brainlife/fsl repository overview

⁠fsl-docker

A Docker image for FSL, providing a lightweight containerized environment for structural MRI, diffusion MRI, and functional MRI processing.

The image installs FSL using the official installer and configures the runtime environment so that FSL tools are immediately available inside the container. It is intended for reproducible neuroimaging workflows across Docker, Singularity, and HPC environments.

⁠Maintainers

Gabriele Amorosino ([email protected]⁠)

⁠Run (Docker)

docker run --rm -it \
  brainlife/fsl:latest \
  <your_command>

Example:

docker run --rm -it \
  brainlife/fsl:latest \
  fslmaths --help

⁠Run (Singularity / Apptainer)

⁠From your local Docker image

singularity build fsl.sif \
  docker-daemon://brainlife/fsl:latest

singularity exec \
  --bind $(pwd):/workspace \
  fsl.sif \
  <your_command>

⁠Directly from Docker Hub

singularity exec \
  docker://brainlife/fsl:latest \
  <your_command>

Example:

singularity exec \
  docker://brainlife/fsl:latest \
  topup --help

⁠Contents

• FSL installed via the official installer

• Environment automatically configured through fsl.sh

• Core command-line tools available, including:

  • bet
  • flirt
  • fnirt
  • topup
  • eddy
  • fslmaths
  • fslstats
  • fslroi

The container is designed to remain minimal, reproducible, and HPC-friendly, enabling the same environment across local workstations, clusters, and cloud infrastructures.

⁠Current implementation

The current latest image is built with:

FSL 6.0.7.22

installed under:

/usr/local/fsl

⁠Reference

• Jenkinson, M., Beckmann, C. F., Behrens, T. E., Woolrich, M. W., & Smith, S. M. (2012). Fsl. Neuroimage, 62(2), 782-790.