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<html>
<head>
<link rel="stylesheet" title="normal" type="text/css" href="../fsl.css">
<title>Atlas Reference</title>
</head>
<body>
<br><br><p>
<h3>The atlas tool data and file format reference</h3>
<h4>Introduction</h4>
<p>
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.
</p>
<p>Atlases come in two flavours:
<ul>
<li>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.</li>
<li>Label or "hard" segmentation - a 3D image where each voxel
contains the value corresponding to that voxel's
classification label.</li>
</ul>
</p>
<h4>XML Specification</h4>
<table>
<tr><th>Tag name</th><th>Description</th><th>Attributes</th></tr>
<tr><th colspan="3">Tags in header section</th></tr>
<tr><td>name</td>
<td>A text sting to be displayed in any tools when refering to this atlas.</td>
<td></td></tr>
<tr><td>type</td>
<td>Probabilistic, Label.</td>
<td></td></tr>
<tr><td>imagefile</td>
<td>Relative path to the location of the atlas image</td>
<td></td></tr>
<tr><td>summaryimagefile</td>
<td>Relative path to the location of the atlas summary image</td>
<td></td></tr>
<tr><th colspan="3">Tags in data section</th></tr>
<tr><td>label</td>
<td>Text corresponding to this volume's label</td>
<td>
<dl>
<dt>index</dt><dd></dd>
<dt>x</dt><dd></dd>
<dt>y</dt><dd></dd>
<dt>z</dt><dd></dd>
</dl>
</td>
</table>
<h5>Example</h5>
<pre>
<?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>
</pre>
<h4>Hints and tips for atlas developers</h4>
</body>
</html>
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