Salil, can you run fslregister with --debug as the first option, capture the terminal output, and send it to me? thanks doug
On 03/07/2013 09:02 PM, Anastasia Yendiki wrote:
Hi Salil - I'm cc-ing Doug who may be able to help. The error happens when bbregister invokes fslregister, in this particular line of fslregister: set refvol = `stem2fname $SUBJECTS_DIR/$subjid/mri/$fsvol`
When run on brainmask.mgz, it returns "ERROR: could not determine file".
a.y
On Wed, 6 Mar 2013, Salil Soman wrote:
Thank you for your email. Changing the mask option got me past the error I was having initially, but now I get these new errors:
mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
ter.30396/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/WCA_0226_T1_FS/mri/ERROR:/mnt/glusterfs/salsoman/output/TRACULA/WCA_0226_T1_FS/dmri/xfms/tmp.bbregis
ter.30396/fslregister/refvol.fslregister.nii
Thank you for your consideration.
Best wishes,
-S
On Wed, Mar 6, 2013 at 1:15 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:
Hi Salil - The problem is that you've set dob0 = 1 but you haven't set b0mlist and b0plist, so it doesn't know where to find your field maps to do the B0 unwarping.
a.y