I was hoping the developers might be able to help with a problem I'm having with a sub-step of preproc-sess.
I executed the following:
preproc-sess -s FS_T1_501 -surface self lhrh -fwhm 6 -per-run -fsd bold
In the relevant output, I see mktemplate-sess completed, followed by a call to mkbrainmask-sess, which eventually reported:
# ---------- Using FSL's BET to Extract Brain------------------ # /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold bet.fsl /tmp/mkbrainmask_2623/in.nii /tmp/mkbrainmask_2623/brain -m -f 0.1 /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/remove_ext: not found /usr/local/freesurfer/bin/bet.fsl: 1: /usr/local/freesurfer/bin/bet.fsl: /bin/imtest: not found /usr/local/freesurfer/bin/bet.fsl: 153: [: =: unexpected operator /usr/local/freesurfer/bin/bet.fsl: 231: /usr/local/freesurfer/bin/bet.fsl: /bin/bet2: not found mri_binarize --i /tmp/mkbrainmask_2623/brain_mask.nii --min .01 --o /tmp/mkbrainmask_2623/brain_mask.nii niiRead(): error opening file /tmp/mkbrainmask_2623/brain_mask $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/chris/ubfs/cpmcnorg/openfmri/booth/FS_T1_501/bold cmdline mri_binarize --i /tmp/mkbrainmask_3238/brain_mask.nii --min .01 --o /tmp/mkbrainmask_3238/brain_mask.nii sysname Linux hostname wernickesarea machine x86_64 user chris
input /tmp/mkbrainmask_3238/brain_mask.nii frame 0 nErode3d 0 nErode2d 0 output /tmp/mkbrainmask_3238/brain_mask.nii Binarizing based on threshold min 0.01 max +infinity binval 1 binvalnot 0
It's not obvious from the tail end of the output that this didn't work out, but this process finished in just a couple of seconds (making it unlikely that any smoothing or slice time correction was performed), and there was no brain_mask.nii file to be found either in /tmp/ or in the session folder. Those "not found" errors seem relevant, but I can't imagine what to do about them.