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
Neuroscience Research Australia
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Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883
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