Hi Nazanin
the nonlinear registration is actually to our segmentation atlas (*.gca). I guess you could try using something else, but you should extract a mean intensity image from the gca as a target, not the MNI305. You can do this with:
mri_convert -nth 0 <file>.gca mean_gca.mgz
FYI, this:
mri_convert -nth 1 <file>.gca labels_gca.mgz
would give you the highest prior label at each spot (and 2 would give you the prior)
cheers Bruce
On Mon, 30 Oct 2017, N Saf wrote:
Dear Experts, In the volume-based stream, if I'm right the FreeSurfer does two registration with MNI305 ,one affine and one nonlinear , is it possible to perform the nonlinear registration somewhere else and then use the result in FreeSurfer and run the rest of the analysis ?
thank's alot for your great support.
BRG, Nazanin