[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Wed Dec 4 08:03:32 EST 2019
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
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>>>>>>>>>>>>>>>>>>
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>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> 1. Re: Import mri - scripts (Sotirios Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>> <CAKHj7uST=
>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com>
>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized dicom files
>>>>>>>>>>>>>>>>>> to diagnose the
>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a tool to check if
>>>>>>>>>>>>>>>>>> there are problems
>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to upload them.
>>>>>>>>>>>>>>>>>> Something that could
>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the front-page. Also
>>>>>>>>>>>>>>>>>> which attributes of the
>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is there a dcm file
>>>>>>>>>>>>>>>>>> header
>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into unix_timestamp function it
>>>>>>>>>>>>>>>>>> worked,but i
>>>>>>>>>>>>>>>>>> >> thought that something else was causing the 2nd issue.
>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours Boucher, Mr, <
>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The first error occurs because the QCFirstChangeTime
>>>>>>>>>>>>>>>>>> and columns are of
>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not `datatime`. You
>>>>>>>>>>>>>>>>>> should be using
>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The second error occurs because the trigger triggers
>>>>>>>>>>>>>>>>>> a rollback of the
>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger error handling.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or AFTER trigger
>>>>>>>>>>>>>>>>>> results in failure of
>>>>>>>>>>>>>>>>>> >>> the entire statement that caused trigger invocation.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it helps.
>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their corresponding rows at
>>>>>>>>>>>>>>>>>> the file table are
>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at file_qcstatus as
>>>>>>>>>>>>>>>>>> well, because i
>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as passed throught
>>>>>>>>>>>>>>>>>> the interface
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>> >>> SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>> >>> EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>> >>> QCStatus = "Pass",
>>>>>>>>>>>>>>>>>> >>> QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>> >>> QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range value for
>>>>>>>>>>>>>>>>>> column
>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>>>>>>>>>>>>>>>>>> 823.
>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a
>>>>>>>>>>>>>>>>>> child row: a foreign
>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`parameter_file`,
>>>>>>>>>>>>>>>>>> CONSTRAINT
>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY (`FileID`)
>>>>>>>>>>>>>>>>>> REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>> >>> at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm
>>>>>>>>>>>>>>>>>> line 848.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a TarchiveID column
>>>>>>>>>>>>>>>>>> associated with
>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this value is NULL,
>>>>>>>>>>>>>>>>>> it means no DICOMs
>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables. At the end of
>>>>>>>>>>>>>>>>>> the insertion of the
>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this value is updated
>>>>>>>>>>>>>>>>>> with the correct
>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want to do?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this table is only
>>>>>>>>>>>>>>>>>> linked to the files
>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You could always
>>>>>>>>>>>>>>>>>> create a new table for
>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the tarchive table?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is imported to mark all
>>>>>>>>>>>>>>>>>> their
>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I was thinking of
>>>>>>>>>>>>>>>>>> creating a trigger for
>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add entries to?
>>>>>>>>>>>>>>>>>> So far from what i see
>>>>>>>>>>>>>>>>>> >>> i need to add entres at the table "files" whenever
>>>>>>>>>>>>>>>>>> an insertion happens to
>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for StudyID, at the
>>>>>>>>>>>>>>>>>> beginning of my email
>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the StudyID. So
>>>>>>>>>>>>>>>>>> the StudyID i am
>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the database?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the DicomArchiveID field of
>>>>>>>>>>>>>>>>>> the
>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in the metadata
>>>>>>>>>>>>>>>>>> field but it is mixed
>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the tables? At the
>>>>>>>>>>>>>>>>>> tarchive table,
>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata column i found
>>>>>>>>>>>>>>>>>> something called
>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but that must be
>>>>>>>>>>>>>>>>>> the Study Instance UID.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little explanation
>>>>>>>>>>>>>>>>>> below.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI violation tables
>>>>>>>>>>>>>>>>>> if:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> - the scan type could not be identified (not
>>>>>>>>>>>>>>>>>> matching an entry in
>>>>>>>>>>>>>>>>>> >>> the mri_protocol table)
>>>>>>>>>>>>>>>>>> >>> - one parameter of the scan type is out of the
>>>>>>>>>>>>>>>>>> expected range
>>>>>>>>>>>>>>>>>> >>> present in the mri_protocol_checks (extra
>>>>>>>>>>>>>>>>>> filtering in case you need to be
>>>>>>>>>>>>>>>>>> >>> stricker on some parameters not present in the
>>>>>>>>>>>>>>>>>> mri_protocol table)
>>>>>>>>>>>>>>>>>> >>> - if the CandID and PSCID do not match
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the MRI violation
>>>>>>>>>>>>>>>>>> tables as it happens
>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to MINC files and
>>>>>>>>>>>>>>>>>> only MINC files
>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> - "No single DICOM" (since no valid DICOM could be
>>>>>>>>>>>>>>>>>> found to convert
>>>>>>>>>>>>>>>>>> >>> to MINC)
>>>>>>>>>>>>>>>>>> >>> - "Study already inserted" (duplicate StudyUID)
>>>>>>>>>>>>>>>>>> since this error
>>>>>>>>>>>>>>>>>> >>> happens at the dicomTar.pl level (way before
>>>>>>>>>>>>>>>>>> conversion into MINC files)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it consumed 5.12GB of
>>>>>>>>>>>>>>>>>> ram. Now about the
>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to be inserted
>>>>>>>>>>>>>>>>>> there only if there is
>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in general for its
>>>>>>>>>>>>>>>>>> header parameter?
>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No single dicom" or
>>>>>>>>>>>>>>>>>> with the 2 studyiuid
>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues with the memory.
>>>>>>>>>>>>>>>>>> I think most of our
>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with 4GB you should
>>>>>>>>>>>>>>>>>> be fine.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> about that dicom that had that insertion error it's
>>>>>>>>>>>>>>>>>> about 30mb and when
>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being drastically
>>>>>>>>>>>>>>>>>> increased from 2gb to
>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine is frozen.
>>>>>>>>>>>>>>>>>> What is the recommended
>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?., ?/? Cecile
>>>>>>>>>>>>>>>>>> Madjar <
>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem was fixed!
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are absolutely
>>>>>>>>>>>>>>>>>> certain that no
>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID, you can update
>>>>>>>>>>>>>>>>>> the mri_upload table
>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0 instead of 1 for
>>>>>>>>>>>>>>>>>> that uploadID. It
>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts did not update
>>>>>>>>>>>>>>>>>> this field when it
>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why that would be the
>>>>>>>>>>>>>>>>>> case though.
>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are certain that
>>>>>>>>>>>>>>>>>> there is no processing
>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't have a
>>>>>>>>>>>>>>>>>> StudyID they actually do
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> I thought that this might be a permission because "w"
>>>>>>>>>>>>>>>>>> was missing at the
>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only 102809579
>>>>>>>>>>>>>>>>>> passed, but with no mnic
>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 34 -ignore
>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI pipeline is
>>>>>>>>>>>>>>>>>> currently processing it.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python script:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the Patient header
>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in finding TR_min,
>>>>>>>>>>>>>>>>>> TR_max, TE_min,
>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do an update at
>>>>>>>>>>>>>>>>>> the mri_protocol table
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Also about the first patient with DC0000 had a
>>>>>>>>>>>>>>>>>> violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE of 17 nowhere
>>>>>>>>>>>>>>>>>> and i find that weird
>>>>>>>>>>>>>>>>>> >>> since Loris detects the SeriesDescription.
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The target directory
>>>>>>>>>>>>>>>>>> does not contain a
>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are missing their
>>>>>>>>>>>>>>>>>> StudyUID
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use it with data
>>>>>>>>>>>>>>>>>> from multiple
>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be converted into valid
>>>>>>>>>>>>>>>>>> MINC files.
>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be considered!" What is
>>>>>>>>>>>>>>>>>> this?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of 102327840,
>>>>>>>>>>>>>>>>>> 102809579 and 102506134
>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of the folder at
>>>>>>>>>>>>>>>>>> dicom_output.txt.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete imaging data is
>>>>>>>>>>>>>>>>>> fully documented here
>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the answers you
>>>>>>>>>>>>>>>>>> were looking for there.
>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in *mri_scanner* seen in
>>>>>>>>>>>>>>>>>> your database
>>>>>>>>>>>>>>>>>> >>> management software is a visual placeholder for you
>>>>>>>>>>>>>>>>>> as the user? I'm not
>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be registered with
>>>>>>>>>>>>>>>>>> ID='0' as your screenshot
>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using the API, is
>>>>>>>>>>>>>>>>>> there something
>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i receive a 500
>>>>>>>>>>>>>>>>>> internal error? In the
>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is something
>>>>>>>>>>>>>>>>>> wrong with token, but i
>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a string.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019] [php7:error] [pid
>>>>>>>>>>>>>>>>>> 4535] [client
>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error: Uncaught
>>>>>>>>>>>>>>>>>> TypeError: Argument 1
>>>>>>>>>>>>>>>>>> >>> passed to SinglePointLogin::JWTAuthenticate() must be
>>>>>>>>>>>>>>>>>> of the type string,
>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>> >>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>> >>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>> >>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>> >>> Loris\\API\\Candidates->__construct('POST',
>>>>>>>>>>>>>>>>>> Array)\n#5 {main}\n thrown in
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete candidates? Just to let
>>>>>>>>>>>>>>>>>> you know what i
>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe i may have
>>>>>>>>>>>>>>>>>> missed dependencies.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID 13 etc ( is
>>>>>>>>>>>>>>>>>> there a way to omit
>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner candidates, so i
>>>>>>>>>>>>>>>>>> deleted all the entries
>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't delete this
>>>>>>>>>>>>>>>>>> entry with the 0 ID.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then the candidate
>>>>>>>>>>>>>>>>>> table.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing tools for
>>>>>>>>>>>>>>>>>> creating new candidates
>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are using a PHP
>>>>>>>>>>>>>>>>>> script, by calling the Candidate
>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>> >>> These will create the necessary records for you.
>>>>>>>>>>>>>>>>>> (It's not recommended to
>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql database tables in
>>>>>>>>>>>>>>>>>> your script, if I
>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6 digit randomized
>>>>>>>>>>>>>>>>>> ID, and there are
>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for project-specific IDs and
>>>>>>>>>>>>>>>>>> the External ID field
>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used for any
>>>>>>>>>>>>>>>>>> values you like.
>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs can be added
>>>>>>>>>>>>>>>>>> in parallel - these
>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate Information
>>>>>>>>>>>>>>>>>> module and added in the
>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto insert the
>>>>>>>>>>>>>>>>>> candidates based on
>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know whethere when
>>>>>>>>>>>>>>>>>> we are creating a new
>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we also have to
>>>>>>>>>>>>>>>>>> insert a new record at
>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a problem that in
>>>>>>>>>>>>>>>>>> our case CandID won't
>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from 100000?)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?., ?/? Melanie
>>>>>>>>>>>>>>>>>> Legault, Mrs <
>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the numeric part
>>>>>>>>>>>>>>>>>> of the PSCID get
>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID of `ABC` plus
>>>>>>>>>>>>>>>>>> 4 numerical char
>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence would be:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always get the
>>>>>>>>>>>>>>>>>> latest value generated
>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is varchar(255), it
>>>>>>>>>>>>>>>>>> must be stored
>>>>>>>>>>>>>>>>>> >>> within a specific length of characters. Otherwise if
>>>>>>>>>>>>>>>>>> we were to sort
>>>>>>>>>>>>>>>>>> >>> strings with different lengths the result would not
>>>>>>>>>>>>>>>>>> be sorted correctly (
>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result to 1, 10, 11,
>>>>>>>>>>>>>>>>>> 2 ).
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?., ?/? Melanie
>>>>>>>>>>>>>>>>>> Legault, Mrs <
>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored anywhere.
>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with the max value
>>>>>>>>>>>>>>>>>> and increase that
>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the next PSCID.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer | Faculty of
>>>>>>>>>>>>>>>>>> Medicine | McGill
>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>> >>> *From:* loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca> on behalf of
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri - scripts
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next available PSCID
>>>>>>>>>>>>>>>>>> value for a new
>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is sequential, but
>>>>>>>>>>>>>>>>>> where do we store the
>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you have assigned
>>>>>>>>>>>>>>>>>> are global
>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial and error?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup of your tables
>>>>>>>>>>>>>>>>>> to match your
>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according to
>>>>>>>>>>>>>>>>>> instructions --
>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation recommends
>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first deleting prior
>>>>>>>>>>>>>>>>>> uploads).
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to resolve what
>>>>>>>>>>>>>>>>>> would happen?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at the
>>>>>>>>>>>>>>>>>> brainbrowser from the
>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are stored at
>>>>>>>>>>>>>>>>>> /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to resolve what would
>>>>>>>>>>>>>>>>>> happend? would they
>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists in my local
>>>>>>>>>>>>>>>>>> database. If i adjust
>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min the mincs
>>>>>>>>>>>>>>>>>> will be uploaded?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up your
>>>>>>>>>>>>>>>>>> mri_protocol table ? (and
>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional types of
>>>>>>>>>>>>>>>>>> scans)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a pre-requisite for the
>>>>>>>>>>>>>>>>>> Imaging insertion
>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup documentation :
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert statements.
>>>>>>>>>>>>>>>>>> You can adapt the
>>>>>>>>>>>>>>>>>> >>> insert statements which load the default table values
>>>>>>>>>>>>>>>>>> --> e.g. Here on
>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but not how to
>>>>>>>>>>>>>>>>>> insert new rows.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then will the minc be
>>>>>>>>>>>>>>>>>> inserted?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked correctly.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the screenshot is
>>>>>>>>>>>>>>>>>> enough.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type", which we knew
>>>>>>>>>>>>>>>>>> already. Did you
>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of the module,
>>>>>>>>>>>>>>>>>> showing for each scan
>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will also show for
>>>>>>>>>>>>>>>>>> comparison what's
>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>> >>> Compare these values to find which parameter was not
>>>>>>>>>>>>>>>>>> correct according
>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type definitions.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> You may end up broadening your mri_protocol value
>>>>>>>>>>>>>>>>>> ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by editing the
>>>>>>>>>>>>>>>>>> database table
>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI Violations
>>>>>>>>>>>>>>>>>> module.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are explained in
>>>>>>>>>>>>>>>>>> more detail in the
>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS (click the
>>>>>>>>>>>>>>>>>> ["?"] icon in the menu
>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting guide
>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >>> : no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> looks like my previous email's attachment wasn't
>>>>>>>>>>>>>>>>>> delivered due to
>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at google drive
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify worked in both
>>>>>>>>>>>>>>>>>> cases
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the .html output
>>>>>>>>>>>>>>>>>> from webbrowser, so
>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not sure why you're
>>>>>>>>>>>>>>>>>> getting an Endian
>>>>>>>>>>>>>>>>>> >>> warning. (it's a warning not an error, correct?)
>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers (PatientName)
>>>>>>>>>>>>>>>>>> all successfully
>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM headers -- though
>>>>>>>>>>>>>>>>>> your dcmodify command is
>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk header updates.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being changed (e.g.
>>>>>>>>>>>>>>>>>> "(2001,105f)" from
>>>>>>>>>>>>>>>>>> >>> the warning message) - you can also dcmdump a DICOM
>>>>>>>>>>>>>>>>>> slice before and look
>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to backup your
>>>>>>>>>>>>>>>>>> DICOMS before/after
>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on each version to
>>>>>>>>>>>>>>>>>> diff the outputs --
>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Re the protocol violation -- AcquisitionProtocol not
>>>>>>>>>>>>>>>>>> recognized or
>>>>>>>>>>>>>>>>>> >>> unknown : this means your scans did not match what
>>>>>>>>>>>>>>>>>> is stored in your
>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end module -- can you
>>>>>>>>>>>>>>>>>> see why they didn't
>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the contents of
>>>>>>>>>>>>>>>>>> the mri_protocol
>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of the mismatch.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Here is the psc table
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through the interface
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom file
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> dcmodify -ma PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>> >>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined
>>>>>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined
>>>>>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN and undefined
>>>>>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN and undefined
>>>>>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN and undefined
>>>>>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN and undefined
>>>>>>>>>>>>>>>>>> length, reading a
>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax LittleEndianImplicit
>>>>>>>>>>>>>>>>>> (CP-246)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show warnings. Below
>>>>>>>>>>>>>>>>>> you can see the
>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics could not be
>>>>>>>>>>>>>>>>>> inserted due to
>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod -upload_id 12
>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> find -path \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>> -name '__MACOSX'
>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> dicomTar.pl \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/ -database -profile
>>>>>>>>>>>>>>>>>> prod -verbose
>>>>>>>>>>>>>>>>>> >>> Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> You will archive the dir : ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the following command:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> * Taken from dir :
>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>> >>> * Archive target location :
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1
>>>>>>>>>>>>>>>>>> >>> * Name of host OS : Linux
>>>>>>>>>>>>>>>>>> >>> * Created by user : lorisadmin
>>>>>>>>>>>>>>>>>> >>> * Archived on : 2019-09-06
>>>>>>>>>>>>>>>>>> 18:36:50
>>>>>>>>>>>>>>>>>> >>> * dicomSummary version : 1
>>>>>>>>>>>>>>>>>> >>> * dicomTar version : 1
>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball :
>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive :
>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>> >>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target location
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>> >>> md5sum
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be considered for
>>>>>>>>>>>>>>>>>> inserting into the
>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and log file is
>>>>>>>>>>>>>>>>>> >>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>> >>> CandID id: 602102
>>>>>>>>>>>>>>>>>> >>> visit_label is: V1
>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>> >>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>> >>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --> md5: 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --> The minc file cannot be registered since the
>>>>>>>>>>>>>>>>>> AcquisitionProtocol
>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets with the
>>>>>>>>>>>>>>>>>> *delete_imaging_upload*
>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table? (Is it properly
>>>>>>>>>>>>>>>>>> populated? This is a
>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the candidate
>>>>>>>>>>>>>>>>>> record is curious.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> There are also a few options for creating candidates
>>>>>>>>>>>>>>>>>> when inserting
>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API then DICOM
>>>>>>>>>>>>>>>>>> insertion pipeline
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the candidates (and
>>>>>>>>>>>>>>>>>> visits, optionally I
>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID assigned by LORIS.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the PatientName
>>>>>>>>>>>>>>>>>> header in the DICOMs
>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly labelled with
>>>>>>>>>>>>>>>>>> PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s* options when running
>>>>>>>>>>>>>>>>>> the bids_import script,
>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates and sessions.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime do i have to
>>>>>>>>>>>>>>>>>> create a new
>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//)
>>>>>>>>>>>>>>>>>> at ./
>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or update a
>>>>>>>>>>>>>>>>>> child row: a foreign
>>>>>>>>>>>>>>>>>> >>> key constraint fails (`LORIS`.`candidate`, CONSTRAINT
>>>>>>>>>>>>>>>>>> `FK_candidate_1`
>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc`
>>>>>>>>>>>>>>>>>> (`CenterID`)) at
>>>>>>>>>>>>>>>>>> >>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line
>>>>>>>>>>>>>>>>>> 1060.
>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table mri_scanner:
>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>> >>> (CandID,Model,Software,Serial_number,Manufacturer)
>>>>>>>>>>>>>>>>>> VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a child row: a
>>>>>>>>>>>>>>>>>> foreign key
>>>>>>>>>>>>>>>>>> >>> constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT
>>>>>>>>>>>>>>>>>> `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES `candidate`
>>>>>>>>>>>>>>>>>> (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ERROR: The validation has failed. Either re-run the
>>>>>>>>>>>>>>>>>> validation again
>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run tarchiveLoader.pl
>>>>>>>>>>>>>>>>>> using -force to force the
>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> (loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl -profile prod <
>>>>>>>>>>>>>>>>>> ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in pattern match (m//)
>>>>>>>>>>>>>>>>>> at ./
>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 144.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already inserted this study.
>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>> >>> This is the information retained from the first time
>>>>>>>>>>>>>>>>>> the study was
>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> * Taken from dir :
>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>> >>> * Archive target location :
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>> >>> * Name of creating host : 127.0.1.1
>>>>>>>>>>>>>>>>>> >>> * Name of host OS : Linux
>>>>>>>>>>>>>>>>>> >>> * Created by user : lorisadmin
>>>>>>>>>>>>>>>>>> >>> * Archived on : 2019-09-04
>>>>>>>>>>>>>>>>>> 18:33:05
>>>>>>>>>>>>>>>>>> >>> * dicomSummary version : 1
>>>>>>>>>>>>>>>>>> >>> * dicomTar version : 1
>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball :
>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive :
>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>> >>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or directory at ./
>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress. Let us know when
>>>>>>>>>>>>>>>>>> you next encounter
>>>>>>>>>>>>>>>>>> >>> issues as you progress through the Imaging
>>>>>>>>>>>>>>>>>> Install/Setup docs
>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle the incoming/
>>>>>>>>>>>>>>>>>> directory next
>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is 'port' :
>>>>>>>>>>>>>>>>>> ''. Also i have tested
>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with lorisuser.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> I executed the script again, because the only error i
>>>>>>>>>>>>>>>>>> had previously was
>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't exist and there
>>>>>>>>>>>>>>>>>> are no errors
>>>>>>>>>>>>>>>>>> >>> reported back except of warnings <<mysql: [Warning]
>>>>>>>>>>>>>>>>>> Using a password on the
>>>>>>>>>>>>>>>>>> >>> command line interface can be insecure>>.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was unable to connect
>>>>>>>>>>>>>>>>>> to the database
>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the password),
>>>>>>>>>>>>>>>>>> that would explain the
>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI code path you
>>>>>>>>>>>>>>>>>> saw in the Config
>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the output from your
>>>>>>>>>>>>>>>>>> script run -- Did
>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> For example, check if the database connection
>>>>>>>>>>>>>>>>>> information was populated
>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> If you are referring to the imaging_install.sh here
>>>>>>>>>>>>>>>>>> is an image with the
>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the problem is
>>>>>>>>>>>>>>>>>> somewhere at the last part
>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as possible
>>>>>>>>>>>>>>>>>> automatically?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?., ?/? Christine
>>>>>>>>>>>>>>>>>> Rogers, Ms. <
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is up and
>>>>>>>>>>>>>>>>>> working and all the
>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$ chmod
>>>>>>>>>>>>>>>>>> 775 project
>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have 775
>>>>>>>>>>>>>>>>>> permissions and that
>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers group, per step 1
>>>>>>>>>>>>>>>>>> in the install
>>>>>>>>>>>>>>>>>> >>> Readme <https://github.com/aces/Loris#install-steps>.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and Image should
>>>>>>>>>>>>>>>>>> change LORIS to
>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated during your
>>>>>>>>>>>>>>>>>> imaging installation
>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> by an
>>>>>>>>>>>>>>>>>> automated script --
>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually via the Config
>>>>>>>>>>>>>>>>>> module.
>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup Guide
>>>>>>>>>>>>>>>>>> >>> <https://github.com/aces/Loris/wiki/Setup> for
>>>>>>>>>>>>>>>>>> detailed steps to follow.
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and Image should
>>>>>>>>>>>>>>>>>> change LORIS to loris,
>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?., ?/? Sotirios
>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> curl -sL https://deb.nodesource.com/setup_8.x | sudo
>>>>>>>>>>>>>>>>>> -E bash -
>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make worked and now i
>>>>>>>>>>>>>>>>>> can see all the
>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i don't need make
>>>>>>>>>>>>>>>>>> install?
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>> _______________________________________________
>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience | MCIN.ca
>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
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