Index TableOfContents

Labels, Color Lookup Tables and Annotation Files

This page discusses the basic concepts of FreeSurfer files that relate to identifying regions-of-interest for surfaces and volumes.

Label

A label is an integer value which can be associated with a surface mesh vertex, or with a voxel, to indicate that it belongs to some region of interest. This could mark the vertex or voxel as part of an anatomical region, or it could mark the vertex/voxel as part of a region for analysis.

Sometimes when speaking or writing loosely, the word "label" is used as shorthand for "the set of vertices marked with a particular label". Sometimes vertices are said to "belong to a label", meaning that these vertics belong to the set marked by that label. "Saving a label" refers to saving into a file the list of vertices marked by a particular label value.

Label file

A label file is a text file capturing a list of vertices belonging to a region, including their spatial positions(using R,A,S coordinates). Because both vertex number and corresponding position are listed, a label file can be used by either tksurfer or tkmedit to identify surface or volume locations belonging to the region.

It should be noted that a label file's vertex numbers will apply to several surfaces of a subject: for example the white surface, the pial surface, the inflated surface and so on. However the R,A,S positions are those of a particular one of these surfaces, according to selections in effect when the label file was saved by tksurfer.

Perhaps surprisingly, a label file contains neither the label code nor label name that it pertains to. Instead it is conventional to name the label file in a manner that indicates the label intended, though this naming convention has varied over the years. Examples:

Label file format

1806
7  -22.796  -66.405  -29.582 0.000000
89  -22.273  -43.118  -24.069 0.000000
138  -14.142  -81.495  -30.903 0.000000
[...]

Row

Col1

Col2

Col3

Col4

Col5

1

Comment

2

Count of subsequent rows

3..end

Vertex num

R coord

A coord

S coord

Don't know

Color Lookup Table

In FreeSurfer a "color lookup table" is a table cross-referencing the integer label code to a name, and to a color (Red, Green, Blue and Opacity values). Although called a "color lookup", in many usages it is the cross-reference to name, or simply the list of names, which is important.

Details

Labels

x

Color Lookup Tables

x

Annotations

x

Related pages

Document Author/s

GrahamWideman