gz ./$subject_$visit_processed_data.gz (then tell the pipeline to load each $subject_$visit_processed_data.gz ) Again, this no-duplicate check exists to help ensure duplicate data isn't inserted, which is a protection we try to preserve as much as possible. Since all the code is customizable, this check could be manually bypassed, but ideally this workaround will help keep the error-proofing intact. Let us know how this goes - We'll be offline for Labour day weekend but back in the office next Tuesday. Best, Christine On Fri, Aug 30, 2019 at 12:53 PM Morales Pinzon, Alfredo > wrote: Hi Christine, Thank you for your answer. Here are the answers to your questions: Can you use distinct filenames ? We could but we already have all the images, thousands, with a pre-defined convention. One solution could be to make a copy with a different name before uploading. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Yes, we are uploading the result of a couple of pipelines for each participant for each label. Let me know if you can find a workaround, in the mean time I will check with Pisti if we can make a copy of the files with a different name before uploading. Best, Alfredo. ________________________________ From: Christine Rogers, Ms. > Sent: Friday, August 30, 2019 11:17 AM To: Morales Pinzon, Alfredo > Cc: loris-dev at bic.mni.mcgill.ca >; Cecile Madjar >; Sridar Narayanan, Dr. >; Rozie Arnaoutelis, Ms. >; Douglas Arnold, Dr. >; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. To provide a quick answer (since most of our imaging team is on vacation this week) : Yes the MD5hash seems to require a unique filename (* below). Can you use distinct filenames ? i.e. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Or, are you trying to load more than one participant/session at a time? (*) This line in the actual MRIProcessingUtility library: (around Line 617) $md5hash = &NeuroDB::MRI::compute_hash(\$file); and my $unique = &NeuroDB::MRI::is_unique_hash(\$file); I'll check with other imaging devs to see if we have a workaround while our senior devs are away -- I think there must be some solution... Meanwhile, the MD5hash for imaging files is documented here (per this script documentation) : computeMd5Hash($file, $upload_id) Computes the MD5 hash of a file and makes sure it is unique. INPUTS: * $file : file to use to compute the MD5 hash * $upload_id: upload ID of the study RETURNS: 1 if the file is unique, 0 otherwise Best, Christine On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo > wrote: Dear DevLoris Team, I started the uploading process of processed files, segmentations and transformations, using the file "register_processed_data.pl" but some files are not being uploaded. The error reported in "data/logs/registerProcessed" show the following log for one of the files that could not be inserted: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-29_19:08:17 ==>Mapped DICOM parameters -> using user-defined filterParameters for /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: w024 -> Set SessionID to 28269. -> Set SourceFileID to 49598. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to ConsensusGd. -> Set PipelineDate to 2019-08-29. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be added to database. ------------------------------------------------------------------------------- I checked the md5hash for a previous uploaded file, which is different from the previous, but the same "md5hash" was calculated. See the following log: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-19_10:11:53 ==>Mapped DICOM parameters -> using user-defined filterParameters for ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: baseline -> Set SessionID to 28268. -> Set SourceFileID to 49593. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to T2Vol. -> Set PipelineDate to 2019-08-19. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz moved to: /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! Making JIV ==> Registered /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz in database, given FileID: 112945 ------------------------------------------------------------------------------- Here are the corresponding md5 for each file calculated using the command md5sum: /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. Let me know if you need more information. 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 -- 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 -------------- An embedded and charset-unspecified text was scrubbed... Name: ct2f_ISPC-stx152lsq6.mnc.gz.txt URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: gvf_ISPC-stx152lsq6.mnc.gz.txt URL: From cecile.madjar at mcin.ca Tue Sep 17 15:15:52 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 17 Sep 2019 15:15:52 -0400 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: Message-ID: Hi Alfredo, The "processing" entry I was talking about would need to be created by your wrapper script before calling register_processed_data to create the MINC header in the processed data. A bit like it is done in that function of the DTIPrep pipeline used with LORIS. Then you could use a combination of these new processing tags to differentiate the processed data from the native one. You could always bypass the md5sum check if you prefer but that would mean then that you will not be able to detect duplicated files when inserting a new file. Hope this helps! Let me know how things go, C?cile On Tue, Sep 17, 2019 at 8:08 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi C?cile, > > I tried your solution but it didn't work as the mnc headers do not contain > any information about patient nor "processing". The headers only have > information about the spacing and intensity of the image and are almost > similar among them. Attached I'm sending the header for two different mnc > files. > > Is there another way to make the images have different hash? Or maybe > bypass the hash check? > > Best, > Alfredo. > ------------------------------ > *From:* Cecile Madjar > *Sent:* Tuesday, September 10, 2019 11:59 AM > *To:* Christine Rogers, Ms. > *Cc:* Morales Pinzon, Alfredo ; > loris-dev at bic.mni.mcgill.ca ; Rozie > Arnaoutelis, Ms. ; Sridar Narayanan, Dr. < > sridar.narayanan at mcgill.ca>; Douglas Arnold, Dr. ; > Guttmann, Charles,M.D. > *Subject:* Re: [Loris-dev] Error "not a unique file" inserting > segmentation files in LORIS > > > External Email - Use Caution > > Hi Alfredo, > > Sorry, I just came back from vacation. I don't know if you still have > issues inserting the data. > > Just in case and to let you know, the MD5SUM is computed on the MINC files > based on the following list of MINC headers: > > - patient:full_name > - study:start_time > - patient:identification > - patient:sex > - patient:age > - patient:birthdate > - study_instance_uid > - series_description > - processing:intergradient_rejected > > The code with the list of headers to use to create an MD5sum is in the > MRI.pm library (function called compute_hash > > ). > > When I had to develop the insertion of processed DWI images into the > database, most of the headers used were identical to the native image which > resulted in the duplicate error message you got. To bypass that, I created > a new MINC header (under a processing category) in the processed images > that I wanted to insert with some parameters specific to that processed > image and modified the code in the compute_hash > > function to include that new header when computing the MD5sum. You would > just need to add an additional if statement like in line 1198 of MRI.pm > > . > > Let me know if you have questions or if something is not clear. > > Best, > > C?cile > > On Fri, Aug 30, 2019 at 3:35 PM Christine Rogers, Ms. < > christine.rogers at mcgill.ca> wrote: > > Hi Alfredo, > > Great, this is helpful to know. If I understand you - the filename is the > same for all the packages of processed data you are trying to upload, for > various subject-visits. > e.g. you may have organized them in subdirectories like: > $subject/$visit/processed_data.gz > > One solution could be to make a copy with a different name before > uploading. > > > Instead of making a copy (or renaming) -- try a unique soft-link for each > package. I should think that would work (though can't confirm right now). > e.g. Use a simple bash command to execute for each package: > > ln -s $subject/$visit/processed_data.gz > ./$subject_$visit_processed_data.gz > (then tell the pipeline to load each $subject_$visit_processed_data.gz ) > > Again, this no-duplicate check exists to help ensure duplicate data isn't > inserted, which is a protection we try to preserve as much as possible. > Since all the code is customizable, this check could be manually bypassed, > but ideally this workaround will help keep the error-proofing intact. > > Let us know how this goes - > We'll be offline for Labour day weekend but back in the office next > Tuesday. > Best, > Christine > > > On Fri, Aug 30, 2019 at 12:53 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Hi Christine, > > Thank you for your answer. > > Here are the answers to your questions: > > Can you use distinct filenames ? > We could but we already have all the images, thousands, with a pre-defined > convention. One solution could be to make a copy with a different name > before uploading. > > Are you are trying to load additional data for a participant session (i.e. > same IDs and visit label) ? > Yes, we are uploading the result of a couple of pipelines for each > participant for each label. > > Let me know if you can find a workaround, in the mean time I will check > with Pisti if we can make a copy of the files with a different name before > uploading. > > Best, > Alfredo. > > ------------------------------ > *From:* Christine Rogers, Ms. > *Sent:* Friday, August 30, 2019 11:17 AM > *To:* Morales Pinzon, Alfredo > *Cc:* loris-dev at bic.mni.mcgill.ca ; Cecile > Madjar ; Sridar Narayanan, Dr. < > sridar.narayanan at mcgill.ca>; Rozie Arnaoutelis, Ms. < > rozie.arnaoutelis at mcgill.ca>; Douglas Arnold, Dr. < > douglas.arnold at mcgill.ca>; Guttmann, Charles,M.D. < > guttmann at bwh.harvard.edu> > *Subject:* Re: [Loris-dev] Error "not a unique file" inserting > segmentation files in LORIS > > > External Email - Use Caution > > Hi Alfredo, > > Could you please help me inserting those files which are different in size > and md5 from previous uploaded files? > > > > The only similarity between the previous uploaded files and the ones that > could not be uploaded is the filename. > > > To provide a quick answer (since most of our imaging team is on vacation > this week) : > > Yes the MD5hash seems to require a unique filename (* below). > Can you use distinct filenames ? i.e. Are you are trying to load > additional data for a participant session (i.e. same IDs and visit label) > ? > Or, are you trying to load more than one participant/session at a time? > > (*) This line in the actual MRIProcessingUtility library > : > (around Line 617) > > $md5hash = &NeuroDB::MRI::compute_hash(\$file); > > and > > my $unique = &NeuroDB::MRI::is_unique_hash(\$file); > > > > I'll check with other imaging devs to see if we have a workaround while > our senior devs are away -- I think there must be some solution... > Meanwhile, the MD5hash for imaging files is documented here (per this > script documentation > ) > : > > computeMd5Hash($file, $upload_id) > Computes the MD5 hash of a file and makes sure it is unique. > INPUTS: > > - $file : file to use to compute the MD5 hash > > > - $upload_id: upload ID of the study > > RETURNS: 1 if the file is unique, 0 otherwise > > > > Best, > Christine > > > > On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > > Dear DevLoris Team, > > I started the uploading process of processed files, segmentations and > transformations, using the file "register_processed_data.pl" but some > files are not being uploaded. The error reported in > "data/logs/registerProcessed" show the following log for one of the files > that could not be inserted: > > > ------------------------------------------------------------------------------- > ==> Successfully connected to database > Log file, 2019-08-29_19:08:17 > > > ==>Mapped DICOM parameters > -> using user-defined filterParameters for > /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz > > ==> Verifying acquisition center > - Center Name : UNKN > - CenterID : 0 > -> Set ScannerID to 0. > > ==> Data found for candidate : 123456 - Visit: w024 > -> Set SessionID to 28269. > -> Set SourceFileID to 49598. > -> Set AcquisitionProtocolID to 1013. > -> Set CoordinateSpace to stx152lsq6. > -> Set SourcePipeline to ConsensusGd. > -> Set PipelineDate to 2019-08-29. > -> Set OutputType to gvf. > -> Set md5hash to *b877648ed0ef9a7458ad4931f4dbfd11*. > > ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be > added to database. > > ------------------------------------------------------------------------------- > > I checked the md5hash for a previous uploaded file, which is different > from the previous, but the same "md5hash" was calculated. See the following > log: > > > ------------------------------------------------------------------------------- > > ==> Successfully connected to database > Log file, 2019-08-19_10:11:53 > > > ==>Mapped DICOM parameters > -> using user-defined filterParameters for > > ==> Verifying acquisition center > - Center Name : UNKN > - CenterID : 0 > -> Set ScannerID to 0. > > ==> Data found for candidate : 123456 - Visit: baseline > -> Set SessionID to 28268. > -> Set SourceFileID to 49593. > -> Set AcquisitionProtocolID to 1013. > -> Set CoordinateSpace to stx152lsq6. > -> Set SourcePipeline to T2Vol. > -> Set PipelineDate to 2019-08-19. > -> Set OutputType to gvf. > -> Set md5hash to *b877648ed0ef9a7458ad4931f4dbfd11*. > File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz > moved to: > > /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz > > ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! > > Making JIV > > ==> Registered > /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz > in database, given FileID: 112945 > > ------------------------------------------------------------------------------- > > Here are the corresponding md5 for each file calculated using the command > md5sum: > /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c > /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 > > Could you please help me inserting those files which are different in size > and md5 from previous uploaded files? The only similarity between the > previous uploaded files and the ones that could not be uploaded is the > filename. > > Let me know if you need more information. > > 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 > > > > -- > > 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 sotirisnik at gmail.com Tue Sep 17 19:31:14 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Wed, 18 Sep 2019 02:31:14 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 44901 bytes Desc: not available URL: From AMORALESPINZON at bwh.harvard.edu Wed Sep 18 16:06:54 2019 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Wed, 18 Sep 2019 20:06:54 +0000 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: , Message-ID: Hi C?cile, I added the "filename" to the hash calculation in order to be able to insert the files. Once I finish the insertion of transformations and masks I will remove the line so that it won't change the importing behavior for other images. The modification actually prevents inserting the same exact file based on the filepath. This is the modification: _____________________________________ sub compute_hash { ... if($fileType eq 'mnc') { ... $ctx->add($file->getFileDatum('File')); } ... } _____________________________________ Thank you for the help. Best, Alfredo. ________________________________ From: Cecile Madjar Sent: Tuesday, September 17, 2019 3:15 PM To: Morales Pinzon, Alfredo Cc: Christine Rogers, Ms. ; loris-dev at bic.mni.mcgill.ca ; Rozie Arnaoutelis, Ms. ; Sridar Narayanan, Dr. ; Douglas Arnold, Dr. ; Guttmann, Charles,M.D. Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, The "processing" entry I was talking about would need to be created by your wrapper script before calling register_processed_data to create the MINC header in the processed data. A bit like it is done in that function of the DTIPrep pipeline used with LORIS. Then you could use a combination of these new processing tags to differentiate the processed data from the native one. You could always bypass the md5sum check if you prefer but that would mean then that you will not be able to detect duplicated files when inserting a new file. Hope this helps! Let me know how things go, C?cile On Tue, Sep 17, 2019 at 8:08 AM Morales Pinzon, Alfredo > wrote: Hi C?cile, I tried your solution but it didn't work as the mnc headers do not contain any information about patient nor "processing". The headers only have information about the spacing and intensity of the image and are almost similar among them. Attached I'm sending the header for two different mnc files. Is there another way to make the images have different hash? Or maybe bypass the hash check? Best, Alfredo. ________________________________ From: Cecile Madjar > Sent: Tuesday, September 10, 2019 11:59 AM To: Christine Rogers, Ms. > Cc: Morales Pinzon, Alfredo >; loris-dev at bic.mni.mcgill.ca >; Rozie Arnaoutelis, Ms. >; Sridar Narayanan, Dr. >; Douglas Arnold, Dr. >; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, Sorry, I just came back from vacation. I don't know if you still have issues inserting the data. Just in case and to let you know, the MD5SUM is computed on the MINC files based on the following list of MINC headers: * patient:full_name * study:start_time * patient:identification * patient:sex * patient:age * patient:birthdate * study_instance_uid * series_description * processing:intergradient_rejected The code with the list of headers to use to create an MD5sum is in the MRI.pm library (function called compute_hash). When I had to develop the insertion of processed DWI images into the database, most of the headers used were identical to the native image which resulted in the duplicate error message you got. To bypass that, I created a new MINC header (under a processing category) in the processed images that I wanted to insert with some parameters specific to that processed image and modified the code in the compute_hash function to include that new header when computing the MD5sum. You would just need to add an additional if statement like in line 1198 of MRI.pm. Let me know if you have questions or if something is not clear. Best, C?cile On Fri, Aug 30, 2019 at 3:35 PM Christine Rogers, Ms. > wrote: Hi Alfredo, Great, this is helpful to know. If I understand you - the filename is the same for all the packages of processed data you are trying to upload, for various subject-visits. e.g. you may have organized them in subdirectories like: $subject/$visit/processed_data.gz One solution could be to make a copy with a different name before uploading. Instead of making a copy (or renaming) -- try a unique soft-link for each package. I should think that would work (though can't confirm right now). e.g. Use a simple bash command to execute for each package: > ln -s $subject/$visit/processed_data.gz ./$subject_$visit_processed_data.gz (then tell the pipeline to load each $subject_$visit_processed_data.gz ) Again, this no-duplicate check exists to help ensure duplicate data isn't inserted, which is a protection we try to preserve as much as possible. Since all the code is customizable, this check could be manually bypassed, but ideally this workaround will help keep the error-proofing intact. Let us know how this goes - We'll be offline for Labour day weekend but back in the office next Tuesday. Best, Christine On Fri, Aug 30, 2019 at 12:53 PM Morales Pinzon, Alfredo > wrote: Hi Christine, Thank you for your answer. Here are the answers to your questions: Can you use distinct filenames ? We could but we already have all the images, thousands, with a pre-defined convention. One solution could be to make a copy with a different name before uploading. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Yes, we are uploading the result of a couple of pipelines for each participant for each label. Let me know if you can find a workaround, in the mean time I will check with Pisti if we can make a copy of the files with a different name before uploading. Best, Alfredo. ________________________________ From: Christine Rogers, Ms. > Sent: Friday, August 30, 2019 11:17 AM To: Morales Pinzon, Alfredo > Cc: loris-dev at bic.mni.mcgill.ca >; Cecile Madjar >; Sridar Narayanan, Dr. >; Rozie Arnaoutelis, Ms. >; Douglas Arnold, Dr. >; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. To provide a quick answer (since most of our imaging team is on vacation this week) : Yes the MD5hash seems to require a unique filename (* below). Can you use distinct filenames ? i.e. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Or, are you trying to load more than one participant/session at a time? (*) This line in the actual MRIProcessingUtility library: (around Line 617) $md5hash = &NeuroDB::MRI::compute_hash(\$file); and my $unique = &NeuroDB::MRI::is_unique_hash(\$file); I'll check with other imaging devs to see if we have a workaround while our senior devs are away -- I think there must be some solution... Meanwhile, the MD5hash for imaging files is documented here (per this script documentation) : computeMd5Hash($file, $upload_id) Computes the MD5 hash of a file and makes sure it is unique. INPUTS: * $file : file to use to compute the MD5 hash * $upload_id: upload ID of the study RETURNS: 1 if the file is unique, 0 otherwise Best, Christine On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo > wrote: Dear DevLoris Team, I started the uploading process of processed files, segmentations and transformations, using the file "register_processed_data.pl" but some files are not being uploaded. The error reported in "data/logs/registerProcessed" show the following log for one of the files that could not be inserted: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-29_19:08:17 ==>Mapped DICOM parameters -> using user-defined filterParameters for /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: w024 -> Set SessionID to 28269. -> Set SourceFileID to 49598. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to ConsensusGd. -> Set PipelineDate to 2019-08-29. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be added to database. ------------------------------------------------------------------------------- I checked the md5hash for a previous uploaded file, which is different from the previous, but the same "md5hash" was calculated. See the following log: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-19_10:11:53 ==>Mapped DICOM parameters -> using user-defined filterParameters for ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: baseline -> Set SessionID to 28268. -> Set SourceFileID to 49593. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to T2Vol. -> Set PipelineDate to 2019-08-19. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz moved to: /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! Making JIV ==> Registered /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz in database, given FileID: 112945 ------------------------------------------------------------------------------- Here are the corresponding md5 for each file calculated using the command md5sum: /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. Let me know if you need more information. 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 -- 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 christine.rogers at mcgill.ca Thu Sep 19 12:57:19 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Thu, 19 Sep 2019 16:57:19 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > 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.png] ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs > ??????: 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 > ??????: 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 > 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 > ??????: 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. > ??????: 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 > wrote: *if i were to change their status to resolve what would happen? ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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? ). [https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y] ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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.png] [image.png] Thanks ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: I see that i can edit the values but not how to insert new rows. [image.png] If i choose Inserted with flag then will the minc be inserted? [image.png] ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > 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 > ??????: Hi, From Dicat's view seems that dcmodify worked in both cases [image.png] [image.png] For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier. [image.png] Thanks ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [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. > ??????: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 135445 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 16405 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44301 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 84052 bytes Desc: image.png URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 44901 bytes Desc: image.png URL: From sotirisnik at gmail.com Fri Sep 20 07:39:36 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 20 Sep 2019 14:39:36 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 24658 bytes Desc: not available URL: From sotirisnik at gmail.com Fri Sep 20 09:37:37 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 20 Sep 2019 16:37:37 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 >> > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 95725 bytes Desc: not available URL: From sotirisnik at gmail.com Fri Sep 20 09:44:37 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 20 Sep 2019 16:44:37 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 >>> >> -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 95725 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 5062 bytes Desc: not available URL: From christine.rogers at mcgill.ca Fri Sep 20 09:54:20 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Fri, 20 Sep 2019 13:54:20 +0000 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > wrote: I fixed it with this [image.png] ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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.png] ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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.png] Lastly i deleted the session and then the candidate table. Thanks ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > 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.png] ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie Legault, Mrs > ??????: 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 > ??????: 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 > 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 > ??????: 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. > ??????: 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 > wrote: *if i were to change their status to resolve what would happen? ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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? ). [https://lh5.googleusercontent.com/0G4f5Ms034ZaYEwHLLOzo4YBjQwcKxjSLRrE0XLZAR86JhsPocXi5tkAvgbELadS63HWgJ_A6eGF0BitFWhf4DCVx5EEFzThQm19QfKDpgrrIfGFZjdy4BanrmRjawJeo3kYt-5y] ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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.png] [image.png] Thanks ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: I see that i can edit the values but not how to insert new rows. [image.png] If i choose Inserted with flag then will the minc be inserted? [image.png] ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > 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 > ??????: Hi, From Dicat's view seems that dcmodify worked in both cases [image.png] [image.png] For the mri_violations i attached the .html output from webbrowser, so that you can check the filelds easier. [image.png] Thanks ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 > wrote: Here is the psc table [image.png] I created 2 candidates profiles through the interface [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. > ??????: 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 > 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. > ??????: 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 > 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 <>. ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine Rogers, Ms. > ??????: 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 $mridir/dicom-archive/.loris_mri/database_config.py Best, Christine On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos > wrote: Hi Christine, If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically? Thanks [https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs] ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. > ??????: Hi Sotirios, Glad to hear your LORIS core install is up and working and all the front-end pages are loading. > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 > wrote: As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right? [image.png] ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios Nikoloutsopoulos > ??????: 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 -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 5062 bytes Desc: image.png URL: From sotirisnik at gmail.com Mon Sep 23 19:30:01 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 24 Sep 2019 02:30:01 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 51135 bytes Desc: not available URL: -------------- next part -------------- (loris-mri-python) lorisadmin at loris-VirtualBox:~/DataQualityControlTool/mipqctool$ python dicom_uploader.py ./102788419/7/1.3.12.2.1107.5.2.30.27245.2015122209062920279710806.0.0.0_0007_000048_15169884000bff.dcm 102788419 Creating candidate Update externalid Create candidate Candidate Info 868341 DCC0000 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 22 /data/incoming/DCC0000_868341_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-1\-8\-pmFnoJ -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-1\-8\-pmFnoJ \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-1-8-pmFnoJ Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-1-8-pmFnoJ You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-1-8-pmFnoJ.tar ImagingUpload-1-8-pmFnoJ getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-1-8-pmFnoJ * Archive target location : /data/loris/data/tarchive/DCM_2015-12-22_ImagingUpload-1-8-pmFnoJ.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-24 01:08:36 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 3a213c69e608266355f11494e8253c02 ImagingUpload-1-8-pmFnoJ.tar * md5sum for DICOM tarball gzipped : 5740530dbe533d843884b1a4f86c7f83 ImagingUpload-1-8-pmFnoJ.tar.gz * md5sum for complete archive : 946c5a419e46f49912cc586fc7522a9b DCM_2015-12-22_ImagingUpload-1-8-pmFnoJ.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_2015\-12\-22_ImagingUpload\-1\-8\-pmFnoJ\.tar -uploadID 22 -verbose md5sum /data/loris/data/tarchive/DCM_2015-12-22_ImagingUpload-1-8-pmFnoJ.tar PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 candidate id 868341 Set centerID = 1 PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 5 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-8-pLTyn6.log PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 candidate id 868341 Finished file: assembly/868341/V1/mri/native/loris_868341_V1_t1_001.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 256 0.976562 1 1 2 1 256 0.976562 2 0 0 1 176 1.000000 Restructuring... log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-8-BlB4D6.log PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 candidate id 868341 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-9-aj183j.log PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 candidate id 868341 Finished file: assembly/868341/V1/mri/native/loris_868341_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 30 4.940154 1 1 1 1 256 0.976562 2 0 2 1 256 0.976562 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-9-pqkH2B.log PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 candidate id 868341 Finished file: assembly/868341/V1/mri/native/loris_868341_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 1 256 0.976562 1 1 0 1 30 5.233743 2 0 2 1 256 0.976562 Restructuring... log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-9-re4bXt.log PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 PSCID is: DCC0000 CandID id: 868341 visit_label is: V1 candidate id 868341 Finished file: assembly/868341/V1/mri/native/loris_868341_V1_t1_004.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 256 0.976562 1 1 2 1 256 0.976562 2 0 0 1 30 4.465090 Restructuring... noise_estimate --snr /data/loris/data//assembly/868341/V1/mri/native/loris_868341_V1_t1_001.mnc SNR is: 30.9451 noise_estimate --snr /data/loris/data//assembly/868341/V1/mri/native/loris_868341_V1_t1_002.mnc SNR is: 62.5745 noise_estimate --snr /data/loris/data//assembly/868341/V1/mri/native/loris_868341_V1_t1_003.mnc SNR is: 61.2643 noise_estimate --snr /data/loris/data//assembly/868341/V1/mri/native/loris_868341_V1_t1_004.mnc SNR is: 56.031 Creating Minc Pics TarchiveSource is 11 Connecting to database. FileID from mass_pic.pl is: 15 FileID from mass_pic.pl is: 16 FileID from mass_pic.pl is: 17 FileID from mass_pic.pl is: 18 Finished mass_pic.pl execution Cleaning up temp files: rm -rf /tmp/TarLoad-1-8-Q5zNUp/ImagingUpload-1-8-pmFnoJ* Can't exec "mail": No such file or directory at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 665. print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 666. print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 667. print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 668. print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 669. find /data/loris/data/tarchive// -name *ImagingUpload-1-8-pmFnoJ* rm /data/incoming/DCC0000_868341_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. 1940 ./102327840/6/1.3.12.2.1107.5.2.18.41881.2015052614223027481362738.0.0.0_0006_000030_151783708598e6.dcm 102327840 Creating candidate Update externalid Create candidate Candidate Info 627229 DCC0001 Next Visit Label 1 ./102327840/6/1.3.12.2.1107.5.2.18.41881.2015052614223027481362738.0.0.0_0006_000088_1517837174996a.dcm does not have Protocolname 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 23 /data/incoming/DCC0001_627229_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-1\-9\-gE48TD -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-1\-9\-gE48TD \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-1-9-gE48TD 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 ./102809579/10/1.3.12.2.1107.5.2.30.27780.2017071115494453951663644.0.0.0_0010_000030_1518430122f026.dcm 102809579 Creating candidate Update externalid Create candidate Candidate Info 167757 DCC0002 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 24 /data/incoming/DCC0002_167757_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-1\-9\-71OIUb -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-1\-9\-71OIUb \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-1-9-71OIUb 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 ./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 210134 DCC0003 Next Visit Label 1 ./000535670/501/1.3.46.670589.11.34037.5.0.6020.2012120510342515883_0501_000111_151810731519ee.dcm does not have Protocolname 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 25 /data/incoming/DCC0003_210134_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-1\-9\-XnnapL -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-1\-9\-XnnapL \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-1-9-XnnapL Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-1-9-XnnapL You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-1-9-XnnapL.tar ImagingUpload-1-9-XnnapL getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-1-9-XnnapL * Archive target location : /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-1-9-XnnapL.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-24 01:09:33 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : af694b3303426fd5bc116be614ca4d68 ImagingUpload-1-9-XnnapL.tar * md5sum for DICOM tarball gzipped : b0e25d740a22cf6b04548825f77577c7 ImagingUpload-1-9-XnnapL.tar.gz * md5sum for complete archive : 54a456d222aa37b80bbedd3be843150e DCM_2012-12-05_ImagingUpload-1-9-XnnapL.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_2012\-12\-05_ImagingUpload\-1\-9\-XnnapL\.tar -uploadID 25 -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-1-9-XnnapL.tar PSCID is: DCC0003 CandID id: 210134 visit_label is: V1 PSCID is: DCC0003 CandID id: 210134 visit_label is: V1 candidate id 210134 Set centerID = 1 PSCID is: DCC0003 CandID id: 210134 visit_label is: V1 PSCID is: DCC0003 CandID id: 210134 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-9-mWwIoL.log PSCID is: DCC0003 CandID id: 210134 visit_label is: V1 PSCID is: DCC0003 CandID id: 210134 visit_label is: V1 candidate id 210134 Finished file: assembly/210134/V1/mri/native/loris_210134_V1_t1_001.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 256 1.000000 1 1 2 1 256 1.000000 2 0 0 1 91 1.766667 Restructuring... noise_estimate --snr /data/loris/data//assembly/210134/V1/mri/native/loris_210134_V1_t1_001.mnc SNR is: 23.989 Creating Minc Pics TarchiveSource is 12 Connecting to database. FileID from mass_pic.pl is: 19 Finished mass_pic.pl execution Cleaning up temp files: rm -rf /tmp/TarLoad-1-9-jRPp63/ImagingUpload-1-9-XnnapL* find /data/loris/data/tarchive// -name *ImagingUpload-1-9-XnnapL* rm /data/incoming/DCC0003_210134_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. 9.90050029754638 ./000998448/205/1.3.46.670589.11.70598.5.0.7280.2016082207333647000_0205_000024_1518217540255b.dcm 000998448 Creating candidate Update externalid Create candidate Candidate Info 183367 DCC0004 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 26 /data/incoming/DCC0004_183367_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-1\-9\-aRk36X -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-1\-9\-aRk36X \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-1-9-aRk36X Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-1-9-aRk36X You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-1-9-aRk36X.tar ImagingUpload-1-9-aRk36X getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-1-9-aRk36X * Archive target location : /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-1-9-aRk36X.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-24 01:10:01 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : ea44c342cc95679c8d1da95b0c2bb4d4 ImagingUpload-1-9-aRk36X.tar * md5sum for DICOM tarball gzipped : 42971f1828c465ea9e4c87a4ccbcef14 ImagingUpload-1-9-aRk36X.tar.gz * md5sum for complete archive : 9f7a31a61a15ee4b7f8cbadad7e94599 DCM_2016-08-22_ImagingUpload-1-9-aRk36X.tar Adding archive info into database DBD::mysql::st execute failed: Data truncated for column 'EchoTime' at row 1 at /data/loris/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 340. 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\-1\-9\-aRk36X\.tar -uploadID 26 -verbose md5sum /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-1-9-aRk36X.tar PSCID is: DCC0004 CandID id: 183367 visit_label is: V1 PSCID is: DCC0004 CandID id: 183367 visit_label is: V1 candidate id 183367 Set centerID = 1 PSCID is: DCC0004 CandID id: 183367 visit_label is: V1 PSCID is: DCC0004 CandID id: 183367 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-1-10-RG9p3u.log PSCID is: DCC0004 CandID id: 183367 visit_label is: V1 PSCID is: DCC0004 CandID id: 183367 visit_label is: V1 candidate id 183367 Finished file: assembly/183367/V1/mri/native/loris_183367_V1_t1_001.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 384 0.623811 1 1 2 1 384 0.623811 2 0 0 1 180 0.950000 Restructuring... log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-1-10-oy2BKe.log PSCID is: DCC0004 CandID id: 183367 visit_label is: V1 PSCID is: DCC0004 CandID id: 183367 visit_label is: V1 candidate id 183367 Finished file: assembly/183367/V1/mri/native/loris_183367_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 29 4.660714 1 1 1 1 384 0.623811 2 0 2 1 384 0.623811 noise_estimate --snr /data/loris/data//assembly/183367/V1/mri/native/loris_183367_V1_t1_001.mnc SNR is: 102.424 noise_estimate --snr /data/loris/data//assembly/183367/V1/mri/native/loris_183367_V1_t1_002.mnc SNR is: 136.395 Creating Minc Pics TarchiveSource is 13 Connecting to database. FileID from mass_pic.pl is: 20 FileID from mass_pic.pl is: 21 Finished mass_pic.pl execution Cleaning up temp files: rm -rf /tmp/TarLoad-1-10-_QDxoy/ImagingUpload-1-9-aRk36X* find /data/loris/data/tarchive// -name *ImagingUpload-1-9-aRk36X* rm /data/incoming/DCC0004_183367_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. 7.96409988403320 ./102761034/301/1.3.46.670589.11.34037.5.0.4664.2016120612342878292_0301_000022_151699185019fa.dcm 102761034 Creating candidate Update externalid Create candidate Candidate Info 651370 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 27 /data/incoming/DCC0005_651370_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-1\-10\-oNM8vm -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-1\-10\-oNM8vm \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-1-10-oNM8vm Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-1-10-oNM8vm You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-1-10-oNM8vm.tar ImagingUpload-1-10-oNM8vm getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-1-10-oNM8vm * Archive target location : /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-1-10-oNM8vm.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-24 01:10:57 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : b2932757fc7666efad789a82d43d706e ImagingUpload-1-10-oNM8vm.tar * md5sum for DICOM tarball gzipped : a23f143d37f98f5126e9791919e08191 ImagingUpload-1-10-oNM8vm.tar.gz * md5sum for complete archive : 8afe8a06f52d5ff956b4d97a7bd8ac8a DCM_2016-12-06_ImagingUpload-1-10-oNM8vm.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\-12\-06_ImagingUpload\-1\-10\-oNM8vm\.tar -uploadID 27 -verbose md5sum /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-1-10-oNM8vm.tar PSCID is: DCC0005 CandID id: 651370 visit_label is: V1 PSCID is: DCC0005 CandID id: 651370 visit_label is: V1 candidate id 651370 Set centerID = 1 PSCID is: DCC0005 CandID id: 651370 visit_label is: V1 PSCID is: DCC0005 CandID id: 651370 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 ./102506134/401/1.3.46.670589.11.34037.5.0.4800.2015021615033196828_0401_000098_1517388840aea6.dcm 102506134 Creating candidate Update externalid Create candidate Candidate Info 638739 DCC0006 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 28 /data/incoming/DCC0006_638739_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-1\-11\-3ZZg0p -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-1\-11\-3ZZg0p \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-1-11-3ZZg0p 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. From christine.rogers at mcgill.ca Tue Sep 24 09:46:43 2019 From: christine.rogers at mcgill.ca (Christine Rogers, Ms.) Date: Tue, 24 Sep 2019 13:46:43 +0000 Subject: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS In-Reply-To: References: Message-ID: Hi Alfredo, Thanks for sharing your modification with us and the community. Best, Christine On Wed, Sep 18, 2019 at 4:07 PM Morales Pinzon, Alfredo > wrote: Hi C?cile, I added the "filename" to the hash calculation in order to be able to insert the files. Once I finish the insertion of transformations and masks I will remove the line so that it won't change the importing behavior for other images. The modification actually prevents inserting the same exact file based on the filepath. This is the modification: _____________________________________ sub compute_hash { ... if($fileType eq 'mnc') { ... $ctx->add($file->getFileDatum('File')); } ... } _____________________________________ Thank you for the help. Best, Alfredo. ________________________________ From: Cecile Madjar > Sent: Tuesday, September 17, 2019 3:15 PM To: Morales Pinzon, Alfredo > Cc: Christine Rogers, Ms. >; loris-dev at bic.mni.mcgill.ca >; Rozie Arnaoutelis, Ms. >; Sridar Narayanan, Dr. >; Douglas Arnold, Dr. >; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, The "processing" entry I was talking about would need to be created by your wrapper script before calling register_processed_data to create the MINC header in the processed data. A bit like it is done in that function of the DTIPrep pipeline used with LORIS. Then you could use a combination of these new processing tags to differentiate the processed data from the native one. You could always bypass the md5sum check if you prefer but that would mean then that you will not be able to detect duplicated files when inserting a new file. Hope this helps! Let me know how things go, C?cile On Tue, Sep 17, 2019 at 8:08 AM Morales Pinzon, Alfredo > wrote: Hi C?cile, I tried your solution but it didn't work as the mnc headers do not contain any information about patient nor "processing". The headers only have information about the spacing and intensity of the image and are almost similar among them. Attached I'm sending the header for two different mnc files. Is there another way to make the images have different hash? Or maybe bypass the hash check? Best, Alfredo. ________________________________ From: Cecile Madjar > Sent: Tuesday, September 10, 2019 11:59 AM To: Christine Rogers, Ms. > Cc: Morales Pinzon, Alfredo >; loris-dev at bic.mni.mcgill.ca >; Rozie Arnaoutelis, Ms. >; Sridar Narayanan, Dr. >; Douglas Arnold, Dr. >; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, Sorry, I just came back from vacation. I don't know if you still have issues inserting the data. Just in case and to let you know, the MD5SUM is computed on the MINC files based on the following list of MINC headers: * patient:full_name * study:start_time * patient:identification * patient:sex * patient:age * patient:birthdate * study_instance_uid * series_description * processing:intergradient_rejected The code with the list of headers to use to create an MD5sum is in the MRI.pm library (function called compute_hash). When I had to develop the insertion of processed DWI images into the database, most of the headers used were identical to the native image which resulted in the duplicate error message you got. To bypass that, I created a new MINC header (under a processing category) in the processed images that I wanted to insert with some parameters specific to that processed image and modified the code in the compute_hash function to include that new header when computing the MD5sum. You would just need to add an additional if statement like in line 1198 of MRI.pm. Let me know if you have questions or if something is not clear. Best, C?cile On Fri, Aug 30, 2019 at 3:35 PM Christine Rogers, Ms. > wrote: Hi Alfredo, Great, this is helpful to know. If I understand you - the filename is the same for all the packages of processed data you are trying to upload, for various subject-visits. e.g. you may have organized them in subdirectories like: $subject/$visit/processed_data.gz One solution could be to make a copy with a different name before uploading. Instead of making a copy (or renaming) -- try a unique soft-link for each package. I should think that would work (though can't confirm right now). e.g. Use a simple bash command to execute for each package: > ln -s $subject/$visit/processed_data.gz ./$subject_$visit_processed_data.gz (then tell the pipeline to load each $subject_$visit_processed_data.gz ) Again, this no-duplicate check exists to help ensure duplicate data isn't inserted, which is a protection we try to preserve as much as possible. Since all the code is customizable, this check could be manually bypassed, but ideally this workaround will help keep the error-proofing intact. Let us know how this goes - We'll be offline for Labour day weekend but back in the office next Tuesday. Best, Christine On Fri, Aug 30, 2019 at 12:53 PM Morales Pinzon, Alfredo > wrote: Hi Christine, Thank you for your answer. Here are the answers to your questions: Can you use distinct filenames ? We could but we already have all the images, thousands, with a pre-defined convention. One solution could be to make a copy with a different name before uploading. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Yes, we are uploading the result of a couple of pipelines for each participant for each label. Let me know if you can find a workaround, in the mean time I will check with Pisti if we can make a copy of the files with a different name before uploading. Best, Alfredo. ________________________________ From: Christine Rogers, Ms. > Sent: Friday, August 30, 2019 11:17 AM To: Morales Pinzon, Alfredo > Cc: loris-dev at bic.mni.mcgill.ca >; Cecile Madjar >; Sridar Narayanan, Dr. >; Rozie Arnaoutelis, Ms. >; Douglas Arnold, Dr. >; Guttmann, Charles,M.D. > Subject: Re: [Loris-dev] Error "not a unique file" inserting segmentation files in LORIS External Email - Use Caution Hi Alfredo, Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. To provide a quick answer (since most of our imaging team is on vacation this week) : Yes the MD5hash seems to require a unique filename (* below). Can you use distinct filenames ? i.e. Are you are trying to load additional data for a participant session (i.e. same IDs and visit label) ? Or, are you trying to load more than one participant/session at a time? (*) This line in the actual MRIProcessingUtility library: (around Line 617) $md5hash = &NeuroDB::MRI::compute_hash(\$file); and my $unique = &NeuroDB::MRI::is_unique_hash(\$file); I'll check with other imaging devs to see if we have a workaround while our senior devs are away -- I think there must be some solution... Meanwhile, the MD5hash for imaging files is documented here (per this script documentation) : computeMd5Hash($file, $upload_id) Computes the MD5 hash of a file and makes sure it is unique. INPUTS: * $file : file to use to compute the MD5 hash * $upload_id: upload ID of the study RETURNS: 1 if the file is unique, 0 otherwise Best, Christine On Thu, Aug 29, 2019 at 9:46 PM Morales Pinzon, Alfredo > wrote: Dear DevLoris Team, I started the uploading process of processed files, segmentations and transformations, using the file "register_processed_data.pl" but some files are not being uploaded. The error reported in "data/logs/registerProcessed" show the following log for one of the files that could not be inserted: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-29_19:08:17 ==>Mapped DICOM parameters -> using user-defined filterParameters for /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: w024 -> Set SessionID to 28269. -> Set SourceFileID to 49598. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to ConsensusGd. -> Set PipelineDate to 2019-08-29. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. ==> NeuroDB::File=HASH(0x136baa8) is not a unique file and will not be added to database. ------------------------------------------------------------------------------- I checked the md5hash for a previous uploaded file, which is different from the previous, but the same "md5hash" was calculated. See the following log: ------------------------------------------------------------------------------- ==> Successfully connected to database Log file, 2019-08-19_10:11:53 ==>Mapped DICOM parameters -> using user-defined filterParameters for ==> Verifying acquisition center - Center Name : UNKN - CenterID : 0 -> Set ScannerID to 0. ==> Data found for candidate : 123456 - Visit: baseline -> Set SessionID to 28268. -> Set SourceFileID to 49593. -> Set AcquisitionProtocolID to 1013. -> Set CoordinateSpace to stx152lsq6. -> Set SourcePipeline to T2Vol. -> Set PipelineDate to 2019-08-19. -> Set OutputType to gvf. -> Set md5hash to b877648ed0ef9a7458ad4931f4dbfd11. File /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz moved to: /yyy/data/assembly/123456/baseline/mri/processed/T2Vol/IPMSA_123456_baseline_t1c_001_gvf_001.mnc.gz ==> FAILED TO INSERT INTERMEDIARY FILES FOR 112945! Making JIV ==> Registered /data_/ipmsa/loris_data/IPMSA/data/assembly/307024/baseline/mri/processed/T2Vol/IPMSA_307024_baseline_t1c_001_gvf_001.mnc.gz in database, given FileID: 112945 ------------------------------------------------------------------------------- Here are the corresponding md5 for each file calculated using the command md5sum: /xxx/w024/gvf_ISPC-stx152lsq6.mnc.gz 7306010346c4614d8e338595b386ca5c /xxx/baseline/gvf_ISPC-stx152lsq6.mnc.gz 22107253f8b87c9918ac7f82fdc22c36 Could you please help me inserting those files which are different in size and md5 from previous uploaded files? The only similarity between the previous uploaded files and the ones that could not be uploaded is the filename. Let me know if you need more information. 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 -- 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 _______________________________________________ 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 sotirisnik at gmail.com Tue Sep 24 11:56:45 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Tue, 24 Sep 2019 18:56:45 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 >>>>>>>> ??????: >>>>>>>> >>>>>>>> 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 <>>>>>>> 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 >>>>>>>> >>>>>>>> ) >>>>>>>> >>>>>>>> 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 >> > -------------- next part -------------- An HTML attachment was scrubbed... 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Name: image.png Type: image/png Size: 10443 bytes Desc: not available URL: From cecile.madjar at mcin.ca Tue Sep 24 16:24:16 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 24 Sep 2019 16:24:16 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 ??????: >>>>>>>>> >>>>>>>>> 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 >>>>>>>>> ??????: >>>>>>>>> >>>>>>>>> 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 >>>>>>>>> ??????: >>>>>>>>> >>>>>>>>> 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 >>>>>>>>> ??????: >>>>>>>>> >>>>>>>>> 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 <>>>>>>>> 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 >>>>>>>>> >>>>>>>>> ) >>>>>>>>> >>>>>>>>> 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 >>>>>>>>> ??????: >>>>>>>>> >>>>>>>>> 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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Name: image.png Type: image/png Size: 10443 bytes Desc: not available URL: From sotirisnik at gmail.com Thu Sep 26 09:48:03 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Thu, 26 Sep 2019 16:48:03 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 ??????: >>>>>>>>>> >>>>>>>>>> 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 ??????: >>>>>>>>>> >>>>>>>>>> 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 ??????: >>>>>>>>>> >>>>>>>>>> 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 ??????: >>>>>>>>>> >>>>>>>>>> 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 <>>>>>>>>> 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 >>>>>>>>>> >>>>>>>>>> ) >>>>>>>>>> >>>>>>>>>> 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 ??????: >>>>>>>>>> >>>>>>>>>> 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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Name: image.png Type: image/png Size: 10443 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: From cecile.madjar at mcin.ca Thu Sep 26 10:07:21 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Thu, 26 Sep 2019 10:07:21 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 ??????: >>>>>>>>>>> >>>>>>>>>>> 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 ??????: >>>>>>>>>>> >>>>>>>>>>> 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 ??????: >>>>>>>>>>> >>>>>>>>>>> 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 ??????: >>>>>>>>>>> >>>>>>>>>>> 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 <>>>>>>>>>> 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 >>>>>>>>>>> >>>>>>>>>>> ) >>>>>>>>>>> >>>>>>>>>>> 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 ??????: >>>>>>>>>>> >>>>>>>>>>> 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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Name: image.png Type: image/png Size: 10443 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: From sotirisnik at gmail.com Fri Sep 27 06:17:36 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Fri, 27 Sep 2019 13:17:36 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 >>>>>>>> ??????: >>>>>>>> >>>>>>>>> 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 ??????: >>>>>>>>>>>> >>>>>>>>>>>> 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. >>>>>>>>>>>> ??????: >>>>>>>>>>>> >>>>>>>>>>>> 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 ??????: >>>>>>>>>>>> >>>>>>>>>>>> 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 ??????: >>>>>>>>>>>> >>>>>>>>>>>> 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 ??????: >>>>>>>>>>>> >>>>>>>>>>>> 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. >>>>>>>>>>>> ??????: >>>>>>>>>>>> >>>>>>>>>>>> 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 <>>>>>>>>>>> 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 >>>>>>>>>>>> >>>>>>>>>>>> ) >>>>>>>>>>>> >>>>>>>>>>>> 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 ??????: >>>>>>>>>>>> >>>>>>>>>>>> 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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Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: -------------- next part -------------- (loris-mri-python) lorisadmin at loris-VirtualBox:~/DataQualityControlTool/mipqctool$ python dicom_uploader.py ./102788419/7/1.3.12.2.1107.5.2.30.27245.2015122209062920279710806.0.0.0_0007_000048_15169884000bff.dcm 102788419 Creating candidate Update externalid Create candidate Candidate Info 282430 DCC0000 Next Visit Label 1 ./102788419/7/1.3.12.2.1107.5.2.30.27245.2015122209062920279710806.0.0.0_0007_000158_15169884100c6f.dcm does not have Protocolname ./102788419/7/1.3.12.2.1107.5.2.30.27245.2015122209062920279710806.0.0.0_0007_000158_15169884100c6f.dcm does not have SeriesDescription 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 47 /data/incoming/DCC0000_282430_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-4\-55\-UvVoD1 -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-4\-55\-UvVoD1 \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-4-55-UvVoD1 Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-4-55-UvVoD1 You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-4-55-UvVoD1.tar ImagingUpload-4-55-UvVoD1 getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-4-55-UvVoD1 * Archive target location : /data/loris/data/tarchive/DCM_2015-12-22_ImagingUpload-4-55-UvVoD1.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-27 04:55:32 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 14adb7eef8c44ba8155bd21ba53c7ccc ImagingUpload-4-55-UvVoD1.tar * md5sum for DICOM tarball gzipped : 0761dd6b8cd49b6f47041c3fdb91c36f ImagingUpload-4-55-UvVoD1.tar.gz * md5sum for complete archive : 780bc49bbbb615f17f338fb34afcb40f DCM_2015-12-22_ImagingUpload-4-55-UvVoD1.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_2015\-12\-22_ImagingUpload\-4\-55\-UvVoD1\.tar -uploadID 47 -verbose md5sum /data/loris/data/tarchive/DCM_2015-12-22_ImagingUpload-4-55-UvVoD1.tar PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 candidate id 282430 Set centerID = 1 PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 5 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-55-NF3beZ.log PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 candidate id 282430 Finished file: assembly/282430/V1/mri/native/loris_282430_V1_t1_001.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 256 0.976562 1 1 2 1 256 0.976562 2 0 0 1 175 1.005747 Restructuring... log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-55-3SdUJ3.log PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 candidate id 282430 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-55-ascm1w.log PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 candidate id 282430 Finished file: assembly/282430/V1/mri/native/loris_282430_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 30 4.940154 1 1 1 1 256 0.976562 2 0 2 1 256 0.976562 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-55-PIcp0N.log PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 candidate id 282430 Finished file: assembly/282430/V1/mri/native/loris_282430_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 1 256 0.976562 1 1 0 1 30 5.233743 2 0 2 1 256 0.976562 Restructuring... log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-55-cY5KRd.log PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 PSCID is: DCC0000 CandID id: 282430 visit_label is: V1 candidate id 282430 Finished file: assembly/282430/V1/mri/native/loris_282430_V1_t1_004.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 256 0.976562 1 1 2 1 256 0.976562 2 0 0 1 30 4.465090 Restructuring... noise_estimate --snr /data/loris/data//assembly/282430/V1/mri/native/loris_282430_V1_t1_001.mnc SNR is: 30.8967 noise_estimate --snr /data/loris/data//assembly/282430/V1/mri/native/loris_282430_V1_t1_002.mnc SNR is: 62.5745 noise_estimate --snr /data/loris/data//assembly/282430/V1/mri/native/loris_282430_V1_t1_003.mnc SNR is: 61.2643 noise_estimate --snr /data/loris/data//assembly/282430/V1/mri/native/loris_282430_V1_t1_004.mnc SNR is: 56.031 Creating Minc Pics TarchiveSource is 25 Connecting to database. FileID from mass_pic.pl is: 44 FileID from mass_pic.pl is: 45 FileID from mass_pic.pl is: 46 FileID from mass_pic.pl is: 47 Finished mass_pic.pl execution Cleaning up temp files: rm -rf /tmp/TarLoad-4-55-BWCHDs/ImagingUpload-4-55-UvVoD1* Can't exec "mail": No such file or directory at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 665. print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 666. print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 667. print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 668. print() on closed filehandle MAIL at /data/loris/bin/mri//uploadNeuroDB/tarchiveLoader.pl line 669. find /data/loris/data/tarchive// -name *ImagingUpload-4-55-UvVoD1* rm /data/incoming/DCC0000_282430_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. 1940 ./102327840/6/1.3.12.2.1107.5.2.18.41881.2015052614223027481362738.0.0.0_0006_000030_151783708598e6.dcm 102327840 Creating candidate Update externalid Create candidate Candidate Info 122941 DCC0001 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 48 /data/incoming/DCC0001_122941_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-4\-56\-JBLS6f -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-4\-56\-JBLS6f \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-4-56-JBLS6f 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 ./102809579/10/1.3.12.2.1107.5.2.30.27780.2017071115494453951663644.0.0.0_0010_000030_1518430122f026.dcm 102809579 Creating candidate Update externalid Create candidate Candidate Info 153533 DCC0002 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 49 /data/incoming/DCC0002_153533_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-4\-56\-djVIXf -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-4\-56\-djVIXf \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-4-56-djVIXf Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-4-56-djVIXf You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-4-56-djVIXf.tar ImagingUpload-4-56-djVIXf getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-4-56-djVIXf * Archive target location : /data/loris/data/tarchive/DCM_2017-07-11_ImagingUpload-4-56-djVIXf.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-27 04:56:16 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 5f55a5556596ed5f44b0f908711a7114 ImagingUpload-4-56-djVIXf.tar * md5sum for DICOM tarball gzipped : 2bf98abfdaf85756cc5f2ccca7eca152 ImagingUpload-4-56-djVIXf.tar.gz * md5sum for complete archive : 5eadd7a9f46d7574f1cdf15b2509fef8 DCM_2017-07-11_ImagingUpload-4-56-djVIXf.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_2017\-07\-11_ImagingUpload\-4\-56\-djVIXf\.tar -uploadID 49 -verbose md5sum /data/loris/data/tarchive/DCM_2017-07-11_ImagingUpload-4-56-djVIXf.tar PSCID is: DCC0002 CandID id: 153533 visit_label is: V1 PSCID is: DCC0002 CandID id: 153533 visit_label is: V1 candidate id 153533 Set centerID = 1 PSCID is: DCC0002 CandID id: 153533 visit_label is: V1 PSCID is: DCC0002 CandID id: 153533 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-56-Jwsdtf.log PSCID is: DCC0002 CandID id: 153533 visit_label is: V1 PSCID is: DCC0002 CandID id: 153533 visit_label is: V1 candidate id 153533 Finished file: assembly/153533/V1/mri/native/loris_153533_V1_t1_001.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 640 0.437500 1 1 2 1 540 0.437500 2 0 0 1 43 1.000000 Restructuring... noise_estimate --snr /data/loris/data//assembly/153533/V1/mri/native/loris_153533_V1_t1_001.mnc SNR is: 206.057 Creating Minc Pics TarchiveSource is 26 Connecting to database. FileID from mass_pic.pl is: 48 Finished mass_pic.pl execution Cleaning up temp files: rm -rf /tmp/TarLoad-4-56-adLn78/ImagingUpload-4-56-djVIXf* find /data/loris/data/tarchive// -name *ImagingUpload-4-56-djVIXf* rm /data/incoming/DCC0002_153533_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. 1800 ./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 756939 DCC0003 Next Visit Label 1 ./000535670/501/1.3.46.670589.11.34037.5.0.6020.2012120510342515883_0501_000111_151810731519ee.dcm does not have Protocolname ./000535670/501/1.3.46.670589.11.34037.5.0.6020.2012120510342515883_0501_000111_151810731519ee.dcm does not have SeriesDescription 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 50 /data/incoming/DCC0003_756939_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-4\-58\-yNHgRZ -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-4\-58\-yNHgRZ \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-4-58-yNHgRZ Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-4-58-yNHgRZ You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-4-58-yNHgRZ.tar ImagingUpload-4-58-yNHgRZ getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-4-58-yNHgRZ * Archive target location : /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-4-58-yNHgRZ.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-27 04:58:35 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : c7b421c10fa2c6b4db057d2c942da9d4 ImagingUpload-4-58-yNHgRZ.tar * md5sum for DICOM tarball gzipped : c14ee5bab7cc0e91884911fc50a72e6f ImagingUpload-4-58-yNHgRZ.tar.gz * md5sum for complete archive : ff1de3b94301c8b0ace9d13d057c0ccc DCM_2012-12-05_ImagingUpload-4-58-yNHgRZ.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_2012\-12\-05_ImagingUpload\-4\-58\-yNHgRZ\.tar -uploadID 50 -verbose md5sum /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-4-58-yNHgRZ.tar PSCID is: DCC0003 CandID id: 756939 visit_label is: V1 PSCID is: DCC0003 CandID id: 756939 visit_label is: V1 candidate id 756939 Set centerID = 1 PSCID is: DCC0003 CandID id: 756939 visit_label is: V1 PSCID is: DCC0003 CandID id: 756939 visit_label is: V1 Number of MINC files that will be considered for inserting into the database: 1 log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-58-clwvUZ.log PSCID is: DCC0003 CandID id: 756939 visit_label is: V1 PSCID is: DCC0003 CandID id: 756939 visit_label is: V1 candidate id 756939 Finished file: assembly/756939/V1/mri/native/loris_756939_V1_t1_001.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 256 1.000000 1 1 2 1 256 1.000000 2 0 0 1 91 1.766667 Restructuring... noise_estimate --snr /data/loris/data//assembly/756939/V1/mri/native/loris_756939_V1_t1_001.mnc SNR is: 23.989 Creating Minc Pics TarchiveSource is 27 Connecting to database. FileID from mass_pic.pl is: 49 Finished mass_pic.pl execution Cleaning up temp files: rm -rf /tmp/TarLoad-4-58-buXWmO/ImagingUpload-4-58-yNHgRZ* find /data/loris/data/tarchive// -name *ImagingUpload-4-58-yNHgRZ* rm /data/incoming/DCC0003_756939_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. 9.90050029754638 ./000998448/205/1.3.46.670589.11.70598.5.0.7280.2016082207333647000_0205_000024_1518217540255b.dcm 000998448 Creating candidate Update externalid Create candidate Candidate Info 280768 DCC0004 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 51 /data/incoming/DCC0004_280768_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-4\-58\-JfECYF -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-4\-58\-JfECYF \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-4-58-JfECYF Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-4-58-JfECYF You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-4-58-JfECYF.tar ImagingUpload-4-58-JfECYF getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-4-58-JfECYF * Archive target location : /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-4-58-JfECYF.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-27 04:59:01 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 6d21df8cc0996eafa317f6ac9cc64123 ImagingUpload-4-58-JfECYF.tar * md5sum for DICOM tarball gzipped : a198063eb18cfa4dc0591357c20dd1c2 ImagingUpload-4-58-JfECYF.tar.gz * md5sum for complete archive : 3aad64442f6f8233690e645c4fd05fc5 DCM_2016-08-22_ImagingUpload-4-58-JfECYF.tar Adding archive info into database DBD::mysql::st execute failed: Data truncated for column 'EchoTime' at row 1 at /data/loris/bin/mri/dicom-archive/DICOM/DCMSUM.pm line 340. 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\-4\-58\-JfECYF\.tar -uploadID 51 -verbose md5sum /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-4-58-JfECYF.tar PSCID is: DCC0004 CandID id: 280768 visit_label is: V1 PSCID is: DCC0004 CandID id: 280768 visit_label is: V1 candidate id 280768 Set centerID = 1 PSCID is: DCC0004 CandID id: 280768 visit_label is: V1 PSCID is: DCC0004 CandID id: 280768 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-4-59-NFKgPt.log PSCID is: DCC0004 CandID id: 280768 visit_label is: V1 PSCID is: DCC0004 CandID id: 280768 visit_label is: V1 candidate id 280768 Finished file: assembly/280768/V1/mri/native/loris_280768_V1_t1_001.mnc Creating NIfTI files found zspace at 1 0 found yspace at 2 1 found xspace at 0 2 0 2 1 1 384 0.623811 1 1 2 1 384 0.623811 2 0 0 1 180 0.950000 Restructuring... log dir is /data/loris/data//logs and log file is /data/loris/data//logs/TarLoad-4-59-EbeiH8.log PSCID is: DCC0004 CandID id: 280768 visit_label is: V1 PSCID is: DCC0004 CandID id: 280768 visit_label is: V1 candidate id 280768 Finished file: assembly/280768/V1/mri/native/loris_280768_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 29 4.660714 1 1 1 1 384 0.623811 2 0 2 1 384 0.623811 noise_estimate --snr /data/loris/data//assembly/280768/V1/mri/native/loris_280768_V1_t1_001.mnc SNR is: 102.424 noise_estimate --snr /data/loris/data//assembly/280768/V1/mri/native/loris_280768_V1_t1_002.mnc SNR is: 136.395 Creating Minc Pics TarchiveSource is 28 Connecting to database. FileID from mass_pic.pl is: 50 FileID from mass_pic.pl is: 51 Finished mass_pic.pl execution Cleaning up temp files: rm -rf /tmp/TarLoad-4-59-P26NrA/ImagingUpload-4-58-JfECYF* find /data/loris/data/tarchive// -name *ImagingUpload-4-58-JfECYF* rm /data/incoming/DCC0004_280768_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. 7.96409988403320 ./102761034/301/1.3.46.670589.11.34037.5.0.4664.2016120612342878292_0301_000022_151699185019fa.dcm 102761034 Creating candidate Update externalid Create candidate Candidate Info 592193 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 52 /data/incoming/DCC0005_592193_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-4\-59\-udVPCy -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-4\-59\-udVPCy \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-4-59-udVPCy Target: /data/loris/data/tarchive Testing for database connectivity. Database is available. You will archive the dir : ImagingUpload-4-59-udVPCy You are creating a tar with the following command: tar -cf /data/loris/data/tarchive/ImagingUpload-4-59-udVPCy.tar ImagingUpload-4-59-udVPCy getting md5sums and gzipping!! * Taken from dir : /tmp/ImagingUpload-4-59-udVPCy * Archive target location : /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-4-59-udVPCy.tar * Name of creating host : 127.0.1.1 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2019-09-27 04:59:51 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : f56ffbbc4a49d937d401291b5dfdcc5d ImagingUpload-4-59-udVPCy.tar * md5sum for DICOM tarball gzipped : 6b5ded248549f251c3c874a285bc7691 ImagingUpload-4-59-udVPCy.tar.gz * md5sum for complete archive : a1fa979684d637c23d6a6fc7d4266bd3 DCM_2016-12-06_ImagingUpload-4-59-udVPCy.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\-12\-06_ImagingUpload\-4\-59\-udVPCy\.tar -uploadID 52 -verbose md5sum /data/loris/data/tarchive/DCM_2016-12-06_ImagingUpload-4-59-udVPCy.tar PSCID is: DCC0005 CandID id: 592193 visit_label is: V1 PSCID is: DCC0005 CandID id: 592193 visit_label is: V1 candidate id 592193 Set centerID = 1 PSCID is: DCC0005 CandID id: 592193 visit_label is: V1 PSCID is: DCC0005 CandID id: 592193 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 ./102506134/401/1.3.46.670589.11.34037.5.0.4800.2015021615033196828_0401_000098_1517388840aea6.dcm 102506134 Creating candidate Update externalid Create candidate Candidate Info 976678 DCC0006 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/bin/mri//uploadNeuroDB/imaging_upload_file.pl -profile prod -upload_id 53 /data/incoming/DCC0006_976678_V1.tar.gz -verbose find -path \/tmp\/ImagingUpload\-5\-0\-nJMgpV -name '__MACOSX' -delete dicomTar.pl \/tmp\/ImagingUpload\-5\-0\-nJMgpV \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose Source: /tmp/ImagingUpload-5-0-nJMgpV 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: '1.3.51.0.1.1.10.49.10.222.3332609.3331661' '1.3.51.0.1.1.10.49.10.222.2753369.2752207' 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 2500.1000 From cecile.madjar at mcin.ca Fri Sep 27 09:22:15 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Fri, 27 Sep 2019 09:22:15 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 >>>>>>>> ??????: >>>>>>>> >>>>>>>>> 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 ??????: >>>>>>>>> >>>>>>>>>> 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 >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Christine >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>> >>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, Ms. >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>> >>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and all >>>>>>>>>>>>> the front-end pages are loading. >>>>>>>>>>>>> >>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>> >>>>>>>>>>>>> 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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Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: From sotirisnik at gmail.com Mon Sep 30 06:00:01 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 30 Sep 2019 13:00:01 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 ??????: >>>>>>>>> >>>>>>>>>> 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 ??????: >>>>>>>>>> >>>>>>>>>>> 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 >>>>>>>>>>>>> ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Christine >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>> >>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>>> all the front-end pages are loading. >>>>>>>>>>>>>> >>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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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Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: From cecile.madjar at mcin.ca Mon Sep 30 08:38:33 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 30 Sep 2019 08:38:33 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 ??????: >>>>>>>>>> >>>>>>>>>>> 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 ??????: >>>>>>>>>>> >>>>>>>>>>>> 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. >>>>>>>>>>>> ??????: >>>>>>>>>>>> >>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>>>> all the front-end pages are loading. >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 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Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: From sotirisnik at gmail.com Mon Sep 30 08:55:44 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 30 Sep 2019 15:55:44 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 >>>>>>>> ??????: >>>>>>>> >>>>>>>>> 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 ??????: >>>>>>>>>>> >>>>>>>>>>>> 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 ??????: >>>>>>>>>>>> >>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>>>>> all the front-end pages are loading. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>> 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Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42208 bytes Desc: not available URL: From cecile.madjar at mcin.ca Mon Sep 30 09:04:12 2019 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 30 Sep 2019 09:04:12 -0400 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: Ooops, sorry. I read to quickly... You are right. It does not look like we are storing that information at the DICOM level. However, you can see that information in the parameter_file table once the MINC file has been inserted into the database using the following query: SELECT File, Name, Value FROM files JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Name='study:study_id'; Hope this helps and sorry again for the confusion... C?cile On Mon, Sep 30, 2019 at 8:56 AM Sotirios Nikoloutsopoulos < sotirisnik at gmail.com> wrote: > 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 ??????: >>>>>>>>> >>>>>>>>>> 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 ??????: >>>>>>>>>>>> >>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>>>>>> all the front-end pages are loading. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 | 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Name: image.png Type: image/png Size: 175139 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 42208 bytes Desc: not available URL: From sotirisnik at gmail.com Mon Sep 30 09:04:37 2019 From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos) Date: Mon, 30 Sep 2019 16:04:37 +0300 Subject: [Loris-dev] Import mri - scripts In-Reply-To: References: Message-ID: 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 ??????: >>>>>>>>> >>>>>>>>>> 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 ??????: >>>>>>>>>>>> >>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>> >>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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 $mridir >>>>>>>>>>>>>>>>> /dicom-archive/.loris_mri/database_config.py >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>>> Christine >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos < >>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Christine, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If you are referring to the imaging_install.sh here is an >>>>>>>>>>>>>>>>> image with the configurations i typed. Maybe the problem is somewhere at >>>>>>>>>>>>>>>>> the last part which asks to configure as much as possible automatically? >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Thanks >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine Rogers, >>>>>>>>>>>>>>>>> Ms. ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Sotirios, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Glad to hear your LORIS core install is up and working and >>>>>>>>>>>>>>>>> all the front-end pages are loading. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> > lorisadmin at loris-VirtualBox:/var/www/loris$ 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 ??????: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> 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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