>From the gcaFormat freesurfer wiki page I know that:

The .gca file is composed of three volumes, which can be extracted like this:

mri_convert atlas.gca -nth 0 means.mgz
mri_convert atlas.gca -nth 1 labels.mgz
mri_convert atlas.gca -nth 2 priors.mgz

where:

means --> the mean intensity of the most likely label
labels --> indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt)
priors --> the probability that that label occurs at that voxel

Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert.

Can this be done?

Thank you,

Jeff Thompson