Thank you for your answer. I don't want the transformation to distort my image. Is there a command to "apply" the transformation to both the files? Like: $ <some_command> brainmask.mgz brainmask_registered.mgz --apply_transf talairach.lta $ <some_command> lh.white lh_registered.white --apply_transf talairach.lta
I aim to do this an all subjects: will they be aligned between themselves after the process?
Thanks
2017-03-31 15:59 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Paolo
if a linear transform is sufficient for your purposes you could just use the talairach.lta in the subjects/transforms dir. If you want nonlinear you could use talairach.m3z, but it will distort things (of course)
cheers Bruce
On Fri, 31 Mar 2017, Paolo wrote:
TO: freesurfer@nmr.mgh.harvard.edu SUBJECT: Registration of both the brain and the "surf" files to the same
tem
plate. AIM: register e.g. brainmask.mgz and ?h.white for many subjects all to
the s
ame template, so that I can then take slices of brainmask.mgz and the
superi
mposed WM surface accross subjects and compare them, confident that they
are
well alligned. WHAT I TRIED: used mri_robust_register to register all the brainmask.mgz
ima
ges to a T1_1mm_template. I looked for the respective "surface" template
to
register the surfaces, and maybe use mri_surf2surf, cannot find a
"surface"
template that corresponds to the "T1" template. Ideally I would like to
use
the same .lta transformation BOTH for the T1 image and the surface. As I
und
erstand (?) they have a different mesh-transformation matrix. Best regards, Paolo
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