Dear FS experts,
Freesurfer could provide for every participant a standardized partition of the cortex into 66 regional areas. My aim is to use freesurfer to subdivide these regional areas into a set of small and compact regions, resulting in high resolution atlas covering the entire cortex (taken from Hagmann et al. (2008) in PLoS Biol). We tried to used the
mris_divide_parcellation fsaverage rh aparc.annot 100 rh_annot_100 (However, this creates a parcellation of long strips per region, that is not a good partition for what we want.)
Then, we used the
"mris_make_face_parcellation lh.orig $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot". The results look nice, but I have the following questions:
(1)Can i used the "mris_make_face_parcellation" based on the "aparc.annot"?
(2)How can i conver the .annot file into .hdr/.img mask files? I read the introduction about "mri_label2vol", but i was still confused. If i want to convert aparc.annot files in fsaverage, what the input files are for "--temp" and "--seg"?
(3)I read the "lh.ic3.annot" in Matlab (read_annotation.m). For "colortable.struct_names", the name is "ic3.tri_vertex_0"(to "ic3.tri_vertex_641"), how to know which brain regions it belong to? how to know each vertex's MNI coordinate?
(4)"mris_make_face_parcellation lh.orig $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot" . I only see 7 options in: $FREESURFER_HOME/lib/bem/ic[1-7].tri (as per the program usage). Can I specify custom ic*.tri files (and also, how would those be generated)?
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Good Luck
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Life Sciences Research Center
Xidian University
Xi'an China
http://life.xidian.edu.cn
liujixin@life.xidian.edu.cnliujixin2010@gmail.com============================================