Related papers: Portable simulation framework for diffusion MRI
In this paper we present the Neuron Module that we implemented within the Matlab-based diffusion MRI simulation toolbox SpinDoctor. SpinDoctor uses finite element discretization and adaptive time integration to solve the Bloch-Torrey…
Purpose: Conventional MRI is relying on the assumption of the magnetic field being homogeneous in direction and amplitude. However, with the growing interest in portable, affordable point-of-care MRI systems, these assumptions do not…
We propose ReMiDi, a novel method for inferring neuronal microstructure as arbitrary 3D meshes using a differentiable diffusion Magnetic Resonance Imaging (dMRI) simulator. We first implemented in PyTorch a differentiable dMRI simulator…
Open-source simulation frameworks are evolving rapidly to provide accessible tools for the numerical solution of partial differential equations. Modern finite element (FEM) software such as FEniCS, Firedrake, or dune-fem alleviates the need…
The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium such as brain tissue can be modeled by the Bloch-Torrey partial differential equation. The spatial…
A new discretization approach is presented for the simulation of flow in complex poro-fractured media described by means of the Discrete Fracture and Matrix Model. The method is based on the numerical optimization of a properly defined…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
We have developed a finite-element micromagnetic simulation code based on the FEniCS package called magnum.fe. Here we describe the numerical methods that are applied as well as their implementation with FEniCS. We apply a transformation…
FEMPAR is an open source object oriented Fortran200X scientific software library for the high-performance scalable simulation of complex multiphysics problems governed by partial differential equations at large scales, by exploiting…
Simulations with high accuracy are an essential part of scientific research to accelerate the innovation process. They are especially useful for finding novel approaches or optimizing existing methods. Today, powerful software tools are…
Purpose: To present a fully open-source framework for quasi-real-time streaming and cloud-based processing of low-field (LF) MRI data, addressing the growing computational demands of advanced reconstruction and post-processing pipelines in…
We present a finite element scheme for fractional diffusion problems with varying diffusivity and fractional order. We consider a symmetric integral form of these nonlocal equations defined on general geometries and in arbitrary bounded…
We introduce a new Eulerian simulation framework for liquid animation that leverages both finite element and finite volume methods. In contrast to previous methods where the whole simulation domain is discretized either using the finite…
Fitting multi-exponential models to Diffusion MRI (dMRI) data has always been challenging due to various underlying complexities. In this work, we introduce a novel and robust fitting framework for the standard two-compartment IVIM…
Magnetic Resonance Imaging (MRI), including diffusion MRI (dMRI), serves as a ``microscope'' for anatomical structures and routinely mitigates the influence of low signal-to-noise ratio scans by compromising temporal or spatial resolution.…
The Bloch equation describes the evolution of classical particles tagged with a magnetisation vector in a strong magnetic field and is fundamental to many NMR and MRI contrast methods. The equation can be generalised to include the effects…
Soft biological tissues demonstrate strong time-dependent and strain-rate mechanical behavior, arising from their intrinsic visco-elasticity and fluid-solid interactions (especially at sufficiently large time scales). The time-dependent…
Magnetic Resonance Imaging (MRI) is a widely applied non-invasive imaging modality based on non-ionizing radiation which gives excellent images and soft tissue contrast of living tissues. We consider the modified Bloch problem as a model of…
Numerical simulations of flow and transport in porous media usually rely on hybrid-dimensional models, i.e., the fracture is considered as objects of a lower dimension compared to the embedding matrix. Such models are usually combined with…
Many medical imaging techniques utilize fitting approaches for quantitative parameter estimation and analysis. Common examples are pharmacokinetic modeling in DCE MRI/CT, ADC calculations and IVIM modeling in diffusion-weighted MRI and…