| Deletions are marked like this. | Additions are marked like this. |
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| * Perhaps starting with an existing annotation, such as rh.aparc.annot... | |
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| * ... and finally save your work in a new annotation file, eg: rh.myparc.annot. | |
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| As a starting point, let us assume that you understand what you are looking at in the following picture: | As a starting point, let us review what you are looking at in the following picture: |
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| Now, as you float the mouse over the surface, you will see the Label and Annotation fields update. |
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. Annotation value is actually just an alternate representation of the color: Annot = R |
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:
- Perhaps starting with an existing annotation, such as rh.aparc.annot...
- 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).
- ... and finally save your work in a new annotation file, eg: rh.myparc.annot.
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:
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. 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.
Annotation value is actually just an alternate representation of the color: Annot = R
Author(s)
GrahamWideman, Ari Dubin