Differences between revisions 42 and 43
Deletions are marked like this. Additions are marked like this.
Line 234: Line 234:
GrahamWideman, Ari Dubin, Cyndi Schumann Graham Wideman (GrahamWideman), Ari Dubin, Cyndi Schumann

Editing labels/annotations in tksurfer

Index

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: SurfaceLabelAtlas

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 we are looking at in the following picture:

tksurfer_annot1.jpg

You 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.

tksurfer_toolwin.gif

To select a region, click on it, and tksurfer redraws it with a yellow outline. We will later draw our own "outlines" (paths), and these can also be selected, which highlights then in yellow. (This requires paying some attention as to whether it's a region or an outline that's selected.)

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).
  • You might 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 quite 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 we are interested in counting each vertex just once, so a single label value per vertex is a fine restriction. But the multi-labels-per-vertex situation can arise during editing, so we have to handle it.
    tksurfer_1others.gif

  • A vertex can have only one annotation value, which usually follows from the structure number but sometimes not.

  • A vertex's color can actually diverge from the annotation value.

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

Edits

Change the label (structure number) of an existing region

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

  • Resist playing around with all the possible options unless you first read gwissue_labeledit. Instead...

  • Note that the region you selected on the surface 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 of structure numbers on the right. So far this only applies the color of the just-clicked structure (and the color changes immediately in the surface window)

  • Important: Also click "Set Name" to actually apply the desired structure number (as you can judge by mousing over the region and looking at the Label field in the Tool window).

Given an 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 as part of the procedure for new regions that we create later.

Here's a picture of the Labels dialog, for reference: tksurfer_labels_dlog_editsX.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.
    • Create outline path:
      • Possibly start with Edit > Unmark all vertices

      • Make a series of clicks along the desired outline path. tksurfer shows marked vertices.
        tksurfer_dots.jpg

      • Press the "Make closed path" button: tksurfer draws path
        tksurfer_path.jpg

    • Click in the interior of the enclosed region
    • Press the "Custom Fill" button to invoke the Custom Fill dialog.
    • tksurfer_customfill_callouts2.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

    • Clean up:
      • Unmark the vertices: Edit > Unmark all vertices

      • Remove the path: Click on the path to select it, then press the Remove Selected Path button

At this point the suface view should show the desired outcome.
tksurfer_surface_expandedrgn1.jpg

Save the annotation: File > Label > Export Annotation. Probably choose a new name rather than writing over an existing file.

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:

tksurfer_1others.gif

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

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

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.

Bottom line: to avoid confusion, remove all labels from region before applying new ones.

Create a brand new region

Conceptually this is really two operations:

  • Introduce a new structure number, caption and color to tksurfer
  • Create an outline path around the new region and Fill with the new label (ie: structure number).

You may have noticed that the Custom Fill dialog offers "Create a new label" as a possibility. However, this area of functionality is incomplete so this is not the way to proceed (details of why are here: gwissue_labeledit.

Preparation: new look-up table

Instead, we need an alternate way to augment the structures look-up table that tksurfer got from the annotation file. As it turns out, we can simply provide a replacement lookup-table file. This needs to be in the same format as the LUT provided with FreeSurfer: FreeSurferColorLUT.txt.

You probably want to add on to the info that's in the annotation file's LUT, rather than starting from scratch. We couldn't find a program to extract LUT info from an annotation file, so we created one (available: see below), which gave us, for lh.aparc.annot, the following output:

# Freesurfer LUT information extracted from annotation file:
# lh.aparc.annot
# 2008-02-29 23:58:32
# This file can be used as the basis for a new LUT file for annotations purposes
# which can be loaded into tksurfer using File > Label > Load color table

#No.    Label Name:                                  R     G     B     A
0       unknown                                     25     5    25     0
1       bankssts                                    25   100    40     0
2       caudalanteriorcingulate                    125   100   160     0
3       caudalmiddlefrontal                        100    25     0     0
4       corpuscallosum                             120    70    50     0
5       cuneus                                     220    20   100     0
6       entorhinal                                 220    20    10     0
7       fusiform                                   180   220   140     0
8       inferiorparietal                           220    60   220     0
9       inferiortemporal                           180    40   120     0
10      isthmuscingulate                           140    20   140     0
11      lateraloccipital                            20    30   140     0
12      lateralorbitofrontal                        35    75    50     0
13      lingual                                    225   140   140     0
14      medialorbitofrontal                        200    35    75     0
15      middletemporal                             160   100    50     0
16      parahippocampal                             20   220    60     0
17      paracentral                                 60   220    60     0
18      parsopercularis                            220   180   140     0
19      parsorbitalis                               20   100    50     0
20      parstriangularis                           220    60    20     0
21      pericalcarine                              120   100    60     0
22      postcentral                                220    20    20     0
23      posteriorcingulate                         220   180   220     0
24      precentral                                  60    20   220     0
25      precuneus                                  160   140   180     0
26      rostralanteriorcingulate                    80    20   140     0
27      rostralmiddlefrontal                        75    50   125     0
28      superiorfrontal                             20   220   160     0
29      superiorparietal                            20   180   140     0
30      superiortemporal                           140   220   220     0
31      supramarginal                               80   160    20     0
32      frontalpole                                100     0   100     0
33      temporalpole                                70    70    70     0
34      transversetemporal                         150   150   200     0

You would add lines to this table. Suggestions:

  • Use numbers starting at, say, 70, so that if MGH adds more aparc regions in future versions of FreeSurfer you have some hope of avoiding a collision.

  • Choose colors that are not already used. This is mandatory as discussed here: LabelsClutsAnnotationFiles, section "Annotation file design surprise".

Actually creating the new region

  • Load the surface and existing annotation file
  • Load the enhanced look-up-table: File > Label > Load Color Table

  • Draw outline path:
    • 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.
  • Set
    • Fill conditions: Up to and including paths
    • Fill from: Last clicked vertex
    • Action: First remove the enclosed vertices from all labels that your outline encloses, before applying the new structure label.:
      • For each current label: Remove from label... dropdown > region-whatever... click Fill

      • Add to existing label... dropdown > your-new-label ... click Fill

At this point the surface view should be showing your outlined region containing the color of your new structure, and floating the mouse over that region should show the new label and annotation values.

Save the annotation: File > Label > Export Annotation. Probably choose a new name rather than writing over an existing file.

Merging Two Regions

Conceptually, this is two moves:

  • Introduce a new label (structure entry) to be applied to the combo region. Follow the steps described above under "Preparation: new look-up table"
  • Apply the new label to the two regions. Follow the instructions above under "Change the label (structure number) of an existing region"

Additional Comments

Alternate editing techniques

  • As with most software, there are alternative menu choices or buttons for some of the actions discussed.
  • There are also additional techniques for using paths in combination with existing region boundaries to specify the sets of vertices you want to affect.

Clarification of the role of provided LUT files

Since this article mentions lookup-table files, a clarification might be useful on the role of FreeSurferColorLUT.txt.

  • FreeSurferColorLUT.txt might seem to be somehow the "authoritative LUT file". In a sense this is true, but indirectly...
  • FreeSurferColorLUT.txt is not used by tksurfer; tksurfer doesn't secretly read it.
  • The structure numbers (label numbers) in FreeSurferColorLUT.txt are numbers used in the voxel version of data, for example in aseg and aparc+aseg files.
  • The structure numbers used for surface parcellation, for example in a surface annotation file (like rh.aparc.annot), are numbers in the range of 0 to 34 (currently). These structure names do not corresepond to same-numbered structures in FreeSurferColorLUT.txt, but do correspond to FreeSurferColorLUT.txt's range 1000-1034 (lh) and 2000-2034 (rh).

  • The process which maps surface-parcellation into voxel space (mri_aparc2aseg) is responsible for adding 1000 or 2000 to the parcellation numbers. (At least, I assume so, haven't actually checked -- GW). There is no other mechanism that enforces this relationship, so care is needed when adding parcellation regions to coordinate those with +1000 and +2000 number in your enhanced version of FreeSurferColorLUT.txt

Program to extract lookup-table from annotation file

For linux, Centos 5. Not tested on other versions.

Invocation: GWFSAnnotToLUT annot_file_path output_LUTfile_path

Download: GWFSAnnotToLUT

Related Articles

Author(s)

Graham Wideman (GrahamWideman), Ari Dubin, Cyndi Schumann

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