pet-surface pipeline will crash when folder names are too long (macOS)

[alexandreroutier]

Hi,

When running pet-surface on macOS (Mojave), I noticed that pet-surface or pet-surface-longitudinal pipeline is crashing when the pipeline is executed on very long path.

gtmseg from FreeSurfer (6.0) will crash without any clear indications about the error:

Abort
ERROR: mri_gtmseg --s sub-ADNI011S4105_ses-M00 --usf 2 --o gtmseg.mgz --apas apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo
gtmseg exited with errors
Standard error:
Saving result to '/Users/alexandre.routier/PET-Surface-WithVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryLongPath/in/caps/subjects/sub-ADNI011S4105/ses-M00/t1/freesurfer_cross_sectional/sub-ADNI011S4105_ses-M00/tmp/tmpdir.xcerebralseg.50819/tmpdir.fscalc.53505/tmp.mgh' (type = MGH )                       [ ok ]
Saving result to '/Users/alexandre.routier/PET-Surface-WithVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryLongPath/in/caps/subjects/sub-ADNI011S4105/ses-M00/t1/freesurfer_cross_sectional/sub-ADNI011S4105_ses-M00/tmp/tmpdir.xcerebralseg.50819/tmpdir.fscalc.53727/tmp.mgh' (type = MGH )                       [ ok ]
Saving result to '/Users/alexandre.routier/PET-Surface-WithVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryVeryLongPath/in/caps/subjects/sub-ADNI011S4105/ses-M00/t1/freesurfer_cross_sectional/sub-ADNI011S4105_ses-M00/tmp/tmpdir.xcerebralseg.50819/tmpdir.fscalc.53946/tmp.mgh' (type = MGH )                       [ ok ]
Return code: 1

Based on some runs, my feeling is that when working on shorter path, pet-surface* will work without issue. I will also investigate if this error occurs on Linux.

Best, Alex

[omar-rifai]

@MatthieuJoulot this is probably linked to the issue discovered on t1-freesurfer. Please create a separate issue linking to this one.