https://doi.org/10.5281/zenodo.18718434

Susceptibility-Weighted Imaging (SWI)

Susceptibility-Weighted Imaging (SWI)#

Author: Steffen Bollmann, Michèle Masson-Trottier

The University of Queensland

GitHub ORCID
GitHub ORCID

Date: 16/03/2026

License:

Purpose#

Susceptibility-weighted imaging (SWI) is an MRI technique that exploits differences in magnetic susceptibility between tissues to generate contrast. It is particularly useful for visualising venous vasculature, microbleeds, calcifications, and iron deposits in the brain.

This tutorial demonstrates how to:

  1. Download a demo MRI dataset containing magnitude and phase images

  2. Use the CLEAR-SWI Julia package within Neurodesk to compute SWI maps

  3. Generate a minimum intensity projection (mIP) for enhanced vein visualisation

  4. Inspect the results in an image viewer

Learning Objectives

By the end of this tutorial you will be able to:

  • Understand what SWI is and why it is clinically relevant

  • Run the CLEAR-SWI pipeline on magnitude and phase data

  • Create and interpret minimum intensity projections

Citation and Resources#

Tools used in this workflow#

CLEAR-SWI

Eckstein, K., et al. (2023). CLEAR-SWI — Coil-combined Low-artifact Enhanced Arbitrary Resolution SWI. Zeitschrift für Medizinische Physik. https://doi.org/10.1016/j.zemedi.2023.01.001

Educational resources#

Prerequisites#

Before you begin

Make sure you have access to a running Neurodesk instance. See Getting Set Up with Neurodesk for instructions.

  • A running Neurodesk environment

  • Familiarity with basic terminal commands

  • No additional software installation required — CLEAR-SWI is pre-installed in Neurodesk

Load software tools and download demo data#

First, we install osfclient to download the demo dataset from the Open Science Framework, then fetch and unzip the BIDS-formatted data. We use the same demo dataset as the Unwrapping tutorial.

To do so, open a Neurodesktop session, launch a terminal and run the following commands.

Tip

To paste in Neurodesktop, best to use the right click on your mouse!

The terminal in Neurodesktop The terminal in Neurodesktop.

pip install osfclient
cd ~/neurodesktop-storage/
osf -p ru43c fetch -f 01_bids.zip ~/neurodesktop-storage/swi-demo/01_bids.zip

unzip -o ~/neurodesktop-storage/swi-demo/01_bids.zip -d ~/neurodesktop-storage/swi-demo/

The Neurodesktop terminal outpu The Neurodesktop terminal outputs after running the command.

You may wish to confirm the download was successful. You can locate the files in your neurodesktop-storage folder using the file manager. You will see the swi-demo folder containing a zipped and unzipped 01_bids folder.

The Neurodesktop file manager The Neurodesktop file manager showing the downloaded data.

Run CLEAR-SWI#

Write a Julia script that will perform three steps:

  1. Read the magnitude and phase NIfTI files

  2. Compute the SWI volume using calculateSWI

  3. Generate a minimum intensity projection (mIP) using createMIP

Note

The echo time (TEs) must match your acquisition. For this single-echo demo dataset, TEs = [20] (in ms).

Using the command

nano ~/neurodesktop-storage/clearswi.jl

create a file called clearswi.jl with the following contents :

using CLEARSWI

TEs = [20]
nifti_folder = joinpath(homedir(), "neurodesktop-storage/swi-demo/01_bids/sub-170705134431std1312211075243167001/ses-1/anat")
magfile = joinpath(nifti_folder, "sub-170705134431std1312211075243167001_ses-1_run-1_part-mag_T2starw.nii")
phasefile = joinpath(nifti_folder, "sub-170705134431std1312211075243167001_ses-1_run-1_part-phase_T2starw.nii")

println("Loading magnitude and phase data...")
mag = readmag(magfile);
phase = readphase(phasefile);
data = Data(mag, phase, mag.header, TEs);

println("Computing SWI...")
swi = calculateSWI(data);

println("Creating minimum intensity projection...")
mip = createMIP(swi);

outdir = joinpath(homedir(), "neurodesktop-storage/swi-demo")
println("Saving outputs...")
savenii(swi, joinpath(outdir, "swi.nii"); header=mag.header)
savenii(mip, joinpath(outdir, "mip.nii"); header=mag.header)

println("Done! Output saved to ~/neurodesktop-storage/swi-demo/")

Save the file using Ctrl+X (confirm by hitting Y followed by Enter).

The Neurodesktop terminal with the Julia script The Neurodesktop terminal with the Julia script.

Open the CLEAR-SWI tool from the Neurodesk application menu.

Opening CLEAR-SWI in Neurodesktop Opening CLEAR-SWI in Neurodesktop.

Then run your newly written file from the CLEAR-SWI container terminal:

cd ~/neurodesktop-storage/
julia clearswi.jl

The CLEAR-SWI container terminal after running the script The CLEAR-SWI container terminal after running the script.

Inspect the results#

Fig. 1 Opening ITK-SNAP from the Neurodesk Visualisation menu.#

Open ITK-SNAP from the Neurodesk Visualisation menu and load the output files:

  • ~/neurodesktop-storage/swi-demo/swi.nii — the susceptibility-weighted image

  • ~/neurodesktop-storage/swi-demo/mip.nii — the minimum intensity projection

Tip

The mIP highlights venous structures as dark lines. Compare the SWI and mIP side by side to appreciate how the projection enhances vein visibility.

SWI result in ITK-SNAP

Summary#

In this tutorial you:

  1. Downloaded a demo magnitude/phase MRI dataset from the Open Science Framework

  2. Used the CLEAR-SWI Julia package to compute susceptibility-weighted images

  3. Generated a minimum intensity projection for enhanced venous visualisation

  4. Inspected the outputs using ITK-SNAP

See also