Publications by authors named "Jan Sijbers"

137 Publications

Extended imaging volume in cone-beam x-ray tomography using the weighted simultaneous iterative reconstruction technique.

Phys Med Biol 2021 Jul 21. Epub 2021 Jul 21.

Physics, Universiteit Antwerpen, Antwerpen, BELGIUM.

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 artifacts in the obtained reconstructions, caused by projection truncation and data redundancy. These issues can be addressed by incorporating an additional data weighting step in the reconstruction algorithms, known as redundancy weighting. In this work, we present an implementation of redundancy weighting in the widely-used Simultaneous Iterative Reconstruction Technique (SIRT), yielding the W-SIRT method. The new technique is validated using geometric phantoms and a rabbit specimen, by performing both simulation studies as well as physical experiments. The experiments are carried out in a highly flexible stereoscopic X-ray system equipped with X-ray image intensifiers (XRIIs). The simulations showed that higher values of CNR could be obtained using the W-SIRT approach as compared to a weighted implementation of SART. The convergence rate of the W-SIRT was accelerated by including a relaxation parameter in the W-SIRT algorithm, creating the aW-SIRT algorithm. This allowed to obtain the same results as the W-SIRT algorithm, but at half the number of iterations, yielding a much shorter computation time. The aW-SIRT algorithm has proven to perform well for both large as well as small regions of overlap, outperforming the pre-convolutional Feldkamp-David-Kress (FDK) algorithm for small overlap regions (or large detector offsets). The experiments confirmed the results of the simulations. Using the aW-SIRT algorithm, the effective FOV was increased by >75%, only limited by experimental constraints. Although an XRII is used in this work, the method readily applies to flat-panel detectors as well.
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http://dx.doi.org/10.1088/1361-6560/ac16bcDOI Listing
July 2021

On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: Chronicles of the MEMENTO challenge.

Neuroimage 2021 Jul 6;240:118367. Epub 2021 Jul 6.

National Institute of Health, Bethesda, USA.

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 such properties. Most methods, however, are tested and developed on a limited amount of data, and their applicability to other acquisition schemes remains unknown. With this work, we aimed to shed light on the generalizability of existing dMRI signal representations to different diffusion encoding parameters and brain tissue types. To this end, we organized a community challenge - named MEMENTO, making available the same datasets for fair comparisons across algorithms and techniques. We considered two state-of-the-art diffusion datasets, including single-diffusion-encoding (SDE) spin-echo data from a human brain with over 3820 unique diffusion weightings (the MASSIVE dataset), and double (oscillating) diffusion encoding data (DDE/DODE) of a mouse brain including over 2520 unique data points. A subset of the data sampled in 5 different voxels was openly distributed, and the challenge participants were asked to predict the remaining part of the data. After one year, eight participant teams submitted a total of 80 signal fits. For each submission, we evaluated the mean squared error, the variance of the prediction error and the Bayesian information criteria. The received submissions predicted either multi-shell SDE data (37%) or DODE data (22%), followed by cartesian SDE data (19%) and DDE (18%). Most submissions predicted the signals measured with SDE remarkably well, with the exception of low and very strong diffusion weightings. The prediction of DDE and DODE data seemed more challenging, likely because none of the submissions explicitly accounted for diffusion time and frequency. Next to the choice of the model, decisions on fit procedure and hyperparameters play a major role in the prediction performance, highlighting the importance of optimizing and reporting such choices. This work is a community effort to highlight strength and limitations of the field at representing dMRI acquired with trending encoding schemes, gaining insights into how different models generalize to different tissue types and fiber configurations over a large range of diffusion encodings.
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http://dx.doi.org/10.1016/j.neuroimage.2021.118367DOI Listing
July 2021

FleXCT: a flexible X-ray CT scanner with 10 degrees of freedom.

Opt Express 2021 Feb;29(3):3438-3457

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 object to be scanned. Hence, they are less suited for industrial X-ray imaging settings that require advanced scanning modes, such as laminography, conveyor belt scanning, or time-resolved imaging (4DCT). We introduce a new X-ray scanner FleXCT that consists of a total of ten motorized axes, which allow a wide range of non-standard XCT scans such as tiled and off-centre scans, laminography, helical tomography, conveyor belt, dynamic zooming, and X-ray phase contrast imaging. Additionally, a new software tool 'FlexRayTools' was created that enables reconstruction of non-standard XCT projection data of the FleXCT instrument using the ASTRA Toolbox, a highly efficient and open source set of tools for tomographic projection and reconstruction.
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http://dx.doi.org/10.1364/OE.409982DOI Listing
February 2021

Analysis and comparison of algorithms for the tomographic reconstruction of curved fibres.

Nondestruct Test Eval 2020 Jun 29;35(3):328-341. Epub 2020 Jun 29.

Research Group Computed Tomography, University of Applied Sciences Upper Austria, Wels, Austria.

We present visual methods for the analysis and comparison of the results of curved fibre reconstruction algorithms, i.e., of algorithms extracting characteristics of curved fibres from X-ray computed tomography scans. In this work, we extend previous methods for the analysis and comparison of results of different fibre reconstruction algorithms or parametrisations to the analysis of curved fibres. We propose fibre dissimilarity measures for such curved fibres and apply these to compare multiple results to a specified reference. We further propose visualisation methods to analyse differences between multiple results quantitatively and qualitatively. In two case studies, we show that the presented methods provide valuable insights for advancing and parametrising fibre reconstruction algorithms, and support in improving their results in characterising curved fibres.
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http://dx.doi.org/10.1080/10589759.2020.1774583DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7932496PMC
June 2020

EquiSim: An Open-Source Articulatable Statistical Model of the Equine Distal Limb.

Front Vet Sci 2021 3;8:623318. Epub 2021 Mar 3.

imec-Vision Lab, University of Antwerp, Antwerp, Belgium.

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 in bone geometry while maintaining proper jointspace distances to support model articulation toward different poses. Shape variation modes are explained in terms of common biometrics in order to ease model interpretation from a veterinary point of view. The model is publicly available through a graphical user interface (https://github.com/jvhoutte/equisim) in order to facilitate future digitalization in veterinary research, such as computer-aided designs, three-dimensional printing of bone implants, bone fracture risk assessment through finite element methods, and data registration and segmentation problems for clinical practices.
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http://dx.doi.org/10.3389/fvets.2021.623318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7982960PMC
March 2021

Constrained spherical deconvolution of nonspherically sampled diffusion MRI data.

Hum Brain Mapp 2021 02 10;42(2):521-538. Epub 2020 Nov 10.

Imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium.

Constrained spherical deconvolution (CSD) of diffusion-weighted MRI (DW-MRI) is a popular analysis method that extracts the full white matter (WM) fiber orientation density function (fODF) in the living human brain, noninvasively. It assumes that the DW-MRI signal on the sphere can be represented as the spherical convolution of a single-fiber response function (RF) and the fODF, and recovers the fODF through the inverse operation. CSD approaches typically require that the DW-MRI data is sampled shell-wise, and estimate the RF in a purely spherical manner using spherical basis functions, such as spherical harmonics (SH), disregarding any radial dependencies. This precludes analysis of data acquired with nonspherical sampling schemes, for example, Cartesian sampling. Additionally, nonspherical sampling can also arise due to technical issues, for example, gradient nonlinearities, resulting in a spatially dependent bias of the apparent tissue densities and connectivity information. Here, we adopt a compact model for the RFs that also describes their radial dependency. We demonstrate that the proposed model can accurately predict the tissue response for a wide range of b-values. On shell-wise data, our approach provides fODFs and tissue densities indistinguishable from those estimated using SH. On Cartesian data, fODF estimates and apparent tissue densities are on par with those obtained from shell-wise data, significantly broadening the range of data sets that can be analyzed using CSD. In addition, gradient nonlinearities can be accounted for using the proposed model, resulting in much more accurate apparent tissue densities and connectivity metrics.
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http://dx.doi.org/10.1002/hbm.25241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7776001PMC
February 2021

X-ray phase contrast simulation for grating-based interferometry using GATE.

Opt Express 2020 Oct;28(22):33390-33412

The overall importance of x-ray phase contrast (XPC) imaging has grown substantially in the last decades, in particular with the recent advent of compact lab-based XPC systems. For optimizing the experimental XPC setup, as well as benchmarking and testing new acquisition and reconstruction techniques, Monte Carlo (MC) simulations are a valuable tool. GATE, an open source application layer on top of the Geant4 simulation software, is a versatile MC tool primarily intended for various types of medical imaging simulations. To our knowledge, however, there is no GATE-based academic simulation software available for XPC imaging. In this paper, we extend the GATE framework with new physics-based tools for accurate XPC simulations. Our approach combines Monte Carlo simulations in GATE for modelling the x-ray interactions in the sample with subsequent numerical wave propagation, starting from the GATE output.
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http://dx.doi.org/10.1364/OE.392337DOI Listing
October 2020

Accelerating in vivo fast spin echo high angular resolution diffusion imaging with an isotropic resolution in mice through compressed sensing.

Magn Reson Med 2021 03 3;85(3):1397-1413. Epub 2020 Oct 3.

Bio-Imaging Lab, University of Antwerp, Antwerp, Belgium.

Purpose: Echo planar imaging (EPI) is commonly used to acquire the many volumes needed for high angular resolution diffusion Imaging (HARDI), posing a higher risk for artifacts, such as distortion and deformation. An alternative to EPI is fast spin echo (FSE) imaging, which has fewer artifacts but is inherently slower. The aim is to accelerate FSE such that a HARDI data set can be acquired in a time comparable to EPI using compressed sensing.

Methods: Compressed sensing was applied in either q-space or simultaneously in k-space and q-space, by undersampling the k-space in the phase-encoding direction or retrospectively eliminating diffusion directions for different degrees of undersampling. To test the replicability of the acquisition and reconstruction, brain data were acquired from six mice, and a numerical phantom experiment was performed. All HARDI data were analyzed individually using constrained spherical deconvolution, and the apparent fiber density and complexity metric were evaluated, together with whole-brain tractography.

Results: The apparent fiber density and complexity metric showed relatively minor differences when only q-space undersampling was used, but deteriorate when k-space undersampling was applied. Likewise, the tract density weighted image showed good results when only q-space undersampling was applied using 15 directions or more, but information was lost when fewer volumes or k-space undersampling were used.

Conclusion: It was found that acquiring 15 to 20 diffusion directions with a full k-space and reconstructed using compressed sensing could suffice for a replicable measurement of quantitative measures in mice, where areas near the sinuses and ear cavities are untainted by signal loss.
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http://dx.doi.org/10.1002/mrm.28520DOI Listing
March 2021

Unveiling water dynamics in fuel cells from time-resolved tomographic microscopy data.

Sci Rep 2020 10 2;10(1):16388. Epub 2020 Oct 2.

Swiss Light Source, Paul Scherrer Institut, Forschungsstrasse 111, 5232, Villigen, Aargau, Switzerland.

X-ray dynamic tomographic microscopy offers new opportunities in the volumetric investigation of dynamic processes. Due to data complexity and their sheer amount, extraction of comprehensive quantitative information remains challenging due to the intensive manual interaction required. Particularly for dynamic investigations, these intensive manual requirements significantly extend the total data post-processing time, limiting possible dynamic analysis realistically to a few samples and time steps, hindering full exploitation of the new capabilities offered at dedicated time-resolved X-ray tomographic stations. In this paper, a fully automatized iterative tomographic reconstruction pipeline (rSIRT-PWC-DIFF) designed to reconstruct and segment dynamic processes within a static matrix is presented. The proposed algorithm includes automatic dynamic feature separation through difference sinograms, a virtual sinogram step for interior tomography datasets, time-regularization extended to small sub-regions for increased robustness and an automatic stopping criterion. We demonstrate the advantages of our approach on dynamic fuel cell data, for which the current data post-processing pipeline heavily relies on manual labor. The proposed approach reduces the post-processing time by at least a factor of 4 on limited computational resources. Full independence from manual interaction additionally allows straightforward up-scaling to efficiently process larger data, extensively boosting the possibilities in future dynamic X-ray tomographic investigations.
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http://dx.doi.org/10.1038/s41598-020-73036-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7532214PMC
October 2020

Macro- and microstructural changes in cosmonauts' brains after long-duration spaceflight.

Sci Adv 2020 Sep 4;6(36). Epub 2020 Sep 4.

imec-Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium.

Long-duration spaceflight causes widespread physiological changes, although its effect on brain structure remains poorly understood. In this work, we acquired diffusion magnetic resonance imaging to investigate alterations of white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) compositions in each voxel, before, shortly after, and 7 months after long-duration spaceflight. We found increased WM in the cerebellum after spaceflight, providing the first clear evidence of sensorimotor neuroplasticity. At the region of interest level, this increase persisted 7 months after return to Earth. We also observe a widespread redistribution of CSF, with concomitant changes in the voxel fractions of adjacent GM. We show that these GM changes are the result of morphological changes rather than net tissue loss, which remained unclear from previous studies. Our study provides evidence of spaceflight-induced neuroplasticity to adapt motor strategies in space and evidence of fluid shift-induced mechanical changes in the brain.
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http://dx.doi.org/10.1126/sciadv.aaz9488DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7473746PMC
September 2020

Small medial femoral condyle morphotype is associated with medial compartment degeneration and distinct morphological characteristics: a comparative pilot study.

Knee Surg Sports Traumatol Arthrosc 2021 Jun 14;29(6):1777-1789. Epub 2020 Aug 14.

Antwerp Surgical Training, Anatomy and Research Centre (ASTARC), University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium.

Purpose: Early-onset degeneration of the knee is linked to genetics, overload, injury, and potentially, knee morphology. The purpose of this study is to explore the characteristics of the small medial femoral condyle, as a distinct knee morphotype, by means of a landmark-based three-dimensional (3D) analysis and statistical parametric mapping.

Methods: Sixteen knees with a small medial femoral condyle (SMC) were selected from a database of patients with distinct knee joint anatomy and 16 gender-matched knees were selected from a control group database. 3D models were generated from the medical imaging. After normalization for size, a set of pre-defined landmark-based parameters was analysed for the femur and tibia. Local shape differences were evaluated by matching all bone surfaces onto each other and comparing the distances to the mean control group bone shape.

Results: The small medial condyle group showed a significant association with medial compartment degeneration and had a 4% and 13% smaller medial condyle anteroposteriorly and mediolaterally, whereas the distal femur was 3% wider mediolaterally. The lateral condyle was 2% smaller anteroposteriorly and 8% wider mediolaterally. The complete tibial plateau was 3% smaller mediolaterally and the medial tibial plateau was 6% smaller.

Conclusion: A new knee morphotype demonstrated an increased risk for medial compartment degeneration and was differentiated from a healthy control group based on the following morphological characteristics: a smaller medial femoral condyle and medial tibial plateau, a wider lateral femoral condyle and a wider distal femur on a smaller tibial plateau. This pilot study suggests a role for the SMC knee morphotype in the multifactorial process of medial compartment degeneration.

Level Of Evidence: III.
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http://dx.doi.org/10.1007/s00167-020-06218-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8126545PMC
June 2021

Diffusion tensor imaging of the anterior cruciate ligament graft following reconstruction: a longitudinal study.

Eur Radiol 2020 Dec 14;30(12):6673-6684. Epub 2020 Jul 14.

Department of Radiology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.

Objective: To longitudinally monitor remodeling of human autograft following anterior cruciate ligament (ACL) reconstruction with DTI.

Methods: Twenty-eight patients underwent DTI follow-up at 3, 8, and 14 months after clinically successful ACL reconstruction with tendon autograft. Among these, 18 patients had a concomitant lateral extra-articular procedure (LET). DTI data from 7 healthy volunteers was also obtained. Diffusion parameters (fractional anisotropy, FA; mean diffusivity, MD; axial diffusivity, AD; and radial diffusivity, RD) were evaluated within the fiber tractography volumes of the ACL graft and posterior cruciate ligament (PCL) in all patients. Data were analyzed using a linear mixed-effects model with post hoc testing using Bonferroni-Holm correction for multiple testing. The effect of additional LET was studied.

Results: The ACL graft showed a significant decrease of FA over time (F = 4.00, p = 0.025), while the diffusivities did not significantly change over time. For PCL there were no significant DTI changes over time. A different evolution over time between patients with and without LET was noted for all diffusivity values of the ACL graft with reduced AD values in patients with LET at 8 months postoperatively (p = 0.048; adjusted p = 0.387). DTI metrics of the ACL graft differed largely from both native ACL and tendon at 14 months postoperatively.

Conclusion: Our study has shown the potential of DTI to longitudinally monitor the remodeling process in human ACL reconstruction. DTI analysis indicates that graft remodeling is incomplete at 14 months postoperatively.

Key Points: • DTI can be used to longitudinally monitor the remodeling process in human ACL reconstruction. • DTI analysis indicates that autograft remodeling is incomplete at 14 months postoperatively. • DTI may be helpful for evaluating new ACL treatments.
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http://dx.doi.org/10.1007/s00330-020-07051-wDOI Listing
December 2020

Harmonization of Brain Diffusion MRI: Concepts and Methods.

Front Neurosci 2020 6;14:396. Epub 2020 May 6.

imec-Vision Lab, University of Antwerp, Antwerp, Belgium.

MRI diffusion data suffers from significant inter- and intra-site variability, which hinders multi-site and/or longitudinal diffusion studies. This variability may arise from a range of factors, such as hardware, reconstruction algorithms and acquisition settings. To allow a reliable comparison and joint analysis of diffusion data across sites and over time, there is a clear need for robust data harmonization methods. This review article provides a comprehensive overview of diffusion data harmonization concepts and methods, and their limitations. Overall, the methods for the harmonization of multi-site diffusion images can be categorized in two main groups: diffusion parametric map harmonization (DPMH) and diffusion weighted image harmonization (DWIH). Whereas DPMH harmonizes the diffusion parametric maps (e.g., FA, MD, and MK), DWIH harmonizes the diffusion-weighted images. Defining a gold standard harmonization technique for dMRI data is still an ongoing challenge. Nevertheless, in this paper we provide two classification tools, namely a feature table and a flowchart, which aim to guide the readers in selecting an appropriate harmonization method for their study.
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http://dx.doi.org/10.3389/fnins.2020.00396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7218137PMC
May 2020

Supporting measurements or more averages? How to quantify cerebral blood flow most reliably in 5 minutes by arterial spin labeling.

Magn Reson Med 2020 11 19;84(5):2523-2536. Epub 2020 May 19.

imec - Vision Lab, Department of Physics, University of Antwerp, Antwerp, Belgium.

Purpose: To determine whether sacrificing part of the scan time of pseudo-continuous arterial spin labeling (PCASL) for measurement of the labeling efficiency and blood is beneficial in terms of CBF quantification reliability.

Methods: In a simulation framework, 5-minute scan protocols with different scan time divisions between PCASL data acquisition and supporting measurements were evaluated in terms of CBF estimation variability across both noise and ground truth parameter realizations taken from the general population distribution. The entire simulation experiment was repeated for a single-post-labeling delay (PLD), multi-PLD, and free-lunch time-encoded (te-FL) PCASL acquisition strategy. Furthermore, a real data study was designed for preliminary validation.

Results: For the considered population statistics, measuring the labeling efficiency and the blood proved beneficial in terms of CBF estimation variability for any distribution of the 5-minute scan time compared to only acquiring ASL data. Compared to single-PLD PCASL without support measurements as recommended in the consensus statement, a 26%, 33%, and 42% reduction in relative CBF estimation variability was found for optimal combinations of supporting measurements with single-PLD, free-lunch, and multi-PLD PCASL data acquisition, respectively. The benefit of taking the individual variation of blood into account was also demonstrated in the real data experiment.

Conclusions: Spending time to measure the labeling efficiency and the blood instead of acquiring more averages of the PCASL data proves to be advisable for robust CBF quantification in the general population.
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http://dx.doi.org/10.1002/mrm.28314DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402018PMC
November 2020

Super-Resolution Magnetic Resonance Imaging of the Knee Using 2-Dimensional Turbo Spin Echo Imaging.

Invest Radiol 2020 08;55(8):481-493

imec-Vision Lab, Department of Physics, University of Antwerp, Wilrijk, Belgium.

Objectives: The purpose of this study was to assess the technical feasibility of 3-dimensional (3D) super-resolution reconstruction (SRR) of 2D turbo spin echo (TSE) knee magnetic resonance imaging (MRI) and to compare its image quality with conventional 3D TSE sampling perfection with application optimized contrast using different flip angle evolutions (SPACE) MRI.

Materials And Methods: Super-resolution reconstruction 2D TSE MRI and 3D TSE SPACE images were acquired from a phantom and from the knee of 22 subjects (8 healthy volunteers and 14 patients) using a clinical 3-T scanner. For SRR, 7 anisotropic 2D TSE stacks (voxel size, 0.5 × 0.5 × 2.0 mm; scan time per stack, 1 minute 55 seconds; total scan time, 13 minutes 25 seconds) were acquired with the slice stack rotated around the phase-encoding axis. Super-resolution reconstruction was performed at an isotropic high-resolution grid with a voxel size of 0.5 × 0.5 × 0.5 mm. Direct isotropic 3D image acquisition was performed with the conventional SPACE sequence (voxel size, 0.5 × 0.5 × 0.5 mm; scan time, 12 minutes 42 seconds). For quantitative evaluation, perceptual blur metrics and edge response functions were obtained in the phantom image, and signal-to-noise and contrast-to-noise ratios were measured in the images from the healthy volunteers. Images were qualitatively evaluated by 2 independent radiologists in terms of overall image quality, edge blurring, anatomic visibility, and diagnostic confidence to assess normal and abnormal knee structures. Nonparametric statistical analysis was performed, and significance was defined for P values less than 0.05.

Results: In the phantom, perceptual blur metrics and edge response functions demonstrated a clear improvement in spatial resolution for SRR compared with conventional 3D SPACE. In healthy subjects, signal-to-noise and contrast-to-noise ratios in clinically relevant structures were not significantly different between SRR and 3D SPACE. Super-resolution reconstruction provided better overall image quality and less edge blurring than conventional 3D SPACE, yet the perceived image contrast was better for 3D SPACE. Super-resolution reconstruction received significantly better visibility scores for the menisci, whereas the visibility of cartilage was significantly higher for 3D SPACE. Ligaments had high visibility on both SRR and 3D SPACE images. The diagnostic confidence for assessing menisci was significantly higher for SRR than for conventional 3D SPACE, whereas there were no significant differences between SRR and 3D SPACE for cartilage and ligaments. The interreader agreement for assessing menisci was substantial with 3D SPACE and almost perfect with SRR, and the agreement for assessing cartilage was almost perfect with 3D SPACE and moderate with SRR.

Conclusions: We demonstrate the technical feasibility of SRR for high-resolution isotropic knee MRI. Our SRR results show superior image quality in terms of edge blurring, but lower image contrast and fluid brightness when compared with conventional 3D SPACE acquisitions. Further contrast optimization and shortening of the acquisition time with state-of-the-art acceleration techniques are necessary for future clinical validation of SRR knee MRI.
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http://dx.doi.org/10.1097/RLI.0000000000000676DOI Listing
August 2020

Diffusion tensor imaging of the anterior cruciate ligament following primary repair with internal bracing: A longitudinal study.

J Orthop Res 2021 Jun 15;39(6):1318-1330. Epub 2020 Apr 15.

Icometrix, Leuven, Belgium.

Diffusion tensor imaging (DTI) provides information about tissue microstructure and its degree of organization by quantifying water diffusion. We aimed to monitor longitudinal changes in DTI parameters (fractional isotropy, FA; mean diffusivity, MD; axial diffusivity, AD; radial diffusivity, RD) of the anterior cruciate ligament (ACL) following primary repair with internal bracing (IBLA). Fourteen patients undergoing IBLA were enrolled prospectively and scheduled for clinical follow-up, including instrumented laxity testing, and DTI at 3, 6, 12, and 24 months postoperatively. DTI was also performed in seven healthy subjects. Fiber tractography was used for 3D segmentation of the whole ACL volume, from which median DTI parameters were calculated. The posterior cruciate ligament (PCL) served as a control. Longitudinal DTI changes were assessed using a linear mixed model, and repeated measures correlations were calculated between DTI parameters and clinical laxity tests. At follow-up, thirteen patients had a stable knee and one patient sustained an ACL rerupture after 12 months postoperatively. The ACL repair showed a significant decrease of FA within the first 12 months after surgery, followed by stable FA values thereafter, while ACL diffusivities decreased over time returning towards normal values at 24 months postoperatively. For PCL there were no significant DTI changes over time. There was a significant correlation between ACL FA and laxity tests (r = -0.42, P = .017). This study has shown the potential of DTI to longitudinally monitor diffusion changes in the ACL following IBLA. The DTI findings suggest that healing of the ACL repair is incomplete at 24 months postoperatively.
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http://dx.doi.org/10.1002/jor.24684DOI Listing
June 2021

PAPPI: Personalized analysis of plantar pressure images using statistical modelling and parametric mapping.

PLoS One 2020 27;15(2):e0229685. Epub 2020 Feb 27.

Department of Research, Sint Maartenskliniek, Nijmegen, The Netherlands.

Quantitative analyses of plantar pressure images typically occur at the group level and under the assumption that individuals within each group display homogeneous pressure patterns. When this assumption does not hold, a personalized analysis technique is required. Yet, existing personalized plantar pressure analysis techniques work at the image level, leading to results that can be unintuitive and difficult to interpret. To address these limitations, we introduce PAPPI: the Personalized Analysis of Plantar Pressure Images. PAPPI is built around the statistical modelling of the relationship between plantar pressures in healthy controls and their demographic characteristics. This statistical model then serves as the healthy baseline to which an individual's real plantar pressures are compared using statistical parametric mapping. As a proof-of-concept, we evaluated PAPPI on a cohort of 50 hallux valgus patients. PAPPI showed that plantar pressures from hallux valgus patients did not have a single, homogeneous pattern, but instead, 5 abnormal pressure patterns were observed in sections of this population. When comparing these patterns to foot pain scores (i.e. Foot Function Index, Manchester-Oxford Foot Questionnaire) and radiographic hallux angle measurements, we observed that patients with increased pressure under metatarsal 1 reported less foot pain than other patients in the cohort, while patients with abnormal pressures in the heel showed more severe hallux valgus angles and more foot pain. Also, incidences of pes planus were higher in our hallux valgus cohort compared to the modelled healthy controls. PAPPI helped to clarify recent discrepancies in group-level plantar pressure studies and showed its unique ability to produce quantitative, interpretable, and personalized analyses for plantar pressure images.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229685PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7046232PMC
May 2020

The effect of nasal shape on the thermal conditioning of inhaled air: Using clinical tomographic data to build a large-scale statistical shape model.

Comput Biol Med 2020 02 3;117:103600. Epub 2020 Jan 3.

Physics Department, University of Antwerp, Laboratory of Biophysics and Biomedical Physics, Groenenborgerlaan 171, 2020, Antwerp, Belgium.

In this paper, we investigate the heating function of the nasal cavity qualitatively, using a high-quality, large-scale statistical shape model. This model consists of a symmetrical and an asymmetrical part and provides a new and unique way of examining changes in nasal heating function resulting from natural variations in nasal shape (as obtained from 100 clinical CT scans). Data collected from patients suffering from different nasal or sinus-related complaints are included. Parameterized models allow us to investigate the effect of continuous deviations in shape from the mean nasal cavity. This approach also enables us to avoid many of the compounded effects on flow and heat exchange, which one would encounter when comparing different patient-specific models. The effects of global size, size-related features, and turbinate size are investigated using the symmetrical shape model. The asymmetrical model is used to investigate different types of septal deviation using Mladina's classification. The qualitative results are discussed and compared with findings from the existing literature.
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http://dx.doi.org/10.1016/j.compbiomed.2020.103600DOI Listing
February 2020

A Machine Learning Approach to Growth Direction Finding for Automated Planting of Bulbous Plants.

Sci Rep 2020 01 20;10(1):661. Epub 2020 Jan 20.

Imec-Vision Lab, Department of Physics, University of Antwerp, B-2610, Antwerp, Belgium.

In agricultural robotics, a unique challenge exists in the automated planting of bulbous plants: the estimation of the bulb's growth direction. To date, no existing work addresses this challenge. Therefore, we propose the first robotic vision framework for the estimation of a plant bulb's growth direction. The framework takes as input three x-ray images of the bulb and extracts shape, edge, and texture features from each image. These features are then fed into a machine learning regression algorithm in order to predict the 2D projection of the bulb's growth direction. Using the x-ray system's geometry, these 2D estimates are then mapped to the 3D world coordinate space, where a filtering on the estimate's variance is used to determine whether the estimate is reliable. We applied our algorithm on 27,200 x-ray simulations from T. Apeldoorn bulbs on a standard desktop workstation. Results indicate that our machine learning framework is fast enough to meet industry standards (<0.1 seconds per bulb) while providing acceptable accuracy (e.g. error < 30° in 98.40% of cases using an artificial 3-layer neural network). The high success rates of the proposed framework indicate that it is worthwhile to proceed with the development and testing of a physical prototype of a robotic bulb planting system.
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http://dx.doi.org/10.1038/s41598-019-57405-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6971015PMC
January 2020

poly-DART: A discrete algebraic reconstruction technique for polychromatic X-ray CT.

Opt Express 2019 Nov;27(23):33670-33682

The discrete algebraic reconstruction technique (DART) is a tomographic method to reconstruct images from X-ray projections in which prior knowledge on the number of object materials is exploited. In monochromatic X-ray CT (e.g., synchrotron), DART has been shown to lead to high-quality reconstructions, even with a low number of projections or a limited scanning view. However, most X-ray sources are polychromatic, leading to beam hardening effects, which significantly degrade the performance of DART. In this work, we propose a new discrete tomography algorithm, poly-DART, that exploits sparsity in the attenuation values using DART and simultaneously accounts for the polychromatic nature of the X-ray source. The results show that poly-DART leads to a vastly improved segmentation on polychromatic data obtained from Monte Carlo simulations as well as on experimental data, compared to DART.
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http://dx.doi.org/10.1364/OE.27.033670DOI Listing
November 2019

The costs and benefits of estimating T of tissue alongside cerebral blood flow and arterial transit time in pseudo-continuous arterial spin labeling.

NMR Biomed 2020 12 17;33(12):e4182. Epub 2019 Nov 17.

imec-Vision Lab, Department of Physics, University of Antwerp, 2610, Antwerp, Belgium.

Multi-post-labeling-delay pseudo-continuous arterial spin labeling (multi-PLD PCASL) allows for absolute quantification of the cerebral blood flow (CBF) as well as the arterial transit time (ATT). Estimating these perfusion parameters from multi-PLD PCASL data is a non-linear inverse problem, which is commonly tackled by fitting the single-compartment model (SCM) for PCASL, with CBF and ATT as free parameters. The longitudinal relaxation time of tissue T is an important parameter in this model, as it governs the decay of the perfusion signal entirely upon entry in the imaging voxel. Conventionally, T is fixed to a population average. This approach can cause CBF quantification errors, as T can vary significantly inter- and intra-subject. This study compares the impact on CBF quantification, in terms of accuracy and precision, of either fixing T , the conventional approach, or estimating it alongside CBF and ATT. It is shown that the conventional approach can cause a significant bias in CBF. Indeed, simulation experiments reveal that if T is fixed to a value that is 10% off its true value, this may already result in a bias of 15% in CBF. On the other hand, as is shown by both simulation and real data experiments, estimating T along with CBF and ATT results in a loss of CBF precision of the same order, even if the experiment design is optimized for the latter estimation problem. Simulation experiments suggest that an optimal balance between accuracy and precision of CBF estimation from multi-PLD PCASL data can be expected when using the two-parameter estimator with a fixed T value between population averages of T and the longitudinal relaxation time of blood T .
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http://dx.doi.org/10.1002/nbm.4182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685117PMC
December 2020

Aortic root sizing for transcatheter aortic valve implantation using a shape model parameterisation.

Med Biol Eng Comput 2019 Oct;57(10):2081-2092

Faculty of Medicine and Health Sciences, Department of Translational Pathophysiological Research, Cardiovascular diseases, University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium.

During a transcatheter aortic valve implantation, an axisymmetric implant is placed in an irregularly shaped aortic root. Implanting an incorrect size can cause complications such as leakage of blood alongside or through the implant. The aim of this study was to construct a method that determines the optimal size of the implant based on the three-dimensional shape of the aortic root. Based on the pre-interventional computed tomography scan of 89 patients, a statistical shape model of their aortic root was constructed. The weights associated with the principal components and the volume of calcification in the aortic valve were used as parameters in a classification algorithm. The classification algorithm was trained using the patients with no or mild leakage after their intervention. Subsequently, the algorithms were applied to the patients with moderate to severe leakage. Cross validation showed that a random forest classifier assigned the same size in 65 ± 7% of the training cases, while 57 ± 8% of the patients with moderate to severe leakage were assigned a different size. This initial study showed that this semi-automatic method has the potential to correctly assign an implant size. Further research is required to assess whether the different size implants would improve the outcome of those patients.
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http://dx.doi.org/10.1007/s11517-019-01996-xDOI Listing
October 2019

Alterations of Functional Brain Connectivity After Long-Duration Spaceflight as Revealed by fMRI.

Front Physiol 2019 4;10:761. Epub 2019 Jul 4.

Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, Russia.

The present study reports alterations of task-based functional brain connectivity in a group of 11 cosmonauts after a long-duration spaceflight, compared to a healthy control group not involved in the space program. To elicit the postural and locomotor sensorimotor mechanisms that are usually most significantly impaired when space travelers return to Earth, a plantar stimulation paradigm was used in a block design fMRI study. The motor control system activated by the plantar stimulation involved the pre-central and post-central gyri, SMA, SII/operculum, and, to a lesser degree, the insular cortex and cerebellum. While no post-flight alterations were observed in terms of activation, the network-based statistics approach revealed task-specific functional connectivity modifications within a broader set of regions involving the activation sites along with other parts of the sensorimotor neural network and the visual, proprioceptive, and vestibular systems. The most notable findings included a post-flight increase in the stimulation-specific connectivity of the right posterior supramarginal gyrus with the rest of the brain; a strengthening of connections between the left and right insulae; decreased connectivity of the vestibular nuclei, right inferior parietal cortex (BA40) and cerebellum with areas associated with motor, visual, vestibular, and proprioception functions; and decreased coupling of the cerebellum with the visual cortex and the right inferior parietal cortex. The severity of space motion sickness symptoms was found to correlate with a post- to pre-flight difference in connectivity between the right supramarginal gyrus and the left anterior insula. Due to the complex nature and rapid dynamics of adaptation to gravity alterations, the post-flight findings might be attributed to both the long-term microgravity exposure and to the readaptation to Earth's gravity that took place between the landing and post-flight MRI session. Nevertheless, the results have implications for the multisensory reweighting and gravitational motor system theories, generating hypotheses to be tested in future research.
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http://dx.doi.org/10.3389/fphys.2019.00761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6621543PMC
July 2019

Assessment of Anterior Cruciate Ligament Graft Maturity With Conventional Magnetic Resonance Imaging: A Systematic Literature Review.

Orthop J Sports Med 2019 Jun 3;7(6):2325967119849012. Epub 2019 Jun 3.

Imec/Vision Lab, Department of Physics, University of Antwerp, Wilrijk, Belgium.

Background: Magnetic resonance imaging (MRI) signal intensity (SI) measurements are being used increasingly in both clinical and research studies to assess the maturity of anterior cruciate ligament (ACL) grafts in humans. However, SI in conventional MRI with weighted images is a nonquantitative measure dependent on hardware and software.

Purpose: To conduct a systematic review of studies that have used MRI SI as a proxy for ACL graft maturity and to identify potential confounding factors in assessing the ACL graft in conventional MRI studies.

Study Design: Systematic review; Level of evidence, 4.

Methods: A systematic review was conducted by searching the MEDLINE/PubMed, Scopus, and Cochrane Library electronic databases according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines to identify studies that examined the healing of the intra-articular portion of the ACL graft by assessing SI on MRIs.

Results: A total of 34 studies were selected for inclusion in this systematic review. The MRI acquisition techniques and methods to evaluate the ACL graft SI differed greatly across the studies. No agreement was found regarding the time frames of SI changes in MRI reflecting normal healing of the ACL tendon graft, and the graft SI and clinical outcomes after ACL reconstruction were found to be poorly correlated.

Conclusion: The MRI acquisition and evaluation methods used to assess ACL grafts are very heterogeneous, impeding comparisons of SI between successive scans and between independent studies. Therefore, quantitative MRI-based biomarkers of ACL graft healing are greatly needed to guide the appropriate time of returning to sports after ACL reconstruction.
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http://dx.doi.org/10.1177/2325967119849012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6547178PMC
June 2019

Brain ventricular volume changes induced by long-duration spaceflight.

Proc Natl Acad Sci U S A 2019 05 6;116(21):10531-10536. Epub 2019 May 6.

Lab for Equilibrium Investigations and Aerospace, University of Antwerp, 2610 Antwerp, Belgium.

Long-duration spaceflight induces detrimental changes in human physiology. Its residual effects and mechanisms remain unclear. We prospectively investigated the changes in cerebrospinal fluid (CSF) volume of the brain ventricular regions in space crew by means of a region of interest analysis on structural brain scans. Cosmonaut MRI data were investigated preflight ( = 11), postflight ( = 11), and at long-term follow-up 7 mo after landing ( = 7). Post hoc analyses revealed a significant difference between preflight and postflight values for all supratentorial ventricular structures, i.e., lateral ventricle (mean % change ± SE = 13.3 ± 1.9), third ventricle (mean % change ± SE = 10.4 ± 1.1), and the total ventricular volume (mean % change ± SE = 11.6 ± 1.5) (all < 0.0001), with higher volumes at postflight. At follow-up, these structures did not quite reach baseline levels, with still residual increases in volume for the lateral ventricle (mean % change ± SE = 7.7 ± 1.6; = 0.0009), the third ventricle (mean % change ± SE = 4.7 ± 1.3; = 0.0063), and the total ventricular volume (mean % change ± SE = 6.4 ± 1.3; = 0.0008). This spatiotemporal pattern of CSF compartment enlargement and recovery points to a reduced CSF resorption in microgravity as the underlying cause. Our results warrant more detailed and longer longitudinal follow-up. The clinical impact of our findings on the long-term cosmonauts' health and their relation to ocular changes reported in space travelers requires further prospective studies.
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http://dx.doi.org/10.1073/pnas.1820354116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6535034PMC
May 2019

An assessment of the information lost when applying data reduction techniques to dynamic plantar pressure measurements.

J Biomech 2019 04 23;87:161-166. Epub 2019 Feb 23.

imec-Vision Lab, Department of Physics, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium; Section on Applied Ergonomics & Design, Faculty of Industrial Design Engineering, Delft University of Technology, Landbergstraat 15, 2628 CE Delft, the Netherlands. Electronic address:

Data reduction techniques are commonly applied to dynamic plantar pressure measurements, often prior to the measurement's analysis. In performing these data reductions, information is discarded from the measurement before it can be evaluated, leading to unkonwn consequences. In this study, we aim to provide the first assessment of what impact data reduction techniques have on plantar pressure measurements. Specifically, we quantify the extent to which information of any kind is discarded when performing common data reductions. Plantar pressure measurements were collected from 33 healthy controls, 8 Hallux Valgus patients, and 10 Metatarsalgia patients. Eleven common data reductions were then applied to the measurements, and the resulting datasets were compared to the original measurement in three ways. First, information theory was used to estimate the information content present in the original and reduced datasets. Second, principal component analysis was used to estimate the number of intrinsic dimensions present. Finally, a permutational multivariate ANOVA was performed to evaluate the significance of group differences between the healthy controls, Hallux Valgus, and Metatarsalgia groups. The evaluated data reductions showed a minimum of 99.1% loss in information content and losses of dimensionality between 20.8% and 83.3%. Significant group differences were also lost after each of the 11 data reductions (α=0.05), but these results may differ for other patient groups (especially those with highly-deformed footprints) or other region of interest definitions. Nevertheless, the existence of these results suggest that the diagnostic content of dynamic plantar pressure measurements is yet to be fully exploited.
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http://dx.doi.org/10.1016/j.jbiomech.2019.02.008DOI Listing
April 2019

Posture normalisation of 3D body scans.

Ergonomics 2019 Jun 25;62(6):834-848. Epub 2019 Mar 25.

a imec - Vision Lab, Department of Physics , University of Antwerp , Belgium Universiteitsplein 1, B-2610 , Antwerp , Belgium.

For product developers that design near-body products, virtual mannequins that represent realistic body shapes, are valuable tools. With statistical shape modelling, the variability of such body shapes can be described. Shape variation captured by statistical shape models (SSMs) is often polluted by posture variations, leading to less compact models. In this paper, we propose a framework that has low computational complexity to build a posture invariant SSM, by capturing and correcting the posture of an instance. The posture-normalised SSM is shown to be substantially more compact than the non-posture-normalised SSM. Statistical shape modelling is a technique to map out the variability of (body) shapes. This variability is often polluted by variations in posture. In this paper, we propose a framework to build a posture invariant statistical shape model. SSM: statistical shape model; 1D: one-dimensional; 3D: three-dimensional; DHM: digital human model; LBS: linear blend skinning; PCA: princial component analysis; PC: principal component; TTR: thumb tip reach.
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http://dx.doi.org/10.1080/00140139.2019.1581262DOI Listing
June 2019

Normalized averaged range (nAR), a robust quantification method for MPIO-content.

J Magn Reson 2019 03 21;300:18-27. Epub 2018 Dec 21.

Bio-Imaging Lab, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium.

Micron-sized paramagnetic iron oxide particles (MPIO) are commonly used as contrast agents in magnetic resonance imaging (MRI) that produce negative contrast enhancement, i.e. darkening, on T2-weighted images. However, estimation and quantification of MPIO in vivo is still challenging. This limitation mainly arises from smearing and displacement of the negative contrast of the MPIO, so-called blooming, potentially leading to false-positive detection. Further, the bias field induced by the MR coils also hinders visualization and quantification of the MPIO. To mitigate these drawbacks, a positive contrast image can be generated, for example by using a frequency offset technique, which can significantly improve the accuracy of quantification methods. In this research, we introduce the normalized average range (nAR) as a new way to quantify the relative MPIO content within a study. The method compares the average value of test ROIs to that of a control ROI in range filtered images. The nAR can be used on both positive and negative contrast images. The nAR was tested on agar phantoms containing various MPIO concentrations, and on a rostral migration model for MPIO labeled stem cells in mice. The amount of MPIO was quantified for biased and unbiased data, and both for positive and negative contrast images. In addition, the presence of MPIOs in the olfactory bulb was verified by histology. The results show the nAR can indicate the presence and relative content of MPIO for both negative and positive images. However, the nAR showed slightly higher sensitivity in optimized positive contrast images compared to negative contrast images. In all cases, the bias field played a minor role in the quantification, making debiasing less of a concern. The dependency of the nAR values on the MPIO content in the ROI was further validated histologically. Thus, the nAR provides a robust and reliable tool for quantification of MPIO in mice.
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http://dx.doi.org/10.1016/j.jmr.2018.12.019DOI Listing
March 2019

High quality statistical shape modelling of the human nasal cavity and applications.

R Soc Open Sci 2018 Dec 19;5(12):181558. Epub 2018 Dec 19.

Physics Department, University of Antwerp, Laboratory of Biophysics and Biomedical Physics, Groenenborgerlaan 171, 2020 Antwerp, Belgium.

The human nose is a complex organ that shows large morphological variations and has many important functions. However, the relation between shape and function is not yet fully understood. In this work, we present a high quality statistical shape model of the human nose based on clinical CT data of 46 patients. A technique based on cylindrical parametrization was used to create a correspondence between the nasal shapes of the population. Applying principal component analysis on these corresponded nasal cavities resulted in an average nasal geometry and geometrical variations, known as principal components, present in the population with a high precision. The analysis led to 46 principal components, which account for 95% of the total geometrical variation captured. These variations are first discussed qualitatively, and the effect on the average nasal shape of the first five principal components is visualized. Hereafter, by using this statistical shape model, two application examples that lead to quantitative data are shown: nasal shape in function of age and gender, and a morphometric analysis of different anatomical regions. Shape models, as the one presented here, can help to get a better understanding of nasal shape and variation, and their relationship with demographic data.
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http://dx.doi.org/10.1098/rsos.181558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304114PMC
December 2018

Parametric Reconstruction of Glass Fiber-reinforced Polymer Composites from X-ray Projection Data-A Simulation Study.

J Nondestr Eval 2018 30;37(3):62. Epub 2018 Jul 30.

1imec-VisionLab, Department of Physics, University of Antwerp, Universiteitsplein 1, 2610 Antwerpen, Belgium.

We present a new approach to estimate geometry parameters of glass fibers in glass fiber-reinforced polymers from simulated X-ray micro-computed tomography scans. Traditionally, these parameters are estimated using a multi-step procedure including image reconstruction, pre-processing, segmentation and analysis of features of interest. Each step in this chain introduces errors that propagate through the pipeline and impair the accuracy of the estimated parameters. In the approach presented in this paper, we reconstruct volumes from a low number of projection angles using an iterative reconstruction technique and then estimate position, direction and length of the contained fibers incorporating knowledge about their shape, modeled as a geometric representation, which is then optimized. Using simulation experiments, we show that our method can estimate those representations even in presence of noisy data and only very few projection angles available.
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http://dx.doi.org/10.1007/s10921-018-0514-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6314276PMC
July 2018
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