Motion-compensated image reconstruction for improved kidney function assessment using dynamic contrast-enhanced MRI.

Accurately measuring renal function is crucial for pediatric patients with kidney conditions. Traditional methods have limitations, but dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) provides a safe and efficient approach for detailed anatomical evaluation and renal function assessment. However, motion artifacts during DCE-MRI can degrade image quality and introduce misalignments, leading to unreliable results. This study introduces a motion-compensated reconstruction technique for DCE-MRI data acquired using golden-angle radial sampling. Our proposed method achieves three key objectives: (1) identifying and removing corrupted data (outliers) using a Gaussian process model fitting with a k -space center navigator, (2) efficiently clustering the data into motion phases and performing interphase registration, and (3) utilizing a novel formulation of motion-compensated radial reconstruction. We applied the proposed motion correction (MoCo) method to DCE-MRI data affected by varying degrees of motion, including both respiratory and bulk motion. We compared the outcomes with those obtained from the conventional radial reconstruction. Our evaluation encompassed assessing the quality of images, concentration curves, and tracer kinetic model fitting, and estimating renal function. The proposed MoCo reconstruction improved the temporal signal-to-noise ratio for all subjects, with a 21.8% increase on average, while total variation values of the aorta, right, and left kidney concentration were improved for each subject, with 32.5%, 41.3%, and 42.9% increases on average, respectively. Furthermore, evaluation of tracer kinetic model fitting indicated that the median standard deviation of the estimated filtration rate ( σ F T ), mean normalized root-mean-squared error (nRMSE), and chi-square goodness-of-fit of tracer kinetic model fit were decreased from 0.10 to 0.04, 0.27 to 0.24, and, 0.43 to 0.27, respectively. The proposed MoCo technique enabled more reliable renal function assessment and improved image quality for detailed anatomical evaluation in the case of bulk and respiratory motion during the acquisition of DCE-MRI.

Prospective motion correction in kidney MRI using FID navigators.

PURPOSE: Abdominal MRI scans may require breath-holding to prevent image quality degradation, which can be challenging for patients, especially children. In this study, we evaluate whether FID navigators can be used to measure and correct for motion prospectively, in real-time. METHODS: FID navigators were inserted into a 3D radial sequence with stack-of-stars sampling. MRI experiments were conducted on 6 healthy volunteers. A calibration scan was first acquired to create a linear motion model that estimates the kidney displacement due to respiration from the FID navigator signal. This model was then applied to predict and prospectively correct for motion in real time during deep and continuous deep breathing scans. Resultant images acquired with the proposed technique were compared with those acquired without motion correction. Dice scores were calculated between inhale/exhale motion states. Furthermore, images acquired using the proposed technique were compared with images from extra-dimensional golden-angle radial sparse parallel, a retrospective motion state binning technique. RESULTS: Images reconstructed for each motion state show that the kidneys' position could be accurately tracked and corrected with the proposed method. The mean of Dice scores computed between the motion states were improved from 0.93 to 0.96 using the proposed technique. Depiction of the kidneys was improved in the combined images of all motion states. Comparing results of the proposed technique and extra-dimensional golden-angle radial sparse parallel, high-quality images can be reconstructed from a fraction of spokes using the proposed method. CONCLUSION: The proposed technique reduces blurriness and motion artifacts in kidney imaging by prospectively correcting their position both in-plane and through-slice.

Self-supervised IVIM DWI parameter estimation with a physics based forward model.

PURPOSE: To assess the robustness and repeatability of intravoxel incoherent motion model (IVIM) parameter estimation for the diffusion-weighted MRI in the abdominal organs under the constraints of noisy diffusion signal using a novel neural network method. METHODS: Clinically acquired abdominal scans of Crohn's disease patients were retrospectively analyzed with regions segmented in the kidney cortex, spleen, liver, and bowel. A novel IVIM parameter fitting method based on the principle of a physics guided self-supervised convolutional neural network that does not require reference parameter estimates for training was compared to a conventional non-linear least squares (NNLS) algorithm, and a voxelwise trained artificial neural network (ANN). RESULTS: Results showed substantial increase in parameter robustness to the noise corrupted signal. In an intra-session repeatability experiment, the proposed method showed reduced coefficient of variation (CoV) over multiple acquisitions in comparison to conventional NLLS method and comparable performance to ANN. The use of D and f estimates from the proposed method led to the smallest misclassification error in linear discriminant analysis for characterization between normal and abnormal Crohn's disease bowel tissue. The fitting of D∗ parameter remains to be challenging. CONCLUSION: The proposed method yields robust estimates of D and f IVIM parameters under the constraints of noisy diffusion signal. This indicates a potential for the use of the proposed method in conjunction with accelerated DW-MRI acquisition strategies, which would typically result in lower signal to noise ratio.

Quantitative renal magnetic resonance imaging: magnetic resonance urography.

The goal of functional renal imaging is to identify and quantitate irreversible renal damage and nephron loss, as well as potentially reversible hemodynamic changes. MR urography has evolved into a comprehensive evaluation of the urinary tract that combines anatomical imaging with functional evaluation in a single test without ionizing radiation. Quantitative functional MR imaging is based on dynamic contrast-enhanced MR acquisitions that provide progressive, visible enhancement of the renal parenchyma and urinary tract. The signal changes related to perfusion, concentration and excretion of the contrast agent can be evaluated using both quantitative and qualitative measures. Functional evaluation with MR has continued to improve as a result of significant technical advances allowing for faster image acquisition as well as the development of new tracer kinetic models of renal function. The most common indications for MR urography in children are the evaluation of congenital anomalies of the kidney and urinary tract including hydronephrosis and renal malformations, and the identification of ectopic ureters in children with incontinence. In this paper, we review the underlying acquisition schemes and techniques used to generate quantitative functional parameters including the differential renal function (DRF), asymmetry index, mean transit time (MTT), signal intensity versus time curves as well as the calculation of individual kidney glomerular filtration rate (GFR). Visual inspection and semi-quantitative assessment using the renal transit time (RTT) and calyceal transit times (CTT) are fundamental to accurate diagnosis and are used as a basis for the interpretation of the quantitative data. The importance of visual assessment of the images cannot be overstated when analyzing the quantitative measures of renal function.

Normative values for ureteral diameter in children.

BACKGROUND: Assessment of the ureter is a fundamental part of the radiologic evaluation of the urinary tract. Abnormal ureteral dilation warrants further investigation to assess the etiology, which includes obstruction and/or reflux. Despite this fundamental need, there are no established normative values in children based on imaging. OBJECTIVE: To provide normative values for ureteral diameter in pediatric patients with age-related ranges. MATERIALS AND METHODS: We retrospectively reviewed all magnetic resonance (MR) urography studies and chose only normal ureters for assessment. The images were analyzed on commercially available software to assess maximum internal diameter. Manual measurements were done in cases where the images were below the resolution for automated assessment. Maximum intraluminal ureteral diameters were measured in upper, mid and lower thirds and the average of the three maximum ureteral diameters was used to obtain the average widest internal ureteral diameter. Multivariable linear regression was performed to test the association between the calculated diameter and gender. Differences in sizes between the left and right ureter were assessed using paired Wilcoxon signed rank test. RESULTS: One hundred twenty-one MR urography studies were selected, which included 160 ureter units. The diameter increases progressively with age, ranging from 3.2 mm during infancy to 5.0 mm in patients older than 16 years of age. After 9 years of age, the average widest internal ureteral diameter is slightly larger in males compared to females (odds ratio [OR]=1.91, 95% confidence interval [CI] [1.63, 2.25], P<0.0001). The right ureter was slightly larger than the left (3.9 mm vs. 3.7 mm, P=0.004) among 39 patients in whom both right and left ureter units were included. The average mid ureteral diameter is widest, followed by the distal third then proximal third. CONCLUSION: We present the normative values for the average widest internal ureteral diameter based on laterality and different segments. In the pediatric population, 3.8 mm should be considered the average widest internal ureteral diameter.

Retrospective Distortion and Motion Correction for Free-Breathing DW-MRI of the Kidneys Using Dual-Echo EPI and Slice-to-Volume Registration.

BACKGROUND: Diffusion-weighted MRI (DW-MRI) of the kidneys is a technique that provides information about the microstructure of renal tissue without requiring exogenous contrasts such as gadolinium, and it can be used for diagnosis in cases of renal disease and assessing response-to-therapy. However, physiological motion and large geometric distortions due to main B0 field inhomogeneities degrade the image quality, reduce the accuracy of quantitative imaging markers, and impede their subsequent clinical applicability. PURPOSE: To retrospectively correct for geometric distortion for free-breathing DW-MRI of the kidneys at 3T, in the presence of a nonstatic distortion field due to breathing and bulk motion. STUDY TYPE: Prospective. SUBJECTS: Ten healthy volunteers (ages 29-38, four females). FIELD STRENGTH/SEQUENCE: 3T; DW-MR dual-echo echo-planar imaging (EPI) sequence (10 b-values and 17 directions) and a T2 volume. ASSESSMENT: The distortion correction was evaluated subjectively (Likert scale 0-5) and numerically with cross-correlation between the DW images at b = 0 s/mm2 and a T2 volume. The intravoxel incoherent motion (IVIM) and diffusion tensor (DTI) model-fitting performance was evaluated using the root-mean-squared error (nRMSE) and the coefficient of variation (CV%) of their parameters. STATISTICAL TESTS: Statistical comparisons were done using Wilcoxon tests. RESULTS: The proposed method improved the Likert scores by 1.1 ± 0.8 (P < 0.05), the cross-correlation with the T2 reference image by 0.13 ± 0.05 (P < 0.05), and reduced the nRMSE by 0.13 ± 0.03 (P < 0.05) and 0.23 ± 0.06 (P < 0.05) for IVIM and DTI, respectively. The CV% of the IVIM parameters (slow and fast diffusion, and diffusion fraction for IVIM and mean diffusivity, and fractional anisotropy for DTI) was reduced by 2.26 ± 3.98% (P = 6.971 × 10-2 ), 11.24 ± 26.26% (P = 6.971 × 10-2 ), 4.12 ± 12.91% (P = 0.101), 3.22 ± 0.55% (P < 0.05), and 2.42 ± 1.15% (P < 0.05). DATA CONCLUSION: The results indicate that the proposed Di + MoCo method can effectively correct for time-varying geometric distortions and for misalignments due to breathing motion. Consequently, the image quality and precision of the DW-MRI model parameters improved. LEVEL OF EVIDENCE: 2 TECHNICAL EFFICACY STAGE: 1.

Improving Automatic Renal Segmentation in Clinically Normal and Abnormal Paediatric DCE-MRI via Contrast Maximisation and Convolutional Networks for Computing Markers of Kidney Function.

There is a growing demand for fast, accurate computation of clinical markers to improve renal function and anatomy assessment with a single study. However, conventional techniques have limitations leading to overestimations of kidney function or failure to provide sufficient spatial resolution to target the disease location. In contrast, the computer-aided analysis of dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) could generate significant markers, including the glomerular filtration rate (GFR) and time-intensity curves of the cortex and medulla for determining obstruction in the urinary tract. This paper presents a dual-stage fully modular framework for automatic renal compartment segmentation in 4D DCE-MRI volumes. (1) Memory-efficient 3D deep learning is integrated to localise each kidney by harnessing residual convolutional neural networks for improved convergence; segmentation is performed by efficiently learning spatial-temporal information coupled with boundary-preserving fully convolutional dense nets. (2) Renal contextual information is enhanced via non-linear transformation to segment the cortex and medulla. The proposed framework is evaluated on a paediatric dataset containing 60 4D DCE-MRI volumes exhibiting varying conditions affecting kidney function. Our technique outperforms a state-of-the-art approach based on a GrabCut and support vector machine classifier in mean dice similarity (DSC) by 3.8% and demonstrates higher statistical stability with lower standard deviation by 12.4% and 15.7% for cortex and medulla segmentation, respectively.

Bulk motion-compensated DCE-MRI for functional imaging of kidneys in newborns.

BACKGROUND: Evaluation of kidney function in newborns with hydronephrosis is important for clinical decisions. Dynamic contrast-enhanced (DCE) MRI can provide the necessary anatomical and functional information. Golden angle dynamic radial acquisition and compressed sensing reconstruction provides sufficient spatiotemporal resolution to achieve accurate parameter estimation for functional imaging of kidneys. However, bulk motion during imaging (rigid or nonrigid movement of the subject resulting in signal dropout) remains an unresolved challenge. PURPOSE: To evaluate a motion-compensated (MoCo) DCE-MRI technique for robust evaluation of kidney function in newborns. Our method includes: 1) motion detection, 2) motion-robust image reconstruction, 3) joint realignment of the volumes, and 4) tracer-kinetic (TK) model fitting to evaluate kidney function parameters. STUDY TYPE: Retrospective. SUBJECTS: Eleven newborn patients (ages <6 months, 6 female). FIELD STRENGTH/SEQUENCE: 3T; dynamic "stack-of-stars" 3D fast low-angle shot (FLASH) sequence using a multichannel body-matrix coil. ASSESSMENT: We evaluated the proposed technique in terms of the signal-to-noise ratio (SNR) of the reconstructed images, the presence of discontinuities in the contrast agent concentration time curves due to motion with a total variation (TV) metric and the goodness of fit of the TK model, and the standard variation of its parameters. STATISTICAL TESTS: We used a paired t-test to compare the MoCo and no-MoCo results. RESULTS: The proposed MoCo method successfully detected motion and improved the SNR by 3.3 (P = 0.012) and decreased TV by 0.374 (P = 0.017) across all subjects. Moreover, it decreased nRMSE of the TK model fit for the subjects with less than five isolated bulk motion events in 6 minutes (mean 1.53, P = 0.043), but not for the subjects with more frequent events or no motion (P = 0.745 and P = 0.683). DATA CONCLUSION: Our results indicate that the proposed MoCo technique improves the image quality and accuracy of the TK model fit for subjects who present isolated bulk motion events. LEVEL OF EVIDENCE: 3 Technical Efficacy Stage: 1 J. Magn. Reson. Imaging 2020;52:207-216.

Prospective pediatric study comparing glomerular filtration rate estimates based on motion-robust dynamic contrast-enhanced magnetic resonance imaging and serum creatinine (eGFR) to 99mTc DTPA.

BACKGROUND: Current methods to estimate glomerular filtration rate (GFR) have shortcomings. Estimates based on serum creatinine are known to be inaccurate in the chronically ill and during acute changes in renal function. Gold standard methods such as inulin and 99mTc diethylenetriamine pentaacetic acid (DTPA) require blood or urine sampling and thus can be difficult to perform in children. Motion-robust radial volumetric interpolated breath-hold examination (VIBE) dynamic contrast-enhanced MRI represents a novel tool for estimating GFR that has not been validated in children. OBJECTIVE: The purpose of our study was to determine the feasibility and accuracy of GFR measured by motion-robust radial VIBE dynamic contrast-enhanced MRI compared to estimates by serum creatinine (eGFR) and 99mTc DTPA in children. MATERIALS AND METHODS: We enrolled children, 0-18 years of age, who were undergoing both a contrast-enhanced MRI and nuclear medicine 99mTc DTPA glomerular filtration rate (NM-GFR) within 2 weeks of each other. Enrolled children consented to an additional 6-min dynamic contrast-enhanced MRI scan using the motion-robust high spatiotemporal resolution prototype dynamic radial VIBE sequence (Siemens, Erlangen, Germany) at 3 tesla (T). The images were reconstructed offline with high temporal resolution (~3 s/volume) using compressed sensing image reconstruction including regularization in temporal dimension to improve image quality and reduce streaking artifacts. Images were then automatically post-processed using in-house-developed software. Post-processing steps included automatic segmentation of kidney parenchyma and aorta using convolutional neural network techniques and tracer kinetic model fitting using the Sourbron two-compartment model to calculate the MR-based GFR (MR-GFR). The NM-GFR was compared to MR-GFR and estimated GFR based on serum creatinine (eGFR) using Pearson correlation coefficient and Bland-Altman analysis. RESULTS: Twenty-one children (7 female, 14 male) were enrolled between February 2017 and May 2018. Data from six of these children were not further analyzed because of deviations from the MRI protocol. Fifteen patients were analyzed (5 female, 10 male; average age 5.9 years); the method was technically feasible in all children. The results showed that the MR-GFR correlated with NM-GFR with a Pearson correlation coefficient (r-value) of 0.98. Bland-Altman analysis (i.e. difference of MR-GFR and NM-GFR versus mean of NM-GFR and MR-GFR) showed a mean difference of -0.32 and reproducibility coefficient of 18 with 95% confidence interval, and the coefficient of variation of 6.7% with values between -19 (-1.96 standard deviation) and 18 (+1.96 standard deviation). In contrast, serum creatinine compared with NM-GFR yielded an r-value of 0.73. Bland-Altman analysis (i.e. difference of eGFR and NM-GFR versus mean of NM-GFR and eGFR) showed a mean difference of 2.9 and reproducibility coefficient of 70 with 95% confidence interval, and the coefficient of variation of 25% with values between -67 (-1.96 standard deviation) and 73 (+1.96 standard deviation). CONCLUSION: MR-GFR is a technically feasible and reliable method of measuring GFR when compared to the reference standard, NM-GFR by serum 99mTc DTPA, and MR-GFR is more reliable than estimates based on serum creatinine.

Correction to: Prospective pediatric study comparing glomerular filtration rate estimates based on motion-robust dynamic contrast-enhanced magnetic resonance imaging and serum creatinine (eGFR) to 99mTc DTPA.

The originally published version of this article contained a typographical error. In the text under the subheading "Dynamic contrast-enhanced MRI method, post-processing, and MR-GFR calculation" and in Table 1 the intravenous injection rate of gadobutrol was incorrectly listed as 0.2 mL/s.

Curved planar reformatting and convolutional neural network-based segmentation of the small bowel for visualization and quantitative assessment of pediatric Crohn's disease from MRI.

BACKGROUND: Contrast-enhanced MRI of the small bowel is an effective imaging sequence for the detection and characterization of disease burden in pediatric Crohn's disease (CD). However, visualization and quantification of disease burden requires scrolling back and forth through 3D images to follow the anatomy of the bowel, and it can be difficult to fully appreciate the extent of disease. PURPOSE: To develop and evaluate a method that offers better visualization and quantitative assessment of CD from MRI. STUDY TYPE: Retrospective. POPULATION: Twenty-three pediatric patients with CD. FIELD STRENGTH/SEQUENCE: 1.5T MRI system and T1 -weighted postcontrast VIBE sequence. ASSESSMENT: The convolutional neural network (CNN) segmentation of the bowel's lumen, wall, and background was compared with manual boundary delineation. We assessed the reproducibility and the capability of the extracted markers to differentiate between different levels of disease defined after a consensus review by two experienced radiologists. STATISTICAL TESTS: The segmentation algorithm was assessed using the Dice similarity coefficient (DSC) and boundary distances between the CNN and manual boundary delineations. The capability of the extracted markers to differentiate between different disease levels was determined using a t-test. The reproducibility of the extracted markers was assessed using the mean relative difference (MRD), Pearson correlation, and Bland-Altman analysis. RESULTS: Our CNN exhibited DSCs of 75 ± 18%, 81 ± 8%, and 97 ± 2% for the lumen, wall, and background, respectively. The extracted markers of wall thickness at the location of min radius (P = 0.0013) and the median value of relative contrast enhancement (P = 0.0033) could differentiate active and nonactive disease segments. Other extracted markers could differentiate between segments with strictures and segments without strictures (P < 0.05). The observers' agreement in measuring stricture length was >3 times superior when computed on curved planar reformatting images compared with the conventional scheme. DATA CONCLUSION: The results of this study show that the newly developed method is efficient for visualization and assessment of CD. LEVEL OF EVIDENCE: 4 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2019;49:1565-1576.

Development and Progression of Interstitial Lung Abnormalities in the Framingham Heart Study.

RATIONALE: The relationship between the development and/or progression of interstitial lung abnormalities (ILA) and clinical outcomes has not been previously investigated. OBJECTIVES: To determine the risk factors for, and the clinical consequences of, having ILA progression in participants from the Framingham Heart Study. METHODS: ILA were assessed in 1,867 participants who had serial chest computed tomography (CT) scans approximately 6 years apart. Mixed effect regression (and Cox) models were used to assess the association between ILA progression and pulmonary function decline (and mortality). MEASUREMENTS AND MAIN RESULTS: During the follow-up period 660 (35%) participants did not have ILA on either CT scan, 37 (2%) had stable to improving ILA, and 118 (6%) had ILA with progression (the remaining participants without ILA were noted to be indeterminate on at least one CT scan). Increasing age and increasing copies of the MUC5B promoter polymorphism were associated with ILA progression. After adjustment for covariates, ILA progression was associated with a greater FVC decline when compared with participants without ILA (20 ml; SE, ±6 ml; P = 0.0005) and with those with ILA without progression (25 ml; SE, ±11 ml; P = 0.03). Over a median follow-up time of approximately 4 years, after adjustment, ILA progression was associated with an increase in the risk of death (hazard ratio, 3.9; 95% confidence interval, 1.3-10.9; P = 0.01) when compared with those without ILA. CONCLUSIONS: These findings demonstrate that ILA progression in the Framingham Heart Study is associated with an increased rate of pulmonary function decline and increased risk of death.

MUC5B promoter polymorphism and interstitial lung abnormalities.

BACKGROUND: A common promoter polymorphism (rs35705950) in MUC5B, the gene encoding mucin 5B, is associated with idiopathic pulmonary fibrosis. It is not known whether this polymorphism is associated with interstitial lung disease in the general population. METHODS: We performed a blinded assessment of interstitial lung abnormalities detected in 2633 participants in the Framingham Heart Study by means of volumetric chest computed tomography (CT). We evaluated the relationship between the abnormalities and the genotype at the rs35705950 locus. RESULTS: Of the 2633 chest CT scans that were evaluated, interstitial lung abnormalities were present in 177 (7%). Participants with such abnormalities were more likely to have shortness of breath and chronic cough and reduced measures of total lung and diffusion capacity, as compared with participants without such abnormalities. After adjustment for covariates, for each copy of the minor rs35705950 allele, the odds of interstitial lung abnormalities were 2.8 times greater (95% confidence interval [CI], 2.0 to 3.9; P<0.001), and the odds of definite CT evidence of pulmonary fibrosis were 6.3 times greater (95% CI, 3.1 to 12.7; P<0.001). Although the evidence of an association between the MUC5B genotype and interstitial lung abnormalities was greater among participants who were older than 50 years of age, a history of cigarette smoking did not appear to influence the association. CONCLUSIONS: The MUC5B promoter polymorphism was found to be associated with interstitial lung disease in the general population. Although this association was more apparent in older persons, it did not appear to be influenced by cigarette smoking. (Funded by the National Institutes of Health and others; ClinicalTrials.gov number, NCT00005121.).

Improved myelin water fraction mapping with deep neural networks using synthetically generated 3D data.

We introduce a generative model for synthesis of large scale 3D datasets for quantitative parameter mapping of myelin water fraction (MWF). Our model combines a MR physics signal decay model with an accurate probabilistic multi-component parametric T2 model. We synthetically generate a wide variety of high quality signals and corresponding parameters from a wide range of naturally occurring prior parameter values. To capture spatial variation, the generative signal decay model is combined with a generative spatial model conditioned on generic tissue segmentations. Synthesized 3D datasets can be used to train any convolutional neural network (CNN) based architecture for MWF estimation. Our source code is available at: https://github.com/quin-med-harvard-edu/synthmap Reduction of acquisition time at the expense of lower SNR, as well as accuracy and repeatability of MWF estimation techniques, are key factors that affect the adoption of MWF mapping in clinical practice. We demonstrate that the synthetically trained CNN provides superior accuracy over the competing methods under the constraints of naturally occurring noise levels as well as on the synthetically generated images at low SNR levels. Normalized root mean squared error (nRMSE) is less than 7% on synthetic data, which is significantly lower than competing methods. Additionally, the proposed method yields a coefficient of variation (CoV) that is at least 4x better than the competing method on intra-session test-retest reference dataset.

IVIM-Morph: Motion-compensated quantitative Intra-voxel Incoherent Motion (IVIM) analysis for functional fetal lung maturity assessment from diffusion-weighted MRI data.

Quantitative analysis of pseudo-diffusion in diffusion-weighted magnetic resonance imaging (DWI) data shows potential for assessing fetal lung maturation and generating valuable imaging biomarkers. Yet, the clinical utility of DWI data is hindered by unavoidable fetal motion during acquisition. We present IVIM-morph, a self-supervised deep neural network model for motion-corrected quantitative analysis of DWI data using the Intra-voxel Incoherent Motion (IVIM) model. IVIM-morph combines two sub-networks, a registration sub-network, and an IVIM model fitting sub-network, enabling simultaneous estimation of IVIM model parameters and motion. To promote physically plausible image registration, we introduce a biophysically informed loss function that effectively balances registration and model-fitting quality. We validated the efficacy of IVIM-morph by establishing a correlation between the predicted IVIM model parameters of the lung and gestational age (GA) using fetal DWI data of 39 subjects. Our approach was compared against six baseline methods: 1) no motion compensation, 2) affine registration of all DWI images to the initial image, 3) deformable registration of all DWI images to the initial image, 4) deformable registration of each DWI image to its preceding image in the sequence, 5) iterative deformable motion compensation combined with IVIM model parameter estimation, and 6) self-supervised deep-learning-based deformable registration. IVIM-morph exhibited a notably improved correlation with gestational age (GA) when performing in-vivo quantitative analysis of fetal lung DWI data during the canalicular phase. Specifically, over 2 test groups of cases, it achieved an Rf2 of 0.44 and 0.52, outperforming the values of 0.27 and 0.25, 0.25 and 0.00, 0.00 and 0.00, 0.38 and 0.00, and 0.07 and 0.14 obtained by other methods. IVIM-morph shows potential in developing valuable biomarkers for non-invasive assessment of fetal lung maturity with DWI data. Moreover, its adaptability opens the door to potential applications in other clinical contexts where motion compensation is essential for quantitative DWI analysis. The IVIM-morph code is readily available at:https://github.com/TechnionComputationalMRILab/qDWI-Morph.

Self Supervised Denoising Diffusion Probabilistic Models for Abdominal DW-MRI.

Quantitative diffusion weighted MRI in the abdomen provides important markers of disease, however significant limitations exist for its accurate computation. One such limitation is the low signal-to-noise ratio, particularly at high diffusion b-values. To address this, multiple diffusion directional images can be collected at each b-value and geometrically averaged, which invariably leads to longer scan time, blurring due to motion and other artifacts. We propose a novel parameter estimation technique based on self supervised diffusion denoising probabilistic model that can effectively denoise diffusion weighted images and work on single diffusion gradient direction images. Our source code is made available at https://github.com/quin-med-harvard-edu/ssDDPM.

Learning the Regularization in DCE-MR Image Reconstruction for Functional Imaging of Kidneys.

Kidney DCE-MRI aims at both qualitative assessment of kidney anatomy and quantitative assessment of kidney function by estimating the tracer kinetic (TK) model parameters. Accurate estimation of TK model parameters requires an accurate measurement of the arterial input function (AIF) with high temporal resolution. Accelerated imaging is used to achieve high temporal resolution, which yields under-sampling artifacts in the reconstructed images. Compressed sensing (CS) methods offer a variety of reconstruction options. Most commonly, sparsity of temporal differences is encouraged for regularization to reduce artifacts. Increasing regularization in CS methods removes the ambient artifacts but also over-smooths the signal temporally which reduces the parameter estimation accuracy. In this work, we propose a single image trained deep neural network to reduce MRI under-sampling artifacts without reducing the accuracy of functional imaging markers. Instead of regularizing with a penalty term in optimization, we promote regularization by generating images from a lower dimensional representation. In this manuscript we motivate and explain the lower dimensional input design. We compare our approach to CS reconstructions with multiple regularization weights. Proposed approach results in kidney biomarkers that are highly correlated with the ground truth markers estimated using the CS reconstruction which was optimized for functional analysis. At the same time, the proposed approach reduces the artifacts in the reconstructed images.

3D Deep Learning for Anatomical Structure Segmentation in Multiple Imaging Modalities.

Accurate, quantitative segmentation of anatomical structures in radiological scans, such as Magnetic Resonance Imaging (MRI) and Computer Tomography (CT), can produce significant biomarkers and can be integrated into computer-aided assisted diagnosis (CADx) systems to support the interpretation of medical images from multi-protocol scanners. However, there are serious challenges towards developing robust automated segmentation techniques, including high variations in anatomical structure and size, the presence of edge-based artefacts, and heavy un-controlled breathing that can produce blurred motion-based artefacts. This paper presents a novel computing approach for automatic organ and muscle segmentation in medical images from multiple modalities by harnessing the advantages of deep learning techniques in a two-part process. (1) a 3D encoder-decoder, Rb-UNet, builds a localisation model and a 3D Tiramisu network generates a boundary-preserving segmentation model for each target structure; (2) the fully trained Rb-UNet predicts a 3D bounding box encapsulating the target structure of interest, after which the fully trained Tiramisu model performs segmentation to reveal detailed organ or muscle boundaries. The proposed approach is evaluated on six different datasets, including MRI, Dynamic Contrast Enhanced (DCE) MRI and CT scans targeting the pancreas, liver, kidneys and psoas-muscle and achieves quantitative measures of mean Dice similarity coefficient (DSC) that surpass or are comparable with the state-of-the-art. A qualitative evaluation performed by two independent radiologists verified the preservation of detailed organ and muscle boundaries.

Modeling dynamic radial contrast enhanced MRI with linear time invariant systems for motion correction in quantitative assessment of kidney function.

Early identification of kidney function deterioration is essential to determine which newborn patients with congenital kidney disease should be considered for surgical intervention as opposed to observation. Kidney function can be measured by fitting a tracer kinetic (TK) model onto a series of Dynamic Contrast Enhanced (DCE) MR images and estimating the filtration rate parameter from the model. Unfortunately, breathing and large bulk motion events due to patient movement in the scanner create outliers and misalignments that introduce large errors in the TK model parameter estimates even when using a motion-robust dynamic radial VIBE sequence for DCE-MR imaging. The misalignments between the series of volumes are difficult to correct using standard registration due to 1) the large differences in geometry and contrast between volumes of the dynamic sequence and 2) the requirement of fast dynamic imaging to achieve high temporal resolution and motion deteriorates image quality. These difficulties reduce the accuracy and stability of registration over the dynamic sequence. An alternative registration approach is to generate noise and motion free templates of the original data from the TK model and use them to register each volume to its contrast-matched template. However, the TK models used to characterize DCE-MRI are tissue specific, non-linear and sensitive to the same motion and sampling artifacts that hinder registration in the first place. Hence, these can only be applied to register accurately pre-segmented regions of interest, such as kidneys, and might converge to local minima under the presence of large artifacts. Here we introduce a novel linear time invariant (LTI) model to characterize DCE-MR data for different tissue types within a volume. We approximate the LTI model as a sparse sum of first order LTI functions to introduce robustness to motion and sampling artifacts. Hence, this model is well suited for registration of the entire field of view of DCE-MR data with artifacts and outliers. We incorporate this LTI model into a registration framework and evaluate it on both synthetic data and data from 20 children. For each subject, we reconstructed the sequence of DCE-MR images, detected corrupted volumes acquired during motion, aligned the sequence of volumes and recovered the corrupted volumes using the LTI model. The results show that our approach correctly aligned the volumes, provided the most stable registration in time and improved the tracer kinetic model fit.

Simultaneous Motion and Distortion Correction Using Dual-Echo Diffusion-Weighted MRI.

BACKGROUND AND PURPOSE: Geometric distortions resulting from large pose changes reduce the accuracy of motion measurements and interfere with the ability to generate artifact-free information. Our goal is to develop an algorithm and pulse sequence to enable motion-compensated, geometric distortion compensated diffusion-weighted MRI, and to evaluate its efficacy in correcting for the field inhomogeneity and position changes, induced by large and frequent head motions. METHODS: Dual echo planar imaging (EPI) with a blip-reversed phase encoding distortion correction technique was evaluated in five volunteers in two separate experiments and compared with static field map distortion correction. In the first experiment, dual-echo EPI images were acquired in two head positions designed to induce a large field inhomogeneity change. A field map and a distortion-free structural image were acquired at each position to assess the ability of dual-echo EPI to generate reliable field maps and enable geometric distortion correction in both positions. In the second experiment, volunteers were asked to move to multiple random positions during a diffusion scan. Images were reconstructed using the dual-echo correction and a slice-to-volume registration (SVR) registration algorithm. The accuracy of SVR motion estimates was compared to externally measured ground truth motion parameters. RESULTS: Our results show that dual-echo EPI can produce slice-level field maps with comparable quality to field maps generated by the reference gold standard method. We also show that slice-level distortion correction improves the accuracy of SVR algorithms as slices acquired at different orientations have different levels of distortion, which can create errors in the registration process. CONCLUSIONS: Dual-echo acquisitions with blip-reversed phase encoding can be used to generate slice-level distortion-free images, which is critical for motion-robust slice to volume registration. The distortion corrected images not only result in better motion estimates, but they also enable a more accurate final diffusion image reconstruction.