[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Tue Dec 3 15:26:16 EST 2019
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
Στις Δευ, 2 Δεκ 2019 στις 6:59 μ.μ., ο/η Cecile Madjar <
cecile.madjar at mcin.ca> έγραψε:
> 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,
>
> Cécile
>
> 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
>>
>>
>> Στις Τετ, 27 Νοε 2019 στις 4:29 μ.μ., ο/η Cecile Madjar <
>> cecile.madjar at mcin.ca> έγραψε:
>>
>>> Hi Sotirios,
>>>
>>> Thank you for the details!
>>>
>>> A few things to try:
>>>
>>> - modify the TMPDIR to be on your /data directory where there might
>>> be more space to do processing (could create a /data/tmp where the
>>> temporary files would be created)
>>> - how many files are there for that upload in tarchive_files? Are
>>> they different from the ones showing the warning message?
>>> - FYI: query to get that: SELECT tf.* FROM tarchive_files tf JOIN
>>> mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>> output of that query would be very useful if you can provide it)
>>> - how many series are there for that upload in tarchive_series?
>>> - FYI: query to get that: SELECT ts.* FROM tarchive_series ts JOIN
>>> mri_upload USING (TarchiveID) WHERE UploadID=<your uploadID> (the
>>> output of that query would be very useful if you can provide it)
>>> - things are failing when the scripts try running the following
>>> command: find /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO
>>> -type f | /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>> -studyuid -series -echo -image -file -attvalue 0018 0024 -series_descr
>>> -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4 | cut -f 5 | dcm2mnc -dname ''
>>> -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>> - clearly the problems come from get_dicom_info.pl but I cannot
>>> pinpoint the error yet. I will ask around and get back to you
>>>
>>> If I cannot figure it out remotely, is there a way to have a call using
>>> zoom? This way you could share your screen with me and run the debugger on
>>> that script and hopefully we can figure out what is going on with those
>>> datasets?
>>>
>>> Thanks!
>>>
>>> Cécile
>>>
>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios Nikoloutsopoulos <
>>> sotirisnik at gmail.com> wrote:
>>>
>>>> Hi Cecile,
>>>>
>>>> In both my virtual machines
>>>> export TMPDIR=/tmp
>>>>
>>>> In both vm also with dcm2mnc i get this output. Just to verify that
>>>> this passed in my 1st vm and produced mincs.
>>>>
>>>> I attached the spool as a csv.
>>>>
>>>> [image: image.png]
>>>>
>>>> And also one difference i found was this in the Loris-mri code ( left
>>>> 1st workable vm, right 2nd vm that has to be fixed, although i changed it
>>>> seems to be independent of the uninitialized value $_ )
>>>>
>>>>
>>>> [image: image.png]
>>>>
>>>> Thanks,
>>>>
>>>> Sotirios
>>>>
>>>>
>>>>
>>>>
>>>> Στις Τρί, 26 Νοε 2019 στις 11:34 μ.μ., ο/η Cecile Madjar <
>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>
>>>>> Hi Sotirios,
>>>>>
>>>>> that is puzzling... A few additional questions:
>>>>>
>>>>> - what is the bash variable TMPDIR set to on the environment file?
>>>>> - could you try running separately dcm2mnc on the DICOM folder to
>>>>> see if that works?
>>>>> - could you send us the detailed log from the notification spool
>>>>> table (SELECT * FROM notification_spool WHERE UploadID=<your uploadID>) and
>>>>> send it back to us? Maybe there are some additional clues that could help
>>>>> figuring out what is going on.
>>>>>
>>>>> Thank you!
>>>>>
>>>>> Cécile
>>>>>
>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios Nikoloutsopoulos <
>>>>> sotirisnik at gmail.com> wrote:
>>>>>
>>>>>> Hi Cecile,
>>>>>>
>>>>>> I checked for the StudyInstacueUID at the files with "The target
>>>>>> directory does not contain a single DICOM file"" and their attribute has a
>>>>>> value.
>>>>>>
>>>>>> Regarding the scouter and localizer, i modified the settings in the
>>>>>> imaging pipeline and now i don't get that error message, but still it
>>>>>> doesn't create the mnics.
>>>>>>
>>>>>> The errors i am getting are ( uninitialized value $_ is not
>>>>>> important? because i haven't got comments about that )
>>>>>>
>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>> Running now the following command: /data/loris/data//uploadNeuroDB/
>>>>>> imaging_upload_file.pl -profile prod -upload_id 134
>>>>>> /data/incoming/DCC0025_118008_V1.tar.gz -verbose
>>>>>>
>>>>>> and
>>>>>>
>>>>>> Number of MINC files that will be considered for inserting into the
>>>>>> database: 0
>>>>>>
>>>>>> No data could be converted into valid MINC files.
>>>>>>
>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>> Use of uninitialized value $mail_user in concatenation (.) or string
>>>>>> at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>>>>>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/
>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>> batch_uploads_imageuploader.pl line 250.
>>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>>
>>>>>> Thanks
>>>>>>
>>>>>> Sotirios
>>>>>>
>>>>>> Στις Δευ, 25 Νοε 2019 στις 5:22 μ.μ., ο/η Cecile Madjar <
>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> OK. So the issue I mentioned should not be a problem for you.
>>>>>>>
>>>>>>> Is the StudyInstanceUID DICOM header set in your images? If it is
>>>>>>> not set, then you would end up with the error message "The target directory
>>>>>>> does not contain a single DICOM file". So maybe this is the issue you are
>>>>>>> having with those datasets?
>>>>>>>
>>>>>>> Regarding not excluding series descriptions, you can configure that
>>>>>>> in the Config module under the Imaging Pipeline section. Simply remove all
>>>>>>> entries for the "Series description to exclude from imaging insertion"
>>>>>>> setting.
>>>>>>>
>>>>>>> Cécile
>>>>>>>
>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Cecile,
>>>>>>>>
>>>>>>>> We are using this version
>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip. Is it possible
>>>>>>>> to insert low resolution now?
>>>>>>>>
>>>>>>>> Thanks
>>>>>>>>
>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <cecile.madjar at mcin.ca>
>>>>>>>> wrote:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>
>>>>>>>>> There was a bug that got resolved in 20.2 in get_dicom_info.pl.
>>>>>>>>> Basically, if a DICOM did not have the (0020,0032) header,
>>>>>>>>> get_dicom_info.pl considered that the file was not a DICOM, which
>>>>>>>>> was a mistake. This got fixed in version 20.2 of LORIS-MRI. Hopefully this
>>>>>>>>> is the issue you are encountering.
>>>>>>>>>
>>>>>>>>> About scout and localizer, they are a type of short and low
>>>>>>>>> resolution sequence that is used by the tech but is of no interest
>>>>>>>>> scientifically, which is why we tend to no insert them.
>>>>>>>>>
>>>>>>>>> Hope this helps,
>>>>>>>>>
>>>>>>>>> Cécile
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Cecile,
>>>>>>>>>>
>>>>>>>>>> i executed the find command and the output i got per folder was
>>>>>>>>>> "DICOM medical imaging data. Maybe there is something wrong with the find
>>>>>>>>>> command in the warning that it is unable to check if the file is a dicom
>>>>>>>>>> file? Also when i use get_dicom_info.pl i don't get any output
>>>>>>>>>> data. Finally i don't understand what scout or localizer is ( something
>>>>>>>>>> like if and only if a file fails then the whole session is invalid? ).
>>>>>>>>>>
>>>>>>>>>> [image: image.png]
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Sotirios
>>>>>>>>>>
>>>>>>>>>> Στις Τρί, 19 Νοε 2019 στις 9:40 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>
>>>>>>>>>>> I took a closer look to the batch_uploader_multiple_output.txt
>>>>>>>>>>> file you sent. It looks like there are different reasons for failure
>>>>>>>>>>> depending on the DICOM folder uploaded.
>>>>>>>>>>>
>>>>>>>>>>> - For 465466 DCC0000 V1; 727195 DCC0004 V1 and 684908
>>>>>>>>>>> DCC0007 V1: it looks like there is no file of type DICOM in the folder.
>>>>>>>>>>> Have you checked to see if that is indeed the case? Maybe you can try
>>>>>>>>>>> running the following command on that folder to see what are the types of
>>>>>>>>>>> the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>> file, then that is why you get the error message from the pipeline:
>>>>>>>>>>> -
>>>>>>>>>>>
>>>>>>>>>>> find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>
>>>>>>>>>>> - For 864173 DCC0001 V1: it looks like there are two
>>>>>>>>>>> different DICOM studies within the same folder. You will need to split that
>>>>>>>>>>> study in two based on the StudyUID field as the insertion pipeline does not
>>>>>>>>>>> allow for more than one StudyUID per upload.
>>>>>>>>>>> - For 890807 DCC0002 V1; 637025 DCC0005 V1 and 239975
>>>>>>>>>>> DCC0006 V1: it looks like the dcm2mnc command did not produce any MINC
>>>>>>>>>>> files. Can you check in the DICOM archive what are the series present in
>>>>>>>>>>> the tarchive for that visit? Maybe only a scout or localizer was acquired
>>>>>>>>>>> for that session, hence the no valid MINC files (scout and localizer being
>>>>>>>>>>> skipped for the conversion)
>>>>>>>>>>> - For 397410 DCC0003 V1: it looks like everything went well
>>>>>>>>>>> for this one.
>>>>>>>>>>>
>>>>>>>>>>> One script that is called by our pipeline is called
>>>>>>>>>>> get_dicom_info.pl and this does all kind of checks on the DICOM
>>>>>>>>>>> files (it is being called when running the dcm2mnc conversion). You could
>>>>>>>>>>> run it independently on your folder if needed.
>>>>>>>>>>>
>>>>>>>>>>> Since one of the study got in, it does not look like you are
>>>>>>>>>>> having a problem with the setup. It seems more likely to be a problem with
>>>>>>>>>>> the data themselves.
>>>>>>>>>>>
>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>
>>>>>>>>>>> Cécile
>>>>>>>>>>>
>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>
>>>>>>>>>>>> In my first vm i am able to create the minc files and view them
>>>>>>>>>>>> at the mri browser (except of candidate 102761034 ), meanwhile the same
>>>>>>>>>>>> files gives warnings at the 2nd vm. The output of the batch upload can be
>>>>>>>>>>>> seen in the file attached.
>>>>>>>>>>>> Also a colleague of us has built a pre-validation tool for
>>>>>>>>>>>> dicom https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks
>>>>>>>>>>>>
>>>>>>>>>>>> Στις Τετ, 13 Νοε 2019 στις 11:45 μ.μ., ο/η Christine Rogers,
>>>>>>>>>>>> Ms. <christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>> Can you provide us with some fresh particulars of the
>>>>>>>>>>>>> current issue and we'll take it from there?
>>>>>>>>>>>>> Yang's team has built these scripts which can definitely serve
>>>>>>>>>>>>> as a model for your pre-validation of your DICOM collections.
>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> We make use of pydicom library too. Now about the validate.py
>>>>>>>>>>>>>> i see that you check if some attributes are missing such as PatientID,
>>>>>>>>>>>>>> PatientName which all of our files contains that info. Maybe i have missed
>>>>>>>>>>>>>> something on the setup of my other virtual machine ( although one dicom
>>>>>>>>>>>>>> passed on the new vm successfully, the others that were inserted correctly
>>>>>>>>>>>>>> on my old vm fails on the new one ), i think that i had asked about this
>>>>>>>>>>>>>> error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>> 144." but i don't remember the solution.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Στις Τετ, 13 Νοε 2019 στις 5:45 π.μ., ο/η Yang Ding <
>>>>>>>>>>>>>> it at cnbp.ca> έγραψε:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you had some issue
>>>>>>>>>>>>>>> with DICOM. I am a fellow developer for an external project using LORIS,
>>>>>>>>>>>>>>> kind of just like you. We had to implement DICOM upload as well but more as
>>>>>>>>>>>>>>> a fully automated pipeline actually.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> While we were building CNBP, we had coded up some minor
>>>>>>>>>>>>>>> Python functions to check DICOM integrity (and simple validations) and you
>>>>>>>>>>>>>>> might be able to gain some inspiration from it and help you with your
>>>>>>>>>>>>>>> cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#) seems
>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
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>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> 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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