https://pypi.org/project/fsleyes/ https://anaconda.org/conda-forge/fsleyes https://doi.org/10.5281/zenodo.1470761

FSLeyes (pronounced fossilise) is the FSL image viewer, released with FSL 5.0.10 onwards.

Follow FSLeyes on Twitter 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).

Note

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

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 The FSLeyes version which comes bundled with FSL may be slightly out of date, but it is straightforward to update using conda.

Warning

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 Twitter.

FSL 6.0.2 and newer

From FSL 6.0.2 onwards, FSLeyes is installed into the 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

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)

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.

FSLeyes is available on PyPi and should work with Python 3.6 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:

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 run:

pip install fsleyes

Install standalone build (no longer updated)

FSLeyes 0.32.3 is the last version for which standalone builds are provided. From FSLeyes 0.33.0, conda is the recommended installation method.

If you wish to install FSLeyes independently of FSL, you can download FSLeyes 0.32.3 for your OS via the links below. If your OS is not listed, you will need to install FSLeyes via alternate means.

Ubuntu users

Only Ubuntu LTS release are supported - the links below are not guaranteed to work on interim Ubuntu releases.

1. Download the zip or tar.gz file for your platform using the links above.

2. Unzip/untar the downloaded file to a location of your choice.

3. Call FSLeyes like this, replacing the /path/to/downloaded/FSLeyes/ to the path of the location to which you downloaded and unzipped FSLeyes

You may wish to put the directory containing the fsleyes command on your $PATH environment variable - then you can just type 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.

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

If you have found a bug in FSLeyes, you can also open an issue on github.

Development

The source code for FSLeyes and its dependent projects is hosted here:

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:

 

FSLeyes (last edited 10:25:56 04-05-2021 by PaulMcCarthy)