Hi Keith

the average white/pial surface doesn't have any topological or smoothness constraints, which is why we don't really use it. Yes, mris_expand is slow, but that's precisely because it prohibits self-intersection. The good nes is that compared to the rest of the recon stream it doesn't add that much time :)

Bruce

On Sat, 6 Apr 2013, Keith Jamison wrote:

I have seen that the official recommendation for making a mid-gray surface
is to use mris_expand.  This seems to be a very slow procedure on my
machine.  I have also tried just loading the ?h.white and ?h.pial surfaces
into matlab, averaging their vertices, and exporting the result.  This seems
to result in a nearly identical surface as mris_expand.  On a test subject,
only 48 out of 127,998 (0.0375%) vertices differed by more than 0.1mm, and
these were almost entirely around the edges of the corpus callosum. 

Is there a reason this alternative is a bad idea?  I imagine mris_expand
does additional topology checks along the way, but if the vertices vary so
little, can that be a major problem?

I'm inclined to go with the faster solution, but since I'm relatively new to
this procedure, I wanted to see what the community's experience might be.

Thanks!
Keith

_______________________________
Keith Jamison
Graduate Research Assistant

Department of Biomedical Engineering
University of Minnesota
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