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Hello,
I have a tone of FS people who have been run through Recon-all and I am
happy with the output but I would like to expand the existing labels to
include the Buckner 7 tight labels. Is this still the best way to update my
subject labels to include these labels?
On Sat, Nov 26, 2016 at 8:07 PM Thomas Yeo <ytho...@csail.mit.edu> wrote:
> 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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