Hi Ursula,
Since FS 6.0, freeview stopped displaying index 0 in the annotation look
up table which is usually reserved as "unknown 0 0 0 0", so that it
doesn't show a black region on the surface. Would it be possible for you
change your indices starting from 1? I will also update freeview so that
it can check the color of index 0 and handle it more smartly.
Best,
Ruopeng
On 07/14/2017 06:10 PM, Ursula Tooley wrote:
Hi FreeSurfer Experts,
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
---
Ursula Tooley
Ph.D. Student
Neuroscience Graduate Group
University of Pennsylvania
[email protected] <mailto:[email protected]>
202.413.5627
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