yes, but i am confused as to how mris_label2annot uses the color table.  according to http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles, each .label file contains columns of vertex numbers, coordinate values, and a column of zeros.  i assume that mris_label2annot assigns the coordinates in the file to the anatomical name corresponding to the name of the file, but when i tried to set the color table region names to be the same as the names of the .label files, the output was the same as what i sent earlier:

1 11829830 Left-Cerebral-Exterior
2 16119285 Left-Cerebral-White-Matter
...

even though my color table didn't have label numbers 1, 2, etc.!

cheers,
@rno

On Sun, Jun 24, 2012 at 11:22 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
Weren't you concerned that the names in the annotation were incorrect? You get to pick the names and the colors to be whatever you want to be. By default, it uses FreeSurferColorLUT.txt.
doug


On 6/23/12 9:54 PM, Arno Klein wrote:

dear doug,

thank you for your response.  for the custom color table, what do i assign for the different anatomical names and color values?  why wouldn't the names and colors in FreeSurferColorLUT.txt work?

cheers,
@rno