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

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Ursula Tooley Ph.D. Student Neuroscience Graduate Group University of Pennsylvania utooley@gmail.com mailto:utooley@gmail.com 202.413.5627

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