[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Tue Aug 27 19:20:20 EDT 2019
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
>
>
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