[Loris-dev] Import mri - scripts
Cecile Madjar
cecile.madjar at mcin.ca
Mon Dec 9 13:10:11 EST 2019
Hi Sotirios,
The issue you are having is a indeed a dcm2mnc issue. The converter does
not seem to work on your dataset for some reason. Unfortunately, there is
not much we can do on our front to fix this...
I would recommend creating an issue on the MINC tools repository
<https://github.com/BIC-MNI/minc-toolkit-v2/issues> so they can fix your
problem.
Very sorry that you are having that problem.
Best,
Cécile
On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <cecile.madjar at mcin.ca> wrote:
> Hi Sotirios,
>
> Could you please share a dataset with us that produces the error you get
> and the weird display in BrainBrowser? You could use the same SFTP
> credential that Nicolas gave you.
>
> The message errors you got from imaging_install.sh are probably due to the
> fact that you reran the install script and it tried to reinstall something
> that was already there. I would not worry about it. FYI, the only thing you
> needed to do was to update the MINC tools path in the environment file as
> you did after re-running imaging_install.sh and source the environment file.
>
> Best,
>
> Cécile
>
> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi Cecile,
>>
>> We used minctool 1.9.7 and we still get this error
>>
>> <<Restructuring...
>> gsl: bessel_I0.c:216: ERROR: overflow
>> Default GSL error handler invoked.
>> noise_estimate --snr /data/loris/data>>
>>
>
>> One dicom folder hadn't that error and is being viewed fine in the
>> BrainBrowser of Loris.
>>
>
>> When i used dpkg to the 1.9.17 the installation reported fine <<Unpacking
>> minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>
>> and then i used source /opt/minc/1.9.17/minc-toolkit-config.sh
>>
>> and aftewards runned bash ./imaging_install.sh just to be sure.
>>
>> We also had to modify /data/loris/bin/mri/environment because it still
>> pointed to the old version.
>>
>> What i found strange is this during the run of imaging_install.sh
>>
>> <<already using interpreter
>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>> Please use the *system* python to run this script
>> Traceback (most recent call last):
>> File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 2632,
>> in <module>
>> main()
>> File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 870,
>> in main
>> symlink=options.symlink,
>> File "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 1156,
>> in create_environment
>> install_python(home_dir, lib_dir, inc_dir, bin_dir,
>> site_packages=site_packages, clear=clear, symlink=symlink)
>> File
>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>> line 357, in abspath
>> if not isabs(path):
>> File
>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>> line 64, in isabs
>> return s.startswith(sep)
>> AttributeError: 'NoneType' object has no attribute 'startswith'
>> Installing the Python libraries into the loris-mri virtualenv...
>> Requirement already satisfied: mysqlclient in
>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>> Requirement already satisfied: mysql-connector in
>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>> Requirement already satisfied: pybids in
>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>> Requirement already satisfied: nibabel>=2.1 in ./python_virtua>>
>>
>> So should i open an issue for that error? or is there something else to
>> try?
>>
>> Thanks
>>
>> Sotirios
>>
>>
>>
>>
>>
>> Στις Τρί, 3 Δεκ 2019 στις 10:39 μ.μ., ο/η Cecile Madjar <
>> cecile.madjar at mcin.ca> έγραψε:
>>
>>> 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/20191209/83c5fe54/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/20191209/83c5fe54/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/20191209/83c5fe54/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/20191209/83c5fe54/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/20191209/83c5fe54/attachment-0007.png>
More information about the Loris-dev
mailing list