FSLeyes (pronounced fossilise) is the new FSL image viewer, released with FSL 5.0.10.
Follow FSLeyes on Twitter to be notified of new releases.
FSLeyes can either be installed as a standalone application, installed into a conda environment, or installed into a Python environment (for advanced users).
Install standalone application (recommended)
This is currently the recommended way to install FSLeyes.
The links below are currently out of date due to an issue with our web server - click here to download the latest version of FSLeyes.
Download the latest version of FSLeyes for your OS via the links below. If your OS is not listed, you will need to install FSLeyes into a Python environment (outlined below).
Only Ubuntu LTS release are supported - the above builds are not expected to work on interim Ubuntu releases.
If you are installing FSLeyes independently of FSL, simply unzip into a location of your choice.
If you wish to upgrade your version of FSLeyes which was installed as part of FSL (note: you may need to ask your system administrator to do this):
cd $FSLDIR/bin/ sudo mv FSLeyes.app FSLeyes.app_backup sudo unzip /path/to/downloaded/FSLeyes_macos_latest.zip
cd $FSLDIR/bin/ sudo mv FSLeyes FSLeyes_backup sudo unzip /path/to/downloaded/FSLeyes_centos6_latest.zip
If the newly installed version works, you may safely remove the $FSLDIR/bin/FSLeyes.app_backup ($FSLDIR/bin/FSLeyes_backup under Linux) directory.
If you are installing FSLeyes into a version of FSL which is older than 5.0.10, you will also need to create a link to the newly installed FSLeyes:
cd $FSLDIR/bin sudo echo -e '#!/usr/bin/env bash\n$FSLDIR/bin/FSLeyes.app/Contents/MacOS/fsleyes "$@"' > fsleyes sudo chmod a+x fsleyes
cd $FSLDIR/bin sudo ln -s FSLeyes/fsleyes ./fsleyes
Install into conda environment (recommended)
conda install -c conda-forge fsleyes
Install into a Python environment (advanced)
This method is suitable for Python users who are comfortable creating virtual environments.
python -m venv fsleyes-virtualenv . fsleyes-virtualenv/bin/activate
Once you have activated your virtual environment, you should be able to install FSLeyes like so:
pip install fsleyes
Before installing FSLeyes, you first need to install wxPython. The easiest way to do this on Linux is to use the pre-release wxPython builds available at https://extras.wxpython.org/wxPython4/extras/linux/. For example, if you are using CentOS 7:
pip install -f https://extras.wxpython.org/wxPython4/extras/linux/gtk2/centos-7 wxpython pip install fsleyes
You will also need to install the wxPython runtime dependencies. Under CentOS 7, you will need to run the following command:
sudo yum install freeglut SDL
Similarly, under Ubuntu:
sudo apt-get install freeglut3 libsdl1.2debian
Another option is to install wxPython directly from PyPi - if you do this, you will need to have C/C++ compilers installed, and all of the dependencies required to compile wxPython. Under CentOS 7, run the following commands:
sudo yum groupinstall "Development tools" sudo yum install gtk2-devel gtk3-devel webkitgtk-devel webkitgtk3-devel sudo yum install libjpeg-turbo-devel libtiff-devel SDL-devel gstreamer-plugins-base-devel libnotify-devel freeglut-devel
Under Ubuntu, run the following:
sudo apt-get install build-essential sudo apt-get install libgtk2.0-dev libgtk-3-dev libwebkitgtk-dev libwebkitgtk-3.0-dev sudo apt-get install libjpeg-turbo8-dev libtiff5-dev libsdl1.2-dev libgstreamer1.0-dev libgstreamer-plugins-base1.0-dev libnotify-dev freeglut3-dev
Then you should be able to pip install fsleyes as described above.
Help and troubleshooting
User documentation for FSLeyes can be found here.
If you are having trouble getting FSLeyes to run, a solution may be documented on the troubleshooting page.
You may also find a solution to your problem in the FSL mailing list archives.
If you have found a bug in FSLeyes, you can also open an issue on github.
The source code for FSLeyes and its dependent projects is hosted here:
API/developer documentation can be found here:
If you would like to cite FSLeyes or fslpy in your research, refer to their respective Zenodo pages: