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Dear Freesurfer Team,
We would like to perform a striatal parcellation in PD patients and controls using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
We followed the instructions below which allowed us to transform the Choi's striatal atlas to our individual subjects, Here's a (non-ideal) suggestion I previously suggested to another user:
1) Assuming you are quite happy with the freesurfer striatal parcellation in your individual 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) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>> setenv SUBJECTS_DIR <something>>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
>> setenv SUBJECTS_DIR <something>>> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morphThis worked very well (but we have to perform this indicidually for all our subjects). OUr next question is : how can we obtain an "aseg.stat" file from this striatal parcellation, in order to have the volumes of the 7 different régions for each subject?Thanks a lot for yor help!!AnaAna MarquesMD, PhDPraticien HospitalierService de NeurologieHopital Gabriel-MontpiedCHRU Clermont-FerrandTEL: 04 73 751 600FAX: 04 73 751 596
De : freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Thomas Yeo <ythomas@csail.mit.edu>
Envoyé : mardi 16 février 2021 01:02
À : Freesurfer support list
Objet : Re: [Freesurfer] striatal parcellationExternal Email - Use Caution
Hi Ana,
To transform the Choi's striatal atlas to your individual subject, Here's a (non-ideal) suggestion I previously suggested to another user:
1) Assuming you are quite happy with the freesurfer striatal parcellation in your individual 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) warp the Choi_atlas1mm.nii.gz to freesurfer nonlinear volumetric space:
>> setenv SUBJECTS_DIR <something>>> mri_vol2vol_used --mov Choi_atlas1mm.nii.gz --s MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Choi_atlas_freesurfer_internal_space.nii.gz --interp nearest
b) warp the Choi_atlas_freesurfer_internal_space.nii.gz to your subject:
>> setenv SUBJECTS_DIR <something>>> mri_vol2vol --mov $SUBJECTS_DIR/AD_SUBJECT_FS/mri/norm.mgz --s AD_SUBJECT_FS --targ Choi_atlas_freesurfer_internal_space.nii.gz --m3z talairach.m3z --o Choi_atlas_AD_subject.nii.gz --interp nearest --inv-morphThis is not optimal because of the double interpolation. You might want to use the MNI template instead of the Choi_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 Choi_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 Tue, Feb 16, 2021 at 12:02 AM Marques Ana-raquel <ar_marques@chu-clermontferrand.fr> wrote:
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Dear Freesurfer Team,
we would like to perform a volumetric analysis in Parkinson's disease using freesurfer, and we have previously used recon all to perform tha surface based analysis and automate segmentation.
We would also like to extract the different volumes of striatal parcellation using the Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.
However, we can't find how to perform this parcellation, and how to add it to the recon all steps?
Thank you very much for your help!
Ana MarquesMD, PhDService de NeurologieHopital Gabriel-MontpiedCHRU Clermont-FerrandTEL: 04 73 751 600FAX: 04 73 751 596
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