I think Andrew H might have a way to do this, but he's on vacation until
next week. Try back then.
On 3/5/2020 12:29 PM, Ardesch, D.J. wrote:
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Dear FreeSurfer experts,
I am working on some monkey data and trying to get an accurate
nonlinear transform to talairach space (talairach.m3z in the -careg
stage). The problem is that the monkey brains look so different from
the human brain that this registration ends up being very far off,
even with an accurate talairach.lta.
As an alternative, I did a two-stage nonlinear registration using ANTs
(first from subject to a macaque template and then from macaque
template to talairach), which gives an accurate nonlinear transform.
However, I can’t seem to convert this nonlinear transform file
correctly from .nii.gz to the .m3z format that FreeSurfer needs to
continue down the pipeline.
How would one go about converting the nonlinear transform from ANTs to
a correct .m3z file?
Some other things I tried:
* I have tried a workaround in which I applied the inverse ANTs
transform to the first frame of RB_all_2016-05-10.vc700.gca to get
the talairach volume in subject space, and then ran
mri_ca_register on that volume to obtain a talairach.m3z. That
transform works but is still not accurate enough unfortunately.
* The nonlinear transform itself seems correct because when I apply
it to the movable volume using ANTs the results are similar to:
mri_convert movable.mgz –apply_transform talairach.m3z -oc 0 0 0
movable_in_talairach.mgz
where movable.mgz is the talairach volume in subject space and
talairach.m3z is the transform made by mri_ca_register.
The dimensions, orientation, and voxel size of
movable_in_talairach.mgz and my own transformed volume are identical.
Any help would be greatly appreciated!
Platform: MacOS Mojave
Version: FreeSurfer 6.0.0
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