[Loris-dev] Import mri - scripts
Sotirios Nikoloutsopoulos
sotirisnik at gmail.com
Fri Jan 31 09:23:07 EST 2020
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
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>
>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> 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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