Dataset Information

New 3D phase-unwrapping method based on voxel clustering and local polynomial modeling: application to quantitative susceptibility mapping.

ABSTRACT:

Background

To develop an accurate and robust 3-dimensional (3D) phase-unwrapping method that works effectively in the presence of severe noise, disconnected regions, rapid phase changes, and open-ended lines for quantitative susceptibility mapping (QSM).

Methods

We developed a 3D phase-unwrapping method based on voxel clustering and local polynomial modeling named CLOSE3D, which firstly explores the 26-neighborhood to calculate local variation of the phasor and the phase, and then according to the local variation of the phasor, clusters the phase data into easy-to-unwrap blocks and difficult-to-unwrap residual voxels. Next, CLOSE3D sequentially performs intrablock, interblock, and residual-voxel unwrapping by using the region-growing local polynomial modeling method. CLOSED3D was evaluated in simulation and using in vivo brain QSM data, and was compared with classical region-growing and region-expanding labeling for unwrapping estimates methods.

Results

The simulation experiments showed that CLOSE3D achieved accurate phase-unwrapping results with a mean error ratio <0.39%, even in the presence of serious noise, disconnected regions, and rapid phase changes. The error ratios of region-growing (P=0.000 and P=0.000) and region-expanding labeling for unwrapping estimates (P=0.007, P=0.014) methods were both significantly higher than that of CLOSE3D, when the noise level was ≥60%. The results of the in vivo brain QSM experiments showed that CLOSE3D unwrapped the phase data and accurately reconstructed quantitative susceptibility data, even with serious noise, rapid-varying phase, or an open-ended cutline.

Conclusions

CLOSE3D achieves phase unwrapping with high accuracy and robustness, which will help phase-related 3D magnetic resonance imaging (MRI) applications such as QSM and susceptibility weighted imaging.

SUBMITTER: Cheng J

PROVIDER: S-EPMC10006161 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature

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Publications

New 3D phase-unwrapping method based on voxel clustering and local polynomial modeling: application to quantitative susceptibility mapping.

Cheng Junying J Zheng Qian Q Xu Man M Xu Zhongbiao Z Zhu Li L Liu Liang L Han Shaoqiang S Chen Wufan W Feng Yanqiu Y Cheng Jingliang J

Quantitative imaging in medicine and surgery 20221226 3

<h4>Background</h4>To develop an accurate and robust 3-dimensional (3D) phase-unwrapping method that works effectively in the presence of severe noise, disconnected regions, rapid phase changes, and open-ended lines for quantitative susceptibility mapping (QSM).<h4>Methods</h4>We developed a 3D phase-unwrapping method based on voxel clustering and local polynomial modeling named CLOSE3D, which firstly explores the 26-neighborhood to calculate local variation of the phasor and the phase, and then ...[more]

PMID: 36915306

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Project description:BackgroundAccurate phase unwrapping is a critical prerequisite for successful applications in phase-related MRI, including quantitative susceptibility mapping (QSM) and susceptibility weighted imaging. However, many existing 3D phase unwrapping algorithms face challenges in the presence of severe noise, rapidly changing phase, and open-end cutline.MethodsIn this study, we introduce a novel 3D phase unwrapping approach utilizing region partitioning and a local polynomial model. Initially, the method leverages phase partitioning to create initial regions. Noisy voxels connecting areas within these regions are excluded and grouped into residual voxels. The connected regions within the region of interest are then reidentified and categorized into blocks and residual voxels based on voxel count thresholds. Subsequently, the method sequentially performs inter-block and residual voxel phase unwrapping using the local polynomial model. The proposed method was evaluated on simulation and in vivo abdominal QSM data, and was compared with the classical Region-growing, Laplacian_based, Graph-cut, and PRELUDE methods.ResultsSimulation experiments, conducted under different signal-to-noise ratios and phase change levels, consistently demonstrate that the proposed method achieves accurate unwrapping results, with mean error ratios not exceeding 0.01%. In contrast, the error ratios of Region-growing (N/A, 84.47%), Laplacian_based (20.65%, N/A), Graph-cut (2.26%, 20.71%), and PRELUDE (4.28%, 10.33%) methods are all substantially higher than those of the proposed method. In vivo abdominal QSM experiments further confirm the effectiveness of the proposed method in unwrapping phase data and successfully reconstructing susceptibility maps, even in scenarios with significant noise, rapidly changing phase, and open-end cutline in a large field of view.ConclusionThe proposed method demonstrates robust and accurate phase unwrapping capabilities, positioning it as a promising option for abdominal QSM applications.

Project description:The evolution of magnetic susceptibility of the brain is mainly determined by myelin in white matter (WM) and iron deposition in deep gray matter (DGM). However, existing imaging techniques have limited abilities to simultaneously quantify the myelination and iron deposition within a voxel throughout brain development and aging. For instance, the temporal trajectories of iron in the brain WM and myelination in DGM have not been investigated during the aging process. This study aimed to map the age-related iron and myelin changes in the whole brain, encompassing myelin in DGM and iron deposition in WM, using a novel sub-voxel quantitative susceptibility mapping (QSM) method. To achieve this, a cohort of 494 healthy adults (18-80 years old) was studied. The sub-voxel QSM method was employed to obtain the paramagnetic and diamagnetic susceptibility based on the approximated R2' map from acquired R2* map. The linear relationship between R2* and R2' maps was established from the regression coefficients on a small cohort data acquired with both 3D gradient recalled echo data and R2 mapping. Large cohort sub-voxel susceptibility maps were used to create longitudinal and age-specific atlases via group-wise registration. To explore the differential developmental trajectories in the DGM and WM, we employed nonlinear models including exponential and Poisson functions, along with generalized additive models. The constructed atlases reveal the iron accumulation in the posterior part of the putamen and the gradual myelination process in the globus pallidus with aging. Interestingly, the developmental trajectories show that the rate of myelination differs among various DGM regions. Furthermore, the process of myelin synthesis is paralleled by an associated pattern of iron accumulation in the primary WM fiber bundles. In summary, our study offers significant insights into the distinctive developmental trajectories of iron in the brain's WM and myelination/demyelination in the DGM in vivo. These findings highlight the potential of using sub-voxel QSM to uncover new perspectives in neuroscience and improve our understanding of whole-brain myelination and iron deposit processes across the lifespan.

Project description:PurposeBrain iron accumulation has been suggested as a pathomechanism in patients with type 2 diabetes mellitus (T2DM) with cognitive impairment. This research aims to examine the total-brain pattern of iron accumulation in relation to executive function decline in patients with T2DM by voxel-based quantitative susceptibility mapping (QSM) analysis.Materials and methodsA total of 32 patients with T2DM and 34 age- and sex-matched healthy controls (HCs) were enrolled in this study. All participants underwent brain magnetic resonance examination, and 48 individuals underwent cognitive function assessments. Imaging data were collected with three-dimensional fast low-angle shot sequences to achieve magnitude as well as phase images. Using voxel-based QSM analysis, we compared the voxel-wise susceptibility values of the whole brain among groups and explored whether the susceptibility values had correlations with cognitive data.ResultsAmong the 66 participants, cognitive function was estimated in 23 patients with T2DM (11 males and 12 females; average age, 64.65 ± 8.44 years) and 25 HCs (13 males and 12 females; average age, 61.20 ± 7.62 years). T2DM patients exhibited significantly (t = 4.288, P < 0.001) lower Montreal Cognitive Assessment (MoCA) scores [T2DM, 27 (27, 28); HCs, 29 (28, 29); normal standard ≥ 26)] and higher Trail-making Test (TMT)-A/TMT-B scores [71 (51, 100)/185 (149, 260)] than HCs [53 (36.5, 63.5)/150 (103, 172.5)] (Z = 2.612, P = 0.009; Z = 2.797, P = 0.005). Subjects with T2DM showed significantly higher susceptibility values than HCs in the caudate/putamen/pallidum, frontal inferior triangular gyrus, and precentral gyrus on the right hemisphere. In contrast (HC > T2DM), no region showed a significant difference in susceptibility values between the groups. The correlation analysis between susceptibility values and cognitive function scores was tested by voxel-based susceptibility value with sex and age as covariates. After multiple comparison correction, in T2DM patients, the left thalamus showed a significant relationship with TMT-A (R 2 = 0.53, P = 0.001). The right thalamus and left thalamus showed a significant relationship with TMT-B (R 2 = 0.35, P = 0.019; and R 2 = 0.38, P = 0.017, respectively). In HCs, the cluster of right precentral/middle frontal gyrus/inferior frontal gyrus/inferior triangular gyrus showed a significant relationship with TMT-B (R 2 = 0.59, P = 0.010). No relationship was found between the susceptibility values with MoCA in the brain region in both two groups.ConclusionPatients with T2DM presented declined cognitive assessments and elevated iron deposition in the striatum and frontal lobe, suggesting that executive function decline in T2DM might be associated with the cerebral iron burden and that changes in susceptibility values may represent a latent quantitative imaging marker for early assessment of cognitive decline in patients with T2DM.

Project description:BackgroundAccurate measurement of the liver iron concentration (LIC) is needed to guide iron-chelating therapy for patients with transfusional iron overload. In this work, we investigate the feasibility of automated quantitative susceptibility mapping (QSM) to measure the LIC.PurposeTo develop a rapid, robust, and automated liver QSM for clinical practice.Study typeProspective.Population13 healthy subjects and 22 patients.Field strength/sequences1.5 T and 3 T/3D multiecho gradient-recalled echo (GRE) sequence.AssessmentData were acquired using a 3D GRE sequence with an out-of-phase echo spacing with respect to each other. All odd echoes that were in-phase (IP) were used to initialize the fat-water separation and field estimation (T2 *-IDEAL) before performing QSM. Liver QSM was generated through an automated pipeline without manual intervention. This IP echo-based initialization method was compared with an existing graph cuts initialization method (simultaneous phase unwrapping and removal of chemical shift, SPURS) in healthy subjects (n = 5). Reproducibility was assessed over four scanners at two field strengths from two manufacturers using healthy subjects (n = 8). Clinical feasibility was evaluated in patients (n = 22).Statistical testsIP and SPURS initialization methods in both healthy subjects and patients were compared using paired t-test and linear regression analysis to assess processing time and region of interest (ROI) measurements. Reproducibility of QSM, R2 *, and proton density fat fraction (PDFF) among the four different scanners was assessed using linear regression, Bland-Altman analysis, and the intraclass correlation coefficient (ICC).ResultsLiver QSM using the IP method was found to be ~5.5 times faster than SPURS (P < 0.05) in initializing T2 *-IDEAL with similar outputs. Liver QSM using the IP method were reproducibly generated in all four scanners (average coefficient of determination 0.95, average slope 0.90, average bias 0.002 ppm, 95% limits of agreement between -0.06 to 0.07 ppm, ICC 0.97).Data conclusionUse of IP echo-based initialization enables robust water/fat separation and field estimation for automated, rapid, and reproducible liver QSM for clinical applications.Level of evidence1 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019;50:725-732.

Dataset Information

New 3D phase-unwrapping method based on voxel clustering and local polynomial modeling: application to quantitative susceptibility mapping.

Background

Methods

Results

Conclusions

Publications

New 3D phase-unwrapping method based on voxel clustering and local polynomial modeling: application to quantitative susceptibility mapping.

Similar Datasets

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