[Loris-dev] Issue uploading segmentations

Mon Aug 15 13:21:47 EDT 2022

Hi Cécile,

I have indeed a different version from v23.0. This is the version of the MRI.pm I’m using right now:

https://github.com/SPINEProject/Loris-MRI/blob/master/uploadNeuroDB/NeuroDB/MRI.pm

I believe I used this after a fix you wrote.

As you pointed out the inputs for the function findScannerID in the file MRI.pm has changed as I don’t have the parameter $register_new which is why the $db is zero:

https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/register_processed_data.pl#L264

https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/NeuroDB/MRI.pm#L938

I will upgrade my code to the v23.0-release and test. I’ll keep you posted.

Best,
Alfredo.

On Aug 8, 2022, at 5:02 PM, Morales Pinzon, Alfredo <AMORALESPINZON at BWH.HARVARD.EDU<mailto:AMORALESPINZON at BWH.HARVARD.EDU>> wrote:

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Dear LorisDev team,

I am uploading segmentations to images already uploaded into LORIS using the script "register_processed_data.pl". I have used this script before but now I'm getting the following errors:

===
Use of uninitialized value $patientName in pattern match (m//) at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112.
Use of uninitialized value $patientName in pattern match (m//) at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112.
Attribute (db) does not pass the type constraint because: Validation failed for 'NeuroDB::Database' with value 0 (not isa NeuroDB::Database) at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Moose/Object.pm line 24
       Moose::Object::new('NeuroDB::objectBroker::MriScannerOB', 'db', 0) called at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 961
       NeuroDB::MRI::findScannerID(undef, undef, undef, undef, 0, 'REF(0x3ca3fc0)', 0, 'NeuroDB::Database=HASH(0x3d7c8b0)') called at /anom_project/bin/mri/uploadNeuroDB/register_processed_data.pl line 266
Argument "8Exiting now\n\n" isn't numeric in right bitshift (>>) at /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310.
Argument "\nAn error occurred when running register_processed_data..." isn't numeric in right bitshift (>>) at /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310.
0fileLikeName:%710881_m00_t1c%
===

This is command line I'm executing:
===
register_processed_data.pl  -profile prod  -sourcePipeline T2Vol  -tool T2Vol  -pipelineDate 2022-08-08  -coordinateSpace ISPC-t2w  -outputType ct2f  -inputFileIDs 571801  -sourceFileID 571801  -scanType ct2f  -file /anom_project/file.mnc.gz
===

I am using v23.0 of Loris-MRI and LORIS v23.0.2.

Any ideas on how can I solve this issue? Do I have to upgrade Loris-MRI?

Best regards,
Alfredo.
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