you can try mri_coreg with --dof 7
On 4/4/17 2:31 AM, Paolo wrote:
For further clarity, we want to evaluate the geometric distortions to
test how robust different sequences are to the local magnetic
filed/susceptibility variations.
So we want to keep the image as untouched as possible, but possibly
aligned for comparison.
Is there an option in FS to register an image with 7 DOF (global
rescale)? I am thinking of/mri_robust_register,/ for which I see 3, 6,
12 DOF (--transonly, default and --affine).
2017-03-31 19:59 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu
<mailto:fis...@nmr.mgh.harvard.edu>>:
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
<fis...@nmr.mgh.harvard.edu <mailto:fis...@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
<mailto: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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