Hi Noam,
This should be a two step procedure, rather than a one-step procedure.
Here's a previous email I sent to the list about warping Choi's
striatum atlas to individual subject's striatum (which I have modified
for the cerebellum for you). Let us know if this works.
1) Assuming you are quite happy with the freesurfer cerebellum
parcellation in your subjects, then I am assuming freesurfer nonlinear
registration (talairach.m3z) is working quite well. Talairach.m3z
warps your subject to an internal freesurfer space (kinda like MNI305,
but not quite). Let's say the freesurfer recon-all output is at
<something>/SUBJECT_FS/
2) Run the MNI152 1mm template (the one from FSL) through recon-all.
Recon-all will give you a Talairach.m3z that allows you to map the
MNI152 1mm template to the internal freesurfer space. Let's say the
freesurfer recon-all output is at <something>/MNI152_FS/
3) Then do the following:
a) Use mri_vol2vol to upsample the Buckner cerebellum atlas which is
2mm resolution to the 1mm MNI152 template:
>> mri_vol2vol --mov Buckner_atlas.nii.gz --targ MNI152/mri/norm.mgz
>> --regheader --o Buckner_atlas1mm.nii.gz --no-save-reg --interp nearest
Notice that I use norm.mgz of the MNI template rather than the
original MNI template. norm.mgz is the 256 x 256 x 256 conformed
version of the MNI template that recon-all puts through.
b) warp the Buckner_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>> setenv SUBJECTS_DIR <something>
>> mri_vol2vol_used --mov Buckner_atlas1mm.nii.gz --s MNI152_FS --targ
>> $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o
>> Buckner_atlas_freesurfer_internal_space.nii.gz --interp nearest
c) warp the Buckner_atlas_freesurfer_internal_space.nii.gz to your subject:
>> setenv SUBJECTS_DIR <something>
>> mri_vol2vol --mov $SUBJECTS_DIR/SUBJECT_FS/mri/norm.mgz --s SUBJECT_FS
>> --targ Buckner_atlas_freesurfer_internal_space.nii.gz --m3ztalairach.m3z --o
>> Buckner_atlas_subject.nii.gz --interp nearest --inv-morph
This is not optimal because of the double interpolation. You might
want to use the MNI template instead of the Buckner_atlas to test the
above, so you can check the goodness of the warp. The final warped MNI
template should hopefully look identical to your subject. If that
works, then use the Buckner_atlas. Note that mri_vol2vol does not work
properly for talairach.m3z below version 5, so you should use version
5x mri_vol2vol.
Regards,
Thomas
On Thu, Nov 24, 2016 at 6:31 AM, Peled, Noam <npe...@mgh.harvard.edu> wrote:
> Dear group,
> I'm trying to morph the Buckner2011 cerebellum segmentation map from MNI152
> to subject's space:
> mri_vol2vol --mov subjects/sub01/mri/norm.mgz --s sub01 --targ
> Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz --m3z
> talairach.m3z --o sub01_Buckner2011_atlas_17_loose.nii.gz --nearest
> --inv-morph
> It worked with the 17 networks, but didn't work with the 7 networks version.
> Any ideas? This is really strange.
>
> Thanks,
> Noam
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