[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Mon Aug 5 09:05:34 EDT 2019
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
>>
>
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