Good to know. So, if we ever encounter a problem with a pial, white, or orig surface crossing the midline, we should first run -autorecon3 (if not already run, so as to generate the ?h.aparc.annot) and then reprocess from - finalsurfs onward, but without the -noaparc flag in the command for mris_make_surfaces?

Except, I just noticed that there doesn't actually appear to be any way to exclude the -noaparc flag from mris_make_surfaces via recon-all. That is, the default setting for NoAparcMakeSurf is 1, and the only flag in recon-all available for affecting this value is -noaparc-makesurf, which also sets NoAparcMakeSurf to 1.

Did you perhaps intend to NOT include -noaparc as a default flag in 'mris_make_surfaces', such that the default setting of NoAparcMakeSurf in recon-all should be 0 rather than 1?

thanks, Mike H.

On Fri, 2007-12-14 at 14:31 -0500, Bruce Fischl wrote:

Hi Mike,

if noaparc is not given, mris_make_surfaces will look for ?h.aparc.annot and read it in to determine what regions it should disable the deformation in to avoid crossing the midline.

cheers, Bruce

On Fri, 14 Dec 2007, Michael Harms wrote:

...

Hello, What is the role of the -noaparc flag in 'mris_make_surfaces' of FS v4?

thanks, Mike H.