I’ve created a custom annotation file in MATLAB, using read_annotation.m and write_annotation.m, relabeling the Glasser parcellation regions. It seems to display as expected in tksurfer and tkmedit, but in freeview the first annotation is completely transparent (see images below), although if I hover my mouse over the area, it’s labeled with the correct struct_name. I’ve changed the alpha value in the annotation file and see no difference in freeview, and also given some previous listserv posts tried changing the RGB values for that first annotation in colortable.table. 

View in tksurfer:

tksurfer fsaverage lh inflated -annotation my_annotation.annot 

View in freeview:

freeview $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=my_annotation.annot 

Any help would be greatly appreciated. I’m running FS 6.0, Freeview V2, this occurs both locally on my OSX El Capitan and on an HPC running Linux Centos.

Thanks in advance,

Ursula