[Loris-dev] Upgrading to Loris 21 - new make file
Dave MacFarlane
dave.macfarlane at mcin.ca
Thu Aug 8 09:31:49 EDT 2019
It looks like the javascript snippet shown in the error message when trying
to compile the js is truncated. Have you run out of disk space?
On Thu, Aug 8, 2019 at 8:37 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:
> Hi,
>
> I runned make and also included the file it reports at the end.
>
> lorisadmin at hbp:/var/www/loris$ make
> npm install
> npm WARN optional Skipping failed optional dependency /chokidar/fsevents:
> npm WARN notsup Not compatible with your operating system or architecture:
> fsevents at 1.2.9
> npm WARN optional Skipping failed optional dependency
> /watchpack/chokidar/fsevents:
> npm WARN notsup Not compatible with your operating system or architecture:
> fsevents at 1.2.9
> npm run compile
>
> > loris at 1.0.0 compile /var/www/loris
> > webpack
>
> /var/www/loris/node_modules/webpack/bin/webpack.js:86
> let notify =
> ^^^
>
> SyntaxError: Block-scoped declarations (let, const, function, class) not
> yet supported outside strict mode
> at exports.runInThisContext (vm.js:53:16)
> at Module._compile (module.js:374:25)
> at Object.Module._extensions..js (module.js:417:10)
> at Module.load (module.js:344:32)
> at Function.Module._load (module.js:301:12)
> at Function.Module.runMain (module.js:442:10)
> at startup (node.js:136:18)
> at node.js:966:3
>
> npm ERR! Linux 4.15.0-55-generic
> npm ERR! argv "/usr/bin/nodejs" "/usr/bin/npm" "run" "compile"
> npm ERR! node v4.2.6
> npm ERR! npm v3.5.2
> npm ERR! code ELIFECYCLE
> npm ERR! loris at 1.0.0 compile: `webpack`
> npm ERR! Exit status 1
> npm ERR!
> npm ERR! Failed at the loris at 1.0.0 compile script 'webpack'.
> npm ERR! Make sure you have the latest version of node.js and npm
> installed.
> npm ERR! If you do, this is most likely a problem with the loris package,
> npm ERR! not with npm itself.
> npm ERR! Tell the author that this fails on your system:
> npm ERR! webpack
> npm ERR! You can get information on how to open an issue for this project
> with:
> npm ERR! npm bugs loris
> npm ERR! Or if that isn't available, you can get their info via:
> npm ERR! npm owner ls loris
> npm ERR! There is likely additional logging output above.
>
> npm ERR! Please include the following file with any support request:
> npm ERR! /var/www/loris/npm-debug.log
> Makefile:14: recipe for target 'javascript' failed
> make: *** [javascript] Error 1
>
> Thanks,
>
> Sotirios
>
> Στις Τετ, 7 Αυγ 2019 στις 5:41 μ.μ., ο/η Christine Rogers, Ms. <
> christine.rogers at mcgill.ca> έγραψε:
>
>> Hi Sotirios,
>>
>> Thanks, have you tried all of these steps?
>> - clear your browser cache (and refresh a few times)
>> - delete any files in your smarty/templates_c directory (this will clear
>> the template cache - do Not touch smarty/templates/)
>> - run `make` (per the 21 release notes, this replaces the composer
>> commands used in previous releases to update your dependencies)
>> - restart apache (doesn't hurt)
>>
>> Let us know how it goes -- let us know what difference you see after,
>> with your logs. A
>> lso please send us your Config path settings (see these Troubleshooting
>> Queries
>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>)
>> if you're still seeing front-end issues.
>>
>> Thanks,
>> Christine
>>
>> On Wed, Aug 7, 2019 at 8:02 AM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> lorisadmin at hbp:/var/www/loris$ sudo cat /var/log/apache2/error.log
>>> [Wed Aug 07 07:35:02.422501 2019] [mpm_prefork:notice] [pid 1267]
>>> AH00163: Apache/2.4.18 (Ubuntu) OpenSSL/1.0.2g configured -- resuming
>>> normal operations
>>> [Wed Aug 07 07:35:02.422514 2019] [core:notice] [pid 1267] AH00094:
>>> Command line: '/usr/sbin/apache2'
>>>
>>> And as for the access.log the content are empty
>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log
>>> lorisadmin at hbp:/var/www/loris$ sudo ls -l /var/log/apache2/access.log
>>> -rw-r----- 1 root adm 0 Ιούν 28 14:09 /var/log/apache2/access.log
>>>
>>> Also i noticed a loris_access.log.
>>>
>>> The only non-blank pages are:
>>> mri_violations, dataquery does not exist at all, statistics,
>>> data_team_helper, genomic_browser, configuration and
>>> server_processes_manager/ prints "Required configuration settings for
>>> Server Processes Manager are missing. Cannot continue."
>>>
>>> Thanks,
>>> Sotirios
>>>
>>> Στις Τρί, 6 Αυγ 2019 στις 10:13 μ.μ., ο/η Christine Rogers, Ms. <
>>> christine.rogers at mcgill.ca> έγραψε:
>>>
>>>> Hi Sotirios and LORIS community --
>>>>
>>>> When upgrading to brand-new release 21 -- just a reminder to follow
>>>> the release notes and run the new *make* file to update your
>>>> dependencies (instead of using *composer* commands).
>>>> We've also updated the Wiki page
>>>> <https://github.com/aces/Loris/wiki/Updating-your-LORIS> to clarify
>>>> that the release notes for each version will tell you what to run.
>>>>
>>>> If your current version is not the last release (20.3), it's still
>>>> important to upgrade to each minor release increment (e.g. 20.2, 20.3)
>>>> before making the leap to 21.0.
>>>>
>>>> If you're getting blank pages, post-upgrade -- Try clearing your cache.
>>>>
>>>> Got questions or feedback e.g. on the Release Notes? please don't
>>>> hesitate to let us know.
>>>> Thanks,
>>>> Christine
>>>> The LORIS team
>>>>
>>>>
>>>>
>>>> On Tue, Aug 6, 2019 at 10:09 AM Christine Rogers, Ms. <
>>>> christine.rogers at mcgill.ca> wrote:
>>>>
>>>>> Hi Sotirios,
>>>>> Could you also let us know -- on which pages is content visible, and
>>>>> on which pages/modules is content not visible for you?
>>>>> Thanks,
>>>>> Christine
>>>>>
>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. <
>>>>> christine.rogers at mcgill.ca> wrote:
>>>>>
>>>>>> Thanks Sotirios,
>>>>>> That's good to know. It sounds like you've checked that your
>>>>>> /var/www/loris/project/config.xml file get populated properly.
>>>>>>
>>>>>> Please send us the last few errors you're seeing in your apache error
>>>>>> log file, and your config paths and we can see what's happening with your
>>>>>> front end --
>>>>>> Run these Troubleshooting Queries
>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>
>>>>>> to get your config path settings, given your front end is not displaying
>>>>>> fully.
>>>>>>
>>>>>> The Loris-MRI repo
>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0> 21
>>>>>> install/upgrade would then be your next steps.
>>>>>> Best,
>>>>>> Christine
>>>>>>
>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>
>>>>>>> I am using a VM. What i did was:
>>>>>>> 1) Download the files from https://github.com/aces/Loris and
>>>>>>> replace them to my existing /vaw/www/loris folder.
>>>>>>> 2) Execute the composer install --no-dev and then composer
>>>>>>> dump-autoload as mentioned here
>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS.
>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS
>>>>>>> already existed i moved a .config file, then re-executed the install.sh
>>>>>>> successfully
>>>>>>> 4 ) As for the database, i dropped the schema and i executed the
>>>>>>> installdb.php
>>>>>>>
>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 5:22 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>
>>>>>>>> Hi Sotorios,
>>>>>>>>
>>>>>>>> Thanks - when you re-installed did you start on a fresh root path /
>>>>>>>> VM or might some of your old system setting still apply?
>>>>>>>> (And if you did any steps similar to an upgrade, did you follow the
>>>>>>>> Upgrade steps in the Release Notes, from both repos?)
>>>>>>>>
>>>>>>>> About the TR_range column - it was recently split (MRI pr339
>>>>>>>> <https://github.com/aces/Loris-MRI/pull/339>) split into TR_min
>>>>>>>> and _max columns. Given the code was trying to query TR_range which does
>>>>>>>> not exist in your mri_protocol table, double-check which version of the
>>>>>>>> Loris repo (tables) and the Loris-MRI repo (code) you have installed to
>>>>>>>> ensure they match.
>>>>>>>>
>>>>>>>> Christine
>>>>>>>>
>>>>>>>>
>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos <
>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not
>>>>>>>>> visible at all at most pages.
>>>>>>>>>
>>>>>>>>> [image: image.png]
>>>>>>>>>
>>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 3:19 μ.μ., ο/η Sotirios Nikoloutsopoulos
>>>>>>>>> <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>
>>>>>>>>>> Hi,
>>>>>>>>>>
>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails
>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol
>>>>>>>>>> which doesn't have TR_range
>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556
>>>>>>>>>>
>>>>>>>>>> [image: image.png]
>>>>>>>>>>
>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>> ./batch_uploads_imageuploader line 147.
>>>>>>>>>> base is DCC0000_258024_V1
>>>>>>>>>> path is /data/incoming/
>>>>>>>>>> type is .tar.gz
>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz
>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in
>>>>>>>>>> 'where clause' at
>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985.
>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute()
>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line
>>>>>>>>>> 1986.
>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>)
>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line
>>>>>>>>>> 1995.
>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in
>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562.
>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>
>>>>>>>>>> No Mincs inserted
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>>
>>>>>>>>>> Sotirios
>>>>>>>>>>
>>>>>>>>>> Στις Σάβ, 3 Αυγ 2019 στις 1:08 π.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with some
>>>>>>>>>>> major new features and cleanup -- especially if you are early in your setup
>>>>>>>>>>> phase, check out the Release notes for both the LORIS
>>>>>>>>>>> <https://github.com/aces/Loris/releases/tag/v21.0.0> and
>>>>>>>>>>> Loris-MRI
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0> repos.
>>>>>>>>>>>
>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table
>>>>>>>>>>> should be at the root of these issues :
>>>>>>>>>>>
>>>>>>>>>>> The mri_protocol table must be populated
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a
>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't
>>>>>>>>>>> identified or matched to scan types in this table.
>>>>>>>>>>>
>>>>>>>>>>> By default, this table is populated with entries for t1, t2,
>>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are here
>>>>>>>>>>> <https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L591>
>>>>>>>>>>> )
>>>>>>>>>>> Feel free to restore our default records and broaden their
>>>>>>>>>>> parameters to match all your scan types.
>>>>>>>>>>>
>>>>>>>>>>> re Defaced, native, selected -- these filter the scans displayed
>>>>>>>>>>> as you move to the next page (View Session), instead of viewing "all types"
>>>>>>>>>>> of scans from a given session :
>>>>>>>>>>>
>>>>>>>>>>> - "defaced" means that a defacing script
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/scripts_md/run_defacing_script.md>
>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy)
>>>>>>>>>>> - "native" means that no pre-processing has been performed
>>>>>>>>>>> on the scan (it's raw data),
>>>>>>>>>>> - "selected" will show only volumes that have been QC'd and
>>>>>>>>>>> "selected" as the best of their type -- used to display only the best
>>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g.
>>>>>>>>>>>
>>>>>>>>>>> re QC Comments --
>>>>>>>>>>> Once you have successfully loaded scans (matched to the
>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View
>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each
>>>>>>>>>>> visit.
>>>>>>>>>>> These are stored directly in the database, and linked to each
>>>>>>>>>>> scan. (Table name: feedback_mri_comments)
>>>>>>>>>>> (Visit-level QC comments are linked to the session.)
>>>>>>>>>>>
>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging
>>>>>>>>>>> Setup guide
>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md>
>>>>>>>>>>> -
>>>>>>>>>>>
>>>>>>>>>>> An old LORIS walkthrough video
>>>>>>>>>>> <https://www.youtube.com/watch?v=HDWC6RUbI6A> can also walk you
>>>>>>>>>>> through some of the Imaging front-end features, starting at 8:00
>>>>>>>>>>> LORIS' imaging modules have been updated many times since this
>>>>>>>>>>> video, but the functionality and workflow is similar.
>>>>>>>>>>>
>>>>>>>>>>> Let us know how it goes once you have entries in your
>>>>>>>>>>> mri_protocol table -
>>>>>>>>>>> Best,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>
>>>>>>>>>>>> In the candidate_list page i can see this patient
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> If i press the link under PSCID i get to see
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to
>>>>>>>>>>>> imaging_browser
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> At the mri_violations page i also see No results ( neither on
>>>>>>>>>>>> resolved / not resolved ).
>>>>>>>>>>>>
>>>>>>>>>>>> At the imaging_uploader i can see the record that failed.
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name
>>>>>>>>>>>> which i think is the acquisition we wanted?
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> Also my mri_protocol table is empty.
>>>>>>>>>>>>
>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native,
>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc
>>>>>>>>>>>> comments stored?
>>>>>>>>>>>>
>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>
>>>>>>>>>>>> Finally a walkthrough would be helpful.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>
>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>
>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 8:29 μ.μ., ο/η Christine Rogers,
>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>> Glad to hear you're making progress with the visit labels. To
>>>>>>>>>>>>> follow up on your last few emails:
>>>>>>>>>>>>>
>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements
>>>>>>>>>>>>> for the Visit Windows table
>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#iv-visit-windows>
>>>>>>>>>>>>> .
>>>>>>>>>>>>>
>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is
>>>>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use
>>>>>>>>>>>>> V01 by default across all documentation.
>>>>>>>>>>>>>
>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/
>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user
>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User
>>>>>>>>>>>>> passwords in the Wiki's Setup Guide
>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#2-create-front-end-users>
>>>>>>>>>>>>> )
>>>>>>>>>>>>>
>>>>>>>>>>>>> c- The minc file not being registered -- due to
>>>>>>>>>>>>> AcquisitionProtocol unknown.
>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in you
>>>>>>>>>>>>> Dicom header was not matched to any scan listed in the mri_protocol
>>>>>>>>>>>>> database table.
>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide,
>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md> this
>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted").
>>>>>>>>>>>>>
>>>>>>>>>>>>> The MRI Violations module (Readme here)
>>>>>>>>>>>>> <https://github.com/aces/Loris/tree/minor/modules/mri_violations>will show
>>>>>>>>>>>>> you the details of this mismatch --
>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and
>>>>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you
>>>>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table.
>>>>>>>>>>>>>
>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or
>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you
>>>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca
>>>>>>>>>>>>> (MRI Violations module).
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>
>>>>>>>>>>>>> The LORIS team
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit label
>>>>>>>>>>>>>> disappeared.
>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Please see the attached file. Also something i found.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Acquisition protocol is unknown
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --> The minc file cannot be registered since the
>>>>>>>>>>>>>> AcquisitionProtocol is unknown
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:58 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by
>>>>>>>>>>>>>>> deleting the rows from the login_history i was able to login.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:50 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and
>>>>>>>>>>>>>>>> i don't know how to insert it because the record requires lots of
>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and
>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to
>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the
>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still
>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the
>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ).
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Στις Δευ, 29 Ιουλ 2019 στις 5:21 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the
>>>>>>>>>>>>>>>>> Visit_Windows table?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label
>>>>>>>>>>>>>>>>> was V1. Does that refer to the same visit? If so, you might want to
>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a
>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit
>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...).
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>>>>> <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"?
>>>>>>>>>>>>>>>>>> I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but
>>>>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for
>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist
>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to
>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit
>>>>>>>>>>>>>>>>>> label does not exist
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Παρ, 26 Ιουλ 2019 στις 3:02 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of mincs
>>>>>>>>>>>>>>>>>>> fails. Please see the output.txt file i attached. Also is there something
>>>>>>>>>>>>>>>>>>> else i need to change at the paths configuration?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 6:55 μ.μ., ο/η Cecile Madjar
>>>>>>>>>>>>>>>>>>> <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> We are making progress!
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that
>>>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site.
>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this:
>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE
>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center";
>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to
>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique).
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Let me know how it goes!
>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Dear Cecile,
>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the
>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now
>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix
>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that
>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed
>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the
>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i
>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are
>>>>>>>>>>>>>>>>>>>>> okay with that )
>>>>>>>>>>>>>>>>>>>>> Thank you a lot,
>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 5:48 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to
>>>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under
>>>>>>>>>>>>>>>>>>>>>> the Admin menu).
>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png]
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module and
>>>>>>>>>>>>>>>>>>>>>> update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my guess
>>>>>>>>>>>>>>>>>>>>>> is that currently, it is set to /data/LORIS/data) and click on the submit
>>>>>>>>>>>>>>>>>>>>>> button.
>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png]
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the
>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to
>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your
>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the
>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline).
>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png]
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and
>>>>>>>>>>>>>>>>>>>>>> it might be a good idea to update your PERL5LIB variable to the following
>>>>>>>>>>>>>>>>>>>>>> (it has been added to the code a few releases ago as we realized this was
>>>>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using
>>>>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below):
>>>>>>>>>>>>>>>>>>>>>> export
>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much
>>>>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the
>>>>>>>>>>>>>>>>>>>>>>> environment file?
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 12:59 π.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/.
>>>>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the
>>>>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the
>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl "
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it
>>>>>>>>>>>>>>>>>>>>>>>> was repeating a pattern and had LORIS instead of loris ( i think the
>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of
>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris'
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database
>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the
>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable.
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 6:05 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set
>>>>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time).
>>>>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module
>>>>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup).
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second
>>>>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in
>>>>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is
>>>>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did
>>>>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the
>>>>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will
>>>>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal
>>>>>>>>>>>>>>>>>>>>>>>>> during the second run:
>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where
>>>>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It
>>>>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set
>>>>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where
>>>>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri).
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147.
>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01
>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/
>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb
>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256.
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284.
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219.
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270.
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711.
>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735.
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id
>>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs
>>>>>>>>>>>>>>>>>>>>>>>>>> are not inserted and i am getting this error
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id
>>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd
>>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run
>>>>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7.
>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows:
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that
>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last
>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the
>>>>>>>>>>>>>>>>>>>>>>>>>> image ).
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 5:05 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of
>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per
>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session
>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your
>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline can
>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit in the session table as long as the visit label is present
>>>>>>>>>>>>>>>>>>>>>>>>>>> in the Visit_Windows table (which means the visit label stored in the
>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName is a valid visit label).
>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the
>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the
>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here
>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change
>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/dicom-archive/profileTemplate.pl#L59>
>>>>>>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the
>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for
>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are
>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if
>>>>>>>>>>>>>>>>>>>>>>>>>>> you execute the following steps, the pipeline should be able to create
>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates:
>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the
>>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes
>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser
>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until
>>>>>>>>>>>>>>>>>>>>>>>>>>> now.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the patient in the .dcm files and now i am getting an error that the visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>> label does not exist.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically
>>>>>>>>>>>>>>>>>>>>>>>>>>>> created.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered
>>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the database: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 3:38 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate profile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i have to create a new one each time before i try to upload a file? Is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there already a way to create a candidate profile and get the DCCID and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 18 Ιουλ 2019 στις 5:00 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to remove all the entries and files specific to an upload. However, this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release is not yet out. Hopefully in the next few weeks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner";
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it expects
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that the DICOM field PatientName and uploaded filename contains the string
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "phantom". We enforced this behaviour on the imaging uploader side in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> recent releases but I can't remember which one. Probably the upcoming 21.0
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> release.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem cumbersome
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but they are here to ensure that the files inserted are all valid and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled properly as it is a bit messy to have to delete files that were
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> wrongly labelled. At least, the delete script present in release 21.0 will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> make this process easier but it is still good practice to verify those
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> things.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> initial answer I gave Sotirios below. I forgot to cc the loris-dev in my
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> earlier reply...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 16 Ιουλ 2019 στις 12:02 π.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is blank
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on the header?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is blank in the DICOM headers in your DICOM files? Did they go through some
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> processes before upload to LORIS?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it but if you use batch_uploads_imageuploader, the insertion scripts could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started".
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or DICOM archive path from which those MINC files were created from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f; do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl -profile prod -uploadID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1 -mincPath $f; done
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.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
>
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