fsleyes 1.16.3
FSLeyes, the FSL image viewer
License: Apache License Version 2.0
Requires Python: >=3.9

FSLeyes
=======

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

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

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

.. 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/


`FSLeyes <https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes>`_ is the `FSL
<https://fsl.fmrib.ox.ac.uk/fsl/docs/>`_ image viewer.


Installation
------------


FSLeyes is a GUI application written in Python, and built on `wxPython
<https://www.wxpython.org>`_. FSLeyes requires OpenGL for visualisation.


In the majority of cases, you should be able to follow the installation
instructions outlined at the FSLeyes home page:

https://fsl.fmrib.ox.ac.uk/fsl/docs/#/utilities/fsleyes


Dependencies
------------


All of the dependencies of FSLeyes are listed in `pyproject.toml
<pyproject.toml>`_.

Being an OpenGL application, FSLeyes can only be used on computers with
graphics hardware (or a software GL renderer) that supports one of the
following versions:

- OpenGL 3.3

- OpenGL 2.1, with the following extensions:

  - ``EXT_framebuffer_object``
  - ``ARB_instanced_arrays``
  - ``ARB_draw_instanced``

- OpenGL 1.4, with the following extensions:

  - ``ARB_vertex_program``
  - ``ARB_fragment_program``
  - ``EXT_framebuffer_object``
  - ``GL_ARB_texture_non_power_of_two``


Documentation
-------------

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/


The FSLeyes user and API documentation is written in ReStructuredText, and can
be built using `sphinx <http://www.sphinx-doc.org/>`_::

    pip install -e ".[doc]"
    sphinx-build userdoc userdoc/html
    sphinx-build apidoc  apidoc/html

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


Credits
-------


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

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.
  http://dannyruijters.nl/docs/cudaPrefilter3.pdf

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).

The *brain_colours* colour maps were produced and provided by Cyril Pernet
(https://doi.org/10.1111/ejn.14430).

The data files used in the FSLeyes ``tractogram`` unit tests are from the
`DIPY <https://dipy.org/>`_ example data sets
(``dipy.data.fetch_stanford_hardi``).