Hi all,
Since I haven't heard back about my question so far, I'm posting it
again! Sorry about this but I really need your help!
As mentioned in my previous posts, I'm interested in having the GM
volumetric lobar masks (frontal, parietal, temporal, occipital, and
insular) with the final goal of moving them the DTI space to perform
thalamic parcellation. I've ran the following commands:
1- a. mri_annotation2label --subject P2 --hemi lh --lobesStrict
freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot
b. mri_annotation2label --subject P2 --hemi rh --lobesStrict
freeSurfer_Results/P2/label/rh.freeSurfer_lobes.annot
2- mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o
freeSurfer_Results/P2/label/freeSurfer_lobes.nii.gz
I thought after doing this I'm going to get the 5 or 6 lobar labels, but
instead I'm getting a detailed WM + GM segmentation. I looked at
"FreeSurferColorLUT.txt" and tried to manually combine labels in the
range of 1000-1035 for the left and 2000-2035 for the right hemisphere
to get the lobe masks, but after having a closer look I realised that
labels 1002,1008-1035 & 2002,2008-2035 are all empty (ie. I only have 7
labels in each hemisphere)! so, I'm now not sure how to manually combine
these labels either!
Could someone PLEASE PLEASE clarify this for me! I would really
appreciate any help!
Thanks,
-Mojdeh
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