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Hi Katherine,
Yes. This is still the best way if you have already run recon-all.
Regards,
Thomas
On Sat, Oct 6, 2018 at 8:21 AM Katherine Damme <katherine.da...@gmail.com>
wrote:
> 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
>> > (function(){(function n(e) { "use strict"; function t(e) { if
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>> > })()
>> >
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