FSLeyes

FSLeyes (pronounced fossilise) is the FSL image viewer, part of FSL since FSL 5.0.10.

Follow FSLeyes on X to be notified of new releases.

The FSLeyes user guide can be found here, and the release history can be viewed here.

FSLeyes can either be installed as part of FSL, installed into a conda environment, or installed into a Python environment (for advanced users).

Install as part of FSL (recommended)

FSLeyes comes bundled with all versions of FSL from 5.0.10 onwards. So if you have FSL, you already have FSLeyes. The FSLeyes version which comes bundled with FSL may be slightly out of date, but it is straightforward to update using conda.

If you have an older version of FSL, it is recommended to update to the latest available version - you can do this by downloading and running the getfsl.sh or fslinstaller.py script, available on the installation page.

Info

The terminal commands in the instructions below may require administrative privileges, depending on where you have installed FSL. If you encounter permission errors, try repeating the command, but prefixing it with sudo.

FSL 6.0.7

If you have FSL 6.0.7 or newer, you can update to the latest version of FSLeyes by running the following command:

update_fsl_package fsleyes

FSL 6.0.6 or newer

Info

Sometimes it is difficult to update packages within an existing conda environment, due to compatibility problems with packages that are already installed. If you have trouble updating FSLeyes, please get in touch via the FSl mailing list or X.

If you have FSL 6.0.6 or newer, you can update to the latest version by running the following command:

${FSLDIR}/bin/conda update -p ${FSLDIR} fsleyes

FSL 6.0.2 and newer

From FSL 6.0.2 to 6.0.5.2, FSLeyes is installed into the embedded ${FSLDIR}/fslpython conda environment, which is a part of the FSL installation. You can update to the latest version of FSLeyes by running the following command:

${FSLDIR}/fslpython/bin/conda update -n fslpython -c conda-forge --update-all fsleyes

On macOS, if you experience segmentation faults after updating FSLeyes, try running: ${FSLDIR}/fslpython/bin/conda install -n fslpython -c conda-forge libffi=3.3

FSL 6.0.1 and older

Versions of FSL prior to 6.0.2 come with a standalone version of FSLeyes. Before updating, you should remove the old standalone version of FSLeyes. If you are using macOS:

rm ${FSLDIR}/bin/fsleyes
rm -r ${FSLDIR}/bin/FSLeyes.app

Or, if you are using Linux:

rm ${FSLDIR}/bin/fsleyes
rm -r ${FSLDIR}/bin/FSLeyes

Now you can install FSLeyes with the following command:

${FSLDIR}/fslpython/bin/conda install -n fslpython -c conda-forge --update-all fsleyes

When you want to update FSLeyes again in the future, use this command instead:

${FSLDIR}/fslpython/bin/conda update -n fslpython -c conda-forge --update-all fsleyes

Install from conda-forge (recommended)

If you want to install FSLeyes independently of FSL, conda is the recommended method. FSLeyes is available on conda-forge - if you use an anaconda or miniconda environment, you can install FSLeyes into it like so:

conda install -c conda-forge fsleyes

Or you can create a separate conda environment, specifically for FSLeyes, like so:

conda create -c conda-forge -p path/to/fsleyes/environment fsleyes

Install from PyPi (advanced)

Warning

This is an advanced option, recommended only if you are comfortable working with Python environments, and installing packages using your OS package manager. The commands below are suggestions - you will probably need to adapt them to suit your OS and environment.

FSLeyes is available on PyPi and should work with Python 3.9 and newer. The best way to install FSLeyes from PyPi is to create an isolated python environment with a virtual environment, and install FSLeyes into it. To get started:

python -m venv fsleyes-virtualenv
. fsleyes-virtualenv/bin/activate

macOS users

Once you have activated your virtual environment, you should be able to install FSLeyes like so:

pip install fsleyes

Linux users

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 20.04:

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 20.04, 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 run:

pip install fsleyes

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, or on Neurostars.

To ask for help, try the FSL mailing list, Neurostars, or X.

If you have found a bug in FSLeyes, you can also open an issue on github. If you would like to fix a bug or add a new feature, you are also welcome to open a pull request through github (although it is probably best to open an issue first to discuss the proposal).

Development

The source code for FSLeyes and its main dependencies is hosted at:

Mirrors for these projects are also on github - feel free to use the issue tracker, and open a PR if you have something to contribute:

API/developer documentation can be found here:

Citation

If you would like to cite FSLeyes or fslpy in your research, refer to their respective Zenodo pages: