[Loris-dev] Import mri - scripts
Christine Rogers, Ms.
christine.rogers at mcgill.ca
Wed Sep 4 15:46:19 EDT 2019
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<mailto: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<http://batch_uploads_imageuploader.pl> -profile prod < ~/Desktop/input.txt > log.txt
Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 144.
DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`RegistrationCenterID`) REFERENCES `psc` (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1060.
ERROR: Failed to insert record in table mri_scanner:
The following database commands failed:
PREPARE s FROM 'INSERT INTO mri_scanner (CandID,Model,Software,Serial_number,Manufacturer) VALUES (?,?,?,?,?)';
SET @x1='242126', at x2='Achieva', at x3='3.2.2\3.2.2.0', at x4='34037', at x5='Philips Medical Systems';
EXECUTE s USING @x1, at x2, at x3, at x4, at x5;
Error obtained:Cannot add or update a child row: a foreign key constraint fails (`LORIS`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) (error code 1452)
ERROR: The validation has failed. Either re-run the validation again and fix the problem. Or re-run tarchiveLoader.pl using -force to force the execution.
The tarchiveLoader.pl insertion script has failed.
Can't exec "mail": No such file or directory at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 249.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 250.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 251.
And second execution:
(loris-mri-python) lorisadmin at loris-VirtualBox:/data/loris/bin/mri$ ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> -profile prod < ~/Desktop/input.txt > log.txt
Use of uninitialized value $_ in pattern match (m//) at ./batch_uploads_imageuploader.pl<http://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<http://batch_uploads_imageuploader.pl> line 249.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 250.
print() on closed filehandle MAIL at ./batch_uploads_imageuploader.pl<http://batch_uploads_imageuploader.pl> line 251.
Στις Τετ, 4 Σεπ 2019 στις 5:35 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
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<mailto: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>>.
Στις Τετ, 4 Σεπ 2019 στις 4:53 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
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 $mridir/dicom-archive/.loris_mri/database_config.py
Best,
Christine
On Wed, Sep 4, 2019 at 9:34 AM Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> wrote:
Hi Christine,
If you are referring to the imaging_install.sh here is an image with the configurations i typed. Maybe the problem is somewhere at the last part which asks to configure as much as possible automatically?
Thanks
[https://lh5.googleusercontent.com/j0RRFnBHh5ePMY2WuojLIIsv8HZR46fvQUnNU9K0idwkhx_aEdCOMLKUnxI5lVupyRzSsP0weD2UNfywMc9VXykIOu0wJ1ao6cKNwlmJFrC3sJIXXAWT6aM7xHf-J134kCR0gbOs]
Στις Τετ, 4 Σεπ 2019 στις 4:16 μ.μ., ο/η Christine Rogers, Ms. <christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>> έγραψε:
Hi Sotirios,
Glad to hear your LORIS core install is up and working and all the front-end pages are loading.
> lorisadmin at loris-VirtualBox:/var/www/loris$ 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<mailto:sotirisnik at gmail.com>> wrote:
As for the Paths, LORIS-MRI code and Image should change LORIS to loris, right?
[image.png]
Στις Τετ, 4 Σεπ 2019 στις 2:28 μ.μ., ο/η Sotirios Nikoloutsopoulos <sotirisnik at gmail.com<mailto:sotirisnik at gmail.com>> έγραψε:
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
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christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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--
christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
--
christine.rogers at mcgill.ca<mailto:christine.rogers at mcgill.ca>
McGill Centre for Integrative Neuroscience | MCIN.ca
Montreal Neurological Institute
McGill University | Montreal | Canada
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