Try setting SUBJECTS_DIR to the full path rather than just ./
On 10/21/2016 03:03 PM, Russ, Brian (NIH/NIMH) [E] wrote:
Hi,
I’m attempting to use FreeSurfer to create a set of surface and flat maps for use with some macaque data. Using a number of programs prior to FreeSurfer I have created a skull-stripped T1 image and White Matter mask and then successfully used FreeSurfers mksubjdirs, mri_convert, mri_fill, etc, through to mris_inflate to create a set of surfaces. After taking a break from the data I’ve come back to it to try and convert the surface maps into flattened maps. However, tksurfer is not recognizing the subjects directory.
Error: cannot find subject {subject} in ./{subject} input: setenv SUBJECTS_DIR ./ && tksurfer {subject} rh inflated
I can’t seem to find anyway to make FreeSurfer reindex the subject directory without running recon-all, which I don’t want to do as I had to manually edit the masks as this is a macaque data set, and the current surfaces are quite good.
Freesurfer version: free surfer-Linux v5.3.0
any help would be greatly appreciated.
Brian
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