Add basic volume example and clarify basic surface example

Adding underlying files for logo

Adapting MNE Python gen_rst sphinxext for thumbnails

Change name of label example for ordering

Change name of contour example for ordering

Fix gen_rst so example index isn't double-headered

Delete montage example for now

Move view example for ordering

Rename view example

Improve code and aesthetics of parc values example

Updating basic volume example further

Name full and thumb images differently in gen_rst

Track volume mask file

Change datatype of mask file for better storage

Demonstrate alpha in parcellation example

Unify license statements across the package

Change example README as it is now incorporated into the docs page

Change view in label example

Updating website banner

Converting README to markdown and updating some aspects of it

Flattening and tweaking doc index

Increasing the size of the example thumbnails

Update Alex's affiliation

removing large files

Author: mwaskom

LICENSE

@@ -0,0 +1,24 @@
+Copyright (c) 2011, Neuroimaging in Python Team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+    * Redistributions of source code must retain the above copyright
+      notice, this list of conditions and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright
+      notice, this list of conditions and the following disclaimer in the
+      documentation and/or other materials provided with the distribution.
+    * Neither the name of the <organization> nor the
+      names of its contributors may be used to endorse or promote products
+      derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL <COPYRIGHT HOLDER> BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -0,0 +1,64 @@
+PySurfer
+========
+
+![](doc/logo_files/pysurfer_logo_small.png)
+
+PySurfer is a Python package for interacting with a cortical surface
+representations of neuroimaging data. It extends Mayavi's powerful
+visualization engine with a high-level interface for working with MRI and MEG
+data.
+
+PySurfer offers both a command-line interface designed to broadly the
+Freesurfer Tksurfer program and a Python library for writing scripts to
+efficiently explore complex datasets and prepare publication-ready figures.
+
+To goal of the project is to facilitate the production of figures that are both
+beautiful and scientifically informative.
+
+Important Links
+---------------
+
+- Official source code repository: https://github.com/nipy/PySurfer
+- Online documentation (stable): http://pysurfer.github.com/
+- NITRC page: http://www.nitrc.org/projects/pysurfer
+- Freesurfer: http://surfer.nmr.mgh.harvard.edu/
+- Mailing list: http://mail.scipy.org/mailman/listinfo/nipy-devel
+
+Install
+-------
+
+This packages uses setuptools. To install it for all users, run:
+
+    python setup.py build
+    sudo python setup.py install
+
+If you do not have sudo privileges, you can install locally:
+
+    python setup.py install --home
+
+For information about dependencies, please see the [online
+documentation](http://pysurfer.github.com/install.html)
+
+License
+-------
+
+Available under the Revised BSD (3-clause) license.
+
+Testing
+-------
+
+You can launch the test suite by running `nosetests` from the source folder.
+
+Another way to test is to build the documentation, which will run the example
+scripts and automatically generate static image output. From the source
+directory:
+
+    cd doc/
+    make clean
+    make html
+
+The resulting documentation will live at _build/html/index.html, which can be
+compared to the online docs.
+
+Either method will work only if you have Freesurfer installed on your machine
+with a valid SUBJECTS\_DIR folder.

README.rst

@@ -4,6 +4,6 @@
 {% block header %}
 <div style="background-color: white; text-align: left; padding: 10px 10px 15px 15px">
  <a href="{{pathto('index') }}">
-  <img src="{{ pathto("_static/banner.png", 1) }}" alt="PySurfer logo"  border="0" />
+  <img src="{{ pathto("_static/banner.png", 1) }}" alt="PySurfer logo" height=180px width=600px border="0" />
 </div>
 {% endblock %}

doc/_static/banner.png

@@ -1,5 +1,5 @@
-Documentation
-=============
+Detailed Documentation
+======================
 
 .. _doc-index:
 

doc/_static/pysurfer_logo_small.png

@@ -1,22 +1,18 @@
 Introduction
 ============
 
-PySurfer is a Python based program for visualization and interaction
-with cortical surface representations of neuroimaging data from
-`Freesurfer <http://surfer.nmr.mgh.harvard.edu/>`_. It extends
-`Mayavi's <http://github.enthought.com/mayavi/mayavi/index.html>`_ powerful
-visualization engine with a high-level interface for working with
-MRI and MEG data.
+PySurfer is a Python library for visualizing cortical surface representations
+of neuroimaging data. The package is primarily intended for use with
+`Freesurfer <http://surfer.nmr.mgh.harvard.edu/>`_, but it can plot data that
+are drawn from a variety of sources. PySurfer extends `Mayavi's
+<http://github.enthought.com/mayavi/mayavi/index.html>`_ powerful rendering 
+engine with a high-level interface for working with MRI and MEG data.
 
-PySurfer offers both a command-line interface designed to broadly
-replicate Freesurfer's Tksurfer program as well as a Python library
-for writing scripts to efficiently explore complex datasets.
-
-Contents
---------
+More Information
+----------------
 
 .. toctree::
-    :maxdepth: 2
+    :maxdepth: 1
 
     install
     examples/index.rst
@@ -25,20 +21,16 @@ Contents
 Authors
 -------
 
-Michael Waskom, Stanford University
-
-Alexandre Gramfort, Harvard Med. School MGH Martinos Center - INRIA
-
-Scott Burns, Harvard Med. School MGH Martinos Center
-
-Martin Luessi, Harvard Med. School MGH Martinos Center
-
-Eric Larson, University of Washington ILABS
+- Michael Waskom, Stanford University
+- Alexandre Gramfort, Telecom ParisTech - CNRS, CEA - Neurospin
+- Scott Burns, Vanderbilt University
+- Martin Luessi, Harvard Medical School MGH Martinos Center
+- Eric Larson, University of Washington ILABS
 
 License
 -------
 
-The PySurfer source code is available under the simplified BSD license
+The PySurfer source code is available under the Revised BSD (3-Clause) license
 
 Support
 -------