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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.
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This is not a very useful procedure given an initial annotation from recon-all, since it's unlikely you want to give a provide region a new label from the provided list. However, it will come in handy for ''new'' regions that we create later.
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attachment:tksurfer_customfill_dlog.gif
  * attachment:tksurfer_customfill_dlog.gif

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:

  • 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) + (G * 256) + (B * 256^2).
  • One would expect color and annotation value to follow from the structure number, via a color look-up table.

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

  • A vertex can have more than one structure number attached to it (ie: be a "member of more than one label"). Is this a useful state? Not if saving data to an annotation file, as that kind of file prevents multi labels per vertex. For many purposes one is interested in counting each vertex once, so a single label value per vertex is a fine restriction. But the multi-labels-per-vertex can arise during editing, so we have to handle it.
  • A vertex can have only one annotation value, which usually follows from the structure number but not necessarily.
  • The vertex's color can actually diverge from the annotation value.

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

  • Click on region to select
  • Open Labels dialog. (View > Windows > Labels)

  • Don't play around with all the possible options before reading: "gwissue_labeledit". Instead...

  • Note that the region you selected is also selected in the left hand list of existing regions.
  • To apply a different label to that region, select the desired label from the list on the right, (color changes immediately in the surface window), and also click "Set Name".

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...

  • Draw a complete outline path that encloses the desired "incursion" into supramarginal, and also encloses any amount of inferiorparietal.
    • Possibly start with Edit > Unmark all vertices

    • Make a series of clicks along the desired outline path. tksurfer shows marked vertices.
    • Press the "Make closed path" button: tksurfer draws path
    • Click in the interior of the enclosed region
    • Press the "Custom Fill" button to invoke the Custom Fill dialog.
    • attachment:tksurfer_customfill_dlog.gif
    • Set
      • Fill conditions: Up to and including paths
      • Fill from: Last clicked vertex
      • Action: Here's the tricky part! You first remove the enclosed vertices from both labels before (re)applying the desired label. (Not doing so is discussed below):
        • Remove from label... dropdown > supramarginal... click Fill

        • Remove from label... dropdown > inferiorparietal ... click Fill

        • Add to existing label... dropdown > inferiorparietal ... click Fill

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

tksurfer_labeledit (last edited 2010-03-24 19:53:31 by AllisonStevens)