Hi Ruopeng, That works perfectly, thanks so much.
Best, Ursula --- Ursula Tooley Ph.D. Student Neuroscience Graduate Group University of Pennsylvania [email protected] 202.413.5627 > > From: Ruopeng Wang <[email protected] > <mailto:[email protected]>> > Subject: Re: [Freesurfer] Custom Annotation: 1st Annot Visible in TKSurfer > but not Freeview > Date: July 17, 2017 at 11:43:18 AM EDT > To: [email protected] <mailto:[email protected]> > > > 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 >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] <mailto:[email protected]> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > _______________________________________________ > Freesurfer mailing list > [email protected] <mailto:[email protected]> > 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.
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