The atlas tool data and file format reference

Introduction

The atlas data is represented by a set of image files (e.g. 3/4D NIFTI files) along with an atlas description file in XML. The image files contain voxel classification values while the XML file caries the associated label and summary image information.

Atlases come in two flavours:

XML Specification

Tag nameDescriptionAttributes
Tags in header section
name A text sting to be displayed in any tools when refering to this atlas.
type Probabilistic, Label.
imagefile Relative path to the location of the atlas image
summaryimagefile Relative path to the location of the atlas summary image
Tags in data section
label Text corresponding to this volume's label
index
x
y
z
Example
<?xml version="1.0" encoding="ISO-8859-1"?>
<atlas version="1.0">
  <header>
    <name>MNI Structural Probability Atlas</name>
    <type>Probabalistic</type>
    <imagefile>/MNI/MNI-prob-2mm</imagefile>
    <summaryimagefile>/MNI/MNI-maxprob-thr25-2mm</summaryimagefile>
  </header>
  <data>
    <label index="0" x="39" y="73" z="35">Caudate</label>
    <label index="1" x="34" y="32" z="15">Cerebellum</label>
    <label index="2" x="45" y="90" z="29">Frontal Lobe</label>
    <label index="3" x="27" y="73" z="30">Insula</label>
    <label index="4" x="50" y="20" z="37">Occipital Lobe</label>
    <label index="5" x="45" y="33" z="61">Parietal Lobe</label>
    <label index="6" x="56" y="69" z="34">Putamen</label>
    <label index="7" x="16" y="53" z="35">Temporal Lobe</label>
    <label index="8" x="48" y="55" z="38">Thalamus</label>
  </data>
</atlas>

Hints and tips for atlas developers