RS-SWANe Installation & Maintenance Guide

This guide provides step-by-step instructions to install Python3, dcm2niix, FSL, FreeSurfer, 3D Slicer, Graphviz, and SWANe on Ubuntu.

1. Install Python3

Installation

Ensure Python3 is installed and up-to-date:

sudo apt update
sudo apt install python3 python3-pip

Verify Installation

python3 --version
pip3 --version

Maintenance

• Update Python packages:

  pip3 install --upgrade pip
  pip3 list --outdated | cut -d' ' -f1 | xargs -n1 pip3 install --upgrade

2. Install dcm2niix

Installation

1. Via apt:

   sudo apt update
   sudo apt install dcm2niix

2. Alternatively, build from source:

   git clone https://github.com/rordenlab/dcm2niix.git
   cd dcm2niix/console
   mkdir build && cd build
   cmake ..
   make
   sudo make install

Verify Installation

dcm2niix --version

Maintenance

To update, repeat source installation steps.

3. Install FSL

Installation

1. Download and install the FSL installer:

   wget https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py
   python3 fslinstaller.py

2. Add to ~/.bashrc:

   export FSLDIR=/usr/local/fsl
   . ${FSLDIR}/etc/fslconf/fsl.sh
   export PATH=${FSLDIR}/bin:$PATH

3. Reload the shell:

   source ~/.bashrc

Verify Installation

flirt -version

Maintenance

Run the installer script to update:

python3 fslinstaller.py

4. Install FreeSurfer

Installation

1. Download the software from FreeSurfer's Website.

2. Extract and move it:

   tar -xvzf freesurfer-Linux-<version>.tar.gz
   sudo mv freesurfer /usr/local/
   sudo chmod -R 755 /usr/local/freesurfer

3. Add to ~/.bashrc:

   export FREESURFER_HOME=/usr/local/freesurfer
   source $FREESURFER_HOME/SetUpFreeSurfer.sh

4. Register for a license at this link, and copy license.txt:

   cp /path/to/license.txt /usr/local/freesurfer/

5. Reload the shell:

   source ~/.bashrc

Verify Installation

recon-all -version

Maintenance

Reinstall the latest version when required.

5. Install 3D Slicer

Installation

1. Download the latest release from 3D Slicer's website.

2. Extract and move it:

   tar -xvzf Slicer-<version>-linux-amd64.tar.gz
   sudo mv Slicer-<version> /opt/slicer

3. Add to PATH in ~/.bashrc:

   export PATH=/opt/slicer/Slicer-<version>:$PATH

4. Reload the shell:

   source ~/.bashrc

Install SlicerFreeSurfer Extension

1. Open Slicer, navigate to Extensions Manager.
2. Search for "SlicerFreeSurfer" and install it.

6. Install Graphviz

Installation

sudo apt update
sudo apt install graphviz

Verify Installation

dot -version

7. Install and Run SWANe

Installation

1. Create a virtual environment:

   python3 -m venv swane_env

2. Activate the virtual environment:

   source swane_env/bin/activate

3. Install SWANe:

   pip install swane

4. Run SWANe:

   python3 -m swane

5. Exit the virtual environment:

   deactivate

8. Configuration Recap

Ensure your ~/.bashrc includes the following environment variables:

# FreeSurfer
export FREESURFER_HOME=/usr/local/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

# FSL
export FSLDIR=/usr/local/fsl
. ${FSLDIR}/etc/fslconf/fsl.sh
export PATH=${FSLDIR}/bin:$PATH

# Slicer
export PATH=/opt/slicer/Slicer-<version>:$PATH

Reload the shell:

source ~/.bashrc

9. Maintenance

1. Update Tools
   Regularly visit the official websites for updates.

2. Backup Configurations
   Save ~/.bashrc and license.txt for FreeSurfer.

3. Test Environment
   Periodically check installations:

   which python3
   which dcm2niix
   which flirt
   which recon-all
   which dot

4. System Updates
   Keep your system up-to-date:

   sudo apt update && sudo apt upgrade