Hi Doug:

 When you talk about zero out subcortical region, when does this zero

out happen? it should happen after register vertex into functional space, right? Then it happens before functional space interpolation or after interpolation?

It happens after interpolation.

 And one more question about the register.dat file used for this

process. whose resolution info is used in register.dat file ? the low resolution functional image (moving image) or high resolution anatomy image? Is the resolution of fsaverage is 2mm*2mm*0.15mm?

The low resolution (though those numbers are no longer used internally -- the resolution is obtained from the mov volume).

doug

Thanks much!

Jing

Date: Tue, 26 Apr 2011 17:11:45 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] about mri_vol2surf

Hi Jing, by default it does include all the non-cortical structures
in the medial wall, including any subcortical structures. If you
include --cortex in the command-line it zeros them out. The way it
works is that it goes through each vertex on the surface, gets the
RAS coordinate for that vertex, applies the registration matrix to
map it into the function space, then samples the function value
using nearest neighbor (can change to trilinear with --interp
trilin).



doug



On 4/26/11 1:51 PM, Jing Ming wrote:


  Hi Surfers:



    I am using mri_vol2surf to project fMRI result into the
  fsaverage surface. And the fMRI result may contain some
  subcortical regions, so, I wonder mri_vol2surf will automatically
  get rid of the subcortical region and only map cortical area into
  surface right? Is there any material about the mapping algorithm
  of mri_vol2surf? Thanks much!



  Jing

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