From cba0032f88fbe255d84778a529620bee51e7fa6d Mon Sep 17 00:00:00 2001
From: howff <3064316+howff@users.noreply.github.com>
Date: Tue, 28 May 2024 12:56:02 +0100
Subject: [PATCH] FSL README.md - how to run it

using --entrypoint to override the container entrypoint (which is just an interactive shell) that starts the X11 GUI
---
 software/FSL/README.md | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/software/FSL/README.md b/software/FSL/README.md
index ebbc650..a8811f4 100644
--- a/software/FSL/README.md
+++ b/software/FSL/README.md
@@ -10,6 +10,20 @@ A container with a relatively old version (5.0.7) can be build from `fsl5.Docker
 
 Version 6.0.7.9 can be run from https://github.com/smi/SCANDAN/pkgs/container/fsl
 
+To run it:
+```
+XSOCK=/tmp/.X11-unix
+XAUTH=${HOME}/.Xauthority
+podman run --rm -it \
+    -e USER="$USER" \
+    -e DISPLAY="$DISPLAY" \
+    -e XAUTHORITY="$XAUTH" \
+    -v $XSOCK:$XSOCK \
+    -v $XAUTH:$XAUTH \
+    --entrypoint='["/bin/sh", "-c", ". /usr/local/fsl/etc/fslconf/fsl.sh && /usr/local/fsl/bin/fsl"]' \
+    ghcr.io/smi/fsl:latest
+```
+
 ### FSL Documentation
 
 The new FSL site provides [these](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/install/container?id=install-fsl-into-a-dockersingularity-container) instructions. This has been translated into the main `Dockerfile` in this directory.