Hi Jixin,
mris_make_face_parcellation uses an icosahedral sampling, so you cannot use
it with an arbitrary annotation, and the parcels in it will not correspond
to the brain regions in any of the annots but rather will cut across
boundaries. You could certainly use matlab for example to compile a list of
all the different annotation names from the aparc.annot that are in each of
the lh.ic3.annot annotations. For 4), I guess you could generate your own
.tri files that are not supertesselated icosahedra as long as they are
valid tesselations of the sphere, but we don't have any. If you want to
convert to nifti/analyze, you probably want to first sample them into the
volume (mri_label2vol).
cheers
Bruce
On Fri, 22 Jul 2011, Jixin Liu wrote:
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)?
--
Good Luck
============================================
Life Sciences Research Center
Xidian University
Xi'an China
http://life.xidian.edu.cn
liuji...@life.xidian.edu.cn
liujixin2...@gmail.com
============================================
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