[Loris-dev] Import mri - scripts
Shen Wang
wangshen.mcin at gmail.com
Tue Aug 27 14:42:08 EDT 2019
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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