FSL command calls that fail are not printing errors to the terminal
The following command should fail because the output dir betx does not exist:
bet /Users/taylor/data/gui/bet/T1.nii.gz /Users/taylor/data/gui/betx/T1_brain.nii.gz -f 0.5 -g 0
/Users/taylor/fsl-6.0.6.5/share/fsl/bin/bet /Users/taylor/data/gui/bet/T1.nii.gz /Users/taylor/data/gui/betx/T1_brain.nii.gz -f 0.5 -g 0
The error message from bet is:
libc++abi: terminating due to uncaught exception of type NiftiIO::NiftiException: Error: cant open file /Users/taylor/data/gui/betx/T1_brain.nii.gz
/Users/taylor/fsl-6.0.6.5/bin/bet: line 399: 90656 Abort trap: 6 ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
that error does not appear in the terminal where fsl-desktop was launched, but it should!