PurposeQuantitative susceptibility mapping (QSM) is increasingly used for clinical research where oblique image acquisition is commonplace but its effects on QSM accuracy are not well understood.Theory and MethodsThe QSM processing pipeline involves defining the unit magnetic dipole kernel, which requires knowledge of the direction of the main magnetic field with respect to the acquired image volume axes. The direction of is dependent upon the axis and angle of rotation in oblique acquisition. Using both a numerical brain phantom and in-vivo acquisitions, we analysed 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 root-mean-squared error and QSM-tuned structural similarity index (XSIM).ResultsRotation of wrapped phase images gave severe artefacts. Background field removal with projection onto dipole fields gave the most accurate susceptibilities when the field map was first rotated into alignment with . LBV and VSHARP background field removal methods gave accurate results without tilt correction. For susceptibility calculation, thresholded k-space division, iterative Tikhonov regularisation and weighted linear total variation regularisation all performed most accurately when local field maps were rotated into alignment with before susceptibility calculation.ConclusionFor accurate QSM, oblique acquisition must be taken into account. Rotation of images into alignment with 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.
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.
Simultaneous multi-slice (SMS) acquisition is increasingly used to accelerate echo planar imaging (EPI). EPI acquisitions have been used for quantitative susceptibility mapping (QSM) but, to utilise SMS, an investigation into the effect of SMS on EPI-QSM accuracy is necessary. Here, we show that SMS has no significant effect on magnetic susceptibility maps and values, and can, therefore, provide accurate QSM within a short TR. We also show, for the first time, that multi-echo phase images can be acquired using an EPI sequence (highly) accelerated using SMS and parallel imaging, leading to more accurate QSM reconstruction compared to standard single-echo EPI.
Temporal lobe epilepsy (TLE) is associated with widespread brain alterations. Using quantitative susceptibility mapping (QSM) alongside transverse relaxation rate (), we investigated regional brain susceptibility changes in 36 patients with left‐sided (LTLE) or right‐sided TLE (RTLE) secondary to hippocampal sclerosis, and 27 healthy controls (HC). We compared three susceptibility calculation methods to ensure image quality. Correlations of susceptibility and with age of epilepsy onset, frequency of focal‐to‐bilateral tonic–clonic seizures (FBTCS), and neuropsychological test scores were examined. Weak‐harmonic QSM (WH‐QSM) successfully reduced noise and removed residual background field artefacts. Significant susceptibility increases were identified in the left putamen in the RTLE group compared to the LTLE group, the right putamen and right thalamus in the RTLE group compared to HC, and a significant susceptibility decrease in the left hippocampus in LTLE versus HC. LTLE patients who underwent epilepsy surgery showed significantly lower left‐versus‐right hippocampal susceptibility. Significant changes were found between TLE and HC groups in the amygdala, putamen, thalamus, and in the hippocampus. Specifically, decreased R2* was found in the left and right hippocampus in LTLE and RTLE, respectively, compared to HC. Susceptibility and were significantly correlated with cognitive test scores in the hippocampus, globus pallidus, and thalamus. FBTCS frequency correlated positively with ipsilateral thalamic and contralateral putamen susceptibility and with in bilateral globi pallidi. Age of onset was correlated with susceptibility in the hippocampus and putamen, and with in the caudate. Susceptibility and changes observed in TLE groups suggest selective loss of low‐myelinated neurons alongside iron redistribution in the hippocampi, predominantly ipsilaterally, indicating QSM's sensitivity to local pathology. Increased susceptibility and in the thalamus and putamen suggest increased iron content and reflect disease severity.
Although EPI phase images are useful (e.g. for Quantitative Susceptibility Mapping), they often contain phase inconsistencies in the slice-select direction which persist and can degrade QSM results. Here, we analysed three EPI datasets in healthy volunteers to characterise these phase inconsistencies and understand whether they occur or interact with interleaved or sequential slice acquisition order. We characterised a ~2Hz cryogen pump artifact in sequential data and slice-to-slice phase jumps in interleaved data. We modified a previously proposed QSM processing pipeline, including 2D (VSHARP) and 3D (PDF) background field removal that removed all through-slice artifacts observed.
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