Editing labels/annotations in tksurfer

Index TableOfContents

Version applicability

This page covers features in tksurfer in FreeSurfer 4.0.1 and 4.0.2. Later versions may have updated behaviors.

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:

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

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 review 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:

Now, as you float the mouse over the surface, you will see the Label and Annotation fields update. These are the values attached to the individual vertex that the mouse is hovering over.

Editing a region consists of changing the Label and/or Annotation values for the vertices of interest. Of course, editing vertices one at a time would be tedious, so instead tksurfer offers various tools to draw an outline "path" and then "fill" that shape with the desired Label value, or perform other editing operations on the outlined region.

As it turns out, however, none of this is true in tksurfer:

All that said, there is a way to proceed and get the desired results.

xxxxx display of "1 other"

Edits

Change the label (structure number) of an existing region

Given and initial annotation from recon-all, this is not a very useful procedure, since it's unlikely you want to give a provided region a new label from the provided list. However, it will come in handy for new regions that we create later.

Here's a picture of the Labels dialog, for reference: attachment:tksurfer_labels_dlog_edits.jpg

Expand the boundary of an existing region

Supposed you want to expand inferiorparietal into supramarginal...

At this point the suface view should show the desired outcome.

If you do not first remove the labels from the outlined vertices, tksurfer will add the new labels to the vertices resulting in two labels. In regular tksurfer, you see something like this:

xxxxxxxxxxxxxxxxxxxxxxx

We created a custom version that shows the actual labels. Within the "incursion" area of the outline, as perhaps expected you see this:

xxxxx

Unexpectedly, in the entire rest of the region (not just in the outline) you see this:

This appears to be a bug. It turns out to be relatively benign, because when the data is saved the annotation file only captures a single label per vertex.

Author(s)

GrahamWideman, Ari Dubin