Instead of outputting the reconstruction to derivatives/, the invocation script code/fs_extract.sh hands over to the FS default $SUBJECTS_DIR at /applications/freesurfer/subjects/$SUBJ.
I think this is because we styled the internal variable as $DERIVS_DIR instead of $SUBJECTS_DIR
Instead of outputting the reconstruction to
derivatives/, the invocation scriptcode/fs_extract.shhands over to the FS default$SUBJECTS_DIRat/applications/freesurfer/subjects/$SUBJ.I think this is because we styled the internal variable as
$DERIVS_DIRinstead of$SUBJECTS_DIR