Jan Sijbers

University of Antwerp | UA · Department of Physics

Longitudinal MRI is an important diagnostic imaging tool for evaluating the effects of treatment and monitoring disease progression. However, MRI, and particularly longitudinal MRI, is known to be time consuming. To accelerate imaging, compressed sensing (CS) theory has been applied to exploit sparsity, both on single image as on image sequence lev...

The prospect of continued manned space missions warrants an in-depth understanding of how prolonged microgravity affects the human brain. Functional magnetic resonance imaging (fMRI) can pinpoint changes reflecting adaptive neuroplasticity across time. We acquired resting-state fMRI data of cosmonauts before, shortly after, and eight months after s...

A new framework for the parametric reconstruction of curved fibres from glass fibre-reinforced composite X-ray computed tomography data is proposed. It allows us to detect fibres in a fibre-reinforced polymer sample from a low-dose, low resolution computed tomography scan. An efficient curve representation is then used for each detected fibre, of w...

Tensor‐valued diffusion encoding facilitates data analysis by q‐space trajectory imaging. By modeling the diffusion signal of heterogeneous tissues with a diffusion tensor distribution (DTD) and modulating the encoding tensor shape, this novel approach allows disentangling variations in diffusivity from microscopic anisotropy, orientation dispersio...

Multi-slice (MS) super-resolution reconstruction (SRR) methods have been proposed to improve the trade-off between resolution, signal-to-noise ratio and scan time in magnetic resonance imaging. MS-SRR consists in the estimation of an isotropic high-resolution image from a series of anisotropic MS images with a low through-plane resolution, where th...

Transcatheter mitral valve replacement (TMVR) has emerged as a minimally invasive alternative for treating patients suffering from mitral valve disease. The number of TMVR procedures is expected to rise as devices currently in clinical trials obtain approval for commercialization. Automating the planning of such interventions becomes, therefore, mo...

Background: Most studies using diffusion-weighted MRI (DW-MRI) in Alzheimer's disease (AD) have focused their analyses on white matter (WM) microstructural changes using the diffusion (kurtosis) tensor model. Although recent works have addressed some limitations of the tensor model, such as the representation of crossing fibers and partial volume...

The design of new x-ray phase contrast imaging setups often relies on Monte Carlo simulations for prospective parameter studies. Monte Carlo simulations are known to be accurate but time consuming, leading to long simulation times, especially when many parameter variations are required. This is certainly the case for imaging methods relying on abso...

Purpose: To introduce a novel imaging and parameter estimation framework for accurate multi-shot diffusion MRI. Theory and methods: We propose a new framework called ADEPT (Accurate Diffusion Echo-Planar imaging with multi-contrast shoTs) that enables fast diffusion MRI by allowing diffusion contrast settings to change between shots in a multi-s...

X-ray Computed Tomography (CT) is a commonly used imaging technique for non-destructive inspection of manufactured objects. However, a full CT scan requires a long acquisition time, making this method unsuitable for inline applications. In contrast to X-ray CT, inspection can be performed directly in the projection space, using simulated X-ray proj...

In X-ray computed tomography, discrete tomography (DT) algorithms have been successful at reconstructing objects composed of only a few distinct materials. Many DT-based methods rely on a divide-and-conquer procedure to reconstruct the volume in parts, which improves their run-time and reconstruction quality. However, this procedure is based on sta...

The design of new x-ray phase contrast imaging setups often relies on Monte Carlo simulations for prospective parameter studies. Monte Carlo simulations are known to be accurate but time consuming, leading to long simulation times, especially when many parameter variations are required. This is certainly the case for imaging methods relying on abso...

The 3D musculoskeletal motion of animals is of interest for various biological studies and can be derived from X-ray fluoroscopy acquisitions by means of image matching or manual landmark annotation and mapping. While the image matching method requires a robust similarity measure (intensity-based) or an expensive computation (tomographic reconstruc...

Radiography is a common imaging method for non-destructive object inspection. Processing radiographs to detect defects is, however, challenging, especially if the defect type and location are unknown. In other fields, autoencoders (AE) have been largely studied for anomaly detection. While their performance for defect detection has shown promise, m...

To preserve the quality of fresh fruit after harvest and to meet the year-round demand for high-quality fruit, pears are stored under a controlled atmosphere. However, due to preharvest events or suboptimal storage conditions, internal disorders might develop resulting in severe quality loss. Examples include internal browning and cavities, which a...

In this work, we apply and adapt established probability of detection (POD) methods on the in-line inspection of aluminium cylinder heads using X-ray computed tomography (XCT). We propose to use the XCT simulation tool SimCT to simulate virtual X-ray radiographs from the specimen including artificial defects, which avoids the manufacturing of speci...

Quantitative Magnetic Resonance (MR) imaging provides reproducible measurements of biophysical parameters, and has become an essential tool in clinical MR studies. Unfortunately, 3D isotropic high resolution (HR) parameter mapping is hardly feasible in clinical practice due to prohibitively long acquisition times. Moreover, accurate and precise est...

This document includes supplementary material that complements the main body of the paper. In Section 1, we provide analytical derivations of the Jacobian and Hessian of the alternating minimization scheme which was used to obtain the joint Maximum a Posteriori estimates of the tissue and motion parameters. Next, Section 2 elaborates on the impleme...

Long-duration spaceflight induces changes to the brain and cerebrospinal fluid compartments and visual acuity problems known as spaceflight-associated neuro-ocular syndrome (SANS). The clinical relevance of these changes and whether they equally affect crews of different space agencies remain unknown. We used MRI to analyze the alterations occurrin...

Mitral valve disease is a commonly occurring pathology and its incidence is expected to rise in the coming decades. This has led to an increase in the number and complexity of computational models developed to characterize the mitral valve behaviour, resulting in the need for automated segmentation methods. In this study, we evaluated the suitabili...

The free water elimination (FWE) model and its kurtosis variant (DKI-FWE) can separate tissue and free water signal contributions, thus providing tissue-specific diffusional information. However, a downside of these models is that the associated parameter estimation problem is ill-conditioned, necessitating the use of advanced estimation techniques...

Purpose The registration of a 3D atlas image to 2D radiographs enables 3D pre-operative planning without the need to acquire costly and high-dose CT-scans. Recently, many deep-learning-based 2D/3D registration methods have been proposed which tackle the problem as a reconstruction by regressing the 3D image immediately from the radiographs, rather...

Humans undergo extreme physiological changes when subjected to long periods of weightlessness, and as we continue to become a space-faring species, it is imperative that we fully understand the physiological changes that occur in the human body, including the brain. In this study, we present findings of brain structural changes associated with long...

This paper describes a reconstruction method for atom probe tomography based on a bottom-up approach accounting for (i) the final tip morphology (which is frequently induced by inhomogeneous evaporation probabilities across the tip surface due to laser absorption, heat diffusion effects, and inhomogeneous material properties), (ii) the limited (and...

In recent years, terahertz (THz) time-domain imaging attracted significant attention and become a useful tool in many applications. A THz time-domain imaging system measures amplitude changes of the THz radiation across a range of frequencies so the absorption coefficient of the materials in the sample can be obtained. THz time-domain images repres...

X-ray computed tomography (X-CT) plays an important role in non-destructive quality inspection and process evaluation in metal additive manufacturing, as several types of defects such as keyhole and lack of fusion pores can be observed in these 3D images as local changes in material density. Segmentation of these defects often relies on threshold m...

Most lab-based X-ray sources are polychromatic, making the imaging process follow a non-linear model. However, widespread reconstruction algorithms, such as filtered back projection and the simultaneous iterative reconstruction technique, assume the reconstruction to be a linear problem, leading to artifacts in the reconstructions from polychromati...

Due to the rapid nucleation and bubble deformation processes that occur during a foam formation process, 4D-CT scans can only record a small number of X-ray projections per rotation. Current dynamic CT imaging methods compute a series of 3D images, which requires a high number of projections per rotation and thus limits the temporal resolution. In...

The clinical application of diffusion MRI is practically hindered by its long scan time. In this work, we introduce a novel imaging and parameter estimation framework for time-efficient diffusion MRI. To improve the scan efficiency, we propose ADEPT (Accelerated Diffusion EPI with multi-contrast shoTs), in which diffusion contrast settings are allo...

In clinical MRI, direct acquisition at isotropic high resolution (HR) and with high signal-to-noise ratio (SNR) is often infeasible due to the long scan time required. Multi-slice super-resolution reconstruction (MS-SRR) can reduce this limitation by reconstructing an HR 3D isotropic image from a series of MS images with an anisotropy factor (AF, d...

T2* mapping using ultra-short echo time (UTE) MRI enables quantitative evaluation of knee structures with short transverse relaxation times. However, acquisitions with low through-plane resolution are commonly used to obtain T2* maps within reasonable scan time, affecting the estimation accuracy due to partial volume effect. In this work, a model-b...

Current classifications of midshaft clavicle fractures are based on radiography. The aim of the study was to evaluate the fracture pattern of clavicle fractures using 3-dimensional computed tomography (3D CT). A retrospective analysis was performed on CT scans of 65 acute clavicle fractures. Using quantitative 3D CT reconstruction techniques, the f...

In this paper, we propose the use of Recurrent Inference Machines (RIMs) to perform T 1 and T 2 mapping. The RIM is a neural network framework that learns an iterative inference process based on the signal model, similar to conventional statistical methods for quantitative MRI (QMRI), such as the Maximum Likelihood Estimator (MLE). This framework c...

Introduction: Neuropsychological test scores are limited and standard outcomes may mask the heterogeneity of cognitive impairment. This article presents the calculation and evaluation of six composite scores that quantify domain-specific impairment. Methods: Parameters for composite scores calculation were learned by performing confirmatory fact...

Purpose: Adjoint image warping is an important tool to solve image reconstruction problems that warp the unknown image in the forward model. This includes four-dimensional computed tomography (4D-CT) models in which images are compared against recorded projection images of various time frames using image warping as a model of the motion. The inver...

An issue in computerized X-ray tomography is the limited size of available detectors relative to objects of interest. A solution was provided in the past two decades by positioning the detector in a lateral offset position, increasing the effective field of view (FOV) and thus the diameter of the reconstructed volume. However, this introduced artif...

Diffusion MRI (dMRI) has become an invaluable tool to assess the microstructural organization of brain tissue. Depending on the specific acquisition settings, the dMRI signal encodes specific properties of the underlying diffusion process. In the last two decades, several signal representations have been proposed to fit the dMRI signal and decode s...

In this paper, we propose the use of Recurrent Inference Machines (RIMs) to perform T1 and T2 mapping. The RIM is a neural network framework that learns an iterative inference process based on the signal model, similar to conventional statistical methods for quantitative MRI (QMRI), such as the Maximum Likelihood Estimator (MLE). This framework com...

T2* mapping using ultrashort echo time (UTE) MRI allows for quantitative evaluation of collagen-rich knee structures with short mean transverse relaxation times. However, acquisitions with low through-plane resolution are commonly used to obtain T2* maps within reasonable scan times, affecting the accuracy of the estimations because of partial volu...

One of the most commonly used correction methods in X-ray imaging is flat field correction, which corrects for systematic inconsistencies, such as differences in detector pixel response. In conventional X-ray imaging, flat fields are acquired by exposing the detector without any object in the X-ray beam. However, in edge illumination X-ray CT, whic...

Background: Recent research has shown that leg dominance has an impact on gait and that this impact is significant enough that a leg dominance scores are worth developing. However, it remains unclear how leg dominance impacts plantar pressure measurements. Some studies assume that measurements from opposing feet are identical while others assume th...

Beam hardening and scattering effects can seriously degrade image quality in polychromatic X-ray CT imaging. In recent years, polychromatic image reconstruction techniques and scatter estimation using Monte Carlo simulation have been developed to compensate for beam hardening and scattering CT artifacts, respectively. Both techniques require knowle...

X-ray 3D Computed Tomography (3DCT) has great potential for inspection of industrial products. Unfortunately, conventional CT-based workflows to inspect objects created from a CAD model involve a time-consuming acquisition process, computationally expensive image reconstruction, and multiple postprocessing steps, preventing them from inline usage....

Compared to single source systems, stereo X-ray CT systems allow acquiring projection data within a reduced amount of time, for an extended field-of-view, or for dual X-ray energies. To exploit the benefit of a dual X-ray system, its acquisition geometry needs to be calibrated. Unfortunately, in modular stereo X-ray CT setups , geometry misalignmen...

Diffusion MRI (dMRI) has become an invaluable tool to assess the microstructural organization of brain tissue. Depending on the specific acquisition settings, the dMRI signal encodes specific properties of the underlying diffusion process. In the last two decades, several signal representations have been proposed to fit the dMRI signal and decode s...

Most digital models of the equine distal limb that are available in the community are static and/or subject specific; hence, they have limited applications in veterinary research. In this paper, we present an articulatable model of the entire equine distal limb based on statistical shape modeling. The model describes the inter-subject variability i...

Long term storage is required to deliver high quality pear fruit year-round. Under suboptimal storage conditions, internal disorders, such as internal browning and cavity formation, can develop and are often invisible from the outside. We present a non-destructive inspection method to quantify internal disorders in X-ray CT scans of pear fruit usin...

Laboratory based X-ray micro-CT is a non-destructive testing method that enables three dimensional visualization and analysis of the internal and external morphology of samples.Although a wide variety of commercial scanners exist, most of them are limited in the number of degrees of freedom to position the source and detector with respect to the ob...

Restoring high-quality CT images from low-dose CT counterparts is an ill-posed, nonlinear problem to which deep learning approaches have shown promising results compared to classical model-based approaches. Feedforward neural networks, whose output at any given time depends only on their input at that specific time slot, have been widely used to pr...

A new reconstruction method incorporating the beam shape was developed for 3D Terahertz computed tomography using operators instead of matrices, solving data storing problems. We show that this method significantly improves the accuracy of recon- structions.

In this paper, we study the application of a ray tracing technique to terahertz (THz) computed tomography (CT). We evaluate its accuracy by comparing the resulting sinograms with the ones simulated with a Born series approximation.