Re: [Freesurfer] Fwd: gray matter/csf surface reconstruction

Hi Shani

you should be able to use mri_vol2surf. It takes a projfrac or projdist option to select how far out or in along the normal you want to sample.

cheers Bruce

On Sat, 29 Oct 2011, Shani Ben Amitay wrote:

Hi , I have a  diffusion weighted dataset and I would like to perform an analysis along the cortical normals.

Any advice will be appreciated

Thanks, shani

On Sun, Oct 23, 2011 at 5:04 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Shani

  we described in in the recon1 NeuroImage paper (1999) and the
  PNAS paper, I think the next year. We don't impose any
  constrains on the pial surface as it evolves from the white
  surface (e.g. "link" terms in the energy functional), but let
  the vertices move whereever they want to in order to find an
  image intensity that is what we estimate the gray/csf boundary
  to be in that region.

  Can you tell us a bit about what you want to do with the
  normals? We typically don't use them for sampling of hires data
  for example, but rather use mris_expand to generate a series of
  intermediate surfaces.


  cheers
  Bruce

On Sun, 23 Oct 2011, Shani Ben Amitay wrote:

  Dear freesurfers,
  In order to generate cortical vector normals connecting
  homologous vertices
  of the inner and outer surface, I would like to better
  understand how the
  gray matter/csf surface is reconstructed and how
  correspondence between
  inner and outer surfaces is achieved.

  Does anyone can explain or give a reference?

  Thanks ,
  Shani

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