[Loris-dev] Issue uploading segmentations

[Cecile Madjar]

Hi Alfredo,

Looking at the code of LORIS-MRI 23.0, I do not see why the $db variable is
not passed correctly to the function NeuroDB::MRI::findScannerID. The line
numbers in your log and the ones in the code seem to be different. Has
there been any code changes made?

What are the variables passed to the NeuroDB::MRI::findScannerID function
call in register_processed_data.pl and the variables expected by the
function NeuroDB/MRI.pm findScannerID? There might be some discrepancies
there?

Best,

Cécile

On Mon, Aug 8, 2022 at 5:03 PM Morales Pinzon, Alfredo <
AMORALESPINZON at bwh.harvard.edu> wrote:

> 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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