[Loris-dev] Import mri - scripts

[Nicolas Brossard]

Hi Sotirios,

My name is Nicolas and I am part of the LORIS team. I was told by Cecile
that you were having a problem with the imaging pipeline. Would you be
willing to share your problematic DICOM archive with me? I could set up an
account for you on one of our sftp server and you could upload your data
there. I know patient scans are sensitive data but this would greatly
simplify the debugging process.


Thanks
Nicolas

On Wed, Nov 27, 2019 at 9:30 AM Cecile Madjar <cecile.madjar at mcin.ca> wrote:

> Hi Sotirios,
>
> Thank you for the details!
>
> A few things to try:
>
>    - modify the TMPDIR to be on your /data directory where there might be
>    more space to do processing (could create a /data/tmp where the temporary
>    files would be created)
>    - how many files are there for that upload in tarchive_files? Are they
>    different from the ones showing the warning message?
>       - FYI: query to get that: SELECT tf.* FROM tarchive_files tf JOIN
>       mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>       output of that query would be very useful if you can provide it)
>       - how many series are there for that upload in tarchive_series?
>    - FYI: query to get that: SELECT ts.* FROM tarchive_series ts JOIN
>       mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>       output of that query would be very useful if you can provide it)
>    - things are failing when the scripts try running the following
>    command: find /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO
>    -type f  | /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>       - clearly the problems come from get_dicom_info.pl but I cannot
>       pinpoint the error yet. I will ask around and get back to you
>
> If I cannot figure it out remotely, is there a way to have a call using
> zoom? This way you could share your screen with me and run the debugger on
> that script and hopefully we can figure out what is going on with those
> datasets?
>
> Thanks!
>
> Cécile
>
> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi Cecile,
>>
>> In both my virtual machines
>> export TMPDIR=/tmp
>>
>> In both vm also with dcm2mnc i get this output. Just to verify that this
>> passed in my 1st vm and produced mincs.
>>
>> I attached the spool as a csv.
>>
>> [image: image.png]
>>
>> And also one difference i found was this in the Loris-mri code ( left 1st
>> workable vm, right 2nd vm that has to be fixed, although i changed it seems
>> to be independent of the uninitialized value $_ )
>>
>>
>> [image: image.png]
>>
>> Thanks,
>>
>> Sotirios
>>
>>
>>
>>
>> Στις Τρί, 26 Νοε 2019 στις 11:34 μ.μ., ο/η Cecile Madjar <
>> cecile.madjar at mcin.ca> έγραψε:
>>
>>> Hi Sotirios,
>>>
>>> that is puzzling... A few additional questions:
>>>
>>>    - what is the bash variable TMPDIR set to on the environment file?
>>>    - could you try running separately dcm2mnc on the DICOM folder to
>>>    see if that works?
>>>    - could you send us the detailed log from the notification spool
>>>    table (SELECT * FROM notification_spool WHERE UploadID=<your uploadID>) and
>>>    send it back to us? Maybe there are some additional clues that could help
>>>    figuring out what is going on.
>>>
>>> Thank you!
>>>
>>> Cécile
>>>
>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi Cecile,
>>>>
>>>> I checked for the StudyInstacueUID at the files with "The target
>>>> directory does not contain a single DICOM file"" and their attribute has a
>>>> value.
>>>>
>>>> Regarding the scouter and localizer, i modified the settings in the
>>>> imaging pipeline and now i don't get that error message, but still it
>>>> doesn't create the mnics.
>>>>
>>>> The errors i am getting are ( uninitialized value $_ is not important?
>>>> because i haven't got comments about that )
>>>>
>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>>> imaging_upload_file.pl -profile prod -upload_id 134
>>>> /data/incoming/DCC0025_118008_V1.tar.gz -verbose
>>>>
>>>> and
>>>>
>>>> Number of MINC files that will be considered for inserting into the
>>>> database: 0
>>>>
>>>> No data could be converted into valid MINC files.
>>>>
>>>> The tarchiveLoader.pl insertion script has failed.
>>>> Use of uninitialized value $mail_user in concatenation (.) or string at
>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>>>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/
>>>> batch_uploads_imageuploader.pl line 249.
>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>> batch_uploads_imageuploader.pl line 250.
>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>> batch_uploads_imageuploader.pl line 251.
>>>>
>>>> Thanks
>>>>
>>>> Sotirios
>>>>
>>>> Στις Δευ, 25 Νοε 2019 στις 5:22 μ.μ., ο/η Cecile Madjar <
>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> OK. So the issue I mentioned should not be a problem for you.
>>>>>
>>>>> Is the StudyInstanceUID DICOM header set in your images? If it is not
>>>>> set, then you would end up with the error message "The target directory
>>>>> does not contain a single DICOM file". So maybe this is the issue you are
>>>>> having with those datasets?
>>>>>
>>>>> Regarding not excluding series descriptions, you can configure that in
>>>>> the Config module under the Imaging Pipeline section. Simply remove all
>>>>> entries for the "Series description to exclude from imaging insertion"
>>>>> setting.
>>>>>
>>>>> Cécile
>>>>>
>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> Hi Cecile,
>>>>>>
>>>>>> We are using this version
>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible to
>>>>>> insert low resolution now?
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <cecile.madjar at mcin.ca>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>
>>>>>>> There was a bug that got resolved in 20.2 in get_dicom_info.pl.
>>>>>>> Basically, if a DICOM did not have the (0020,0032) header,
>>>>>>> get_dicom_info.pl considered that the file was not a DICOM, which
>>>>>>> was a mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this
>>>>>>> is the issue you are encountering.
>>>>>>>
>>>>>>> About scout and localizer, they are a type of short and low
>>>>>>> resolution sequence that is used by the tech but is of no interest
>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>
>>>>>>> Hope this helps,
>>>>>>>
>>>>>>> Cécile
>>>>>>>
>>>>>>>
>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Cecile,
>>>>>>>>
>>>>>>>> i executed the find command and the output i got per folder was
>>>>>>>> "DICOM medical imaging data. Maybe there is something wrong with the find
>>>>>>>> command in the warning that it is unable to check if the file is a dicom
>>>>>>>> file? Also when i use get_dicom_info.pl i don't get any output
>>>>>>>> data. Finally i don't understand what scout or localizer is ( something
>>>>>>>> like if and only if a file fails then the whole session is invalid? ).
>>>>>>>>
>>>>>>>> [image: image.png]
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> Sotirios
>>>>>>>>
>>>>>>>> Στις Τρί, 19 Νοε 2019 στις 9:40 μ.μ., ο/η Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> I took a closer look to the batch_uploader_multiple_output.txt
>>>>>>>>> file you sent. It looks like there are different reasons for failure
>>>>>>>>> depending on the DICOM folder uploaded.
>>>>>>>>>
>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908 DCC0007
>>>>>>>>>    V1: it looks like there is no file of type DICOM in the folder. Have you
>>>>>>>>>    checked to see if that is indeed the case? Maybe you can try running the
>>>>>>>>>    following command on that folder to see what are the types of the files? If
>>>>>>>>>    it does not return at least one DICOM medical imaging data file, then that
>>>>>>>>>    is why you get the error message from the pipeline:
>>>>>>>>>       -
>>>>>>>>>
>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>
>>>>>>>>>       - For 864173 DCC0001 V1: it looks like there are two
>>>>>>>>>    different DICOM studies within the same folder. You will need to split that
>>>>>>>>>    study in two based on the StudyUID field as the insertion pipeline does not
>>>>>>>>>    allow for more than one StudyUID per upload.
>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975 DCC0006
>>>>>>>>>    V1: it looks like the dcm2mnc command did not produce any MINC files. Can
>>>>>>>>>    you check in the DICOM archive what are the series present in the tarchive
>>>>>>>>>    for that visit? Maybe only a scout or localizer was acquired for that
>>>>>>>>>    session, hence the no valid MINC files (scout and localizer being skipped
>>>>>>>>>    for the conversion)
>>>>>>>>>    - For 397410 DCC0003 V1: it looks like everything went well
>>>>>>>>>    for this one.
>>>>>>>>>
>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>> get_dicom_info.pl and this does all kind of checks on the DICOM
>>>>>>>>> files (it is being called when running the dcm2mnc conversion). You could
>>>>>>>>> run it independently on your folder if needed.
>>>>>>>>>
>>>>>>>>> Since one of the study got in, it does not look like you are
>>>>>>>>> having a problem with the setup. It seems more likely to be a problem with
>>>>>>>>> the data themselves.
>>>>>>>>>
>>>>>>>>> Hope this helps.
>>>>>>>>>
>>>>>>>>> Cécile
>>>>>>>>>
>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Christine,
>>>>>>>>>>
>>>>>>>>>> In my first vm i am able to create the minc files and view them
>>>>>>>>>> at the mri browser (except of candidate 102761034 ), meanwhile the same
>>>>>>>>>> files gives warnings at the 2nd vm. The output  of the batch upload can be
>>>>>>>>>> seen in the file attached.
>>>>>>>>>> Also a colleague of us has built a pre-validation tool for dicom
>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/ which had
>>>>>>>>>> found all the files that Loris gave as warning . Basically I confirmed that
>>>>>>>>>> the total amount of files per dicom was the same amount as stated in Loris
>>>>>>>>>> and checked some filenames given from warning to confirm that they match
>>>>>>>>>> with our tool. But that was months ago and my colleague had changed some
>>>>>>>>>> parameters for MIP and now our tool doesn't find all the invalid files,
>>>>>>>>>> that's why i asked for the dicom header specification of Loris. In a
>>>>>>>>>> discussion we had he mentioned that he doesn't check for some tags e.x.
>>>>>>>>>> orientation. Lastly to mention that in my first vm i didn't use our tool to
>>>>>>>>>> remove invalid dcm files.
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Στις Τετ, 13 Νοε 2019 στις 11:45 μ.μ., ο/η Christine Rogers, Ms. <
>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>> Can you provide us with some fresh particulars of the
>>>>>>>>>>> current issue and we'll take it from there?
>>>>>>>>>>> Yang's team has built these scripts which can definitely serve
>>>>>>>>>>> as a model for your pre-validation of your DICOM collections.
>>>>>>>>>>> cheers,
>>>>>>>>>>> Christine
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>
>>>>>>>>>>>> We make use of pydicom library too. Now about the validate.py i
>>>>>>>>>>>> see that you check if some attributes are missing such as PatientID,
>>>>>>>>>>>> PatientName which all of our files contains that info. Maybe i have missed
>>>>>>>>>>>> something on the setup of my other virtual machine ( although one dicom
>>>>>>>>>>>> passed on the new vm successfully, the others that were inserted correctly
>>>>>>>>>>>> on my old vm fails on the new one ), i think that i had asked about this
>>>>>>>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144."
>>>>>>>>>>>> but i don't remember the solution.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks
>>>>>>>>>>>>
>>>>>>>>>>>> Στις Τετ, 13 Νοε 2019 στις 5:45 π.μ., ο/η Yang Ding <it at cnbp.ca>
>>>>>>>>>>>> έγραψε:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Christine from the LORIS team mentioned you had some issue
>>>>>>>>>>>>> with DICOM.  I am a fellow developer for an external project using LORIS,
>>>>>>>>>>>>> kind of just like you. We had to implement DICOM upload as well but more as
>>>>>>>>>>>>> a fully automated pipeline actually.
>>>>>>>>>>>>>
>>>>>>>>>>>>> While we were building CNBP, we had coded up some minor Python
>>>>>>>>>>>>> functions to check DICOM integrity (and simple validations) and you might
>>>>>>>>>>>>> be able to gain some inspiration from it and help you with your cause. For
>>>>>>>>>>>>> more comprehensive solution, PyDICOM (
>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> To subscribe or unsubscribe via the World Wide Web, visit
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>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>> or, via email, send a message with subject or body 'help' to
>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> You can reach the person managing the list at
>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> When replying, please edit your Subject line so it is more
>>>>>>>>>>>>>> specific
>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com>
>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom files to
>>>>>>>>>>>>>> diagnose the
>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to check if
>>>>>>>>>>>>>> there are problems
>>>>>>>>>>>>>> > with the dcm files, before trying to upload them. Something
>>>>>>>>>>>>>> that could
>>>>>>>>>>>>>> > provide the same results provided in the warning_output,
>>>>>>>>>>>>>> this is the
>>>>>>>>>>>>>> > summary from the mri_upload at the front-page. Also which
>>>>>>>>>>>>>> attributes of the
>>>>>>>>>>>>>> > dcm header would trigger a warning? is there a dcm file
>>>>>>>>>>>>>> header
>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it
>>>>>>>>>>>>>> worked,but i
>>>>>>>>>>>>>> >> thought that something else was causing the 2nd issue.
>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, <
>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime and
>>>>>>>>>>>>>> columns are of
>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You should be
>>>>>>>>>>>>>> using
>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The second error occurs because the trigger triggers a
>>>>>>>>>>>>>> rollback of the
>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>> >>> See mysql documentation for trigger error handling.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger results
>>>>>>>>>>>>>> in failure of
>>>>>>>>>>>>>> >>> the entire statement that caused trigger invocation.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of
>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding rows at the
>>>>>>>>>>>>>> file table are
>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as
>>>>>>>>>>>>>> well, because i
>>>>>>>>>>>>>> >>> don't want manually to label them as passed throught the
>>>>>>>>>>>>>> interface
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for column
>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child
>>>>>>>>>>>>>> row: a foreign
>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`) REFERENCES
>>>>>>>>>>>>>> `files` (`FileID`))
>>>>>>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>>>>>>>>>>>>>> 848.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column
>>>>>>>>>>>>>> associated with
>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL, it
>>>>>>>>>>>>>> means no DICOMs
>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the end of the
>>>>>>>>>>>>>> insertion of the
>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated with
>>>>>>>>>>>>>> the correct
>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only linked
>>>>>>>>>>>>>> to the files
>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could always create a
>>>>>>>>>>>>>> new table for
>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to mark all
>>>>>>>>>>>>>> their
>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of
>>>>>>>>>>>>>> creating a trigger for
>>>>>>>>>>>>>> >>> that, but which tables do i need to add entries to? So
>>>>>>>>>>>>>> far from what i see
>>>>>>>>>>>>>> >>> i need to add entres at  the table "files" whenever an
>>>>>>>>>>>>>> insertion happens to
>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the
>>>>>>>>>>>>>> beginning of my email
>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So the
>>>>>>>>>>>>>> StudyID i am
>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of the
>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the metadata
>>>>>>>>>>>>>> field but it is mixed
>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the
>>>>>>>>>>>>>> tarchive table,
>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found
>>>>>>>>>>>>>> something called
>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be the
>>>>>>>>>>>>>> Study Instance UID.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Your observation is correct. A little explanation below.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation tables if:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>    - the scan type could not be identified (not matching
>>>>>>>>>>>>>> an entry in
>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>> >>>    - one parameter of the scan type is out of the
>>>>>>>>>>>>>> expected range
>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks (extra filtering in
>>>>>>>>>>>>>> case you need to be
>>>>>>>>>>>>>> >>>    stricker on some parameters not present in the
>>>>>>>>>>>>>> mri_protocol table)
>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not match
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The following cases do not get in the MRI violation
>>>>>>>>>>>>>> tables as it happens
>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC files and only
>>>>>>>>>>>>>> MINC files
>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid DICOM could be
>>>>>>>>>>>>>> found to convert
>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>> >>>    - "Study already inserted" (duplicate StudyUID) since
>>>>>>>>>>>>>> this error
>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level (way before
>>>>>>>>>>>>>> conversion into MINC files)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of
>>>>>>>>>>>>>> ram. Now about the
>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted there
>>>>>>>>>>>>>> only if there is
>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its header
>>>>>>>>>>>>>> parameter?
>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or
>>>>>>>>>>>>>> with the 2 studyiuid
>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the memory. I
>>>>>>>>>>>>>> think most of our
>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should be
>>>>>>>>>>>>>> fine.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> about that dicom that had that insertion error it's about
>>>>>>>>>>>>>> 30mb and when
>>>>>>>>>>>>>> >>> it is being processed the ram is being drastically
>>>>>>>>>>>>>> increased from 2gb to
>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen. What
>>>>>>>>>>>>>> is the recommended
>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed!
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> For the delete script issue, if you are absolutely
>>>>>>>>>>>>>> certain that no
>>>>>>>>>>>>>> >>> processes are run for that uploadID, you can update the
>>>>>>>>>>>>>> mri_upload table
>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for that
>>>>>>>>>>>>>> uploadID. It
>>>>>>>>>>>>>> >>> looks like for some reason the scripts did not update
>>>>>>>>>>>>>> this field when it
>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would be the
>>>>>>>>>>>>>> case though.
>>>>>>>>>>>>>> >>> Note: only do that update if you are certain that there
>>>>>>>>>>>>>> is no processing
>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a StudyID
>>>>>>>>>>>>>> they actually do
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> I thought that this might be a permission because "w" was
>>>>>>>>>>>>>> missing at the
>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579 passed,
>>>>>>>>>>>>>> but with no mnic
>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is currently
>>>>>>>>>>>>>> processing it.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python script:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header
>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min,
>>>>>>>>>>>>>> TR_max, TE_min,
>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at the
>>>>>>>>>>>>>> mri_protocol table
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a violation
>>>>>>>>>>>>>> "T1 AXIAL SE
>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere and
>>>>>>>>>>>>>> i find that weird
>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory
>>>>>>>>>>>>>> does not contain a
>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are missing their
>>>>>>>>>>>>>> StudyUID
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data from
>>>>>>>>>>>>>> multiple
>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted into valid MINC
>>>>>>>>>>>>>> files.
>>>>>>>>>>>>>> >>> localizer, scout will not be considered!" What is this?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> If i wanted to force the insertion of 102327840,
>>>>>>>>>>>>>> 102809579 and 102506134
>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the folder at
>>>>>>>>>>>>>> dicom_output.txt.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging data is fully
>>>>>>>>>>>>>> documented here
>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers you were
>>>>>>>>>>>>>> looking for there.
>>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in
>>>>>>>>>>>>>> your database
>>>>>>>>>>>>>> >>> management software is a visual placeholder for you as
>>>>>>>>>>>>>> the user?  I'm not
>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered with ID='0'
>>>>>>>>>>>>>> as your screenshot
>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> I tried to create a new candidate using the API, is there
>>>>>>>>>>>>>> something
>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a 500
>>>>>>>>>>>>>> internal error? In the
>>>>>>>>>>>>>> >>> loris-error log it state that there is something wrong
>>>>>>>>>>>>>> with token, but i
>>>>>>>>>>>>>> >>> verfied that the type of the token is a string.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid 4535]
>>>>>>>>>>>>>> [client
>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:  Uncaught TypeError:
>>>>>>>>>>>>>> Argument 1
>>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be of
>>>>>>>>>>>>>> the type string,
>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc
>>>>>>>>>>>>>> on line 169 and
>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST', Array)\n#5
>>>>>>>>>>>>>> {main}\n  thrown in
>>>>>>>>>>>>>> >>> /var/www/loris/php/libraries/SinglePointLogin.class.inc
>>>>>>>>>>>>>> on line 192
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just to let you
>>>>>>>>>>>>>> know what i
>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may have missed
>>>>>>>>>>>>>> dependencies.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is there a
>>>>>>>>>>>>>> way to omit
>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i deleted
>>>>>>>>>>>>>> all the entries
>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete this entry
>>>>>>>>>>>>>> with the 0 ID.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the candidate table.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> We recommend that you use our existing tools for creating
>>>>>>>>>>>>>> new candidates
>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP script,
>>>>>>>>>>>>>> by calling the Candidate
>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>> >>> These will create the necessary records for you.  (It's
>>>>>>>>>>>>>> not recommended to
>>>>>>>>>>>>>> >>> make direct modifications to mysql database tables in
>>>>>>>>>>>>>> your script, if I
>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized ID,
>>>>>>>>>>>>>> and there are
>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs and the
>>>>>>>>>>>>>> External ID field
>>>>>>>>>>>>>> >>> in the candidate table can also be used for any values
>>>>>>>>>>>>>> you like.
>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be added in
>>>>>>>>>>>>>> parallel - these
>>>>>>>>>>>>>> >>> are entered/visible in the Candidate Information module
>>>>>>>>>>>>>> and added in the
>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> We are building a script that will auto insert the
>>>>>>>>>>>>>> candidates based on
>>>>>>>>>>>>>> >>> their ExternalID. We would like to know whethere when we
>>>>>>>>>>>>>> are creating a new
>>>>>>>>>>>>>> >>> profile in the candidate table, if we also have to insert
>>>>>>>>>>>>>> a new record at
>>>>>>>>>>>>>> >>> another table? Furthermore is there a problem that in our
>>>>>>>>>>>>>> case CandID won't
>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie
>>>>>>>>>>>>>> Legault, Mrs <
>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> That would normally be the case but the numeric part of
>>>>>>>>>>>>>> the PSCID get
>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus 4
>>>>>>>>>>>>>> numerical char
>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> thus sorting them ascending will always get the latest
>>>>>>>>>>>>>> value generated
>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it must
>>>>>>>>>>>>>> be stored
>>>>>>>>>>>>>> >>> within a specific length of characters. Otherwise if we
>>>>>>>>>>>>>> were to sort
>>>>>>>>>>>>>> >>> strings with different lengths the result would not be
>>>>>>>>>>>>>> sorted correctly (
>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11, 2 ).
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie
>>>>>>>>>>>>>> Legault, Mrs <
>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the max value and
>>>>>>>>>>>>>> increase that
>>>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of
>>>>>>>>>>>>>> Medicine | McGill
>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of
>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> how does Loris determine the next available PSCID value
>>>>>>>>>>>>>> for a new
>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but
>>>>>>>>>>>>>> where do we store the
>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have assigned are
>>>>>>>>>>>>>> global
>>>>>>>>>>>>>> >>> standard? or were assigned after trial and error?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Given you have done the initial setup of your tables to
>>>>>>>>>>>>>> match your
>>>>>>>>>>>>>> >>> intended protocol/parameters according to instructions --
>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation recommends
>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting prior
>>>>>>>>>>>>>> uploads).
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> *if i were to change their status to resolve what would
>>>>>>>>>>>>>> happen?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the brainbrowser
>>>>>>>>>>>>>> from the
>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at
>>>>>>>>>>>>>> /data/loris/data/trashbin/
>>>>>>>>>>>>>> >>> if i were to click their issue to resolve what would
>>>>>>>>>>>>>> happend? would they
>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The defaut values of the schema exists in my local
>>>>>>>>>>>>>> database. If i adjust
>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs will be
>>>>>>>>>>>>>> uploaded?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your mri_protocol
>>>>>>>>>>>>>> table ?   (and
>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types of scans)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the
>>>>>>>>>>>>>> Imaging insertion
>>>>>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert statements.  You
>>>>>>>>>>>>>> can adapt the
>>>>>>>>>>>>>> >>> insert statements which load the default table values -->
>>>>>>>>>>>>>> e.g. Here on
>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> I see that i can edit the values but not how to insert
>>>>>>>>>>>>>> new rows.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the minc be
>>>>>>>>>>>>>> inserted?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot is enough.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> It says "could not identify scan type", which we knew
>>>>>>>>>>>>>> already.  Did you
>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> It will take you to the next page of the module, showing
>>>>>>>>>>>>>> for each scan
>>>>>>>>>>>>>> >>> what the scan parameters were, and will also show for
>>>>>>>>>>>>>> comparison what's
>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>> >>> Compare these values to find which parameter was not
>>>>>>>>>>>>>> correct according
>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type definitions.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol value ranges
>>>>>>>>>>>>>> (e.g. TR, TE)
>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>> >>> This can be done in the front-end, by editing the
>>>>>>>>>>>>>> database table
>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI Violations module.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The MRI Violations module features are explained in more
>>>>>>>>>>>>>> detail in the
>>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click the  ["?"]
>>>>>>>>>>>>>> icon in the menu
>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> looks like my previous email's attachment wasn't
>>>>>>>>>>>>>> delivered due to
>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at google drive
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both cases
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html output from
>>>>>>>>>>>>>> webbrowser, so
>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're
>>>>>>>>>>>>>> getting an Endian
>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error, correct?)
>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName) all
>>>>>>>>>>>>>> successfully
>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers -- though your
>>>>>>>>>>>>>> dcmodify command is
>>>>>>>>>>>>>> >>> a great and fast solution for bulk header updates.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> If you're concerned about fields being changed (e.g.
>>>>>>>>>>>>>> "(2001,105f)" from
>>>>>>>>>>>>>> >>> the warning message)  - you can also dcmdump a DICOM
>>>>>>>>>>>>>> slice before and look
>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your DICOMS
>>>>>>>>>>>>>> before/after
>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to diff
>>>>>>>>>>>>>> the outputs --
>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not
>>>>>>>>>>>>>> recognized or
>>>>>>>>>>>>>> >>> unknown :   this means your scans did not match what is
>>>>>>>>>>>>>> stored in your
>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module -- can you see
>>>>>>>>>>>>>> why they didn't
>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>> >>> Send us an example, in addition to the contents of the
>>>>>>>>>>>>>> mri_protocol
>>>>>>>>>>>>>> >>> table, if you can't find the source of the mismatch.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the interface
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined
>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined
>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined
>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined
>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined
>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined
>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below you
>>>>>>>>>>>>>> can see the
>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could not be
>>>>>>>>>>>>>> inserted due to
>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12
>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>  find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name
>>>>>>>>>>>>>> '__MACOSX'
>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile prod
>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> You are creating a tar with the following command:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>> >>> * Name of creating host            :    127.0.1.1
>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>> >>> * Created by user                  :    lorisadmin
>>>>>>>>>>>>>> >>> * Archived on                      :    2019-09-06
>>>>>>>>>>>>>> 18:36:50
>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>> >>>  DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl
>>>>>>>>>>>>>> -globLocation
>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Number of MINC files that will be considered for
>>>>>>>>>>>>>> inserting into the
>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>   --> The minc file cannot be registered since the
>>>>>>>>>>>>>> AcquisitionProtocol
>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the
>>>>>>>>>>>>>> *delete_imaging_upload*
>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it properly populated?
>>>>>>>>>>>>>> This is a
>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>> >>> The foreign key constraint error on the candidate record
>>>>>>>>>>>>>> is curious.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> There are also a few options for creating candidates when
>>>>>>>>>>>>>> inserting
>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM
>>>>>>>>>>>>>> insertion pipeline
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and
>>>>>>>>>>>>>> visits, optionally I
>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>> >>> You will want to first ensure that the PatientName header
>>>>>>>>>>>>>> in the DICOMs
>>>>>>>>>>>>>> >>> as well as tar package are correctly labelled with
>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running the
>>>>>>>>>>>>>> bids_import script,
>>>>>>>>>>>>>> >>> to automatically create your candidates and sessions.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i have to
>>>>>>>>>>>>>> create a new
>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./
>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a child
>>>>>>>>>>>>>> row: a foreign
>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT
>>>>>>>>>>>>>> `FK_candidate_1`
>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc`
>>>>>>>>>>>>>> (`CenterID`)) at
>>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>>>>>>>>>>>>>> 1060.
>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner:
>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES
>>>>>>>>>>>>>> (?,?,?,?,?)';
>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a
>>>>>>>>>>>>>> foreign key
>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT
>>>>>>>>>>>>>> `FK_mri_scanner_1`
>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`))
>>>>>>>>>>>>>> (error code 1452)
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>  ERROR: The validation has failed. Either re-run the
>>>>>>>>>>>>>> validation again
>>>>>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl using
>>>>>>>>>>>>>> -force to force the
>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//) at ./
>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study.
>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>> >>> This is the information retained from the first time the
>>>>>>>>>>>>>> study was
>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>> >>> * Name of creating host            :    127.0.1.1
>>>>>>>>>>>>>> >>> * Name of host OS                  :    Linux
>>>>>>>>>>>>>> >>> * Created by user                  :    lorisadmin
>>>>>>>>>>>>>> >>> * Archived on                      :    2019-09-04
>>>>>>>>>>>>>> 18:33:05
>>>>>>>>>>>>>> >>> * dicomSummary version             :    1
>>>>>>>>>>>>>> >>> * dicomTar version                 :    1
>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>> >>>  DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.  Let us know when you
>>>>>>>>>>>>>> next encounter
>>>>>>>>>>>>>> >>> issues as you progress through the Imaging Install/Setup
>>>>>>>>>>>>>> docs
>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>> >>> I'll look into how we can better handle the incoming/
>>>>>>>>>>>>>> directory next
>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios Nikoloutsopoulos
>>>>>>>>>>>>>> <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>> >>> populated correctly except its port is  'port'    : ''.
>>>>>>>>>>>>>> Also i have tested
>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> I executed the script again, because the only error i had
>>>>>>>>>>>>>> previously was
>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and there are
>>>>>>>>>>>>>> no errors
>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql: [Warning] Using
>>>>>>>>>>>>>> a password on the
>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> It's possible -- if the script was unable to connect to
>>>>>>>>>>>>>> the database
>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the password), that
>>>>>>>>>>>>>> would explain the
>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you saw
>>>>>>>>>>>>>> in the Config
>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output from your
>>>>>>>>>>>>>> script run -- Did
>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>> >>> The Config fields are populated by the imaging_install.sh
>>>>>>>>>>>>>> script (starting
>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> For example, check if the database connection information
>>>>>>>>>>>>>> was populated
>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh here is an
>>>>>>>>>>>>>> image with the
>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is somewhere at
>>>>>>>>>>>>>> the last part
>>>>>>>>>>>>>> >>> which asks to configure as much as possible automatically?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine
>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and working
>>>>>>>>>>>>>> and all the
>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod 775
>>>>>>>>>>>>>> project
>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775 permissions
>>>>>>>>>>>>>> and that
>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1 in
>>>>>>>>>>>>>> the install
>>>>>>>>>>>>>> >>> Readme <https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should
>>>>>>>>>>>>>> change LORIS to
>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> These imaging paths will be updated during your imaging
>>>>>>>>>>>>>> installation
>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> by an
>>>>>>>>>>>>>> automated script --
>>>>>>>>>>>>>> >>> you do not need to set them manually via the Config
>>>>>>>>>>>>>> module.
>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> for detailed
>>>>>>>>>>>>>> steps to follow.
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should change
>>>>>>>>>>>>>> LORIS to loris,
>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios
>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo -E
>>>>>>>>>>>>>> bash -
>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> you had suggested in the past, make worked and now i can
>>>>>>>>>>>>>> see all the
>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't need make
>>>>>>>>>>>>>> install?
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>> >>> 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
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> 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
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>> 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
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>> _______________________________________________
> Loris-dev mailing list
> Loris-dev at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>
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