Re: [Freesurfer] Registration of both the brain and the "surf" files to the same template.

for volumes you can use either

mri_convert -at <transform>

or

mri_vol2vol.

For surfaces I think mris_transform should do the trick (and possibly mri_surf2surf, but I defer to Doug on this)

Bruce On Fri, 31 Mar 2017, Paolo wrote:

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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