Install FSL into a Docker/Singularity container

FSL can easily be installed into a Docker or Singularity container. If you would like to have a complete FSL installation, follow the standard instructions for a Linux installation. Here is an example Dockerfile which installs FSL into an Ubuntu 20.04 image:

FROM ubuntu:20.04

ENV FSLDIR          "/usr/local/fsl"
ENV DEBIAN_FRONTEND "noninteractive"
ENV LANG            "en_GB.UTF-8"

RUN apt update  -y && \
    apt upgrade -y && \
    apt install -y    \
      python          \
      wget            \
      file            \
      dc              \
      mesa-utils      \
      pulseaudio      \
      libquadmath0    \
      libgtk2.0-0     \
      firefox         \
      libgomp1

RUN wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py
RUN python ./fslinstaller.py -d /usr/local/fsl/

ENTRYPOINT [ "sh", "-c", ". /usr/local/fsl/etc/fslconf/fsl.sh && /bin/bash" ]

If you need to install optional/extra components, such as truenet, adjust the fslinstaller.py invocation accordingly, e.g.:

RUN python ./fslinstaller.py -d /usr/local/fsl --extra truenet

If you only need specific FSL commands, you can use conda to install only the FSL components that you need - see here for more details.