Hi, We're trying to create some customized annotations in matlab, and then write them out to an .annot file.
Some of these annotations are dense (e.g., ~1000 ROIs). However, if we defined more than 30 or so colours, tksufrer crashes.
Does this limit have something to do with what is specified in the colortable.orig_tab structure?
We simply read in the standard lh.aparc.annot output by freesurfer and made all the necessary changes before using write_annotation to create a new .annot file, but were not sure what to change the orig_tab field to so we left it blank. Do I need to change this to something else?
Thanks for your help, Alex
Hi Alex,
what version are you using? I have used thousands of colors in the current version to build icosahedral (mostly uniform) parcellations of the surface.
cheers, Bruce On Thu, 9 Apr 2009, Alex Fornito wrote:
Hi, We're trying to create some customized annotations in matlab, and then write them out to an .annot file.
Some of these annotations are dense (e.g., ~1000 ROIs). However, if we defined more than 30 or so colours, tksufrer crashes.
Does this limit have something to do with what is specified in the colortable.orig_tab structure?
We simply read in the standard lh.aparc.annot output by freesurfer and made all the necessary changes before using write_annotation to create a new .annot file, but were not sure what to change the orig_tab field to so we left it blank. Do I need to change this to something else?
Thanks for your help, Alex
Sorry, I should clarify what I mean by tksurfer crashing: When I define 1000 different colours, only half of the brain gets displayed. I.e. when I click to add the annotation file, it refreshes the image from one side, everything begins as expected, but when it gets to half way across the brain, it seems to runs out of memory and just does not bother displaying the parcellation for that half.
On 09/04/2009 13:59, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Alex,
what version are you using? I have used thousands of colors in the current version to build icosahedral (mostly uniform) parcellations of the surface.
cheers, Bruce On Thu, 9 Apr 2009, Alex Fornito wrote:
Hi, We're trying to create some customized annotations in matlab, and then write them out to an .annot file.
Some of these annotations are dense (e.g., ~1000 ROIs). However, if we defined more than 30 or so colours, tksufrer crashes.
Does this limit have something to do with what is specified in the colortable.orig_tab structure?
We simply read in the standard lh.aparc.annot output by freesurfer and made all the necessary changes before using write_annotation to create a new .annot file, but were not sure what to change the orig_tab field to so we left it blank. Do I need to change this to something else?
Thanks for your help, Alex
I think this was a tksurfer bug that I fixed a few months ago. Can you try grabbing a current version of tksurfer and see if it is fixed?
Bruce
On Thu, 9 Apr 2009, Alex Fornito wrote:
Sorry, I should clarify what I mean by tksurfer crashing: When I define 1000 different colours, only half of the brain gets displayed. I.e. when I click to add the annotation file, it refreshes the image from one side, everything begins as expected, but when it gets to half way across the brain, it seems to runs out of memory and just does not bother displaying the parcellation for that half.
On 09/04/2009 13:59, "Bruce Fischl" fischl@nmr.mgh.harvard.edu wrote:
Hi Alex,
what version are you using? I have used thousands of colors in the current version to build icosahedral (mostly uniform) parcellations of the surface.
cheers, Bruce On Thu, 9 Apr 2009, Alex Fornito wrote:
Hi, We're trying to create some customized annotations in matlab, and then write them out to an .annot file.
Some of these annotations are dense (e.g., ~1000 ROIs). However, if we defined more than 30 or so colours, tksufrer crashes.
Does this limit have something to do with what is specified in the colortable.orig_tab structure?
We simply read in the standard lh.aparc.annot output by freesurfer and made all the necessary changes before using write_annotation to create a new .annot file, but were not sure what to change the orig_tab field to so we left it blank. Do I need to change this to something else?
Thanks for your help, Alex
freesurfer@nmr.mgh.harvard.edu
-
Alex Fornito -
Bruce Fischl