[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Mon Aug 5 08:19:24 EDT 2019
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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