Hi Mailing List,

I am attempting to apply the Yeo 2011 7-network fucntional parcellations to a set of fs MRIs processed with v5.1.0. Below are listed the first three steps I plan to take and I am seeking advice as to:

A) Whether this approach is valid.
B) Steps to take next.


Steps 1-3:

1. Run MNI152 1mm template through recon-all
recon-all -i FSL_MNI152_FreeSurferConformed_1mm.nii -subjid Yeo2011_MNI152_FS
recon-all -all -subjid Yeo2011_MNI152_FS

2. Warp the Yeo_atlas1mm.nii.gz to freesurfer nonlinear volumetric space
mri_vol2vol --mov Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii --s Yeo2011_MNI152_FS --targ $FREESURFER_HOME/average/mni305.cor.mgz --m3z talairach.m3z --o Yeo2011_atlas_FSI.nii.gz --nearest

3. warp the Yeo_atlas_freesurfer_internal_space.nii.gz to each subject:
mri_vol2vol --mov $SUBJECTS_DIR/subjID/mri/norm.mgz --s subjID --targ Yeo2011_atlas_FSI.nii.gz --m3z talairach.m3z --o Yeo2011_atlas_subjID.nii.gz --nearest --inv-morph


When previously mapping the Choi 2012 straital parcellations, steps 4 and 5 were: 

4. Creating a striatal mask in the native subject's space from freesurfer segmented Caudate (11 & 50), Putamen (12 & 51), and Accumbens (26 & 58):
mri_binarize --i subjID/mri/aparc+aseg.mgz --match 11 --match 12 --match 26 --match 50 --match 51 --match 58 --o striatum_mask.nii.gz

5. Using this mask to mask the choi striatal parcellations
fslmaths Choi2012_atlas_subjID.nii.gz -mas striatum_mask_subjID.nii.gz Yeo_atlas_subjID_mask.nii.gz


Do I need to do a similar thing for the Yeo cortical parcellations and if so what regions should I include in the cortical mask?

--

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
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