[Loris-dev] Import mri - scripts

[Cecile Madjar]

Hi Sotirios,

It looks like xargs is not installed in your docker environment.

This is being used by the following command in dicomTar.pl (and a few other
places but that is the one causing the error at the moment):

$cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs* rm -f";

So you need to install xargs in your docker for the command to run.

Hope this helps,

Cécile
On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hello,
>
> We are making a dockerized version of Loris 21 and when we execute the
> batch_uploads_imageuploader.pl we get an error about xargs. What could be
> the casue?
>
> 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 13
> /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>
>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name '__MACOSX'
> -delete
> xargs: file: No such file or directory
>
> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
> Target: /data/loris/data/tarchive
>
> Thanks
>
> Στις Τρί, 10 Δεκ 2019 στις 7:21 μ.μ., ο/η Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> έγραψε:
>
>> Hi,
>>
>> i opened an issue and looked up for the values of Volume they suggested
>> https://github.com/BIC-MNI/minc-toolkit-v2/issues/95. The only
>> attributes associated with it i saw are [0x00089206] and [0x00089207]
>>
>> [image: image.png]
>>
>> I looked up for the file that was being viewed fine in the BrainBrowser
>> and saw that it had that attribute empty so i used this command because i
>> couldn't find a way to modify the attribute via pydicom
>>
>> dcmodify -ma "(0008,9206)=" *.dcm
>>
>> and that command reported the warning about the Endian Syntax. I also
>> used the corresponding command for 9207 and got the message "Tag not found'
>>
>> Lastly I tried to upload some dicoms and now i am getting the SNR and i
>> can view them fine. I believe now that all of them will pass successfully,
>> i will report back later.
>>
>> Thanks,
>>
>> Sotirios
>>
>> Στις Δευ, 9 Δεκ 2019 στις 8:10 μ.μ., ο/η Cecile Madjar <
>> cecile.madjar at mcin.ca> έγραψε:
>>
>>> 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
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
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