fsleyes

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).