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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>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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