From cecile.madjar at mcin.ca  Mon Dec  2 11:58:47 2019
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 2 Dec 2019 11:58:47 -0500
Subject: [Loris-dev] Import mri - scripts
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Message-ID: <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>

Hi Sotirios,

It looks like for some reason your binary mnc2nii is not working and
reports that error. Do you want to create NIfTI files or are you happy with
just the MINC files?

If you don't need the NIfTI files, then maybe you can set the Config
setting "NIfTI file creation" to No instead of Yes and this error will not
appear anymore.

If you need the NIfTI files to be created, then I would
recommend installing the latest version of the MINC tools (1.9.17). They
can be found there:

   - pre-built packages: https://packages.bic.mni.mcgill.ca/minc-toolkit/
   - from the source code with installation instructions in the README:
   https://github.com/BIC-MNI/minc-toolkit-v2

If the problem persists by using the latest release of MINC tools, then
create an issue on Github for the MINC developers here
<https://github.com/BIC-MNI/minc-toolkit-v2/issues>.

Hope this helps,

C?cile

On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hi Cecile,
>
> Thanks to Nicholas i was able to create all the mincs images. The problem
> was that the files were in Little-Endian-Implicit transfer syntax and i had
> to convert them Little-Endian-Explicit transfer syntax with this command
>
> find <root_of_my_DICOM_files_directory> -type f | xargs -i
> dcmconv --write-xfer-little {} {}
>
>
> Looking back at our mails i saw that Little-Endian error had occurred when
> i used dcmodify, but i switcthed to using pydicom instead.
>
>
> [image: image.png]
>
>
> In the output i see an error sometimes about "gsl: bessel_I0.c:216: ERROR:
> overflow". Is this okay?
>
> Restructuring...
> gsl: bessel_I0.c:216: ERROR: overflow
> Default GSL error handler invoked.
> noise_estimate --snr
> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
> SNR is:
> gsl: bessel_I0.c:216: ERROR: overflow
> Default GSL error handler invoked.
>
> Thanks,
>
> Sotirios
>
>
> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
> cecile.madjar at mcin.ca> ??????:
>
>> 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!
>>
>> C?cile
>>
>> 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
>>>
>>>
>>>
>>>
>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>> cecile.madjar at mcin.ca> ??????:
>>>
>>>> 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!
>>>>
>>>> C?cile
>>>>
>>>> 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
>>>>>
>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>
>>>>>> 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.
>>>>>>
>>>>>> C?cile
>>>>>>
>>>>>> 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,
>>>>>>>>
>>>>>>>> C?cile
>>>>>>>>
>>>>>>>>
>>>>>>>> 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
>>>>>>>>>
>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>
>>>>>>>>>> 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.
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers, Ms.
>>>>>>>>>>> <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>
>>>>>>>>>>>> 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
>>>>>>>>>>>>>
>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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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>>>>>>>>>>>>>>> or, via email, send a message with subject or body 'help' to
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>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>
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From joh17964 at umn.edu  Mon Dec  2 12:43:23 2019
From: joh17964 at umn.edu (Eli Johnson)
Date: Mon, 2 Dec 2019 11:43:23 -0600
Subject: [Loris-dev] Importing spreadsheet/csv to LORIS
Message-ID: <CAKcpJh7y09Z+rn2--sK_sVg7vsC7+cnLgk9sOpk+6-Muccqbkg@mail.gmail.com>

Hi all,

I am interested in importing large datasets currently saved as csv or xlsx
into our instance of LORIS. I know that some instruments (like the
Vineland) are able to parse a text file and map the variables from the file
to the corresponding MySQL field in the database. Are there tools already
out there or ideas for how to implement this for a csv containing multiple
candidates and visits? Does LORIS contain any built in functions in it's
libraries that could help with this?

I wanted to check what already exists or if anyone is already working on
this before writing something custom. I'm also happy to collaborate if
there is already something in the works for this.

Thanks,

Eli Johnson
Researcher
Institute of Child Development
University of Minnesota
joh17964 at umn.edu
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From leigh.ibis at gmail.com  Mon Dec  2 13:29:46 2019
From: leigh.ibis at gmail.com (Leigh MacIntyre)
Date: Mon, 2 Dec 2019 13:29:46 -0500
Subject: [Loris-dev] Importing spreadsheet/csv to LORIS
In-Reply-To: <CAKcpJh7y09Z+rn2--sK_sVg7vsC7+cnLgk9sOpk+6-Muccqbkg@mail.gmail.com>
References: <CAKcpJh7y09Z+rn2--sK_sVg7vsC7+cnLgk9sOpk+6-Muccqbkg@mail.gmail.com>
Message-ID: <2AFF6D4A-2C7B-4561-9235-DF416F57E116@gmail.com>

Hi Eli,

We (IBIS) have this feature. Sruthy Mathew would probably be the best person to speak with regarding the code to do this. You (may)? Have to adapt it to allow for multiple visits contained in one spreadsheet but I am sure we have the function for multiple candidates in the same visit in one file. 


L
Sent from my iPhone

> On Dec 2, 2019, at 12:43 PM, Eli Johnson <joh17964 at umn.edu> wrote:
> 
> ?
> Hi all, 
> 
> I am interested in importing large datasets currently saved as csv or xlsx into our instance of LORIS. I know that some instruments (like the Vineland) are able to parse a text file and map the variables from the file to the corresponding MySQL field in the database. Are there tools already out there or ideas for how to implement this for a csv containing multiple candidates and visits? Does LORIS contain any built in functions in it's libraries that could help with this? 
> 
> I wanted to check what already exists or if anyone is already working on this before writing something custom. I'm also happy to collaborate if there is already something in the works for this. 
> 
> Thanks, 
> 
> Eli Johnson
> Researcher
> Institute of Child Development
> University of Minnesota
> joh17964 at umn.edu
> _______________________________________________
> 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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From AMORALESPINZON at bwh.harvard.edu  Mon Dec  2 13:33:17 2019
From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo)
Date: Mon, 2 Dec 2019 18:33:17 +0000
Subject: [Loris-dev] LORIS Error: The target directory does not contain
 a single DICOM file.
In-Reply-To: <88DDA28F-928E-4923-99AE-81FF0E63B622@bwh.harvard.edu>
References: <4A0C0CF2-B5BC-47F1-84F9-287D4BD9B547@bwh.harvard.edu>
 <CAMkiY3eb8EDto_g3Ma-r2sJCMp3JBKEHfhPbezB-OXjoMMadnw@mail.gmail.com>
 <88DDA28F-928E-4923-99AE-81FF0E63B622@bwh.harvard.edu>
Message-ID: <51B93D39-60D4-4E79-A521-AB07EDDC0E96@bwh.harvard.edu>

Hi C?cile,

Apparently the changes we made, fixed StudyInstanceUID and StudyID, worked as we don?t see the error ?The target directory does not contain a single DICOM file? anymore. However, now I am getting the following error for all the cases that were fixed:

----------------------------------
Running now the following command: /xxx/bin/mri/uploadNeuroDB/imaging_upload_file.pl<http://imaging_upload_file.pl/> -profile prod -upload_id 20925 /yyy/AAA10001_111222_baseline.tar.gz -verbose Spool message is: The Scan for the uploadID 20925 has already been run with tarchiveID: 20738. To continue with the rest of the insertion pipeline, please run tarchiveLoader from a terminal as follows: /xxx/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar -verbose
----------------------------------

When I run the suggested command line I get the following message:

----------------------------------
$ /xxx/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar -verbose

md5sum /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar

PSCID is: AAA10001
 CandID id: 111222
 visit_label is: baseline
candidate id 111222
PSCID is: AAA10001
 CandID id: 111222
 visit_label is: baseline
WARNING: Age was not numeric!!
WARNING: Age was not numeric!!
WARNING: Age was not numeric!!
WARNING: Age was not numeric!!
WARNING: Age was not numeric!!
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
Error reading file.
Mincinfo_wrapper: crashed while running mincinfo (termination status=256)

Number of MINC files that will be considered for inserting into the database: 0

No data could be converted into valid MINC files. Localizers will not be considered!
----------------------------------

I tested the conversion of one the DICOM folder to minc and then executed mincinfo but I didn?t get any errors.

Do you know why this might be happening?

Is there an issue with the files created by LORIS in the first attempt I tried to upload these images (see uploadId 20925)?

Let me know if you need more information from my side to help overcome this issue.

Best regards,
Alfredo.

On Nov 25, 2019, at 10:25 AM, Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.EDU>> wrote:

Hi C?cile,

Thank you for your prompt response. We will make the changes, try again, and report back to this thread.

Best regards,
Alfredo.

On Nov 25, 2019, at 10:06 AM, Cecile Madjar <cecile.madjar at mcin.ca<mailto:cecile.madjar at mcin.ca>> wrote:


        External Email - Use Caution

Hi Alfredo,

Indeed, the StudyInstanceUID needs to have a value for the insertion pipeline to work so that could explain the no DICOM found error.

FYI - StudyInstanceUID also needs to be unique for each uploaded study otherwise insertion in the tarchive tables would fail with the error: "the study has already been uploaded"

Hope this helps,

C?cile

On Mon, Nov 25, 2019 at 10:02 AM Morales Pinzon, Alfredo <AMORALESPINZON at bwh.harvard.edu<mailto:AMORALESPINZON at bwh.harvard.edu>> wrote:
Dear LorisDev team,

I am batch uploading images to imaging visits using the script batch_uploads_imageuploader but for some images I get the following error:

The target directory does not contain a single DICOM file.

I had seen this error previously due to missing dicom fields like StudyID (0020,0010) and ImagePositionPatient (0020,0032). However, after checking these particular dicom fields and setting StudyID it to '0' I am still getting the same error. What other dicom fields should I check?

Is there a log where I can exactly find the error? Does the "StudyInstanceUID" need to have a value?

I'm pasting the dcmdump of a dicom at the end of this email in case this might help figuring out what is the issue.

I am using LORIS v at 20.1.1.<mailto:v at 20.1.1.>

Thank you in advance for your help.

Best regards,
Alfredo.

--------------------------------------------------------------------------------------

# Dicom-File-Format

# Dicom-Meta-Information-Header
# Used TransferSyntax: Little Endian Explicit
(0002,0000) UL 230                                      #   4, 1 FileMetaInformationGroupLength
(0002,0001) OB 00\01                                    #   2, 1 FileMetaInformationVersion
(0002,0002) UI =MRImageStorage                          #  26, 1 MediaStorageSOPClassUID
(0002,0003) UI [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] #  64, 1 MediaStorageSOPInstanceUID
(0002,0010) UI =LittleEndianImplicit                    #  18, 1 TransferSyntaxUID
(0002,0012) UI [1.2.276.0.7230010.3.0.3.6.0]            #  28, 1 ImplementationClassUID
(0002,0013) SH [OFFIS_DCMTK_360]                        #  16, 1 ImplementationVersionName
(0002,0016) AE [GDCM/ITK 3.17.0]                        #  16, 1 SourceApplicationEntityTitle

# Dicom-Data-Set
# Used TransferSyntax: Little Endian Implicit
(0008,0008) CS [DERIVED\SECONDARY]                      #  18, 2 ImageType
(0008,0016) UI =MRImageStorage                          #  26, 1 SOPClassUID
(0008,0018) UI [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] #  64, 1 SOPInstanceUID
(0008,0020) DA [20000101]                               #   8, 1 StudyDate
(0008,0021) DA [20000101]                               #   8, 1 SeriesDate
(0008,0022) DA [20000101]                               #   8, 1 AcquisitionDate
(0008,0030) TM (no value available)                     #   0, 0 StudyTime
(0008,0031) TM [085517]                                 #   6, 1 SeriesTime
(0008,0032) TM [085517]                                 #   6, 1 AcquisitionTime
(0008,0060) CS [MR]                                     #   2, 1 Modality
(0008,0070) LO [AAABBBCCC]                                 #   6, 1 Manufacturer
(0008,0104) LO [Anonymized]                             #  10, 1 CodeMeaning
(0008,103e) LO [t1c]                                    #   4, 1 SeriesDescription
(0008,1090) LO [nifti2dicom]                            #  12, 1 ManufacturerModelName
(0010,0010) PN [10041]                                  #   6, 1 PatientName
(0010,0020) LO [10041]                                  #   6, 1 PatientID
(0010,0021) LO [Anonymized]                             #  10, 1 IssuerOfPatientID
(0010,0030) DA [19650101]                               #   8, 1 PatientBirthDate
(0010,0040) CS [Anonymized]                             #  10, 1 PatientSex
(0010,1010) AS [Anonymized]                             #  10, 1 PatientAge
(0010,1030) DS (no value available)                     #   0, 0 PatientWeight
(0010,2150) LO [Anonymized]                             #  10, 1 CountryOfResidence
(0010,2152) LO [Anonymized]                             #  10, 1 RegionOfResidence
(0010,21f0) LO [Anonymized]                             #  10, 1 PatientReligiousPreference
(0012,0050) LO [baseline]                               #   8, 1 ClinicalTrialTimePointID
(0012,0062) CS [Yes]                                    #   4, 1 PatientIdentityRemoved
(0012,0063) LO [Genentech]                              #  10, 1 DeidentificationMethod
(0018,0050) DS [3]                                      #   2, 1 SliceThickness
(0018,0088) DS [3]                                      #   2, 1 SpacingBetweenSlices
(0020,000d) UI (no value available)                     #   0, 0 StudyInstanceUID
(0020,000e) UI [1.2.826.0.1.3680043.2.1143.2737712182581015462892759360372011946] #  64, 1 SeriesInstanceUID
(0020,0010) SH [0]                                      #   2, 1 StudyID
(0020,0011) IS [901]                                    #   4, 1 SeriesNumber
(0020,0012) IS [1]                                      #   2, 1 AcquisitionNumber
(0020,0013) IS [1]                                      #   2, 1 InstanceNumber
(0020,0020) CS [L\R]                                    #   4, 2 PatientOrientation
(0020,0032) DS [-116.48152160645\-118.93698120117\-275.82513427734] #  50, 3 ImagePositionPatient
(0020,0037) DS [1\0\0\0\1\0]                            #  12, 6 ImageOrientationPatient
(0020,0052) UI [1.2.826.0.1.3680043.2.1143.263896814292546686535778822643473818] #  64, 1 FrameOfReferenceUID
(0028,0002) US 1                                        #   2, 1 SamplesPerPixel
(0028,0004) CS [MONOCHROME2]                            #  12, 1 PhotometricInterpretation
(0028,0010) US 256                                      #   2, 1 Rows
(0028,0011) US 256                                      #   2, 1 Columns
(0028,0030) DS [1\1]                                    #   4, 2 PixelSpacing
(0028,0100) US 16                                       #   2, 1 BitsAllocated
(0028,0101) US 16                                       #   2, 1 BitsStored
(0028,0102) US 15                                       #   2, 1 HighBit
(0028,0103) US 1                                        #   2, 1 PixelRepresentation
(0032,1033) LO [Anonymized]                             #  10, 1 RequestingService
(0040,0280) ST [Anonymized]                             #  10, 1 CommentsOnThePerformedProcedureStep
(0400,0563) LO [Anonymized]                             #  10, 1 ModifyingSystem
(0400,0564) LO [Anonymized]                             #  10, 1 SourceOfPreviousValues
(0400,0565) CS [Anonymized]                             #  10, 1 ReasonForTheAttributeModification
(1110,21b0) ?? 0a\00                                    #   2, 1 Unknown Tag & Data
(7fe0,0010) OW 0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000... # 131072, 1 PixelData


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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From cecile.madjar at mcin.ca  Mon Dec  2 14:14:07 2019
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 2 Dec 2019 14:14:07 -0500
Subject: [Loris-dev] LORIS Error: The target directory does not contain
 a single DICOM file.
In-Reply-To: <51B93D39-60D4-4E79-A521-AB07EDDC0E96@bwh.harvard.edu>
References: <4A0C0CF2-B5BC-47F1-84F9-287D4BD9B547@bwh.harvard.edu>
 <CAMkiY3eb8EDto_g3Ma-r2sJCMp3JBKEHfhPbezB-OXjoMMadnw@mail.gmail.com>
 <88DDA28F-928E-4923-99AE-81FF0E63B622@bwh.harvard.edu>
 <51B93D39-60D4-4E79-A521-AB07EDDC0E96@bwh.harvard.edu>
Message-ID: <CAMkiY3exr6_Wq90_ZXr-627myKau4gosNi3WmKXjGcjE15rCCg@mail.gmail.com>

Hi Alfredo,

see below in blue for answers to the different cases.

Hope that will help,

C?cile

On Mon, Dec 2, 2019 at 1:33 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> Hi C?cile,
>
> Apparently the changes we made, fixed StudyInstanceUID and StudyID, worked
> as we don?t see the error ?The target directory does not contain a single
> DICOM file? anymore. However, now I am getting the following error for all
> the cases that were fixed:
>
> ----------------------------------
> Running now the following command: /xxx/bin/mri/uploadNeuroDB/
> imaging_upload_file.pl -profile prod -upload_id 20925
> /yyy/AAA10001_111222_baseline.tar.gz -verbose Spool message is: The Scan
> for the uploadID 20925 has already been run with tarchiveID: 20738. To
> continue with the rest of the insertion pipeline, please run tarchiveLoader
> from a terminal as follows: /xxx/bin/mri/uploadNeuroDB/tarchiveLoader
> -globLocation -profile prod
> /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar -verbose
> ----------------------------------
>

The important message is "The Scan for the uploadID 20925 has already been
run with tarchiveID: 20738.". This means that there is already a study that
was inserted in the tarchive tables that is using the same StudyInstanceUID
as the one being uploaded. So you would need to generate new *unique*
StudyInstanceUID per DICOM study you wish to upload (since as I understand,
that field has been erased for ethical purposes). Each StudyInstanceUID has
to be unique otherwise the pipeline thinks you are trying to upload a
duplicate dataset.

FYI - The terminal output with the tarchiveLoader command is actually
suggesting to run the tarchiveLoader on the previous upload that was found
to have the same StudyInstanceUID (and that has tarchiveID=20738 associated
with the previous upload).


When I run the suggested command line I get the following message:
>

> ----------------------------------
> $ /xxx/bin/mri/uploadNeuroDB/tarchiveLoader -globLocation -profile prod
> /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar -verbose
>
> md5sum /yyy/data/tarchive/DCM_2011-08-19_ImagingUpload-9-52-PPfWPd.tar
>
> PSCID is: AAA10001
>  CandID id: 111222
>  visit_label is: baseline
> candidate id 111222
> PSCID is: AAA10001
>  CandID id: 111222
>  visit_label is: baseline
> WARNING: Age was not numeric!!
> WARNING: Age was not numeric!!
> WARNING: Age was not numeric!!
> WARNING: Age was not numeric!!
> WARNING: Age was not numeric!!
> Error reading file.
> Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
> Error reading file.
> Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
> Error reading file.
> Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
> Error reading file.
> Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
> Error reading file.
> Mincinfo_wrapper: crashed while running mincinfo (termination status=256)
>
> Number of MINC files that will be considered for inserting into the
> database: 0
>
> No data could be converted into valid MINC files. Localizers will not be
> considered!
> ----------------------------------
>
> I tested the conversion of one the DICOM folder to minc and then executed
> mincinfo but I didn?t get any errors.
>
> Do you know why this might be happening?
>

Is it possible that the encoding of the DICOMs are not "little endian
explicit" by any chance? If that is the case, you would need to convert
them so that the encoding is "little endian explicit".

FYI: command to convert the encoding of the DICOMs
find <root_of_my_DICOM_files_directory> -type f | xargs -i
dcmconv --write-xfer-little {} {}

Once done, you would need to remove the partial upload and reupload. This
can be done using the delete_imaging_upload.pl script in the tools
directory. Run the -h option and you will see the explanation on how this
script can be run and detailed information about the options.

Is there an issue with the files created by LORIS in the first attempt I
> tried to upload these images (see uploadId 20925)?
>
> Let me know if you need more information from my side to help overcome
> this issue.
>

> Best regards,
> Alfredo.
>
> On Nov 25, 2019, at 10:25 AM, Morales Pinzon, Alfredo <
> AMORALESPINZON at BWH.HARVARD.EDU> wrote:
>
> Hi C?cile,
>
> Thank you for your prompt response. We will make the changes, try again,
> and report back to this thread.
>
> Best regards,
> Alfredo.
>
> On Nov 25, 2019, at 10:06 AM, Cecile Madjar <cecile.madjar at mcin.ca> wrote:
>
>         External Email - Use Caution
>
> Hi Alfredo,
>
> Indeed, the StudyInstanceUID needs to have a value for the insertion
> pipeline to work so that could explain the no DICOM found error.
>
> FYI - StudyInstanceUID also needs to be unique for each uploaded study
> otherwise insertion in the tarchive tables would fail with the error: "the
> study has already been uploaded"
>
> Hope this helps,
>
> C?cile
>
> On Mon, Nov 25, 2019 at 10:02 AM Morales Pinzon, Alfredo <
> AMORALESPINZON at bwh.harvard.edu> wrote:
>
>> Dear LorisDev team,
>>
>> I am batch uploading images to imaging visits using the script
>> batch_uploads_imageuploader but for some images I get the following error:
>>
>> *The target directory does not contain a single DICOM file.*
>>
>> I had seen this error previously due to missing dicom fields like StudyID
>> (0020,0010) and ImagePositionPatient (0020,0032). However, after checking
>> these particular dicom fields and setting StudyID it to '0' I am still
>> getting the same error. What other dicom fields should I check?
>>
>> Is there a log where I can exactly find the error? Does the
>> "StudyInstanceUID" need to have a value?
>>
>> I'm pasting the dcmdump of a dicom at the end of this email in case this
>> might help figuring out what is the issue.
>>
>> I am using LORIS v at 20.1.1.
>>
>> Thank you in advance for your help.
>>
>> Best regards,
>> Alfredo.
>>
>>
>> --------------------------------------------------------------------------------------
>>
>> # Dicom-File-Format
>>
>> # Dicom-Meta-Information-Header
>> # Used TransferSyntax: Little Endian Explicit
>> (0002,0000) UL 230                                      #   4, 1
>> FileMetaInformationGroupLength
>> (0002,0001) OB 00\01                                    #   2, 1
>> FileMetaInformationVersion
>> (0002,0002) UI =MRImageStorage                          #  26, 1
>> MediaStorageSOPClassUID
>> (0002,0003) UI
>> [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] #  64, 1
>> MediaStorageSOPInstanceUID
>> (0002,0010) UI =LittleEndianImplicit                    #  18, 1
>> TransferSyntaxUID
>> (0002,0012) UI [1.2.276.0.7230010.3.0.3.6.0]            #  28, 1
>> ImplementationClassUID
>> (0002,0013) SH [OFFIS_DCMTK_360]                        #  16, 1
>> ImplementationVersionName
>> (0002,0016) AE [GDCM/ITK 3.17.0]                        #  16, 1
>> SourceApplicationEntityTitle
>>
>> # Dicom-Data-Set
>> # Used TransferSyntax: Little Endian Implicit
>> (0008,0008) CS [DERIVED\SECONDARY]                      #  18, 2 ImageType
>> (0008,0016) UI =MRImageStorage                          #  26, 1
>> SOPClassUID
>> (0008,0018) UI
>> [1.2.826.0.1.3680043.2.1125.1.62497394598874749597838823223385071] #  64, 1
>> SOPInstanceUID
>> (0008,0020) DA [20000101]                               #   8, 1 StudyDate
>> (0008,0021) DA [20000101]                               #   8, 1
>> SeriesDate
>> (0008,0022) DA [20000101]                               #   8, 1
>> AcquisitionDate
>> (0008,0030) TM (no value available)                     #   0, 0 StudyTime
>> (0008,0031) TM [085517]                                 #   6, 1
>> SeriesTime
>> (0008,0032) TM [085517]                                 #   6, 1
>> AcquisitionTime
>> (0008,0060) CS [MR]                                     #   2, 1 Modality
>> (0008,0070) LO [AAABBBCCC]                                 #   6, 1
>> Manufacturer
>> (0008,0104) LO [Anonymized]                             #  10, 1
>> CodeMeaning
>> (0008,103e) LO [t1c]                                    #   4, 1
>> SeriesDescription
>> (0008,1090) LO [nifti2dicom]                            #  12, 1
>> ManufacturerModelName
>> (0010,0010) PN [10041]                                  #   6, 1
>> PatientName
>> (0010,0020) LO [10041]                                  #   6, 1 PatientID
>> (0010,0021) LO [Anonymized]                             #  10, 1
>> IssuerOfPatientID
>> (0010,0030) DA [19650101]                               #   8, 1
>> PatientBirthDate
>> (0010,0040) CS [Anonymized]                             #  10, 1
>> PatientSex
>> (0010,1010) AS [Anonymized]                             #  10, 1
>> PatientAge
>> (0010,1030) DS (no value available)                     #   0, 0
>> PatientWeight
>> (0010,2150) LO [Anonymized]                             #  10, 1
>> CountryOfResidence
>> (0010,2152) LO [Anonymized]                             #  10, 1
>> RegionOfResidence
>> (0010,21f0) LO [Anonymized]                             #  10, 1
>> PatientReligiousPreference
>> (0012,0050) LO [baseline]                               #   8, 1
>> ClinicalTrialTimePointID
>> (0012,0062) CS [Yes]                                    #   4, 1
>> PatientIdentityRemoved
>> (0012,0063) LO [Genentech]                              #  10, 1
>> DeidentificationMethod
>> (0018,0050) DS [3]                                      #   2, 1
>> SliceThickness
>> (0018,0088) DS [3]                                      #   2, 1
>> SpacingBetweenSlices
>> (0020,000d) UI (no value available)                     #   0, 0
>> StudyInstanceUID
>> (0020,000e) UI
>> [1.2.826.0.1.3680043.2.1143.2737712182581015462892759360372011946] #  64, 1
>> SeriesInstanceUID
>> *(0020,0010) SH [0]                                      #   2, 1 StudyID*
>> (0020,0011) IS [901]                                    #   4, 1
>> SeriesNumber
>> (0020,0012) IS [1]                                      #   2, 1
>> AcquisitionNumber
>> (0020,0013) IS [1]                                      #   2, 1
>> InstanceNumber
>> (0020,0020) CS [L\R]                                    #   4, 2
>> PatientOrientation
>> (0020,0032) DS [-116.48152160645\-118.93698120117\-275.82513427734] #
>>  50, 3 ImagePositionPatient
>> (0020,0037) DS [1\0\0\0\1\0]                            #  12, 6
>> ImageOrientationPatient
>> (0020,0052) UI
>> [1.2.826.0.1.3680043.2.1143.263896814292546686535778822643473818] #  64, 1
>> FrameOfReferenceUID
>> (0028,0002) US 1                                        #   2, 1
>> SamplesPerPixel
>> (0028,0004) CS [MONOCHROME2]                            #  12, 1
>> PhotometricInterpretation
>> (0028,0010) US 256                                      #   2, 1 Rows
>> (0028,0011) US 256                                      #   2, 1 Columns
>> (0028,0030) DS [1\1]                                    #   4, 2
>> PixelSpacing
>> (0028,0100) US 16                                       #   2, 1
>> BitsAllocated
>> (0028,0101) US 16                                       #   2, 1
>> BitsStored
>> (0028,0102) US 15                                       #   2, 1 HighBit
>> (0028,0103) US 1                                        #   2, 1
>> PixelRepresentation
>> (0032,1033) LO [Anonymized]                             #  10, 1
>> RequestingService
>> (0040,0280) ST [Anonymized]                             #  10, 1
>> CommentsOnThePerformedProcedureStep
>> (0400,0563) LO [Anonymized]                             #  10, 1
>> ModifyingSystem
>> (0400,0564) LO [Anonymized]                             #  10, 1
>> SourceOfPreviousValues
>> (0400,0565) CS [Anonymized]                             #  10, 1
>> ReasonForTheAttributeModification
>> (1110,21b0) ?? 0a\00                                    #   2, 1 Unknown
>> Tag & Data
>> (7fe0,0010) OW
>> 0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000\0000... #
>> 131072, 1 PixelData
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>> _______________________________________________
>> 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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From sotirisnik at gmail.com  Tue Dec  3 15:26:16 2019
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Tue, 3 Dec 2019 22:26:16 +0200
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
Message-ID: <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>

Hi Cecile,

Yes, Nifti files are mandatory for our work. From what we saw at a 3rd vm
we setted up, the nifti files are being created ( i haven't verified if
that is the case at the 2nd vm ). I will install the latest version and
will report back, but do you know any nifti/minc viewer? because the
Brainbrowser of Loris does not output them well, it's like it is loading
only 1 slice and we would like to verify it with another tool too. We
verified that the dcmconv command didn't affect the quality of the .dcm
files.

Thanks,

Sotirios

???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
cecile.madjar at mcin.ca> ??????:

> Hi Sotirios,
>
> It looks like for some reason your binary mnc2nii is not working and
> reports that error. Do you want to create NIfTI files or are you happy with
> just the MINC files?
>
> If you don't need the NIfTI files, then maybe you can set the Config
> setting "NIfTI file creation" to No instead of Yes and this error will
> not appear anymore.
>
> If you need the NIfTI files to be created, then I would
> recommend installing the latest version of the MINC tools (1.9.17). They
> can be found there:
>
>    - pre-built packages: https://packages.bic.mni.mcgill.ca/minc-toolkit/
>    - from the source code with installation instructions in the README:
>    https://github.com/BIC-MNI/minc-toolkit-v2
>
> If the problem persists by using the latest release of MINC tools, then
> create an issue on Github for the MINC developers here
> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>
> Hope this helps,
>
> C?cile
>
> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi Cecile,
>>
>> Thanks to Nicholas i was able to create all the mincs images. The problem
>> was that the files were in Little-Endian-Implicit transfer syntax and i had
>> to convert them Little-Endian-Explicit transfer syntax with this command
>>
>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>> dcmconv --write-xfer-little {} {}
>>
>>
>> Looking back at our mails i saw that Little-Endian error had occurred
>> when i used dcmodify, but i switcthed to using pydicom instead.
>>
>>
>> [image: image.png]
>>
>>
>> In the output i see an error sometimes about "gsl: bessel_I0.c:216:
>> ERROR: overflow". Is this okay?
>>
>> Restructuring...
>> gsl: bessel_I0.c:216: ERROR: overflow
>> Default GSL error handler invoked.
>> noise_estimate --snr
>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>> SNR is:
>> gsl: bessel_I0.c:216: ERROR: overflow
>> Default GSL error handler invoked.
>>
>> Thanks,
>>
>> Sotirios
>>
>>
>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>> cecile.madjar at mcin.ca> ??????:
>>
>>> 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!
>>>
>>> C?cile
>>>
>>> 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
>>>>
>>>>
>>>>
>>>>
>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>> cecile.madjar at mcin.ca> ??????:
>>>>
>>>>> 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!
>>>>>
>>>>> C?cile
>>>>>
>>>>> 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
>>>>>>
>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>
>>>>>>> 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.
>>>>>>>
>>>>>>> C?cile
>>>>>>>
>>>>>>> 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,
>>>>>>>>>
>>>>>>>>> C?cile
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>
>>>>>>>>>>> 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.
>>>>>>>>>>>
>>>>>>>>>>> C?cile
>>>>>>>>>>>
>>>>>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers,
>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>
>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>
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From cecile.madjar at mcin.ca  Tue Dec  3 15:39:36 2019
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Tue, 3 Dec 2019 15:39:36 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
Message-ID: <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>

Hi Sotirios,

Does the pic screenshot in the imaging browser module also shows 1 slice?
If so, that would mean there was an issue with the dcm2mnc conversion. Once
again, installing the latest version of the MINC tools should help but if
this issue persists I would recommend creating an issue for that too on
their repository <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if
not already reported there, there are a few known issue reported).

Other viewer for MINCs are register and Display (both part of the MINC
tools). For NIfTI, you have FSLeye, MRICron and probably many other viewers
that exists.

Hope this helps,

C?cile

On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hi Cecile,
>
> Yes, Nifti files are mandatory for our work. From what we saw at a 3rd vm
> we setted up, the nifti files are being created ( i haven't verified if
> that is the case at the 2nd vm ). I will install the latest version and
> will report back, but do you know any nifti/minc viewer? because the
> Brainbrowser of Loris does not output them well, it's like it is loading
> only 1 slice and we would like to verify it with another tool too. We
> verified that the dcmconv command didn't affect the quality of the .dcm
> files.
>
> Thanks,
>
> Sotirios
>
> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
> cecile.madjar at mcin.ca> ??????:
>
>> Hi Sotirios,
>>
>> It looks like for some reason your binary mnc2nii is not working and
>> reports that error. Do you want to create NIfTI files or are you happy with
>> just the MINC files?
>>
>> If you don't need the NIfTI files, then maybe you can set the Config
>> setting "NIfTI file creation" to No instead of Yes and this error will
>> not appear anymore.
>>
>> If you need the NIfTI files to be created, then I would
>> recommend installing the latest version of the MINC tools (1.9.17). They
>> can be found there:
>>
>>    - pre-built packages: https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>    - from the source code with installation instructions in the README:
>>    https://github.com/BIC-MNI/minc-toolkit-v2
>>
>> If the problem persists by using the latest release of MINC tools, then
>> create an issue on Github for the MINC developers here
>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>
>> Hope this helps,
>>
>> C?cile
>>
>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi Cecile,
>>>
>>> Thanks to Nicholas i was able to create all the mincs images. The
>>> problem was that the files were in Little-Endian-Implicit transfer syntax
>>> and i had to convert them Little-Endian-Explicit transfer syntax with this
>>> command
>>>
>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>> dcmconv --write-xfer-little {} {}
>>>
>>>
>>> Looking back at our mails i saw that Little-Endian error had occurred
>>> when i used dcmodify, but i switcthed to using pydicom instead.
>>>
>>>
>>> [image: image.png]
>>>
>>>
>>> In the output i see an error sometimes about "gsl: bessel_I0.c:216:
>>> ERROR: overflow". Is this okay?
>>>
>>> Restructuring...
>>> gsl: bessel_I0.c:216: ERROR: overflow
>>> Default GSL error handler invoked.
>>> noise_estimate --snr
>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>> SNR is:
>>> gsl: bessel_I0.c:216: ERROR: overflow
>>> Default GSL error handler invoked.
>>>
>>> Thanks,
>>>
>>> Sotirios
>>>
>>>
>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>> cecile.madjar at mcin.ca> ??????:
>>>
>>>> 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!
>>>>
>>>> C?cile
>>>>
>>>> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>
>>>>>> 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!
>>>>>>
>>>>>> C?cile
>>>>>>
>>>>>> 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
>>>>>>>
>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>
>>>>>>>> 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.
>>>>>>>>
>>>>>>>> C?cile
>>>>>>>>
>>>>>>>> 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,
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>
>>>>>>>>>>>> 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.
>>>>>>>>>>>>
>>>>>>>>>>>> C?cile
>>>>>>>>>>>>
>>>>>>>>>>>> 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
>>>>>>>>>>>>>
>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers,
>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>
>>>>>>>>>>>>
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From sotirisnik at gmail.com  Wed Dec  4 08:03:32 2019
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Wed, 4 Dec 2019 15:03:32 +0200
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
Message-ID: <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>

 Hi Cecile,

We used minctool 1.9.7 and we still get this error

<<Restructuring...
gsl: bessel_I0.c:216: ERROR: overflow
Default GSL error handler invoked.
noise_estimate --snr /data/loris/data>>

One dicom folder hadn't that error and is being viewed fine in the
BrainBrowser of Loris.

When i used dpkg to the 1.9.17 the installation reported fine <<Unpacking
minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>

and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh

and aftewards runned bash ./imaging_install.sh just to be sure.

We also had to modify /data/loris/bin/mri/environment because it still
pointed to the old version.

What i found strange is this during the run of imaging_install.sh

<<already using interpreter
/data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
Please use the *system* python to run this script
Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 2632,
in <module>
    main()
  File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 870, in
main
    symlink=options.symlink,
  File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 1156,
in create_environment
    install_python(home_dir, lib_dir, inc_dir, bin_dir,
site_packages=site_packages, clear=clear, symlink=symlink)
  File
"/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
line 357, in abspath
    if not isabs(path):
  File
"/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
line 64, in isabs
    return s.startswith(sep)
AttributeError: 'NoneType' object has no attribute 'startswith'
Installing the Python libraries into the loris-mri virtualenv...
Requirement already satisfied: mysqlclient in
./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
Requirement already satisfied: mysql-connector in
./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
Requirement already satisfied: pybids in
./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>

So should i open an issue for that error? or is there something else to try?

Thanks

Sotirios





???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
cecile.madjar at mcin.ca> ??????:

> Hi Sotirios,
>
> Does the pic screenshot in the imaging browser module also shows 1 slice?
> If so, that would mean there was an issue with the dcm2mnc conversion. Once
> again, installing the latest version of the MINC tools should help but if
> this issue persists I would recommend creating an issue for that too on
> their repository <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if
> not already reported there, there are a few known issue reported).
>
> Other viewer for MINCs are register and Display (both part of the MINC
> tools). For NIfTI, you have FSLeye, MRICron and probably many other viewers
> that exists.
>
> Hope this helps,
>
> C?cile
>
> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi Cecile,
>>
>> Yes, Nifti files are mandatory for our work. From what we saw at a 3rd vm
>> we setted up, the nifti files are being created ( i haven't verified if
>> that is the case at the 2nd vm ). I will install the latest version and
>> will report back, but do you know any nifti/minc viewer? because the
>> Brainbrowser of Loris does not output them well, it's like it is loading
>> only 1 slice and we would like to verify it with another tool too. We
>> verified that the dcmconv command didn't affect the quality of the .dcm
>> files.
>>
>> Thanks,
>>
>> Sotirios
>>
>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>> cecile.madjar at mcin.ca> ??????:
>>
>>> Hi Sotirios,
>>>
>>> It looks like for some reason your binary mnc2nii is not working and
>>> reports that error. Do you want to create NIfTI files or are you happy with
>>> just the MINC files?
>>>
>>> If you don't need the NIfTI files, then maybe you can set the Config
>>> setting "NIfTI file creation" to No instead of Yes and this error will
>>> not appear anymore.
>>>
>>> If you need the NIfTI files to be created, then I would
>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>> can be found there:
>>>
>>>    - pre-built packages:
>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>    - from the source code with installation instructions in the README:
>>>    https://github.com/BIC-MNI/minc-toolkit-v2
>>>
>>> If the problem persists by using the latest release of MINC tools, then
>>> create an issue on Github for the MINC developers here
>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>
>>> Hope this helps,
>>>
>>> C?cile
>>>
>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi Cecile,
>>>>
>>>> Thanks to Nicholas i was able to create all the mincs images. The
>>>> problem was that the files were in Little-Endian-Implicit transfer syntax
>>>> and i had to convert them Little-Endian-Explicit transfer syntax with this
>>>> command
>>>>
>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>> dcmconv --write-xfer-little {} {}
>>>>
>>>>
>>>> Looking back at our mails i saw that Little-Endian error had occurred
>>>> when i used dcmodify, but i switcthed to using pydicom instead.
>>>>
>>>>
>>>> [image: image.png]
>>>>
>>>>
>>>> In the output i see an error sometimes about "gsl: bessel_I0.c:216:
>>>> ERROR: overflow". Is this okay?
>>>>
>>>> Restructuring...
>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>> Default GSL error handler invoked.
>>>> noise_estimate --snr
>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>> SNR is:
>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>> Default GSL error handler invoked.
>>>>
>>>> Thanks,
>>>>
>>>> Sotirios
>>>>
>>>>
>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>> cecile.madjar at mcin.ca> ??????:
>>>>
>>>>> 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!
>>>>>
>>>>> C?cile
>>>>>
>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>
>>>>>>> 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!
>>>>>>>
>>>>>>> C?cile
>>>>>>>
>>>>>>> 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
>>>>>>>>
>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>
>>>>>>>>> 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.
>>>>>>>>>
>>>>>>>>> C?cile
>>>>>>>>>
>>>>>>>>> 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,
>>>>>>>>>>>
>>>>>>>>>>> C?cile
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>
>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>
>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>
>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers,
>>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
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From cecile.madjar at mcin.ca  Wed Dec  4 08:59:10 2019
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Wed, 4 Dec 2019 08:59:10 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
Message-ID: <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>

Hi Sotirios,

Could you please share a dataset with us that produces the error you get
and the weird display in BrainBrowser? You could use the same SFTP
credential that Nicolas gave you.

The message errors you got from imaging_install.sh are probably due to the
fact that you reran the install script and it tried to reinstall something
that was already there. I would not worry about it. FYI, the only thing you
needed to do was to update the MINC tools path in the environment file as
you did after re-running imaging_install.sh and source the environment file.

Best,

C?cile

On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

>  Hi Cecile,
>
> We used minctool 1.9.7 and we still get this error
>
> <<Restructuring...
> gsl: bessel_I0.c:216: ERROR: overflow
> Default GSL error handler invoked.
> noise_estimate --snr /data/loris/data>>
>

> One dicom folder hadn't that error and is being viewed fine in the
> BrainBrowser of Loris.
>

> When i used dpkg to the 1.9.17 the installation reported fine <<Unpacking
> minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>
> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>
> and aftewards runned bash ./imaging_install.sh just to be sure.
>
> We also had to modify /data/loris/bin/mri/environment because it still
> pointed to the old version.
>
> What i found strange is this during the run of imaging_install.sh
>
> <<already using interpreter
> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
> Please use the *system* python to run this script
> Traceback (most recent call last):
>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 2632,
> in <module>
>     main()
>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 870,
> in main
>     symlink=options.symlink,
>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 1156,
> in create_environment
>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
> site_packages=site_packages, clear=clear, symlink=symlink)
>   File
> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
> line 357, in abspath
>     if not isabs(path):
>   File
> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
> line 64, in isabs
>     return s.startswith(sep)
> AttributeError: 'NoneType' object has no attribute 'startswith'
> Installing the Python libraries into the loris-mri virtualenv...
> Requirement already satisfied: mysqlclient in
> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
> Requirement already satisfied: mysql-connector in
> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
> Requirement already satisfied: pybids in
> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>
> So should i open an issue for that error? or is there something else to
> try?
>
> Thanks
>
> Sotirios
>
>
>
>
>
> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
> cecile.madjar at mcin.ca> ??????:
>
>> Hi Sotirios,
>>
>> Does the pic screenshot in the imaging browser module also shows 1 slice?
>> If so, that would mean there was an issue with the dcm2mnc conversion. Once
>> again, installing the latest version of the MINC tools should help but if
>> this issue persists I would recommend creating an issue for that too on
>> their repository <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if
>> not already reported there, there are a few known issue reported).
>>
>> Other viewer for MINCs are register and Display (both part of the MINC
>> tools). For NIfTI, you have FSLeye, MRICron and probably many other viewers
>> that exists.
>>
>> Hope this helps,
>>
>> C?cile
>>
>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi Cecile,
>>>
>>> Yes, Nifti files are mandatory for our work. From what we saw at a 3rd
>>> vm we setted up, the nifti files are being created ( i haven't verified if
>>> that is the case at the 2nd vm ). I will install the latest version and
>>> will report back, but do you know any nifti/minc viewer? because the
>>> Brainbrowser of Loris does not output them well, it's like it is loading
>>> only 1 slice and we would like to verify it with another tool too. We
>>> verified that the dcmconv command didn't affect the quality of the .dcm
>>> files.
>>>
>>> Thanks,
>>>
>>> Sotirios
>>>
>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>> cecile.madjar at mcin.ca> ??????:
>>>
>>>> Hi Sotirios,
>>>>
>>>> It looks like for some reason your binary mnc2nii is not working and
>>>> reports that error. Do you want to create NIfTI files or are you happy with
>>>> just the MINC files?
>>>>
>>>> If you don't need the NIfTI files, then maybe you can set the Config
>>>> setting "NIfTI file creation" to No instead of Yes and this error will
>>>> not appear anymore.
>>>>
>>>> If you need the NIfTI files to be created, then I would
>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>> can be found there:
>>>>
>>>>    - pre-built packages:
>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>    - from the source code with installation instructions in the
>>>>    README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>
>>>> If the problem persists by using the latest release of MINC tools, then
>>>> create an issue on Github for the MINC developers here
>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>
>>>> Hope this helps,
>>>>
>>>> C?cile
>>>>
>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> Hi Cecile,
>>>>>
>>>>> Thanks to Nicholas i was able to create all the mincs images. The
>>>>> problem was that the files were in Little-Endian-Implicit transfer syntax
>>>>> and i had to convert them Little-Endian-Explicit transfer syntax with this
>>>>> command
>>>>>
>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>> dcmconv --write-xfer-little {} {}
>>>>>
>>>>>
>>>>> Looking back at our mails i saw that Little-Endian error had occurred
>>>>> when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>
>>>>>
>>>>> [image: image.png]
>>>>>
>>>>>
>>>>> In the output i see an error sometimes about "gsl: bessel_I0.c:216:
>>>>> ERROR: overflow". Is this okay?
>>>>>
>>>>> Restructuring...
>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>> Default GSL error handler invoked.
>>>>> noise_estimate --snr
>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>> SNR is:
>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>> Default GSL error handler invoked.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Sotirios
>>>>>
>>>>>
>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>
>>>>>> 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!
>>>>>>
>>>>>> C?cile
>>>>>>
>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>
>>>>>>>> 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!
>>>>>>>>
>>>>>>>> C?cile
>>>>>>>>
>>>>>>>> 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
>>>>>>>>>
>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>
>>>>>>>>>> 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.
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>> 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,
>>>>>>>>>>>>
>>>>>>>>>>>> C?cile
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> 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
>>>>>>>>>>>>>
>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine Rogers,
>>>>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
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From iris.rodriguez at cneuro.edu.cu  Fri Dec  6 14:29:55 2019
From: iris.rodriguez at cneuro.edu.cu (=?iso-8859-1?Q?Iris_Rodr=EDguez_Gil?=)
Date: Fri, 6 Dec 2019 14:29:55 -0500
Subject: [Loris-dev] BIds Insertion
Message-ID: <C3A14E086354C04B8DB16023948F98BA01A25CC7AB98@exchange.cneuro.edu.cu>

Hi all,

I have problem with the insertion of the bids dataset in my server with loris 22.0.
I am testing with a short dataset and passing this parameters:

Python bids_import -d /dataset_bids -p database_config.py  -c  -s  -v


Trace and Error:

Connecting to:
        database: CBMCUBA
        username: lorisuser
        hostname: localhost
        port    : 3306


Executing query:
        SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);

With arguments:
        ('default_bids_vl',)


Executing query:
        SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = %s);

With arguments:
        ('dataDirBasepath',)

Loading the BIDS dataset with BIDS layout library...

        => BIDS dataset loaded with BIDS layout

Grepping candidates from the BIDS layout...
Validating the list of participants...
        => Passed validation of the list of participants

        => List of participants found:
                MC0002270
                MC0002275
                MC0002339
                MC0002347
                MC0002352
                MC0002362


Grepping list of sessions from the BIDS layout...
        => List of sessions found:

                MC0002270: 1
                MC0002339: 1
                MC0002275: 1
                MC0002362: 1
                MC0002352: 1
                MC0002347: 1


Grepping the different modalities from the BIDS layout...
        => Done grepping the different modalities from the BIDS layout

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/
Copying file /home/lorisadmin/dataset_test/dataset_description.json to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/dataset_description.json
Copying file /home/lorisadmin/dataset_test/README to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/README
Copying file /home/lorisadmin/dataset_test/participants.tsv to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/participants.tsv

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s

With arguments:
        ('MC0002270',)

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270

Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('586022', '1')

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s

With arguments:
        ('MC0002275',)

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002275

Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('531254', '1')

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002275/ses-1

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s

With arguments:
        ('MC0002339',)

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002339

Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('854503', '1')

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002339/ses-1

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s

With arguments:
        ('MC0002347',)

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002347

Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('615335', '1')

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002347/ses-1

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s

With arguments:
        ('MC0002352',)

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002352

Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('606661', '1')

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002352/ses-1

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s

With arguments:
        ('MC0002362',)

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002362

Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('827956', '1')

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002362/ses-1
Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/anat/

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s

With arguments:
        ('MC0002270',)


Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('586022', '1')

Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/anat/sub-MC0002270_T1w.json to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/anat/sub-MC0002270_T1w.json

Executing query:
        SELECT type FROM ImagingFileTypes


Executing query:
        SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s

With arguments:
        ('2bc67d1f0ffa5f5860f0c71f31cc517adf364d5a9503ab402758fa0e0836e14e956354fd992be4a0dbaf3f0454ead82b824a718853b09ab3ed83503ead37e7ab',)

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s

With arguments:
        ('MC0002270',)


Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('586022', '1')

Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.json to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.json

Executing query:
        SELECT type FROM ImagingFileTypes

Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.bvec to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.bvec
Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.bval to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.bval

Executing query:
        SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s

With arguments:
        ('1a075f0c10b856888e728c5421791cf6d18e363ca45255df46f4161460173f8153907173ae3840ac383e68d5f271eadc54bf03ea52fae737f758f376819295b3',)

Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.json to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.json

Executing query:
        SELECT type FROM ImagingFileTypes

Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.bvec to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.bvec
Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.bval to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.bval

Executing query:
        SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s

With arguments:
        ('bef678b4383bde1df93411e05bf75d8bccb5adf985e610ee7029c74056397ca43449dc20c187fa553ac0487a5adff67dc9e49827a8c227382768968c0444c9e7',)

Creating directory /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/

Executing query:
        SELECT * FROM candidate WHERE PSCID = %s
/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/site-packages/sklearn/externals/joblib/__init__.py:15: FutureWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
  warnings.warn(msg, category=FutureWarning)
/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/site-packages/sklearn/utils/deprecation.py:144: FutureWarning: The sklearn.utils.testing module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.utils. Anything that cannot be imported from sklearn.utils is now part of the private API.
  warnings.warn(message, FutureWarning)
/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/site-packages/sklearn/utils/deprecation.py:144: FutureWarning: The sklearn.datasets.base module is  deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.datasets. Anything that cannot be imported from sklearn.datasets is now part of the private API.
  warnings.warn(message, FutureWarning)

With arguments:
        ('MC0002270',)


Executing query:
        SELECT * FROM session WHERE CandID = %s AND Visit_label = %s

With arguments:
        ('586022', '1')

Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.json to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.json

Executing query:
        SELECT type FROM ImagingFileTypes


Executing query:
        SELECT  PhysiologicalOutputTypeID FROM    physiological_output_type WHERE   OutputTypeName = %s

With arguments:
        ('raw',)


Executing query:
        SELECT pf.PhysiologicalFileID, pf.FilePath FROM physiological_file AS pf JOIN physiological_parameter_file USING (PhysiologicalFileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s

With arguments:
        ('2962f54555ebd038297d3056cbad12379a3a293cb2128930f76a1da8e033987e7f6440632b00e585c22826879108c00f535e5e2f205ed5107c04ee7ae51c3282',)


Executing query:
        SELECT  PhysiologicalModalityID FROM    physiological_modality WHERE   PhysiologicalModality = %s

With arguments:
        ('eeg',)

Copying file /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.edf to /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.edf

Executing query:
        INSERT INTO physiological_file (AcquisitionTime, SessionID, PhysiologicalOutputTypeID, FileType, InsertedByUser, PhysiologicalModalityID, FilePath) VALUES (%s,%s,%s,%s,%s,%s,%s)
With arguments:
        [(None, 1, 1, 'set', 'lorisadmin', 1, 'bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.edf')]


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('json_file',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 109, 'bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.json')


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('EMGChannelCount',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 101, 0)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('PowerLineFrequency',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 108, 60)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('EEGPlacementScheme',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 116, '10-10')


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('ECGChannelCount',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 112, 0)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('physiological_file_blake2b_hash',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 107, '2962f54555ebd038297d3056cbad12379a3a293cb2128930f76a1da8e033987e7f6440632b00e585c22826879108c00f535e5e2f205ed5107c04ee7ae51c3282')


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('TriggerChannelCount',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 115, 0)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('physiological_json_file_blake2b_hash',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 105, 'b3c94060b316453cfc2816eb57cc9012377bcfe345dab476a2b6507651d1fd0b79b5987635659439c91ac44156d49ec191c9faf694e788d7919be79e8d87e3ad')


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('TaskDescription',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 104, 'Protocol used in Cuban Brain Mapping Project')


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('SoftwareFilters',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 100, 'n/a')


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('EOGChannelCount',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 106, 0)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('SamplingFrequency',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 102, 200)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('MiscChannelCount',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 110, 0)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('RecordingType',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 114, 'continuous')


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('EEGChannelCount',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 99, 62)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('RecordingDuration',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 111, 1801.42)


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('EEGReference',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 113, 'common')


Executing query:
        SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND SourceFrom='physiological_parameter_file'

With arguments:
        ('TaskName',)


Executing query:
        INSERT INTO physiological_parameter_file (PhysiologicalFileID, ParameterTypeID, Value) VALUES (%s,%s,%s)
With arguments:
        (3, 103, 'protmap')

Traceback (most recent call last):
  File "bids_import.py", line 431, in <module>
    main()
  File "bids_import.py", line 75, in main
    read_and_insert_bids(bids_dir, config_file, verbose, createcand, createvisit)
  File "bids_import.py", line 216, in read_and_insert_bids
    loris_bids_root_dir    = loris_bids_root_dir
  File "/data/loris/bin/mri/python/lib/eeg.py", line 143, in __init__
    self.register_raw_data()
  File "/data/loris/bin/mri/python/lib/eeg.py", line 264, in register_raw_data
    inserted_eeg  = self.fetch_and_insert_eeg_file()
  File "/data/loris/bin/mri/python/lib/eeg.py", line 473, in fetch_and_insert_eeg_file
    fdt_full_path = eeg_file_data['fdt_file']
KeyError: 'fdt_file'


But with this error I can see that the candidates was inserted in the database, so which I can't see in the formulary?



[cid:image003.jpg at 01D5AC41.A11DBCB0]


How I can solve this problem, any idea?,

Thanks,
Iris



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From cecile.madjar at mcin.ca  Fri Dec  6 15:10:58 2019
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Fri, 6 Dec 2019 15:10:58 -0500
Subject: [Loris-dev] BIds Insertion
In-Reply-To: <C3A14E086354C04B8DB16023948F98BA01A25CC7AB98@exchange.cneuro.edu.cu>
References: <C3A14E086354C04B8DB16023948F98BA01A25CC7AB98@exchange.cneuro.edu.cu>
Message-ID: <CAMkiY3ficwPGjzdrNVeXdmGF7xTQoJ_Age22WA0LZZsB-txKgw@mail.gmail.com>

Hi Iris,

I am a bit puzzled by your error message.

I see you are inserting EDF files but somehow the pipeline is going into an
if statement reserved to '.set' files (which sometimes can come with '.fdt'
files, see link here
<https://github.com/aces/Loris-MRI/blob/96a026ffc48af5c408d037a1bbaecc58619066ce/python/lib/eeg.py#L471>).
Was the code modified on your end by any chance?

C?cile

On Fri, Dec 6, 2019 at 2:30 PM Iris Rodr?guez Gil <
iris.rodriguez at cneuro.edu.cu> wrote:

> Hi all,
>
>
>
> I have problem with the insertion of the bids dataset in my server with
> loris 22.0.
>
> I am testing with a short dataset and passing this parameters:
>
>
>
> *Python bids_import ?d /dataset_bids ?p database_config.py  ?c  ?s  -v*
>
>
>
>
>
> Trace and Error:
>
>
>
> Connecting to:
>
>         database: CBMCUBA
>
>         username: lorisuser
>
>         hostname: localhost
>
>         port    : 3306
>
>
>
>
>
> Executing query:
>
>         SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM
> ConfigSettings WHERE Name = %s);
>
>
>
> With arguments:
>
>         ('default_bids_vl',)
>
>
>
>
>
> Executing query:
>
>         SELECT Value FROM Config WHERE ConfigID = (SELECT ID FROM
> ConfigSettings WHERE Name = %s);
>
>
>
> With arguments:
>
>         ('dataDirBasepath',)
>
>
>
> Loading the BIDS dataset with BIDS layout library...
>
>
>
>         => BIDS dataset loaded with BIDS layout
>
>
>
> Grepping candidates from the BIDS layout...
>
> Validating the list of participants...
>
>         => Passed validation of the list of participants
>
>
>
>         => List of participants found:
>
>                 MC0002270
>
>                 MC0002275
>
>                 MC0002339
>
>                 MC0002347
>
>                 MC0002352
>
>                 MC0002362
>
>
>
>
>
> Grepping list of sessions from the BIDS layout...
>
>         => List of sessions found:
>
>
>
>                 MC0002270: 1
>
>                 MC0002339: 1
>
>                 MC0002275: 1
>
>                 MC0002362: 1
>
>                 MC0002352: 1
>
>                 MC0002347: 1
>
>
>
>
>
> Grepping the different modalities from the BIDS layout...
>
>         => Done grepping the different modalities from the BIDS layout
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/
>
> Copying file /home/lorisadmin/dataset_test/dataset_description.json to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/dataset_description.json
>
> Copying file /home/lorisadmin/dataset_test/README to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/README
>
> Copying file /home/lorisadmin/dataset_test/participants.tsv to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/participants.tsv
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
>
>
> With arguments:
>
>         ('MC0002270',)
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('586022', '1')
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
>
>
> With arguments:
>
>         ('MC0002275',)
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002275
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('531254', '1')
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002275/ses-1
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
>
>
> With arguments:
>
>         ('MC0002339',)
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002339
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('854503', '1')
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002339/ses-1
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
>
>
> With arguments:
>
>         ('MC0002347',)
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002347
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('615335', '1')
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002347/ses-1
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
>
>
> With arguments:
>
>         ('MC0002352',)
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002352
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('606661', '1')
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002352/ses-1
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
>
>
> With arguments:
>
>         ('MC0002362',)
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002362
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('827956', '1')
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002362/ses-1
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/anat/
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
>
>
> With arguments:
>
>         ('MC0002270',)
>
>
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('586022', '1')
>
>
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/anat/sub-MC0002270_T1w.json
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/anat/sub-MC0002270_T1w.json
>
>
>
> Executing query:
>
>         SELECT type FROM ImagingFileTypes
>
>
>
>
>
> Executing query:
>
>         SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING
> (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s
>
>
>
> With arguments:
>
>
> ('2bc67d1f0ffa5f5860f0c71f31cc517adf364d5a9503ab402758fa0e0836e14e956354fd992be4a0dbaf3f0454ead82b824a718853b09ab3ed83503ead37e7ab',)
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
>
>
> With arguments:
>
>         ('MC0002270',)
>
>
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('586022', '1')
>
>
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.json
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.json
>
>
>
> Executing query:
>
>         SELECT type FROM ImagingFileTypes
>
>
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.bvec
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.bvec
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.bval
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-01_dwi.bval
>
>
>
> Executing query:
>
>         SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING
> (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s
>
>
>
> With arguments:
>
>
> ('1a075f0c10b856888e728c5421791cf6d18e363ca45255df46f4161460173f8153907173ae3840ac383e68d5f271eadc54bf03ea52fae737f758f376819295b3',)
>
>
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.json
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.json
>
>
>
> Executing query:
>
>         SELECT type FROM ImagingFileTypes
>
>
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.bvec
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.bvec
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.bval
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/dwi/sub-MC0002270_run-02_dwi.bval
>
>
>
> Executing query:
>
>         SELECT f.FileID, f.File FROM files AS f JOIN parameter_file USING
> (FileID) JOIN parameter_type USING (ParameterTypeID) WHERE Value=%s
>
>
>
> With arguments:
>
>
> ('bef678b4383bde1df93411e05bf75d8bccb5adf985e610ee7029c74056397ca43449dc20c187fa553ac0487a5adff67dc9e49827a8c227382768968c0444c9e7',)
>
>
>
> Creating directory
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/
>
>
>
> Executing query:
>
>         SELECT * FROM candidate WHERE PSCID = %s
>
> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/site-packages/sklearn/externals/joblib/__init__.py:15:
> FutureWarning: sklearn.externals.joblib is deprecated in 0.21 and will be
> removed in 0.23. Please import this functionality directly from joblib,
> which can be installed with: pip install joblib. If this warning is raised
> when loading pickled models, you may need to re-serialize those models with
> scikit-learn 0.21+.
>
>   warnings.warn(msg, category=FutureWarning)
>
> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/site-packages/sklearn/utils/deprecation.py:144:
> FutureWarning: The sklearn.utils.testing module is  deprecated in version
> 0.22 and will be removed in version 0.24. The corresponding classes /
> functions should instead be imported from sklearn.utils. Anything that
> cannot be imported from sklearn.utils is now part of the private API.
>
>   warnings.warn(message, FutureWarning)
>
> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/site-packages/sklearn/utils/deprecation.py:144:
> FutureWarning: The sklearn.datasets.base module is  deprecated in version
> 0.22 and will be removed in version 0.24. The corresponding classes /
> functions should instead be imported from sklearn.datasets. Anything that
> cannot be imported from sklearn.datasets is now part of the private API.
>
>   warnings.warn(message, FutureWarning)
>
>
>
> With arguments:
>
>         ('MC0002270',)
>
>
>
>
>
> Executing query:
>
>         SELECT * FROM session WHERE CandID = %s AND Visit_label = %s
>
>
>
> With arguments:
>
>         ('586022', '1')
>
>
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.json
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.json
>
>
>
> Executing query:
>
>         SELECT type FROM ImagingFileTypes
>
>
>
>
>
> Executing query:
>
>         SELECT  PhysiologicalOutputTypeID FROM
> physiological_output_type WHERE   OutputTypeName = %s
>
>
>
> With arguments:
>
>         ('raw',)
>
>
>
>
>
> Executing query:
>
>         SELECT pf.PhysiologicalFileID, pf.FilePath FROM physiological_file
> AS pf JOIN physiological_parameter_file USING (PhysiologicalFileID) JOIN
> parameter_type USING (ParameterTypeID) WHERE Value=%s
>
>
>
> With arguments:
>
>
> ('2962f54555ebd038297d3056cbad12379a3a293cb2128930f76a1da8e033987e7f6440632b00e585c22826879108c00f535e5e2f205ed5107c04ee7ae51c3282',)
>
>
>
>
>
> Executing query:
>
>         SELECT  PhysiologicalModalityID FROM    physiological_modality
> WHERE   PhysiologicalModality = %s
>
>
>
> With arguments:
>
>         ('eeg',)
>
>
>
> Copying file
> /home/lorisadmin/dataset_test/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.edf
> to
> /data/loris/data/bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.edf
>
>
>
> Executing query:
>
>         INSERT INTO physiological_file (AcquisitionTime, SessionID,
> PhysiologicalOutputTypeID, FileType, InsertedByUser,
> PhysiologicalModalityID, FilePath) VALUES (%s,%s,%s,%s,%s,%s,%s)
>
> With arguments:
>
>         [(None, 1, 1, 'set', 'lorisadmin', 1,
> 'bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.edf')]
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('json_file',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 109,
> 'bids_imports/Dataset_containing_Cuban_Brain_Mapping_database_BIDSVersion_1.2.1/sub-MC0002270/ses-1/eeg/sub-MC0002270_task-protmap_eeg.json')
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('EMGChannelCount',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 101, 0)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('PowerLineFrequency',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 108, 60)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('EEGPlacementScheme',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 116, '10-10')
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('ECGChannelCount',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 112, 0)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('physiological_file_blake2b_hash',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 107,
> '2962f54555ebd038297d3056cbad12379a3a293cb2128930f76a1da8e033987e7f6440632b00e585c22826879108c00f535e5e2f205ed5107c04ee7ae51c3282')
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('TriggerChannelCount',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 115, 0)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('physiological_json_file_blake2b_hash',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 105,
> 'b3c94060b316453cfc2816eb57cc9012377bcfe345dab476a2b6507651d1fd0b79b5987635659439c91ac44156d49ec191c9faf694e788d7919be79e8d87e3ad')
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('TaskDescription',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 104, 'Protocol used in Cuban Brain Mapping Project')
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('SoftwareFilters',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 100, 'n/a')
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('EOGChannelCount',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 106, 0)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('SamplingFrequency',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 102, 200)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('MiscChannelCount',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 110, 0)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('RecordingType',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 114, 'continuous')
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('EEGChannelCount',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 99, 62)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('RecordingDuration',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 111, 1801.42)
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('EEGReference',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 113, 'common')
>
>
>
>
>
> Executing query:
>
>         SELECT ParameterTypeID FROM parameter_type WHERE Name = %s AND
> SourceFrom='physiological_parameter_file'
>
>
>
> With arguments:
>
>         ('TaskName',)
>
>
>
>
>
> Executing query:
>
>         INSERT INTO physiological_parameter_file (PhysiologicalFileID,
> ParameterTypeID, Value) VALUES (%s,%s,%s)
>
> With arguments:
>
>         (3, 103, 'protmap')
>
>
>
> Traceback (most recent call last):
>
>   File "bids_import.py", line 431, in <module>
>
>     main()
>
>   File "bids_import.py", line 75, in main
>
>     read_and_insert_bids(bids_dir, config_file, verbose, createcand,
> createvisit)
>
>   File "bids_import.py", line 216, in read_and_insert_bids
>
>     loris_bids_root_dir    = loris_bids_root_dir
>
>   File "/data/loris/bin/mri/python/lib/eeg.py", line 143, in __init__
>
>     self.register_raw_data()
>
>   File "/data/loris/bin/mri/python/lib/eeg.py", line 264, in
> register_raw_data
>
>     inserted_eeg  = self.fetch_and_insert_eeg_file()
>
>   File "/data/loris/bin/mri/python/lib/eeg.py", line 473, in
> fetch_and_insert_eeg_file
>
>     fdt_full_path = eeg_file_data['fdt_file']
>
> KeyError: 'fdt_file'
>
>
>
>
>
> But with this error I can see that the candidates was inserted in the
> database, so which I can't see in the formulary?
>
>
>
>
>
>
>
>
>
>
>
> How I can solve this problem, any idea?,
>
>
>
> Thanks,
>
> Iris
>
>
>
>
>
>
>
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From iris.rodriguez at cneuro.edu.cu  Fri Dec  6 16:25:11 2019
From: iris.rodriguez at cneuro.edu.cu (=?iso-8859-1?Q?Iris_Rodr=EDguez_Gil?=)
Date: Fri, 6 Dec 2019 16:25:11 -0500
Subject: [Loris-dev] HELP!!
Message-ID: <C3A14E086354C04B8DB16023948F98BA01A25CC7ABFA@exchange.cneuro.edu.cu>

Hi all,

I can't visualize my candidates in Loris formulary, but, in the genomic browser they are show.
Any Idea?
Thanks.


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From cecile.madjar at mcin.ca  Mon Dec  9 13:10:11 2019
From: cecile.madjar at mcin.ca (Cecile Madjar)
Date: Mon, 9 Dec 2019 13:10:11 -0500
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
Message-ID: <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>

Hi Sotirios,

The issue you are having is a indeed a dcm2mnc issue. The converter does
not seem to work on your dataset for some reason. Unfortunately, there is
not much we can do on our front to fix this...

I would recommend creating an issue on the MINC tools repository
<https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix your
problem.

Very sorry that you are having that problem.

Best,

C?cile

On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca> wrote:

> Hi Sotirios,
>
> Could you please share a dataset with us that produces the error you get
> and the weird display in BrainBrowser? You could use the same SFTP
> credential that Nicolas gave you.
>
> The message errors you got from imaging_install.sh are probably due to the
> fact that you reran the install script and it tried to reinstall something
> that was already there. I would not worry about it. FYI, the only thing you
> needed to do was to update the MINC tools path in the environment file as
> you did after re-running imaging_install.sh and source the environment file.
>
> Best,
>
> C?cile
>
> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>>  Hi Cecile,
>>
>> We used minctool 1.9.7 and we still get this error
>>
>> <<Restructuring...
>> gsl: bessel_I0.c:216: ERROR: overflow
>> Default GSL error handler invoked.
>> noise_estimate --snr /data/loris/data>>
>>
>
>> One dicom folder hadn't that error and is being viewed fine in the
>> BrainBrowser of Loris.
>>
>
>> When i used dpkg to the 1.9.17 the installation reported fine <<Unpacking
>> minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>
>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>
>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>
>> We also had to modify /data/loris/bin/mri/environment because it still
>> pointed to the old version.
>>
>> What i found strange is this during the run of imaging_install.sh
>>
>> <<already using interpreter
>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>> Please use the *system* python to run this script
>> Traceback (most recent call last):
>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 2632,
>> in <module>
>>     main()
>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 870,
>> in main
>>     symlink=options.symlink,
>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 1156,
>> in create_environment
>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>> site_packages=site_packages, clear=clear, symlink=symlink)
>>   File
>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>> line 357, in abspath
>>     if not isabs(path):
>>   File
>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>> line 64, in isabs
>>     return s.startswith(sep)
>> AttributeError: 'NoneType' object has no attribute 'startswith'
>> Installing the Python libraries into the loris-mri virtualenv...
>> Requirement already satisfied: mysqlclient in
>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>> Requirement already satisfied: mysql-connector in
>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>> Requirement already satisfied: pybids in
>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>
>> So should i open an issue for that error? or is there something else to
>> try?
>>
>> Thanks
>>
>> Sotirios
>>
>>
>>
>>
>>
>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>> cecile.madjar at mcin.ca> ??????:
>>
>>> Hi Sotirios,
>>>
>>> Does the pic screenshot in the imaging browser module also shows 1
>>> slice? If so, that would mean there was an issue with the dcm2mnc
>>> conversion. Once again, installing the latest version of the MINC tools
>>> should help but if this issue persists I would recommend creating an issue
>>> for that too on their repository
>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not already
>>> reported there, there are a few known issue reported).
>>>
>>> Other viewer for MINCs are register and Display (both part of the MINC
>>> tools). For NIfTI, you have FSLeye, MRICron and probably many other viewers
>>> that exists.
>>>
>>> Hope this helps,
>>>
>>> C?cile
>>>
>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi Cecile,
>>>>
>>>> Yes, Nifti files are mandatory for our work. From what we saw at a 3rd
>>>> vm we setted up, the nifti files are being created ( i haven't verified if
>>>> that is the case at the 2nd vm ). I will install the latest version and
>>>> will report back, but do you know any nifti/minc viewer? because the
>>>> Brainbrowser of Loris does not output them well, it's like it is loading
>>>> only 1 slice and we would like to verify it with another tool too. We
>>>> verified that the dcmconv command didn't affect the quality of the
>>>> .dcm files.
>>>>
>>>> Thanks,
>>>>
>>>> Sotirios
>>>>
>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>> cecile.madjar at mcin.ca> ??????:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> It looks like for some reason your binary mnc2nii is not working and
>>>>> reports that error. Do you want to create NIfTI files or are you happy with
>>>>> just the MINC files?
>>>>>
>>>>> If you don't need the NIfTI files, then maybe you can set the Config
>>>>> setting "NIfTI file creation" to No instead of Yes and this error
>>>>> will not appear anymore.
>>>>>
>>>>> If you need the NIfTI files to be created, then I would
>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>> can be found there:
>>>>>
>>>>>    - pre-built packages:
>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>    - from the source code with installation instructions in the
>>>>>    README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>
>>>>> If the problem persists by using the latest release of MINC tools,
>>>>> then create an issue on Github for the MINC developers here
>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>
>>>>> Hope this helps,
>>>>>
>>>>> C?cile
>>>>>
>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> Hi Cecile,
>>>>>>
>>>>>> Thanks to Nicholas i was able to create all the mincs images. The
>>>>>> problem was that the files were in Little-Endian-Implicit transfer syntax
>>>>>> and i had to convert them Little-Endian-Explicit transfer syntax with this
>>>>>> command
>>>>>>
>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>
>>>>>>
>>>>>> Looking back at our mails i saw that Little-Endian error had occurred
>>>>>> when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>
>>>>>>
>>>>>> [image: image.png]
>>>>>>
>>>>>>
>>>>>> In the output i see an error sometimes about "gsl: bessel_I0.c:216:
>>>>>> ERROR: overflow". Is this okay?
>>>>>>
>>>>>> Restructuring...
>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>> Default GSL error handler invoked.
>>>>>> noise_estimate --snr
>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>> SNR is:
>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>> Default GSL error handler invoked.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Sotirios
>>>>>>
>>>>>>
>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>
>>>>>>> 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!
>>>>>>>
>>>>>>> C?cile
>>>>>>>
>>>>>>> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>
>>>>>>>>> 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!
>>>>>>>>>
>>>>>>>>> C?cile
>>>>>>>>>
>>>>>>>>> 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
>>>>>>>>>>
>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>
>>>>>>>>>>> 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.
>>>>>>>>>>>
>>>>>>>>>>> C?cile
>>>>>>>>>>>
>>>>>>>>>>> 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,
>>>>>>>>>>>>>
>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine
>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>> >>>
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>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> _______________________________________________
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>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> 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
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From sotirisnik at gmail.com  Tue Dec 10 12:21:28 2019
From: sotirisnik at gmail.com (Sotirios Nikoloutsopoulos)
Date: Tue, 10 Dec 2019 19:21:28 +0200
Subject: [Loris-dev] Import mri - scripts
In-Reply-To: <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
References: <mailman.1851.1573565332.16403.loris-dev@bic.mni.mcgill.ca>
 <CAEfMBom1HCWLo4NWgt5XG4625tCBfRT_Z_HepvtT_Er2LKbJoA@mail.gmail.com>
 <CAKHj7uS1AdMDjnacouTvxZgziYVgp5NNUeOuMkpDyrTskGTh-Q@mail.gmail.com>
 <CALbt7NDej8FGUUS6_oKbK5Fp-FnwsVz9AgZ6ZcJEZhmoKZmv8w@mail.gmail.com>
 <CAKHj7uSx-qqcXHZsWsZmSJ7sC1DgF+XapT5Y1+QdoVic37_DDg@mail.gmail.com>
 <CAMkiY3fQBGDGeNO8EHxwYAgbhTggNSQ+AVuCfdraDXwULMjjUg@mail.gmail.com>
 <CAKHj7uT5xXi=pOPdH=W9BroSphMHdTszdgW+GxuES=8wZox9eQ@mail.gmail.com>
 <CAMkiY3eUouxaRVdC4wH+vdjeQ=q_Nx8bcDNzcWgD_OgN77m3mw@mail.gmail.com>
 <CAKHj7uSxu4+tm+=x4+qJ1sAbrjmxG2H7LovDb7-2KMnyYQhrgg@mail.gmail.com>
 <CAMkiY3fdPZec2jx-cc2Zq37j3ekmTu_o819yBUv-bC7M98bkVw@mail.gmail.com>
 <CAKHj7uSZHozpuQ_YwGmy6wQ4tm43vJa556V0o2+JGDVsYaqN4g@mail.gmail.com>
 <CAMkiY3dge=x93bQDv0fHGMcrX0PA8Z_imLb_zSTh=nTrx5weFg@mail.gmail.com>
 <CAKHj7uR81gCkjvccMxwMA08dGSEgyTLJBJ+pZPkoUQDtGP_hFA@mail.gmail.com>
 <CAMkiY3fGhvExZ-JOvxeHe7dJQPvtPAHx3oJuiMVX7f1JgF1GAg@mail.gmail.com>
 <CAKHj7uRExO98Yyn9_07aw44wbh0bCL9_C1VFTAURKsxQLUuAeQ@mail.gmail.com>
 <CAMkiY3cbJLKncAiGWX51=Drp6vQp8SyxZOsj7LCBcVSVSQp9dA@mail.gmail.com>
 <CAKHj7uRueb5fgh4VVCAyaq8tC9WM4gJ7k6Q=dxsqWzFgDqPfVQ@mail.gmail.com>
 <CAMkiY3d-Vt=3gQqwJ+GSRSacbLp2QxrB0g-_C7ONd8j_g1ipoQ@mail.gmail.com>
 <CAKHj7uQt9=nokz5g1zBuBx1-rJ8q7qKOuNVkQugC9wfvNFcjVA@mail.gmail.com>
 <CAMkiY3cAuQfT_5iMzYoF2BXVceu_vgz4eCq2sAtoyse+zUYeSg@mail.gmail.com>
 <CAMkiY3dq1O3V8+r4tTAWQ8N=rVFg=DNY-UPeMqbec+MSayj=Cg@mail.gmail.com>
Message-ID: <CAKHj7uSEegvE1apPBGVyHmjyVzF+YxJjDMg0b+hDE4_-ON+dYw@mail.gmail.com>

Hi,

i opened an issue and looked up for the values of Volume they suggested
https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The only attributes
associated with it i saw are [0x00089206] and [0x00089207]

[image: image.png]

I looked up for the file that was being viewed fine in the BrainBrowser and
saw that it had that attribute empty so i used this command because i
couldn't find a way to modify the attribute via pydicom

dcmodify -ma "(0008,9206)=" *.dcm

and that command reported the warning about the Endian Syntax. I also used
the corresponding command for 9207 and got the message "Tag not found'

Lastly I tried to upload some dicoms and now i am getting the SNR and i can
view them fine. I believe now that all of them will pass successfully, i
will report back later.

Thanks,

Sotirios

???? ???, 9 ??? 2019 ???? 8:10 ?.?., ?/? Cecile Madjar <
cecile.madjar at mcin.ca> ??????:

> Hi Sotirios,
>
> The issue you are having is a indeed a dcm2mnc issue. The converter does
> not seem to work on your dataset for some reason. Unfortunately, there is
> not much we can do on our front to fix this...
>
> I would recommend creating an issue on the MINC tools repository
> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix your
> problem.
>
> Very sorry that you are having that problem.
>
> Best,
>
> C?cile
>
> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca>
> wrote:
>
>> Hi Sotirios,
>>
>> Could you please share a dataset with us that produces the error you get
>> and the weird display in BrainBrowser? You could use the same SFTP
>> credential that Nicolas gave you.
>>
>> The message errors you got from imaging_install.sh are probably due to
>> the fact that you reran the install script and it tried to reinstall
>> something that was already there. I would not worry about it. FYI, the only
>> thing you needed to do was to update the MINC tools path in the environment
>> file as you did after re-running imaging_install.sh and source the
>> environment file.
>>
>> Best,
>>
>> C?cile
>>
>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>>  Hi Cecile,
>>>
>>> We used minctool 1.9.7 and we still get this error
>>>
>>> <<Restructuring...
>>> gsl: bessel_I0.c:216: ERROR: overflow
>>> Default GSL error handler invoked.
>>> noise_estimate --snr /data/loris/data>>
>>>
>>
>>> One dicom folder hadn't that error and is being viewed fine in the
>>> BrainBrowser of Loris.
>>>
>>
>>> When i used dpkg to the 1.9.17 the installation reported fine
>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>
>>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>>
>>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>>
>>> We also had to modify /data/loris/bin/mri/environment because it still
>>> pointed to the old version.
>>>
>>> What i found strange is this during the run of imaging_install.sh
>>>
>>> <<already using interpreter
>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>> Please use the *system* python to run this script
>>> Traceback (most recent call last):
>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>> 2632, in <module>
>>>     main()
>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 870,
>>> in main
>>>     symlink=options.symlink,
>>>   File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line
>>> 1156, in create_environment
>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>   File
>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>> line 357, in abspath
>>>     if not isabs(path):
>>>   File
>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>> line 64, in isabs
>>>     return s.startswith(sep)
>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>> Installing the Python libraries into the loris-mri virtualenv...
>>> Requirement already satisfied: mysqlclient in
>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>> Requirement already satisfied: mysql-connector in
>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>> Requirement already satisfied: pybids in
>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>>
>>> So should i open an issue for that error? or is there something else to
>>> try?
>>>
>>> Thanks
>>>
>>> Sotirios
>>>
>>>
>>>
>>>
>>>
>>> ???? ???, 3 ??? 2019 ???? 10:39 ?.?., ?/? Cecile Madjar <
>>> cecile.madjar at mcin.ca> ??????:
>>>
>>>> Hi Sotirios,
>>>>
>>>> Does the pic screenshot in the imaging browser module also shows 1
>>>> slice? If so, that would mean there was an issue with the dcm2mnc
>>>> conversion. Once again, installing the latest version of the MINC tools
>>>> should help but if this issue persists I would recommend creating an issue
>>>> for that too on their repository
>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not already
>>>> reported there, there are a few known issue reported).
>>>>
>>>> Other viewer for MINCs are register and Display (both part of the MINC
>>>> tools). For NIfTI, you have FSLeye, MRICron and probably many other viewers
>>>> that exists.
>>>>
>>>> Hope this helps,
>>>>
>>>> C?cile
>>>>
>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> Hi Cecile,
>>>>>
>>>>> Yes, Nifti files are mandatory for our work. From what we saw at a 3rd
>>>>> vm we setted up, the nifti files are being created ( i haven't verified if
>>>>> that is the case at the 2nd vm ). I will install the latest version and
>>>>> will report back, but do you know any nifti/minc viewer? because the
>>>>> Brainbrowser of Loris does not output them well, it's like it is loading
>>>>> only 1 slice and we would like to verify it with another tool too. We
>>>>> verified that the dcmconv command didn't affect the quality of the
>>>>> .dcm files.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Sotirios
>>>>>
>>>>> ???? ???, 2 ??? 2019 ???? 6:59 ?.?., ?/? Cecile Madjar <
>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>
>>>>>> Hi Sotirios,
>>>>>>
>>>>>> It looks like for some reason your binary mnc2nii is not working and
>>>>>> reports that error. Do you want to create NIfTI files or are you happy with
>>>>>> just the MINC files?
>>>>>>
>>>>>> If you don't need the NIfTI files, then maybe you can set the Config
>>>>>> setting "NIfTI file creation" to No instead of Yes and this error
>>>>>> will not appear anymore.
>>>>>>
>>>>>> If you need the NIfTI files to be created, then I would
>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>> can be found there:
>>>>>>
>>>>>>    - pre-built packages:
>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>    - from the source code with installation instructions in the
>>>>>>    README: https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>
>>>>>> If the problem persists by using the latest release of MINC tools,
>>>>>> then create an issue on Github for the MINC developers here
>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>
>>>>>> Hope this helps,
>>>>>>
>>>>>> C?cile
>>>>>>
>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>
>>>>>>> Hi Cecile,
>>>>>>>
>>>>>>> Thanks to Nicholas i was able to create all the mincs images. The
>>>>>>> problem was that the files were in Little-Endian-Implicit transfer syntax
>>>>>>> and i had to convert them Little-Endian-Explicit transfer syntax with this
>>>>>>> command
>>>>>>>
>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs -i
>>>>>>> dcmconv --write-xfer-little {} {}
>>>>>>>
>>>>>>>
>>>>>>> Looking back at our mails i saw that Little-Endian error had
>>>>>>> occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>
>>>>>>>
>>>>>>> [image: image.png]
>>>>>>>
>>>>>>>
>>>>>>> In the output i see an error sometimes about "gsl: bessel_I0.c:216:
>>>>>>> ERROR: overflow". Is this okay?
>>>>>>>
>>>>>>> Restructuring...
>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>> Default GSL error handler invoked.
>>>>>>> noise_estimate --snr
>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>> SNR is:
>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>> Default GSL error handler invoked.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Sotirios
>>>>>>>
>>>>>>>
>>>>>>> ???? ???, 27 ??? 2019 ???? 4:29 ?.?., ?/? Cecile Madjar <
>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>
>>>>>>>> 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!
>>>>>>>>
>>>>>>>> C?cile
>>>>>>>>
>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ???? ???, 26 ??? 2019 ???? 11:34 ?.?., ?/? Cecile Madjar <
>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>
>>>>>>>>>> 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!
>>>>>>>>>>
>>>>>>>>>> C?cile
>>>>>>>>>>
>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>> ???? ???, 25 ??? 2019 ???? 5:22 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>
>>>>>>>>>>>> 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.
>>>>>>>>>>>>
>>>>>>>>>>>> C?cile
>>>>>>>>>>>>
>>>>>>>>>>>> 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,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> ???? ???, 19 ??? 2019 ???? 9:40 ?.?., ?/? Cecile Madjar <
>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 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.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> C?cile
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 11:45 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>> Rogers, Ms. <christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> ???? ???, 13 ??? 2019 ???? 5:45 ?.?., ?/? Yang Ding <
>>>>>>>>>>>>>>>>>>> it at cnbp.ca> ??????:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
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From alsneuroimagingresearchunit at gmail.com  Wed Dec 18 18:22:06 2019
From: alsneuroimagingresearchunit at gmail.com (ALS Neuroimaging Research Unit)
Date: Wed, 18 Dec 2019 16:22:06 -0700
Subject: [Loris-dev] Normalizing/breaking down instruments
Message-ID: <CABJp3aDaJ2dYYB34v_shBj=3Nqq+C3VFh5ygZC4y6C5w9shSoA@mail.gmail.com>

 Hi!

Currently our instruments are quite long, and we would like to break them
down into separate instruments.
The code is easy to break down and separate. However, what would be the
best way to import the data from the larger instrument and into to the new
smaller instruments, given that the CommentIDs will be different.

Also is there any documentation that I could refer to to understand the
relationship between the individual instrument tables and the flag table?
The LORIS database schema
<https://github.com/aces/Loris/wiki/LORIS-database-schema> on GitHub is not
updated and is redirected to a dead link on the LORIS demo instance,

Thanks!
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From melanie.legault2 at mcgill.ca  Thu Dec 19 07:25:14 2019
From: melanie.legault2 at mcgill.ca (Melanie Legault, Mrs)
Date: Thu, 19 Dec 2019 12:25:14 +0000
Subject: [Loris-dev] Normalizing/breaking down instruments
In-Reply-To: <CABJp3aDaJ2dYYB34v_shBj=3Nqq+C3VFh5ygZC4y6C5w9shSoA@mail.gmail.com>
References: <CABJp3aDaJ2dYYB34v_shBj=3Nqq+C3VFh5ygZC4y6C5w9shSoA@mail.gmail.com>
Message-ID: <YTOPR0101MB2027DDDF5C982163FC03B60DCF520@YTOPR0101MB2027.CANPRD01.PROD.OUTLOOK.COM>

Hello,

There is no easy, fit all answer to your question about importing the instrument's data.
It depend on a few factors:

  *   the number of candidates you already have and amount of data that would need to be migrated.
  *   if you have access to a software developer (or at least someone who knows MySQL (MariaDB) and how to code scripts.
  *   If you have another instance of LORIS to develop a script without affecting the production instance.
  *   the time that you have to complete this task.

Depending on the answer to these questions, there are a few options:

  *   If you only have a few candidates, it might be easier to just manually enter the same data in the new instruments via LORIS web interface as it was done in the first place.
  *   If you have a lot of instruments from many candidates to import, then it might be preferable to write a script that would work directly in the back-end (database) to import the data from the old instruments to the new one.
     *   Write the script.
     *   Test and validate your script on a separate LORIS instance to ensure that it would do the data transfer properly and without errors.
     *   Backup your production database in case something goes wrong.
     *   Run the script on the production instance at an appropriate time.

As for the relationship of the instruments with flag table, you can refer to the "SQL/0000-00-00-schema.sql" file in your LORIS directory for the exact version for your instance.
In the latest releases

  *   The "CommentID" field of the instruments table refer to the "CommentID" of the "flag" table.
  *   In the same row on the "flag" table, the "SessionID" field refer to the "ID" field of the "session" table.
  *   In the same row on the "session" table, the "CandID" field refer to the "CandID" field of the candidate table.

If you need more info, it will be a pleasure to answer your questions.


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 ALS Neuroimaging Research Unit <alsneuroimagingresearchunit at gmail.com>
Sent: December 18, 2019 18:22
To: loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
Subject: [Loris-dev] Normalizing/breaking down instruments

Hi!

Currently our instruments are quite long, and we would like to break them down into separate instruments.
The code is easy to break down and separate. However, what would be the best way to import the data from the larger instrument and into to the new smaller instruments, given that the CommentIDs will be different.

Also is there any documentation that I could refer to to understand the relationship between the individual instrument tables and the flag table? The LORIS database schema<https://github.com/aces/Loris/wiki/LORIS-database-schema> on GitHub is not updated and is redirected to a dead link on the LORIS demo instance,

Thanks!
-------------- next part --------------
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From justin.kat at mcin.ca  Thu Dec 19 14:36:32 2019
From: justin.kat at mcin.ca (Justin Kat)
Date: Thu, 19 Dec 2019 14:36:32 -0500
Subject: [Loris-dev] Normalizing/breaking down instruments
In-Reply-To: <YTOPR0101MB2027DDDF5C982163FC03B60DCF520@YTOPR0101MB2027.CANPRD01.PROD.OUTLOOK.COM>
References: <CABJp3aDaJ2dYYB34v_shBj=3Nqq+C3VFh5ygZC4y6C5w9shSoA@mail.gmail.com>
 <YTOPR0101MB2027DDDF5C982163FC03B60DCF520@YTOPR0101MB2027.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <CAC4yyo2hNNpPBcB07GRrXZPbPTA1b-gDtwM85nvvcyebZrpupg@mail.gmail.com>

Hi,

To help answer your first question, just in case you're looking to split up
the large instrument in terms of the frontend, ie. the display and/or data
entry aspect, you can have a look into the instrument_subtests and
test_names tables in conjunction with this template that outlines how to
split the form fields into respective subpages:
https://github.com/aces/Loris/blob/master/docs/instruments/NDB_BVL_Instrument_TEMPLATE.class.inc

Justin

On Thu, Dec 19, 2019 at 7:25 AM Melanie Legault, Mrs <
melanie.legault2 at mcgill.ca> wrote:

> Hello,
>
> There is no easy, fit all answer to your question about importing the
> instrument's data.
> It depend on a few factors:
>
>    - the number of candidates you already have and amount of data that
>    would need to be migrated.
>    - if you have access to a software developer (or at least someone who
>    knows MySQL (MariaDB) and how to code scripts.
>    - If you have another instance of LORIS to develop a script without
>    affecting the production instance.
>    - the time that you have to complete this task.
>
> Depending on the answer to these questions, there are a few options:
>
>    - If you only have a few candidates, it might be easier to just
>    manually enter the same data in the new instruments via LORIS web interface
>    as it was done in the first place.
>    - If you have a lot of instruments from many candidates to import,
>    then it might be preferable to write a script that would work directly in
>    the back-end (database) to import the data from the old instruments to the
>    new one.
>    - Write the script.
>       - Test and validate your script on a separate LORIS instance to
>       ensure that it would do the data transfer properly and without errors.
>       - Backup your production database in case something goes wrong.
>       - Run the script on the production instance at an appropriate time.
>
> As for the relationship of the instruments with flag table, you can refer
> to the "SQL/0000-00-00-schema.sql" file in your LORIS directory for the
> exact version for your instance.
> In the latest releases
>
>    - The "CommentID" field of the instruments table refer to the
>    "CommentID" of the "flag" table.
>    - In the same row on the "flag" table, the "SessionID" field refer to
>    the "ID" field of the "session" table.
>    - In the same row on the "session" table, the "CandID" field refer to
>    the "CandID" field of the candidate table.
>
> If you need more info, it will be a pleasure to answer your questions.
>
> 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 ALS Neuroimaging
> Research Unit <alsneuroimagingresearchunit at gmail.com>
> *Sent:* December 18, 2019 18:22
> *To:* loris-dev at bic.mni.mcgill.ca <loris-dev at bic.mni.mcgill.ca>
> *Subject:* [Loris-dev] Normalizing/breaking down instruments
>
> Hi!
>
> Currently our instruments are quite long, and we would like to break them
> down into separate instruments.
> The code is easy to break down and separate. However, what would be the
> best way to import the data from the larger instrument and into to the new
> smaller instruments, given that the CommentIDs will be different.
>
> Also is there any documentation that I could refer to to understand the
> relationship between the individual instrument tables and the flag table?
> The LORIS database schema
> <https://github.com/aces/Loris/wiki/LORIS-database-schema> on GitHub is
> not updated and is redirected to a dead link on the LORIS demo instance,
>
> Thanks!
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> Loris-dev at bic.mni.mcgill.ca
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>
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