"uuid","repository link","title","author","contributor","publication year","abstract","subject topic","language","publication type","publisher","isbn","issn","patent","patent status","bibliographic note","access restriction","embargo date","faculty","department","research group","programme","project","coordinates"
"uuid:70213029-2de4-4fab-b0ca-b5ebb27188e6","http://resolver.tudelft.nl/uuid:70213029-2de4-4fab-b0ca-b5ebb27188e6","On the identification of hypoxic regions in subject-specific cerebral vasculature by combined CFD/MRI","Perinajová, R. (TU Delft ChemE/Transport Phenomena; J.M. Burgers Centre for Fluid Mechanics); van Ooij, Pim (Amsterdam UMC); Kenjeres, S. (TU Delft ChemE/Transport Phenomena; J.M. Burgers Centre for Fluid Mechanics)","","2023","A long-time exposure to lack of oxygen (hypoxia) in some regions of the cerebrovascular system is believed to be one of the causes of cerebral neurological diseases. In the present study, we show how a combination of magnetic resonance imaging (MRI) and computational fluid dynamics (CFD) can provide a noninvasive alternative for studying blood flow and transport of oxygen within the cerebral vasculature. We perform computer simulations of oxygen mass transfer in the subject-specific geometry of the circle of Willis. The computational domain and boundary conditions are based on four-dimensional (4D)-flow MRI measurements. Two different oxygen mass transfer models are considered: passive (where oxygen is treated as a dilute chemical species in plasma) and active (where oxygen is bonded to haemoglobin) models. We show that neglecting haemoglobin transport results in a significant underestimation of the arterial wall mass transfer of oxygen. We identified the hypoxic regions along the arterial walls by introducing the critical thresholds that are obtained by comparison of the estimated range of Damköhler number (Da, 〈9; 57〉) with the local Sherwood number. Finally, we recommend additional validations of the combined MRI/CFD approach proposed here for larger groups of subject- or patient-specific brain vasculature systems.","Alzheimer; brain; CFD; hypoxia; MRI; oxygen transport","en","journal article","","","","","","","","","","","ChemE/Transport Phenomena","","",""
"uuid:c93aa17f-7fdb-49c9-a513-fe2d99ac290c","http://resolver.tudelft.nl/uuid:c93aa17f-7fdb-49c9-a513-fe2d99ac290c","Subclinical liver traits are associated with structural and hemodynamic brain imaging markers","Yilmaz, Pinar (Erasmus MC); Alferink, Louise J.M. (Erasmus MC); Cremers, Lotte G.M. (Erasmus MC); Murad, Sarwa D. (Erasmus MC); Niessen, W.J. (TU Delft ImPhys/Vos group; TU Delft ImPhys/Computational Imaging; Erasmus MC); Ikram, M. Arfan (Erasmus MC); Vernooij, Meike W. (Erasmus MC)","","2023","Background & Aims: Impaired liver function affects brain health and therefore understanding potential mechanisms for subclinical liver disease is essential. We assessed the liver–brain associations using liver measures with brain imaging markers, and cognitive measures in the general population. Methods: Within the population-based Rotterdam Study, liver serum and imaging measures (ultrasound and transient elastography), metabolic dysfunction-associated fatty liver disease (MAFLD), non-alcoholic fatty liver disease (NAFLD) and fibrosis phenotypes, and brain structure were determined in 3493 non-demented and stroke-free participants in 2009–2014. This resulted in subgroups of n = 3493 for MAFLD (mean age 69 ± 9 years, 56% ♀), n = 2938 for NAFLD (mean age 70 ± 9 years, 56% ♀) and n = 2252 for fibrosis (mean age 65 ± 7 years, 54% ♀). Imaging markers of small vessel disease and neurodegeneration, cerebral blood flow (CBF) and brain perfusion (BP) were acquired from brain MRI (1.5-tesla). General cognitive function was assessed by Mini-Mental State Examination and the g-factor. Multiple linear and logistic regression models were used for liver-brain associations and adjusted for age, sex, intracranial volume, cardiovascular risk factors and alcohol use. Results: Higher gamma-glutamyltransferase (GGT) levels were significantly associated with smaller total brain volume (TBV, standardized mean difference (SMD), −0.02, 95% confidence interval (CI) (−0.03 to −0.01); p = 8.4·10−4), grey matter volumes, and lower CBF and BP. Liver serum measures were not related to small vessel disease markers, nor to white matter microstructural integrity or general cognition. Participants with ultrasound-based liver steatosis had a higher fractional anisotropy (FA, SMD 0.11, 95% CI (0.04 to 0.17), p = 1.5·10−3) and lower CBF and BP. MAFLD and NAFLD phenotypes were associated with alterations in white matter microstructural integrity (NAFLD ~ FA, SMD 0.14, 95% CI (0.07 to 0.22), p = 1.6·10−4; NAFLD ~ mean diffusivity, SMD −0.12, 95% CI (−0.18 to −0.05), p = 4.7·10−4) and also with lower CBF and BP (MAFLD ~ CBF, SMD −0.13, 95% CI (−0.20 to −0.06), p = 3.1·10−4; MAFLD ~ BP, SMD −0.12, 95% CI (−0.20 to −0.05), p = 1.6·10−3). Furthermore, fibrosis phenotypes were related to TBV, grey and white matter volumes. Conclusions: Presence of liver steatosis, fibrosis and elevated serum GGT are associated with structural and hemodynamic brain markers in a population-based cross-sectional setting. Understanding the hepatic role in brain changes can target modifiable factors and prevent brain dysfunction.","brain; fibrosis; liver; MRI; non-alcoholic fatty liver disease","en","journal article","","","","","","","","","","","ImPhys/Vos group","","",""
"uuid:03e92f25-9e64-45ea-a096-540fe212834a","http://resolver.tudelft.nl/uuid:03e92f25-9e64-45ea-a096-540fe212834a","MRI-based synthetic CT in the detection of knee osteoarthritis: Comparison with CT","Arbabi, Saeed (University Medical Center Utrecht); Foppen, Wouter (University Medical Center Utrecht); Gielis, Willem Paul (University Medical Center Utrecht); van Stralen, Marijn (MRIguidance B.V); Jansen, Mylène (University Medical Center Utrecht); Arbabi, Vahid (University Medical Center Utrecht; Orthopaedic‐ Biomechanics Research Group); de Jong, Pim A. (University Medical Center Utrecht); Weinans, Harrie (TU Delft Biomaterials & Tissue Biomechanics; University Medical Center Utrecht); Seevinck, Peter (Image Sciences Institute; MRIguidance B.V)","","2023","Magnetic resonance Imaging is the gold standard for assessment of soft tissues; however, X-ray-based techniques are required for evaluating bone-related pathologies. This study evaluated the performance of synthetic computed tomography (sCT), a novel MRI-based bone visualization technique, compared with CT, for the scoring of knee osteoarthritis. sCT images were generated from the 3T T1-weighted gradient-echo MR images using a trained machine learning algorithm. Two readers scored the severity of osteoarthritis in tibiofemoral and patellofemoral joints according to OACT, which enables the evaluation of osteoarthritis, from its characteristics of joint space narrowing, osteophytes, cysts and sclerosis in CT (and sCT) images. Cohen's κ was used to assess the interreader agreement for each modality, and intermodality agreement of CT- and sCT-based scores for each reader. We also compared the confidence level of readers for grading CT and sCT images using confidence scores collected during grading. Inter-reader agreement for tibiofemoral and patellofemoral joints were almost-perfect for both modalities (κ = 0.83–0.88). The intermodality agreement of osteoarthritis scores between CT and sCT was substantial to almost-perfect for tibiofemoral (κ = 0.63 and 0.84 for the two readers) and patellofemoral joints (κ = 0.78 and 0.81 for the two readers). The analysis of diagnosis confidence scores showed comparable visual quality of the two modalities, where both are showing acceptable confidence levels for scoring OA. In conclusion, in this single-center study, sCT and CT were comparable for the scoring of knee OA.","CT; MRI; neural networks; osteoarthritis; synthetic CT","en","journal article","","","","","","","","","","","Biomaterials & Tissue Biomechanics","","",""
"uuid:a1317215-c660-437c-84c0-caa969b4c6f5","http://resolver.tudelft.nl/uuid:a1317215-c660-437c-84c0-caa969b4c6f5","Nanoprobes for PET/MR Imaging","Liu, Huanhuan (Zhengzhou University); Wang, R. (TU Delft RST/Applied Radiation & Isotopes); Gao, Haiyan (Zhengzhou University); Chen, Lijuan (Zhengzhou University); Li, Xiaochen (Zhengzhou University); Yu, Xuan (Zhengzhou University); Wu, Yaping (Zhengzhou University); Bai, Yan (Zhengzhou University); Wei, W. (Zhengzhou University); Wang, Meiyun (Zhengzhou University; Henan University)","","2023","The development of clinical imaging techniques significantly improves diagnostic accuracy and provides guidance for personalized treatment of individuals. However, every single imaging modality has its distinct drawbacks that cannot fully fulfil the diagnosis requirement. Thus, rational combination of different imaging modalities can achieve more comprehensive information of disease and in this way provide better personalized treatment strategy. The hybrid PET/MRI has drawn increasing attention since its first clinical application. Imaging probes play an essential role in achieving qualified figures with accurate information of diseases. The application of nanotechnology promotes the development of versatile molecular probes for PET/MRI technique. Though there is an emerging clinical requirement, only a small number of multimodal PET/MRI probes have been investigated in preclinical research. Thus, this review tries to thoroughly summarize the nano-sized PET/MRI probes on their design, preparation and biological application. By discussing the strength and limitations of these current available PET/MRI multimodal probes, this work aims to figure out the further research direction and promote the possible clinic translation of the novel PET/MRI probes.","dual-modality imaging; MRI; nanoprobes; PET; radiolabeling","en","review","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2024-04-17","","","RST/Applied Radiation & Isotopes","","",""
"uuid:8375af69-7ca4-47d8-b7f6-4f002ee3755d","http://resolver.tudelft.nl/uuid:8375af69-7ca4-47d8-b7f6-4f002ee3755d","Learning-based method for k-space trajectory design in MRI","Sharma, Shubham (Indian Institute of Science); Hari, K.V.S. (Indian Institute of Science); Leus, G.J.T. (TU Delft Signal Processing Systems)","","2022","Variable density sampling of the k-space in MRI is an integral part of trajectory design. It has been observed that data-driven trajectory design methods provide a better image reconstruction as compared to trajectories obtained from a fixed or a parametric density function. In this paper, a data-driven strategy has been proposed to obtain non-Cartesian continuous k-space sampling trajectories for MRI under the compressed sensing framework (greedy non-Cartesian (GNC)). A stochas-tic version of the algorithm (stochastic greedy non-Cartesian (SGNC)) is also proposed that reduces the computation time. We compare the proposed trajectory with a traveling salesman problem (TSP)-based trajectory and an echo planar imaging-like trajectory obtained by a greedy method called stochastic greedy-Cartesian (SGC) algorithm. The training images are taken from knee images of the fastMRI dataset. It is observed that the proposed algorithms outperform the TSP-based and the SGC trajectories for similar read-out times.","MRI; variable-density samplin; data-driven; k-space trajectory design","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2023-03-08","","","Signal Processing Systems","","",""
"uuid:5e5974a7-4b7e-4cbe-be48-67f928bd2094","http://resolver.tudelft.nl/uuid:5e5974a7-4b7e-4cbe-be48-67f928bd2094","The Correlation Between Wall Shear Stress and Plaque Composition in Advanced Human Carotid Atherosclerosis","Moerman, A. M. (Erasmus MC); Korteland, S. (Erasmus MC); Dilba, K. (Erasmus MC); van Gaalen, K. (Erasmus MC); Poot, D. H.J. (Erasmus MC); van Der Lugt, A. (Erasmus MC); Verhagen, H. J.M. (Erasmus MC); Wentzel, J. J. (Erasmus MC); van Der Steen, A. F.W. (Erasmus MC); Gijsen, F.J.H. (TU Delft Medical Instruments & Bio-Inspired Technology; Erasmus MC); Van der Heiden, K. (Erasmus MC)","","2022","The role of wall shear stress (WSS) in atherosclerotic plaque development is evident, but the relation between WSS and plaque composition in advanced atherosclerosis, potentially resulting in plaque destabilization, is a topic of discussion. Using our previously developed image registration pipeline, we investigated the relation between two WSS metrics, time-averaged WSS (TAWSS) and the oscillatory shear index (OSI), and the local histologically determined plaque composition in a set of advanced human carotid plaques. Our dataset of 11 carotid endarterectomy samples yielded 87 histological cross-sections, which yielded 511 radial bins for analysis. Both TAWSS and OSI values were subdivided into patient-specific low, mid, and high tertiles. This cross-sectional study shows that necrotic core (NC) size and macrophage area are significantly larger in areas exposed to high TAWSS or low OSI. Local TAWSS and OSI tertile values were generally inversely related, as described in the literature, but other combinations were also found. Investigating the relation between plaque vulnerability features and different combinations of TAWSS and OSI tertile values revealed a significantly larger cap thickness in areas exposed to both low TAWSS and low OSI. In conclusion, our study confirmed previous findings, correlating high TAWSS to larger macrophage areas and necrotic core sizes. In addition, our study demonstrated new relations, correlating low OSI to larger macrophage areas, and a combination of low TAWSS and low OSI to larger cap thickness.","atherosclerosis; image registration pipeline; MRI; oscillatory shear index; plaque composition; vulnerable plaque; wall shear stress","en","journal article","","","","","","","","","","","Medical Instruments & Bio-Inspired Technology","","",""
"uuid:ef358b0d-e8d3-448f-ac3c-72fed411bf95","http://resolver.tudelft.nl/uuid:ef358b0d-e8d3-448f-ac3c-72fed411bf95","Assessment of data consistency through cascades of independently recurrent inference machines for fast and robust accelerated MRI reconstruction","Karkalousos, D. (Universiteit van Amsterdam); Noteboom, S. (Vrije Universiteit Amsterdam); Hulst, H. E. (Vrije Universiteit Amsterdam; Universiteit Leiden); Vos, F.M. (TU Delft ImPhys/Computational Imaging; TU Delft ImPhys/Medical Imaging); Caan, M.W.A. (TU Delft ImPhys/Computational Imaging; Universiteit van Amsterdam)","","2022","Objective. Machine Learning methods can learn how to reconstruct magnetic resonance images (MRI) and thereby accelerate acquisition, which is of paramount importance to the clinical workflow. Physics-informed networks incorporate the forward model of accelerated MRI reconstruction in the learning process. With increasing network complexity, robustness is not ensured when reconstructing data unseen during training. We aim to embed data consistency (DC) in deep networks while balancing the degree of network complexity. While doing so, we will assess whether either explicit or implicit enforcement of DC in varying network architectures is preferred to optimize performance. Approach. We propose a scheme called Cascades of Independently Recurrent Inference Machines (CIRIM) to assess DC through unrolled optimization. Herein we assess DC both implicitly by gradient descent and explicitly by a designed term. Extensive comparison of the CIRIM to compressed sensing as well as other Machine Learning methods is performed: the End-to-End Variational Network (E2EVN), CascadeNet, KIKINet, LPDNet, RIM, IRIM, and UNet. Models were trained and evaluated on T1-weighted and FLAIR contrast brain data, and T2-weighted knee data. Both 1D and 2D undersampling patterns were evaluated. Robustness was tested by reconstructing 7.5× prospectively undersampled 3D FLAIR MRI data of multiple sclerosis (MS) patients with white matter lesions. Main results. The CIRIM performed best when implicitly enforcing DC, while the E2EVN required an explicit DC formulation. Through its cascades, the CIRIM was able to score higher on structural similarity and PSNR compared to other methods, in particular under heterogeneous imaging conditions. In reconstructing MS patient data, prospectively acquired with a sampling pattern unseen during model training, the CIRIM maintained lesion contrast while efficiently denoising the images. Significance. The CIRIM showed highly promising generalization capabilities maintaining a very fair trade-off between reconstructed image quality and fast reconstruction times, which is crucial in the clinical workflow.","compressed sensing; data consistency; image reconstruction; machine learning; MRI","en","journal article","","","","","","","","","","","ImPhys/Computational Imaging","","",""
"uuid:188064e2-1680-490e-8ca1-216c1ff4c6ca","http://resolver.tudelft.nl/uuid:188064e2-1680-490e-8ca1-216c1ff4c6ca","A Dictionary Learning Approach for Joint Reconstruction and Denoising in Low Field Magnetic Resonance Imaging","Ahishakiye, Emmanuel (Kyambogo University; Mbarara University of Science and Technology); van Gijzen, M.B. (TU Delft Numerical Analysis); Shan, X. (Harbin Institute of Technology); Tumwiine, Julius (Mbarara University of Science and Technology); Obungoloch, Johnes (Mbarara University of Science and Technology)","","2021","Currently, many children with hydrocephalus in East Africa and other resource-constrained countries do not have access to Magnetic Resonance Imaging (MRI) scanners, the preferred imaging tool during the disease administration and treatment. Conventional MRI scanners are costly to buy and manage, which limits their utilization in low-income countries. Low-field MRI scanners can offer an affordable, sustainable, and safe imaging alternative to high-field MRI. However, they are associated with a low signal-to-noise ratio (SNR), and therefore the images obtained are noisy. In this study, we propose an algorithm that may help to alleviate the drawbacks of low-field MRI by improving the quality of images obtained. The proposed algorithm combines our previous proposed algorithm known as AS-DLMRI for image reconstruction and a nonlinear diffusion filter for image denoising. The formulation is capable of removing additive zero-mean white and homogeneous Gaussian noise, as well as other noise types that could be present in the original signal. Experiments on visual quality revealed that the proposed algorithm is effective in denoising images during reconstruction. The proposed algorithm effectively denoised a noisy phantom, and a noisy MRI image, and had better performance when compared to DLMRI and AS-DLMRI in terms of Peak Signal to Noise ratio (PSNR) and High-Frequency Error Norm (HFEN). Integrating AS-DLMRI and the nonlinear diffusion filter proved to be effective in improving the quality of the images during the experiments performed. The hybrid algorithm may be of great use in imaging modalities like low-field MRI that are associated with low SNR.","MRI; low-field MRI; image reconstruction; Dictionary learning; Image denoising","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2022-03-31","","","Numerical Analysis","","",""
"uuid:4956949f-3e54-45e0-a8cb-4479b1437715","http://resolver.tudelft.nl/uuid:4956949f-3e54-45e0-a8cb-4479b1437715","Transceive phase corrected 2D contrast source inversion-electrical properties tomography","Stijnman, Peter R.S. (University Medical Center Utrecht; Eindhoven University of Technology); Mandija, Stefano (University Medical Center Utrecht); Fuchs, P.S. (TU Delft Signal Processing Systems); van den Berg, Cornelis A.T. (University Medical Center Utrecht); Remis, R.F. (TU Delft Signal Processing Systems)","","2021","Purpose: To remove the necessity of the tranceive phase assumption for CSI-EPT and show electrical properties maps reconstructed from measured data obtained using a standard 3T birdcage body coil setup. Methods: The existing CSI-EPT algorithm is reformulated to use the transceive phase rather than relying on the transceive phase assumption. Furthermore, the radio frequency (RF)-shield is numerically implemented to accurately model the RF fields inside the MRI scanner. We verify that the reformulated two-dimensional (2D) CSI-EPT algorithm can reconstruct electrical properties maps given 2D electromagnetic simulations. Afterward, the algorithm is tested with three-dimensional (3D) FDTD simulations to investigate if the 2D CSI-EPT can retrieve the electrical properties for 3D RF fields. Finally, an MR experiment at 3T with a phantom is performed. Results: From the results of the 2D simulations, it is seen that CSI-EPT can reconstruct the electrical properties using MRI accessible quantities. For 3D simulations, it is observed that the electrical properties are underestimated, nonetheless, CSI-EPT has a lower standard deviation than the standard Helmholtz based methods. Finally, the first CSI-EPT reconstructions based on measured data are presented showing comparable accuracy and precision to reconstructions based on simulated data, and demonstrating the feasibility of CSI-EPT. Conclusions: The CSI-EPT algorithm was rewritten to use MRI accessible quantities. This allows for CSI-EPT to fully exploit the benefits of the higher static magnetic field strengths with a standard quadrature birdcage coil setup.","contrast source inversion; dielectric tissue mapping; electrical properties tomography; EPT; MRI; RF-shield; transceive phase","en","journal article","","","","","","","","","","","Signal Processing Systems","","",""
"uuid:468a143c-4eb9-49db-bde2-5954c17f417f","http://resolver.tudelft.nl/uuid:468a143c-4eb9-49db-bde2-5954c17f417f","A multi-center, multi-vendor study to evaluate the generalizability of a radiomics model for classifying prostate cancer: High grade vs. low grade","Castillo, J.M. (Erasmus MC); Starmans, M.P.A. (Erasmus MC); Arif, M. (Erasmus MC); Niessen, W.J. (TU Delft ImPhys/Computational Imaging; TU Delft ImPhys/Medical Imaging; Erasmus MC); Klein, Stefan (Erasmus MC); Bangma, Chris H. (Erasmus MC); Schoots, Ivo G. (Erasmus MC); Veenland, J.F. (Erasmus MC)","","2021","Radiomics applied in MRI has shown promising results in classifying prostate cancer lesions. However, many papers describe single-center studies without external validation. The issues of using radiomics models on unseen data have not yet been sufficiently addressed. The aim of this study is to evaluate the generalizability of radiomics models for prostate cancer classification and to compare the performance of these models to the performance of radiologists. Multiparametric MRI, photographs and histology of radical prostatectomy specimens, and pathology reports of 107 patients were obtained from three healthcare centers in the Netherlands. By spatially correlating the MRI with histology, 204 lesions were identified. For each lesion, radiomics features were extracted from the MRI data. Radiomics models for discriminating high-grade (Gleason score ≥ 7) versus low-grade lesions were automatically generated using open-source machine learning software. The performance was tested both in a single-center setting through cross-validation and in a multi-center setting using the two unseen datasets as external validation. For comparison with clinical practice, a multi-center classifier was tested and compared with the Prostate Imaging Reporting and Data System version 2 (PIRADS v2) scoring performed by two expert radiologists. The three single-center models obtained a mean AUC of 0.75, which decreased to 0.54 when the model was applied to the external data, the radiologists obtained a mean AUC of 0.46. In the multi-center setting, the radiomics model obtained a mean AUC of 0.75 while the radiologists obtained a mean AUC of 0.47 on the same subset. While radiomics models have a decent performance when tested on data from the same center(s), they may show a significant drop in performance when applied to external data. On a multi-center dataset our radiomics model outperformed the radiologists, and thus, may represent a more accurate alternative for malignancy prediction.","Machine learning; MRI; Prostate carcinoma; Radiomics","en","journal article","","","","","","","","","","","ImPhys/Computational Imaging","","",""
"uuid:de026467-b52f-4727-8d2c-b3609a1cba69","http://resolver.tudelft.nl/uuid:de026467-b52f-4727-8d2c-b3609a1cba69","Geometrically induced wall shear stress variability in CFD-MRI coupled simulations of blood flow in the thoracic aortas","Perinajová, R. (TU Delft ChemE/Transport Phenomena); Juffermans, Joe F. (Leiden University Medical Center); Westenberg, Jos J.M. (Leiden University Medical Center); van der Palen, Roel L.F. (Leiden University Medical Center); van den Boogaard, Pieter J. (Leiden University Medical Center); Lamb, Hildo J. (Leiden University Medical Center); Kenjeres, S. (TU Delft ChemE/Transport Phenomena)","","2021","Aortic aneurysm is associated with aberrant blood flow and wall shear stress (WSS). This can be studied by coupling magnetic resonance imaging (MRI) with computational fluid dynamics (CFD). For patient-specific simulations, extra attention should be given to the variation in segmentation of the MRI data-set and its effect on WSS. We performed CFD simulations of blood flow in the aorta for ten different volunteers and provided corresponding WSS distributions. The aorta of each volunteer was segmented four times. The same inlet and outlet boundary conditions were applied for all segmentation variations of each volunteer. Steady-state CFD simulations were performed with inlet flow based on phase-contrast MRI during peak systole. We show that the commonly used comparison of mean and maximal values of WSS, based on CFD in the different segments of the thoracic aorta, yields good to excellent correlation (0.78–0.95) for rescan and moderate to excellent correlation (0.64–1.00) for intra- and interobserver reproducibility. However, the effect of geometrical variations is higher for the voxel-to-voxel comparison of WSS. With this analysis method, the correlation for different segments of the whole aorta is poor to moderate (0.43–0.66) for rescan and poor to good (0.48–0.73) for intra- and interobserver reproducibility. Therefore, we advise being critical about the CFD results based on the MRI segmentations to avoid possible misinterpretation. While the global values of WSS are similar for different modalities, the variation of results is high when considering the local distributions.","Aorta; CFD; MRI; Segmentation; Wall shear stress","en","journal article","","","","","","","","","","","ChemE/Transport Phenomena","","",""
"uuid:cfe63e61-212a-4ac1-b964-6a6f0e762e51","http://resolver.tudelft.nl/uuid:cfe63e61-212a-4ac1-b964-6a6f0e762e51","A calibrated physical flow standard for medical perfusion imaging","Kok, G. (VSL Dutch Metrology Institute); Pelevic, N. (VSL Dutch Metrology Institute); Chiribiri, A. (King’s College London); Milidonis, X. (King’s College London); Nazir, M. (King’s College London); Capstick, M. (Zurich MedTech AG, Zurich); Drost, S.; Poelma, C. (TU Delft Multi Phase Systems); Schaeffter, T. (Physikalisch-Technische Bundesanstalt)","","2021","In the medical sector, various imaging methodologies or modalities (e.g. MRI, PET, CT) are used to assess the health of various parts of the bodies of patients. One such investigation is the blood flow or perfusion of the heart muscle, expressed as the (blood) flow rate normalized by the mass of the volume of interest. Currently there is no physical flow standard for the validation of quantitative perfusion measurements. This need has been addressed in the EMPIR 15HLT05 PerfusImaging project. A phantom simulating the heart muscle has been developed with the capability that it can reproducibly generate a flow profile with individual flow rates known with a relative uncertainty of about 10% (k = 2) and total flow rate known with an uncertainty of 1% (k = 2). An overview of the phantom and its validation is given. Next, a new analysis method is presented to analyse the sequence of images which are acquired when using a standard dynamic imaging protocol. It is concluded that the new, alternative approach gives results comparable to the standard analysis method.","Calibration; CFD; Modelling; MRI; Perfusion; UIV","en","journal article","","","","","","","","","","","Multi Phase Systems","","",""
"uuid:78d96af2-fb96-4a6e-a51e-ea4236fdf2d7","http://resolver.tudelft.nl/uuid:78d96af2-fb96-4a6e-a51e-ea4236fdf2d7","Electromagnetic Fields in MRI: Analytical Methods and Applications","Fuchs, P.S. (TU Delft Signal Processing Systems)","Remis, R.F. (promotor); Leus, G.J.T. (promotor); Hari, K.V.S. (promotor); Delft University of Technology (degree granting institution)","2020","Electrical properties, the conductivity and permittivity of tissue, are quantities that describe the interaction of an object and electromagnetic fields. These properties influence electromagnetic fields and are influenced themselves by physiological phe- nomena such as lesions or a stroke. Therefore, they are important in identifying or diagnosing the severity of pathologies, and they are essential in magnetic resonance imaging (MRI) safety and efficiency by determining tissue heating or sensitivity to excitation pulses and antenna designs. In two-dimensional electromagnetic fields, which occur in specific measurement geometries, it is possible to simplify the relationship between electromagnetic fields and electrical properties, and reconstruct these properties using essentially a forward operation, foregoing a full inversion scheme. These insights also help to find, and ex- plain, the cause of specific artefacts, such as those caused by mismatches in incident field used in the computation of the full electromagnetic fields. The two-dimensional field assumption necessary for the simplified relationship described above is subsequently tested, and it is shown that this assumption does not hold when the object is sufficiently translation variant in the longitudinal direction. That is, even if the fields for a translation invariant object would be two-dimensional, they become three-dimensional through the interaction of the tissue parameters with the fields, which cause out of plane current and field contributions. Another interesting application of closed form expressions between currents and fields is the target field method, which solves the inverse source problem between electric currents and static magnetic fields in a regularised manner by constraining their relationship to a cylindrical geometry. This method is adapted for transverse oriented magnetic fields to be used with Halbach type magnet arrays, and an open source tool is developed to make the method easy to apply for various design con- siderations. Moving away from constraints on the field or current structure, we show the intri- cate relationship between electrical properties and the measured signal in an MRI scanner. This is done by deriving the electro- (and magneto-) motive force for a typ- ical MRI scenario without any assumptions on the object or electro-magnetic fields. This model can then even be used to reconstruct electrical properties from the sim- plest MRI signal, namely the free induced decay (FID) signal. To round off our investigation of tissue properties we take a small detour to the magnetic tissue property, the permeability or magnetic susceptibility. For reconstruct- ing this tissue property a dipole deconvolution is required, where the dipole convolu- tion loses information of the original object through the zeros of the dipole kernel. A new machine learning based approach to reconstruct the lost information is investi- gated in the final chapter of this thesis.","MRI; Electromagnetic FIelds; Inverse Problems; Coil Design; Electrical Properties","en","doctoral thesis","","978-94-6416-342-1","","","","","","","","","Signal Processing Systems","","",""
"uuid:61dc6d60-c2f0-407a-b698-ff0d8850976a","http://resolver.tudelft.nl/uuid:61dc6d60-c2f0-407a-b698-ff0d8850976a","Towards a general framework for fast and feasible k-space trajectories for MRI based on projection methods","Sharma, Shubham (Indian Institute of Science); Coutino, Mario (TU Delft Signal Processing Systems); Chepuri, Sundeep Prabhakar (Indian Institute of Science); Leus, G.J.T. (TU Delft Signal Processing Systems); Hari, K. V.S. (Indian Institute of Science)","","2020","The design of feasible trajectories to traverse the k-space for sampling in magnetic resonance imaging (MRI) is important while considering ways to reduce the scan time. Over the recent years, non-Cartesian trajectories have been observed to result in benign artifacts and being less sensitive to motion. In this paper, we propose a generalized framework that encompasses projection-based methods to generate feasible non-Cartesian k-space trajectories. This framework allows to construct feasible trajectories from both random or structured initial trajectories, e.g., based on the traveling salesman problem (TSP). We evaluate the performance of the proposed methods by simulating the reconstruction of 128 × 128 and 256 × 256 phantom and brain MRI images in terms of structural similarity (SSIM) index and peak signal-to-noise ratio (PSNR) using compressed sensing techniques. It is observed that the TSP-based trajectories from the proposed projection method with constant acceleration parameterization (CAP) result in better reconstruction compared to the projection method with constant velocity parameterization (CVP) and this for a similar read-out time. Further, random-like trajectories are observed to be better than TSP-based trajectories as they reduce the read-out time while providing better reconstruction quality. A reduction in read-out time by upto 67% is achieved using the proposed projection with permutation (PP) method.","compressed sensing; k-space sampling; MRI; projection methods; trajectory design","en","journal article","","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2021-04-30","","","Signal Processing Systems","","",""
"uuid:5cac3120-16ac-4b06-977e-c703d37bb342","http://resolver.tudelft.nl/uuid:5cac3120-16ac-4b06-977e-c703d37bb342","PC-MRI Blood-Flow measurements: Visualization and Data Assimilation","de Hoon, N.H.L.C. (TU Delft Computer Graphics and Visualisation)","Vilanova Bartroli, A. (promotor); Eisemann, E. (promotor); Jalba, A.C. (promotor); Delft University of Technology (degree granting institution)","2020","Heart and vessel diseases, or cardiovascular diseases (CVDs), are globally the main cause of mortality and morbidity. The blood flow plays an important role in their occurrence and progression. Therefore, knowledge of the blood flow is of key importance to reduce and threat these diseases. This knowledge requires both high-quality data and an insightful visual representation. Using advanced imaging techniques, for example phase-contrast magnetic resonance imaging (PC-MRI), the blood flow in a patient can be measured. This technique provides patient-specific 3D data over time, that is, for every measured position, a so-called voxel, the velocity of the blood is measured in all three directions. From these three values per voxel, a vector can then be reconstructed that tells us how fast and in which direction the blood was flowing at the measured location. By doing this for multiple moments one can obtain this data throughout a heart cycle. Since this data is three dimensional and changing over time generating a visual representation of this data is challenging for multiple reasons. One such reason is occlusion where part of the visualization is hidden by the rest of the visualization. Another is visual clutter where the visualization is ``too busy'' and therefore unclear. Moreover, the measured data is subject to noise and artefacts which further hinder the visualization. In this dissertation, novel visualization approaches are presented that address these and other visualization challenges of PC-MRI data. Besides PC-MRI data, blood flow data can be created using computer simulation models, for example using computational fluid dynamics (CFD) models, that are based on physical models. For this usually the shape of the blood vessel is measured using imaging techniques which is in turn used to simulate the blood flow inside the vessel. However, both measuring and modelling the blood flow have their own advantages and disadvantages. For example, PC-MRI measurements suffer from the inevitable effects of measurement noise which causes the data to deviate from the actual blood flow in the patient. Simulations, on the other hand, require detailed input information and are based on model assumptions, and hence result in data that is not always representative for the patient, however, the resulting data does correspond to the physical model. In addition to visualization approaches, this work also presents novel methods that combine PC-MRI measurements and simulations such that the resulting data is both physically-plausible and patient-specific.","visualization; Medical imaging; MRI; simulation; CFD; Data assimilation","en","doctoral thesis","","","","","","","","","","","Computer Graphics and Visualisation","","",""
"uuid:9eabdf99-580c-4358-a0b6-786e04f4f27e","http://resolver.tudelft.nl/uuid:9eabdf99-580c-4358-a0b6-786e04f4f27e","Space Filling Curves for MRI Sampling","Sharma, S. (Indian Institute of Science); Hari, K.V.S. (Indian Institute of Science); Leus, G.J.T. (TU Delft Signal Processing Systems)","","2020","A novel class of k-space trajectories for magnetic resonance imaging (MRI) sampling using space filling curves (SFCs) is presented here. More specifically, Peano, Hilbert and Sierpinski curves are used. We propose 1-shot and 4-shot variable density SFCs by utilizing the space coverage provided by SFCs in different iterations. The proposed trajectories are compared with state-of-the-art echo planar imaging (EPI) trajectories for 128 × 128 and 256 × 256 phantom and brain images. The simulation results show that the readout time is reduced by up to 45% for the 128 × 128 image with little compromise in reconstruction quality. Also, the peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) index are improved by 2.32 dB and 0.1009, respectively, with an 18% shorter readout time using the 4-shot Hilbert SFC trajectory for reconstructing a 256 × 256 brain MRI image.","MRI; k-space trajectories; space filling curves","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2020-11-14","","","Signal Processing Systems","","",""
"uuid:f8787d94-836d-48dc-951c-2c92ad982f5b","http://resolver.tudelft.nl/uuid:f8787d94-836d-48dc-951c-2c92ad982f5b","K-Space Trajectory Design for Reduced MRI Scan Time","Sharma, S. (Indian Institute of Science); Hari, K.V.S. (Indian Institute of Science); Leus, G.J.T. (TU Delft Signal Processing Systems)","","2020","The development of compressed sensing (CS) techniques for magnetic resonance imaging (MRI) is enabling a speedup of MRI scanning. To increase the incoherence in the sampling, a random selection of points on the k-space is deployed and a continuous trajectory is obtained by solving a traveling salesman problem (TSP) through these points. A feasible trajectory satisfying the gradient constraints is then obtained by parameterizing it using state-of-the-art methods. In this paper, a constrained convex optimization based method to obtain feasible trajectories is proposed. The method is motivated by the fact that the readout time is proportional to the number of sample points and includes the lengths of the segments of the trajectory in the cost function to obtain variable length trajectories. The proposed method provides a reduction in readout time by more than 50% for random-like trajectories with an improvement of about 1.5 dB in peak signal-to-noise ratio (PSNR) and 0.0762 in structural similarity (SSIM) index on average for a realistic brain phantom MRI image adopting single-shot trajectories.","MRI; compressed sensing; k-space trajectories","en","conference paper","IEEE","","","","","Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.","","2020-11-14","","","Signal Processing Systems","","",""
"uuid:ed5426d7-5135-4dfa-aadb-da2f93d3b89b","http://resolver.tudelft.nl/uuid:ed5426d7-5135-4dfa-aadb-da2f93d3b89b","Characterizing the structure of aerobic granular sludge using ultra-high field magnetic resonance","Kirkland, Catherine M. (Montana State University - Bozeman); Seymour, Joseph D. (Montana State University - Bozeman); Krug, Julia R. (Wageningen University & Research); Velders, Aldrik H. (Wageningen University & Research); Vergeldt, Frank J. (Wageningen University & Research); Van As, Henk (Wageningen University & Research); van den Berg, L. (TU Delft Sanitary Engineering); de Kreuk, M.K. (TU Delft Sanitary Engineering); Codd, Sarah L. (Montana State University - Bozeman)","","2020","Despite aerobic granular sludge wastewater treatment plants operating around the world, our understanding of internal granule structure and its relation to treatment efficiency remains limited. This can be attributed in part to the drawbacks of time-consuming, labor-intensive, and invasive microscopy protocols which effectively restrict samples sizes and may introduce artefacts. Time-domain nuclear magnetic resonance (NMR) allows non-invasive measurements which describe internal structural features of opaque, complex materials like biofilms. NMR was used to image aerobic granules collected from five full-scale wastewater treatment plants in the Netherlands and United States, as well as laboratory granules and control beads. T1 and T2 relaxation-weighted images reveal heterogeneous structures that include high- and low-density biofilm regions, water-like voids, and solid-like inclusions. Channels larger than approximately 50 μm and connected to the bulk fluid were not visible. Both cluster and ring-like structures were observed with each granule source having a characteristic structural type. These structures, and their NMR relaxation behavior, were stable over several months of storage. These observations reveal the complex structures within aerobic granules from a range of sources and highlight the need for non-invasive characterization methods like NMR to be applied in the ongoing effort to correlate structure and function.","Aerobic granular sludge; Biofilm; EPS; MRI; Nuclear magnetic resonance; Wastewater","en","journal article","","","","","","","","","","","Sanitary Engineering","","",""
"uuid:f36c8037-d9d3-460d-b51d-4860516d0d8b","http://resolver.tudelft.nl/uuid:f36c8037-d9d3-460d-b51d-4860516d0d8b","Weakly supervised object detection with 2D and 3D regression neural networks","Dubost, Florian (Erasmus MC); Adams, Hieab (Erasmus MC); Yilmaz, Pinar (Erasmus MC); Bortsova, Gerda (Erasmus MC); Tulder, Gijs van (Erasmus MC); Ikram, M. Arfan (Erasmus MC); Niessen, W.J. (TU Delft ImPhys/Medical Imaging; TU Delft ImPhys/Computational Imaging; Erasmus MC); Vernooij, Meike W. (Erasmus MC); Bruijne, Marleen de (Erasmus MC; University of Copenhagen)","","2020","Finding automatically multiple lesions in large images is a common problem in medical image analysis. Solving this problem can be challenging if, during optimization, the automated method cannot access information about the location of the lesions nor is given single examples of the lesions. We propose a new weakly supervised detection method using neural networks, that computes attention maps revealing the locations of brain lesions. These attention maps are computed using the last feature maps of a segmentation network optimized only with global image-level labels. The proposed method can generate attention maps at full input resolution without need for interpolation during preprocessing, which allows small lesions to appear in attention maps. For comparison, we modify state-of-the-art methods to compute attention maps for weakly supervised object detection, by using a global regression objective instead of the more conventional classification objective. This regression objective optimizes the number of occurrences of the target object in an image, e.g. the number of brain lesions in a scan, or the number of digits in an image. We study the behavior of the proposed method in MNIST-based detection datasets, and evaluate it for the challenging detection of enlarged perivascular spaces – a type of brain lesion – in a dataset of 2202 3D scans with point-wise annotations in the center of all lesions in four brain regions. In MNIST-based datasets, the proposed method outperforms the other methods. In the brain dataset, the weakly supervised detection methods come close to the human intrarater agreement in each region. The proposed method reaches the best area under the curve in two out of four regions, and has the lowest number of false positive detections in all regions, while its average sensitivity over all regions is similar to that of the other best methods. The proposed method can facilitate epidemiological and clinical studies of enlarged perivascular spaces and help advance research in the etiology of enlarged perivascular spaces and in their relationship with cerebrovascular diseases.","Brain; Count; Deep learning; Detection; Enlarged perivascular spaces; Lesion; MRI; Perivascular spaces; Regression; Weak-labels; Weakly-supervised","en","journal article","","","","","","","","","","","ImPhys/Medical Imaging","","",""
"uuid:e42bf1dd-ea66-4ae1-b93f-c7d23a6ec9a0","http://resolver.tudelft.nl/uuid:e42bf1dd-ea66-4ae1-b93f-c7d23a6ec9a0","An adaptive intelligence algorithm for undersampled knee MRI reconstruction","Pezzotti, Nicola (Philips Research); Yousefi, Sahar (Leiden University Medical Center); Elmahdy, Mohamed S. (Leiden University Medical Center); van Gemert, Jeroen Hendrikus Fransiscus (Philips Healthcare Nederland); Schuelke, Christophe (Philips Innovation Services); Doneva, Mariya (Philips Innovation Services); Nielsen, Tim (Philips Innovation Services); Lelieveldt, B.P.F. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center); Staring, M. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center)","","2020","Adaptive intelligence aims at empowering machine learning techniques with the additional use of domain knowledge. In this work, we present the application of adaptive intelligence to accelerate MR acquisition. Starting from undersampled k-space data, an iterative learning-based reconstruction scheme inspired by compressed sensing theory is used to reconstruct the images. We developed a novel deep neural network to refine and correct prior reconstruction assumptions given the training data. The network was trained and tested on a knee MRI dataset from the 2019 fastMRI challenge organized by Facebook AI Research and NYU Langone Health. All submissions to the challenge were initially ranked based on similarity with a known groundtruth, after which the top 4 submissions were evaluated radiologically. Our method was evaluated by the fastMRI organizers on an independent challenge dataset. It ranked #1, shared #1, and #3 on respectively the 8× accelerated multi-coil, the 4× multi-coil, and the 4× single-coil tracks. This demonstrates the superior performance and wide applicability of the method.","Deep learning; FastMRI challenge; Image reconstruction; ISTA; MRI","en","journal article","","","","","","","","","","","Pattern Recognition and Bioinformatics","","",""
"uuid:9d22f175-0fc0-489e-83b7-30ffd9996b3b","http://resolver.tudelft.nl/uuid:9d22f175-0fc0-489e-83b7-30ffd9996b3b","Efficient computational methods in Magnetic Resonance Imaging: From optimal dielectric pad design to effective preconditioned imaging techniques","van Gemert, J.H.F. (TU Delft Microwave Sensing, Signals & Systems)","Remis, R.F. (promotor); Webb, A. (promotor); Delft University of Technology (degree granting institution)","2019","This dissertation describes how to design dielectric pads that can be used to increase image quality in Magnetic Resonance Imaging, and how to accelerate image reconstruction times using a preconditioner.
Image quality is limited by the signal to noise ratio of a scan. This ratio is increased for higher static magnetic field strengths and therefore there is great interest in high-field MRI. The wavelength of the transmitted magnetic RF field decreases for higher field strengths, and it becomes comparable to the dimensions of the human body. Consequently, RF interference patterns are encountered which can severely degrade image quality because of a low transmit efficiency or because of inhomogeneities in the field distribution. Dielectric pads can be used to improve this distribution as the pads tailor the field by inducing a secondary magnetic field due to its high permittivity. Typically, the pads are placed tangential to the body and in the vicinity of the region of interest. The exact location, dimensions, and constitution of the pad need to be carefully determined, however, and depend on the application and the MR configuration. Normally, parametric design studies are carried out using electromagnetic field solvers to find a suitable pad, but this is a very time consuming process which can last hours to days. In contrast with these design studies, we present methods to efficiently model and design the dielectric pads using reduced order modeling and optimization techniques. Subsequently, we have created a design tool to bridge the gap between the advanced design methods and the practical application by the MR community. Now, pads can be designed for any 7T neuroimaging and 3T body imaging application within minutes.
In the second part of the thesis a preconditioner is designed for parallel imaging (PI) and compressed sensing (CS) reconstructions. MRI acquisition times can be strongly reduced by using PI and CS techniques by acquiring less data than prescribed by the Nyquist criterion to fully reconstruct the anatomic image; this is beneficial for patient's comfort and for minimizing the risk of patient's movement. Although acquisition times are reduced, the reconstruction times are increased significantly. The reconstruction times can be reduced when a preconditioner is used. In this thesis, we construct such a preconditioner for the frequently used iterative Split Bregman framework. We have tested the performance in a conjugate gradient framework, and show that for different coil configurations, undersampling patterns, and anatomies, a five-fold acceleration can be obtained for solving the linear system part of Split Bregman.","Maxwell Equations; Dielectric pad; High-permittivity pads; Reduced order modeling; MRI; Preconditioning; Reconstruction","en","doctoral thesis","","978-94-028-1334-0","","","","","","","","","Microwave Sensing, Signals & Systems","","",""
"uuid:412600ec-ff91-45bf-b85e-a891b2f2090a","http://resolver.tudelft.nl/uuid:412600ec-ff91-45bf-b85e-a891b2f2090a","Detection of mild cognitive impairment in a community-dwelling population using quantitative, multiparametric MRI-based classification","Bouts, Mark J.R.J. (Universiteit Leiden; Leiden University Medical Center); van der Grond, Jeroen (Leiden University Medical Center); Vernooij, Meike W. (Erasmus MC); Koini, Marisa (Medical University Graz); Schouten, T.M. (TU Delft YES! Delft; Universiteit Leiden; Leiden University Medical Center); de Vos, Frank (Universiteit Leiden; Leiden University Medical Center); Feis, Rogier A. (Leiden University Medical Center; Universiteit Leiden); Lechner, Anita (Medical University Graz); Niessen, W.J. (TU Delft ImPhys/Quantitative Imaging; Erasmus MC)","","2019","Early and accurate mild cognitive impairment (MCI) detection within a heterogeneous, nonclinical population is needed to improve care for persons at risk of developing dementia. Magnetic resonance imaging (MRI)-based classification may aid early diagnosis of MCI, but has only been applied within clinical cohorts. We aimed to determine the generalizability of MRI-based classification probability scores to detect MCI on an individual basis within a general population. To determine classification probability scores, an AD, mild-AD, and moderate-AD detection model were created with anatomical and diffusion MRI measures calculated from a clinical Alzheimer's Disease (AD) cohort and subsequently applied to a population-based cohort with 48 MCI and 617 normal aging subjects. Each model's ability to detect MCI was quantified using area under the receiver operating characteristic curve (AUC) and compared with an MCI detection model trained and applied to the population-based cohort. The AD-model and mild-AD identified MCI from controls better than chance level (AUC = 0.600, p = 0.025; AUC = 0.619, p = 0.008). In contrast, the moderate-AD-model was not able to separate MCI from normal aging (AUC = 0.567, p = 0.147). The MCI-model was able to separate MCI from controls better than chance (p = 0.014) with mean AUC values comparable with the AD-model (AUC = 0.611, p = 1.0). Within our population-based cohort, classification models detected MCI better than chance. Nevertheless, classification performance rates were moderate and may be insufficient to facilitate robust MRI-based MCI detection on an individual basis. Our data indicate that multiparametric MRI-based classification algorithms, that are effective in clinical cohorts, may not straightforwardly translate to applications in a general population.","Alzheimer's disease; classification; community-dwelling cohort; diffusion tensor imaging; machine learning; mild cognitive impairment; MRI","en","journal article","","","","","","","","","","YES! Delft","ImPhys/Quantitative Imaging","","",""
"uuid:85dc0984-2fb6-473c-841e-8442bdca36b2","http://resolver.tudelft.nl/uuid:85dc0984-2fb6-473c-841e-8442bdca36b2","Combining deep learning and 3D contrast source inversion in MR-based electrical properties tomography","Leijsen, R.L. (Leiden University Medical Center); van den Berg, Cornelis (University Medical Center Utrecht; Universiteit Utrecht); Webb, A. (Leiden University Medical Center); Remis, R.F. (TU Delft Signal Processing Systems); Mandija, Stefano (University Medical Center Utrecht; Universiteit Utrecht)","","2019","Magnetic resonance electrical properties tomography (MR-EPT) is a technique used to estimate the conductivity and permittivity of tissues from MR measurements of the transmit magnetic field. Different reconstruction methods are available; however, all these methods present several limitations, which hamper the clinical applicability. Standard Helmholtz-based MR-EPT methods are severely affected by noise. Iterative reconstruction methods such as contrast source inversion electrical properties tomography (CSI-EPT) are typically time-consuming and are dependent on their initialization. Deep learning (DL) based methods require a large amount of training data before sufficient generalization can be achieved. Here, we investigate the benefits achievable using a hybrid approach, that is, using MR-EPT or DL-EPT as initialization guesses for standard 3D CSI-EPT. Using realistic electromagnetic simulations at 3 and 7 T, the accuracy and precision of hybrid CSI reconstructions are compared with those of standard 3D CSI-EPT reconstructions. Our results indicate that a hybrid method consisting of an initial DL-EPT reconstruction followed by a 3D CSI-EPT reconstruction would be beneficial. DL-EPT combined with standard 3D CSI-EPT exploits the power of data-driven DL-based EPT reconstructions, while the subsequent CSI-EPT facilitates a better generalization by providing data consistency.","conductivity; contrast source inversion EPT; deep learning EPT; electrical properties tomography; MR-EPT; MRI; permittivity","en","journal article","","","","","","","","","","","Signal Processing Systems","","",""
"uuid:ffb8551f-c339-400d-8c96-595682567329","http://resolver.tudelft.nl/uuid:ffb8551f-c339-400d-8c96-595682567329","The value of hippocampal volume, shape, and texture for 11-year prediction of dementia: a population-based study","Achterberg, Hakim C. (Erasmus MC); Sørensen, Lauge (University of Copenhagen); Wolters, Frank J. (Erasmus MC); Niessen, W.J. (TU Delft ImPhys/Quantitative Imaging; Erasmus MC); Vernooij, Meike W. (Erasmus MC); Ikram, M. Arfan (Erasmus MC); Nielsen, Mads (University of Copenhagen; Biomediq A/S, Copenhagen); de Bruijne, Marleen (Erasmus MC; University of Copenhagen)","","2019","Hippocampal volume and shape are known magnetic resonance imaging biomarkers of neurodegeneration. Recently, hippocampal texture has been shown to improve prediction of dementia in patients with mild cognitive impairment, but it is unknown whether texture adds prognostic information beyond volume and shape and whether the predictive value extends to cognitively healthy individuals. Using 510 subjects from the Rotterdam Study, a prospective, population-based cohort study, we investigated if hippocampal volume, shape, texture, and their combination were predictive of dementia and determined how predictive performance varied with time to diagnosis and presence of early clinical symptoms of dementia. All features showed significant predictive performance with the area under the receiver operating characteristic curve ranging from 0.700 for texture alone to 0.788 for the combination of volume and texture. Although predictive performance extended to those without objective cognitive complaints or mild cognitive impairment, performance decreased with increasing follow-up time. We conclude that a combination of multiple hippocampal features on magnetic resonance imaging performs better in predicting dementia in the general population than any feature by itself.","Dementia; Hippocampal shape; Hippocampal texture; MRI; Population-based; Prediction","en","journal article","","","","","","","","","","","ImPhys/Quantitative Imaging","","",""
"uuid:724f270c-53c2-44c2-a2c3-42805452b44d","http://resolver.tudelft.nl/uuid:724f270c-53c2-44c2-a2c3-42805452b44d","Normative brain volumetry derived from different reference populations: impact on single-subject diagnostic assessment in dementia","Vinke, Elisabeth J. (Erasmus MC); Huizinga, W. (Erasmus MC); Bergtholdt, Martin (Philips Innovation Services); Adams, Hieab H. (Erasmus MC); Steketee, Rebecca M.E. (Erasmus MC); Papma, Janne M. (Erasmus MC); De Jong, Frank Jan; Niessen, W.J. (TU Delft ImPhys/Quantitative Imaging; Erasmus MC); Ikram, M. Arfan (Erasmus MC)","","2019","Brain imaging data are increasingly made publicly accessible, and volumetric imaging measures derived from population-based cohorts may serve as normative data for individual patient diagnostic assessment. Yet, these normative cohorts are usually not a perfect reflection of a patient's base population, nor are imaging parameters such as field strength or scanner type similar. In this proof of principle study, we assessed differences between reference curves of subcortical structure volumes of normal controls derived from two population-based studies and a case-control study. We assessed the impact of any differences on individual assessment of brain structure volumes. Percentile curves were fitted on the three healthy cohorts. Next, percentile values for these subcortical structures for individual patients from these three cohorts, 91 mild cognitive impairment and 95 Alzheimer's disease cases and patients from the Alzheimer Center, were calculated, based on the distributions of each of the three cohorts. Overall, we found that the subcortical volume normative data from these cohorts are highly interchangeable, suggesting more flexibility in clinical implementation.","Imaging; MRI; Normative data; Subcortical brain volume","en","journal article","","","","","","","","","","","ImPhys/Quantitative Imaging","","",""
"uuid:c71e1484-3459-4c48-bc86-37c348dc0e5b","http://resolver.tudelft.nl/uuid:c71e1484-3459-4c48-bc86-37c348dc0e5b","Trajectories of imaging markers in brain aging: the Rotterdam Study","Vinke, Elisabeth J. (Erasmus MC); de Groot, Marius (Erasmus MC); Venkatraghavan, Vikram (Erasmus MC); Klein, S. (Erasmus MC); Niessen, W.J. (TU Delft ImPhys/Quantitative Imaging; Erasmus MC); Ikram, M. Arfan (Erasmus MC); Vernooij, Meike W. (Erasmus MC)","","2018","With aging, the brain undergoes several structural changes. These changes reflect the normal aging process and are therefore not necessarily pathologic. In fact, better understanding of these normal changes is an important cornerstone to also disentangle pathologic changes. Several studies have investigated normal brain aging, both cross-sectional and longitudinal, and focused on a broad range of magnetic resonance imaging (MRI) markers. This study aims to comprise the different aspects in brain aging, by performing a comprehensive longitudinal assessment of brain aging, providing trajectories of volumetric (global and lobar; subcortical and cortical), microstructural, and focal (presence of microbleeds, lacunar or cortical infarcts) brain imaging markers in aging and the sequence in which these markers change in aging. Trajectories were calculated on 10,755 MRI scans that were acquired between 2005 and 2016 among 5286 persons aged 45 years and older from the population-based Rotterdam Study. The average number of MRI scans per participant was 2 scans (ranging from 1 to 4 scans), with a mean interval between MRI scans of 3.3 years (ranging from 0.2 to 9.5 years) and an average follow-up time of 5.2 years (ranging from 0.3 to 9.8 years). We found that trajectories of the different volumetric, microstructural, and focal markers show nonlinear curves, with accelerating change with advancing age. We found earlier acceleration of change in global and lobar volumetric and microstructural markers in men compared with women. For subcortical and cortical volumes, results show a mix of more linear and nonlinear trajectories, either increasing, decreasing, or stable over age for the subcortical and cortical volume and thickness. Differences between men and women are visible in several parcellations; however, the direction of these differences is mixed. The presence of focal markers show a nonlinear increase with age, with men having a higher probability for cortical or lacunar infarcts. The data presented in this study provide insight into the normal aging process in the brain, and its variability.","Diffusion-MRI; Epidemiology; Gray matter; Longitudinal; MRI; Neurodegeneration; Population-based; White matter","en","journal article","","","","","","","","","","","ImPhys/Quantitative Imaging","","",""
"uuid:b0c0e88a-6da0-45ca-bea9-ebd501c49a90","http://resolver.tudelft.nl/uuid:b0c0e88a-6da0-45ca-bea9-ebd501c49a90","MRI Mouse Brain Data of Ischemic Lesion after Transient Middle Cerebral Artery Occlusion","Mulder, Inge A. (Leiden University Medical Center); Khmelinskii, Artem (Leiden University Medical Center; University of Twente; Netherlands Cancer Institute); Dzyubachyk, Oleh (Leiden University Medical Center); De Jong, Sebastiaan (Max Planck Institute for Metabolism Research); Wermer, Marieke J.H. (Leiden University Medical Center); Hoehn, Mathias (Leiden University Medical Center; University of Twente; Max Planck Institute for Metabolism Research); Lelieveldt, B.P.F. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center); van den Maagdenberg, Arn M.J.M. (Leiden University Medical Center)","","2017","In this data report we make available to the community a highly variable longitudinal MRI mouse brain data set of ischemic lesion after transient middle cerebral artery occlusion (tMCAo). Together with the provided semi-automated and automated segmentations, these data can be used to further improve the method proposed by Mulder et al. (2017) and also to serve as a benchmark for comparison between different approaches to segment ischemic lesions in MRI mouse brain data. It can also be used to develop and validate algorithms that further classify the stroke area into core and penumbra.
• The data were collected from mice: (i) of different ages, (ii) of two different strains, (iii) at different time points after the ischemic infarct induction, (iv) from two laboratories, (v) using two different MRI systems, and (vi) using three different sets of acquisition parameters.
• Segmentations of the ischemic lesions are provided as well. These were obtained by: (i) two observers using a semi-automated method and (ii) using the novel automated segmentation approach described by Mulder et al. (2017).
• Type/format of data: raw files, MetaImage files, text/Excel files, analyzed data.
• The following set of images associated with each of the 121 scans is included: raw Bruker MRI data (reference scan, T2 scan with all echoes, calculated T2-weighted map), automated segmentations of the ischemic lesions and semi-automated segmentations by two observers.
• For 99 of these scans, an accompanying set of Bruker MR diffusion maps, containing the Diffusion-Weighted Image (DWI) and calculated Apparent Diffusion Coefficient (ADC) maps, is included.
• Acquisition hardware: small-animal Bruker MRI systems (7 T and 11.7 T).
• Experimental set-up: infarct was induced in male mice of different age and background, using the tMCAo model. After that, MRI scans at different time points after infarct induction were acquired.
• Data sources: Leiden, Netherlands; Cologne, Germany.
• Data accessibility: all related data sets (121 T2 scans + template + 99 diffusion scans) were deposited in the public Dryad Digital Repository (https://doi.org/10.5061/dryad.1m528).","Brain; Data collection; Ischemic stroke; Mouse; MRI","en","journal article","","","","","","","","","","","Pattern Recognition and Bioinformatics","","",""
"uuid:71b81644-e487-4fc1-aa6b-b691e2d90de2","http://resolver.tudelft.nl/uuid:71b81644-e487-4fc1-aa6b-b691e2d90de2","Automated Ischemic Lesion Segmentation in MRI Mouse Brain Data after Transient Middle Cerebral Artery Occlusion","Mulder, Inge A. (Leiden University Medical Center); Khmelinskii, Artem (Leiden University Medical Center; Percuros B.V); Dzyubachyk, Oleh (Leiden University Medical Center); de Jong, Sebastiaan (Leiden University Medical Center); Rieff, Nathalie (Leiden University Medical Center); Wermer, Marieke J.H. (Leiden University Medical Center); Hoehn, Mathias (Leiden University Medical Center; Percuros B.V; Max Planck Institute for Metabolism Research); Lelieveldt, B.P.F. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center); van den Maagdenberg, Arn M.J.M. (Leiden University Medical Center)","","2017","Magnetic resonance imaging (MRI) has become increasingly important in ischemic stroke experiments in mice, especially because it enables longitudinal studies. Still, quantitative analysis of MRI data remains challenging mainly because segmentation of mouse brain lesions in MRI data heavily relies on time-consuming manual tracing and thresholding techniques. Therefore, in the present study, a fully automated approach was developed to analyze longitudinal MRI data for quantification of ischemic lesion volume progression in the mouse brain. We present a level-set-based lesion segmentation algorithm that is built using a minimal set of assumptions and requires only one MRI sequence (T2) as input. To validate our algorithm we used a heterogeneous data set consisting of 121 mouse brain scans of various age groups and time points after infarct induction and obtained using different MRI hardware and acquisition parameters. We evaluated the volumetric accuracy and regional overlap of ischemic lesions segmented by our automated method against the ground truth obtained in a semi-automated fashion that includes a highly time-consuming manual correction step. Our method shows good agreement with human observations and is accurate on heterogeneous data, whilst requiring much shorter average execution time. The algorithm developed here was compiled into a toolbox and made publically available, as well as all the data sets.","Automated segmentation; Ischemic stroke; Lesion; Mouse; MRI; Quantification; Volume","en","journal article","","","","","","","","","","","Pattern Recognition and Bioinformatics","","",""
"uuid:909d94e7-2818-4614-8c96-4191f0aa631c","http://resolver.tudelft.nl/uuid:909d94e7-2818-4614-8c96-4191f0aa631c","Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington’s Disease","Keo, D.L. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center); Aziz, N. Ahmad (Leiden University Medical Center); Dzyubachyk, Oleh (Leiden University Medical Center); Van Der Grond, Jeroen (Leiden University Medical Center); van Roon-Mom, Willeke M.C. (Leiden University Medical Center); Lelieveldt, B.P.F. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center); Reinders, M.J.T. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center); Mahfouz, A.M.E.T.A. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center)","","2017","Cytosine-adenine-guanine (CAG) repeat expansions in the coding regions of nine polyglutamine (polyQ) genes (HTT, ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, ATN1, AR, and TBP) are the cause of several neurodegenerative diseases including Huntington’s disease (HD), six different spinocerebellar ataxias (SCAs), dentatorubral-pallidoluysian atrophy, and spinobulbar muscular atrophy. The expanded CAG repeat length in the causative gene is negatively related to the age-at-onset (AAO) of clinical symptoms. In addition to the expanded CAG repeat length in the causative gene, the normal CAG repeats in the other polyQ genes can affect the AAO, suggesting functional interactions between the polyQ genes. However, there is no detailed assessment of the relationships among polyQ genes in pathologically relevant brain regions. We used gene co-expression analysis to study the functional relationships among polyQ genes in different brain regions using the Allen Human Brain Atlas (AHBA), a spatial map of gene expression in the healthy brain. We constructed co-expression networks for seven anatomical brain structures, as well as a region showing a specific pattern of atrophy in HD patients detected by magnetic resonance imaging (MRI) of the brain. In this HD-associated region, we found that ATN1 and ATXN2 were co-expressed and shared co-expression partners which were enriched for DNA repair genes. We observed a similar co-expression pattern in the frontal lobe, parietal lobe, and striatum in which this relation was most pronounced. Given that the co-expression patterns for these anatomical structures were similar to those for the HD-associated region, our results suggest that their disruption is likely involved in HD pathology. Moreover, ATN1 and ATXN2 also shared many co-expressed genes with HTT, the causative gene of HD, across the brain. Although this triangular relationship among these three polyQ genes may also be dysregulated in other polyQ diseases, stronger co-expression patterns between ATN1 and ATXN2 observed in the HD-associated region, especially in the striatum, may be more specific to HD.","gene co-expression; polyglutamine diseases; human brain; Huntington’s diseas; neurodegeneration; MRI; spinocerebellar ataxias; OA-Fund TU Delft","en","journal article","","","","","","","","","","","Pattern Recognition and Bioinformatics","","",""
"uuid:ab9f68e7-4a52-44e3-b343-0c917de50d85","http://resolver.tudelft.nl/uuid:ab9f68e7-4a52-44e3-b343-0c917de50d85","Detection of Conversion from Mild Cognitive Impairment to Alzheimer’s Disease Using Longitudinal Brain MRI","Sun, Zhuo (Leiden University Medical Center); van de Giessen, M. (Leiden University Medical Center); Lelieveldt, B.P.F. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center); Staring, M. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center)","","2017","Mild Cognitive Impairment (MCI) is an intermediate stage between healthy and Alzheimer’s disease (AD). To enable early intervention it is important to identify the MCI subjects that will convert to AD in an early stage. In this paper, we provide a new method to distinguish between MCI patients that either convert to Alzheimer’s Disease (MCIc) or remain stable (MCIs), using only longitudinal T1-weighted MRI. Currently, most longitudinal studies focus on volumetric comparison of a few anatomical structures, thereby ignoring more detailed development inside and outside those structures. In this study we propose to exploit the anatomical development within the entire brain, as found by a non-rigid registration approach. Specifically, this anatomical development is represented by the Stationary Velocity Field (SVF) from registration between the baseline and follow-up images. To make the SVFs comparable among subjects, we use the parallel transportmethod to align themin a common space. The normalized SVF together with derived features are then used to distinguish between MCIc and MCIs subjects. This novel feature space is reduced using a Kernel Principal Component Analysis method, and a linear support vector machine is used as a classifier. Extensive comparative experiments are performed to inspect the influence of several aspects of our method on classification performance, specifically the feature choice, the smoothing parameter in the registration and the use of dimensionality reduction. The optimal result from a 10-fold cross-validation using 36 month follow-up data shows competitive results: accuracy 92%, sensitivity 95%, specificity 90%, and AUC 94%. Based on the same dataset, the proposed approach outperforms two alternative ones that either depends on the baseline image only, or uses longitudinal information from larger brain areas. Good results were also obtained when scans at 6, 12, or 24 months were used for training the classifier. Besides the classification power, the proposed method can quantitatively compare brain regions that have a significant difference in development between the MCIc and MCIs groups.","Alzheimer’s disease; Conversion; Mild cognitive impairment (MCI); MRI; Non-rigid registration; Parallel transport; Stationary velocity field (SVF); SVM classification","en","journal article","","","","","","","","","","","Pattern Recognition and Bioinformatics","","",""
"uuid:13e1f7b0-a570-46e5-a299-bcfeed05f758","http://resolver.tudelft.nl/uuid:13e1f7b0-a570-46e5-a299-bcfeed05f758","Morphological maturation of the mouse brain: An in vivo MRI and histology investigation","Hammelrath, Luam (Max Planck Institute for Metabolism Research); Škokić, Siniša (Max Planck Institute for Metabolism Research; University of Zagreb); Khmelinskii, Artem (Leiden University Medical Center; Percuros B.V); Hess, Andreas (Friedrich-Alexander-Universität Erlangen-Nürnberg); van der Knaap, Noortje (Max Planck Institute for Metabolism Research; Radboud Universiteit Nijmegen); Staring, M. (Leiden University Medical Center); Lelieveldt, B.P.F. (TU Delft Pattern Recognition and Bioinformatics; Leiden University Medical Center); Wiedermann, Dirk (Max Planck Institute for Metabolism Research); Hoehn, Mathias (Max Planck Institute for Metabolism Research; Leiden University Medical Center; Percuros B.V)","","2016","With the wide access to studies of selected gene expressions in transgenic animals,mice have become the dominant species as cerebral diseasemodels. Many of these studies are performed on animals of not more than eight weeks, declared as adult animals. Based on the earlier reports that full brain maturation requires at least three months in rats, there is a clear need to discern the corresponding minimal animal age to provide an “adult brain” in mice in order to avoid modulation of disease progression/therapy studies by ongoing developmental changes. For this purpose, we have studied anatomical brain alterations of mice during their first six months of age. Using T2-weighted and diffusion-weightedMRI, structural and volume changes of the brain were identified and compared with histological analysis of myelination. Mouse brain volume was found to be almost stable already at three weeks, but cortex thickness kept decreasing continuously with maximal changes during the first
three months. Myelination is still increasing between three and six months, although most dramatic changes are over by three months. While our results emphasize that mice should be at least three months old when adult animals are needed for brain studies, preferred choice of one particular metric for future investigation goals will result in somewhat varying age windows of stabilization.","MRI; Mouse brain; Brain development; Cortex; Myelination; DTI","en","journal article","","","","","","","","","","","Pattern Recognition and Bioinformatics","","",""
"uuid:7437598a-bf01-4837-b699-b8bc17a13965","http://resolver.tudelft.nl/uuid:7437598a-bf01-4837-b699-b8bc17a13965","Mini-review: novel non-destructive in situ biofilm characterization techniques in membrane systems","Valladares Linares, R. (King Abdullah University of Science and Technology); Fortunato, L (King Abdullah University of Science and Technology); Farhat, N. M. (King Abdullah University of Science and Technology); Bucs, S. S. (King Abdullah University of Science and Technology); Staal, M.J. (TU Delft BT/Environmental Biotechnology); Fridjonsson, E. O. (University of Western Australia); Johns, M. L. (University of Western Australia); Vrouwenvelder, J.S. (TU Delft BT/Environmental Biotechnology; King Abdullah University of Science and Technology; Wetsus, Centre for Sustainable Water Technology); Leiknes, TO (King Abdullah University of Science and Technology)","","2016","Membrane systems are commonly used in the water industry to produce potable water and for advanced wastewater treatment. One of the major drawbacks of membrane systems is biofilm formation (biofouling), which results in an unacceptable decline in membrane performance. Three novel in situ biofouling characterization techniques were assessed: (i) optical coherence tomography (OCT), (ii) planar optodes, and (iii) nuclear magnetic resonance (NMR). The first two techniques were assessed using a biofilm grown on the surface of nanofiltration (NF) membranes using a transparent membrane fouling simulator that accurately simulates spiral wound modules, modified for in situ biofilm imaging. For the NMR study, a spiral wound reverse osmosis membrane module was used. Results show that these techniques can provide information to reconstruct the biofilm accurately, either with 2-D (OCT, planar optodes and NMR), or 3-D (OCT and NMR) scans. These non-destructive tools can elucidate the interaction of hydrodynamics and mass transport on biofilm accumulation in membrane systems. Oxygen distribution in the biofilm can be mapped and linked to water flow and substrate characteristics; insights on the effect of crossflow velocity, flow stagnation, and feed spacer presence can be obtained, and in situ information on biofilm structure, thickness, and spatial distribution can be quantitatively assessed. The combination of these novel non-destructive in situ biofilm characterization techniques can provide real-time observation of biofilm formation at the mesoscale. The information obtained with these tools could potentially be used for further improvement in the design of membrane systems and operational parameters to reduce impact of biofouling on membrane performance.","Biofouling; Drinking water; MRI; Optical coherence tomography; Water treatment and reuse","en","review","","","","","","","","","","","BT/Environmental Biotechnology","","",""
"uuid:5648e091-ebb2-4ac9-b2de-82ec3bd3146e","http://resolver.tudelft.nl/uuid:5648e091-ebb2-4ac9-b2de-82ec3bd3146e","Subject-specific upper extremity modelling","Bolsterlee, B.","Van der Helm, F.C.T. (promotor); Veeger, H.E.J. (promotor)","2014","Insight into the mechanical interaction between muscles and bones can be of great help to understand normal function of the human body and to improve diagnoses and treatments of musculoskeletal disorders. This research presented in this thesis aims to improve the predictions of a musculoskeletal model of the shoulder and elbow (the Delft Shoulder and Elbow Model or DSEM) by extracting anatomical information from MRI scans and other imaging modalities. Several techniques are presented to personalise anatomical parameters and the effect on muscle and joint force predictions are calculated. Due to difficulties related to validation of modelling results and the limited ability to measure all relevant model parameters in vivo, it is concluded that subject-specific models are not likely to lead to a vast new range of applications in the near future.","biomechanics; musculoskeletal model; shoulder and elbow; MRI; ultrasound","en","doctoral thesis","","","","","","","","","Mechanical, Maritime and Materials Engineering","BioMechanical Engineering","","","",""
"uuid:c11ff40a-cf64-4459-95df-6908b6245354","http://resolver.tudelft.nl/uuid:c11ff40a-cf64-4459-95df-6908b6245354","Smart needles for percutaneous interventions","Henken, K.R.","Dankelman, J. (promotor); van den Dobbelsteen, J.J. (copromotor)","2014","The development of advanced needles for diagnostic and therapeutic purposes such as ablation and brachytherapy in the liver has offered minimally invasive therapies to patients that were previously untreatable. This thesis focuses on accurate placement of such needles guided by magnetic resonance imaging (MRI) to maximize the effect of the treatment and to minimize unwanted side-effects. To this end, an MRI-compatible steerable needle is developed which consists of a cable-actuated tip and a passively flexible shaft. The trajectory of this needle can be adjusted after the needle has been inserted. In addition, shape sensing based on optical strain sensors (fiber Bragg gratings or FBGs) is investigated aiming at feeding back information about the position and orientation of the needle tip in real-time. This is essential for accurate targeting, particularly when the needle trajectory is curved. Finally, steerability and shape sensing are integrated in a robotic system for needle steering in MRI-guided percutaneous interventions in the liver. The master-slave system comprises a steerable needle equipped with FBGs for tracking and a piezoelectric actuator unit. Needle insertion and steering is controlled by the physician through a master device, while FBG-based visual feedback of the needle shape is provided.","needle; robotics; FBG; biomedical engineering; sensors; MRI; medical instruments; shape sensing; needle steering","en","doctoral thesis","","","","","","","","2015-09-30","Mechanical, Maritime and Materials Engineering","BioMechanical Engineering","","","",""
"uuid:2a9e6349-9269-4281-ae00-b952921ece6f","http://resolver.tudelft.nl/uuid:2a9e6349-9269-4281-ae00-b952921ece6f","Multi-modal image registration: Matching MRI with histology","Alic, L.; Haeck, J.C.; Klein, S.; Bol, K.; Van Tiel, S.T.; Wielepolski, P.A.; Bijster, M.; Niessen, W.J.; Bernsen, M.; Veenland, J.F.; De Jong, M.","","2010","","multi-modal registration; MRI; histology; tumor; tissue characterization","en","conference paper","SPIE","","","","","","","","Applied Sciences","Imaging Science and Technology","","","",""
"uuid:ae10097a-68e8-41a2-a51e-593c985c818d","http://resolver.tudelft.nl/uuid:ae10097a-68e8-41a2-a51e-593c985c818d","Biofouling of spiral wound membrane systems","Vrouwenvelder, J.S.","Van Loosdrecht, M.C.M. (promotor)","2009","Biofouling of spiral wound membrane systems High quality drinking water can be produced with membrane filtration processes like reverse osmosis (RO) and nanofiltration (NF). Because the global demand for fresh clean water is increasing, these membrane technologies will increase in importance in the coming decades. One of the most serious problems in RO/NF applications is biofouling - excessive growth of biomass - affecting the performance of the RO/NF systems due to e.g. (i) increase in pressure drop across membrane elements (feed-concentrate channel), (ii) decrease in membrane permeability, (iii) increase in salt passage. These phenomena result in the need to increase the feed pressure to maintain constant production and to clean the membrane elements chemically. In practice, the first phenomenon is most dominant. The objective of this study was to relate biomass accumulation in spiral wound RO and NF membrane elements with membrane performance and hydrodynamics and to determine parameters influencing biofouling. The focus of this research was on the development of biomass in the feed-concentrate (feed-spacer) channel and its effect on pressure drop and flow distribution. These detailed studies can be used to develop an integral strategy to control biofouling in spiral wound membrane systems. Problem analysis Studies to diagnose biofouling in 15 full-scale RO and NF membrane installations with varying feed water types showed that (i) highest biomass concentrations were found at the installation feed side, (ii) the biomass related parameter adenosine-tri-phosphate was suitable for biofouling diagnosis in membrane element autopsies, (iii) measurements of biological parameters in the water were not appropriate in quantifying biofouling, and (iv) there is a need for a representative monitor and sensitive accurate pressure data to enable a reliable evaluation of the development of biofouling (Chapter 2). Based on the practical observations it was decided to develop a set of tools to study biofouling at controlled conditions. Method development A monitor was developed (Chapter 3) in combination with testing of a sensitive differential pressure drop transmitter (Chapter 4). This small monitor named Membrane Fouling Simulator (MFS) uses the same membranes and spacers as present in commercial membrane elements, has similar hydrodynamics and is equipped with a sight window. The MFS is an effective scaled-down version of a full-scale system and allows to study the biofouling process occurring in the first 0.20 m of RO/NF elements. Magnetic Resonance Imaging (MRI) provided in-situ, non-invasive, and spatially-resolved measurements of biofouling and its impact on hydrodynamics and mass transport in spiral wound membrane elements as well as in the MFS (Chapter 5). A three-dimensional computational model was developed to simulate biofouling in membrane elements, with feed spacer geometry as used in practice (Chapter 6). The model combines fluid dynamics, solute transport and biofouling. The methods described in the first part of the thesis have been used to increase the understanding of fundamental aspects of biofouling. Basic studies The development of biomass and related increase in pressure drop was not influenced by the permeate production in the elements (Chapter 7). Irrespective whether a flux was applied or not, the feed-concentrate channel pressure drop and biofilm amount increased in RO and NF membranes in monitor, test-rig, pilot and full-scale installation. Mass transport calculations supported that permeate production plays a minor role in the development of biofouling. Since fouling occurred irrespective of permeate production, the critical flux concept stating that “below a critical flux no fouling occurs” is not applicable to control RO/NF biofouling in extensively pretreated water. In essence, biofouling is a feed spacer channel problem (Chapter 8). This observation is based on (i) practical data and supported by (ii) in-situ visual observations of fouling accumulation using the MFS sight window, (iii) in-situ non-destructive observations of fouling accumulation and velocity distribution profiles using MRI, and (iv) differences in pressure drop and biomass development in monitors with and without feed spacer. MRI studies showed that already a restricted biofilm accumulation on the feed channel spacer influenced the velocity distribution profile strongly, leading to a strong decrease of the effective surface area in the membrane module and probably increasing the salt concentration in the dead-zones of the element leading to increased salt passage. Three-dimensional numerical simulations of biofilm formation and fluid flow were executed and compared with MRI and MFS studies (Chapter 9). The simulations showed similar (i) pressure drop development and (ii) patterns in flow distribution and channelling as observed in MRI and MFS studies. Feed spacers showed to have an essential role in biofouling, and are considered a prime target for improving the membrane elements. Based on the gained insights several potential methodologies to minimize the impact of biofouling have been studied and described in the last chapters of the thesis. Control studies The effect of substrate concentration, linear flow velocity, substrate load and flow direction on pressure drop development and biofilm accumulation was investigated in MFSs (Chapter 10). The pressure drop increase was related to the amount of accumulated biomass and linear flow velocity. Biomass accumulation was related to the substrate load. A flow direction change in the pressure vessels instantaneously reduced the pressure drop, accentuating that hydrodynamics, spacers and pressure vessel configuration offer possibilities to restrict the pressure drop increase caused by accumulated biomass. The impact of flow regime on pressure drop, biomass accumulation and morphology was studied (Chapter 11). In RO and NF membrane elements, at linear flow velocities as applied in practice voluminous and filamentous biofilm structures developed in the feed spacer channel, causing a significant increase in feed channel pressure drop. The amount of accumulated biomass was independent of the applied shear, depending on the substrate load. A high shear force resulted in more compact and less filamentous biofilm structure compared to a low shear force, causing a lower pressure drop increase. A biofilm grown at low shear was easier to remove during water flushing compared to a biofilm grown at high shear. Flow regimes manipulated biofilm morphology affecting membrane performance, enabling new approaches to control biofouling. Phosphate limitation as a method to control biofouling was investigated at a full-scale RO installation, characterized by low phosphate and substrate concentrations in the feed water and low biomass amounts in lead membrane modules. MFS studies showed that phosphate limitation restricted the pressure drop increase and biomass accumulation, even in the presence of high substrate concentrations (Chapter 12). Outlook Most past and present methods to control biofouling have not been very successful. Based on insights obtained by the studies described in this thesis, an overview is given of several potential complementary approaches to solve biofouling (Chapter 13). An integrated approach for biofouling control is proposed, based on three corner stones: (i) equipment design and operation, (ii) biomass growth conditions, and (iii) cleaning agents. Although in this stage chemical cleaning and biofouling inhibitor dosing seem inevitable to control biofouling, it is expected that in future – also because of sustainability and costs reasons - membrane systems will be operated without or with minimal chemical cleaning and dosing.","biofouling; hydrodynamics; nanofiltration; reverse osmosis; biofilm; 3D CFD model; membrane fouling; drinking water; feed spacer; flux; NMR; MRI; NF; RO; pressure drop increase; concentration polarization","en","doctoral thesis","","","","","","","","2009-10-30","Applied Sciences","Biotechnology","","","",""
"uuid:16aa52d8-cfc3-4790-9fea-75ff731afb7a","http://resolver.tudelft.nl/uuid:16aa52d8-cfc3-4790-9fea-75ff731afb7a","Calix[4]arenes as Molecular Platforms in Magnetic Resonance Imaging","Schühle, D.T.","Sheldon, R.A. (promotor); Schatz, J. (promotor); Peters, J.A. (promotor)","2009","Magnetic resonance imaging (MRI) is an important tool in medical diagnosis. It uses non-ionizing radio-frequency radiation and produces images with excellent resolution. To increase the contrast, Gd(III)-containing compounds are applied leading to a brightening of the area of interest. The performance of a contrast agent can be enhanced by using large and at the same time rigid systems to bind the paramagnetic Gd(III). Since calix[4]arenes can be rigidified and functionalized easily, they were chosen as molecular building blocks to attach Gd(III)-containing units to them. Those conjugates were optimized to yield highly efficient MRI contrast agents that self-assemble in water to nano-sized aggregates. Their interaction with the plasma protein human serum albumin gives them the potential to be used in angiography. To extend their application even further, nano-vesicles (liposomes) were prepared that contain such a conjugate in their walls. Thanks to the presence of the calix[4]arene core, those liposomes have unprecedentedly high contrast enhancement properties. Due to this and the fact that liposomes are known to accumulate in tumours, this probe is a promising candidate for cancer imaging. The broad applicability of the calix[4]arene core in medical sciences is further demonstrated in investigations towards sodium-selective artificial ion channels as well as towards a deeper understanding of the functioning of model compounds that mimic the hydrophobic active pocket of enzymes.","Calixarene; MRI; Self-aggregation; albumin; Imidazolium salt","en","doctoral thesis","","","","","","","","2009-10-09","Applied Sciences","Biotechnology","","","",""
"uuid:39df65bc-92c5-4df3-bf58-8a1e1ec11bc9","http://resolver.tudelft.nl/uuid:39df65bc-92c5-4df3-bf58-8a1e1ec11bc9","The anatomy of the thoracic spinal canal investigated with magnetic resonance imaging (MRI)","Lee, R.A.; Van Zundert, A.A.; Breedveld, P.; Wondergem, J.H.; Peek, D.; Wieringa, P.A.","","2007","Background and Objectives : Anesthesiologists are reluctant to consider higher levels for spinal anesthesia, largely due to direct threats to the spinal cord. The goal of this study is to investigate, with magnetic resonance imaging (MRI), the distances between the relevant structures of the spinal canal (spinal cord, thecal tissue, etc.) to determine modal anatomical positions for neuraxial anesthesia. Method : A group of 19 patients were imaged with an MRI scanner in supine position. Medial sagittal slices of the thoracic and lumbar spine were measured for the relative distances between anatomical structures, including epidural space, dura, and spinal cord. Results : The posterior dura – spinal cord distance is significantly greater in the middle thoracic region than at upper and lower thoracic levels (e.g. T6 9.5 ± 1.8 mm, T12 3.7 ± 1.2 mm, p < 0.001, T1 4.7 ± 1.7 mm, p < 0.001). There is variation in modal distances between the structures important for neuraxial anesthesia, at different levels of the spinal canal. Conclusions : The spinal cord tends to follow the straightest line through the imposed geometry of the spine. Considering the necessary angle of entry of the needle at mid-thoracic levels, there is relatively (more than at upper thoracic and lumbar levels) substantial separation of cord and surrounding thecal tissue. Anesthesiologists perform spinal blockades up to the L2-L3 interspace, but avoid higher levels for fear of neurological damage. The information that there is substantially more space in the dorsal subarachnoid space at thoracic level, might lead to potential applications in regional anesthesia. In contrast, the cauda equina sits more dorsally in the lumbar region.","anatomy; intrathecal; MRI; neuraxial; spinal cord","en","journal article","Amb Acta Medica Belgica","","","","","","","","Mechanical, Maritime and Materials Engineering","Biomedical Engineering","","","",""
"uuid:3227d30a-4672-4ed9-9e62-0a85f14b1e39","http://resolver.tudelft.nl/uuid:3227d30a-4672-4ed9-9e62-0a85f14b1e39","Lanthanide-Loaded Liposomes for Multimodality Imaging and Therapy","Zielhuis, S.W.; Seppenwoolde, J.H.; Mateus, V.A.P.; Bakker, C.J.G.; Krijger, G.C.; Storm, G.; Zonnenberg, B.A.; Van het Schip, A.D.; Koning, G.A.; Nijsen, J.F.W.","","2006","Many advanced molecular imaging agents are currently being investigated preclinically. Especially, liposomes, have proven to be very promising carrier systems for diagnostic agents for use in single-photon emission computed tomography (SPECT) or magnetic resonance imaging (MRI), as well as for therapeutic agents to treat diseases such as cancer. In this study, nanosized liposomes were designed and labeled with the radionuclides, holmium-166 (both a beta- and gamma-emitter and also highly paramagnetic) or technetium-99m, and coloaded with paramagnetic gadolinium allowing multimodality SPECT and MR imaging and radionuclide therapy with one single agent. Methods: Diethylenetriaminepentaacetic acid bisoctadecylamide (an amphiphilic molecule with a chelating group suitable for labeling with radionuclides) and gadoliniumacetylacetonate (GdAcAc) (a small lipophilic paramagnetic molecule) were incorporated in liposomes. The liposomes were characterized by measuring their mean size and size distribution, gadolinium content, and radiochemical stability after incubation in human serum at 37°C. The MRI properties (in vitro) were determined by use of relaxivity measurements at 1.5 and 3.0 Tesla in order to evaluate their potency as imaging agents. Results: The liposomes were successfully labeled with holmium-166, resulting in a high labeling efficiency (95% ± 1%) and radiochemical stability (> 98% after 48 hours of incubation), and coloaded with GdAcAc. Labeling of liposomes with technetium-99m was somewhat less efficient (85% ± 2%), although their radiochemical stability was sufficient (95% ± 1% after 6 hours of incubation). MRI measurements showed that the incorporation of GdAcAc had a strong effect on the MRI relaxivity. Conclusions: The synthesized liposomes allow for multimodality imaging and therapy, which makes these new agents highly attractive for future applications","liposomes; molecular imaging; MRI; gadolinium; holmium; SPECT; technetium","en","journal article","Mary Ann Liebert","","","","","","","","Applied Sciences","Radiation, Radionuclides and Reactors","","","",""