Editing labels/annotations in tksurfer

Index TableOfContents

Overview

This page describes the process of editing labels using tksurfer. Surface label data can be stored in individual label files, or the data of many labels can be stored in an annotation file. This page focuses on the annotation file way of doing things, though much of the following is relevant to the separate-label-files approach too.

Editing might be desired for a couple of reasons:

• You have an individual subject where you don't like the region boundaries that FreeSurfer produced.

• You are editing many cases on the way to producing a new atlas.

At any rate, you will want to know how to perform the following editing moves:

• Expand the boundary of a region into a neighboring region (or vice versa).
• Create an entirely new label (ie: new structure Id number and caption), draw a region and label it with the new structure number.
• Merge two regions (and presumably apply a new structure number etc).

Editing labels turns out to be reasonably straightforward, but there are a number of idiosyncratic features to work around in tksurfer.

Background

As a starting point, let us assume that you understand what you are looking at in the following picture:

xxxxxx surface with annot xxxxxxxxx

One can arrive at this picture by:

tksurfer -annot aparc subjectid rh inflated

In addition:

• View > Information > Annotation to turn on display of the Annotation value in the Tool window.

• View > Auto-redraw

Now, as you float the mouse over the surface, you will see the Label and Annotation fields update.

Author(s)

GrahamWideman, Ari Dubin