add license page;

_sources/document.txt

@@ -4,7 +4,7 @@
    contain the root `toctree` directive.
 
 ========
-Homepage
+Document
 ========
 
 Table of Contents

_sources/download.txt

@@ -19,23 +19,36 @@ Download Links
 |winlogo| `Windows Installer (x86) 
 <static/DiffusionKitSetup-WIN32-v1.1-r151109.exe>`_
 
-|rellogo| `Linux Binary Package (x86) 
+|rellogo| `Linux Binary Package (x86-64) 
 <static/DiffusionKitSetup-x86_64-v1.1-r151109.tar.gz>`_
 
 System requirement
 ==================
 
-Basically this software can run in any system, including 32/64-bit MS Windows/Linux OS, although currently we only tested and released the binary packages for Windows/Linux OS. The software is developed based on C/C++, and some platform independent packages, including ITK, VTK, and OpenCV, etc. However, for high-performance data processing and visualization, we recommend using 64-bit OS with multi-core CPU and standalone video card.
+Basically this software can run in any system, including 32/64-bit MS Windows/Linux OS, 
+although currently we only tested and released the binary packages for Windows/Linux OS. 
+The software is developed based on C/C++, and some platform independent packages, 
+including ITK, VTK, and OpenCV, etc. 
+However, for high-performance data processing and visualization, 
+we recommend using 64-bit OS with multi-core CPU and standalone video card.
 
 Install/Uninstall
 =================
 
-Please download the package from http://brainnetome.org/dmri , according to your own OS. Unpack the files to where you want and you can enjoy the software. The 64-bit OS is recommended for high-performance data processing. Each installation package is completely standalone so you DO NOT need to install ANY other dependency to run the software. If you encounter any dependency problem please DO `contact us <mailto:[email protected]>`_.
+Please download the package from http://diffusion.brainnetome.org , 
+according to your own OS. Unpack the files to where you want and you can enjoy the software. 
+The 64-bit OS is recommended for high-performance data processing. 
+Each installation package is completely standalone so you DO NOT need to 
+install ANY other dependency to run the software. 
+If you encounter any dependency problem please DO `contact us <mailto:[email protected]>`_.
 
 For MS Windows OS
 -----------------
 
-Double click the ``DiffusionKitSetup-v1.1.exe`` file and then choose the destination path according to the wizard. You may need to provide administrator permission if you want to put the files into the system path. Similarly, to uninstall you only need to hit the menu of “uninstall” in the MS Windows start menu.
+Double click the ``DiffusionKitSetup-v1.1.exe`` file and then choose the destination path 
+according to the wizard. You may need to provide administrator permission 
+if you want to put the files into the system path. 
+Similarly, to uninstall you only need to hit the menu of “uninstall” in the MS Windows start menu.
 
 For Linux OS
 ------------

_sources/fileformat.txt

@@ -38,6 +38,7 @@ The .fiber format is as following ::
 
 The first and second line indicates who produces the file and the version of the file format, and line 3 to line 7 characterize several main attributes of this fiber bundle. From line 8, fiber-wise node descriptions are presented; for example, for one fiber on line 8, [80 101.378 0.5 0.1] corresponds to the total number of nodes, length, mean FA and mean MD of this fiber. Starting from line 9, properties of each node of the fiber are described, e.g., [110.758 148.574 124.982 0.166754 0.3] denote x-, y- and z-coordinate, FA and MD of this node.
 
+.. [4] http://www.mccauslandcenter.sc.edu/mricro
 .. [17] http://trackvis.org
 
 .. include:: common.txt

_sources/index.txt

@@ -65,6 +65,7 @@ material contained within.
    document.rst
    screenshot.rst
    download.rst
+   license.rst
    feedback.rst
 
 Reference

_sources/license.txt

@@ -0,0 +1,22 @@
+.. diffusionkit documentation master file, created by
+   sphinx-quickstart on Mon Oct 26 10:48:55 2015.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+=======
+License
+=======
+
+Copyright |copy|  2013-2015 `Brainnetome Center <http://www.brainnetome.org/>`_, CASIA
+
+This software is provided 'as-is', without any express or implied warranty. 
+In no event will the authors be held liable for any damages arising from the use of this software.
+
+Permission is granted to use this software for any purpose, 
+including research purpose and commercial applications, subject to the following restrictions:
+
+1. The origin of this software must not be misrepresented; If you use this software in your work, an acknowledgment is required. A written permission is also required for commercial use.
+2. Altered versions must be plainly marked as such, and must not be misrepresented as being the original software.
+3. This notice may not be removed or altered from any distribution.
+
+.. include:: common.txt

document.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Homepage &mdash; diffusionkit 1.1 beta documentation</title>
+  <title>Document &mdash; diffusionkit 1.1 beta documentation</title>
 
 
 
@@ -82,7 +82,7 @@
 
 
                 <ul class="current">
-<li class="toctree-l1 current"><a class="current reference internal" href="">Homepage</a><ul>
+<li class="toctree-l1 current"><a class="current reference internal" href="">Document</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="overview.html">Overivew</a></li>
 <li class="toctree-l2"><a class="reference internal" href="userguide.html">User Guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
@@ -93,6 +93,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="screenshot.html">Screenshots</a></li>
 <li class="toctree-l1"><a class="reference internal" href="download.html">Download</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="feedback.html">Support</a></li>
 </ul>
 
@@ -124,7 +125,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="index.html">Docs</a> &raquo;</li>
 
-    <li>Homepage</li>
+    <li>Document</li>
       <li class="wy-breadcrumbs-aside">
 
 
@@ -136,8 +137,8 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <div class="section" id="homepage">
-<h1>Homepage<a class="headerlink" href="#homepage" title="Permalink to this headline">¶</a></h1>
+  <div class="section" id="document">
+<h1>Document<a class="headerlink" href="#document" title="Permalink to this headline">¶</a></h1>
 <p>Table of Contents</p>
 <div class="toctree-wrapper compound">
 <ul>
@@ -221,7 +222,7 @@ <h1>Homepage<a class="headerlink" href="#homepage" title="Permalink to this head
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2015, Brainnetome Center, CASIA.
+        &copy; Copyright 2013-2015, Brainnetome Center, CASIA.
 
     </p>
   </div> 

download.html

@@ -31,7 +31,7 @@
 
 
     <link rel="top" title="diffusionkit 1.1 beta documentation" href="index.html"/>
-        <link rel="next" title="Support" href="feedback.html"/>
+        <link rel="next" title="License" href="license.html"/>
         <link rel="prev" title="Screenshots" href="screenshot.html"/> 
 
 
@@ -82,7 +82,7 @@
 
 
                 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="document.html">Homepage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="document.html">Document</a></li>
 <li class="toctree-l1"><a class="reference internal" href="screenshot.html">Screenshots</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="">Download</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#download-links">Download Links</a></li>
@@ -94,6 +94,7 @@
 </li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="feedback.html">Support</a></li>
 </ul>
 
@@ -143,18 +144,31 @@ <h1>Download<a class="headerlink" href="#download" title="Permalink to this head
 <h2>Download Links<a class="headerlink" href="#download-links" title="Permalink to this headline">¶</a></h2>
 <p><img alt="winlogo" src="_images/winlogo.jpg" /> <a class="reference external" href="static/DiffusionKitSetup-WIN64-v1.1-r151109.exe">Windows Installer (x86-64)</a></p>
 <p><img alt="winlogo" src="_images/winlogo.jpg" /> <a class="reference external" href="static/DiffusionKitSetup-WIN32-v1.1-r151109.exe">Windows Installer (x86)</a></p>
-<p><img alt="rellogo" src="_images/rellogo.jpg" /> <a class="reference external" href="static/DiffusionKitSetup-x86_64-v1.1-r151109.tar.gz">Linux Binary Package (x86)</a></p>
+<p><img alt="rellogo" src="_images/rellogo.jpg" /> <a class="reference external" href="static/DiffusionKitSetup-x86_64-v1.1-r151109.tar.gz">Linux Binary Package (x86-64)</a></p>
 </div>
 <div class="section" id="system-requirement">
 <h2>System requirement<a class="headerlink" href="#system-requirement" title="Permalink to this headline">¶</a></h2>
-<p>Basically this software can run in any system, including 32/64-bit MS Windows/Linux OS, although currently we only tested and released the binary packages for Windows/Linux OS. The software is developed based on C/C++, and some platform independent packages, including ITK, VTK, and OpenCV, etc. However, for high-performance data processing and visualization, we recommend using 64-bit OS with multi-core CPU and standalone video card.</p>
+<p>Basically this software can run in any system, including 32/64-bit MS Windows/Linux OS,
+although currently we only tested and released the binary packages for Windows/Linux OS.
+The software is developed based on C/C++, and some platform independent packages,
+including ITK, VTK, and OpenCV, etc.
+However, for high-performance data processing and visualization,
+we recommend using 64-bit OS with multi-core CPU and standalone video card.</p>
 </div>
 <div class="section" id="install-uninstall">
 <h2>Install/Uninstall<a class="headerlink" href="#install-uninstall" title="Permalink to this headline">¶</a></h2>
-<p>Please download the package from <a class="reference external" href="http://brainnetome.org/dmri">http://brainnetome.org/dmri</a> , according to your own OS. Unpack the files to where you want and you can enjoy the software. The 64-bit OS is recommended for high-performance data processing. Each installation package is completely standalone so you DO NOT need to install ANY other dependency to run the software. If you encounter any dependency problem please DO <a class="reference external" href="mailto:diffusion&#46;kit&#37;&#52;&#48;nlpr&#46;ia&#46;ac&#46;cn">contact us</a>.</p>
+<p>Please download the package from <a class="reference external" href="http://diffusion.brainnetome.org">http://diffusion.brainnetome.org</a> ,
+according to your own OS. Unpack the files to where you want and you can enjoy the software.
+The 64-bit OS is recommended for high-performance data processing.
+Each installation package is completely standalone so you DO NOT need to
+install ANY other dependency to run the software.
+If you encounter any dependency problem please DO <a class="reference external" href="mailto:diffusion&#46;kit&#37;&#52;&#48;nlpr&#46;ia&#46;ac&#46;cn">contact us</a>.</p>
 <div class="section" id="for-ms-windows-os">
 <h3>For MS Windows OS<a class="headerlink" href="#for-ms-windows-os" title="Permalink to this headline">¶</a></h3>
-<p>Double click the <code class="docutils literal"><span class="pre">DiffusionKitSetup-v1.1.exe</span></code> file and then choose the destination path according to the wizard. You may need to provide administrator permission if you want to put the files into the system path. Similarly, to uninstall you only need to hit the menu of “uninstall” in the MS Windows start menu.</p>
+<p>Double click the <code class="docutils literal"><span class="pre">DiffusionKitSetup-v1.1.exe</span></code> file and then choose the destination path
+according to the wizard. You may need to provide administrator permission
+if you want to put the files into the system path.
+Similarly, to uninstall you only need to hit the menu of “uninstall” in the MS Windows start menu.</p>
 </div>
 <div class="section" id="for-linux-os">
 <h3>For Linux OS<a class="headerlink" href="#for-linux-os" title="Permalink to this headline">¶</a></h3>
@@ -193,7 +207,7 @@ <h3>For Linux OS<a class="headerlink" href="#for-linux-os" title="Permalink to t
 
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
-        <a href="feedback.html" class="btn btn-neutral float-right" title="Support" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="license.html" class="btn btn-neutral float-right" title="License" accesskey="n">Next <span class="fa fa-arrow-circle-right"></span></a>
 
 
         <a href="screenshot.html" class="btn btn-neutral" title="Screenshots" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
@@ -205,7 +219,7 @@ <h3>For Linux OS<a class="headerlink" href="#for-linux-os" title="Permalink to t
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2015, Brainnetome Center, CASIA.
+        &copy; Copyright 2013-2015, Brainnetome Center, CASIA.
 
     </p>
   </div> 

feedback.html

@@ -32,7 +32,7 @@
 
 
     <link rel="top" title="diffusionkit 1.1 beta documentation" href="index.html"/>
-        <link rel="prev" title="Download" href="download.html"/> 
+        <link rel="prev" title="License" href="license.html"/> 
 
 
   <script src="_static/js/modernizr.min.js"></script>
@@ -82,9 +82,10 @@
 
 
                 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="document.html">Homepage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="document.html">Document</a></li>
 <li class="toctree-l1"><a class="reference internal" href="screenshot.html">Screenshots</a></li>
 <li class="toctree-l1"><a class="reference internal" href="download.html">Download</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="">Support</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#feedback">Feedback</a></li>
 </ul>
@@ -164,7 +165,7 @@ <h2>Feedback<a class="headerlink" href="#feedback" title="Permalink to this head
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
 
 
-        <a href="download.html" class="btn btn-neutral" title="Download" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="license.html" class="btn btn-neutral" title="License" accesskey="p"><span class="fa fa-arrow-circle-left"></span> Previous</a>
 
     </div>
 
@@ -173,7 +174,7 @@ <h2>Feedback<a class="headerlink" href="#feedback" title="Permalink to this head
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2015, Brainnetome Center, CASIA.
+        &copy; Copyright 2013-2015, Brainnetome Center, CASIA.
 
     </p>
   </div> 

fileformat.html

@@ -32,7 +32,7 @@
 
 
     <link rel="top" title="diffusionkit 1.1 beta documentation" href="index.html"/>
-        <link rel="up" title="Homepage" href="document.html"/>
+        <link rel="up" title="Document" href="document.html"/>
         <link rel="next" title="TO-DO List" href="todo.html"/>
         <link rel="prev" title="Tutorial" href="tutorial.html"/> 
 
@@ -84,7 +84,7 @@
 
 
                 <ul class="current">
-<li class="toctree-l1 current"><a class="reference internal" href="document.html">Homepage</a><ul class="current">
+<li class="toctree-l1 current"><a class="reference internal" href="document.html">Document</a><ul class="current">
 <li class="toctree-l2"><a class="reference internal" href="overview.html">Overivew</a></li>
 <li class="toctree-l2"><a class="reference internal" href="userguide.html">User Guide</a></li>
 <li class="toctree-l2"><a class="reference internal" href="tutorial.html">Tutorial</a></li>
@@ -99,6 +99,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="screenshot.html">Screenshots</a></li>
 <li class="toctree-l1"><a class="reference internal" href="download.html">Download</a></li>
+<li class="toctree-l1"><a class="reference internal" href="license.html">License</a></li>
 <li class="toctree-l1"><a class="reference internal" href="feedback.html">Support</a></li>
 </ul>
 
@@ -130,7 +131,7 @@
   <ul class="wy-breadcrumbs">
     <li><a href="index.html">Docs</a> &raquo;</li>
 
-          <li><a href="document.html">Homepage</a> &raquo;</li>
+          <li><a href="document.html">Document</a> &raquo;</li>
 
     <li>Data format</li>
       <li class="wy-breadcrumbs-aside">
@@ -152,11 +153,11 @@
 <h1>Data format<a class="headerlink" href="#data-format" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="input">
 <h2>Input<a class="headerlink" href="#input" title="Permalink to this headline">¶</a></h2>
-<p>Since we apply the dcm2nii to unify the format of input data, it can support most types of DICOM files (in folders). Please refer to the author’s webpage for more information <a href="#id4"><span class="problematic" id="id5"><span id="id1"></span>[4]_</span></a>. Please also get back to us if you encounter any problems.</p>
+<p>Since we apply the dcm2nii to unify the format of input data, it can support most types of DICOM files (in folders). Please refer to the author’s webpage for more information <a class="footnote-reference" href="#id3" id="id1">[4]</a>. Please also get back to us if you encounter any problems.</p>
 </div>
 <div class="section" id="output">
 <h2>Output<a class="headerlink" href="#output" title="Permalink to this headline">¶</a></h2>
-<p>All the intermediate files are in compressed NIFTI format (.nii.gz). The final track file is in .fiber/.fbr or .trk format, where the former is a short version of the later one. The .trk format is from the TrackVis <a class="footnote-reference" href="#id3" id="id2">[17]</a>.</p>
+<p>All the intermediate files are in compressed NIFTI format (.nii.gz). The final track file is in .fiber/.fbr or .trk format, where the former is a short version of the later one. The .trk format is from the TrackVis <a class="footnote-reference" href="#id4" id="id2">[17]</a>.</p>
 <p>The .fiber format is as following</p>
 <div class="highlight-python"><div class="highlight"><pre>Brainnetome fiber tracking
 Version 1
@@ -174,6 +175,12 @@ <h2>Output<a class="headerlink" href="#output" title="Permalink to this headline
 <table class="docutils footnote" frame="void" id="id3" rules="none">
 <colgroup><col class="label" /><col /></colgroup>
 <tbody valign="top">
+<tr><td class="label"><a class="fn-backref" href="#id1">[4]</a></td><td><a class="reference external" href="http://www.mccauslandcenter.sc.edu/mricro">http://www.mccauslandcenter.sc.edu/mricro</a></td></tr>
+</tbody>
+</table>
+<table class="docutils footnote" frame="void" id="id4" rules="none">
+<colgroup><col class="label" /><col /></colgroup>
+<tbody valign="top">
 <tr><td class="label"><a class="fn-backref" href="#id2">[17]</a></td><td><a class="reference external" href="http://trackvis.org">http://trackvis.org</a></td></tr>
 </tbody>
 </table>
@@ -211,7 +218,7 @@ <h2>Output<a class="headerlink" href="#output" title="Permalink to this headline
 
   <div role="contentinfo">
     <p>
-        &copy; Copyright 2015, Brainnetome Center, CASIA.
+        &copy; Copyright 2013-2015, Brainnetome Center, CASIA.
 
     </p>
   </div>