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QuantitativeSusceptibilityMappingTGV

Build Status Coverage Aqua QA

This project is an improvement of the TGV-QSM method in terms of speed, artefacts and ease of use. Oblique orientations and anisotropic voxel sizes are supported.

References

  • Bredies, K., Ropele, S., Poser, B. A., Barth, M., & Langkammer, C. (2014). Single-step quantitative susceptibility mapping using total generalized variation and 3D EPI. In Proceedings of the 22nd Annual Meeting ISMRM (Vol. 62, p. 604).

  • Langkammer, C., Bredies, K., Poser, B. A., Barth, M., Reishofer, G., Fan, A. P., ... & Ropele, S. (2015). Fast quantitative susceptibility mapping using 3D EPI and total generalized variation. Neuroimage, 111, 622-630.

Further points to consider

Masking for QSM, Run on GPU, Rotated Data

Command line usage

Command line Setup (Windows, Linux, Mac)

  1. Install Julia (v1.10+ recommended)
  2. Make sure julia can be executed from the command line
  3. Download the single file tgv_qsm.jl

Run script

julia <folder>/tgv_qsm.jl --help

On the first usage, the script will download all dependencies.

Optional configuration

Under Linux: Make the file executable with chmod +x tgv_qsm.jl and run directly via

<folder>/tgv_qsm.jl --help

Number of threads

In case Julia uses only 1 CPU thread, you can use the command

julia --threads=auto <folder>/tgv_qsm.jl <arguments>

Run in Julia

Setup

  1. Install Julia (v1.10+ recommended)

  2. Install this package
    Open the julia REPL and type:

    julia> ] # enters package manager
pkg> add QuantitativeSusceptibilityMappingTGV MriResearchTools

    or

    import Pkg
Pkg.add(["QuantitativeSusceptibilityMappingTGV", "MriResearchTools"])

Example to run TGV

  1. Prepare files
    3D mask and phase NIfTI files are required

  2. Run the following commands in an interactive julia REPL or a julia source file

    using QuantitativeSusceptibilityMappingTGV, MriResearchTools

mask = niread("<mask-path>") .!= 0; # convert to boolean
phase = readphase("<phase-path>");

voxel_size = header(phase).pixdim[2:4] # in [mm]
TE = 0.004 # in [s]
fieldstrength = 3 # in [T]

chi = qsm_tgv(phase, mask, res; TE=TE, fieldstrength=fieldstrength);

savenii(chi, "chi", "<folder-to-save>")
    # Change regularization strength (1-4)
chi = qsm_tgv(phase, mask, voxel_size; TE, fieldstrength, regularization=1);
    # Optionally obtain settings from BIDS JSON file
using JSON
settings = JSON.parse(read("<phase-json>", String))
fieldstrength = settings["MagneticFieldStrength"]
TE = settings["EchoTime"]

The first execution might take some time to compile the kernels (~1min).

Julia IDE

For convenient scripting in Julia, vscode with the julia extension is recommended. NIfTI files can be viewed in vscode with the niivue extension.

Settings

The default settings were optimized for brain QSM and should lead to good results independently of the acquired resolution.

It uses the number of CPU threads julia was started with. You can use julia --threads=auto or set it to a specific number of threads.

List of optional keyword arguments

regularization=2 : change the strength of the regularization from 1-4
erosions=3: number of erosion steps applied to the mask
B0_dir=[0, 0, 1]: direction of the B0 field for oblique orientations

For most applications the following options don't have to be adjusted:

alpha=[0.002, 0.003]: manually choose regularization parameters (overwrites regularization)
step_size=3: requires less iterations with higher step size, but might lead to artefacts or iteration instabilities. step_size=1 is the behaviour of the publication
iterations=1000: manually choose the number of iteration steps
dedimensionalize=false: optionally apply a dedimensionalization step
laplacian=get_laplace_phase_del: options are get_laplace_phase3 (corresponds to Python version), get_laplace_phase_romeo and get_laplace_phase_del (default). get_laplace_phase_del is selected as default as it improves the robustness when imperfect phase values are present
correct_laplacian=true: subtracts the mean of the Laplacian inside the mask, which avoids edge artefacts in certain cases
original_kernel=false : select the kernel that was used in the Python version. This doesn't support oblique orientations

Rotated Data

A new kernel was implemented that supports oblique acquisitions. The direction of the B0 field needs to be given as a vector e.g. B0_dir=[0,0,1] for the B0 field in z-direction.
(This should be retrievable with something like B0_dir = nifti_phase.affine * [0,0,1]. Needs confirming)

Self contained example to test if package works

using QuantitativeSusceptibilityMappingTGV

sz = (20, 20, 20);
res = [1, 1, 1];
TE = 0.01;

phase = randn(sz);
mask = trues(sz);

chi = qsm_tgv(phase, mask, res; TE);

Settings to reproduce the original version

Beside one regularization bug-fix, this should produce identical results to the original Python code

qsm = qsm_tgv(phase, mask, res; TE, fieldstrength, laplacian=get_laplace_phase3, step_size=1, iterations=1000, alpha=[0.003, 0.001], erosions=5, dedimensionalize=false, correct_laplacian=false, original_kernel=true)

Speed

The parallel CPU version is about twice as fast as the Cython version, the GPU version is about 10x faster than the Cython version (on a RTX 3060 Laptop GPU 6GB)

Run on GPU

Command line script are provided for processing on the GPU e.g. (tgv_qsm_cuda.jl) and also for the other GPU types. In Julia the GPU processing can be activated via:

using CUDA
chi = qsm_tgv(phase, mask, res; TE, fieldstrength, gpu=CUDA);
using AMDGPU
chi = qsm_tgv(phase, mask, res; TE, fieldstrength, gpu=AMDGPU);

For Intel GPU:

using oneAPI
chi = qsm_tgv(phase, mask, res; TE, fieldstrength, gpu=oneAPI);

For Mac GPU:

using Metal
chi = qsm_tgv(phase, mask, res; TE, fieldstrength, gpu=Metal);

Masking for QSM

Masking for QSM is a challenge, since including corrupted phase areas can cause global artefacts in the QSM result. See the publications QSMxT and phase based masking.

A simple solution is to remove areas based on phase quality using ROMEO

using MriResearchTools
mask_phase = robustmask(romeovoxelquality(phase; mag=mag))
mask_combined = mask_phase .& mask_brain

The mask might contain holes, and a more sophisticated approach is taken in the QSMxT toolbox.