FSLeyes, the FSL image viewer
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
All of the core dependencies of FSLeyes are listed in requirements.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:
- OpenGL 2.1, with the following extensions:
FSLeyes also requires the presence of GLUT, or FreeGLUT.
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/.
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).
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