Application of Laplacian-based Methods to Multi-echo Phase Data for Accurate Susceptibility Mapping

In Susceptibility Mapping (SM) using multi-echo gradient-echo phase data, unwrapping and/or background-Òeld removal is often performed using Laplacian-based methods. However, SM pipelines in the literature have applied these methods at di×erent stages. Here, using simulated and acquired images, we compared the performance of three pipelines that apply Laplacian-based methods at di× erent stages. We showed that Laplacian-based methods alter the linearity of the phase over time. We demonstrated that only a processing pipeline that takes this into account, i.e. by Òtting the multi-echo data over time to correctly estimate a Òeld map before applying Laplacian-based methods, gives accurate susceptibility values

The Effect of Oblique Image Slices on the Accuracy of Quantitative Susceptibility Mapping and a Robust Tilt Correction Method

Quantitative susceptibility mapping (QSM) using the MRI phase to calculate tissue magnetic susceptibility is finding increasing clinical applications. Oblique image slices are often acquired to facilitate radiological viewing and reduce artifacts. Here, we show that artifacts and errors arise in susceptibility maps if oblique acquisition is not properly taken into account in QSM. We performed a comprehensive analysis of the effects of oblique acquisition on brain susceptibility maps and compared tilt correction schemes for three susceptibility calculation methods, using a numerical phantom and human in-vivo images. We demonstrate a robust tilt correction method for accurate QSM with oblique acquisition

SAS: Symmetric Analysis of Z-Spectra, a Method to Evaluate B0 Correction Techniques for CEST Data in Clinical Systems Using Non-Exchanging Phantoms

Presentation of a method for the comparison of B0 correction methods. This method is based on non-exchanging phantoms to remove CEST effects. SAS method proposed to inform studies

Investigating the accuracy and precision of TE‐dependent versus multi‐echo QSM using Laplacian‐based methods at 3 T

Purpose: Multi‐echo gradient‐recalled echo acquisitions for QSM enable optimizing the SNR for several tissue types through multi‐echo (TE) combination or investigating temporal variations in the susceptibility (potentially reflecting tissue microstructure) by calculating one QSM image at each TE (TE‐dependent QSM). In contrast with multi‐echo QSM, applying Laplacian‐based methods (LBMs) for phase unwrapping and background field removal to single TEs could introduce nonlinear temporal variations (independent of tissue microstructure) into the measured susceptibility. Here, we aimed to compare the effect of LBMs on the QSM susceptibilities in TE‐dependent versus multi‐echo QSM. Methods: TE–dependent recalled echo data simulated in a numerical head phantom and gradient‐recalled echo images acquired at 3 T in 10 healthy volunteers. Several QSM pipelines were tested, including four distinct LBMs: sophisticated harmonic artifact reduction for phase data (SHARP), variable‐radius sophisticated harmonic artifact reduction for phase data (V‐SHARP), Laplacian boundary value background field removal (LBV), and one‐step total generalized variation (TGV). Results from distinct pipelines were compared using visual inspection, summary statistics of susceptibility in deep gray matter/white matter/venous regions of interest, and, in the healthy volunteers, regional susceptibility bias analysis and nonparametric tests. Results: Multi‐echo versus TE‐dependent QSM had higher regional accuracy, especially in high‐susceptibility regions and at shorter TEs. Everywhere except in the veins, a processing pipeline incorporating TGV provided the most temporally stable TE‐dependent QSM results with an accuracy similar to multi‐echo QSM. Conclusions: For TE‐dependent QSM, carefully choosing LBMs can minimize the introduction of LBM‐related nonlinear temporal susceptibility variations

Susceptibility Mapping in Sickle Cell Anaemia Patients with and Without Chronic Blood Transfusions

Sickle cell anaemia (SCA) is a genetic disorder affecting haemoglobin. Previous studies suggest that the iron content in some deep-brain regions is higher in transfused SCA patients (TSCA) than in healthy controls (HC). We hypothesised that iron content in those regions is lower in non-transfused patients (NSCA) than in controls as NSCA have low haematocrit. A pilot study (5 TSCA, 5 NSCA, 5 HC) showed that susceptibility values were significantly lower in the globus pallidus of both TSCA and NSCA than in HC, supporting our second hypothesis. A larger study (20 NSCA, 18 HC) showed a trend in this direction

Investigating the effect of flow compensation and quantitative susceptibility mapping method on the accuracy of venous susceptibility measurement

Quantitative susceptibility mapping (QSM) is a promising non-invasive method for obtaining information relating to oxygen metabolism. However, the optimal acquisition sequence and QSM reconstruction method for reliable venous susceptibility measurements are unknown. Full flow compensation is generally recommended to correct for the influence of venous blood flow, although the effect of flow compensation on the accuracy of venous susceptibility values has not been systematically evaluated. In this study, we investigated the effect of different acquisition sequences, including different flow compensation schemes, and different QSM reconstruction methods on venous susceptibilities. Ten healthy subjects were scanned with five or six distinct QSM sequence designs using monopolar readout gradients and different flow compensation schemes. All data sets were processed using six different QSM pipelines and venous blood susceptibility was evaluated in whole-brain segmentations of the venous vasculature and single veins. The quality of vein segmentations and the accuracy of venous susceptibility values were analyzed and compared between all combinations of sequences and reconstruction methods. The influence of the QSM reconstruction method on average venous susceptibility values was found to be 2.7–11.6 times greater than the influence of the acquisition sequence, including flow compensation. The majority of the investigated QSM reconstruction methods tended to underestimate venous susceptibility values in the vein segmentations that were obtained. In summary, we found that multi-echo gradient-echo acquisition sequences without full flow compensation yielded venous susceptibility values comparable to sequences with full flow compensation. However, the QSM reconstruction method had a great influence on susceptibility values and thus needs to be selected carefully for accurate venous QSM

SEGUE: a Speedy rEgion-Growing algorithm for Unwrapping Estimated phase

Recent Magnetic Resonance Imaging (MRI) techniques, such as Quantitative magnetic Susceptibility Mapping (QSM), employ the signal phase to reveal disease-related changes in tissue composition including iron or calcium content. The MRI phase is also routinely used in functional and diffusion MRI for distortion correction. However, phase images are wrapped into a range of 2π radians. PRELUDE is the gold standard method for robust, spatial, 3-dimensional, MRI phase unwrapping. Unfortunately, PRELUDE's computation time can reach 15 minutes for a severely wrapped brain image and nearly 10 hours to unwrap a full head-and-neck image on a standard PC. Here we develop a Speedy rEgion-Growing algorithm for Unwrapping Estimated phase (SEGUE) based on similar principles to PRELUDE, implemented with additional methods for acceleration. We compared PRELUDE and SEGUE in numerical phantoms, and using in-vivo images of the brain, head-and-neck, and pelvis acquired in 4-5 healthy volunteers and at 4-6 echo times. To overcome chemical-shift-induced errors within the head-and-neck and pelvic images, we also investigated applying both techniques within fat and water masks separately. SEGUE provided almost identical unwrapped phase maps to the gold standard PRELUDE. SEGUE was (1.5 to 70 times) faster than PRELUDE, especially in severely wrapped images at later echoes as well as in the head-and-neck and pelvic images. Applying these techniques within fat and water masks separately successfully removed chemical-shiftinduced errors. SEGUE's MATLAB implementation is available for download. SEGUE is a general unwrapping algorithm not specific to MRI and could, therefore, be used in images acquired with other modalities

Phase unwrapping with a rapid opensource minimum spanning tree algorithm (ROMEO)

PURPOSE: To develop a rapid and accurate MRI phase-unwrapping technique for challenging phase topographies encountered at high magnetic fields, around metal implants, or postoperative cavities, which is sufficiently fast to be applied to large-group studies including Quantitative Susceptibility Mapping and functional MRI (with phase-based distortion correction). METHODS: The proposed path-following phase-unwrapping algorithm, ROMEO, estimates the coherence of the signal both in space-using MRI magnitude and phase information-and over time, assuming approximately linear temporal phase evolution. This information is combined to form a quality map that guides the unwrapping along a 3D path through the object using a computationally efficient minimum spanning tree algorithm. ROMEO was tested against the two most commonly used exact phase-unwrapping methods, PRELUDE and BEST PATH, in simulated topographies and at several field strengths: in 3T and 7T in vivo human head images and 9.4T ex vivo rat head images. RESULTS: ROMEO was more reliable than PRELUDE and BEST PATH, yielding unwrapping results with excellent temporal stability for multi-echo or multi-time-point data. It does not require image masking and delivers results within seconds, even in large, highly wrapped multi-echo data sets (eg, 9 seconds for a 7T head data set with 31 echoes and a 208 × 208 × 96 matrix size). CONCLUSION: Overall, ROMEO was both faster and more accurate than PRELUDE and BEST PATH, delivering exact results within seconds, which is well below typical image acquisition times, enabling potential on-console application

Quantitative susceptibility mapping of carotid arterial tissue ex vivo: Assessing sensitivity to vessel microstructural composition

PURPOSE: To characterize microstructural contributions to the magnetic susceptibility of carotid arteries. METHOD: Arterial vessels were scanned using high-resolution quantitative susceptibility mapping (QSM) at 7 Tesla. Models of vessel degradation were generated using ex vivo porcine carotid arteries that were subjected to several different enzymatic digestion treatments that selectively removed microstructural components (smooth muscle cells, collagen, and elastin). Magnetic susceptibilities measured in these tissue models were compared to those in untreated (native) porcine arteries. Magnetic susceptibility measured in native porcine carotid arteries was further compared to the susceptibility of cadaveric human carotid arteries to investigate their similarity. RESULTS: The magnetic susceptibility of native porcine vessels was diamagnetic (χnative = -0.1820 ppm), with higher susceptibilities in all models of vessel degradation (χelastin-degraded = -0.0163 ppm; χcollagen-degraded = -0.1158 ppm; χdecellularized = -0.1379 ppm; χfixed native = -0.2199 ppm). Magnetic susceptibility was significantly higher in collagen-degraded compared to native porcine vessels (Tukey-Kramer, P .05). CONCLUSIONS: Magnetic susceptibility measured using QSM is sensitive to the microstructural composition of arterial vessels-most notably to collagen. The similarity of human and porcine arterial tissue susceptibility values provides a solid basis for translational studies. Because vessel microstructure becomes disrupted during the onset and progression of carotid atherosclerosis, QSM has the potential to provide a sensitive and specific marker of vessel disease