Index: fslview/doc/fslview/atlas-descriptions.html
===================================================================
--- /dev/null	1970-01-01 00:00:00.000000000 +0000
+++ fslview/doc/fslview/atlas-descriptions.html	2010-06-30 19:14:39.913565850 -0400
@@ -0,0 +1,223 @@
+<html>
+  <head>
+    <link rel="stylesheet" title="normal" type="text/css" href="fslview.css">
+    <title>FSL</title>
+  </head>
+  <body>
+    <h2>Brain Atlases included with FSL</h2>
+
+    <ul>
+      <li><a href="#ho">Harvard-Oxford cortical and subcortical structural atlases</a></li>
+      <li><a href="#jul">J&uuml;lich histological atlas</a></li>
+      <li><a href="#wm">JHU DTI-based white-matter atlases</a></li>
+      <li><a href="#thal">Oxford thalamic connectivity atlas</a></li>
+      <li><a href="#tal">Talairach atlas</a></li>
+      <li><a href="#mni">MNI structural atlas</a></li>
+    </ul>
+
+    <table cellpadding="10" cellspacing="0">
+
+      <tr><td colspan="2"><hr></td></tr>
+      <tr valign="top">
+	<td rowspan="2">
+	  <p><b><a name="ho"></a>Harvard-Oxford cortical and subcortical structural atlases</b></p>
+	  <p>Probabilistic atlases covering 48 cortical and 21
+	    subcortical structural areas, derived from structural data
+	    and segmentations kindly provided by
+	    the <a href="http://www.cma.mgh.harvard.edu/">Harvard
+	    Center for Morphometric Analysis</a>.</p>
+	  <p>T1-weighted images of 21 healthy male and 16 healthy
+	    female subjects (ages 18-50) were individually segmented
+	    by the CMA using semi-automated tools developed
+	    in-house. The T1-weighted images were affine-registered to
+	    MNI152 space using FLIRT (FSL), and the transforms then
+	    applied to the individual labels. Finally, these were
+	    combined across subjects to form population probability
+	    maps for each label.</p>
+	  <p>We are very grateful to the following for providing the
+	    segmentations used to create these atlases: David Kennedy
+	    and Christian
+	    Haselgrove, Centre for
+	    Morphometric Analysis, Harvard; Bruce Fischl,
+	    the Martinos Center
+	    for Biomedical Imaging, MGH (NIH grants
+	    P41-RR14075, R01 RR16594-01A1, R01 NS052585-01); Janis
+	    Breeze and Jean Frazier from
+	    the Child
+	    and Adolescent Neuropsychiatric Research Program,
+	    Cambridge Health Alliance; Larry Seidman and Jill
+	    Goldstein from
+	    the Department of
+	    Psychiatry of Harvard Medical School.</p>
+	</td>
+	<td><img src="atlas-hocort.png" width="100">
+	</td>
+      </tr>
+      <tr>
+	<td><img src="atlas-hosub.png" width="100"></td>
+      </tr>
+
+      <tr><td colspan="2"><hr></td></tr>
+      <tr valign="top">
+	<td>
+	  <p><b><a name="jul"></a>J&uuml;lich histological (cyto- and myelo-architectonic) atlas</b></p>
+
+          <p>A probabilistic atlas created by averaging multi-subject
+	    post-mortem cyto- and myelo-architectonic segmentations,
+	    performed by the team of Profs Zilles and Amunts at the <a
+	    href="http://www.fz-juelich.de/inb/inb-3/Home">Research
+	    Center J&uuml;lich</a> and kindly provided by Simon
+	    Eickhoff.</p>
+
+	  <p>The atlas contains 32 grey matter structures and 10 white
+	    matter structures. This is the same data as used in
+	    Eickhoff's <a
+	    href="http://www.fz-juelich.de/inb/inb-3/spm_anatomy_toolbox">
+	    Anatomy Toolbox</a> v1.5. The atlas is based on the
+	    miscroscopic and quantitative histological examination of
+	    ten human post-mortem brains. The histological volumes of
+	    these brains were 3D reconstructed and spatially
+	    normalised into the space of the MNI single subject
+	    template to create a probabilistic map of each area. For
+	    the FSL version of this atlas, these probabilistic maps
+	    were then linearly transformed into MNI152 space.</p>
+
+	  <p>Main references (to reference individual
+	    structures' maps, please see the publication list at the start
+	    of the <a href="http://www.fz-juelich.de/inb/inb-3/datapool/SPM/Manual_v15.pdf">Anatomy Toolbox manual</a>):<ul>
+	      <li>Amunts et al. Neuroanatomical Tract-Tracing 3:
+		Molecules, Neurons and Systems, ch18. Springer (2006)</li>
+	      <li>Eickhoff et al. A new SPM toolbox for combining
+		probabilistic cytoarchitectonic maps and functional imaging
+		data. Neuroimage 25(4):1325-35 (2005)</li>
+	      <li>Toga et al. Towards multimodal atlases of the human
+		brain. Nature Reviews Neuroscience 7:952-966 (2006)</li>
+<li>Eickhoff et al., Assignment of functional activations to probabilistic cytoarchitectonic areas revisited. NeuroImage, 36(3): 511-521 (2007)</li>
+	    </ul>
+	  </p>
+	</td>
+	<td><img src="atlas-juelich.png" width="100"></td>
+      </tr>
+
+      <tr><td colspan="2"><hr></td></tr>
+      <tr valign="top">
+	<td>
+	  <p><b><a name="wm"></a>JHU DTI-based white-matter atlases</b></p>
+	  <p>There are two white-matter atlases, both kindly provided
+	    by Dr. Susumu
+	    Mori, <a href="http://cmrm.med.jhmi.edu/">Laboratory of
+	    Brain Anatomical MRI</a>, Johns Hopkins
+	    University:</p>
+
+	  <p>In the <b>ICBM-DTI-81 white-matter labels atlas</b>, 50 white
+	    matter tract labels were created by hand segmentation of a
+	    standard-space average of diffusion MRI tensor maps from
+	    81 subjects; mean age 39 (18:59), M:42, F: 39. The
+	    diffusion data was kindly provided by the ICBM DTI
+	    workgroup.</p>
+
+	  <p>In the <b>JHU white-matter tractography atlas</b>, 20
+	    structures were identified probabilistically by averaging
+	    the results of running deterministic tractography on 28
+	    normal subjects (mean age 29, M:17, F:11).</P>
+
+	  <p>References:
+	    <ul>
+	      <li>Mori et al. MRI Atlas of Human White
+		Matter. Elsevier, Amsterdam, The Netherlands
+		(2005)</li>
+	      <li>Wakana et al. Reproducibility of quantitative tractography methods applied to cerebral white matter. NeuroImage 36:630-644 (2007)</li>
+	      <li>Hua et al. Tract probability maps in stereotaxic spaces: analysis of white matter anatomy and tract-specific quantification. NeuroImage, in press</li>
+	    </ul>
+	  </p>
+	<td><img src="atlas-jhuwm.png" width="100"></td>
+      </tr>
+
+      <tr><td colspan="2"><hr></td></tr>
+      <tr valign="top">
+	<td><p><b><a name="thal"></a>Oxford thalamic connectivity atlas</b></p>
+	  <p>A probabilistic atlas of 7 sub-thalamic regions, segmented according to their
+	    white-matter connectivity to cortical areas, kindly provided
+	    by Heidi Johansen-Berg and Timothy Behrens, FMRIB.</p>
+	  <p>This connectivity atlas reports probability of anatomical
+	    connection from points in the thalamus to each of 7 cortical
+	    zones. These probabilties are calculated using
+	    probabilistic diffusion tractography in multiple
+	    subjects. For more details see
+	    the <a href="http://www.fmrib.ox.ac.uk/connect/">Thalamic
+	      Connectivity Atlas</a> web page.</p>
+	  <p>References:<ul>
+	      <li>Behrens et al. Non-invasive mapping of connections
+		between human thalamus and cortex using diffusion imaging.  Nature
+		Neuroscience 6(7):750-757 (2003)</li>
+	      <li>Behrens et al. Characterisation and propagation of
+		uncertainty in diffusion weighted MR imaging.  Magnetic Resonance in
+		Medicine  50:1077-1088 (2003)</li></ul></p></td>
+	<td><img src="atlas-thalamic.png" width="100"></td>
+      </tr>
+
+     <tr><td colspan="2"><hr></td></tr>
+      <tr valign="top">
+	<td>
+	  <p><b><a name="tal"></a>Talairach atlas</b></p>
+	  <p>A conversion of the original Talairach structural
+	    labellings, kindly provided by Jack Lancaster and Diana
+	    Tordesillas Guti&eacute;rrez at
+	    the <a href="http://ric.uthscsa.edu/">Research Imaging
+	    Center</a>, UTHSCSA, Texas.</p>
+	  <p>This is a digitised version of the original (coarsely
+	    sliced) Talairach atlas (Lancaster 2000) after the
+	    application of a correcting affine transform (Lancaster
+	    2007) to register it into MNI152 space.</p>
+	  <p>References:
+	    <ul>
+	      <li>Talairach et al. Co-planar stereotaxic atlas of the
+		human brain. Thieme, New York. (1988)</li>
+	      <li>Lancaster et al. Bias between MNI and Talairach
+		coordinates analyzed using the ICBM-152 brain
+		template. Human Brain Mapping (in press) (2007)</li>
+	      <li>Lancaster et al. Automated Talairach Atlas labels for
+		functional brain mapping. Human Brain Mapping 10:120-131 (2000)</li>
+	    </ul>
+	  </p>
+	<td><img src="atlas-tal.png" width="100"></td>
+      </tr>
+
+      <tr><td colspan="2"><hr></td></tr>
+      <tr valign="top">
+	<td>
+	  <p><b><a name="mni"></a>MNI structural atlas</b></p>
+	  <p>9 anatomical structural regions, kindly provided by Jack
+	    Lancaster at
+	    the <a href="http://ric.uthscsa.edu/">Research Imaging
+	    Center</a>, UTHSCSA, Texas (originally from
+	    the <a
+	    href="http://www.bic.mni.mcgill.ca/bic_welcome.html">McConnell
+	    Brain Imaging Centre</a>, MNI).</p>
+	  <p>A single subject's structural image was hand segmented,
+	    and the labels were then propagated to more than 50
+	    subjects' structural images using nonlinear
+	    registration. Each resulting labelled brain was then
+	    transformed into MNI152 space using affine registration,
+	    before averaging segmentations across subjects to produce
+	    the final probability images. For more details see the
+	    <a href="http://ric.uthscsa.edu/resources/body.html">Talairach Daemon</a>.</p>
+	  <p>References:
+	    <ul>
+	      <li>Collins et al. Automatic 3-D model-based
+		neuroanatomical segmentation. Human Brain Mapping
+		3(3): 190-208. (1995)</li>
+	      <li>Mazziotta et al. A probabilistic atlas and reference
+		system for the human brain: International Consortium
+		for Brain Mapping (ICBM). Phil. Trans. Royal Soc. B
+		Biol. Sci.  356(1412):1293-1322 (2001) </li>
+	    </ul>
+	  </p>
+	</td>
+	<td><img src="atlas-mni.png" width="100"></td>
+      </tr>
+
+     <tr><td colspan="2"><hr></td></tr>
+   </table>
+  </body>
+</html>
Index: fslview/doc/fslview/atlas-reference.html
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--- /dev/null	1970-01-01 00:00:00.000000000 +0000
+++ fslview/doc/fslview/atlas-reference.html	2010-06-30 19:14:39.917560147 -0400
@@ -0,0 +1,94 @@
+<html>
+  <head>
+    <link rel="stylesheet" title="normal" type="text/css" href="fslview.css">
+    <title>Atlas Reference</title>
+  </head>
+  <body>
+    <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>
+&lt;?xml version="1.0" encoding="ISO-8859-1"?&gt;
+&lt;atlas version="1.0"&gt;
+  &lt;header&gt;
+    &lt;name&gt;MNI Structural Probability Atlas&lt;/name&gt;
+    &lt;type&gt;Probabalistic&lt;/type&gt;
+    &lt;images&gt;
+      &lt;imagefile&gt;/MNI/MNI-prob-2mm&lt;/imagefile&gt;
+      &lt;summaryimagefile&gt;/MNI/MNI-maxprob-thr25-2mm&lt;/summaryimagefile&gt;
+    &lt;images&gt;
+  &lt;/header&gt;
+  &lt;data&gt;
+    &lt;label index="0" x="39" y="73" z="35"&gt;Caudate&lt;/label&gt;
+    &lt;label index="1" x="34" y="32" z="15"&gt;Cerebellum&lt;/label&gt;
+    &lt;label index="2" x="45" y="90" z="29"&gt;Frontal Lobe&lt;/label&gt;
+    &lt;label index="3" x="27" y="73" z="30"&gt;Insula&lt;/label&gt;
+    &lt;label index="4" x="50" y="20" z="37"&gt;Occipital Lobe&lt;/label&gt;
+    &lt;label index="5" x="45" y="33" z="61"&gt;Parietal Lobe&lt;/label&gt;
+    &lt;label index="6" x="56" y="69" z="34"&gt;Putamen&lt;/label&gt;
+    &lt;label index="7" x="16" y="53" z="35"&gt;Temporal Lobe&lt;/label&gt;
+    &lt;label index="8" x="48" y="55" z="38"&gt;Thalamus&lt;/label&gt;
+  &lt;/data&gt;
+&lt;/atlas&gt;
+</pre>
+
+
+    <h4>Hints and tips for atlas developers</h4>
+
+
+
+  </body>
+</html>
Index: fslview/doc/fslview/atlas.html
===================================================================
--- fslview.orig/doc/fslview/atlas.html	2010-06-30 19:12:01.126482703 -0400
+++ fslview/doc/fslview/atlas.html	2010-06-30 19:14:39.921559671 -0400
@@ -7,7 +7,7 @@
     <h3>Anatomical atlas tools</h3>
 
     <p>These tools provide feedback via various <a
-      href="../data/atlas-descriptions.html">atlases</a> included in the
+      href="atlas-descriptions.html">atlases</a> included in the
       FSL/FSLView distributions. Labels from selected atlases can be
       displayed, summary images overlaid, structures located and
       single structure probabilty maps shown.</p>
Index: fslview/doc/fslview/fslview.adp
===================================================================
--- fslview.orig/doc/fslview/fslview.adp	2010-06-30 19:12:01.126482703 -0400
+++ fslview/doc/fslview/fslview.adp	2010-06-30 19:14:39.921559671 -0400
@@ -72,7 +72,7 @@
   </DCF>
 
   <DCF ref="atlas.html" icon="./atlashelp.png" title="Anatomical atlas tools">
-    <section ref="../data/atlas-descriptions.html" title="The bundled atlases"></section>
+    <section ref="./atlas-descriptions.html" title="The bundled atlases"></section>
     <section ref="./atlas-tool.html" title="The atlas tool"></section>
     <section ref="./atlas-select.html" title="The atlas selection dialog"></section>
     <section ref="./atlas-inspect.html" title="The atlas inspector dialog"></section>
