Hi Bruce,

I am wondering whether I can get the white matter volume of the single label by using mri_aparc2aseg -s <subjid> --labelwm ... But mri_aparc2aseg only works for annotation not the label. Maybe this is not the right way. Any suggestion would be appreciated.

Wayne

On 28/04/09 11:00 AM, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:

Hi Wayne,

why are you trying to convert the label to an annotation? Not sure why it's not working, but I don't know that I've ever used the tksurfer export feature.

Bruce

On Tue, 28 Apr 2009, Wayne Su wrote:

...

I have the trouble to convert the BA label to annotation file. The Freesurfer 4.3.0 is on Mac OS 10.5.6. First, I got the BA label: mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/lh.BA1.label --trgsubject 001 --trglabel 001/label/lh.BA1.label --hemi lh --regmethod surface This works. I can load the label onto the surface by using tksurfer. Select File->Label->Export Annotation. The Terminal window shows ³writing color table into annotation file...² and stop here. I checked the lh.BA1.annot, it¹s about 1MB. But when I try to load this annotation, the surfer warning me no lables imported and annotation was empty. I went to the command line and type in: mris_label2annot --s 001 --h lh --ctab 001/label/ba1.annot.ctab --l 001/label/lh.BA1.label --a BA1 Here is the message. subject 001 hemi lh SUBJECTS_DIR /Applications/freesurfer4.3/subjects ColorTable 001/label/ba1.annot.ctab AnnotName BA1 nlables 1 Loading /Applications/freesurfer4.3/subjects/001/surf/lh.orig 001/label/lh.BA1.label 001/label/lh.BA1.label 1 14465659 BA1 Mapping unhit to unknown Found 129453 unhit vertices Writing annot to /Applications/freesurfer4.3/subjects/001/label/lh.BA1.annot writing colortable into annotation file...

This seems work because I can load the annotation onto the surface. But what are the ³unhit vertices²? Is this normal?

The last question: how can I get the voxel number (volume) of this label?

Thanks.

Wayne