Atlas Reference

### 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:

- Probabilistic - a 4D image where each volume contains voxel values [0:100] indicating the probability that a given voxel is classified as belonging to the structure represented by that volume.
- Label or "hard" segmentation - a 3D image where each voxel contains the value corresponding to that voxel's classification label.

#### XML Specification

Tag name | Description | Attributes
--- | --- | ---
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