I have performed make_face_parcellation on fsaverage (with ic5) (Darwin-leopard-i686-stable-pub-v5.1.0). I read_annotation ed the parcellation into matlab an noticed that while colortable.table has 10242 rows (as expected), length(unique(colortable.table(:,5))) produces 9834 => some entries are in the list more than once. If I grasped the procedure correctly, the entries in label are determined by colortable.table(:,5) and colortable.table(:,5) is determined by:

% Column 5 is the structure ID, calculated from

% R + G*2^8 + B*2^16 + flag*2^24

One example for this problem is colortable.table(43,:) and colortable.table(86,:) both read:

0 0 170 0 11141120

How are Rm G, B determined?

I guess one quick fix would be to introduce flags >0. Would that affect anything else? Or, is there a way to force my own indices onto colortable.table(:,5)? (if I change this entry, save the annot and load the annot, the entry is at R + G*2^8 + B*2^16 + flag*2^24 again

(I already encountered the effects of this problem a couple of months ago (2. in this post http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21189.html).)

Thank you so much for your help,

Franz