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Add a narrative intro explaining what PySurfer is
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doc/index.rst

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.. toctree::
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:maxdepth: 1
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intro
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install
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examples/index.rst
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documentation/index.rst

doc/intro.rst

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.. _intro:
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What is PySurfer?
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=================
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PySurfer is a Python library and application for visualizing brain imaging
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data. It is specifically useful for plotting data on a three-dimensional mesh
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representing the cortical surface of the brain. If you have functional MRI,
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magnetoencephalography, or anatomical measurements from cortex, PySurfer can
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help you turn them into beautiful and reproducible graphics.
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PySurfer uses an explicit model of cortical geometry to generate
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highly-accurate images of neuroimaging data. This is preferable to other
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approaches that use simple 3D renderings of a brain volume because the
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underlying topology of the cortex is a two-dimensional sheet. PySurfer can
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read cortical models that have been processed using Freesurfer_ to "inflate"
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the cortical folds and reveal activations that are buried within deep sulci.
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This presentation is much closer to how cortical areas are laid out, and it can
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help you understand and communicate your efforts to map functional or
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morphometric organization.
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PySurfer and its dependencies are written in Python and released with a liberal
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open source license. PySurfer can be combined with other tools from the nipy_
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ecosystem to manipulate and plot data in the same script or interactive
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session. The visualization is primarily controlled with a high-level API that
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allow you to draw a complex scene with just a few lines of code. This means
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that PySurfer is naturally scriptable. Once you have developed a basic
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visualization, it's easy to add a for-loop and generate the same image for
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every subject in your experiment. It also aids the reproducibility of graphics
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you create for conferences or papers, as each figure can be associated with a
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short script that shows exactly how the visualization was produced.
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To see a set of examples demonstrating some of PySurfer's capabilities, you can
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check out the :ref:`example gallery <examples>`.
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.. include:: links_names.txt
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examples/README.rst

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.. _examples:
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PySurfer Example Gallery
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========================
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examples/index.rst

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.. _examples:
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This page offers a set of example scripts intended to demonstrate the
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functionality offered by PySurfer, from the most basic tasks to more complex
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visualizations.

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