Re: [Freesurfer] lh.orig.nofix vs. lh.white

no, the smoothing is done irrespective of the intensity volume (in mris_smooth). The smoothness constraints in mris_make_surfaces are more sophisticated (they assume that the surfaces are well-fit by quadratic patches, not planes) and also move the surface to lie at large intensity gradients

On Wed, 4 Sep 2013, David Romano wrote:

Thanks, Doug; this helps me to formulate my second question better, which is:

2. Assuming that no change in intensity is necessary, would the files

lh.white, lh.area, and lh.curv produced by the mri_make_surfaces command (in the -white subsection of the -autorecon2 section) be the same as the files produced by the command

mri_smooth lh.orig lh.white?

(Note that I dropped the flag -nw, so this will produce lh.area and lh.curv files.)

Thanks again, David

On Wed, Sep 4, 2013 at 4:10 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

  lh.orig.nofix is the original tesselation without anything done
  to it.
  To get to lh.white, the defects are automatically corrected to
  create
  lh.orig. lh.orig is then refined with smoothness and intensity
  constraints to produce lh.white
  doug


  On 09/04/2013 07:07 PM, David Romano wrote:
  > Hi everyone,
  >
  > I've been trying to go through the various steps described on
  the page:
  >
  > http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
  >
  > and I'm trying to understand part of the -autorecon2 section,
  and in
  > particular,
  >
  > 1) how the lh.orig.nofix file that is produced by the end of
  the
  > -tessellate subsection is different from the the lh.white file
  that is
  > produced by the -white subsection, and
  >
  > 2) whether the area and curvature files produced by the
  command
  >
  >
  >
  >
  >

...

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