[Loris-dev] Import mri - scripts

[Sotirios Nikoloutsopoulos]

Hi,

loris-access.log reports HTTP 500 error and loris-error reports that some
files are missing e.x. autoload.php from
/var/www/loris/htdocs/../vendor/autoload.php (
https://github.com/aces/Loris/tree/minor/htdocs/vendor and as i can verify
those files do not exist in the github folder )

Thanks



Στις Πέμ, 29 Αυγ 2019 στις 4:04 μ.μ., ο/η Christine Rogers, Ms. <
christine.rogers at mcgill.ca> έγραψε:

> Hi Sotirios,
>
> > Any suggestion why Loris is not showing up in the browser?
>
>
> - What are the last few lines of your loris-access and loris-error apache
> logs?
>
> - What are the URL and host in your Config table?  (run these queries
> from the wiki
> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>
> )
>
> - Are you using https, are the certificates in place, etc?
>
> - Do any of the wiki's Troubleshooting steps
> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>
>  help?
>
> Best,
> Christine
>
> On Wed, Aug 28, 2019 at 9:30 PM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Any suggestion why Loris is not showing up in the browser?
>>
>> Thanks
>>
>>
>> Στις Τετ, 28 Αυγ 2019 στις 2:30 π.μ., ο/η Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> έγραψε:
>>
>>> Also to mention that in the picture i opened the 000-default.conf which
>>> is just a copy of loris.conf by using cp
>>>
>>> Στις Τετ, 28 Αυγ 2019 στις 2:20 π.μ., ο/η Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> έγραψε:
>>>
>>>> Ok that fixed the install.sh problem. Now it doesn't show loris to the
>>>> browser, although everything seems right ( also
>>>>
>>>>  /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ).
>>>>
>>>>
>>>> And apache is running
>>>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl
>>>> status apache2[sudo] password for lorisadmin:
>>>> ● apache2.service - LSB: Apache2 web server
>>>>    Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
>>>>   Drop-In: /lib/systemd/system/apache2.service.d
>>>>            └─apache2-systemd.conf
>>>>    Active: active (running) since Τετ 2019-08-28 02:15:12 EEST; 3min
>>>> 34s ago
>>>>
>>>> [image: image.png]
>>>>
>>>> Στις Τρί, 27 Αυγ 2019 στις 9:42 μ.μ., ο/η Shen Wang <
>>>> wangshen.mcin at gmail.com> έγραψε:
>>>>
>>>>> Hi,
>>>>> This is a bug for install.sh file, we will fix it later.
>>>>> Thank for letting me know your Loris install situation.
>>>>> regards
>>>>> Shen
>>>>>
>>>>>
>>>>> On Tue, 27 Aug 2019 at 14:28, Shen Wang <wangshen.mcin at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>> Please remove "set -euo pipefail" line 10 in the install.sh file.
>>>>>> Then try again.
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> i still haven't resolved the previous issue. Also i tried to install
>>>>>>> Loris to a new virtual machine and when i execute install.sh i get the
>>>>>>> following error
>>>>>>>
>>>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh
>>>>>>> LORIS Installation Script starting at 2019-08-27T21:00:42
>>>>>>> The log for this session will be stored in file
>>>>>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log
>>>>>>> ---------------------------------------------------------------------
>>>>>>>                    LORIS Installation Script
>>>>>>> ---------------------------------------------------------------------
>>>>>>>
>>>>>>> PHP appears to be installed.
>>>>>>>
>>>>>>> PHP Composer appears to be installed.
>>>>>>>
>>>>>>> This install script will ask you to provide inputs for different
>>>>>>> steps.
>>>>>>> Please ensure you have the following information ready (if
>>>>>>> applicable):
>>>>>>>
>>>>>>>   1) Your project directory name.
>>>>>>>      (Will be used to modify the paths for Imaging data in the
>>>>>>> generated
>>>>>>>      config.xml file for LORIS, and may also be used to automatically
>>>>>>>      create/install apache config files.) If unsure, a default like
>>>>>>> "LORIS"
>>>>>>>      should be acceptable.
>>>>>>>
>>>>>>> Please also consult the Loris WIKI on GitHub for more information on
>>>>>>> these
>>>>>>> Install Script input parameters.
>>>>>>>
>>>>>>> Ready to continue? [yn] y
>>>>>>>
>>>>>>> ./install.sh: line 132: projectname: unbound variable
>>>>>>>
>>>>>>> Thanks
>>>>>>>
>>>>>>> Στις Τρί, 6 Αυγ 2019 στις 5:09 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>
>>>>>>>> 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
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Shen Wang
>>>>>> Loris <https://github.com/aces/Loris>  Developer
>>>>>> Montreal Neurological Institute
>>>>>> McGill University
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Shen Wang
>>>>> Loris <https://github.com/aces/Loris>  Developer
>>>>> Montreal Neurological Institute
>>>>> McGill University
>>>>>
>>>>> _______________________________________________
>> Loris-dev mailing list
>> Loris-dev at bic.mni.mcgill.ca
>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>
>
>
> --
>
> christine.rogers at mcgill.ca
> McGill Centre for Integrative Neuroscience | MCIN.ca
> Montreal Neurological Institute
> McGill University | Montreal | Canada
>
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