Install FreeSurfer 8.2.0 and all patches on an Ubuntu 24.04 machine

install-freesurfer-8.2.0-ubuntu-24.04.bash

#!/usr/bin/env bash
#
# Install FreeSurfer 8.2.0 on Ubuntu 24.04
#
# Ported from:
#  - https://github.com/pwighton/fs-docker/blob/master/freesurfer/Dockerfile.8.2.0
# See also:
#  - https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads/rel8notes

set -euo pipefail
FS_VERSION="8.2.0"
DEB_NAME="freesurfer_ubuntu24-${FS_VERSION}_amd64.deb"
DEB_URL="https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FS_VERSION}/${DEB_NAME}"
UPDATES_URL="https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/${FS_VERSION}/fs820_updates.sh"
FREESURFER_HOME="/usr/local/freesurfer/${FS_VERSION}"
SUBJECTS_DIR="$HOME/freesurfer-subjects"

mkdir -p $SUBJECTS_DIR
WORKDIR="$(mktemp -d)"
cd "$WORKDIR"

# Install pre-reqs
sudo apt-get -y update
sudo apt-get -y install wget findutils libgomp1 procps libxt6 libxext6 libncurses6 unzip

# Install FreeSurfer
# - see: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
wget --progress=bar:force:noscroll "$DEB_URL"
sudo apt-get -y install ./"$DEB_NAME"

# Apply point-release updates/bug fixes (same idea as fs820_updates.sh in the
# Rocky Dockerfile, just with the Ubuntu FREESURFER_HOME path)
wget --progress=bar:force:noscroll "$UPDATES_URL"

# Note: yes/tr get SIGPIPE once fs820_updates.sh finishes reading stdin and
# exits, which would trip `pipefail` above even on a successful update run.
# So pipefail is disabled just for this pipeline and we check the exit status
# of the actual update script (the rightmost command) instead.
set +o pipefail
yes y | tr -d '\n' | sudo FREESURFER_HOME="$FREESURFER_HOME" bash fs820_updates.sh
updates_status=${PIPESTATUS[-1]}
set -o pipefail
if [ "$updates_status" -ne 0 ]; then
  echo "fs820_updates.sh exited with status $updates_status" >&2
  exit "$updates_status"
fi

# Clean up
cd /
rm -rf "$WORKDIR"

# Set up FreeSurfer environment on login
{
  echo ""
  echo "# FreeSurfer ${FS_VERSION} setup (added by install_freesurfer_${FS_VERSION}.sh)"
  echo "export FREESURFER_HOME=\"${FREESURFER_HOME}\""
  echo "export SUBJECTS_DIR=\"${SUBJECTS_DIR}\""
  echo "source \"\$FREESURFER_HOME/SetUpFreeSurfer.sh\""
} >> "$HOME/.bashrc"

echo ""
echo ""
echo "FreeSurfer ${FS_VERSION} installed to ${FREESURFER_HOME}"
echo "Environment setup added to $HOME/.bashrc - run 'source $HOME/.bashrc' or open a new shell"