Dear Doug,
We have encountered errors running preproc-sess (FSFAST v5.1) command with the flag "-per-session". The command line is
on machine adapt (same result on machine avml) cd /space/adapt/1/users/raij/AVISI_FSFAST5.1/avml07 setenv SUBJECTS_DIR /space/adapt/1/users/tapsya/subject_MRIs setenv SUBJECT avml07 nmr-std-env (=FS 5.1)
preproc-sess \ -sf subjectname -df sessdir \ -mni305 \ -per-session \ -sliceorder siemens \ -fsd bold \ -fwhm 5 \
The error message: ... stc-sess Done avml07 To MNI305 ---------------- rawfunc2tal-sess -fwhm 5 -s avml07 -d /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1 -fsd bold -stc siemens -update -subcort-mask ---------------- 1/1 avml07 1/1 avml07 002 ---------------- "ERROR: could not determine file for /autofs/space/adapt_001/users/raij/AVISI_FSFAST5.1/avml07/bold/002/fmcpr.siemens"
Hence it looks like rawfunc2tal-sess is searching for -per-run files (stem fmcpr*) rather than -per-session files (stem fmc*).
We tried to take control over the stems and added the following lines:
-mcin f \ -mcout fmc \ -stcin fmc \ -stcout fmcstc \ -smin fmcstc \ -smout fmcstcsm5 \
OR (modern naming conventions):
-mcin f -mcout fmc -stcin fmc -stcout fmc.siemens \ -smin fmc.siemens \ -smout fmc.siemens.sm5.mni305.2mm \
However, these resulted in the same error.
We also tried this on a more recent data set and received the same error.
In summary, it appears that rawfunc2tal-sess (and in fact also rawfunc2surf-sess) expect the stem fmcpr even when we use per-session (where they should expect the stem fmc).
Any help would be greatly appreciated!
Best regards,
Tapsya