[Loris-dev] Import mri - scripts
Ling Ma
lingyun.ma at mcin.ca
Thu Jan 30 11:21:52 EST 2020
Oh, I just found that you are using Loris-mri 21.0, as I stated in the
previous email, the "$_" could not find any matches, so your command might
not be correctly entered.
On Thu, Jan 30, 2020 at 10:35 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
> Hi Sotirios,
>
> By curiosity, I just looked at the error message, "Use of uninitialized
> value $_ in pattern match (m//) at /data/loris/bin/mri/
> batch_uploads_imageuploader.pl line 144." clearly means that there is no
> match, but 144 line has no such code related with $_ in recent versions of
> the batch_uploads_imageuploader.pl. There is something in the line 165
> for a few recent versions.
>
> As to "xargs: file: No such file or directory", it could be due to a
> command unable to find anything using the directory provided as the message
> suggested.
>
> In both cases, I feel that it could be helpful if you provide more details
> such as which Loris_MRI version you are running, what is the exact command
> line you are using to help supporters to understand.
>
> Thanks.
>
> Best regards,
> Ling Ma
> Consultant
>
> On Wed, Jan 29, 2020 at 6:57 PM Sotirios Nikoloutsopoulos <
> sotirisnik at gmail.com> wrote:
>
>> Hi Cecile,
>>
>> it seems that xargs is already installed in our docker container.
>>
>> [image: image.png]
>>
>>
>> Στις Τετ, 29 Ιαν 2020 στις 7:59 μ.μ., ο/η Cecile Madjar <
>> cecile.madjar at mcin.ca> έγραψε:
>>
>>> 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
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>> 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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