[FIX] Fix t1-freesurfer pipeline handler #1240
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NicolasGensollen
merged commit 687a824
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aramis-lab:maint-0.8
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AliceJoubert
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Aug 22, 2024
* fix bad kwargs passing to pipeline handlers * use t1-freesurfer for name * fix handling of ignore_groups * fix special case for segmentationVolumes * add unit tests * trigger CI
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This PR fixes a couple bugs on the iotools
merge-tsvwhich occurs when providing a CAPS folder forT1Freesurfer.These bugs were introduced in #869 (from clinica
0.7.4).group_selectionwas not properly handledT1Freesurferpipeline has no groups in its CAPS and the metric extraction logic is thus a bit different. More precisely, the segmentation volume metrics were not extracted correctly.This PR proposes to add some basic fixes as well as some unit tests.