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

ps. Please remember to send to the list and not to me directly. That way others can benefit from the exchange and the record goes into our mail archive.

On 05/09/2013 11:07 AM, Glen Lee wrote:

Hi Doug

See below for the command line that I used.

smoothK=4;

mri_surf2surf --hemi lh --s fsaverage_sym --fwhm ' ...
                    num2str(smoothK) ' --cortex --sval ' Functional_dir Subj '/GLM/all_base-sym_R.mgh '...

On Wed, May 8, 2013 at 11:31 PM, Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    Hi Glen, can you give us more information about what you did? Eg,
    command line?
    doug



    On 5/8/13 8:53 PM, Glen Lee wrote:

    Hello freesurfer experts,

    I'm a newbie for freesurfer and would like to ask a naive question.

    I've just applied smoothing onto a single surface mgh file using
    mri_surf2surf (with fwhm ==4) and examined the values in the
    output map.

    As it turns out, values become 0 in a number of vertices after
    smoothing while those in many other vertices look normal (i.e.,
    more or less similar to the values in the vertex of unsmoothed map).
    I'm not sure why this happened as smoothing average values
    locally within the kernel (4mm).

    Any helpful answers would be greatly appreciated.

    Glen

    p.s) fyi, the original EPI is a slap data covering only the
    temporal & occipital cortex.








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