I had this problem - adding it as an overlay doesn't help, and that's what you said you were doing anyway it seems - looks like its because there are voxels outside of the brain in your overlap image. Mask it to a standard brain mask by: fslmaths MNI152_T1_2mm_brain_mask.nii.gz -mul CombLesionMap.nii.gz CombLesionMapMasked.nii.gz

(i.e. masked binarised standard brain file - your lesion file - name for new masked file). Then reload your new masked lesion map into MRIcroGL and it should allow you to change the overlay colour.