[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Fri Feb 7 10:44:23 EST 2020
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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