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FSLeyes
=======

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.. image:: https://img.shields.io/pypi/v/fsleyes.svg
   :target: https://pypi.python.org/pypi/fsleyes/

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.. image:: https://anaconda.org/conda-forge/fsleyes/badges/version.svg
   :target: https://anaconda.org/conda-forge/fsleyes

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.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1470761.svg
   :target: https://doi.org/10.5281/zenodo.1470761

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.. image:: https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/badges/master/coverage.svg
   :target: https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/commits/master/
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`FSLeyes <https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes>`_ is the `FSL
<http://fsl.fmrib.ox.ac.uk/fsl/fslwiki>`_ image viewer.
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Installation
------------


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FSLeyes is a GUI application written in Python, and built on `wxPython
<https://www.wxpython.org>`_. FSLeyes requires OpenGL for visualisation.
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In the majority of cases, you should be able to follow the installation
instructions outlined at the FSLeyes home page:
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https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes.
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Dependencies
------------


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All of the core dependencies of FSLeyes are listed in `requirements.txt
<requirements.txt>`_.


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Some extra dependencies, which provide additional functionality, are listed in
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`requirements-extra.txt <requirements-extra.txt>`_ and
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`requirements-notebook.txt <requirements-notebook.txt>`_.


Dependencies for running tests and building the documentation are listed
in `requirements-dev.txt <requirements-dev.txt>`_.
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Being an OpenGL application, FSLeyes can only be used on computers with
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graphics hardware (or a software GL renderer) that supports one of the
following versions:
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- OpenGL 1.4, with the following extensions:
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  - ``ARB_vertex_program``
  - ``ARB_fragment_program``
  - ``EXT_framebuffer_object``
  - ``GL_ARB_texture_non_power_of_two``
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- OpenGL 2.1, with the following extensions:
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  - ``EXT_framebuffer_object``
  - ``ARB_instanced_arrays``
  - ``ARB_draw_instanced``
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Documentation
-------------

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The FSLeyes user and API documentation are hosted at:

 - https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/userdoc/
 - https://open.win.ox.ac.uk/pages/fsl/fsleyes/fsleyes/apidoc/

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The FSLeyes user and API documentation is written in ReStructuredText, and can
be built using `sphinx <http://www.sphinx-doc.org/>`_::
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    pip install -r requirements-dev.txt
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    python setup.py userdoc
    python setup.py apidoc

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The documentation will be generated and saved in ``userdoc/html/`` and
``apidoc/html/``.
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Credits
-------


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Some of the FSLeyes icons are derived from the Freeline icon set, by Enes Dal,
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available at https://www.iconfinder.com/Enesdal, and released under the
Creative Commons (Attribution 3.0 Unported) license.
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The volumetric spline interpolation routine uses code from:

Daniel Ruijters and Philippe Thévenaz,
GPU Prefilter for Accurate Cubic B-Spline Interpolation,
The Computer Journal, vol. 55, no. 1, pp. 15-20, January 2012.
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http://dannyruijters.nl/docs/cudaPrefilter3.pdf
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The GLSL parser is based on code by Nicolas P . Rougier, available at
https://github.com/rougier/glsl-parser, and released under the BSD license.

DICOM to NIFTI conversion is performed with Chris Rorden's dcm2niix
(https://github.com/rordenlab/dcm2niix).
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The *brain_colours* colour maps were produced and provided by Cyril Pernet
(https://doi.org/10.1111/ejn.14430).