fsleyes 0.30.1

FSLeyes, the FSL image viewer

FSLeyes is the FSL image viewer.

Installation

These instructions pertain to manual installation of FSLeyes into a Python environment. Standalone versions of FSLeyes can be downloaded from https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes.

FSLeyes is a wxPython application. If you are on Linux, you will need to install wxPython first - head to https://extras.wxpython.org/wxPython4/extras/linux/ and find the directory that matches your OS. Then run this command (change the URL accordingly):

pip install --only-binary wxpython -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/ubuntu-16.04/ wxpython

Once wxPython has been installed, you can install FSLeyes like so:

pip install fsleyes

To install FSLeyes with all of the optional dependencies (for additional functionality):

pip install fsleyes[extras]

As an alternate to using pip, FSLeyes is also available on conda-forge:

conda install -c conda-forge fsleyes

Dependencies

All of the core dependencies of FSLeyes are listed in requirements.txt.

Some extra dependencies, which provide additional functionality, are listed in requirements-extras.txt and requirements-notebook.txt.

Dependencies for running tests and building the documentation are listed in requirements-dev.txt.

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 1.4, with the following extensions:

  • ARB_vertex_program

  • ARB_fragment_program

  • EXT_framebuffer_object

  • GL_ARB_texture_non_power_of_two

• OpenGL 2.1, with the following extensions:

  • EXT_framebuffer_object

  • ARB_instanced_arrays

  • ARB_draw_instanced

FSLeyes also requires the presence of GLUT, or FreeGLUT.

Documentation

The FSLeyes user and API documentation is written in ReStructuredText, and can be built using sphinx:

pip install -r requirements-dev.txt
python setup.py userdoc
python setup.py apidoc

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).