Re: [Freesurfer] how to get the displacement from template to the linearly registered image

Hi Ping

the displacement fields are stored in m3z format in the file talairach.m3z. They are a vector field over the atlas that maps points in the atlas to points in the original (not linearly aligned) space.

cheers Bruce

On Wed, 28 Aug 2019, ping cao wrote:

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Dear expert，   I saw a paper mentioned this ：

              By using the  deformation field  from
              nonlinear registration, we can build the
              correspondence between voxels in the
              template and each linearly-aligned image.
              For instance, for each voxel (x, y, z) in
              the template image, we can find its
              corresponding voxel (x + dx, y + dy, z +
              dz) in each linearly-aligned image, where
              (dx, dy, dz) is the displacement from the
              template image to the linearly-aligned
              image defined by the deformation field. 

         

  So, I want to get the deformation field from the template to the
  linearly registered image(flirt_T1). 

Can Freesurfer do this?  Which file is a linearly registered image that does not contain an affine transformation? How can I get this deformation field?

  Your help is greatly appreciated.  

Best, ping