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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.

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 not 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:

  • lh.cortex.label
  • lh-avg_calcarine_sulcus.label.

Label file format

  • { { {

#!ascii label , from subject 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.

  • Annotation: An annotation

Details

Labels

x

Color Lookup Tables

x

Annotations

x

Related pages

  • AnnotFiles : Some brief end-user notes on annotation files, plus MatLab and C developer notes.

  • ["mris_label2annot"] : Documentation for the command-line program that amalgamates label files (plus optional color lookup table file) into a single annotation file.
  • ["mri_annotation2label"] : Documentation for the command-line program that breaks an annotation file into individual label files
  • EditingLabels : Pointers to a couple of pages about labels

  • TkSurferGuide/TkSurferWorkingWithData/TkSurferLabel : Working with labels

Document Author/s

GrahamWideman

LabelsClutsAnnotationFiles (last edited 2018-09-28 13:42:03 by 66)