Investigating the effect of oblique image acquisition on the accuracy of QSM and a robust tilt correction method

Abstract

Purpose: Quantitative susceptibility mapping (QSM) is used increasingly for clinical research where oblique image acquisition is commonplace, but its effects on QSM accuracy are not well understood. Theory and Methods:The QSM processing pipeline involves defining the unit magnetic dipole kernel, which requires knowledge of the direction of the main magnetic field B0 with respect to the acquired image volume axes. The direction of B0 is dependent on the axis and angle of rotation in oblique acquisition. Using both a numerical brain phantom and in vivo acquisitions in 5 healthy volunteers, we analyzed the effects of oblique acquisition on magnetic susceptibility maps. We compared three tilt-correction schemes at each step in the QSM pipeline: phase unwrapping, background field removal and susceptibility calculation, using the RMS error and QSM-tuned structural similarity index.Results: Rotation of wrapped phase images gave severe artifacts. Background field removal with projection onto dipole fields gave the most accurate susceptibilities when the field map was first rotated into alignment with B0 . Laplacian boundary value and variable-kernel sophisticated harmonic artifact reduction for phase data background field removal methods gave accurate results without tilt correction. For susceptibility calculation, thresholded k-space division, iterative Tikhonov regularization, and weighted linear total variation regularization, all performed most accurately when local field maps were rotated into alignment with B0 before susceptibility calculation. Conclusion:For accurate QSM, oblique acquisition must be taken into account.Rotation of images into alignment with B0 should be carried out after phase unwrapping and before background-field removal. We provide open-source tilt-correction code to incorporate easily into existing pipelines: https://github.com/o-snow/QSM_ TiltCorrection.git.

Quantitative susceptibility mapping identifies hippocampal and other subcortical grey matter tissue composition changes in temporal lobe epilepsy

“…To remove other noisy regions, the brain mask was eroded via thresholding at the mean of the inverse noise map (MEDI Toolbox, n.d.; Karsa et al, 2019; Kressler et al, 2010) except within ROIs. To account for oblique slice acquisition, the total field map was rotated into alignment with the scanner axes, using FSL FLIRT (Jenkinson et al, 2012) with trilinear interpolation, after phase unwrapping and prior to BFR (Kiersnowski et al, 2022). The brain mask was then eroded by three voxels to improve the performance of BFR using projection onto dipole fields (PDF) (Liu et al, 2011).…”

A guide to advanced MRI processing for clinical glioma research

“…Recently, the ISMRM Electro-Magnetic Tissue Properties Study Group provided recommendations for implementing QSM in clinical brain research [136]. The acquisition should be performed with an axial orientation and -in contrast to SWI -isotropic voxels [137].…”

Normative trajectories of R1, R2* and magnetic susceptibility in basal ganglia on healthy ageing

“…𝜒 maps were derived using SEPIA v1.2.2.4 (Chan and Marques, 2021) with the following pipeline: bipolar gradient phase correction (Li et al, 2015), ROMEO (Dymerska et al, 2021) for total field computation, V-SHARP for background field removal and LP-CNN (Lai et al, 2020) for dipole field inversion. A retrospective correction method was implemented to correct those datasets acquired with a tiled field-of-view with respect to the main magnetic field direction before the dipole field inversion step (Kiersnowski et al, 2023). The mean susceptibility value across the whole brain was used as a reference.…”