QSMxT: Robust masking and artifact reduction for quantitative susceptibility mapping

Abstract

Purpose: Quantitative susceptibility mapping (QSM) estimates the spatial distribution of tissue magnetic susceptibilities from the phase of a gradient-echo signal. QSM algorithms require a signal mask to delineate regions with reliable phase for subsequent susceptibility estimation. Existing masking techniques used in QSM have limitations that introduce artifacts, exclude anatomical detail, and rely on parameter tuning and anatomical priors that narrow their application. Here, a robust masking and reconstruction procedure is presented to overcome these limitations and enable automated QSM processing. Moreover, this method is integrated within an open-source software framework: QSMxT.

Methods: A robust masking technique that automatically separates reliable from less reliable phase regions was developed and combined with a two-pass reconstruction procedure that operates on the separated sources before combination, extracting more information and suppressing streaking artifacts.

Results: Compared with standard masking and reconstruction procedures, the two-pass inversion reduces streaking artifacts caused by unreliable phase and high dynamic ranges of susceptibility sources. It is also robust across a range of acquisitions at 3 T in volunteers and phantoms, at 7 T in tumor patients, and in an in silico head phantom, with significant artifact and error reductions, greater anatomical detail, and minimal parameter tuning.

Conclusion: The two-pass masking and reconstruction procedure separates reliable from less reliable phase regions, enabling a more accurate QSM reconstruction that mitigates artifacts, operates without anatomical priors, and requires minimal parameter tuning. The technique and its integration within QSMxT makes QSM processing more accessible and robust to streaking artifacts.

Keywords: QSM masking; QSM pipeline; QSM software; quantitative imaging; quantitative susceptibility mapping (QSM).

Figure 1

QSMxT processing pipeline and outputs after automated conversion to the Brain Imaging Data Structure standard. Outputs for each subject include masks, T1-weighted images, segmentations registered to the quantitative susceptibility mapping (QSM) space, QSM images, as well as quantitative data for analysis and figure generation. Outputs for the whole group include magnitude and QSM templates

Figure 2

Two-pass QSM masking and reconstruction process for one subject with one echo. A mask is initially produced by thresholding either the magnitude or the spatial phase coherence. A second mask is then produced after applying the hole-filling algorithm. Both masks are then used in parallel QSM reconstruction steps before combination. The images shown were produced using the QSM challenge 2.0 data, and are included for illustrative purposes

Figure 3

QSM results from a volunteer brain (3 T; multi-echo; axial slice) calculated using two-pass QSM with a range of magnitude signal thresholds. The slice shown intersects the top portion of the lateral ventricles. At some thresholds, dark artifacts are visible toward the center of the brain caused by the dephased signal in the lateral ventricles. With a threshold set to the 50th percentile of the magnitude distribution, the artifacts are kept to a minimum

Figure 4

In silico head phantom ground truth and QSM reconstructions using single- and two-pass QSM (7 T; single-echo; simulated; sagittal slice). The zoomed area (yellow rectangle) shows a cortical and two subcortical lesions in close proximity. Two-pass QSM reduces streaking artifacts near the lesions (green arrow), and includes more anatomical detail in the brainstem due to threshold-based masking, allowing the brainstem lesion to be recovered (blue arrow). The difference image illustrates that two-pass QSM primarily mitigates the star-shaped streaking artifacts surrounding the lesions

Figure 5

A, Sagittal brain segmentation of the in silico head phantom, with highlighted ROIs in the vicinity of the introduced lesions. B, Susceptibility error in each ROI using three processing methods. All reconstructions used threshold-based masks based on the spatial phase coherence

Figure 6

QSM results using the gel phantom (3 T; multi-echo; axial slice). On the left is a photo of the gel phantom containing a Gold Anchor MR+™ with 1.5% iron content (yellow square), a pure gold fiducial marker (blue square), and a tooth piece (green square). The latter three images depict the same slice from the magnitude, as well as single- and two-pass QSM results. The two-pass QSM image has a clear reduction of streaking artifacts surrounding the strong sources

Figure 7

QSM templates generated using 46 volunteer brains (3 T; multi-echo; coronal slice). When BET-generated masks are used, strong artifacts near the transverse and superior sagittal sinuses are visible (left; arrow). The artifacts are mitigated using two-pass QSM (center; arrow), with dipole-shaped streaking visible in the difference image (right; arrow)

Figure 8. Measured susceptibility values in 46 volunteer brains across seven ROIs using single-pass and two-pass QSM. Both methods used threshold based masking, and produced similar quantitative measurements across all ROIs tested

Figure 9

QSM results of a brain tumor patient computed using single- and two-pass QSM (7 T; multi-echo; axial slice region). The BET-generated mask excluded part of the tumor included by thresholding (yellow rectangle), as well as areas of the cortex (pink arrow). The two-pass inversion suppresses streaking artifacts near the tumor (orange arrow), and potentially near veins where some differences can be seen (aquamarine arrow)

Figure 10. QSM results of a brain tumor patient (7 T; multi-echo; axial slices) computed using single- and two-pass QSM. Significant reductions of artifacts can be seen near vessels and within tumors after two-pass combination (yellow arrows)