command looks ok. Just using a slab would create 0s in a lot of places, but those 0s should get smoothed with other non 0s


On 05/09/2013 02:06 PM, Glen Lee wrote:

On Thu, May 9, 2013 at 11:28 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto: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'];

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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