[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Wed Aug 28 21:29:40 EDT 2019
Any suggestion why Loris is not showing up in the browser?
Thanks
Στις Τετ, 28 Αυγ 2019 στις 2:30 π.μ., ο/η Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> έγραψε:
> Also to mention that in the picture i opened the 000-default.conf which is
> just a copy of loris.conf by using cp
>
> Στις Τετ, 28 Αυγ 2019 στις 2:20 π.μ., ο/η Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> έγραψε:
>
>> Ok that fixed the install.sh problem. Now it doesn't show loris to the
>> browser, although everything seems right ( also
>>
>> /etc/apache2/sites-enabled/000-default.conf was replaced by loris.config ).
>>
>>
>> And apache is running
>> lorisadmin at loris-VirtualBox:/var/www/loris/htdocs$ sudo systemctl status
>> apache2[sudo] password for lorisadmin:
>> ● apache2.service - LSB: Apache2 web server
>> Loaded: loaded (/etc/init.d/apache2; bad; vendor preset: enabled)
>> Drop-In: /lib/systemd/system/apache2.service.d
>> └─apache2-systemd.conf
>> Active: active (running) since Τετ 2019-08-28 02:15:12 EEST; 3min 34s
>> ago
>>
>> [image: image.png]
>>
>> Στις Τρί, 27 Αυγ 2019 στις 9:42 μ.μ., ο/η Shen Wang <
>> wangshen.mcin at gmail.com> έγραψε:
>>
>>> Hi,
>>> This is a bug for install.sh file, we will fix it later.
>>> Thank for letting me know your Loris install situation.
>>> regards
>>> Shen
>>>
>>>
>>> On Tue, 27 Aug 2019 at 14:28, Shen Wang <wangshen.mcin at gmail.com> wrote:
>>>
>>>> Hi,
>>>> Please remove "set -euo pipefail" line 10 in the install.sh file.
>>>> Then try again.
>>>>
>>>>
>>>>
>>>> On Tue, 27 Aug 2019 at 14:05, Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> i still haven't resolved the previous issue. Also i tried to install
>>>>> Loris to a new virtual machine and when i execute install.sh i get the
>>>>> following error
>>>>>
>>>>> lorisadmin at loris-VirtualBox:/var/www/loris/tools$ ./install.sh
>>>>> LORIS Installation Script starting at 2019-08-27T21:00:42
>>>>> The log for this session will be stored in file
>>>>> /var/www/loris/tools/logs/install-2019-08-27T21:00:42.log
>>>>> ---------------------------------------------------------------------
>>>>> LORIS Installation Script
>>>>> ---------------------------------------------------------------------
>>>>>
>>>>> PHP appears to be installed.
>>>>>
>>>>> PHP Composer appears to be installed.
>>>>>
>>>>> This install script will ask you to provide inputs for different steps.
>>>>> Please ensure you have the following information ready (if applicable):
>>>>>
>>>>> 1) Your project directory name.
>>>>> (Will be used to modify the paths for Imaging data in the
>>>>> generated
>>>>> config.xml file for LORIS, and may also be used to automatically
>>>>> create/install apache config files.) If unsure, a default like
>>>>> "LORIS"
>>>>> should be acceptable.
>>>>>
>>>>> Please also consult the Loris WIKI on GitHub for more information on
>>>>> these
>>>>> Install Script input parameters.
>>>>>
>>>>> Ready to continue? [yn] y
>>>>>
>>>>> ./install.sh: line 132: projectname: unbound variable
>>>>>
>>>>> Thanks
>>>>>
>>>>> Στις Τρί, 6 Αυγ 2019 στις 5:09 μ.μ., ο/η Christine Rogers, Ms. <
>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>
>>>>>> Hi Sotirios,
>>>>>> Could you also let us know -- on which pages is content visible, and
>>>>>> on which pages/modules is content not visible for you?
>>>>>> Thanks,
>>>>>> Christine
>>>>>>
>>>>>> On Tue, Aug 6, 2019 at 9:54 AM Christine Rogers, Ms. <
>>>>>> christine.rogers at mcgill.ca> wrote:
>>>>>>
>>>>>>> Thanks Sotirios,
>>>>>>> That's good to know. It sounds like you've checked that your
>>>>>>> /var/www/loris/project/config.xml file get populated properly.
>>>>>>>
>>>>>>> Please send us the last few errors you're seeing in your apache
>>>>>>> error log file, and your config paths and we can see what's happening with
>>>>>>> your front end --
>>>>>>> Run these Troubleshooting Queries
>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#troubleshooting-configuration-settings>
>>>>>>> to get your config path settings, given your front end is not displaying
>>>>>>> fully.
>>>>>>>
>>>>>>> The Loris-MRI repo
>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0> 21
>>>>>>> install/upgrade would then be your next steps.
>>>>>>> Best,
>>>>>>> Christine
>>>>>>>
>>>>>>> On Tue, Aug 6, 2019 at 7:53 AM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> I am using a VM. What i did was:
>>>>>>>> 1) Download the files from https://github.com/aces/Loris and
>>>>>>>> replace them to my existing /vaw/www/loris folder.
>>>>>>>> 2) Execute the composer install --no-dev and then composer
>>>>>>>> dump-autoload as mentioned here
>>>>>>>> https://github.com/aces/Loris/wiki/Updating-your-LORIS.
>>>>>>>> 3) Execute install.sh from /var/www/loris/tools and because LORIS
>>>>>>>> already existed i moved a .config file, then re-executed the install.sh
>>>>>>>> successfully
>>>>>>>> 4 ) As for the database, i dropped the schema and i executed the
>>>>>>>> installdb.php
>>>>>>>>
>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 5:22 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>
>>>>>>>>> Hi Sotorios,
>>>>>>>>>
>>>>>>>>> Thanks - when you re-installed did you start on a fresh root path
>>>>>>>>> / VM or might some of your old system setting still apply?
>>>>>>>>> (And if you did any steps similar to an upgrade, did you follow
>>>>>>>>> the Upgrade steps in the Release Notes, from both repos?)
>>>>>>>>>
>>>>>>>>> About the TR_range column - it was recently split (MRI pr339
>>>>>>>>> <https://github.com/aces/Loris-MRI/pull/339>) split into TR_min
>>>>>>>>> and _max columns. Given the code was trying to query TR_range which does
>>>>>>>>> not exist in your mri_protocol table, double-check which version of the
>>>>>>>>> Loris repo (tables) and the Loris-MRI repo (code) you have installed to
>>>>>>>>> ensure they match.
>>>>>>>>>
>>>>>>>>> Christine
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Mon, Aug 5, 2019 at 9:06 AM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> I reinstalled LORIS to 21 version and now the content is not
>>>>>>>>>> visible at all at most pages.
>>>>>>>>>>
>>>>>>>>>> [image: image.png]
>>>>>>>>>>
>>>>>>>>>> Στις Δευ, 5 Αυγ 2019 στις 3:19 μ.μ., ο/η Sotirios
>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> Is it easy to upgrade to Loris 21? Also the following fails
>>>>>>>>>>> because the line 1985 of NeuroDB/MRIProcessingUtility.pm query mri_protocol
>>>>>>>>>>> which doesn't have TR_range
>>>>>>>>>>> https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L556
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>> ./batch_uploads_imageuploader line 147.
>>>>>>>>>>> base is DCC0000_258024_V1
>>>>>>>>>>> path is /data/incoming/
>>>>>>>>>>> type is .tar.gz
>>>>>>>>>>> fullpath is /data/incoming/DCC0000_258024_V1.tar.gz
>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in
>>>>>>>>>>> 'where clause' at
>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1985.
>>>>>>>>>>> DBD::mysql::st fetchrow_array failed: fetch() without execute()
>>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line
>>>>>>>>>>> 1986.
>>>>>>>>>>> Use of uninitialized value $count_mri_protocol in numeric gt (>)
>>>>>>>>>>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line
>>>>>>>>>>> 1995.
>>>>>>>>>>> DBD::mysql::st execute failed: Unknown column 'TR_range' in
>>>>>>>>>>> 'field list' at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 562.
>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>
>>>>>>>>>>> No Mincs inserted
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Sotirios
>>>>>>>>>>>
>>>>>>>>>>> Στις Σάβ, 3 Αυγ 2019 στις 1:08 π.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>
>>>>>>>>>>>> First, just a note: we've released LORIS 21 this week with
>>>>>>>>>>>> some major new features and cleanup -- especially if you are early in your
>>>>>>>>>>>> setup phase, check out the Release notes for both the LORIS
>>>>>>>>>>>> <https://github.com/aces/Loris/releases/tag/v21.0.0> and
>>>>>>>>>>>> Loris-MRI
>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/releases/tag/v21.0.0>
>>>>>>>>>>>> repos.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks for your screenshots -- your empty mri_protocol table
>>>>>>>>>>>> should be at the root of these issues :
>>>>>>>>>>>>
>>>>>>>>>>>> The mri_protocol table must be populated
>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database>
>>>>>>>>>>>> in order for your scans to be registered in LORIS -- it serves as a
>>>>>>>>>>>> whitelist for the insertion pipeline which filters out scans that aren't
>>>>>>>>>>>> identified or matched to scan types in this table.
>>>>>>>>>>>>
>>>>>>>>>>>> By default, this table is populated with entries for t1, t2,
>>>>>>>>>>>> fMRI and DTI (Insert statements for 21 release branch are here
>>>>>>>>>>>> <https://github.com/aces/Loris/blob/21.0-release/SQL/0000-00-00-schema.sql#L591>
>>>>>>>>>>>> )
>>>>>>>>>>>> Feel free to restore our default records and broaden their
>>>>>>>>>>>> parameters to match all your scan types.
>>>>>>>>>>>>
>>>>>>>>>>>> re Defaced, native, selected -- these filter the scans
>>>>>>>>>>>> displayed as you move to the next page (View Session), instead of viewing
>>>>>>>>>>>> "all types" of scans from a given session :
>>>>>>>>>>>>
>>>>>>>>>>>> - "defaced" means that a defacing script
>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/master/docs/scripts_md/run_defacing_script.md>
>>>>>>>>>>>> has masked the subject's face in the volume (for patient privacy)
>>>>>>>>>>>> - "native" means that no pre-processing has been performed
>>>>>>>>>>>> on the scan (it's raw data),
>>>>>>>>>>>> - "selected" will show only volumes that have been QC'd
>>>>>>>>>>>> and "selected" as the best of their type -- used to display only the best
>>>>>>>>>>>> quality T1 image instead of all T1s acquired in a session, e.g.
>>>>>>>>>>>>
>>>>>>>>>>>> re QC Comments --
>>>>>>>>>>>> Once you have successfully loaded scans (matched to the
>>>>>>>>>>>> mri_protocol table), you'll be able to use the Imaging Browser's View
>>>>>>>>>>>> Session subpage to enter/view QC comments on each volume, or for each
>>>>>>>>>>>> visit.
>>>>>>>>>>>> These are stored directly in the database, and linked to each
>>>>>>>>>>>> scan. (Table name: feedback_mri_comments)
>>>>>>>>>>>> (Visit-level QC comments are linked to the session.)
>>>>>>>>>>>>
>>>>>>>>>>>> For a walkthrough of the Imaging setup - please see the Imaging
>>>>>>>>>>>> Setup guide
>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md>
>>>>>>>>>>>> -
>>>>>>>>>>>>
>>>>>>>>>>>> An old LORIS walkthrough video
>>>>>>>>>>>> <https://www.youtube.com/watch?v=HDWC6RUbI6A> can also walk
>>>>>>>>>>>> you through some of the Imaging front-end features, starting at 8:00
>>>>>>>>>>>> LORIS' imaging modules have been updated many times since this
>>>>>>>>>>>> video, but the functionality and workflow is similar.
>>>>>>>>>>>>
>>>>>>>>>>>> Let us know how it goes once you have entries in your
>>>>>>>>>>>> mri_protocol table -
>>>>>>>>>>>> Best,
>>>>>>>>>>>> Christine
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> On Fri, Aug 2, 2019 at 7:58 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>
>>>>>>>>>>>>> In the candidate_list page i can see this patient
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> If i press the link under PSCID i get to see
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> and if i press the link under Scan Done it redirects me to
>>>>>>>>>>>>> imaging_browser
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> At the mri_violations page i also see No results ( neither on
>>>>>>>>>>>>> resolved / not resolved ).
>>>>>>>>>>>>>
>>>>>>>>>>>>> At the imaging_uploader i can see the record that failed.
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> If i click on the tarchive info i get to see the Protocol Name
>>>>>>>>>>>>> which i think is the acquisition we wanted?
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> Also my mri_protocol table is empty.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Furthermore i would like to ask about the defaced, native,
>>>>>>>>>>>>> selected. What exactly is native and selected? And where are the qc
>>>>>>>>>>>>> comments stored?
>>>>>>>>>>>>>
>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>
>>>>>>>>>>>>> Finally a walkthrough would be helpful.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>
>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 8:29 μ.μ., ο/η Christine Rogers,
>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>> Glad to hear you're making progress with the visit labels.
>>>>>>>>>>>>>> To follow up on your last few emails:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> a- The Wiki's Setup Guide contains Sample insert statements
>>>>>>>>>>>>>> for the Visit Windows table
>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#iv-visit-windows>
>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> As Cecile mentioned, the consistency of visit label format is
>>>>>>>>>>>>>> important: V01, v01, V1, 01 -- whichever you select to use is fine; we use
>>>>>>>>>>>>>> V01 by default across all documentation.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> b- For Password reset, there is a script in the tools/
>>>>>>>>>>>>>> directory so that a back-end administrator can reset any front-end user
>>>>>>>>>>>>>> password, including Admin. (See info on setting up / resetting User
>>>>>>>>>>>>>> passwords in the Wiki's Setup Guide
>>>>>>>>>>>>>> <https://github.com/aces/Loris/wiki/Project-Customization#2-create-front-end-users>
>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> c- The minc file not being registered -- due to
>>>>>>>>>>>>>> AcquisitionProtocol unknown.
>>>>>>>>>>>>>> This means the SeriesDescription (Acquisition Protocol) in
>>>>>>>>>>>>>> you Dicom header was not matched to any scan listed in the mri_protocol
>>>>>>>>>>>>>> database table.
>>>>>>>>>>>>>> (In the online Loris-MRI Troubleshooting Guide,
>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md> this
>>>>>>>>>>>>>> is Table 3, 2nd-last item "no MINCs inserted").
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The MRI Violations module (Readme here)
>>>>>>>>>>>>>> <https://github.com/aces/Loris/tree/minor/modules/mri_violations>will show
>>>>>>>>>>>>>> you the details of this mismatch --
>>>>>>>>>>>>>> Go to the module (under the Imaging menu), find your scan and
>>>>>>>>>>>>>> click the link "Could not identify scan type" -- in the next subpage you
>>>>>>>>>>>>>> can compare the scan's actual parameters against the mri_protocol table.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> To resolve this, adjust your mri_protocol table values or
>>>>>>>>>>>>>> perhaps ensure your DICOMs are labelled consistently.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Let us know if this works for you -- we can also walk you
>>>>>>>>>>>>>> through an example of non-identified scans on Demo.loris.ca
>>>>>>>>>>>>>> (MRI Violations module).
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> The LORIS team
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> On Tue, Jul 30, 2019 at 10:47 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> I hope this is sufficient as the error for the visit label
>>>>>>>>>>>>>>> disappeared.
>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Please see the attached file. Also something i found.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-17-39-xubBdv.log
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>> /tmp/TarLoad-17-39-UyQcG2/dcc0000_258024_v1_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --> md5: 6b1202fd63e29de4c9be1cd9925888a5
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --> The minc file cannot be registered since the
>>>>>>>>>>>>>>> AcquisitionProtocol is unknown
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:58 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Ok I fixed the login problem by using a known hash and by
>>>>>>>>>>>>>>>> deleting the rows from the login_history i was able to login.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Στις Τρί, 30 Ιουλ 2019 στις 4:50 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> there was no visit label 01 in the Visit_Windows table and
>>>>>>>>>>>>>>>>> i don't know how to insert it because the record requires lots of
>>>>>>>>>>>>>>>>> attributes. Also the system for a reason asked me to update my password and
>>>>>>>>>>>>>>>>> now i don't remember it and my account got suspended. Is there a way to
>>>>>>>>>>>>>>>>> reset it or set a simple password? I updated the password hash in the
>>>>>>>>>>>>>>>>> users table by using the hash from another LORIS setup we had and i still
>>>>>>>>>>>>>>>>> couldn't login ( also the attribute password is always NULL and the
>>>>>>>>>>>>>>>>> expiration date is 1999-01-01 for some reason ).
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Στις Δευ, 29 Ιουλ 2019 στις 5:21 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Can you try adding the visit label v01 to the
>>>>>>>>>>>>>>>>>> Visit_Windows table?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> However, I noticed that in a previous dataset, the label
>>>>>>>>>>>>>>>>>> was V1. Does that refer to the same visit? If so, you might want to
>>>>>>>>>>>>>>>>>> harmonize the visit labels so they are all the same across datasets for a
>>>>>>>>>>>>>>>>>> given timepoint, meaning you will need to relabel scans when the visit
>>>>>>>>>>>>>>>>>> label is different but referring to the same visit label (v01 = V1 etc...).
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> On Mon, Jul 29, 2019 at 10:15 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Could you help me with the "Visit label does not exist"?
>>>>>>>>>>>>>>>>>>> I had changed $subjectID{'createVisitLabel'} to 1 as you had suggested but
>>>>>>>>>>>>>>>>>>> it appears that this problem hasn't been resolved yet.
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> lorisadmin at hbp:/data/loris/bin/mri$ cat
>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-14-58-9Xog7H.log
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> --> using user-defined filterParameters for
>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-14-58-5Z4hYX/dcc0000_258024_v01_20121205_102108_501e1_mri.mnc
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Candidate Mismatch Error is Visit label does not exist
>>>>>>>>>>>>>>>>>>> -> WARNING: This candidate was invalid. Logging to
>>>>>>>>>>>>>>>>>>> MRICandidateErrors table with reason Visit
>>>>>>>>>>>>>>>>>>> label does not exist
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Στις Παρ, 26 Ιουλ 2019 στις 3:02 μ.μ., ο/η Sotirios
>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> The Center error was fixed. Still the insertion of
>>>>>>>>>>>>>>>>>>>> mincs fails. Please see the output.txt file i attached. Also is there
>>>>>>>>>>>>>>>>>>>> something else i need to change at the paths configuration?
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 6:55 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> We are making progress!
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> I have a feeling this error comes from the fact that
>>>>>>>>>>>>>>>>>>>>> your psc table does not have the MRI_alias populated for the DCC site.
>>>>>>>>>>>>>>>>>>>>> Running the following query in the mysql database should fix this:
>>>>>>>>>>>>>>>>>>>>> UPDATE psc SET MRI_alias="DCC", Alias="DCC" WHERE
>>>>>>>>>>>>>>>>>>>>> Name="Data Coordinating Center";
>>>>>>>>>>>>>>>>>>>>> Repeat the same with all your sites (make sure to
>>>>>>>>>>>>>>>>>>>>> change the Aliases between sites, they should all be unique).
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Let me know how it goes!
>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Dear Cecile,
>>>>>>>>>>>>>>>>>>>>>> You were right about your guesses. I did the
>>>>>>>>>>>>>>>>>>>>>> modifications you suggested, i still get the "no mincs inserted" error, now
>>>>>>>>>>>>>>>>>>>>>> i am getting the "No center found this candidate" error ( how do i fix
>>>>>>>>>>>>>>>>>>>>>> that? from what i see the .dcm files contains a 'Institution Name', is that
>>>>>>>>>>>>>>>>>>>>>> the center? ), so i guess that's why the validation fails, but i changed
>>>>>>>>>>>>>>>>>>>>>> the force variable of tarchiveLoader to 1, shouldn't it have inserted the
>>>>>>>>>>>>>>>>>>>>>> mincs then? Also it is optional to have a mail server, right? ( from what i
>>>>>>>>>>>>>>>>>>>>>> see the mail error does not affect the $valid_study, so i assume we are
>>>>>>>>>>>>>>>>>>>>>> okay with that )
>>>>>>>>>>>>>>>>>>>>>> Thank you a lot,
>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 5:48 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> From what I understand, I believe you just need to
>>>>>>>>>>>>>>>>>>>>>>> update a few config settings from the frontend in the Config module (under
>>>>>>>>>>>>>>>>>>>>>>> the Admin menu).
>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.31.35 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Then go to the Paths section of the config module
>>>>>>>>>>>>>>>>>>>>>>> and update the "LORIS-MRI code" config setting to /data/loris/bin/mri (my
>>>>>>>>>>>>>>>>>>>>>>> guess is that currently, it is set to /data/LORIS/data) and click on the
>>>>>>>>>>>>>>>>>>>>>>> submit button.
>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.32.50 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Then, go to Imaging Pipeline section of the
>>>>>>>>>>>>>>>>>>>>>>> Configuration module and update the "Loris-MRI Data Directory" to
>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ (my guess is that it is empty at the moment in your
>>>>>>>>>>>>>>>>>>>>>>> database which is why $data_dir is not defined when you run the
>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader step of the insertion pipeline).
>>>>>>>>>>>>>>>>>>>>>>> [image: Screen Shot 2019-07-25 at 10.40.52 AM.png]
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Finally, I took a look at your environment file and
>>>>>>>>>>>>>>>>>>>>>>> it might be a good idea to update your PERL5LIB variable to the following
>>>>>>>>>>>>>>>>>>>>>>> (it has been added to the code a few releases ago as we realized this was
>>>>>>>>>>>>>>>>>>>>>>> needed for the libraries. Not sure which version of LORIS-MRI you are using
>>>>>>>>>>>>>>>>>>>>>>> but it does not hurt to update this variable to what I suggest below):
>>>>>>>>>>>>>>>>>>>>>>> export
>>>>>>>>>>>>>>>>>>>>>>> PERL5LIB=/data/loris/bin/mri/uploadNeuroDB:/data/loris/bin/mri/dicom-archive:$PERL5LIB
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hope this helps. Sorry you are experiencing so much
>>>>>>>>>>>>>>>>>>>>>>> trouble setting things up. We probably need to update our WIKI.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jul 25, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> The "Loris-MRI Data Directory" should be in the
>>>>>>>>>>>>>>>>>>>>>>>> environment file?
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 25 Ιουλ 2019 στις 12:59 π.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> The scripts are located in /data/loris/bin/mri/.
>>>>>>>>>>>>>>>>>>>>>>>>> Somewhere I might have messed something up but i remember following the
>>>>>>>>>>>>>>>>>>>>>>>>> instructions in the wiki.For example when i tried to execute the
>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader perl script the line
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> my $command = "$bin_dir/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl "
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> was pointing to an invalid path, for example: it
>>>>>>>>>>>>>>>>>>>>>>>>> was repeating a pattern and had LORIS instead of loris ( i think the
>>>>>>>>>>>>>>>>>>>>>>>>> mistake was that in the wiki it suggested to use $PROJECT for the name of
>>>>>>>>>>>>>>>>>>>>>>>>> the folder and i choosed 'loris'
>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Imaging-Database
>>>>>>>>>>>>>>>>>>>>>>>>> ). See also the in image for the modification i did. Also i didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>> section to config the $data_dir variable.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 6:05 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> It looks like you have one Config setting not set
>>>>>>>>>>>>>>>>>>>>>>>>>> (based on the first error message you got when running it the first time).
>>>>>>>>>>>>>>>>>>>>>>>>>> You need to set a value for "Loris-MRI Data Directory" in the Config module
>>>>>>>>>>>>>>>>>>>>>>>>>> under the Imaging pipeline section (from what I can see, it would be
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/ for your setup).
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> The reason you got that error message the second
>>>>>>>>>>>>>>>>>>>>>>>>>> time is that the pipeline checks if the DICOM study was already inserted in
>>>>>>>>>>>>>>>>>>>>>>>>>> the tarchive table. Since you ran the study once already, the study is
>>>>>>>>>>>>>>>>>>>>>>>>>> inserted into the tarchive, hence the message. However, the pipeline did
>>>>>>>>>>>>>>>>>>>>>>>>>> not complete as the MINC files were not created and inserted into the
>>>>>>>>>>>>>>>>>>>>>>>>>> files/parameter_file table. In order to continue the insertion, you will
>>>>>>>>>>>>>>>>>>>>>>>>>> then need to run the tarchiveLoader command suggested in the terminal
>>>>>>>>>>>>>>>>>>>>>>>>>> during the second run:
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, I am a bit confused by your setup. Where
>>>>>>>>>>>>>>>>>>>>>>>>>> are the scripts located? In /data/loris/bin/mri or /data/loris/data? It
>>>>>>>>>>>>>>>>>>>>>>>>>> feels like the Config setting "LORIS-MRI code" in the Paths section was set
>>>>>>>>>>>>>>>>>>>>>>>>>> to "/data/LORIS/data" but it should have been set to the directory where
>>>>>>>>>>>>>>>>>>>>>>>>>> the scripts are located (most probably /data/loris/bin/mri).
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 10:55 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok first i execute this command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at ./batch_uploads_imageuploader line 143.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match
>>>>>>>>>>>>>>>>>>>>>>>>>>> (m//) at ./batch_uploads_imageuploader line 147.
>>>>>>>>>>>>>>>>>>>>>>>>>>> base is DCC0000_258024_V01
>>>>>>>>>>>>>>>>>>>>>>>>>>> path is /data/incoming/
>>>>>>>>>>>>>>>>>>>>>>>>>>> type is .tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>> fullpath is
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V01.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> source /tmp/ImagingUpload-17-43-ZUEFjb
>>>>>>>>>>>>>>>>>>>>>>>>>>> targetlocation /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 256.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 284.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive_validation.pl line 219.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl line 270.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 711.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 721.
>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 722.
>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 723.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 724.
>>>>>>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 725.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $data_dir in
>>>>>>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader line 735.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> No Mincs inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader insertion script has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id
>>>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> I inserted the VisitLabel, but still the Mincs
>>>>>>>>>>>>>>>>>>>>>>>>>>> are not inserted and i am getting this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> "lorisadmin at hbp:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id
>>>>>>>>>>>>>>>>>>>>>>>>>>> 3 /data/incoming/DCC0000_258024_V01.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path \/tmp\/ImagingUpload\-17\-45\-5MsWEd
>>>>>>>>>>>>>>>>>>>>>>>>>>> -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>> The Scan for the uploadID 3 has already been run
>>>>>>>>>>>>>>>>>>>>>>>>>>> with tarchiveID: 7.
>>>>>>>>>>>>>>>>>>>>>>>>>>> To continue with the rest of the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline, please run tarchiveLoader from a terminal as follows:
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//2012/DCM_2012-12-05_ImagingUpload-17-43-ZUEFjb.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose"
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Which files should i delete? I thought that
>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting the files from the tarchive was enough. And i executed the last
>>>>>>>>>>>>>>>>>>>>>>>>>>> proposed command to continue to rest of the insertion pipeline ( check the
>>>>>>>>>>>>>>>>>>>>>>>>>>> image ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 5:05 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sorry I was not clear before. Every visits of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates are created in the session table with one entry per
>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID/VisitLabel. So if the imaging pipeline created visits in the session
>>>>>>>>>>>>>>>>>>>>>>>>>>>> table (that are not attached to instruments) and you want to clean your
>>>>>>>>>>>>>>>>>>>>>>>>>>>> database completely, you can delete entries in that table as well.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Regarding your point 2, the imaging pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>> can create the visit in the session table as long as the visit label is
>>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the Visit_Windows table (which means the visit label stored in
>>>>>>>>>>>>>>>>>>>>>>>>>>>> the PatientName is a valid visit label).
>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, in your prod file, if the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> variable $subjectID{'createVisitLabel'} is set to 1 for candidates, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label should be created in the Visit_Windows table I believe. Here
>>>>>>>>>>>>>>>>>>>>>>>>>>>> is the line of the prod file you would need to change
>>>>>>>>>>>>>>>>>>>>>>>>>>>> <https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/dicom-archive/profileTemplate.pl#L59>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general, we prefer populating the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Visit_Windows table and set the $subjectID{'createVisitLabel'} to 0 for
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate data to avoid insertion of badly labelled MRI data that are
>>>>>>>>>>>>>>>>>>>>>>>>>>>> complex to relabel.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Finally, regarding the candidate creation, if
>>>>>>>>>>>>>>>>>>>>>>>>>>>> you execute the following steps, the pipeline should be able to create
>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates:
>>>>>>>>>>>>>>>>>>>>>>>>>>>> - set in the Imaging Pipeline section of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> config module the config setting "Upload creation of candidates" to Yes
>>>>>>>>>>>>>>>>>>>>>>>>>>>> - manually transfer the scans to the LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>>> server instead of uploading it via the imaging browser
>>>>>>>>>>>>>>>>>>>>>>>>>>>> - run batch_imaging_upload.pl as you did until
>>>>>>>>>>>>>>>>>>>>>>>>>>>> now.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Jul 24, 2019 at 8:47 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About my second question i replaced the name
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the patient in the .dcm files and now i am getting an error that the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label does not exist.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I thought it was supposed to be automatically
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> created.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/LORIS/data//uploadNeuroDB/tarchiveLoader
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -globLocation -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive//DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-15-42-yUwQQV.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit labelVisit label does not exist
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for inserting into the database: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log dir is /logs and log file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /logs/TarLoad-15-42-L6pocU.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID is: DCC0000
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> CandID id: 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate id 258024
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> => No Visit label
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-15-42-J2rQms/ImagingUpload-15-42-yUwQQV*"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 24 Ιουλ 2019 στις 3:38 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the records in the session table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) I tried to upload a non-phantom file like
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> input_file.txt:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0000_258024_V1.tar.gz N
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCC0000_258024_V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Terminal:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./batch_uploads_imageuploader -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> < ~/Desktop/input.txt > log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and i get the following error in the log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 7 /data/incoming/DCC0000_258024_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-14\-56\-FeLCB4 -name '__MACOSX' -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Spool message is:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The PatientName read from the DICOM header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> does not start with DCC0000_258024_V1 from the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and the spool message is repeated for each
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .dcm file. Should i preprocess every .dcm file and change the PatientName
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to "DCC0000_258024_V1"?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) As far as it concerns the candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> profile i have to create a new one each time before i try to upload a file?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there already a way to create a candidate profile and get the DCCID and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID without the user interface?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Πέμ, 18 Ιουλ 2019 στις 5:00 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> See answers to your questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> About the 1st case we had a dicom with a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank studyUID, maybe someone accidentally removed it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> That is strange. Something must have been
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> done to the DICOM files. I have never seen a study with no StudyUID out of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the scanner. Usually, you need to manually erase it with some tool.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, DICOMs never cease to surprise me...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Some other questions:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What are the steps to remove all of my
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patients and uploads?: because i want to try to reupload all the testing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicoms we had with a clean database.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Release 21.0 of LORIS-MRI will offer a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script to remove all the entries and files specific to an upload. However,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> this release is not yet out. Hopefully in the next few weeks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In the meantime, since your case is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> particular and that you just want to start with a clean database, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following deletes should work (hopefully I won't forget any tables):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_violations_log;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_protocol_violated_scans;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from MRICandidateErrors;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from parameter_file;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from files_qcstatus; # (if you played
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the QC part of the imaging browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from feedback_mri_comments; # (if you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> played with the QC part of the imaging browser for testing)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_series;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive_files;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_upload;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from tarchive;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from mri_scanner;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete from candidate where PSCID="scanner";
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I don't know if you want to also delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries in the session and candidate table too?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) We do not need to create the profile of a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient ( are the patients stored in the candidate table? because i can't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see the ghosts ), because will it automatically be created when importing a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure I understand fully this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> question. All candidates are stored in the candidate table. The phantom
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scans however are attached to a scanner candidate depending on where the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scan happened. It is a bit of a weird concept that we have to redesign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> eventually but never got a chance to get to it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hopefully this answered your question,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> otherwise, don't hesitate to let me know.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) What is the difference between uploading
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a dicom as phantom instead of importing as PSCCID_DCCID_VisitLabel?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload the scan as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel, there is a check that makes sure the candidate IDs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and visit label are valid at the time of upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When you upload a scan as phantom, it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> expects that the DICOM field PatientName and uploaded filename contains the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string "phantom". We enforced this behaviour on the imaging uploader side
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in recent releases but I can't remember which one. Probably the upcoming
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 release.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> All those verifications might seem
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cumbersome but they are here to ensure that the files inserted are all
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> valid and labelled properly as it is a bit messy to have to delete files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that were wrongly labelled. At least, the delete script present in release
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 21.0 will make this process easier but it is still good practice to verify
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> those things.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> With pleasure. Hopefully the answers to your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions will be helpful.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PS: loris-dev mailing list: you will find
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the initial answer I gave Sotirios below. I forgot to cc the loris-dev in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> my earlier reply...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 16 Ιουλ 2019 στις 12:02 π.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you for reaching out. Since your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> email was already organized in points, I will reply directly below your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> questions below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1) What do we do when the StudyUID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> blank on the header?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> There solution provided at the table 3 does not guide us how to find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> information ( is possible ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> The StudyUID is the field used in our
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline at the moment to check whether a DICOM study was already inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> into LORIS with that same StudyUID since it is supposed to be unique for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> every single study. Currently, we do not support insertion of DICOM studies
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> if they do not have a StudyUID associated with them.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Is there a specific reason why the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyUID is blank in the DICOM headers in your DICOM files? Did they go
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> through some processes before upload to LORIS?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2) When i am about to upload a non-phanton
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> case i need a 'Visit Label'. Is there already a script that can create a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> new visit label for a specific Candidate, so i can provide it as input
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> afterwards to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader ( See option 5.1.3 https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I am not sure if the front-end allows for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it but if you use batch_uploads_imageuploader, the insertion scripts could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit label for you. However, it does need to be included in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> patient name in order for the script to know which label it should use.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For example: you upload V02 for MTL0123
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (DCCID: 456789) but V02 was not yet created for MTL0123; the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts will create a V02 visit for MTL0123 if the PatientName field for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the dataset is MTL0123_456789_V02 with Stage marked as "Not Started".
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> However, *note that for the script to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> create the visit for the candidate, you have to make sure that all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> visit label of your projects were inserted in the Visit_Windows table*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (otherwise, the visit will never be created as they were not specified as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> being part of the list of visit label to expect). So in the example above,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you should have one row in Visit_Windows with Visit_label="V02" set.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 3) Section 4.3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/04-Scripts.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> What do we do when the folder contains multiple mnc files?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> This is a case by case. Most of the time,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the MINC files that failed insertion into the imaging browser end up in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation module where you can see what went wrong with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> acquisitions not inserted. If you notice that the MINC file should be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted as a specific protocol, you can force the insertion as explained
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in section 4.3.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In your case, I have a feeling that you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> want to be able to insert MINC files that did not go through the whole
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline insertion (DICOM archival, then dcm2mnc, then protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identification, then insertion...). In theory, you could call
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl on any MINC file,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> provided you have at least the following information:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - path to the MINC file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> - uploadID associated with the MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or DICOM archive path from which those MINC files were created from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Then the minc_insertion.pl script will do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the subject information and protocol validation etc...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> If all the MINC files come from the same
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> uploadID or TarchiveID, then you could run a loop in bash calling the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> minc_insertion.pl script like this for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> files deriving from uploadID=1:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ls /path/to/mnc/folder/* | while read f;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do minc_insertion.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -uploadID 1 -mincPath $f; done
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helped!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>>
>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>
>>>>>>>>>>> _______________________________________________
>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>>
>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>> Montreal Neurological Institute
>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Loris-dev mailing list
>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>>
>>>>>>> christine.rogers at mcgill.ca
>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>> Montreal Neurological Institute
>>>>>>> McGill University | Montreal | Canada
>>>>>>> _______________________________________________
>>>>>>> Loris-dev mailing list
>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> christine.rogers at mcgill.ca
>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>> Montreal Neurological Institute
>>>>>> McGill University | Montreal | Canada
>>>>>>
>>>>> _______________________________________________
>>>>> Loris-dev mailing list
>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>
>>>>
>>>>
>>>> --
>>>> Shen Wang
>>>> Loris <https://github.com/aces/Loris> Developer
>>>> Montreal Neurological Institute
>>>> McGill University
>>>>
>>>>
>>>
>>> --
>>> Shen Wang
>>> Loris <https://github.com/aces/Loris> Developer
>>> Montreal Neurological Institute
>>> McGill University
>>>
>>>
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