Identity if you want it int the subject's anatomical coords

Cheers Bruce

On Jul 24, 2011, at 7:27 AM, Jixin Liu liujixin2010@gmail.com wrote:

Hi Bruce,

Thanks very much for your reply. i want to convert the ".annot" files to nifti. When i used "mri_label2vol", I used this command 

mri_label2vol --subject fsaverage --annot $FREESURFER_HOME/subjects/fsaverage/surf/lh.ic3.annot --o test.img --hemi lh

ERROR: you must specify a registration method: Either: --reg, --regheader, or --identity mri_label2vol: must specify template volume with --temp

What files should be the input for "--reg" and "--temp"?

On 22 July 2011 21:00, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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)?

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-- Good Luck ============================================ Life Sciences Research Center Xidian University Xi'an China http://life.xidian.edu.cn liujixin@life.xidian.edu.cn liujixin2010@gmail.com ============================================