Installing FSLeyes¶
There are several ways to obtain and install FSLeyes. FSLeyes comes as a standard component of an FSL installation, but can also be installed independently of FSL.
Note
The terminal commands in these instructions may require administrative privileges, depending on where you have installed FSL.
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with FSL may be slightly out of date, but it is straightforward to update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
.
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-deps 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 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-deps 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
Install from PyPi (advanced)¶
Note
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 3.5 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)¶
Note
FSLeyes 0.32.3 is the last version for which standalone builds are
provided. From FSLeyes 0.33.0 onwards, conda
is the recommended
installation method.
If you wish to install FSLeyes independently of FSL, you can download and install a standalone version from the FSLeyes home page, using these instructions.
Download the
zip
ortar.gz
file for your platform.Unzip/untar the downloaded file to a location of your choice.
Call FSLeyes like this (you may wish to put the directory containing the
fsleyes
command on your$PATH
environment variable):Platform
Command to run FSLeyes
Linux
/path/to/downloaded/FSLeyes/fsleyes
macOS
/path/to/downloaded/FSLeyes.app/Contents/MacOS/fsleyes
Install into a Singularity image¶
FSLeyes can be executed from Singularity containers. Here is an example Singularity definition file which installs a standalone version of FSLeyes:
Bootstrap: docker
From: centos:7
%help
FSLeyes Singularity image
%post
yum -y update
yum -y install epel-release
yum -y install wget \
gtk3 \
SDL \
libSM \
mesa-dri-drivers \
gstreamer-plugins-base \
xorg-x11-server-Xvfb \
libnotify \
freeglut
wget -O /tmp/fsleyes.tar.gz \
https://fsl.fmrib.ox.ac.uk/fsldownloads/fsleyes/FSLeyes-latest-centos7.tar.gz
pushd /usr/local/
tar xf /tmp/fsleyes.tar.gz
echo -e '#!/usr/bin/env bash\n/usr/local/FSLeyes/fsleyes "$@"' > bin/fsleyes
chmod a+x bin/fsleyes
popd
%runscript
fsleyes "$@"