[Loris-dev] Import mri - scripts

[Ling Ma]

Hi Sotirios,

You can check hostname and url using a SQL like "select * from Config where
configid in (select id from ConfigSettings where name = 'url' or name =
'host');"

As a result, you can update the Config value with a script once you have
installed the Loris,

like "UPDATE Config set Value = 'http://localhost:8080' WHERE ConfigID =
(SELECT ID from ConfigSettings WHERE name = 'url');
like "UPDATE Config set Value = 'localhost:8080' WHERE ConfigID = (SELECT
ID from ConfigSettings WHERE name = 'host');

I suppose an easy script in whatever language could do the job, like sh,
python, php, whatever.

Best regards,
Ling Ma


On Fri, Feb 7, 2020 at 10:44 AM Sotirios Nikoloutsopoulos <
sotirisnik at gmail.com> wrote:

> Hi Ling,
>
> are those the entries you meant? If only I execute it from browser it adds
> the port 8088, still I can't see it using the curl query.
>
> [image: image.png]
>
> This time i copied the curl query directly from firefox, I only omitted
> the Cookie parameter below.
>
> curl 'http://localhost/installdb.php' -H 'User-Agent: Mozilla/5.0 (X11;
> Ubuntu; Linux x86_64; rv:72.0) Gecko/20100101 Firefox/72.0' -H 'Accept:
> text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
> -H 'Accept-Language: en-US,en;q=0.5' --compressed -H 'Content-Type:
> application/x-www-form-urlencoded' -H 'Origin: http://localhost:8088' -H
> 'Connection: keep-alive' -H 'Referer: http://localhost:8088/installdb.php'
> --H 'Upgrade-Insecure-Requests: 1' --data
> 'dbhost=172.28.1.2&dbadminuser=root&dbadminpassword=neopass&dbname=LORIS&formname=validaterootaccount'
>
> curl 'http://localhost/installdb.php' -H 'User-Agent: Mozilla/5.0 (X11;
> Ubuntu; Linux x86_64; rv:72.0) Gecko/20100101 Firefox/72.0' -H 'Accept:
> text/html,application/xhtml+xml,application/xml;q=0.9,image/webp,*/*;q=0.8'
> -H 'Accept-Language: en-US,en;q=0.5' --compressed -H 'Content-Type:
> application/x-www-form-urlencoded' -H 'Origin: http://localhost:8088' -H
> 'Connection: keep-alive' -H 'Referer:
> http://localhost:8088/installdb.php'-H 'Upgrade-Insecure-Requests: 1'
> --data
> 'lorismysqluser=lorisuser&lorismysqlpassword=neopass&frontenduser=lorisuser&frontendpassword=1234&formname=createmysqlaccount&dbname=LORIS&dbhost=172.28.1.2&dbadminuser=root&dbadminpassword=neopass'
>
> Thanks
>
> Στις Παρ, 31 Ιαν 2020 στις 5:35 μ.μ., ο/η Ling Ma <lingyun.ma at mcin.ca>
> έγραψε:
>
>> Hi Sotirios,
>>
>> This is because you are runing the installdb from curl, whose host name
>> is not the one you used on the browser. You can modify Config table host
>> and url two configurations or possibly pass a good hostname to curl.
>>
>> Ling
>>
>> On Fri, Jan 31, 2020 at 10:25 AM Sotirios Nikoloutsopoulos <
>> sotirisnik at gmail.com> wrote:
>>
>>> Hi Cecile,
>>>
>>> Indeed 'file' was missing and now it worked. I also wanted to ask about
>>> the installdb.php if it is possible to automate the execution. I tried thse
>>> commands with curl to execute the http queries for the forms. Although I
>>> don't have the error1.html and error2.html files at the moment, their html
>>> code showed that the execution was successful and the config.xml is being
>>> created, but when I login it's like the css is not loading.
>>>
>>> #first query
>>> curl --data "formname=validaterootaccount" --data "dbhost=172.28.1.2"
>>> --data "dbadminuser=root" --data "dbadminpassword=neopass" --data
>>> "dbname=LORIS" http://localhost/installdb.php > error1.html
>>> #second query
>>> curl --data "formname=createmysqlaccount" --data "dbhost=172.28.1.2"
>>> --data "dbadminuser=root" --data "dbadminpassword=neopass" --data
>>> "dbname=LORIS" --data "lorismysqluser=lorisuser" --data
>>> "lorismysqlpassword=neopass" --data "frontenduser=lorisuser" --data
>>> "frontendpassword=1234" http://localhost/installdb.php > error2.html
>>>
>>> If i normally execute installdb.php on the browser, there is no problem.
>>>
>>> Thanks
>>>
>>>
>>>
>>> Στις Παρ, 31 Ιαν 2020 στις 4:39 μ.μ., ο/η Cecile Madjar <
>>> cecile.madjar at mcin.ca> έγραψε:
>>>
>>>> Hi Sotirios,
>>>>
>>>> Actually, is it possible that 'file' is not installed on your VM. I
>>>> misread the error in my earlier email and it might be crashing in MRI.pm at
>>>> line 1523 of your code. In that line, 'file' is used to determine if the
>>>> file is a DICOM, if not, it will show a warning and not count the file as a
>>>> DICOM. So in the end, none of your files are considered DICOM files and
>>>> when it comes to convert the list of DICOMs, there is nothing to convert,
>>>> hence the number of MINC file = 0.
>>>>
>>>> Anyway, I have a feeling this might be the issue you are having.
>>>>
>>>> Let me know how it goes,
>>>>
>>>> Cécile
>>>>
>>>> On Fri, Jan 31, 2020 at 9:23 AM Sotirios Nikoloutsopoulos <
>>>> sotirisnik at gmail.com> wrote:
>>>>
>>>>> Hi Ling,
>>>>>
>>>>> Yes it's Loris-mri 21.0. One thought i had is that maybe i should
>>>>> define root as linux user?
>>>>> https://github.com/aueb-wim/LORIS-for-MIP/blob/master/docs/pics/loris_docker_imaging_install.png.
>>>>> But i see no difference either when i execute it as lorisadmin.
>>>>>
>>>>> Also here are the files we use
>>>>> https://github.com/aueb-wim/LORIS-for-MIP/tree/master/mri_loris
>>>>>
>>>>> And here is the complete output of the batch execution.
>>>>>
>>>>> 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 35
>>>>> /data/incoming/DCC0000_956912_V1.tar.gz -verbose
>>>>>
>>>>>  find -path \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3 -name
>>>>> '__MACOSX' -delete
>>>>> xargs: file: No such file or directory
>>>>>
>>>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-14\-15\-z2B0N3
>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>>  Source: /data/tmp/ImagingUpload-14-15-z2B0N3
>>>>> Target: /data/loris/data/tarchive
>>>>>
>>>>> Testing for database connectivity.
>>>>> Database is available.
>>>>>
>>>>> You will archive the dir : ImagingUpload-14-15-z2B0N3
>>>>>
>>>>> You are creating a tar with the following command:
>>>>>
>>>>> tar -cf /data/loris/data/tarchive/ImagingUpload-14-15-z2B0N3.tar
>>>>> ImagingUpload-14-15-z2B0N3
>>>>>
>>>>>
>>>>> getting md5sums and gzipping!!
>>>>>
>>>>> * Taken from dir                   :
>>>>>  /data/tmp/ImagingUpload-14-15-z2B0N3
>>>>> * Archive target location          :
>>>>>  /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>>>>> * Name of creating host            :    172.28.1.1
>>>>> * Name of host OS                  :    Linux
>>>>> * Created by user                  :    lorisadmin
>>>>> * Archived on                      :    2020-01-31 14:15:04
>>>>> * dicomSummary version             :    1
>>>>> * dicomTar version                 :    1
>>>>> * md5sum for DICOM tarball         :
>>>>>  fcaf54e9078705799b10e08c4d34bf70  ImagingUpload-14-15-z2B0N3.tar
>>>>> * md5sum for DICOM tarball gzipped :
>>>>>  52c96cd08d168e659b5c73cb77b4621b  ImagingUpload-14-15-z2B0N3.tar.gz
>>>>> * md5sum for complete archive      :
>>>>>  f5103ec688a5921a37d3c95cba8598e0
>>>>>  DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>>>>>
>>>>> Adding archive info into database
>>>>>
>>>>>
>>>>> Removing temporary files from target location
>>>>>
>>>>>
>>>>> Done adding archive info into database
>>>>>
>>>>> \/data\/loris\/data\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>> -profile prod
>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2015\-09\-07_ImagingUpload\-14\-15\-z2B0N3\.tar
>>>>> -uploadID 35 -verbose
>>>>>  md5sum
>>>>> /data/loris/data/tarchive/DCM_2015-09-07_ImagingUpload-14-15-z2B0N3.tar
>>>>> PSCID is: DCC0000
>>>>>  CandID id: 956912
>>>>>  visit_label is: V1
>>>>> PSCID is: DCC0000
>>>>>  CandID id: 956912
>>>>>  visit_label is: V1
>>>>> candidate id 956912
>>>>> Set centerID = 1
>>>>> PSCID is: DCC0000
>>>>>  CandID id: 956912
>>>>>  visit_label is: V1
>>>>> PSCID is: DCC0000
>>>>>  CandID id: 956912
>>>>>  visit_label is: V1
>>>>> xargs: file: No such file or directory
>>>>>
>>>>> 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 $mail_user in concatenation (.) or string
>>>>> at /data/loris/bin/mri/batch_uploads_imageuploader.pl line 249.
>>>>> Can't exec "mail": No such file or directory at /data/loris/bin/mri/
>>>>> batch_uploads_imageuploader.pl line 249.
>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>> batch_uploads_imageuploader.pl line 250.
>>>>> print() on closed filehandle MAIL at /data/loris/bin/mri/
>>>>> batch_uploads_imageuploader.pl line 251.
>>>>>
>>>>> Στις Πέμ, 30 Ιαν 2020 στις 6:22 μ.μ., ο/η Ling Ma <lingyun.ma at mcin.ca>
>>>>> έγραψε:
>>>>>
>>>>>> Oh, I just found that you are using Loris-mri 21.0, as I stated in
>>>>>> the previous email, the "$_" could not find any matches, so your command
>>>>>> might not be correctly entered.
>>>>>>
>>>>>> On Thu, Jan 30, 2020 at 10:35 AM Ling Ma <lingyun.ma at mcin.ca> wrote:
>>>>>>
>>>>>>> Hi Sotirios,
>>>>>>>
>>>>>>> By curiosity, I just looked at the error message, "Use of
>>>>>>> uninitialized value $_ in pattern match (m//) at /data/loris/bin/mri/
>>>>>>> batch_uploads_imageuploader.pl line 144." clearly means that there
>>>>>>> is no match, but 144 line has no such code related with $_ in recent
>>>>>>> versions of the batch_uploads_imageuploader.pl. There is something
>>>>>>> in the line 165 for a few recent versions.
>>>>>>>
>>>>>>> As to "xargs: file: No such file or directory", it could be due to a
>>>>>>> command unable to find anything using the directory provided as the message
>>>>>>> suggested.
>>>>>>>
>>>>>>> In both cases, I feel that it could be helpful if you provide more
>>>>>>> details such as which Loris_MRI version you are running, what is the exact
>>>>>>> command line you are using to help supporters to understand.
>>>>>>>
>>>>>>> Thanks.
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Ling Ma
>>>>>>> Consultant
>>>>>>>
>>>>>>> On Wed, Jan 29, 2020 at 6:57 PM Sotirios Nikoloutsopoulos <
>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Cecile,
>>>>>>>>
>>>>>>>> it seems that xargs is already installed in our docker container.
>>>>>>>>
>>>>>>>> [image: image.png]
>>>>>>>>
>>>>>>>>
>>>>>>>> Στις Τετ, 29 Ιαν 2020 στις 7:59 μ.μ., ο/η Cecile Madjar <
>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>
>>>>>>>>> Hi Sotirios,
>>>>>>>>>
>>>>>>>>> It looks like xargs is not installed in your docker environment.
>>>>>>>>>
>>>>>>>>> This is being used by the following command in dicomTar.pl (and a
>>>>>>>>> few other places but that is the one causing the error at the moment):
>>>>>>>>>
>>>>>>>>> $cmd = "cd " . $dcm_source . "; find -type f -name '.*' | *xargs*
>>>>>>>>> rm -f";
>>>>>>>>>
>>>>>>>>> So you need to install xargs in your docker for the command to run.
>>>>>>>>>
>>>>>>>>> Hope this helps,
>>>>>>>>>
>>>>>>>>> Cécile
>>>>>>>>> On Wed, Jan 29, 2020 at 10:35 AM Sotirios Nikoloutsopoulos <
>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hello,
>>>>>>>>>>
>>>>>>>>>> We are making a dockerized version of Loris 21 and when we
>>>>>>>>>> execute the batch_uploads_imageuploader.pl we get an error about
>>>>>>>>>> xargs. What could be the casue?
>>>>>>>>>>
>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl line 144.
>>>>>>>>>> Running now the following command:
>>>>>>>>>> /data/loris/data//uploadNeuroDB/imaging_upload_file.pl -profile
>>>>>>>>>> prod -upload_id 13 /data/incoming/DCC0007_854380_V1.tar.gz -verbose
>>>>>>>>>>
>>>>>>>>>>  find -path \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml -name
>>>>>>>>>> '__MACOSX' -delete
>>>>>>>>>> xargs: file: No such file or directory
>>>>>>>>>>
>>>>>>>>>> dicomTar.pl \/data\/tmp\/ImagingUpload\-15\-31\-U_O5ml
>>>>>>>>>> \/data\/loris\/data\/tarchive\/ -database -profile prod -verbose
>>>>>>>>>>  Source: /data/tmp/ImagingUpload-15-31-U_O5ml
>>>>>>>>>> Target: /data/loris/data/tarchive
>>>>>>>>>>
>>>>>>>>>> Thanks
>>>>>>>>>>
>>>>>>>>>> Στις Τρί, 10 Δεκ 2019 στις 7:21 μ.μ., ο/η Sotirios
>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> έγραψε:
>>>>>>>>>>
>>>>>>>>>>> Hi,
>>>>>>>>>>>
>>>>>>>>>>> i opened an issue and looked up for the values of Volume they
>>>>>>>>>>> suggested https://github.com/BIC-MNI/minc-toolkit-v2/issues/95.
>>>>>>>>>>> The only attributes associated with it i saw are [0x00089206] and
>>>>>>>>>>> [0x00089207]
>>>>>>>>>>>
>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>
>>>>>>>>>>> I looked up for the file that was being viewed fine in the
>>>>>>>>>>> BrainBrowser and saw that it had that attribute empty so i used this
>>>>>>>>>>> command because i couldn't find a way to modify the attribute via pydicom
>>>>>>>>>>>
>>>>>>>>>>> dcmodify -ma "(0008,9206)=" *.dcm
>>>>>>>>>>>
>>>>>>>>>>> and that command reported the warning about the Endian Syntax. I
>>>>>>>>>>> also used the corresponding command for 9207 and got the message "Tag not
>>>>>>>>>>> found'
>>>>>>>>>>>
>>>>>>>>>>> Lastly I tried to upload some dicoms and now i am getting the
>>>>>>>>>>> SNR and i can view them fine. I believe now that all of them will pass
>>>>>>>>>>> successfully, i will report back later.
>>>>>>>>>>>
>>>>>>>>>>> Thanks,
>>>>>>>>>>>
>>>>>>>>>>> Sotirios
>>>>>>>>>>>
>>>>>>>>>>> Στις Δευ, 9 Δεκ 2019 στις 8:10 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>
>>>>>>>>>>>> The issue you are having is a indeed a dcm2mnc issue. The
>>>>>>>>>>>> converter does not seem to work on your dataset for some reason.
>>>>>>>>>>>> Unfortunately, there is not much we can do on our front to fix this...
>>>>>>>>>>>>
>>>>>>>>>>>> I would recommend creating an issue on the MINC tools
>>>>>>>>>>>> repository <https://github.com/BIC-MNI/minc-toolkit-v2/issues> so
>>>>>>>>>>>> they can fix your problem.
>>>>>>>>>>>>
>>>>>>>>>>>> Very sorry that you are having that problem.
>>>>>>>>>>>>
>>>>>>>>>>>> Best,
>>>>>>>>>>>>
>>>>>>>>>>>> Cécile
>>>>>>>>>>>>
>>>>>>>>>>>> On Wed, Dec 4, 2019 at 8:59 AM Cecile Madjar <
>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Could you please share a dataset with us that produces the
>>>>>>>>>>>>> error you get and the weird display in BrainBrowser? You could use the same
>>>>>>>>>>>>> SFTP credential that Nicolas gave you.
>>>>>>>>>>>>>
>>>>>>>>>>>>> The message errors you got from imaging_install.sh are
>>>>>>>>>>>>> probably due to the fact that you reran the install script and it tried to
>>>>>>>>>>>>> reinstall something that was already there. I would not worry about it.
>>>>>>>>>>>>> FYI, the only thing you needed to do was to update the MINC tools path in
>>>>>>>>>>>>> the environment file as you did after re-running imaging_install.sh and
>>>>>>>>>>>>> source the environment file.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Best,
>>>>>>>>>>>>>
>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Wed, Dec 4, 2019 at 8:03 AM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>>  Hi Cecile,
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> We used minctool 1.9.7 and we still get this error
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> <<Restructuring...
>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>> noise_estimate --snr /data/loris/data>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> One dicom folder hadn't that error and is being viewed fine
>>>>>>>>>>>>>> in the BrainBrowser of Loris.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>> When i used dpkg to the 1.9.17 the installation reported fine
>>>>>>>>>>>>>> <<Unpacking minc-toolkit-v2 (1.9.17) over (1.9.16) ...>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> and then i used source
>>>>>>>>>>>>>> /opt/minc/1.9.17/minc-toolkit-config.sh
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> and aftewards runned bash ./imaging_install.sh just to be
>>>>>>>>>>>>>> sure.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> We also had to modify /data/loris/bin/mri/environment because
>>>>>>>>>>>>>> it still pointed to the old version.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> What i found strange is this during the run of
>>>>>>>>>>>>>> imaging_install.sh
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> <<already using interpreter
>>>>>>>>>>>>>> /data/loris/bin/mri/python_virtualenvs/loris-mri-python/bin/python3
>>>>>>>>>>>>>> Please use the *system* python to run this script
>>>>>>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>>>>>>   File
>>>>>>>>>>>>>> "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 2632, in
>>>>>>>>>>>>>> <module>
>>>>>>>>>>>>>>     main()
>>>>>>>>>>>>>>   File
>>>>>>>>>>>>>> "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 870, in main
>>>>>>>>>>>>>>     symlink=options.symlink,
>>>>>>>>>>>>>>   File
>>>>>>>>>>>>>> "/usr/local/lib/python3.5/dist-packages/virtualenv.py", line 1156, in
>>>>>>>>>>>>>> create_environment
>>>>>>>>>>>>>>     install_python(home_dir, lib_dir, inc_dir, bin_dir,
>>>>>>>>>>>>>> site_packages=site_packages, clear=clear, symlink=symlink)
>>>>>>>>>>>>>>   File
>>>>>>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>>>>>>> line 357, in abspath
>>>>>>>>>>>>>>     if not isabs(path):
>>>>>>>>>>>>>>   File
>>>>>>>>>>>>>> "/data/loris/bin/mri/python_virtualenvs/loris-mri-python/lib/python3.5/posixpath.py",
>>>>>>>>>>>>>> line 64, in isabs
>>>>>>>>>>>>>>     return s.startswith(sep)
>>>>>>>>>>>>>> AttributeError: 'NoneType' object has no attribute
>>>>>>>>>>>>>> 'startswith'
>>>>>>>>>>>>>> Installing the Python libraries into the loris-mri
>>>>>>>>>>>>>> virtualenv...
>>>>>>>>>>>>>> Requirement already satisfied: mysqlclient in
>>>>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (1.4.4)
>>>>>>>>>>>>>> Requirement already satisfied: mysql-connector in
>>>>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (2.2.9)
>>>>>>>>>>>>>> Requirement already satisfied: pybids in
>>>>>>>>>>>>>> ./python_virtualenvs/loris-mri-python/lib/python3.5/site-packages (0.9.4)
>>>>>>>>>>>>>> Requirement already satisfied: nibabel>=2.1 in
>>>>>>>>>>>>>> ./python_virtua>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> So should i open an issue for that error? or is there
>>>>>>>>>>>>>> something else to try?
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Στις Τρί, 3 Δεκ 2019 στις 10:39 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Does the pic screenshot in the imaging browser module also
>>>>>>>>>>>>>>> shows 1 slice? If so, that would mean there was an issue with the dcm2mnc
>>>>>>>>>>>>>>> conversion. Once again, installing the latest version of the MINC tools
>>>>>>>>>>>>>>> should help but if this issue persists I would recommend creating an issue
>>>>>>>>>>>>>>> for that too on their repository
>>>>>>>>>>>>>>> <https://github.com/BIC-MNI/minc-toolkit-v2/issues> (if not
>>>>>>>>>>>>>>> already reported there, there are a few known issue reported).
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Other viewer for MINCs are register and Display (both part
>>>>>>>>>>>>>>> of the MINC tools). For NIfTI, you have FSLeye, MRICron and probably many
>>>>>>>>>>>>>>> other viewers that exists.
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> On Tue, Dec 3, 2019 at 3:26 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Yes, Nifti files are mandatory for our work. From what we
>>>>>>>>>>>>>>>> saw at a 3rd vm we setted up, the nifti files are being created ( i haven't
>>>>>>>>>>>>>>>> verified if that is the case at the 2nd vm ). I will install the latest
>>>>>>>>>>>>>>>> version and will report back, but do you know any nifti/minc viewer?
>>>>>>>>>>>>>>>> because the Brainbrowser of Loris does not output them well, it's like it
>>>>>>>>>>>>>>>> is loading only 1 slice and we would like to verify it with another tool
>>>>>>>>>>>>>>>> too. We verified that the dcmconv command didn't affect
>>>>>>>>>>>>>>>> the quality of the .dcm files.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Στις Δευ, 2 Δεκ 2019 στις 6:59 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> It looks like for some reason your binary mnc2nii is not
>>>>>>>>>>>>>>>>> working and reports that error. Do you want to create NIfTI files or are
>>>>>>>>>>>>>>>>> you happy with just the MINC files?
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> If you don't need the NIfTI files, then maybe you can set
>>>>>>>>>>>>>>>>> the Config setting "NIfTI file creation" to No instead of
>>>>>>>>>>>>>>>>> Yes and this error will not appear anymore.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> If you need the NIfTI files to be created, then I would
>>>>>>>>>>>>>>>>> recommend installing the latest version of the MINC tools (1.9.17). They
>>>>>>>>>>>>>>>>> can be found there:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>    - pre-built packages:
>>>>>>>>>>>>>>>>>    https://packages.bic.mni.mcgill.ca/minc-toolkit/
>>>>>>>>>>>>>>>>>    - from the source code with installation instructions
>>>>>>>>>>>>>>>>>    in the README:
>>>>>>>>>>>>>>>>>    https://github.com/BIC-MNI/minc-toolkit-v2
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> If the problem persists by using the latest release of
>>>>>>>>>>>>>>>>> MINC tools, then create an issue on Github for the MINC developers
>>>>>>>>>>>>>>>>> here <https://github.com/BIC-MNI/minc-toolkit-v2/issues>.
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>> On Fri, Nov 29, 2019 at 8:06 PM Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks to Nicholas i was able to create all the mincs
>>>>>>>>>>>>>>>>>> images. The problem was that the files were in Little-Endian-Implicit
>>>>>>>>>>>>>>>>>> transfer syntax and i had to convert them Little-Endian-Explicit transfer
>>>>>>>>>>>>>>>>>> syntax with this command
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> find <root_of_my_DICOM_files_directory> -type f | xargs
>>>>>>>>>>>>>>>>>> -i dcmconv --write-xfer-little {} {}
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Looking back at our mails i saw that Little-Endian error
>>>>>>>>>>>>>>>>>> had occurred when i used dcmodify, but i switcthed to using pydicom instead.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> In the output i see an error sometimes about "gsl:
>>>>>>>>>>>>>>>>>> bessel_I0.c:216: ERROR: overflow". Is this okay?
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Restructuring...
>>>>>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>>>>>> noise_estimate --snr
>>>>>>>>>>>>>>>>>> /data/loris/data//assembly/959679/V1/mri/native/loris_959679_V1_t1_001.mnc
>>>>>>>>>>>>>>>>>> SNR is:
>>>>>>>>>>>>>>>>>> gsl: bessel_I0.c:216: ERROR: overflow
>>>>>>>>>>>>>>>>>> Default GSL error handler invoked.
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>> Στις Τετ, 27 Νοε 2019 στις 4:29 μ.μ., ο/η Cecile Madjar <
>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thank you for the details!
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> A few things to try:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>    - modify the TMPDIR to be on your /data directory
>>>>>>>>>>>>>>>>>>>    where there might be more space to do processing (could create a /data/tmp
>>>>>>>>>>>>>>>>>>>    where the temporary files would be created)
>>>>>>>>>>>>>>>>>>>    - how many files are there for that upload in
>>>>>>>>>>>>>>>>>>>    tarchive_files? Are they different from the ones showing the warning
>>>>>>>>>>>>>>>>>>>    message?
>>>>>>>>>>>>>>>>>>>       - FYI: query to get that: SELECT tf.* FROM
>>>>>>>>>>>>>>>>>>>       tarchive_files tf JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>>>>>>       - how many series are there for that upload in
>>>>>>>>>>>>>>>>>>>    tarchive_series?
>>>>>>>>>>>>>>>>>>>    - FYI: query to get that: SELECT ts.* FROM
>>>>>>>>>>>>>>>>>>>       tarchive_series ts JOIN mri_upload USING (TarchiveID) WHERE UploadID=<your
>>>>>>>>>>>>>>>>>>>       uploadID> (the output of that query would be very
>>>>>>>>>>>>>>>>>>>       useful if you can provide it)
>>>>>>>>>>>>>>>>>>>    - things are failing when the scripts try running
>>>>>>>>>>>>>>>>>>>    the following command: find
>>>>>>>>>>>>>>>>>>>    /tmp/TarLoad-23-43-ccugaa/ImagingUpload-23-43-6JCOTO -type f  |
>>>>>>>>>>>>>>>>>>>    /data/loris/bin/mri/dicom-archive/get_dicom_info.pl
>>>>>>>>>>>>>>>>>>>    -studyuid -series -echo -image -file  -attvalue 0018 0024 -series_descr
>>>>>>>>>>>>>>>>>>>    -stdin | sort -n -k1 -k2 -k7 -k3 -k6 -k4  | cut -f 5 | dcm2mnc -dname ''
>>>>>>>>>>>>>>>>>>>    -stdin -clobber -usecoordinates /tmp/TarLoad-23-43-ccugaa
>>>>>>>>>>>>>>>>>>>       - clearly the problems come from get_dicom_info.pl
>>>>>>>>>>>>>>>>>>>       but I cannot pinpoint the error yet. I will ask around and get back to you
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> If I cannot figure it out remotely, is there a way to
>>>>>>>>>>>>>>>>>>> have a call using zoom? This way you could share your screen with me and
>>>>>>>>>>>>>>>>>>> run the debugger on that script and hopefully we can figure out what is
>>>>>>>>>>>>>>>>>>> going on with those datasets?
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Thanks!
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 5:17 PM Sotirios
>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> In both my virtual machines
>>>>>>>>>>>>>>>>>>>> export TMPDIR=/tmp
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> In both vm also with dcm2mnc i get this output. Just to
>>>>>>>>>>>>>>>>>>>> verify that this passed in my 1st vm and produced mincs.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> I attached the spool as a csv.
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> And also one difference i found was this in the
>>>>>>>>>>>>>>>>>>>> Loris-mri code ( left 1st workable vm, right 2nd vm that has to be fixed,
>>>>>>>>>>>>>>>>>>>> although i changed it seems to be independent of the uninitialized value $_
>>>>>>>>>>>>>>>>>>>> )
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Thanks,
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>> Στις Τρί, 26 Νοε 2019 στις 11:34 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> that is puzzling... A few additional questions:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>    - what is the bash variable TMPDIR set to on the
>>>>>>>>>>>>>>>>>>>>>    environment file?
>>>>>>>>>>>>>>>>>>>>>    - could you try running separately dcm2mnc on the
>>>>>>>>>>>>>>>>>>>>>    DICOM folder to see if that works?
>>>>>>>>>>>>>>>>>>>>>    - could you send us the detailed log from the
>>>>>>>>>>>>>>>>>>>>>    notification spool table (SELECT * FROM notification_spool WHERE
>>>>>>>>>>>>>>>>>>>>>    UploadID=<your uploadID>) and send it back to us? Maybe there are some
>>>>>>>>>>>>>>>>>>>>>    additional clues that could help figuring out what is going on.
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Thank you!
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 26, 2019 at 10:12 AM Sotirios
>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> I checked for the StudyInstacueUID at the files with
>>>>>>>>>>>>>>>>>>>>>> "The target directory does not contain a single DICOM file"" and their
>>>>>>>>>>>>>>>>>>>>>> attribute has a value.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Regarding the scouter and localizer, i modified the
>>>>>>>>>>>>>>>>>>>>>> settings in the imaging pipeline and now i don't get that error message,
>>>>>>>>>>>>>>>>>>>>>> but still it doesn't create the mnics.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> The errors i am getting are ( uninitialized value $_
>>>>>>>>>>>>>>>>>>>>>> is not important? because i haven't got comments about that )
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $_ in pattern match (m//)
>>>>>>>>>>>>>>>>>>>>>> at /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> line 144.
>>>>>>>>>>>>>>>>>>>>>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>> imaging_upload_file.pl -profile prod -upload_id 134
>>>>>>>>>>>>>>>>>>>>>> /data/incoming/DCC0025_118008_V1.tar.gz -verbose
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> and
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Number of MINC files that will be considered for
>>>>>>>>>>>>>>>>>>>>>> inserting into the database: 0
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> No data could be converted into valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> The tarchiveLoader.pl insertion script has failed.
>>>>>>>>>>>>>>>>>>>>>> Use of uninitialized value $mail_user in
>>>>>>>>>>>>>>>>>>>>>> concatenation (.) or string at /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 249.
>>>>>>>>>>>>>>>>>>>>>> Can't exec "mail": No such file or directory at
>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> line 249.
>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> line 250.
>>>>>>>>>>>>>>>>>>>>>> print() on closed filehandle MAIL at
>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>> line 251.
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>> Στις Δευ, 25 Νοε 2019 στις 5:22 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> OK. So the issue I mentioned should not be a problem
>>>>>>>>>>>>>>>>>>>>>>> for you.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Is the StudyInstanceUID DICOM header set in your
>>>>>>>>>>>>>>>>>>>>>>> images? If it is not set, then you would end up with the error message "The
>>>>>>>>>>>>>>>>>>>>>>> target directory does not contain a single DICOM file". So maybe this is
>>>>>>>>>>>>>>>>>>>>>>> the issue you are having with those datasets?
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Regarding not excluding series descriptions, you can
>>>>>>>>>>>>>>>>>>>>>>> configure that in the Config module under the Imaging Pipeline section.
>>>>>>>>>>>>>>>>>>>>>>> Simply remove all entries for the "Series description to exclude from
>>>>>>>>>>>>>>>>>>>>>>> imaging insertion" setting.
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>> On Mon, Nov 25, 2019 at 9:58 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> We are using this version
>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/archive/v21.0.0.zip.
>>>>>>>>>>>>>>>>>>>>>>>> Is it possible to insert low resolution now?
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>> On Mon, 25 Nov 2019, 16:53 Cecile Madjar, <
>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Which version of LORIS-MRI are you using?
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> There was a bug that got resolved in 20.2 in
>>>>>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl. Basically, if a DICOM did not
>>>>>>>>>>>>>>>>>>>>>>>>> have the (0020,0032) header, get_dicom_info.pl
>>>>>>>>>>>>>>>>>>>>>>>>> considered that the file was not a DICOM, which was a mistake. This got
>>>>>>>>>>>>>>>>>>>>>>>>> fixed in version 20.2 of LORIS-MRI. Hopefully this is the issue you are
>>>>>>>>>>>>>>>>>>>>>>>>> encountering.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> About scout and localizer, they are a type of
>>>>>>>>>>>>>>>>>>>>>>>>> short and low resolution sequence that is used by the tech but is of no
>>>>>>>>>>>>>>>>>>>>>>>>> interest scientifically, which is why we tend to no insert them.
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>> On Sat, Nov 23, 2019 at 7:28 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> i executed the find command and the output i got
>>>>>>>>>>>>>>>>>>>>>>>>>> per folder was "DICOM medical imaging data. Maybe there is something wrong
>>>>>>>>>>>>>>>>>>>>>>>>>> with the find command in the warning that it is unable to check if the file
>>>>>>>>>>>>>>>>>>>>>>>>>> is a dicom file? Also when i use
>>>>>>>>>>>>>>>>>>>>>>>>>> get_dicom_info.pl i don't get any output data.
>>>>>>>>>>>>>>>>>>>>>>>>>> Finally i don't understand what scout or localizer is ( something like if
>>>>>>>>>>>>>>>>>>>>>>>>>> and only if a file fails then the whole session is invalid? ).
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τρί, 19 Νοε 2019 στις 9:40 μ.μ., ο/η Cecile
>>>>>>>>>>>>>>>>>>>>>>>>>> Madjar <cecile.madjar at mcin.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> I took a closer look to the
>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploader_multiple_output.txt file you sent. It looks like there are
>>>>>>>>>>>>>>>>>>>>>>>>>>> different reasons for failure depending on the DICOM folder uploaded.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>    - For 465466 DCC0000 V1; 727195 DCC0004 V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>    and 684908 DCC0007 V1: it looks like there is no file of type DICOM in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>    folder. Have you checked to see if that is indeed the case? Maybe you can
>>>>>>>>>>>>>>>>>>>>>>>>>>>    try running the following command on that folder to see what are the types
>>>>>>>>>>>>>>>>>>>>>>>>>>>    of the files? If it does not return at least one DICOM medical imaging data
>>>>>>>>>>>>>>>>>>>>>>>>>>>    file, then that is why you get the error message from the pipeline:
>>>>>>>>>>>>>>>>>>>>>>>>>>>       -
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>       find <my_dicom_archive_root_folder> -type f | xargs -i file {}|cut -d: -f2|sort|uniq
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>       - For 864173 DCC0001 V1: it looks like
>>>>>>>>>>>>>>>>>>>>>>>>>>>    there are two different DICOM studies within the same folder. You will need
>>>>>>>>>>>>>>>>>>>>>>>>>>>    to split that study in two based on the StudyUID field as the insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>    pipeline does not allow for more than one StudyUID per upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>    - For 890807 DCC0002 V1; 637025 DCC0005 V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>    and 239975 DCC0006 V1: it looks like the dcm2mnc command did not produce
>>>>>>>>>>>>>>>>>>>>>>>>>>>    any MINC files. Can you check in the DICOM archive what are the series
>>>>>>>>>>>>>>>>>>>>>>>>>>>    present in the tarchive for that visit? Maybe only a scout or localizer was
>>>>>>>>>>>>>>>>>>>>>>>>>>>    acquired for that session, hence the no valid MINC files (scout and
>>>>>>>>>>>>>>>>>>>>>>>>>>>    localizer being skipped for the conversion)
>>>>>>>>>>>>>>>>>>>>>>>>>>>    - For 397410 DCC0003 V1: it looks like
>>>>>>>>>>>>>>>>>>>>>>>>>>>    everything went well for this one.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> One script that is called by our pipeline is
>>>>>>>>>>>>>>>>>>>>>>>>>>> called get_dicom_info.pl and this does all kind
>>>>>>>>>>>>>>>>>>>>>>>>>>> of checks on the DICOM files (it is being called when running the dcm2mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>> conversion). You could run it independently on your folder if needed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Since one of the study got in, it does not look
>>>>>>>>>>>>>>>>>>>>>>>>>>> like you are having a problem with the setup. It seems more likely to be a
>>>>>>>>>>>>>>>>>>>>>>>>>>> problem with the data themselves.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Hope this helps.
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> Cécile
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 5:56 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> In my first vm i am able to create the minc
>>>>>>>>>>>>>>>>>>>>>>>>>>>> files and view them at the mri browser (except of candidate 102761034 ),
>>>>>>>>>>>>>>>>>>>>>>>>>>>> meanwhile the same files gives warnings at the 2nd vm. The output  of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch upload can be seen in the file attached.
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Also a colleague of us has built a
>>>>>>>>>>>>>>>>>>>>>>>>>>>> pre-validation tool for dicom
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/
>>>>>>>>>>>>>>>>>>>>>>>>>>>> which had found all the files that Loris gave as warning . Basically I
>>>>>>>>>>>>>>>>>>>>>>>>>>>> confirmed that the total amount of files per dicom was the same amount as
>>>>>>>>>>>>>>>>>>>>>>>>>>>> stated in Loris and checked some filenames given from warning to confirm
>>>>>>>>>>>>>>>>>>>>>>>>>>>> that they match with our tool. But that was months ago and my colleague had
>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed some parameters for MIP and now our tool doesn't find all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>> invalid files, that's why i asked for the dicom header specification of
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris. In a discussion we had he mentioned that he doesn't check for some
>>>>>>>>>>>>>>>>>>>>>>>>>>>> tags e.x. orientation. Lastly to mention that in my first vm i didn't use
>>>>>>>>>>>>>>>>>>>>>>>>>>>> our tool to remove invalid dcm files.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 13 Νοε 2019 στις 11:45 μ.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Can you provide us with some fresh particulars
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of the current issue and we'll take it from there?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yang's team has built these scripts which can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> definitely serve as a model for your pre-validation of your DICOM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> collections.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, Nov 13, 2019 at 4:23 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> HI Yang,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> We make use of pydicom library too. Now about
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the validate.py i see that you check if some attributes are missing such as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientID, PatientName which all of our files contains that info. Maybe i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have missed something on the setup of my other virtual machine ( although
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> one dicom passed on the new vm successfully, the others that were inserted
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> correctly on my old vm fails on the new one ), i think that i had asked
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> about this error "Use of uninitialized value $_ in pattern match (m//) at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl line 144."
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> but i don't remember the solution.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Στις Τετ, 13 Νοε 2019 στις 5:45 π.μ., ο/η
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yang Ding <it at cnbp.ca> έγραψε:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hey, Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christine from the LORIS team mentioned you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> had some issue with DICOM.  I am a fellow developer for an external project
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using LORIS, kind of just like you. We had to implement DICOM upload as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> well but more as a fully automated pipeline actually.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> While we were building CNBP, we had coded up
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> some minor Python functions to check DICOM integrity (and simple
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> validations) and you might be able to gain some inspiration from it and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> help you with your cause. For more comprehensive solution, PyDICOM (
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://pydicom.github.io/pydicom/stable/getting_started.html#)  seems
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> like a descent python package to help out with a lot of DICOM data checks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (I was essentially just building customized wrapper calls to them). You can
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> see some example scripts here as part of our DICOM submodule. It is pretty
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> rough around the edges but hopefully point you in the right direcitons
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/CNBP/DICOMTransit/blob/Dev/DICOMTransit/DICOM/validate.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cheers,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Yang Ding, PhD.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Canadian Neonatal Brain Platform Architect
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, Nov 12, 2019 at 8:29 AM <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-request at bic.mni.mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Send Loris-dev mailing list submissions to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To subscribe or unsubscribe via the World
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Wide Web, visit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or, via email, send a message with subject
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> or body 'help' to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-request at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You can reach the person managing the list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         loris-dev-owner at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> When replying, please edit your Subject
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> line so it is more specific
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> than "Re: Contents of Loris-dev digest..."
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Today's Topics:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>    1. Re: Import mri - scripts (Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ----------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Message: 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Date: Tue, 12 Nov 2019 15:28:26 +0200
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> From: Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> To: Cecile Madjar <cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Cc: loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Subject: Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Message-ID:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>         <CAKHj7uST=
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 92717of_4Npd6pt-gxnhoYAWMUnG8s8D2066kPsLQ at mail.gmail.com
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Content-Type: text/plain; charset="utf-8"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Could we send you a link with 10 anonymized
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dicom files to diagnose the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings we get?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ???? ???, 9 ??? 2019 ???? 12:38 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Hi Cecile,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > We were wondering whether Loris has a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tool to check if there are problems
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > with the dcm files, before trying to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> upload them. Something that could
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > provide the same results provided in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warning_output, this is the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > summary from the mri_upload at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> front-page. Also which attributes of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > dcm header would trigger a warning? is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> there a dcm file header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > specification for Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > ???? ???, 2 ??? 2019 ???? 12:07 ?.?., ?/?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Yes, by parsing now() into
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unix_timestamp function it worked,but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> thought that something else was causing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the 2nd issue.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> On Tue, 1 Oct 2019, 18:36 Xavier Lecours
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Boucher, Mr, <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> xavier.lecoursboucher at mcgill.ca> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The first error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> QCFirstChangeTime and columns are of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> type `unsigned integer` and not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `datatime`. You should be using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> UNIX_TIMESTAMP() instead of NOW().
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The second error occurs because the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> trigger triggers a rollback of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statement in the files table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See mysql documentation for trigger
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> error handling.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> An error during either a BEFORE or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AFTER trigger results in failure of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the entire statement that caused
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> trigger invocation.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you for sharing that. I hope it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> helps.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Xavier
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* October 1, 2019 8:33 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cecile.madjar at mcin.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> When mincs are inserted their
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> corresponding rows at the file table are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted too
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like to insert their rows at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file_qcstatus as well, because i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> don't want manually to label them as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> passed throught the interface
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That is the trigger i wrote
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> CREATE DEFINER = CURRENT_USER TRIGGER
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `LORIS`.`files_AFTER_INSERT` AFTER
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT ON `files` FOR EACH ROW
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> BEGIN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> INSERT INTO files_qcstatus
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET FileID = NEW.FileID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      SeriesUID = NEW.SeriesUID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      EchoTime = NEW.EchoTime,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCStatus = "Pass",
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCFirstChangeTime = NOW(),
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>      QCLastChangeTime = NOW();
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> END
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> although it contains some errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Out of range
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value for column
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'QCFirstChangeTime' at row 1 at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 823.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`parameter_file`, CONSTRAINT
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> `FK_parameter_file_1` FOREIGN KEY
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`FileID`) REFERENCES `files` (`FileID`))
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 848.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 1 ??? 2019 ???? 4:21 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In the mri_upload table, there is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> TarchiveID column associated with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the MRI upload you inserted. When this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value is NULL, it means no DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> were inserted into the tarchive tables.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> At the end of the insertion of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DICOMs in the tarchive tables, this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> value is updated with the correct
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TarchiveID associated with the upload.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Could this correspond to what you want
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to do?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Regarding the files_qcstatus, this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> table is only linked to the files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table (hence, the MINC files). You
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could always create a new table for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicom_qcstatus and link it to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchive table?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Oct 1, 2019 at 6:56 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i would like whenever a dicom is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imported to mark all their
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> coressponding qc_status to "pass". I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was thinking of creating a trigger for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that, but which tables do i need to add
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> entries to? So far from what i see
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i need to add entres at  the table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> "files" whenever an insertion happens to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files_qcstatus.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 4:04 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Oh, sorry i should have asked for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyID, at the beginning of my email
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i sent 3 hours ago (not StudyUID).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:55 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that's the Study Instance UID, not the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> StudyID. So the StudyID i am
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looking for is not stored in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 30 ??? 2019 ???? 3:38 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The StudyUID is stored in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DicomArchiveID field of the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tarchive table. It can also be found in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the metadata field but it is mixed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with many other information.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Mon, Sep 30, 2019 at 6:00 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is StudyUID stored somewhere at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tables? At the tarchive table,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> specifically at the AcquisitonMetadata
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> column i found something called
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 'Unique Study ID" in its context, but
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that must be the Study Instance UID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 27 ??? 2019 ???? 4:22 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Your observation is correct. A little
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explanation below.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> MINC files get inserted into the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> violation tables if:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - the scan type could not be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> identified (not matching an entry in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - one parameter of the scan type is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> out of the expected range
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    present in the mri_protocol_checks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (extra filtering in case you need to be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    stricker on some parameters not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> present in the mri_protocol table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - if the CandID and PSCID do not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> match
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following cases do not get in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MRI violation tables as it happens
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> before the conversion of the DICOM to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MINC files and only MINC files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> violations are logged there:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "No single DICOM" (since no valid
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DICOM could be found to convert
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    to MINC)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    - "Study already inserted"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (duplicate StudyUID) since this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>    happens at the dicomTar.pl level
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (way before conversion into MINC files)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad everything is working out!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 27, 2019 at 6:17 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the mri passed, for some reason it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> consumed 5.12GB of ram. Now about the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations, dicoms are triggered to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> be inserted there only if there is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a violation for Tr_min, Tr_max, in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> general for its header parameter?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Because i don't see the cases of 'No
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> single dicom" or with the 2 studyiuid
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to be there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 26 ??? 2019 ???? 5:07 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sorry to hear you are having issues
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the memory. I think most of our
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> VMs are set up with 4GB of RAM so with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 4GB you should be fine.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> C?cile
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Thu, Sep 26, 2019 at 9:48 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about that dicom that had that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insertion error it's about 30mb and when
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> it is being processed the ram is being
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> drastically increased from 2gb to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3.28 and then the whole virtual machine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> is frozen. What is the recommended
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> size of ram for using Loris?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 11:24 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Cecile Madjar <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> cecile.madjar at mcin.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to see that the StudyUID problem
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> was fixed!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the delete script issue, if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> absolutely certain that no
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> processes are run for that uploadID,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you can update the mri_upload table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and set the column Inserting to 0
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> instead of 1 for that uploadID. It
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like for some reason the scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> did not update this field when it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stopped the insertion. Not sure why
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that would be the case though.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Note: only do that update if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> certain that there is no processing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> happening.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this helps!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 24, 2019 at 11:57 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> about the Dicoms i reported that didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have a StudyID they actually do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I thought that this might be a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> permission because "w" was missing at the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> group. After using chmod -R 775 only
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 102809579 passed, but with no mnic
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> files. Also now i have this error
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> :/data/loris/bin/mri/tools$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 34 -ignore
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cannot delete upload 34: the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pipeline is currently processing it.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How can solve this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 24 ??? 2019 ???? 2:30 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Here is our auto dicom uploading python
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> script:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To give you a brief idea:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Per folder it will:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 1) Delete all the .bak files
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 2) Locate .dcm files and update the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Patient header
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3) Furthermore we are interesting in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> finding TR_min, TR_max, TE_min,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> TE_max parameters of T1 protocol and do
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> an update at the mri_protocol table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aueb-wim/DataQualityControlTool/blob/loris1/mipqctool/dicom_uploader.py#L205
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For some reason some files are missing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription/ProtocolName
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> In total i have 7 folders
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3/7 passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Also about the first patient with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DC0000 had a violation "T1 AXIAL SE
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GADO", but my script didn't output a TE
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of 17 nowhere and i find that weird
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> since Loris detects the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SeriesDescription.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Now about the 4/7 that didn't passed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102327840 and 102809579 outputs "The
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> target directory does not contain a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> single DICOM file.", therefore they are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> missing their StudyUID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 102506134 has 2 studyuid "You can't use
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> it with data from multiple
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> studies."
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and 102761034 "No data could be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> converted into valid MINC files.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> localizer, scout will not be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered!" What is this?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i wanted to force the insertion of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 102327840, 102809579 and 102506134
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> can i just pass a flag parameter to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl? or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> modify imaging_upload_file.pl?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thank you,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To diagnose a folder search the name of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the folder at dicom_output.txt.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:54 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear about your progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, the script you used to delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging data is fully documented here
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/81bae73ea6e86c9498519dadf574468ee1d992ca/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- let us know if you didn't find the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> answers you were looking for there.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (Is it possible the null row in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> *mri_scanner* seen in your database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> management software is a visual
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> placeholder for you as the user?  I'm not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sure why a scanner would ever be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered with ID='0' as your screenshot
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> showed.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 20, 2019 at 9:45 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I fixed it with this
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 4:37 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I tried to create a new candidate using
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the API, is there something
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> wrong with the structure? why did i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> receive a 500 internal error? In the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-error log it state that there is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> something wrong with token, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verfied that the type of the token is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> string.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [Fri Sep 20 16:35:26.874732 2019]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [php7:error] [pid 4535] [client
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 127.0.0.1:59674] PHP Fatal error:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Uncaught TypeError: Argument 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> passed to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SinglePointLogin::JWTAuthenticate() must be of the type string,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> null given, called in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 169 and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> defined in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc:192\nStack
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> trace:\n#0
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc(169):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SinglePointLogin->JWTAuthenticate(NULL)\n#1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc(171):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SinglePointLogin->authenticate()\n#2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/APIBase.php(73):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> NDB_Client->initialize('/var/www/loris/...')\n#3
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(44):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris\\API\\APIBase->__construct('POST')\n#4
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/htdocs/api/v0.0.2/Candidates.php(244):
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris\\API\\Candidates->__construct('POST', Array)\n#5 {main}\n  thrown in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/SinglePointLogin.class.inc on line 192
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 20 ??? 2019 ???? 2:39 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is there a way also to delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates? Just to let you know what i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> did to clear candidates, because maybe
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> i may have missed dependencies.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> First i deleted all their uploads
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ./delete_imaging_upload.pl -uploadID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 13 etc ( is there a way to omit
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the backup file ? )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Afterwards i had some scanner
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates, so i deleted all the entries
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> from mri_scanner except that i couldn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> delete this entry with the 0 ID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Lastly i deleted the session and then
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the candidate table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 19 ??? 2019 ???? 7:57 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We recommend that you use our existing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tools for creating new candidates
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> - either the LORIS API or if you are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> using a PHP script, by calling the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> class's createNew()
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/php/libraries/Candidate.class.inc#L200
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >function.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These will create the necessary records
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for you.  (It's not recommended to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> make direct modifications to mysql
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> database tables in your script, if I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> understand you.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The CandID should be a randomized 6
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> digit randomized ID, and there are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> multiple reasons for this.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use the PSCID for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> project-specific IDs and the External ID field
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> in the candidate table can also be used
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for any values you like.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Additionally, any number of custom IDs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> can be added in parallel - these
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> are entered/visible in the Candidate
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Information module and added in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> back-end as candidate parameters.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Tue, Sep 17, 2019 at 7:31 PM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> We are building a script that will auto
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insert the candidates based on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> their ExternalID. We would like to know
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> whethere when we are creating a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> profile in the candidate table, if we
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also have to insert a new record at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> another table? Furthermore is there a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem that in our case CandID won't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> be a 6digit? ( should we start it from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 100000?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 5:38 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> That would normally be the case but the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> numeric part of the PSCID get
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> paded with 0 on the left.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ex. for sequential ID made of center ID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of `ABC` plus 4 numerical char
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> with a min value of 1, the sequence
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> would be:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0002
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ABC0010
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> thus sorting them ascending will always
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> get the latest value generated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as the max value.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:* Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 10:15
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> melanie.legault2 at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see, although the PSCID value is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> varchar(255), it must be stored
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> within a specific length of characters.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Otherwise if we were to sort
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> strings with different lengths the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> result would not be sorted correctly (
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x. 1,2,10,11 as strings would result
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to 1, 10, 11, 2 ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 13 ??? 2019 ???? 4:52 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Melanie Legault, Mrs <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> melanie.legault2 at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hello Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There is no `last value` stored
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> anywhere.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The code simply look for the PSCID with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the max value and increase that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> value by 1 in order to generate the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> next PSCID.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hope this info help.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> M?lanie Legault | Software developer |
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Faculty of Medicine | McGill
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> University
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 3801 University, Montr?al, QC H3A 2B4
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *From:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev-bounces at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris-dev-bounces at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> on behalf of Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Nikoloutsopoulos <sotirisnik at gmail.com>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Sent:* September 13, 2019 9:43
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *To:* Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Cc:* loris-dev at bic.mni.mcgill.ca <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> loris-dev at bic.mni.mcgill.ca>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *Subject:* Re: [Loris-dev] Import mri -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> scripts
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> how does Loris determine the next
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> available PSCID value for a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Project-Customization
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> e.x in the default case the PSCID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sequential, but where do we store the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> last value for the sequential sequence?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 10 ??? 2019 ???? 4:00 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the parameters in the mri_protocol you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have assigned are global
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> standard? or were assigned after trial
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and error?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 10:11 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Given you have done the initial setup
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> of your tables to match your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> intended protocol/parameters according
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> to instructions --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the Troubleshooting guide documentation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> recommends
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md#a4-insertion-script-troubleshooting-notes
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> re-running the pipeline (and first
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> deleting prior uploads).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Sun, Sep 8, 2019 at 10:22 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *if i were to change their status to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resolve what would happen?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 5:12 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I noticed that i can view the mnics at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the brainbrowser from the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_violations page ( those mnics are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> stored at /data/loris/data/trashbin/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> if i were to click their issue to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> resolve what would happend? would they
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> appear in the dicom_archive view too? ).
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 8 ??? 2019 ???? 4:17 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The defaut values of the schema exists
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in my local database. If i adjust
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the default values of TR_min and TE_min
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mincs will be uploaded?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 5:48 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Is it possible that you haven't set up
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> your mri_protocol table ?   (and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_scan_type table too, for additional
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> types of scans)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Like the psc table, this is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pre-requisite for the Imaging insertion
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> setup : See the install/setup
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> documentation :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To add new rows, just use MySQL insert
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> statements.  You can adapt the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> insert statements which load the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> default table values --> e.g. Here on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> GitHub :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/SQL/0000-00-00-schema.sql#L718
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (see also the mri_scan_type table)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:32 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I see that i can edit the values but
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not how to insert new rows.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If i choose Inserted with flag then
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> will the minc be inserted?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:21 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear that *dcmodify* worked
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> correctly.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the MRI Violations module, the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> screenshot is enough.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It says "could not identify scan type",
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> which we knew already.  Did you
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> click on the link on those words?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It will take you to the next page of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the module, showing for each scan
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> what the scan parameters were, and will
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> also show for comparison what's
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> stored in your *mri_protocol* table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Compare these values to find which
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> parameter was not correct according
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to your *mri_protocol* table scan type
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> definitions.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You may end up broadening your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_protocol value ranges (e.g. TR, TE)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> for scans.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This can be done in the front-end, by
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> editing the database table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> directly in the same subpage of the MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Violations module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The MRI Violations module features are
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> explained in more detail in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Help text for this module inside LORIS
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (click the  ["?"] icon in the menu
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> bar.)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> See also: Loris-MRI troubleshooting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/AppendixA-Troubleshooting_guideline.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> :  no MINCs inserted- violated scans
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 8:11 PM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> looks like my previous email's
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> attachment wasn't delivered due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> security reasons, i uploaded my file at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> google drive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://drive.google.com/file/d/1U_TRbo_qGgfpQfs-SqeG9J3bMMqNfUU4/view?usp=sharing
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 7 ??? 2019 ???? 3:02 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> From Dicat's view seems that dcmodify
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> worked in both cases
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For the mri_violations i attached the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> .html output from webbrowser, so
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that you can check the filelds easier.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 6 ??? 2019 ???? 7:49 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Great, sounds like more progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> About the dcmodify command -- I'm not
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sure why you're getting an Endian
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> warning.  (it's a warning not an error,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> correct?)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> To clarify -- Were the DICOM headers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (PatientName) all successfully
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> relabelled, after the command ran?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You can use also our DICAT tool (
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/DICAT) to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> verify and/or update local DICOM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> headers -- though your dcmodify command is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a great and fast solution for bulk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> header updates.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you're concerned about fields being
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> changed (e.g. "(2001,105f)" from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> the warning message)  - you can also
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> dcmdump a DICOM slice before and look
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at these fields specifically.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's also not a bad "sanity check" to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> backup your DICOMS before/after
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> running dcmodify, and use dcmdump on
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> each version to diff the outputs --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> this will pinpoint what changed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Re the protocol violation --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> AcquisitionProtocol not recognized or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> unknown :   this means your scans did
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> not match what is stored in your
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> mri_protocol table.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Check the MRI Violations front-end
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> module -- can you see why they didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> match?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Send us an example, in addition to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> contents of the mri_protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> table, if you can't find the source of
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mismatch.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Fri, Sep 6, 2019 at 12:04 PM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Here is the psc table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I created 2 candidates profiles through
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the interface
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> then runned dcmodify command to a dicom
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify -ma
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName="DCC0000_258024_V1"
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /home/lorisadmin/DICOMS/000535670/501/*.dcm
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and got those warning: is this okay?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1402) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,140f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2001,105f) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> W: Found element (2005,1083) with VR UN
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and undefined length, reading a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sequence with transfer syntax
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> LittleEndianImplicit (CP-246)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dcmodify at another Dicom didn't show
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> warnings. Below you can see the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution for the second dicom. Mnics
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> could not be inserted due to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> AcquisitionProtocol being unknown.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Running now the following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri//uploadNeuroDB/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging_upload_file.pl -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -upload_id 12
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> /data/incoming/DCC0001_602102_V1.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  find -path
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs -name '__MACOSX'
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -delete
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> dicomTar.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/tmp\/ImagingUpload\-18\-36\-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> \/data\/loris\/data\/tarchive\/
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -database -profile prod -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  Source: /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Target: /data/loris/data/tarchive
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Testing for database connectivity.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Database is available.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will archive the dir :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You are creating a tar with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> following command:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> tar -cf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> getting md5sums and gzipping!!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-36-mTrxXs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-06 18:36:50
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> b1dcdc8903dd2d9a5443227db2aa2814
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> aeae87f20155a6805f7e0cfe5212ea5f
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-36-mTrxXs.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1d9258d1f077ebc49111ab7ba22a8d6e
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Removing temporary files from target
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> location
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Done adding archive info into database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/bin\/mri\//uploadNeuroDB/tarchiveLoader.pl -globLocation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -profile prod
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> \/data\/loris\/data\/tarchive\/\/DCM_2016\-08\-22_ImagingUpload\-18\-36\-mTrxXs\.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -uploadID 12 -verbose
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  md5sum
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2016-08-22_ImagingUpload-18-36-mTrxXs.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Set centerID = 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Number of MINC files that will be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> considered for inserting into the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> database: 2
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-31ajWx.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log dir is /data/loris/data//logs and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> log file is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data//logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PSCID is: DCC0001
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  CandID id: 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  visit_label is: V1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate id 602102
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Cleaning up temp files: rm -rf
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/ImagingUpload-18-36-mTrxXs*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> cat
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/logs/TarLoad-18-37-fanZFj.log
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> Loading file from disk
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> mapping DICOM parameter for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/TarLoad-18-37-to5pYZ/dcc0001_602102_v1_20160822_072406_205e1d1_mri.mnc
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> computing md5 hash for MINC body.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --> md5:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 02022dda60d9de429340fec838f50cfe
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ==> verifying acquisition protocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Acquisition protocol is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>   --> The minc file cannot be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> registered since the AcquisitionProtocol
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> is unknown
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 10:46 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Sure -- you can delete imaging datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> with the *delete_imaging_upload*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> script --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> details here:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/scripts_md/delete_imaging_upload.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> What's in your *psc* table?  (Is it
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> properly populated? This is a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> pre-requisite to loading imaging data.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/docs/02-Install.md#221-database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The foreign key constraint error on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidate record is curious.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> There are also a few options for
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> creating candidates when inserting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> imaging data:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 1 : in 2 steps with the API
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> then DICOM insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> a. via the LORIS API -- Create the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> candidates (and visits, optionally I
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> think)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/blob/master/docs/API/LorisRESTAPI.md#30-candidate-api
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ensure you get the DCCID/CandID
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> assigned by LORIS.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Then as a second step:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> b. Use the imaging insertion pipeline
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/05-PipelineLaunchOptions.md#51---pipeline-launch-options-for-dicom-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to load your DICOMs.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> You will want to first ensure that the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> PatientName header in the DICOMs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> as well as tar package are correctly
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> labelled with PSCID_DCCID_VisitLabel
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> -- Method 2: for BIDS-format datasets:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How to :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/master/docs/05-PipelineLaunchOptions.md#52---pipeline-launch-for-bids-datasets
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Be sure to use the *-c* and *-s*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> options when running the bids_import script,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> to automatically create your candidates
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> and sessions.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 11:43 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> How do i delete a Study? And everytime
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> do i have to create a new
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> candidate to get DCCID and a PSCID?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *First execution:*
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> DBD::mysql::db do failed: Cannot add or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> update a child row: a foreign
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> key constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`RegistrationCenterID`)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> REFERENCES `psc` (`CenterID`)) at
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ERROR: Failed to insert record in table
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> mri_scanner:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The following database commands failed:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PREPARE s FROM 'INSERT INTO mri_scanner
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> SET
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Medical Systems';
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Error obtained:Cannot add or update a
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> child row: a foreign key
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> constraint fails
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1`
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> FOREIGN KEY (`CandID`) REFERENCES
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> `candidate` (`CandID`)) (error code 1452)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ERROR: The validation has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Either re-run the validation again
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> and fix the problem. Or re-run
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> tarchiveLoader.pl using -force to force the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> execution.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The tarchiveLoader.pl insertion script
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> *And second execution: *
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> (loris-mri-python)
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin at loris-VirtualBox:/data/loris/bin/mri$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -profile prod < ~/Desktop/input.txt >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> log.txt
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Use of uninitialized value $_ in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> pattern match (m//) at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 144.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> PROBLEM:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The user 'lorisadmin' has already
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> inserted this study.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The unique study ID is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> '1.3.51.0.1.1.10.49.10.222.1422753.1420953'.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> This is the information retained from
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the first time the study was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> inserted:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Taken from dir                   :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /tmp/ImagingUpload-18-33-Qq7HGy
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archive target location          :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/data/tarchive/DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of creating host            :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 127.0.1.1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Name of host OS                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Linux
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Created by user                  :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisadmin
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * Archived on                      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 2019-09-04 18:33:05
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomSummary version             :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * dicomTar version                 :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 1
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball         :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 4a301b0318178b09b91e63544282364d
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for DICOM tarball gzipped :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 9d95ea2b9111be236808bfd65d7e65ec
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>  ImagingUpload-18-33-Qq7HGy.tar.gz
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> * md5sum for complete archive      :
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ab19a86357f1d4053aa3b81c8a071053
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DCM_2012-12-05_ImagingUpload-18-33-Qq7HGy.tar
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Last update of record:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The dicomTar.pl execution has failed.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Can't exec "mail": No such file or
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> directory at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> batch_uploads_imageuploader.pl line
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 249.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 250.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> print() on closed filehandle MAIL at ./
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> batch_uploads_imageuploader.pl
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> line 251.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 5:35 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Ok, this sounds like good progress.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Let us know when you next encounter
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> issues as you progress through the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Imaging Install/Setup docs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/minor/docs/02-Install.md
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I'll look into how we can better handle
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the incoming/ directory next
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> time.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 10:23 AM
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /data/loris/bin/mri/dicom-archive/.loris_mri/database_config.py is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> populated correctly except its port is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 'port'    : ''. Also i have tested
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that i can connect to MySQL with
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> lorisuser.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> I executed the script again, because
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the only error i had previously was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> that the /data/incoming folder didn't
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exist and there are no errors
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> reported back except of warnings
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <<mysql: [Warning] Using a password on the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> command line interface can be
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> insecure>>.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:53 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's possible -- if the script was
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> unable to connect to the database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> during its execution (e.g. typo in the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> password), that would explain the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> underpopulated Image path and Loris-MRI
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> code path you saw in the Config
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> It's hard to tell without seeing the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> output from your script run -- Did
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you see a sign of any such error?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> The Config fields are populated by the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh script (starting
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> at line 222
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris-MRI/blob/21.0-dev/imaging_install.sh#L222
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> )
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> For example, check if the database
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> connection information was populated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> accurately in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> $mridir/dicom-archive/.loris_mri/database_config.py
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 9:34 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Christine,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> If you are referring to the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> imaging_install.sh here is an image with the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> configurations i typed. Maybe the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> problem is somewhere at the last part
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> which asks to configure as much as
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> possible automatically?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 4:16 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Christine Rogers, Ms. <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi Sotirios,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Glad to hear your LORIS core install is
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> up and working and all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> front-end pages are loading.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > lorisadmin at loris-VirtualBox:/var/www/loris$
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> chmod 775 project
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > and the web interface worked.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Yes, it's important that project/ have
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 775 permissions and that
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> lorisadmin be part of the sudoers
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> group, per step 1 in the install
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Readme <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris#install-steps
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> > As for the Paths, LORIS-MRI code and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Image should change LORIS to
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> loris, right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> These imaging paths will be updated
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> during your imaging installation
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> by an automated script --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you do not need to set them manually
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> via the Config module.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Please continue to follow the Setup
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Guide
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/aces/Loris/wiki/Setup>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for detailed steps to follow.
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Best,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Christine
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> On Wed, Sep 4, 2019 at 8:05 AM Sotirios
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> wrote:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> As for the Paths, LORIS-MRI code and
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Image should change LORIS to loris,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> right?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> [image: image.png]
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> ???? ???, 4 ??? 2019 ???? 2:28 ?.?.,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ?/? Sotirios Nikoloutsopoulos <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sotirisnik at gmail.com> ??????:
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Hi,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> i used
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> curl -sL
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://deb.nodesource.com/setup_8.x |
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sudo -E bash -
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> sudo apt-get install -y nodejs
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> /0/#inbox/FMfcgxwGBmlrdRDRSFqvSfhPwxLQTrhM>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> you had suggested in the past, make
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> worked and now i can see all the
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> contents in the web-interface, but i
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> don't need make install?
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Thanks
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill Centre for Integrative
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Neuroscience | MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -------------- next part --------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> An HTML attachment was scrubbed...
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> URL: <
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> http://mailman.bic.mni.mcgill.ca/pipermail/loris-dev/attachments/20191112/edc06953/attachment.html
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> End of Loris-dev Digest, Vol 64, Issue 16
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> *****************************************
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> christine.rogers at mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill Centre for Integrative Neuroscience |
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MCIN.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Montreal Neurological Institute
>>>>>>>>>>>>>>>>>>>>>>>>>>>>> McGill University | Montreal | Canada
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev mailing list
>>>>>>>>>>>>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> _______________________________________________
>>>>>>>> Loris-dev mailing list
>>>>>>>> Loris-dev at bic.mni.mcgill.ca
>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev
>>>>>>>>
>>>>>>>
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