Hi Ruopeng,

That works perfectly, thanks so much.

Best, Ursula

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

From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview Date: July 17, 2017 at 11:43:18 AM EDT To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu

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 utooley@gmail.com mailto:utooley@gmail.com 202.413.5627

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.