Hi Xinyang

left/right vessel are I believe small labels that the CMA includes for vessels in the basal ganglia that would otherwise be labeled lesion.

The gca is an internal format, but you can view the contents using freeview. Something like:

freeview -v <path to gca file>#<frame>

where the 'frames' show you different information. I think the most interesting would be frame 0 (mean intensity of the most likely label) and frame 1 (label id of the most likely label). The gca has other information in it that couldn't be stored in a nifti file like Markov relations.

cheers Bruce

On Sun, 13 Oct 2013, Xinyang Liu wrote:

Dear all, In the "FreeSurferColorLUT.txt", what brain regions are represented by "right-vessel" and "left-vessel", respectively? Is there a file or document that explains the definition of regions listed in "FreeSurferColorLUT.txt"?

Also, the atlas for subcortical segmentation is in $FREESURFER_HOME/average/RB_all_2008-03-26, which is a ".gca" file. What is this format? Is there a way that I can "see" this atlas in 3D? Can it be transferred to a ".nii" file?

Thanks, Xinyang