SCANDAN Software

This repository hosts several imaging-related software packages which have been compiled into Docker images for use in Trusted Reserach Environments (TREs).

Software	Image	Notes
Freesurfer	ghcr.io/smi/freesurfer:latest	Requires a user-provided license file
FSL	ghcr.io/smi/fsl:latest
MRIcron	ghcr.io/smi/mricron:latest
MRIcroGL	ghcr.io/smi/mricrogl:latest

See EPCC's TRE Container User Guide for more information.

Containers for other applications can be found in EPCC's TRE Container Samples repository.

Usage notes

Running graphical applications via Docker

XSOCK=/tmp/.X11-unix
XAUTH=/tmp/.docker.xauth
xauth nlist "$DISPLAY" | sed -e 's/^..../ffff/' | xauth -f "$XAUTH" nmerge -

docker run --rm -it \
    -e USER="$USER" \
    -e DISPLAY="$DISPLAY" \
    -e XAUTHORITY="$XAUTH" \
    -v $XSOCK:$XSOCK \
    -v $XAUTH:$XAUTH \
    <image-name>