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. > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
