[Loris-dev] Import mri - scripts
Cecile Madjar
cecile.madjar at mcin.ca
Tue Dec 3 15:39:36 EST 2019
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,
Cécile
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
>
> 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
>>>>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>
>>>>>>>>>>>>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191203/24c7b6e4/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 37207 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191203/24c7b6e4/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 92124 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191203/24c7b6e4/attachment-0005.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 62956 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191203/24c7b6e4/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 65585 bytes
Desc: not available
URL: <http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191203/24c7b6e4/attachment-0007.png>
More information about the Loris-dev
mailing list