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?
