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Hi Cécile,
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<div class="">I have indeed a different version from v23.0. This is the version of the MRI.pm I’m using right now:</div>
<div class=""><br class="">
</div>
<div class=""><a href="https://github.com/SPINEProject/Loris-MRI/blob/master/uploadNeuroDB/NeuroDB/MRI.pm" class="">https://github.com/SPINEProject/Loris-MRI/blob/master/uploadNeuroDB/NeuroDB/MRI.pm</a></div>
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</div>
<div class="">I believe I used this after a fix you wrote. </div>
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</div>
<div class="">As you pointed out the inputs for the function findScannerID in the file MRI.pm has changed as I don’t have the parameter <span style="color: rgb(36, 41, 47); font-family: ui-monospace, SFMono-Regular, "SF Mono", Menlo, Consolas, "Liberation Mono", monospace; font-variant-ligatures: normal; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 248, 197); text-decoration-thickness: initial;" class="">$register_new</span><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""> which
is why the $db is zero:</span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class="">
</span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><a href="https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/register_processed_data.pl#L264" class="">https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/register_processed_data.pl#L264</a></span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class="">
</span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><a href="https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/NeuroDB/MRI.pm#L938" class="">https://github.com/SPINEProject/Loris-MRI/blob/19f469cce904ebe93ba5f641533e4c0ef39fadab/uploadNeuroDB/NeuroDB/MRI.pm#L938</a></span></font></div>
<div class=""><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""> </span></font></div>
<div class="">
<div><font color="#000000" class="">I will upgrade my code to the v23.0-release and test. I’ll keep <span style="caret-color: rgb(0, 0, 0);" class="">you posted.</span></font></div>
<div><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class="">
</span></font></div>
<div><font color="#000000" class="">Best,</font></div>
<div><font color="#000000" class="">Alfredo.</font></div>
<div><font color="#000000" class=""><span style="caret-color: rgb(0, 0, 0);" class=""><br class="">
</span></font>
<blockquote type="cite" class="">
<div class="">On Aug 8, 2022, at 5:02 PM, Morales Pinzon, Alfredo <<a href="mailto:AMORALESPINZON@BWH.HARVARD.EDU" class="">AMORALESPINZON@BWH.HARVARD.EDU</a>> wrote:</div>
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<div class="">
<div class=""> External Email - Use Caution <br class="">
<br class="">
Dear LorisDev team,<br class="">
<br class="">
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:<br class="">
<br class="">
===<br class="">
Use of uninitialized value $patientName in pattern match (m//) at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112.<br class="">
Use of uninitialized value $patientName in pattern match (m//) at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 1112.<br class="">
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<br class="">
Moose::Object::new('NeuroDB::objectBroker::MriScannerOB', 'db', 0) called at /anom_project/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 961<br class="">
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<br class="">
Argument "8Exiting now\n\n" isn't numeric in right bitshift (>>) at /anom_project/bin/mri/uploadNeuroDB/run_insert_TransSegs_IPMSA.pl line 310.<br class="">
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.<br class="">
0fileLikeName:%710881_m00_t1c%<br class="">
===<br class="">
<br class="">
This is command line I'm executing:<br class="">
===<br class="">
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<br class="">
===<br class="">
<br class="">
I am using v23.0 of Loris-MRI and LORIS v23.0.2.<br class="">
<br class="">
Any ideas on how can I solve this issue? Do I have to upgrade Loris-MRI?<br class="">
<br class="">
Best regards,<br class="">
Alfredo.<br class="">
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