Hi Karen

I guess I would do it in matlab - load the face parcellation and the aparc.annot, then count the number of vertices in each parcel in the face parcellation that is in a non-cortical aparc.annot parcel, and set a threshold for discarding them.

cheers Bruce

On Wed, 2 Apr 2014, Karen Marie Sandø Ambrosen wrote:

Hi Bruce,

How can I remove the non-cortical parcels from the annotation file created by mris_make_face_parcellation, such that I obtain an annotation file with approx. the same number of parcels as ?h.aparc.annot.

Best, Karen

On 04/01/2014 02:05 PM, Bruce Fischl wrote: Hi Karen

  sorry, I don't think so. You could certainly discard parcels
  that have a substantial non-cortical component to them, but
  parcellating the remainder of the surface uniformly isn't
  trivial.

  cheers
  Bruce
  On Tue, 1 Apr 2014, Karen Marie Sandø Ambrosen wrote:

        Hi Freesurfer experts,

        I first parcellated the ?h.aparc.annot using the
        mris_divide_parcellation and at first glance it
        seems fine. However, I
        experienced that the size of the regions varies a
        lot. I then found the
        mris_make_face_parcellation, that parcellate the
        surface in regions of
        more equal sizes. Unfortunately the
        mris_make_face_parcallation uses the
        whole surface including the medial wall. Is there
        any way I can get rid
        of the labels covering the medial wall and obtain a
        parcellation with
        the same number of vertices as ?h.apac.annot, but
        with regions of equal
        size?

        Best,
        Karen
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