On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Does the cortex label have any holes in it and do the holes in your output correspond? Try it with out the --cortex flag.
doug
-> there was some improvement when I did smoothing after removed '-- cortex flag', such that the number of vertex with '0' was decreased from 35785 to 21898.

I piped in a slab EPI image (covering only temporal regions) to the freesurfer using mri_vol2surf function (see below for more details).

I'm guessing this has caused some holes (i.e., zero-value vertices) in labels during 2D reconstruction?

Or alternatively, do you see any problem in the command below?

mri_vol2surf --src ' Functional_dir Subj '/FUNCTIONAL/rabold' num2str(run) zero_digit num2str(TR) '.nii' ...

' --srcreg ~/DMPC/3D/data/' Subj '/ANATOMY_SPM/FS-register.dat --hemi rh --projfrac 0.5 --noreshape --o ~/DMPC/2D/data/' Subj '/MGH/rabold' num2str(run) zero_digit num2str(TR) '_R.mgh'];