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 > <ayend...@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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
