Computer simulation of magnetic resonance angiography imaging: model description and validation

Generating Synthetic Radiological Images with PySynthMRI: An Open-Source Cross-Platform Tool

Synthetic MR Imaging allows for the reconstruction of different image contrasts from a single acquisition, reducing scan times. Commercial products that implement synthetic MRI are used in research. They rely on vendor-specific acquisitions and do not include the possibility of using custom multiparametric imaging techniques. We introduce PySynthMRI, an open-source tool with a user-friendly interface that uses a set of input images to generate synthetic images with diverse radiological contrasts by varying representative parameters of the desired target sequence, including the echo time, repetition time and inversion time(s). PySynthMRI is written in Python 3.6, and it can be executed under Linux, Windows, or MacOS as a python script or an executable. The tool is free and open source and is developed while taking into consideration the possibility of software customization by the end user. PySynthMRI generates synthetic images by calculating the pixelwise signal intensity as a function of a set of input images (e.g., T1 and T2 maps) and simulated scanner parameters chosen by the user via a graphical interface. The distribution provides a set of default synthetic contrasts, including T1w gradient echo, T2w spin echo, FLAIR and Double Inversion Recovery. The synthetic images can be exported in DICOM or NiFTI format. PySynthMRI allows for the fast synthetization of differently weighted MR images based on quantitative maps. Specialists can use the provided signal models to retrospectively generate contrasts and add custom ones. The modular architecture of the tool can be exploited to add new features without impacting the codebase.

Blood flow CFD simulation on a cerebral artery of a stroke patient

Abstract

The purpose of this paper is to conduct a numerical simulation of the stroke patient's cerebral arteries and investigate the flow parameters due to the presence of stenosis. The computational fluid dynamics (CFD) simulations are based on simplified and realistic cerebral artery models. The seven simplified models (benchmarks) include straight cylindrical vessels with idealized stenosis with variable d/D (0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1). The realistic model of the cerebral artery is based on magnetic resonance imaging (MRI) for patient-specific cerebral arteries. The simulation for the realistic model of the cerebral artery is performed at boundary conditions measured by ultrasonography of the input and the output flow profiles (velocity and pressure). The obtained CFD results of the benchmarks are validated with actual data from the literature. Furthermore, a previous vascular contraction is assumed to be exist and the effect of this contraction area ratio on the blood flow regime is discussed and highlighted. Furthermore, CFD results show that a certain vascular contraction area critically affects the blood flow which shows increasing the wall shear stress WSS at the stenosis site. An increase in the blood velocity and vortex appears after the contraction zone, this lead to vessel occlusion and strokes.

Article highlights

Magnetic Resonance Simulation in Education: Quantitative Evaluation of an Actual Classroom Experience

Magnetic resonance is an imaging modality that implies a high complexity for radiographers. Despite some simulators having been developed for training purposes, we are not aware of any attempt to quantitatively measure their educational performance. The present study gives an answer to the question: Does an MRI simulator built on specific functional and non-functional requirements help radiographers learn MRI theoretical and practical concepts better than traditional educational method based on lectures? Our study was carried out in a single day by a total of 60 students of a main hospital in Madrid, Spain. The experiment followed a randomized pre-test post-test design with a control group that used a traditional educational method, and an experimental group that used our simulator. Knowledge level was assessed by means of an instrument with evidence of validity in its format and content, while its reliability was analyzed after the experiment. Statistical differences between both groups were measured. Significant statistical differences were found in favor of the participants who used the simulator for both the post-test score and the gain (difference between post-test and pre-test scores). The effect size turned out to be significant as well. In this work we evaluated a magnetic resonance simulation paradigm as a tool to help in the training of radiographers. The study shows that a simulator built on specific design requirements is a valuable complement to traditional education procedures, backed up with significant quantitative results.

Numerical simulation of time-resolved 3D phase-contrast magnetic resonance imaging

A numerical approach is presented to efficiently simulate time-resolved 3D phase-contrast Magnetic resonance Imaging (or 4D Flow MRI) acquisitions under realistic flow conditions. The Navier-Stokes and Bloch equations are simultaneously solved with an Eulerian-Lagrangian formalism. A semi-analytic solution for the Bloch equations as well as a periodic particle seeding strategy are developed to reduce the computational cost. The velocity reconstruction pipeline is first validated by considering a Poiseuille flow configuration. The 4D Flow MRI simulation procedure is then applied to the flow within an in vitro flow phantom typical of the cardiovascular system. The simulated MR velocity images compare favorably to both the flow computed by solving the Navier-Stokes equations and experimental 4D Flow MRI measurements. A practical application is finally presented in which the MRI simulation framework is used to identify the origins of the MRI measurement errors.

A Multi-Layer Perceptron Network for Perfusion Parameter Estimation in DCE-MRI Studies of the Healthy Kidney

Background: Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is an imaging technique which helps in visualizing and quantifying perfusion—one of the most important indicators of an organ’s state. This paper focuses on perfusion and filtration in the kidney, whose performance directly influences versatile functions of the body. In clinical practice, kidney function is assessed by measuring glomerular filtration rate (GFR). Estimating GFR based on DCE-MRI data requires the application of an organ-specific pharmacokinetic (PK) model. However, determination of the model parameters, and thus the characterization of GFR, is sensitive to determination of the arterial input function (AIF) and the initial choice of parameter values. Methods: This paper proposes a multi-layer perceptron network for PK model parameter determination, in order to overcome the limitations of the traditional model’s optimization techniques based on non-linear least-squares curve-fitting. As a reference method, we applied the trust-region reflective algorithm to numerically optimize the model. The effectiveness of the proposed approach was tested for 20 data sets, collected for 10 healthy volunteers whose image-derived GFR scores were compared with ground-truth blood test values. Results: The achieved mean difference between the image-derived and ground-truth GFR values was 2.35 mL/min/1.73 m2, which is comparable to the result obtained for the reference estimation method (−5.80 mL/min/1.73 m2). Conclusions: Neural networks are a feasible alternative to the least-squares curve-fitting algorithm, ensuring agreement with ground-truth measurements at a comparable level. The advantages of using a neural network are twofold. Firstly, it can estimate a GFR value without the need to determine the AIF for each individual patient. Secondly, a reliable estimate can be obtained, without the need to manually set up either the initial parameter values or the constraints thereof.

Virtual clinical trials in medical imaging: a review

The accelerating complexity and variety of medical imaging devices and methods have outpaced the ability to evaluate and optimize their design and clinical use. This is a significant and increasing challenge for both scientific investigations and clinical applications. Evaluations would ideally be done using clinical imaging trials. These experiments, however, are often not practical due to ethical limitations, expense, time requirements, or lack of ground truth. Virtual clinical trials (VCTs) (also known as in silico imaging trials or virtual imaging trials) offer an alternative means to efficiently evaluate medical imaging technologies virtually. They do so by simulating the patients, imaging systems, and interpreters. The field of VCTs has been constantly advanced over the past decades in multiple areas. We summarize the major developments and current status of the field of VCTs in medical imaging. We review the core components of a VCT: computational phantoms, simulators of different imaging modalities, and interpretation models. We also highlight some of the applications of VCTs across various imaging modalities.

Simulation of phase contrast angiography for renal arterial models

BACKGROUND

With the development of versatile magnetic resonance acquisition techniques there arises a need for more advanced imaging simulation tools to enable adequate image appearance prediction, measurement sequence design and testing thereof. Recently, there is a growing interest in phase contrast angiography (PCA) sequence due to the capabilities of blood flow quantification that it offers. Moreover, as it is a non-contrast enhanced protocol, it has become an attractive option in areas, where usage of invasive contrast agents is not indifferent for the imaged tissue. Monitoring of the kidney function is an example of such an application.

RESULTS

We present a computer framework for simulation of the PCA protocol, both conventional and accelerated with echo-planar imaging (EPI) readout, and its application to the numerical models of kidney vasculatures. Eight patient-specific renal arterial trees were reconstructed following vessel segmentation in real computed tomography angiograms. In addition, a synthetic model was designed using a vascular tree growth simulation algorithm. The results embrace a series of synthetic PCA images of the renal arterial trees giving insight into the image formation and quantification of kidney hemodynamics.

CONCLUSIONS

The designed simulation framework enables quantification of the PCA measurement error in relation to ground-truth flow velocity data. The mean velocity measurement error for the reconstructed renal arterial trees range from 1.5 to 12.8% of the aliasing velocity value, depending on image resolution and flip angle. No statistically significant difference was observed between measurements obtained using EPI with a number of echos (NETL) = 4 and conventional PCA. In case of higher NETL factors peak velocity values can be underestimated up to 34%.

Flow MRI simulation in complex 3D geometries: Application to the cerebral venous network

PURPOSE

Develop and evaluate a complete tool to include 3D fluid flows in MRI simulation, leveraging from existing software. Simulation of MR spin flow motion is of high interest in the study of flow artifacts and angiography. However, at present, only a few simulators include this option and most are restricted to static tissue imaging.

THEORY AND METHODS

An extension of JEMRIS, one of the most advanced high performance open-source simulation platforms to date, was developed. The implementation of a Lagrangian description of the flow allows simulating any MR experiment, including both static tissues and complex flow data from computational fluid dynamics. Simulations of simple flow models are compared with real experiments on a physical flow phantom. A realistic simulation of 3D flow MRI on the cerebral venous network is also carried out.

RESULTS

Simulations and real experiments are in good agreement. The generality of the framework is illustrated in 2D and 3D with some common flow artifacts (misregistration and inflow enhancement) and with the three main angiographic techniques: phase contrast velocimetry (PC), time-of-flight, and contrast-enhanced imaging MRA.

CONCLUSION

The framework provides a versatile and reusable tool for the simulation of any MRI experiment including physiological fluids and arbitrarily complex flow motion.

Simulation of MR angiography imaging for validation of cerebral arteries segmentation algorithms

BACKGROUND AND OBJECTIVE

Accurate vessel segmentation of magnetic resonance angiography (MRA) images is essential for computer-aided diagnosis of cerebrovascular diseases such as stenosis or aneurysm. The ability of a segmentation algorithm to correctly reproduce the geometry of the arterial system should be expressed quantitatively and observer-independently to ensure objectivism of the evaluation.

METHODS

This paper introduces a methodology for validating vessel segmentation algorithms using a custom-designed MRA simulation framework. For this purpose, a realistic reference model of an intracranial arterial tree was developed based on a real Time-of-Flight (TOF) MRA data set. With this specific geometry blood flow was simulated and a series of TOF images was synthesized using various acquisition protocol parameters and signal-to-noise ratios. The synthesized arterial tree was then reconstructed using a level-set segmentation algorithm available in the Vascular Modeling Toolkit (VMTK). Moreover, to present versatile application of the proposed methodology, validation was also performed for two alternative techniques: a multi-scale vessel enhancement filter and the Chan-Vese variant of the level-set-based approach, as implemented in the Insight Segmentation and Registration Toolkit (ITK). The segmentation results were compared against the reference model.

RESULTS

The accuracy in determining the vessels centerline courses was very high for each tested segmentation algorithm (mean error rate = 5.6% if using VMTK). However, the estimated radii exhibited deviations from ground truth values with mean error rates ranging from 7% up to 79%, depending on the vessel size, image acquisition and segmentation method.

CONCLUSIONS

We demonstrated the practical application of the designed MRA simulator as a reliable tool for quantitative validation of MRA image processing algorithms that provides objective, reproducible results and is observer independent.

A computer-simulation study on the effects of MRI voxel dimensions on carotid plaque lipid-core and fibrous cap segmentation and stress modeling

Background

The benefits of a decreased slice thickness and/or in-plane voxel size in carotid MRI for atherosclerotic plaque component quantification accuracy and biomechanical peak cap stress analysis have not yet been investigated in detail because of practical limitations.

Methods

In order to provide a methodology that allows such an investigation in detail, numerical simulations of a T1-weighted, contrast-enhanced, 2D MRI sequence were employed. Both the slice thickness (2 mm, 1 mm, and 0.5 mm) and the in plane acquired voxel size (0.62x0.62 mm² and 0.31x0.31 mm²) were varied. This virtual MRI approach was applied to 8 histology-based 3D patient carotid atherosclerotic plaque models.

Results

A decreased slice thickness did not result in major improvements in lumen, vessel wall, and lipid-rich necrotic core size measurements. At 0.62x0.62 mm² in-plane, only a 0.5 mm slice thickness resulted in improved minimum fibrous cap thickness measurements (a 2–3 fold reduction in measurement error) and only marginally improved peak cap stress computations. Acquiring voxels of 0.31x0.31 mm² in-plane, however, led to either similar or significantly larger improvements in plaque component quantification and computed peak cap stress.

Conclusions

This study provides evidence that for currently-used 2D carotid MRI protocols, a decreased slice thickness might not be more beneficial for plaque measurement accuracy than a decreased in-plane voxel size. The MRI simulations performed indicate that not a reduced slice thickness (i.e. more isotropic imaging), but the acquisition of anisotropic voxels with a relatively smaller in-plane voxel size could improve carotid plaque quantification and computed peak cap stress accuracy.