@article {2432, title = {Investigating the Influence of Individual Physical Effects on Dimensional Measurement Deviations Using XCT Simulations}, journal = {Measurement,}, volume = {263}, year = {2026}, doi = {https://doi.org/10.1016/j.measurement.2025.120168}, author = {Miroslav Yosifov and Thiago Linhares Fernandes and Filippo Zanini and Simone Carmignato and Jan De Beenhouwer and Jan Sijbers and Johann Kastner and Christoph Heinzl} } @article {2457, title = {Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3{\textemdash}Ex vivo imaging: Data processing, comparisons with microscopy, and tractography}, journal = {Magnetic Resonance in Medicine}, volume = {93}, year = {2025}, month = {Jan-06-2025}, pages = {2561 - 2582}, issn = {0740-3194}, doi = {10.1002/mrm.v93.610.1002/mrm.30424}, url = {https://onlinelibrary.wiley.com/toc/15222594/93/6https://onlinelibrary.wiley.com/doi/10.1002/mrm.30424https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.30424}, author = {Schilling, Kurt G. and Howard, Amy F. D. and Grussu, Francesco and Ianus, Andrada and Hansen, Brian and Barrett, Rachel L. C. and Aggarwal, Manisha and Michielse, Stijn and Nasrallah, Fatima and Syeda, Warda and Wang, Nian and Veraart, Jelle and Roebroeck, Alard and Bagdasarian, Andrew F. and Eichner, Cornelius and Sepehrband, Farshid and Zimmermann, Jan and Soustelle, Lucas and Bowman, Christien and Tendler, Benjamin C. and Hertanu, Andreea and Ben Jeurissen and Verhoye, Marleen and Frydman, Lucio and van de Looij, Yohan and Hike, David and Dunn, Jeff F. and Miller, Karla and Landman, Bennett A. and Shemesh, Noam and Anderson, Adam and McKinnon, Emilie and Farquharson, Shawna and Dell{\textquoteright}Acqua, Flavio and Pierpaoli, Carlo and Drobnjak, Ivana and Leemans, Alexander and Harkins, Kevin D. and Descoteaux, Maxime and Xu, Duan and Huang, Hao and Santin, Mathieu D. and Grant, Samuel C. and Obenaus, Andre and Kim, Gene S. and Wu, Dan and Le Bihan, Denis and Blackband, Stephen J. and Ciobanu, Luisa and Els Fieremans and Bai, Ruiliang and Leergaard, Trygve B. and Zhang, Jiangyang and Dyrby, Tim B. and Johnson, G. Allan and Cohen-Adad, Julien and Budde, Matthew D. and Jelescu, Ileana O.} } @article {2456, title = {Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2{\textemdash}Ex vivo imaging: Added value and acquisition}, journal = {Magnetic Resonance in Medicine}, volume = {93}, year = {2025}, month = {Jan-06-2025}, pages = {2535 - 2560}, issn = {0740-3194}, doi = {10.1002/mrm.v93.610.1002/mrm.30435}, url = {https://onlinelibrary.wiley.com/toc/15222594/93/6https://onlinelibrary.wiley.com/doi/10.1002/mrm.30435https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.30435}, author = {Schilling, Kurt G. and Grussu, Francesco and Ianus, Andrada and Hansen, Brian and Howard, Amy F. D. and Barrett, Rachel L. C. and Aggarwal, Manisha and Michielse, Stijn and Nasrallah, Fatima and Syeda, Warda and Wang, Nian and Veraart, Jelle and Roebroeck, Alard and Bagdasarian, Andrew F. and Eichner, Cornelius and Sepehrband, Farshid and Zimmermann, Jan and Soustelle, Lucas and Bowman, Christien and Tendler, Benjamin C. and Hertanu, Andreea and Ben Jeurissen and Verhoye, Marleen and Frydman, Lucio and van de Looij, Yohan and Hike, David and Dunn, Jeff F. and Miller, Karla and Landman, Bennett A. and Shemesh, Noam and Anderson, Adam and McKinnon, Emilie and Farquharson, Shawna and Dell{\textquoteright}Acqua, Flavio and Pierpaoli, Carlo and Drobnjak, Ivana and Leemans, Alexander and Harkins, Kevin D. and Descoteaux, Maxime and Xu, Duan and Huang, Hao and Santin, Mathieu D. and Grant, Samuel C. and Obenaus, Andre and Kim, Gene S. and Wu, Dan and Le Bihan, Denis and Blackband, Stephen J. and Ciobanu, Luisa and Els Fieremans and Bai, Ruiliang and Leergaard, Trygve B. and Zhang, Jiangyang and Dyrby, Tim B. and Johnson, G. Allan and Cohen-Adad, Julien and Budde, Matthew D. and Jelescu, Ileana O.} } @article {2455, title = {Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 1: In vivo small-animal imaging}, journal = {Magnetic Resonance in Medicine}, volume = {93}, year = {2025}, month = {Jan-06-2025}, pages = {2507 - 2534}, issn = {0740-3194}, doi = {10.1002/mrm.v93.610.1002/mrm.30429}, url = {https://onlinelibrary.wiley.com/toc/15222594/93/6https://onlinelibrary.wiley.com/doi/10.1002/mrm.30429https://onlinelibrary.wiley.com/doi/pdf/10.1002/mrm.30429}, author = {Jelescu, Ileana O. and Grussu, Francesco and Ianus, Andrada and Hansen, Brian and Barrett, Rachel L. C. and Aggarwal, Manisha and Michielse, Stijn and Nasrallah, Fatima and Syeda, Warda and Wang, Nian and Veraart, Jelle and Roebroeck, Alard and Bagdasarian, Andrew F. and Eichner, Cornelius and Sepehrband, Farshid and Zimmermann, Jan and Soustelle, Lucas and Bowman, Christien and Tendler, Benjamin C. and Hertanu, Andreea and Ben Jeurissen and Verhoye, Marleen and Frydman, Lucio and van de Looij, Yohan and Hike, David and Dunn, Jeff F. and Miller, Karla and Landman, Bennett A. and Shemesh, Noam and Anderson, Adam and McKinnon, Emilie and Farquharson, Shawna and Dell{\textquoteright}Acqua, Flavio and Pierpaoli, Carlo and Drobnjak, Ivana and Leemans, Alexander and Harkins, Kevin D. and Descoteaux, Maxime and Xu, Duan and Huang, Hao and Santin, Mathieu D. and Grant, Samuel C. and Obenaus, Andre and Kim, Gene S. and Wu, Dan and Le Bihan, Denis and Blackband, Stephen J. and Ciobanu, Luisa and Els Fieremans and Bai, Ruiliang and Leergaard, Trygve B. and Zhang, Jiangyang and Dyrby, Tim B. and Johnson, G. Allan and Cohen-Adad, Julien and Budde, Matthew D. and Schilling, Kurt G.} } @book {2458, title = {Handbook of Diffusion MR Tractography: Multishell models}, year = {2025}, pages = {201 - 220}, publisher = {Elsevier}, organization = {Elsevier}, isbn = {9780128188941}, doi = {10.1016/B978-0-12-818894-1.00008-2}, author = {Morez, Jan and De Luca, Alberto and Pietsch, Maximillian and Christiaens, Daan and Baete, Steven H. and Reisert, Marco and Ben Jeurissen} } @inproceedings {2400, title = {In-depth imaging of in-vitro tissue models using electrical impedance tomography}, booktitle = {iCT 2025 - 14th Conference on Industrial Computed Tomography}, volume = {4 - 7 February}, year = {2025}, doi = {doi.org/10.58286/30763}, author = {Jian Deng and Babu Linkoon P Meenaketan and Saeedeh Ebrahimi Takalloo and Yoke Chin Chai and Tom Torfs and Dries Braeken and Jan De Beenhouwer and Jan Sijbers} } @article {2399, title = {Loss of the Ubiquitin-Associated Domain of sqstm1/p62 in Zebrafish Causes a Phenotype Resembling Paget{\textquoteright}s Disease of Bone}, journal = {Calcified Tissue International}, volume = {116}, year = {2025}, pages = {1-15}, author = {Yentl Huybrechts and Rapha{\"e}l De Ridder and Dylan Bergen and Bjorn De Samber and Eveline Boudin and Francesca Tonelli and Dries Knapen and Lucia Vergauwen and Dorien Schepers and Evelien Van Dijck and Qiao Tong and Anja Verhulst and Jan De Beenhouwer and Jan Sijbers and Chrissy Hammond and Antonella Forlino and Geert Mortier and Paul Coucke and P Eckhard Witten and Ronald Young Kwon and Andy Willaert and Gretl Hendrickx and Wim Van Hul} } @article {2434, title = {Moisture Content Estimation of Porous Building Stones using Hyperspectral Imaging}, journal = {Scientific Data}, volume = {13}, year = {2025}, month = {Dec}, pages = {102}, abstract = {Moisture poses a major threat to built heritage through processes such as frost damage, salt crystallization and biological growth, which accelerate stone deterioration. Stone moisture content can be determined non-destructively by spectral reflectance in the shortwave infrared (SWIR) wavelength range. To validate this, large cubic and small cylindrical samples from six stone types, Brick, Euville, Massangis, Neubrunn, Obernkirchen, and Savonni{\`e}res, with different controlled moisture levels were prepared, and a comprehensive SWIR hyperspectral image dataset was created. The acquired hyperspectral images were processed using the Normalized Relative Arc Lengths (NRAL) method to generate moisture maps that illustrate the spatial distribution of water within each sample. Because moisture distribution is influenced by pore characteristics and grain arrangement, the moisture maps were validated through petrographic examination. For quantitative validation, the mean moisture content of each sample was compared with the corresponding gravimetric moisture content. The results demonstrated strong agreement between the estimated and gravimetric moisture values, with root mean square errors ranging from 1 and 2 g/g ~{\texttimes} 100.}, issn = {2052-4463}, doi = {10.1038/s41597-025-06416-4}, url = {https://doi.org/10.1038/s41597-025-06416-4}, author = {Chaghdo, Danish Ali and Koirala, Bikram and Cristina, Laura and De Kock, Tim and Fontaine, Laurent and Hayen, Roald and Paul Scheunders} } @inproceedings {2392, title = {Proximal Neural Networks based reconstruction for few-view CT applications}, booktitle = {14th Conference on Industrial Computed Tomography (iCT), 4 - 7 February 2025, Antwerp, Belgium}, year = {2025}, author = {H. Le and Caroline Bossuyt and Julie Escoda and Marius Costin and Jan De Beenhouwer and Jan Sijbers} } @inproceedings {2374, title = {Deep image prior for sparse-view reconstruction in static, rectangular multi-source x-ray CT systems for cargo scanning}, booktitle = {SPIE Developments in X-Ray Tomography XV}, volume = {13152}, year = {2024}, doi = {https://doi.org/10.1117/12.3027668}, author = {Caroline Bossuyt and Arnold Jan den Dekker and Domenico Iuso and T. Le Hoang and Julie Escoda and Marius Costin and Jan Sijbers and Jan De Beenhouwer} } @article {2459, title = {Diffusion MRI marks progressive alterations in fiber integrity in the zQ175DN mouse model of Huntington{\textquoteright}s disease}, journal = {Neurobiology of Disease}, volume = {193}, year = {2024}, month = {Jan-04-2024}, pages = {106438}, issn = {09699961}, doi = {10.1016/j.nbd.2024.106438}, author = {Vidas-Guscic, Nicholas and van Rijswijk, Jo{\"e}lle and Van Audekerke, Johan and Ben Jeurissen and Nnah, Israel and Tang, Haiying and Mu{\~n}oz-Sanjuan, Ignacio and Pustina, Dorian and Cachope, Roger and Van der Linden, Annemie and Bertoglio, Daniele and Verhoye, Marleen} } @inproceedings {2398, title = {Exploring the Potential of Hyperspectral Imaging to Estimate the Moisture Content in Natural and Historical Stones}, booktitle = {2024 14th Workshop on Hyperspectral Imaging and Signal Processing: Evolution in Remote Sensing (WHISPERS)}, year = {2024}, pages = {1-5}, keywords = {Building Physics, Cultural differences, Damage Monitoring, Estimation, Hyperspectral imaging, Moisture, Moisture content, Monitoring, Protocols, Reflectivity, Reliability, Signal processing, Water conservation}, doi = {10.1109/WHISPERS65427.2024.10876512}, author = {Chaghdo, Danish Ali and Koirala, Bikram and Cristina, Laura and Hayen, Roald and Paul Scheunders} } @article {2349, title = {Voxel-wise segmentation for porosity investigation of additive manufactured parts with 3D unsupervised and (deeply) supervised neural models}, journal = {Applied Intelligence}, volume = {54}, year = {2024}, pages = { 13160{\textendash}13177}, doi = {https://doi.org/10.1007/s10489-024-05647-z}, author = {Domenico Iuso and Soumick Chatterjee and Sven Cornelissen and Dries Verhees and Jan De Beenhouwer and Jan Sijbers} } @conference {2461, title = {Iterative model-based Rician bias correction and its application to denoising in diffusion MRI}, year = {2023}, pages = {3795}, author = {Tournier, Jacques-Donald and Ben Jeurissen and Christiaens, Daan} } @article {2402, title = {Shadow-aware nonlinear spectral unmixing with spatial regularization}, journal = {IEEE Transactions on Geoscience and Remote Sensing}, volume = {61}, year = {2023}, pages = {5517516}, author = {Guichen Zhang and Paul Scheunders and Daniele Cerra} } @article {2286, title = {Use of support vector machines approach via ComBat harmonized diffusion tensor imaging for the diagnosis and prognosis of mild traumatic brain injury: a CENTER-TBI study}, journal = {Journal of Neurotrauma}, volume = {40}, year = {2023}, pages = {1317-1338}, doi = {https://doi.org/10.1089/neu.2022.0365}, author = {Maira Siqueira Pinto and Stefan Winzeck and Evgenios N. Kornaropoulos and Sophie Richter and Roberto Paolella and Marta M. Correia and Ben Glocker and Guy Williams and Anne Vik and Jussi Posti and Asta Kristine H{\r a}berg and Jonas Stenberg and Pieter-Jan Guns and Arnold Jan den Dekker and David K. Menon and Jan Sijbers and Pieter Van Dyck and Virginia F. J. Newcombe} } @article {2212, title = {A Bottom-Up Volume Reconstruction Method for Atom Probe Tomography}, journal = {Microscopy and Microanalysis}, volume = {28}, year = {2022}, pages = {1-14}, doi = {10.1017/S1431927621012836}, author = {Yu-Ting Ling and Siegfried Cools and Janusz Bogdanowicz and Claudia Fleischmann and Jan De Beenhouwer and Jan Sijbers and Wilfried Vandervorst} } @inproceedings {2311, title = {Deep Blind Unmixing using Minimum Simplex Convolutional Network}, booktitle = {IEEE International Geoscience and Remote Sensing Symposium}, year = {2022}, month = {28/09/2022}, pages = {28-31}, abstract = {This paper proposes a deep blind hyperspectral unmixing network for datasets without pure pixels called minimum simplex convolutional network (MiSiCNet). MiSiCNet is the first deep learning-based blind unmixing method proposed in the literature which incorporates both spatial and geometrical information of the hyperspectral data, in addition to the spectral information. The proposed convolutional encoder-decoder architecture incorporates the spatial information using convolutional filters and implicitly applying a prior on the abundances. We added a minimum simplex volume penalty term to the loss function to exploit the geometrical information. We evaluate the performance of MiSiCNet on simulated and real datasets. The experimental results confirm the robustness of the proposed method to both noise and absence of pure pixels. Additionally, MiSiCNet considerably outperforms the state-of-the-art unmixing approaches. The results are given in terms of spectral angle distance in degree for the endmember estimation, and root mean square error in percentage for the abundance estimation. MiS-iCNet was implemented in Python (3.8) using PyTorch as the platform for the deep network and is available online: https://github.com/BehnoodRasti/MiSiCNet.}, doi = {10.1109/IGARSS46834.2022.9883117}, author = {Behnood Rasti and Bikram Koirala and Paul Scheunders and Jocelyn Chanussot} } @article {2193, title = {Discrete Terahertz tomography: a simulation study}, journal = {e-Journal of Nondestructive Testing}, volume = {27}, year = {2022}, issn = {1435-4934}, doi = {doi.org/10.58286/26608}, author = {Jana Christopher and Lars-Paul Lumbeeck and Pavel Paramonov and Jan De Beenhouwer and Jan Sijbers} } @article {2215, title = {The effect of prolonged Spaceflight on Cerebrospinal Fluid and Perivascular Spaces of Astronauts and Cosmonauts}, journal = {PNAS}, volume = {119}, year = {2022}, chapter = {e2120439119}, doi = {https://doi.org/10.1073/pnas.2120439119}, author = {Giuseppe Barisano and Farshid Sepehrband and Heather R. Collins and Steven Jillings and Ben Jeurissen and Andrew J. Taylor and Catho Schoenmaekers and Chloe De Laet and Ilya Rukavishnikov and Inna Nosikova and Alena Rumshiskaya and Jitka Annen and Jan Sijbers and Steven S L Laureys and Angelique Van Ombergen and Petrovichev, Victor and Valentin Sinitsyn and Ekaterina V. Pechenkova and Alexey Grishin and Peter zu Eulenburg and Meng Law and Stefan Sunaert and Paul M. Parizel and Elena Tomilovskaya and Donna Roberts and Floris L Wuyts} } @inproceedings {2209, title = {Evaluation of a Morphable Anthropomorphic Articulated Total Body Model}, booktitle = {Design Tools and Methods in Industrial Engineering II - Proceedings of the 2nd International Conference on Design Tools and Methods in Industrial Engineering, ADM 2021}, year = {2022}, pages = {761{\textendash}772}, publisher = {Springer}, organization = {Springer}, abstract = {In this work a new approach for the creation of Articulated Total Body (ATB) models for person-specific multi-body simulations is presented, with the main aim of overcoming limitations related to classical multi-ellipsoids ATB models, based on regression equations having only the weight and the height of the subject as input. The new methodology is based on a Statistical Shape Model (SSM), morphable according to up to 24 input parameters: the SSM was obtained from Principal Component Analysis (PCA), applied on a wide database of 3D human scans (CAESAR). The so obtained geometry can be segmented automatically to generate body segments with the respective inertial properties (mass, principal moments of inertia, and centres of mass location). The routine has been tested on a random set of 20 male subjects and the classical multi-ellipsoids models were compared to these in terms of inertial properties and 3D external geometry: the highest differences were registered at the abdomen and the thighs for what concerns the mass (60\%), principal moments (75\%) and centres of mass (50 mm) properties; the trunk, the shoulder and the calves are the most critical areas for the external geometry (average distance between the anthropomorphic and ellipsoids models equal to 50 mm). A contribution has been made to build person-specific multibody models. This is a valuable method since approximations made by multi-ellipsoidal models have resulted to be relevant at specific body areas, and personalised models can be a support to design and to forensic analyses.}, keywords = {3D parametric human model, Articulated total body, Forensic biomechanics, Multibody analysis, principal component analysis (PCA)}, isbn = {978-3-030-91233-8}, doi = {10.1007/978-3-030-91234-5_77}, author = {Giulia Pascoletti and Toon Huysmans and Paolo Conti and Zanetti, Elisabetta M.}, editor = {Caterina Rizzi and Francesca Campana and Michele Bici and Francesco Gherardini and Tommaso Ingrassia and Paolo Cicconi} } @inproceedings {2243, title = {Evaluation of deeply supervised neural networks for 3D pore segmentation in additive manufacturing}, booktitle = {SPIE Optical Engineering: Developments in X-Ray Tomography XIV }, volume = {12242}, year = {2022}, pages = {122421K}, doi = {https://doi.org/10.1117/12.2633318}, author = {Domenico Iuso and Soumick Chatterjee and Rob Heylen and Sven Cornelissen and Jan De Beenhouwer and Jan Sijbers} } @article {2235, title = {Improved diffusion parameter estimation by incorporating T2 relaxation properties into the DKI-FWE model}, journal = {NeuroImage}, volume = {256}, year = {2022}, pages = {119219}, doi = {https://doi.org/10.1016/j.neuroimage.2022.119219}, author = {Vincenzo Anania and Quinten Collier and Jelle Veraart and Annemieke Eline Buikema and Floris Vanhevel and Thibo Billiet and Ben Jeurissen and Arnold Jan den Dekker and Jan Sijbers} } @article {2408, title = {MiSiCNet: Minimum Simplex Convolutional Network for Deep Hyperspectral Unmixing}, journal = {IEEE Transactions on Geoscience and Remote Sensing}, volume = {60}, year = {2022}, pages = {1-15}, keywords = {Blind unmixing, convolutional neural network, Data mining, deep learning, deep prior, endmember extraction, Estimation, hyperspectral image, Hyperspectral imaging, Indexes, Libraries, Minimization, minimum simplex volume, Optimization, unmixing}, doi = {10.1109/TGRS.2022.3146904}, author = {Rasti, Behnood and Koirala, Bikram and Paul Scheunders and Chanussot, Jocelyn} } @article {2220, title = {MiSiCNet: Minimum Simplex Convolutional Network for Deep Hyperspectral Unmixing}, journal = {IEEE Transactions on Geoscience and Remote Sensing}, volume = {60}, year = {2022}, doi = {https://doi.org/10.1109/TGRS.2022.3146904}, author = {Behnood Rasti and Bikram Koirala and Paul Scheunders and Jocelyn Chanussot} } @article {2248, title = {Self-calibration of C-arm imaging system using interventional instruments during an intracranial biplane angiography.}, journal = {Int J Comput Assist Radiol Surg}, year = {2022}, month = {2022 Mar 12}, abstract = {To create an accurate 3D reconstruction of the vascular trees, it is necessary to know the exact geometrical parameters of the angiographic imaging system. Many previous studies used vascular structures to estimate the system{\textquoteright}s exact geometry. However, utilizing interventional devices and their relative features may be less challenging, as they are unique in different views. We present a semi-automatic self-calibration approach considering the markers attached to the interventional instruments to estimate the accurate geometry of a biplane X-ray angiography system for neuroradiologic use.

METHODS: A novel approach is proposed to detect and segment the markers using machine learning classification, a combination of support vector machine and boosted tree. Then, these markers are considered as reference points to optimize the acquisition geometry iteratively.

RESULTS: The method is evaluated on four clinical datasets and three pairs of phantom angiograms. The mean and standard deviation of backprojection error for the catheter or guidewire before and after self-calibration are [Formula: see text]~mm and [Formula: see text]~mm, respectively. The mean and standard deviation of the 3D root-mean-square error (RMSE) for some markers in the phantom reduced from [Formula: see text] to [Formula: see text]~mm.

CONCLUSION: A semi-automatic approach to estimate the accurate geometry of the C-arm system was presented. Results show the reduction in the 2D backprojection error as well as the 3D RMSE after using our proposed self-calibration technique. This approach is essential for 3D reconstruction of the vascular trees or post-processing techniques of angiography systems that rely on accurate geometry parameters.}, issn = {1861-6429}, doi = {10.1007/s11548-022-02580-9}, author = {Chabi, Negar and Domenico Iuso and Beuing, Oliver and Preim, Bernhard and Saalfeld, Sylvia} } @article {2258, title = {Shadow-aware nonlinear spectral unmixing for hyperspectral imagery}, journal = {IEEE-JSTARS, Journal of Selected Topics in Applied Earth Observations and Remote Sensing}, volume = {15}, year = {2022}, pages = {5514-5533}, author = {Guichen Zhang and Paul Scheunders and Daniele Cerra and Rupert Muller} } @article {2249, title = {The sqstm1tmΔUBA zebrafish model, a proof-of-concept in vivo model for Paget{\textquoteright}s disease of bone?}, journal = {Bone Reports}, volume = {16}, year = {2022}, pages = {75-76}, doi = {10.1016/j.bonr.2022.101483}, author = {Yentl Huybrechts and Rapha{\"e}l De Ridder and Bjorn De Samber and Eveline Boudin and Francesca Tonelli and Dries Knapen and Dorien Schepers and Jan De Beenhouwer and Jan Sijbers and Antonella Forlino and Paul Coucke and P. Eckhard Witten and Ronald Kwon and Andy Willaert and Gretl Hendrickx and Wim Van Hul} } @article {2079, title = {Accelerating in vivo fast spin echo high angular resolution diffusion imaging with an isotropic resolution in mice through compressed sensing}, journal = {Magnetic Resonance in Medicine}, volume = {85}, year = {2021}, pages = {1397-1413}, doi = {https://doi.org/10.1002/mrm.28520}, author = {Maarten Naeyaert and Jan Aelterman and Vladimir Golkov and Daniel Cremers and Aleksandra Pizurica and Jan Sijbers and Marleen Verhoye} } @article {2135, title = {Combination of X-ray tube and GMDH neural network as a nondestructive and potential technique for measuring characteristics of gas-oil{\textendash}water three phase flows}, journal = {Measurement}, volume = {168}, year = {2021}, chapter = {108427}, abstract = {In this investigation, a fan-beam photon attenuation based system, including one X-ray tube and two sodium iodide crystal detectors, combined with group method of data handling (GMDH) neural network is proposed to recognize type of flow regime and predict gas-oil{\textendash}water volume fractions of a three phase flow. One GMDH neural network was considered for recognizing flow patterns and two GMDH networks were implemented to predict the volume fractions. The recorded photon energy spectra from the two sodium iodide detectors were defined as the inputs of the three GMDH neural networks. The type of flow pattern and volume fractions were the output obtained from the first and the other two GMDH neural networks, respectively. Through the application of the proposed methodology, all of the flow patterns were recognized correctly except one single case. The volume fraction was also predicted with RMS error of less than 3.1.}, doi = {10.1016/j.measurement.2020.108427}, author = {Mohammadmehdi Roshani and Giang Phan and Gholam Hossein Roshani and Robert Hanus and Enrico Corniani and Ehsan Nazemi} } @article {2137, title = {Evaluation of flow pattern recognition and void fraction measurement in two phase flow independent of oil pipeline{\textquoteright}s scale layer thickness}, journal = {Alexandria Engineering Journal}, volume = {60}, year = {2021}, abstract = {The main objective of the present research is to combine the effect of scale thickness on the flow pattern and characteristics of two-phase flow that is used in oil industry. In this regard, an intelligent nondestructive technique based on combination of gamma radiation attenuation and artificial intelligence is proposed to determine the type of flow pattern and gas volume percentage in two phase flow independent of petroleum pipeline{\textquoteright}s scale layer thickness. The proposed system includes a dual energy gamma source, composed of Barium-133 and Cesium-137 radioisotopes, and two sodium iodide detectors for recording the transmitted and scattered photons. Support Vector Machine was implemented for regime identification and Multi-Layer Perceptron with Levenberg Marquardt algorithm was utilized for void fraction prediction. Total count in the scattering detector and counts under photo peaks of Barium-133 and Cesium-137 were assigned as the inputs of networks. The results show the ability of presented system to identify the annular regime and measure the void fraction independent of petroleum pipeline{\textquoteright}s scale layer thickness.}, author = {Mohammadmehdi Roshani and Giang T.T. Phan and Gholam Hossein Roshani and Robert Hanus and Trung Duong and Enrico Corniani and Ehsan Nazemi and ElMostafa Kalmouni} } @conference {2464, title = {On false positive control in Fixel-Based Analysis}, volume = {29}, year = {2021}, author = {Smith, R E and Christiaens, D and Ben Jeurissen and Pietsch, M and Vaughan, D N and Jackson, G and Tournier, J D} } @conference {2147, title = {Faster and better HARDI using FSE and holistic reconstruction}, year = {2021}, author = {Maarten Naeyaert and Vladimir Golkov and Daniel Cremers and Jan Sijbers and Marleen Verhoye} } @article {2179, title = {On the generalizability of diffusion MRI signal representations across acquisition parameters, sequences and tissue types: chronicles of the MEMENTO challenge}, journal = {NeuroImage}, volume = {240}, year = {2021}, doi = {https://doi.org/10.1016/j.neuroimage.2021.118367}, author = {Alberto De Luca and Andrada Ianus and Alexander Leemans and Marco Palombo and Noam Shemesh and Hui Zhang and Daniel C Alexander and Markus Nilsson and Martijn Froeling and Geert-Jan Biessels and Mauro Zucchelli and Matteo Frigo and Enes Albay and Sara Sedlar and Abib Alimi and Samuel Deslauriers-Gauthier and Rachid Deriche and Rutger Fick and Maryam Afzali and Tomasz Pieciak and Fabian Bogusz and Santiago Aja-Fernandez and Evren Ozarslan and Derek K. Jones and Haoze Chen and Mingwu Jin and Zhijie Zhang and Fenxiang Wang and Vishwesh Nath and Prasanna Parvathaneni and Jan Morez and Jan Sijbers and Ben Jeurissen and Shreyas and Fadnavis and Stefan Endres and Ariel Rokem and Eleftherios Garyfallidis and Irina Sanchez and Vesna Prchkovska and Paulo Rodrigues and Bennet A. Landman and Kurt G Schilling} } @conference {2174, title = {Outcome prediction in Mild Traumatic Brain Injury patients using conventional and diffusion MRI via Support Vector Machine: A CENTER-TBI study}, year = {2021}, author = {Maira Siqueira Pinto and Stefan Winzeck and Marta M. Correia and Evgenios N. Kornaropoulos and David K. Menon and Ben Glocker and Arnold Jan den Dekker and Jan Sijbers and Pieter-Jan Guns and Pieter Van Dyck and Virginia F. J. Newcombe} } @conference {2185, title = {Outcome prediction of mild traumatic brain injury using support vector machine based on longitudinal MRdiffusion imaging from CENTER-TBI}, volume = {34}, year = {2021}, pages = {S54}, doi = {10.1007/s10334-021-00947-8}, author = {Maira Siqueira Pinto and Stefan Winzeck and S. Richter and Marta M. Correia and Evgenios N. Kornaropoulos and David K. Menon and Ben Glocker and Pieter-Jan Guns and Arnold Jan den Dekker and Jan Sijbers and Virginia F. J. Newcombe and Pieter Van Dyck} } @inproceedings {2169, title = {Recurrent Inference Machines as Inverse Problem Solvers for MR Relaxometry}, booktitle = { MIDL 2021 - Medical Imaging with Deep Learning}, year = {2021}, author = {Emanoel Ribeiro Sabidussi and Matthan Caan and Shabab Bazrafkan and Arnold Jan den Dekker and Jan Sijbers and Wiro J Niessen and Dirk H J Poot} } @article {2190, title = {Recurrent Inference Machines as inverse problem solvers for MR relaxometry}, journal = {Medical Image Analysis}, volume = {74}, year = {2021}, pages = {1-11}, doi = {https://doi.org/10.1016/j.media.2021.102220}, author = {Emanoel Ribeiro Sabidussi and Stefan Klein and Matthan Caan and Shabab Bazrafkan and Arnold Jan den Dekker and Jan Sijbers and Wiro J Niessen and Dirk H J Poot} } @article {2136, title = {Application of GMDH neural network technique to improve measuring precision of a simplified photon attenuation based two-phase flowmeter}, journal = {Flow Measurement and Instrumentation}, volume = {75}, year = {2020}, abstract = {Multiphase flowmeters have an important role to play in the industry and any attempts that lead to improvements in this field are of great interest. In the current study, group method of data handling (GMDH) technique was applied in order to increase measuring precision of a simple photon attenuation based two-phase flowmeter that has the ability to estimate the gas volumetric percentage in a two-phase flow without any dependency to flow regime pattern. The simple photon attenuation based system is comprised of a cobalt-60 radioisotope and only one 25.4 mm {\texttimes} 25.4 mm sodium iodide crystal detector. Four extracted features from recorded photon spectrum in sodium iodide crystal detector were used as the inputs of GMDH neural network. Equations related to the combination of the features and the error rate of each approximation is also reported in this paper. Applying the mentioned technique, the gas volumetric percentage in an oil-gas two phase flow was determined with the root mean square error of less than 2.71 without any dependency to the flow pattern. The obtained measuring precision in this study is at least 2.1 times better than reported in previous studies.}, doi = {10.1016/j.flowmeasinst.2020.101804}, author = {Mohammadmehdi Roshani and Mohammad Amir Sattari and Peshawa Jammal Muhammad Ali and Gholam Hossein Roshani and Enrico Corniani and Ehsan Nazemi} } @article {1956, title = {The costs and benefits of estimating T1 of tissue alongside cerebral blood flow and arterial transit time in pseudo-continuous arterial spin labeling}, journal = {NMR in Biomedicine}, volume = {33}, year = {2020}, pages = {1-17}, doi = {https://doi.org/10.1002/nbm.4182}, author = {Piet Bladt and Arnold Jan den Dekker and Clement, Patricia and Eric Achten and Jan Sijbers} } @article {2058, title = {Deep neural network and data augmentation methodology for off-axis iris segmentation in wearable headsets}, journal = {Science Direct Elsevier Neural Networks}, volume = {121}, year = {2020}, month = {01/2020}, pages = {101-121}, chapter = {101-121}, doi = {https://doi.org/10.1016/j.neunet.2019.07.020}, url = {https://www.sciencedirect.com/science/article/pii/S0893608019302163?via\%3Dihub$\#$!}, author = {Viktor Varkarakis and Shabab Bazrafkan and Peter Corcoran} } @article {2016, title = {Effect of sample preparation techniques upon single cell chemical imaging: A practical comparison between synchrotron radiation based X-ray fluorescence (SR-XRF) and Nanoscopic Secondary Ion Mass Spectrometry (nano-SIMS)}, journal = {Analytica Chimica Acta}, volume = {1106}, year = {2020}, pages = {22-32}, abstract = {Analytical capabilities of Nanoscopic Secondary Ion Mass Spectrometry (nano-SIMS) and Synchrotron Radiation based X-ray Fluorescence (SR nano-XRF) techniques were compared for nanochemical imaging of polymorphonuclear human neutrophils (PMNs). PMNs were high pressure frozen (HPF), cryosubstituted, embedded in Spurr{\textquoteright}s resin and cut in thin sections (500 nm and 2 mm for both techniques resp.) Nano-SIMS enabled nanoscale mapping of isotopes of C, N, O, P and S, while SR based nano-XRF enabled trace level imaging of metals like Ca, Mn, Fe, Ni, Cu and Zn at a resolution of approx. 50 nm. The obtained elemental distributions were compared with those of whole, cryofrozen PMNs measured at the newly developed ID16A nano-imaging beamline at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. Similarities were observed for elements more tightly bound to the cell structure such as phosphorus and sulphur, while differences for mobile ions such as chlorine and potassium were more pronounced. Due to the observed elemental redistribution of mobile ions such as potassium and chlorine, elemental analysis of high pressure frozen (HPF), cryo-substituted and imbedded cells should be interpreted critically. Although decreasing analytical sensitivity occurs due to the presence of ice, analysis of cryofrozen cells - close to their native state - remains the golden standard. In general, we found nanoscale secondary ion mass spectrometry (nano-SIMS) and synchrotron radiation based nanoscopic X-ray fluorescence (SR nano-XRF) to be two supplementary alternatives for nanochemical imaging of single cells at the nanoscale.}, doi = {10.1016/j.aca.2020.01.054}, author = {Bjorn De Samber and Riet De Rycke and Michiel De Bruyne and Michiel Kienhuis and Linda Sandblad and Sylvain Bohic and Peter Cloetens and Constantin Urban and Lubos Polerecky and Laszlo Vincze} } @article {2134, title = {Proposing a gamma radiation based intelligent system for simultaneous analyzing and detecting type and amount of petroleum by-products}, journal = {Nuclear Engineering and Technology}, year = {2020}, type = {Research regular paper}, abstract = {It is important for operators of poly-pipelines in petroleum industry to continuously monitor characteristics of transferred fluid such as its type and amount. To achieve this aim, in this study a dual energy gamma attenuation technique in combination with artificial neural network (ANN) is proposed to simultaneously determine type and amount of four different petroleum by-products. The detection system is composed of a dual energy gamma source, including americium-241 and barium-133 radioisotopes, and one 2.54 cm {\texttimes} 2.54 cm sodium iodide detector for recording the transmitted photons. Two signals recorded in transmission detector, namely the counts under photo peak of Americium-241 with energy of 59.5 keV and the counts under photo peak of Barium-133 with energy of 356 keV, were applied to the ANN as the two inputs and volume percentages of petroleum by-products were assigned as the outputs.}, author = {Mohammadmehdi Roshani and Giang Phan and Rezhna Hassan Faraj and Nhut-Huan Phan and Gholam Hossein Roshani and Enrico Corniani and Ehsan Nazemi} } @article {2051, title = {Supporting measurements or more averages? How to quantify cerebral blood flow most reliably in 5 minutes by arterial spin labeling}, journal = {Magnetic Resonance in Medicine}, volume = {84}, year = {2020}, pages = {2523-2536}, doi = {10.1002/mrm.28314}, author = {Piet Bladt and M.J.P van Osch and Clement, Patricia and Eric Achten and Jan Sijbers and Arnold Jan den Dekker} } @article {1964, title = {Alterations of Functional Brain Connectivity After Long-Duration Spaceflight as Revealed by fMRI.}, journal = {Front Physiol}, volume = {10}, year = {2019}, pages = {1-23}, abstract = {

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

}, issn = {1664-042X}, doi = {10.3389/fphys.2019.00761}, author = {Pechenkova, Ekaterina and Nosikova, Inna and Rumshiskaya, Alena and Litvinova, Liudmila and Rukavishnikov, Ilya and Mershina, Elena and Valentin Sinitsyn and Angelique Van Ombergen and Ben Jeurissen and Steven Jillings and Laureys, Steven and Jan Sijbers and Grishin, Alexey and Chernikova, Ludmila and Naumov, Ivan and Kornilova, Ludmila and Floris L Wuyts and Tomilovskaya, Elena and Kozlovskaya, Inessa} } @inproceedings {1854, title = {An Articulating Statistical Shape Model of the Human Hand}, booktitle = {Advances in Human Factors in Simulation and Modeling (AHFE 2018)}, volume = {780}, year = {2019}, pages = {433{\textendash}445}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {This paper presents a registration framework for the construction of a statistical shape model of the human hand in a standard pose. It brings a skeletonized reference model of an individual human hand into correspondence with optical 3D surface scans of hands by sequentially applying articulation-based registration and elastic surface registration. Registered surfaces are then fed into a statistical shape modelling algorithm based on principal component analysis. The model-building technique has been evaluated on a dataset of optical scans from 100 healthy individuals, acquired with a 3dMD scanning system. It is shown that our registration framework provides accurate geometric and anatomical alignment, and that the shape basis of the resulting statistical model provides a compact representation of the specific population. The model also provides insight into the anatomical variation of the lower arm and hand, which is useful information for the design of well-fitting products.}, isbn = {978-3-319-94223-0}, doi = {10.1007/978-3-319-94223-0_41}, author = {Jeroen Van Houtte and Kristina Stankovi{\'c} and Brian G Booth and Femke Danckaers and Bertrand, V{\'e}ronique and Frederik Verstreken and Jan Sijbers and Toon Huysmans}, editor = {Cassenti, Daniel N.} } @inproceedings {1852, title = {Automatic Generation of Statistical Shape Models in Motion}, booktitle = {Advances in Human Factors in Simulation and Modeling (AHFE 2018)}, volume = {780}, year = {2019}, pages = {170{\textendash}178}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {Statistical body shape modeling (SBSM) is a well-known technique to map out the variability of body shapes and is commonly used in 3D anthropometric analyses. In this paper, a new approach to integrate movement acquired by a motion capture system with a body shape is proposed. This was done by selecting landmarks on a body shape model, and predicting a body shape based on features. Then, a virtual skeleton was generated relative to those landmarks. This skeleton was parented to a body shape, allowing to modify its pose and to add pre-recorded motion to different body shapes in a realistic way.}, isbn = {978-3-319-94223-0}, doi = {10.1007/978-3-319-94223-0_16}, author = {Femke Danckaers and Scataglini, Sofia and Haelterman, Robby and Van Tiggelen, Damien and Toon Huysmans and Jan Sijbers}, editor = {Cassenti, Daniel N.} } @article {1962, title = {Cognitive Training in Young Patients With Traumatic Brain Injury: A Fixel-Based Analysis.}, journal = {Neurorehabil Neural Repair}, year = {2019}, month = {2019 Aug 16}, abstract = {Traumatic brain injury (TBI) is associated with altered white matter organization and impaired cognitive functioning. We aimed to investigate changes in white matter and cognitive functioning following computerized cognitive training. Sixteen adolescents with moderate-to-severe TBI (age 15.6 {\textpm} 1.8 years, 1.2-4.6 years postinjury) completed the 8-week BrainGames program and diffusion weighted imaging (DWI) and cognitive assessment at time point 1 (before training) and time point 2 (after training). Sixteen healthy controls (HC) (age 15.6 {\textpm} 1.8 years) completed DWI assessment at time point 1 and cognitive assessment at time point 1 and 2. Fixel-based analyses were used to examine fractional anisotropy (FA), mean diffusivity (MD), and fiber cross-section (FC) on a whole brain level and in tracts of interest. Patients with TBI showed cognitive impairments and extensive areas with decreased FA and increased MD together with an increase in FC in the body of the corpus callosum and left superior longitudinal fasciculus (SLF) at time point 1. Patients improved significantly on the inhibition measure at time point 2, whereas the HC group remained unchanged. No training-induced changes were observed on the group level in diffusion metrics. Exploratory correlations were found between improvements on verbal working memory and reduced MD of the left SLF and between increased performance on an information processing speed task and increased FA of the right precentral gyrus. Results are indicative of positive effects of BrainGames on cognitive functioning and provide preliminary evidence for neuroplasticity associated with cognitive improvements following cognitive intervention in TBI.}, issn = {1552-6844}, doi = {10.1177/1545968319868720}, author = {Verhelst, Helena and Diana Giraldo and Vander Linden, Catharine and Vingerhoets, Guy and Ben Jeurissen and Caeyenberghs, Karen} } @inproceedings {1851, title = {Latent Heat Loss of a Virtual Thermal Manikin for Evaluating the Thermal Performance of Bicycle Helmets}, booktitle = {Advances in Human Factors in Simulation and Modeling}, year = {2019}, pages = {66{\textendash}78}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {Thermal performance of three bicycle helmets for latent heat loss was evaluated through a virtual testing methodology using Computational fluid dynamics (CFD) simulations. The virtual thermal manikin was prescribed with a constant sweat rate of 2~g/h and a constant sweat film thickness of 0.3~mm. The simulations were carried out at 6~m/s until convergence was achieved. The results from steady state simulations show heat loss of 158~W from manikin without helmet and approximately 135~W with helmets. However, the thermal performance of helmets with a sweating manikin has been reduced from 89{\textendash}93{\%} to 84{\textendash}87{\%}. These results imply that evaporative/latent heat loss plays a significant role in thermal performance of helmets. Therefore, thermal performance tests for helmets should also include testing of helmets for evaporative heat loss.}, isbn = {978-3-319-94223-0}, author = {Mukunthan, Shriram and Jochen Vleugels and Toon Huysmans and Guido De Bruyne}, editor = {Cassenti, Daniel N.} } @article {1963, title = {MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation.}, journal = {Neuroimage}, year = {2019}, month = {2019 Aug 29}, pages = {116137}, abstract = {

MRtrix3 is an open-source, cross-platform software package for medical image processing, analysis and visualization, with a particular emphasis on the investigation of the brain using diffusion MRI. It is implemented using a fast, modular and flexible general-purpose code framework for image data access and manipulation, enabling efficient development of new applications, whilst retaining high computational performance and a consistent command-line interface between applications. In this article, we provide a high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software.

}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2019.116137}, author = {Tournier, J-Donald and Smith, Robert and Raffelt, David and Tabbara, Rami and Dhollander, Thijs and Pietsch, Maximilian and Christiaens, Daan and Ben Jeurissen and Yeh, Chun-Hung and Connelly, Alan} } @article {1987, title = {A supervised method for nonlinear hyperspectral unmixing}, journal = {Remote Sensing}, volume = {11}, year = {2019}, month = {10/2019}, abstract = {Due to the complex interaction of light with the Earth surface, reflectance spectra can be described as highly nonlinear mixtures of the reflectances of the material constituents occuring in a given resolution cell of hyperspectral data. Our aim is to estimate the fractional abundance maps of the materials from the nonlinear hyperspectral data. The main disadvantage of using nonlinear mixing models is that the model parameters are not properly interpretable in terms of fractional abundances. Moreover, not all spectra of a hyperspectral dataset necessarily follow the same particular mixing model. In this work, we present a supervised method for nonlinear spectral unmixing. The method learns a mapping from a true hyperspectral dataset to corresponding linear spectra, composed of the same fractional abundances. A simple linear unmixing then reveals the fractional abundances. To learn this mapping, ground truth information is required, in the form of actual spectra and corresponding fractional abundances, along with spectra of the pure materials, obtained from a spectral library or available in the dataset. Three methods are presented for learning the nonlinear mapping, based on gaussian processes, kernel ridge regression, and feedforward neural networks. Experimental results conducted on an artificial dataset, a data set obtained by ray tracing, and a drill core hyperspectral dataset show that this novel methodology is very promising.}, doi = {https://doi.org/10.3390/rs11202458}, url = {https://www.mdpi.com/2072-4292/11/20/2458}, author = {Bikram Koirala and Mahdi Khodadadzadeh and Cecilia Contreras and Zohreh Zahiri and Richard Gloaguen and Paul Scheunders} } @conference {1980, title = {A Trajectory Based Bottom-Up Volume Reconstruction Method for Atom Probe Tomography}, year = {2019}, author = {Yu-Ting Ling and Siegfried Cools and Jan De Beenhouwer and Jan Sijbers and Wilfried Vandervorst} } @conference {1995, title = {Absolute CBF quantification in multi-time point ASL: the T1 issue}, year = {2018}, author = {Piet Bladt and Arnold Jan den Dekker and Clement, Patricia and Eric Achten and Jan Sijbers} } @article {1820, title = {Diffusion kurtosis imaging with free water elimination: a Bayesian estimation approach}, journal = {Magnetic Resonance in Medicine}, volume = {80}, year = {2018}, pages = {802-813}, doi = {10.1002/mrm.27075}, author = {Quinten Collier and Jelle Veraart and Ben Jeurissen and Floris Vanhevel and Pim Pullens and Paul M Parizel and Arnold Jan den Dekker and Jan Sijbers} } @article {1872, title = {Enhanced contrast in X-ray microtomographic images of the membranous labyrinth using different X-ray sources and scanning modes}, journal = {Journal of Anatomy}, volume = {233}, year = {2018}, pages = {770--782}, doi = {doi: 10.1111/joa.12885}, author = {Jana Goyens and Menelia Vasilopoulou-Kampitsi and Raf Claes and Jan Sijbers and Lucia Mancini} } @article {1791, title = {IntensityPatches and RegionPatches for Image Recognition}, journal = {Applied Soft Computing}, volume = {62}, year = {2018}, pages = {176-186}, doi = {https://doi.org/10.1016/j.asoc.2017.09.046}, url = {http://www.sciencedirect.com/science/article/pii/S1568494617305859}, author = {Tiago B. A. de Carvalho and Maria A. Sibaldo and Ing Jyh Tsang and George D C Cavalcanti and Jan Sijbers and Ing Ren Tsang} } @article {1902, title = {Noise reduction in hyperspectral imagery: overview and application}, journal = {Remote Sensing }, volume = {10}, year = {2018}, pages = {482}, author = {B Rasti and Paul Scheunders and P Ghesami and G Licciardi and Jocelyn Chanussot} } @mastersthesis {1911, title = {Robust estimation of diffusion tensor and diffusion kurtosis imaging parameters}, volume = {PhD in Sciences/Physics}, year = {2018}, month = {Oct/2018}, school = {University of Antwerp}, type = {PhD thesis}, address = {Antwerp}, author = {Quinten Collier} } @article {1786, title = {The role of whole-brain diffusion MRI as a tool for studying human in vivo cortical segregation based on a measure of neurite density}, journal = {Magnetic Resonance in Medicine}, volume = {79}, year = {2018}, pages = {2738{\textendash}2744}, keywords = {Brain, cortex, Diffusion MRI, fiber orientation distribution, myeloarchitecture, parcellation}, issn = {1522-2594}, doi = {10.1002/mrm.26917}, url = {http://dx.doi.org/10.1002/mrm.26917}, author = {Fernando Calamante and Ben Jeurissen and Robert Elton Smith and Tournier, Jacques-Donald and Connelly, Alan} } @article {1903, title = {A simple computer vision pipeline reveals the effects of isolation on social interaction dynamics in Drosophila}, journal = {Plos Computational Biology}, volume = {14}, year = {2018}, pages = {e1006410}, author = {G Liu and Tanmay Nath and Z Guo and G Linneweber and A Claeys and J Li and M Bengochea and Steve De Backer and Barbara Weyn and M Sneyders and H Nicasy and P Yu and Paul Scheunders and Bassem Hassan} } @article {1792, title = {TomoBank: A Tomographic Data Repository for Computational X-ray Science}, journal = {Measurement Science and Technology}, volume = {29}, year = {2018}, pages = {1-10}, doi = {https://doi.org/10.1088/1361-6501/aa9c19}, author = {Francesco De Carlo and Doga Gursoy and Daniel Ching and Kees Joost Batenburg and Ludwig, Wolfgang and Lucia Mancini and Federica Marone Welford and Rajmund Mokso and Daan Pelt and Jan Sijbers and Mark Rivers} } @article {1824, title = {White matter microstructural organization of interhemispheric pathways predicts different stages of bimanual coordination learning in young and older adults}, journal = {European Journal of Neuroscience }, volume = {47}, year = {2018}, pages = {446{\textendash}459}, doi = {10.1111/ejn.13841}, author = {Hamed Zivari Adab and Sima Chalavi and Iseult Beets and Jolien Gooijers and Inge Leunissen and Boris Cheval and Quinten Collier and Jan Sijbers and Ben Jeurissen and S. P. Swinnen and Matthieu Boisgontier} } @article {1915, title = {The arcuate fasciculus network and verbal deficits in psychosis}, journal = {Translational Neuroscience}, volume = {8}, year = {2017}, month = {Feb-11-2017}, pages = {117-126}, doi = {10.1515/tnsci-2017-0018}, author = {Kenney, Joanne P.M. and McPhilemy, Genevieve and Scanlon, Cathy and Najt, Pablo and McInerney, Shane and Arndt, Sophia and Scherz, Elisabeth and Byrne, Fintan and Alexander Leemans and Ben Jeurissen and Hallahan, Brian and McDonald, Colm and Cannon, Dara M.} } @article {1789, title = {Can portable tomosynthesis improve the diagnostic value of bedside chest X-ray in the intensive care unit? A proof of concept study}, journal = {European Radiology Experimental}, volume = {1}, year = {2017}, pages = {1-7}, doi = {10.1186/s41747-017-0021-6}, author = {Jeroen Cant and Annemie Snoeckx and Gert Behiels and Paul M Parizel and Jan Sijbers} } @article {1766, title = { Exploring sex differences in the adult zebra finch brain: In vivo diffusion tensor imaging and ex vivo super-resolution track density imaging}, journal = {NeuroImage}, volume = {146}, year = {2017}, pages = {789-803}, doi = {10.1016/j.neuroimage.2016.09.067}, author = {Hamaide, Julie and G. De Groof and Gwendolyn Van Steenkiste and Ben Jeurissen and Johan Van Audekerke and Maarten Naeyaert and Van Ruijssevelt, Lisbeth and Cornil, Charlotte and Jan Sijbers and Marleen Verhoye and Annemie Van Der Linden} } @article {1761, title = {Inline Discrete Tomography system: application to agricultural product inspection}, journal = {Computers and Electronics in Agriculture}, volume = {138}, year = {2017}, pages = {117{\textendash}126}, doi = {https://doi.org/10.1016/j.compag.2017.04.010}, author = {Luis Filipe Alves Pereira and Eline Janssens and George D C Cavalcanti and Ing Ren Tsang and Mattias Van Dael and Pieter Verboven and Bart Nicolai and Jan Sijbers} } @mastersthesis {1738, title = {Iterative reconstruction for mobile chest tomosynthesis}, volume = {PhD in Sciences/Physics}, year = {2017}, type = {PhD thesis}, author = {Jeroen Cant} } @conference {1996, title = {Maximizing precision in PCASL MRI using an optimized sampling strategy}, year = {2017}, author = {Piet Bladt and Arnold Jan den Dekker and Clement, Patricia and Eric Achten and Jan Sijbers} } @conference {1997, title = {Optimal sampling strategy for pseudo-continuous arterial spin labeling MRI}, year = {2017}, author = {Piet Bladt and Arnold Jan den Dekker and Clement, Patricia and Eric Achten and Jan Sijbers} } @conference {1764, title = {Solving the Free Water Elimination Estimation Problem by Incorporating T2 Relaxation Properties}, year = {2017}, author = {Quinten Collier and Jelle Veraart and Arnold Jan den Dekker and Floris Vanhevel and Paul M Parizel and Jan Sijbers} } @conference {1818, title = {Statistically optimal separation of multi-component MR signals with a Majorize-Minimize approach: application to MWF estimation}, year = {2017}, author = {Gabriel Ramos-Llord{\'e}n and Arnold Jan den Dekker and Piet Bladt and A. Cuyt and Jan Sijbers} } @article {1644, title = {3D morphometric analysis of the human incudomallear complex using clinical cone-beam CT}, journal = {Hearing research}, volume = {340}, year = {2016}, pages = {79-88}, abstract = {Human middle ears show large morphological variations. This could affect our perception of hearing and explain large variation in experimentally obtained transfer functions. Most morphological studies focus on capturing variation by using landmarks on cadaveric temporal bones. We present statistical shape analysis based on clinical cone beam CT (CBCT) scans of 100 patients. This allowed us to include surface information on the incudomallear (IM) complex (joint, ligaments and tendon not included) of 123 healthy ears with a scanning resolution of 150~μm and without a priori assumptions. Statistical shape modeling yields an average geometry for the IM complex and the variations present in the population with a high precision. Mean values, variation and correlations among anatomical features (length of manubrium, combined length of malleus head and neck, lengths of incus long and short process, enclosing angles, ossicular lever ratio, incudomallear angle, and principal moments of inertia) are reported and compared to results from the literature. Most variation is found in overall size and the angle between incus and malleus. The compact representation provided by statistical shape modeling is demonstrated and its benefits for surface modeling are discussed.}, issn = {1878-5891}, doi = {10.1016/j.heares.2016.01.014}, author = {Joris Soons and Femke Danckaers and Keustermans, William and Toon Huysmans and Jan Sijbers and Casselman, Jan W and Joris J. J. Dirckx} } @inproceedings {1691, title = {Automatic geometric calibration of chest tomosynthesis using data consistency conditions}, booktitle = {The 4th International Conference on Image Formation in X-Ray Computed Tomography}, year = {2016}, pages = {161-164}, address = {Salt Lake City, Utah, USA}, author = {Jeroen Cant and Gert Behiels and Jan Sijbers} } @article {1683, title = {Chronic exposure to haloperidol and olanzapine leads to common and divergent shape changes in the rat hippocampus in the absence of grey-matter volume loss}, journal = {Psychological Medicine}, volume = {46}, year = {2016}, pages = {3081-3093}, doi = {10.1017/S0033291716001768}, author = {William R Crum and Femke Danckaers and Toon Huysmans and Marie-Caroline Cotel and Sridhar Natesan and Michel M. Modo and Jan Sijbers and Steven C.R. Williams and Shitij Kapur and Anthony C. Vernon} } @article {1716, title = {Computerized Tomographic Image Exposure and Reconstruction Method}, number = {PCT/EP2015/059956}, year = {2016}, abstract = {A method to improve reconstruction quality for continuous projections. The use of continuous projection might be advantageous to use cheaper panels and simpler setups for tomosynthesis and CT reconstruction.}, author = {Jeroen Cant and Jan Sijbers} } @inproceedings {1669, title = {Continuous Digital Laminography}, booktitle = {6th Conference on Industrial Computed Tomography}, year = {2016}, address = {Wels, Austria}, url = {http://www.ndt.net/article/ctc2016/papers/ICT2016_paper_id42.pdf}, author = {Jeroen Cant and Gert Behiels and Jan Sijbers} } @inproceedings {1652, title = {Discrete tomographic reconstruction from deliberately motion blurred X-ray projections}, booktitle = {6th Conference on Industrial Computed Tomography}, year = {2016}, pages = {1-6}, address = {Wels, Austria}, author = {Wim Van Aarle and Jeroen Cant and Jan De Beenhouwer and Jan Sijbers} } @article {1892, title = {EPR and DFT analysis of biologically relevant chromium(V) complexes with d-glucitol and d-glucose}, journal = {Journal of Inorganic Biochemistry}, volume = {162}, year = {2016}, pages = {216 - 226}, keywords = {1, 2-diolato ligands, DFT, ENDOR, EPR, HYSCORE, Oxidochromium(V)}, issn = {0162-0134}, doi = {https://doi.org/10.1016/j.jinorgbio.2016.07.012}, url = {http://www.sciencedirect.com/science/article/pii/S0162013416302136}, author = {Sabine Van Doorslaer and Quinten Beirinckx and Kevin Nys and Mar{\'\i}a Florencia Mangiameli and Bert Cuypers and Freddy Callens and Henk Vrielinck and Juan Carlos Gonz{\'a}lez} } @article {1701, title = {Fast and Flexible X-ray Tomography Using the ASTRA Toolbox}, journal = {Optics Express}, volume = {24}, number = {22}, year = {2016}, pages = {25129-25147}, doi = {10.1364/OE.24.025129}, author = {Wim Van Aarle and Willem Jan Palenstijn and Jeroen Cant and Eline Janssens and Folkert Bleichrodt and Andrei Dabravolski and Jan De Beenhouwer and Kees Joost Batenburg and Jan Sijbers} } @inproceedings {1663, title = {Fast X-ray Computed Tomography via Image Completion}, booktitle = {6th Conference on Industrial Computed Tomography(iCT)}, year = {2016}, pages = {1-5}, address = {Wels, Austria}, author = {Luis Filipe Alves Pereira and Eline Janssens and Mattias Van Dael and Pieter Verboven and Bart Nicolai and George D C Cavalcanti and Ing Jyh Tsang and Jan Sijbers} } @conference {Kenney2016-ju, title = {Lateralisation of the arcuate fasciculus in psychosis \& the role in verbal learning \& auditory verbal hallucinations}, volume = {26}, year = {2016}, pages = {S76{\textendash}S77}, publisher = {Elsevier Science Bv}, address = {Po Box 211, 1000 Ae Amsterdam, Netherlands}, author = {Kenney, J and McInerney, S and McPhilemy, G and Najt, P and Scanlon, C and Arndt, S and Scherz, E and Byrne, F and Leemans, A and Ben Jeurissen and Donohoe, G and Hallahan, B and McDonald, C and Cannon, D} } @inproceedings {1810, title = {Lidar information extraction by attribute filters with partial reconstruction}, booktitle = {IEEE IGARSS 2016, International Geoscience and Remote Sensing Symposium, pp. 1484-1487, Beijing, July 10-15 }, year = {2016}, doi = {10.1109/IGARSS.2016.7729379}, author = {Wenzhi Liao and M Della Mura and X Huang and Jocelyn Chanussot and S Gautama and Paul Scheunders and Wilfried Philips} } @article {1781, title = {Method and system for correcting geometric misalignment during image reconstruction in chest tomosynthesis}, number = {EP16173767.1}, year = {2016}, abstract = {A method to find panel misalignment. Necessary when exact panel position is unknown.}, issn = {EP16173767.1}, author = {Jeroen Cant and Jan Sijbers} } @article {kenney2016p, title = {P. 3.033 Lateralisation of the arcuate fasciculus in psychosis \& the role in verbal learning \& auditory verbal hallucinations}, journal = {European Neuropsychopharmacology}, volume = {26}, year = {2016}, pages = {S76{\textendash}S77}, author = {Kenney, J and McInerney, S and McPhilemy, G and Najt, P and Scanlon, C and Arndt, S and Scherz, E and Byrne, F and Alexander Leemans and Ben Jeurissen and G Donohoe and B Hallahan and C McDonald and D Cannon} } @inproceedings {1710, title = {Pixel clustering for face recognition}, booktitle = {5th Brazilian Conference on Intelligent Systems}, year = {2016}, pages = {121-126}, address = {Brazil}, doi = {https://doi.org/10.1109/BRACIS.2016.032}, author = {Tiago B. A. de Carvalho and Maria A. A. Sibaldo and Ing Ren Tsang and George D C Cavalcanti and Ing Jyh Tsang and Jan Sijbers} } @conference {Collier2016-tu, title = {Robust DKI Parameter Estimation in Case of CSF Partial Volume Effects}, year = {2016}, pages = {1044}, author = {Collier, Quinten and Arnold Jan den Dekker and Ben Jeurissen and Jan Sijbers} } @conference {1672, title = {Robust DKI parameter estimation in case of CSF partial volume effects}, year = {2016}, abstract = {Diffusion kurtosis imaging (DKI) suffers from partial volume effects caused by cerebrospinal fluid (CSF). We propose a DKI+CSF model combined with a framework to robustly estimate the DKI parameters. Since the estimation problem is ill-conditioned, a Bayesian estimation approach with a shrinkage prior is incorporated. Both simulation and real data experiments suggest that the use of this prior leads to a more accurate, precise and robust estimation of the DKI+CSF model parameters. Finally, we show that not correcting for the CSF compartment can lead to severe biases in the parameter estimations.}, author = {Quinten Collier and Arnold Jan den Dekker and Ben Jeurissen and Jan Sijbers} } @conference {1671, title = {A robust framework for combined estimation of DKI and CSF partial volume fraction parameters}, year = {2016}, abstract = {Diffusion kurtosis imaging (DKI) suffers from partial volume effects caused by cerebrospinal fluid (CSF). We propose a DKI+CSF model combined with a framework to robustly estimate the DKI parameters. Since the estimation problem is ill-conditioned, a Bayesian estimation approach with a shrinkage prior is incorporated. Both simulation and real data experiments suggest that the use of this prior leads to a more accurate, precise and robust estimation of the DKI+CSF model parameters. Finally, we show that not correcting for the CSF compartment can lead to severe biases in the parameter estimations.}, author = {Quinten Collier and Arnold Jan den Dekker and Ben Jeurissen and Jan Sijbers} } @article {1612, title = {A segmentation and classification algorithm for online detection of internal disorders in citrus using X-ray radiographs}, journal = {Postharvest Biology and Technology}, volume = {112}, year = {2016}, pages = {205-214}, doi = {10.1016/j.postharvbio.2015.09.020}, author = {Mattias Van Dael and S Lebotsa and E Herremans and Pieter Verboven and Jan Sijbers and U. L. Opara and U. L. Cronje and Bart Nicolai} } @article {1648, title = {Unsupervised Retinal Vessel Segmentation Using Combined Filters}, journal = {Plos One}, volume = {11}, number = {2}, year = {2016}, pages = {1-21}, doi = {10.1371/journal.pone.0149943}, author = {Wendeson S. Oliveira and Joyce Vitor Teixeira and Ing Ren Tsang and George D C Cavalcanti and Jan Sijbers} } @article {1634, title = {Abnormal wiring of the connectome in adults with high-functioning autism spectrum disorder}, journal = {Molecular Autism}, volume = {6}, number = {1}, year = {2015}, pages = {65}, abstract = {Recent brain imaging findings suggest that there are widely distributed abnormalities affecting the brain connectivity in individuals with autism spectrum disorder (ASD). Using graph theoretical analysis, it is possible to investigate both global and local properties of brain{\textquoteright}s wiring diagram, i.e., the connectome. We acquired diffusion-weighted magnetic resonance imaging data from 14 adult males with high-functioning ASD and 19 age-, gender-, and IQ-matched controls. As with diffusion tensor imaging-based tractography, it is not possible to detect complex (e.g., crossing) fiber configurations, present in 60{\textendash}90 \% of white matter voxels; we performed constrained spherical deconvolution-based whole brain tractography. Unweighted and weighted structural brain networks were then reconstructed from these tractography data and analyzed with graph theoretical measures. In subjects with ASD, global efficiency was significantly decreased both in the unweighted and the weighted networks, normalized characteristic path length was significantly increased in the unweighted networks, and strength was significantly decreased in the weighted networks. In the local analyses, betweenness centrality of the right caudate was significantly increased in the weighted networks, and the strength of the right superior temporal pole was significantly decreased in the unweighted networks in subjects with ASD. Our findings provide new insights into understanding ASD by showing that the integration of structural brain networks is decreased and that there are abnormalities in the connectivity of the right caudate and right superior temporal pole in subjects with ASD.}, keywords = {Autism spectrum disorder, Brain networks, Connectivity, Connectome, Diffusion Magnetic Resonance Imaging, Graph theoretical analysis, Tractography, White matter tract}, issn = {2040-2392}, doi = {10.1186/s13229-015-0058-4}, url = {http://dx.doi.org/10.1186/s13229-015-0058-4}, author = {Roine, Ulrika and Timo Roine and Salmi, Juha and Nieminen-von Wendt, Taina and Tani, Pekka and Lepp{\"a}m{\"a}ki, Sami and Rintahaka, Pertti and Caeyenberghs, Karen and Alexander Leemans and Sams, Mikko} } @conference {1624, title = {CSF partial volume modeling in diffusion kurtosis imaging: a comparative parameter estimation study}, year = {2015}, month = {11/2015}, doi = {10.3389/conf.fninf.2015.19.00039}, url = {http://www.frontiersin.org/myfrontiers/events/abstractdetails.aspx?abs_doi=10.3389/conf.fninf.2015.19.00039}, author = {Quinten Collier and Jelle Veraart and Arnold Jan den Dekker and Ben Jeurissen and Jan Sijbers} } @article {1526, title = {A geometric unmixing concept for the selection of optimal binary endmember combinations}, journal = {IEEE Geoscience and Remote Sensing letters}, volume = {12}, number = {1}, year = {2015}, pages = {82-86}, author = {Laurent Tits and Rob Heylen and Ben Somers and Paul Scheunders and Pol Coppin} } @conference {1660, title = {Human In Vivo Myeloarchitecture Using Whole-Brain Diffusion MRI}, year = {2015}, pages = {1679}, address = {Toronto, Ontario, Canada}, author = {Fernando Calamante and Ben Jeurissen and Robert Elton Smith and Jacques-Donald Tournier and Alan Connelly} } @article {1492, title = {Iterative Reweighted Linear Least Squares for Accurate, Fast, and Robust Estimation of Diffusion Magnetic Resonance Parameters}, journal = {Magnetic Resonance in Medicine}, volume = {73}, year = {2015}, pages = {2174{\textendash}2184}, abstract = {Purpose: Diffusion-weighted magnetic resonance imaging suffers from physiological noise, such as artifacts caused by motion or system instabilities. Therefore, there is a need for robust diffusion parameter estimation techniques. In the past, several techniques have been proposed, including RESTORE and iRESTORE. However, these techniques are based on nonlinear estimators and are consequently computationally intensive. Method: In this work, we present a new, robust, iteratively reweighted linear least squares (IRLLS) estimator. IRLLS performs a voxel-wise identification of outliers in diffusion-weighted magnetic resonance images, where it exploits the natural skewness of the data distribution to become more sensitive to both signal hyperintensities and signal dropouts. Results: Both simulations and real data experiments were conducted to compare IRLLS with other state-of-the-art techniques. While IRLLS showed no significant loss in accuracy or precision, it proved to be substantially faster than both RESTORE and iRESTORE. In addition, IRLLS proved to be even more robust when considering the overestimation of the noise level or when the signal-to-noise ratio is low. Conclusion: The substantially shortened calculation time in combination with the increased robustness and accuracy, make IRLLS a practical and reliable alternative to current state-of-theart techniques for the robust estimation of diffusion-weighted magnetic resonance parameters.}, keywords = {diffusion tensor imaging, MRI, outlier detection, robust, weighted linear least squares}, doi = {10.1002/mrm.25351}, author = {Quinten Collier and Jelle Veraart and Ben Jeurissen and Arnold Jan den Dekker and Jan Sijbers} } @article {1563, title = {Modeling blurring effects due to continuous gantry rotation: application to region of interest tomography}, journal = {Medical Physics}, volume = {42}, year = {2015}, pages = {2709-2717}, doi = { http://dx.doi.org/10.1118/1.4914422}, author = {Jeroen Cant and Willem Jan Palenstijn and Gert Behiels and Jan Sijbers} } @article {1540, title = {A multi-level preconditioned Krylov method for the efficient solution of algebraic tomographic reconstruction problems}, journal = {Journal of Computational and Applied Mathematics}, volume = {238}, year = {2015}, pages = {1-16}, abstract = {Classical iterative methods for tomographic reconstruction include the class of Algebraic Reconstruction Techniques (ART). Convergence of these stationary linear iterative methods is however notably slow. In this paper we propose the use of Krylov solvers for tomographic linear inversion problems. These advanced iterative methods feature fast convergence at the expense of a higher computational cost per iteration, causing them to be generally uncompetitive without the inclusion of a suitable preconditioner. Combining elements from standard multigrid (MG) solvers and the theory of wavelets, a novel wavelet-based multi-level (WMG) preconditioner is introduced, which is shown to significantly speed-up Krylov convergence. The performance of the WMG-preconditioned Krylov method is analyzed through a spectral analysis, and the approach is compared to existing methods like the classical Simultaneous Iterative Reconstruction Technique (SIRT) and unpreconditioned Krylov methods on a 2D tomographic benchmark problem. Numerical experiments are promising, showing the method to be competitive with the classical Algebraic Reconstruction Techniques in terms of convergence speed and overall performance (CPU time) as well as precision of the reconstruction. }, doi = {doi:10.1016/j.cam.2014.12.044}, author = {Siegfried Cools and Pieter Ghysels and Wim Van Aarle and Jan Sijbers and Wim Vanroose} } @article {1496, title = {Pore REconstruction and Segmentation (PORES) method for improved porosity quantification of nanoporous materials}, journal = {Ultramicroscopy}, volume = {148}, year = {2015}, pages = {10-19}, abstract = {Electron tomography is currently a versatile tool to investigate the connection between the structure and properties of nanomaterials. However, a quantitative interpretation of electron tomography results is still far from straightforward. Especially accurate quantification of pore-space is hampered by artifacts introduced in all steps of the processing chain, i.e., acquisition, reconstruction, segmentation and quantification. Furthermore, most common approaches require subjective manual user input. In this paper, the PORES algorithm ({\textquotedblleft}POre REconstruction and Segmentation{\textquotedblright}) is introduced; it is a tailor-made, integral approach, for the reconstruction, segmentation, and quantification of porous nanomaterials. The PORES processing chain starts by calculating a reconstruction with a nanoporous-specific reconstruction algorithm: the Simultaneous Update of Pore Pixels by iterative REconstruction and Simple Segmentation algorithm (SUPPRESS). It classifies the interior region to the pores during reconstruction, while reconstructing the remaining region by reducing the error with respect to the acquired electron microscopy data. The SUPPRESS reconstruction can be directly plugged into the remaining processing chain of the PORES algorithm, resulting in accurate individual pore quantification and full sample pore statistics. The proposed approach was extensively validated on both simulated and experimental data, indicating its ability to generate accurate statistics of nanoporous materials.}, doi = {10.1016/j.ultramic.2014.08.008}, author = {Van Eyndhoven, Geert and Mert Kurttepeli and C. J. {Van Oers} and Pegie Cool and Sara Bals and Kees Joost Batenburg and Jan Sijbers} } @conference {1605, title = {Statistical shape modeling of the incudomalleolar complex using micro-CT and clinical cone-beam CT}, year = {2015}, month = {July}, address = {Aalborg, Denmark}, abstract = {Introduction: A large variation in material properties and geometry exists in the human temporal bone. These variations can affect hearing and middle ear sound transmission. Middle ear computer (finite element, FE) models are successfully used to predict sound transmission and its dependence on material properties. The model geometry, however, is mostly based on data of a single sample. Here we use statistical shape models (SSM) to characterize the natural anatomical variations present in the incudomalleolar (IM) complex of humans. SSM can later be used in FE models to study the effect of geometry on sound transmission, or parameters can be fitted to clinical CT data to obtain a patient-specific computer model. Methods and Materials: In this study we combine data of high resolution micro-CT scans (uCT, 20 um resolution) of 6 human cadaveric temporal bones and clinical cone-beam CT scans (CBCT, 150 um resolution) of 100 patients. First, a dense correspondence between the uCT samples is obtained by pair-wise elasticity modulated registration of a reference sample to each of the remaining samples. A SSM is built from these corresponded scans using principal component analysis (PCA), describing the average shape and the main variations of the middle ear within the uCT population. Next this SSM is fitted to clinical CBCT data by elastic registration with the SSM as shape prior. Results and conclusions: We will obtain an average geometrical model for malleus, incus and IM complex and characterize the deviations present in the patient population. We will do this by reporting natural variation of size and thickness of malleus head, neck and manubrium, the long and short process of the incus and relative angles in the IM complex.}, author = {Joris Soons and Femke Danckaers and Toon Huysmans and Jan Sijbers and Jan W. Casselamn and Joris J. J. Dirckx} } @article {forde2015structural, title = {Structural brain network analysis in families multiply affected with bipolar I disorder}, journal = {Psychiatry Research: Neuroimaging}, volume = {234}, number = {1}, year = {2015}, pages = {44{\textendash}51}, publisher = {Elsevier}, author = {Forde, Natalie J and O{\textquoteright}Donoghue, Stefani and Scanlon, Cathy and Louise Emsell and Chaddock, Chris and Alexander Leemans and Ben Jeurissen and Gareth J. Barker and Dara M. Cannon and Murray, Robin M and others} } @article {1535, title = {Subcortical volumetric changes across the adult lifespan: subregional thalamic atrophy accounts for age-related sensorimotor performance declines}, journal = {Cortex}, volume = {65}, year = {2015}, pages = {128-138}, doi = { 10.1016/j.cortex.2015.01.003}, author = {L. Serbruyns and Inge Leunissen and Toon Huysmans and K. Cuypers and R. L. Meesen and P. van Ruitenbeek and Jan Sijbers and S. P. Swinnen} } @conference {1545, title = {Theoretical study of the free water elimination model}, volume = {23}, year = {2015}, pages = {2757}, abstract = {Partial volume effects caused by cerebrospinal fluid are an important issue in diffusion MRI. In this work, we study the free water elimination model by analyzing the Cram{\'e}r-Rao lower bound (CRLB) of its parameters. We show that through optimizing the acquisition protocol by minimizing the trace of the CRLB, a significant gain in the precision of the parameter estimation can be achieved. Moreover, further analysis indicates that regularization and/or constraints are necessary for parameter estimation from voxels with large CSF fractions and/or low FA values. These theoretical findings are confirmed by both simulation and real data experiments.}, author = {Quinten Collier and Jelle Veraart and Ben Jeurissen and Arnold Jan den Dekker and Jan Sijbers} } @conference {Collier2015-pa, title = {Theoretical study of the free water elimination model}, volume = {15}, year = {2015}, pages = {2757}, author = {Collier, Quinten and Veraart, Jelle and Ben Jeurissen and Arnold Jan den Dekker and Jan Sijbers} } @conference {1544, title = {Theoretical study of the free water elimination model}, year = {2015}, pages = {78}, abstract = {Partial volume effects caused by cerebrospinal fluid are an important issue in diffusion MRI. In this work, we study the free water elimination model by analyzing the Cram{\'e}r-Rao lower bound (CRLB) of its parameters. We show that through optimizing the acquisition protocol by minimizing the trace of the CRLB, a significant gain in the precision of the parameter estimation can be achieved. Moreover, further analysis indicates that regularization and/or constraints are necessary for parameter estimation from voxels with large CSF fractions and/or low FA values. These theoretical findings are confirmed by both simulation and real data experiments.}, author = {Quinten Collier and Jelle Veraart and Ben Jeurissen and Arnold Jan den Dekker and Jan Sijbers} } @conference {1662, title = {Time to Move On: An FOD-Based DEC Map to Replace DTI{\textquoteright}s Trademark DEC FA}, year = {2015}, pages = {1027}, author = {Thijs Dhollander and Robert Elton Smith and Jacques-Donald Tournier and Ben Jeurissen and Alan Connelly} } @inproceedings {1635, title = {Two-stage fusion of thermal hyperspectral and visible RGB image by PCA and guided filter}, booktitle = {IEEE Whispers 2015, Workshop on Hyperspectral Image and Signal Processing, June 2-5, Tokyo}, year = {2015}, author = {W. Liao and F. Huang and F. v. Coillie and Guy Thoonen and Aleksandra Pizurica and Paul Scheunders and Wilfried Philips} } @conference {1487, title = {An Anthropometric Shape Model for the Design of Sports Helmets}, year = {2014}, author = {Daniel Lacko and Toon Huysmans and Annelies Claeskens and Stijn Verwulgen and Peter Aerts and Jan Sijbers and Guido De Bruyne} } @inproceedings {1501, title = {Anthropometrics 2.0: Enrichment of Classical Anthropometry through Multidisciplinary Collaboration}, booktitle = {6th International Conference on Engineering \& Product Design Education.}, year = {2014}, author = {Stijn Verwulgen and Daniel Lacko and Guido De Bruyne and Femke Danckaers and Naomi Christis and Jan Sijbers and Toon Huysmans} } @conference {1474, title = {Brain Tissue Types Resolved Using Spherical Deconvolution of Multi-Shell Diffusion MRI Data}, year = {2014}, month = {May}, pages = {973}, address = {Milan, Italy}, author = {Ben Jeurissen and Jacques-Donald Tournier and Thijs Dhollander and Alan Connelly and Jan Sijbers} } @inproceedings {1500, title = {Conveyor belt X-ray CT using Domain Constrained Discrete Tomography}, booktitle = {Sibgrapi conference on Graphics, Patterns and Images}, year = {2014}, pages = {290 - 297}, doi = {10.1109/SIBGRAPI.2014.21}, author = {Luis Filipe Alves Pereira and Andrei Dabravolski and Ing Ren Tsang and George D C Cavalcanti and Jan Sijbers} } @article {1494, title = {Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data}, journal = {NeuroImage}, volume = {103}, year = {2014}, pages = {411{\textendash}426}, abstract = {Constrained spherical deconvolution (CSD) has become one of the most widely used methods to extract white matter (WM) fibre orientation information from diffusion-weighted MRI (DW-MRI) data, overcoming the crossing fibre limitations inherent in the diffusion tensor model. It is routinely used to obtain high quality fibre orientation distribution function (fODF) estimates and fibre tractograms and is increasingly used to obtain apparent fibre density (AFD) measures. Unfortunately, CSD typically only supports data acquired on a single shell in q-space. With multi-shell data becoming more and more prevalent, there is a growing need for CSD to fully support such data. Furthermore, CSD can only provide high quality fODF estimates in voxels containing WM only. In voxels containing other tissue types such as grey matter (GM) and cerebrospinal fluid (CSF), the WM response function may no longer be appropriate and spherical deconvolution produces unreliable, noisy fODF estimates. The aim of this study is to incorporate support for multi-shell data into the CSD approach as well as to exploit the unique b-value dependencies of the different tissue types to estimate a multi-tissue ODF. The resulting approach is dubbed multi-shell, multi-tissue CSD (MSMT-CSD) and is compared to the state-of-the-art single-shell, single-tissue CSD (SSST-CSD) approach. Using both simulations and real data, we show that MSMT-CSD can produce reliable WM/GM/CSF volume fraction maps, directly from the DW data, whereas SSST-CSD has a tendency to overestimate the WM volume in voxels containing GM and/or CSF. In addition, compared to SSST-CSD, MSMT-CSD can substantially increase the precision of the fODF fibre orientations and reduce the presence of spurious fODF peaks in voxels containing GM and/or CSF. Both effects translate into more reliable AFD measures and tractography results with MSMT-CSD compared to SSST-CSD.}, doi = {10.1016/j.neuroimage.2014.07.061}, author = {Ben Jeurissen and Jacques-Donald Tournier and Thijs Dhollander and Alan Connelly and Jan Sijbers} } @conference {1454, title = {Reliable Pore-size Measurements Based on a Procedure Specifically Designed for Electron Tomography Measurements of Nanoporous Samples}, year = {2014}, author = {Van Eyndhoven, Geert and Kees Joost Batenburg and Cynthia Van Oers and Mert Kurttepeli and Sara Bals and Pegie Cool and Jan Sijbers} } @inproceedings {1521, title = {Spectral adaptation of hyperspectral flight lines using VHR contextual information}, booktitle = {Geoscience and Remote Sensing Symposium (IGARSS), 2014 IEEE International}, year = {2014}, pages = {2953-2956}, publisher = {IEEE}, organization = {IEEE}, address = {Quebec City, QC, Canada}, abstract = {Due to technological constraints, hyperspectral earth observation imagery are often a mosaic of overlapping flight lines collected in different passes over the area of interest. This causes variations in aqcuisition conditions such that the reflected spectrum can vary significantly between these flight lines. Partly, this problem is solved by atmospherical correction, but residual spectral differences often remain. A probabilistic domain adaptation framework based on graph matching using Hidden Markov Random Fields was recently proposed for transforming hyperspectral data from one image to better correspond to the other. This paper investigates the use of scale and angle invariant textural features for improving the performance of the used Hidden Markov Random Field matching framework in the case of hyperspectral flight lines. These textural features are derived from the filtering of VHR optical imagery with a bank of Gabor filters with varying orientation, scale and frequency and subsequently rendering them invariant to scale and frequency by applying the 2D DFT on the filter responses in the scale and frequency space.}, doi = {10.1109/IGARSS.2014.6947096}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6947096}, author = {Jan-Pieter Jacobs and Guy Thoonen and Devis Tuia and Gustavo Camps-Valls and Pieter Kempeneers and Paul Scheunders} } @conference {1554, title = {Structural brain network analysis in families multiply affected with bipolar 1 disorder}, year = {2014}, address = {Athens, Greece}, author = {Forde, Natalie J and Scanlon, Cathy and Louise Emsell and O{\textquoteright}Donoghue, S and Chaddock, Chris and Alexander Leemans and Ben Jeurissen and Dara M. Cannon and Murray, R M and Colm McDonald} } @article {1546, title = {Structural neuroimaging correlates of allelic variation of the BDNF val66met polymorphism.}, journal = {NeuroImage}, volume = {90}, year = {2014}, month = {2014 Apr 15}, pages = {280-9}, abstract = {BACKGROUND: The brain-derived neurotrophic factor (BDNF) val66met polymorphism is associated with altered activity dependent secretion of BDNF and a variable influence on brain morphology and cognition. Although a met-dose effect is generally assumed, to date the paucity of met-homozygotes have limited our understanding of the role of the met-allele on brain structure. METHODS: To investigate this phenomenon, we recruited sixty normal healthy subjects, twenty in each genotypic group (val/val, val/met and met/met). Global and local morphology were assessed using voxel based morphometry and surface reconstruction methods. White matter organisation was also investigated using tract-based spatial statistics and constrained spherical deconvolution tractography. RESULTS: Morphological analysis revealed an "inverted-U" shaped profile of cortical changes, with val/met heterozygotes most different relative to the two homozygous groups. These results were evident at a global and local level as well as in tractography analysis of white matter fibre bundles. CONCLUSION: In contrast to our expectations, we found no evidence of a linear met-dose effect on brain structure, rather our results support the view that the heterozygotic BDNF val66met genotype is associated with cortical morphology that is more distinct from the BDNF val66met homozygotes. These results may prove significant in furthering our understanding of the role of the BDNF met-allele in disorders such as Alzheimer{\textquoteright}s disease and depression.}, keywords = {Adolescent, Adult, Alleles, Brain, Brain-Derived Neurotrophic Factor, diffusion tensor imaging, Female, Genotype, Heterozygote, Homozygote, Humans, Image Processing, Computer-Assisted, Male, Middle Aged, Polymorphism, Single Nucleotide, Young Adult}, issn = {1095-9572}, doi = {10.1016/j.neuroimage.2013.12.050}, author = {Forde, Natalie J and Ronan, Lisa and Suckling, John and Scanlon, Cathy and Neary, Simon and Holleran, Laurena and Alexander Leemans and Tait, Roger and Rua, Catarina and Fletcher, Paul C and Ben Jeurissen and Dodds, Chris M and Miller, Sam R and Bullmore, Edward T and Colm McDonald and Nathan, Pradeep J and Dara M. Cannon} } @inproceedings {1495, title = {Tomographic image reconstruction from continuous projections}, booktitle = {The third international conference on image formation in X-ray computed tomography}, year = {2014}, month = {06/2014}, pages = {295-298}, address = {Salt Lake City, USA}, author = {Jeroen Cant and Willem Jan Palenstijn and Gert Behiels and Jan Sijbers} } @inproceedings {1478, title = {Type-2 fuzzy GMMs for robust text-independent speaker verification in noisy environments}, booktitle = {International Conference of Pattern Recognition}, year = {2014}, author = {Hector N. B. Pinheiro and Ing Ren Tsang and George D C Cavalcanti and Ing Jyh Tsang and Jan Sijbers} } @inproceedings {Jacobs13, title = {Domain adaptation with Hidden Markov Random Fields}, booktitle = {Geoscience and Remote Sensing Symposium (IGARSS), 2013 IEEE International}, year = {2013}, month = {July}, pages = {3112-3115}, address = {Melbourne, VIC, Australia}, abstract = {In this paper, we propose a method to match multitemporal sequences of hyperspectral images using Hidden Markov Random Fields. Based on the matching of the data manifold, the algorithm matches the reflectance spectra of the classes, thus allowing the reuse of labeled examples acquired on one image to classify the other. This allows valorization of spectra collected in situ to other acquisitions than the one they were acquired for, without user supervision, prior knowledge of the class reflectance in the new domain or global information about atmospheric conditions.}, keywords = {domain adaptation, graph matching, Hidden Markov Random Fields, Multitemporal classification}, issn = {2153-6996}, doi = {10.1109/IGARSS.2013.6723485}, author = {Jan-Pieter Jacobs and Guy Thoonen and Devis Tuia and Gustavo Camps-Valls and Birgen Haest and Paul Scheunders} } @article {1410, title = {Hyperspectral remote sensing data analysis and future challenges}, journal = {IEEE Geoscience and Remote Sensing Magazine}, volume = {1}, year = {2013}, pages = {6-36}, author = {Jose Bioucas-Dias and Antonio Plaza and Gustavo Camps-Valls and Paul Scheunders and Nasser Nasrabadi and Jocedlyn Chanussot} } @inproceedings {1524, title = {Improving the efficiency of MESMA through geometric unmixing principles}, booktitle = {SPIE Remote Sensing, Drseden, Germany, 23-26 September }, volume = {8892}, number = {UNSP 88920Q}, year = {2013}, author = {Laurent Tits and Ben Somers and Rob Heylen and Paul Scheunders and Pol Coppin} } @conference {1426, title = {Iterative reweighted linear least squares for the accurate, fast, and robust estimation of diffusion magnetic resonance parameters}, year = {2013}, author = {Quinten Collier and Jelle Veraart and Jan Sijbers} } @article {1368, title = {Limbic and callosal white matter changes in euthymic bipolar I disorder: an advanced diffusion MRI tractography study}, journal = {Biologicial Psychiatry}, volume = {73}, year = {2013}, pages = {194-201}, doi = {http://dx.doi.org/10.1016/j.biopsych.2012.09.023}, author = {Louise Emsell and Alexander Leemans and Camilla Langan and Wim Van Hecke and Gareth J. Barker and Peter McCarthy and Ben Jeurissen and Jan Sijbers and Stefan Sunaert and Dara M. Cannon and Colm McDonald} } @inproceedings {Sabino:2013:MCT:2571272.2572228, title = {Motion Compensation Techniques in Permutation-Based Video Encryption}, booktitle = {Proceedings of the 2013 IEEE International Conference on Systems, Man, and Cybernetics}, series = {SMC {\textquoteright}13}, year = {2013}, pages = {1578{\textendash}1581}, publisher = {IEEE Computer Society}, organization = {IEEE Computer Society}, address = {Washington, DC, USA}, keywords = {motion compensation, multimedia data security, spatial correlation, video coding, Video encryption}, isbn = {978-1-4799-0652-9}, doi = {10.1109/SMC.2013.272}, url = {http://dx.doi.org/10.1109/SMC.2013.272}, author = {Sabino, Caio C. and Andrade, Lais S. and Ing Ren Tsang and George D C Cavalcanti and Ing Jyh Tsang and Jan Sijbers} } @article {1396, title = {Subchronic memantine induced concurrent functional disconnectivity and altered ultra-structural tissue integrity in the rodent brain: revealed by multimodal MRI.}, journal = {Psychopharmacology}, volume = {227}, year = {2013}, month = {2013 Jun}, pages = {479-91}, abstract = {BACKGROUND: An effective NMDA antagonist imaging model may find key utility in advancing schizophrenia drug discovery research. We investigated effects of subchronic treatment with the NMDA antagonist memantine by using behavioural observation and multimodal MRI. METHODS: Pharmacological MRI (phMRI) was used to map the neuroanatomical binding sites of memantine after acute and subchronic treatment. Resting state fMRI (rs-fMRI) and diffusion MRI were used to study the changes in functional connectivity (FC) and ultra-structural tissue integrity before and after subchronic memantine treatment. Further corroborating behavioural evidences were documented. RESULTS: Dose-dependent phMRI activation was observed in the prelimbic cortex following acute doses of memantine. Subchronic treatment revealed significant effects in the hippocampus, cingulate, prelimbic and retrosplenial cortices. Decreases in FC amongst the hippocampal and frontal cortical structures (prelimbic, cingulate) were apparent through rs-fMRI investigation, indicating a loss of connectivity. Diffusion kurtosis MRI showed decreases in fractional anisotropy and mean diffusivity changes, suggesting ultra-structural changes in the hippocampus and cingulate cortex. Limited behavioural assessment suggested that memantine induced behavioural effects comparable to other NMDA antagonists as measured by locomotor hyperactivity and that the effects could be reversed by antipsychotic drugs. CONCLUSION: Our findings substantiate the hypothesis that repeated NMDA receptor blockade with nonspecific, noncompetitive NMDA antagonists may lead to functional and ultra-structural alterations, particularly in the hippocampus and cingulate cortex. These changes may underlie the behavioural effects. Furthermore, the present findings underscore the utility and the translational potential of multimodal MR imaging and acute/subchronic memantine model in the search for novel disease-modifying treatments for schizophrenia.}, issn = {1432-2072}, doi = {10.1007/s00213-013-2966-3}, author = {Sekar, S and Jonckers, E and Marleen Verhoye and Willems, R and Jelle Veraart and Johan Van Audekerke and Couto, J and Giugliano, M and Wuyts, K and Dedeurwaerdere, S and Jan Sijbers and Mackie, C and Ver Donck, L and Steckler, T and Annemie Van Der Linden} } @article {CampI.L.N.mverhoyejveraartwvheckeE.S.jsijbersA.avdlinde2011, title = {A complementary DTI-histological study in a model of Huntingtons disease}, journal = {Neurobiology of Aging}, volume = {33}, number = {5}, year = {2012}, pages = {945-959}, doi = {http://dx.doi.org/10.1016/j.neurobiolaging.2010.07.001}, author = {N. Van Camp and Ines Blockx and L. Camon and N. de Vera and Marleen Verhoye and Jelle Veraart and Wim Van Hecke and E. Martinez and Guadelupe S. and Jan Sijbers and A. Planas and Annemie Van Der Linden} } @conference {1366, title = {Discrete algebraic reconstruction in MRI: a simulation study}, volume = {25}, year = {2012}, pages = {480-481}, keywords = {compressed sensing, DART, iterative reconstruction, prior knowledge}, doi = {10.1007/s10334-012-0324-9}, author = {Quinten Collier and Segers, Hilde and Jan Sijbers} } @article {1313, title = {Force Feedback to Assist Active Contour Modelling for Tracheal Stenosis Segmentation}, journal = {Advances in Human-Computer Interaction}, volume = {2012}, year = {2012}, abstract = {Manual segmentation of structures for diagnosis and treatment of various diseases is a very time-consuming procedure. Therefore, some level of automation during the segmentation is desired, as it often significantly reduces the segmentation time. A typical solution is to allow manual interaction to steer the segmentation process, which is known as semiautomatic segmentation. In 2D, such interaction is usually achieved with click-and-drag operations, but in 3D a more sophisticated interface is called for. In this paper, we propose a semi-automatic Active Contour Modelling for the delineation of medical structures in 3D, tomographic images. Interaction is implemented with the employment of a 3D haptic device, which is used to steer the contour deformation towards the correct boundaries. In this way, valuable haptic feedback is provided about the 3D surface and its deformation. Experiments on simulated and real tracheal CT data showed that the proposed technique is an intuitive and effective segmentation mechanism.}, doi = {doi:10.1155/2012/632498}, url = {http://www.hindawi.com/journals/ahci/2012/632498/}, author = {Lode Vanacken and R{\^o}mulo Pinho and Jan Sijbers and Karen Coninx} } @conference {1388, title = {Optimization of Compressed Sensing/RARE Combining Acquisition Schemes}, volume = {25}, year = {2012}, pages = {513-514}, doi = {10.1007/s10334-012-0324-9}, author = {Maarten Naeyaert and Jan Aelterman and Johan Van Audekerke and Kasper Claes and Annemie Van Der Linden and Jan Sijbers and Marleen Verhoye} } @inbook {1257, title = {Wavelet-based Multi/Hyperspectral Image Restoration and Fusion}, booktitle = {Signal and Image Processing for Remote Sensing}, year = {2012}, pages = {505-523}, publisher = {Taylor and Francis}, organization = {Taylor and Francis}, chapter = {25}, author = {Paul Scheunders and A. Duijster and Y. Zhang}, editor = {C.H. Chen} } @inproceedings {1429, title = {Efficient parameter estimation for discrete tomography using adaptive modeling}, booktitle = {11th International Meeting on Fully Three-Dimensional Image Reconstruction in Radiology and Nuclear Medicine}, year = {2011}, month = {07/2011}, author = {Wim Van Aarle and K. Crombecq and I. Couckuyt and Kees Joost Batenburg and Jan Sijbers} } @conference {1553, title = {White Matter Tract Deficits in Schizophrenia}, volume = {7}, year = {2011}, address = {Dublin, Ireland}, author = {Forde, Natalie J and Ellison-Wright, I and Nathan, Pradeep J and Zaman, R and Dudas, R and Agius, M and Fernandez-Egea, E and Alexander Leemans and Ben Jeurissen and Scanlon, Cathy and Colm McDonald and Dara M. Cannon} } @article {Hufkens10, title = {Habitat reporting of a heathland site: Classification probabilities as additional information, a case study}, journal = {Ecological Informatics}, volume = {5}, number = {4}, year = {2010}, pages = {248 - 255}, abstract = {Heathlands are man-made habitats and their decline during the last century can be contributed to shifts in both agricultural and management practices as well as to hydrological and atmospheric changes. As a result, many heathland sites, including the Kalmthoutse Heide in Belgium, were included in the European Natura 2000 program, a network of protected areas across the European Union. To assure an accurate mapping of the Kalmthoutse Heide and other Natura 2000 sites in Belgium a classification framework for habitat status reporting with remote sensing data and in particular high resolution hyperspectral imagery was started. In this study we propose a simple and fast context based method for mapping heathland heterogeneity using the intermediate, otherwise redundant, classification probabilities as generated by a hard classification algorithm. Our study proved to be successful in using intermediate classification probabilities as a valuable source of ecological information. The delineated areas have been shown to be statistically sound and robust compared to a neutral model. The technique is not limited to a particular hard classification technique and can easily be adopted into current vegetation monitoring efforts. The resulting maps provided accessible maps which can support management of the protected site and enhance the accuracy of EU reportage as required by the habitat directive.}, keywords = {Heterogeneity, Hyperspectral, Patch, remote sensing, Uncertainty, Vegetation}, issn = {1574-9541}, doi = {10.1016/j.ecoinf.2009.09.002}, url = {http://www.sciencedirect.com/science/article/pii/S1574954109000740}, author = {Koen Hufkens and Guy Thoonen and Jeroen Vanden Borre and Paul Scheunders and Reinhart Ceulemans} } @article {1479, title = {Morphologic and functional changes in the unilateral 6-hydroxydopamine lesion rat model for Parkinson{\textquoteright}s disease discerned with microSPECT and quantitative MRI.}, journal = {Magnetic Resonance Materials in Physics, Biology and Medicine}, volume = {23}, year = {2010}, month = {04/2010}, pages = {65-75}, abstract = {OBJECT: In the present study, we aimed to evaluate the impact of neurodegeneration of the nigrostriatal tract in a rodent model of Parkinson{\textquoteright}s disease on the different MR contrasts (T(2), T(1), CBF and CBV) measured in the striatum. MATERIAL AND METHODS: Animals were injected with 6-hydroxydopamine (6OHDA) in the substantia nigra resulting in massive loss of nigrostriatal neurons and hence dopamine depletion in the ipsilateral striatum. Using 7T MRI imaging, we have quantified T(2), T(1), CBF and CBV in the striata of 6OHDA and control rats. To validate the lesion size, behavioral testing, dopamine transporter muSPECT and tyrosine hydroxylase staining were performed. RESULTS: No significant differences were demonstrated in the absolute MRI values between 6OHDA animals and controls; however, 6OHDA animals showed significant striatal asymmetry for all MRI parameters in contrast to controls. CONCLUSIONS: These PD-related asymmetry ratios might be the result of counteracting changes in both intact and affected striatum and allowed us to diagnose PD lesions. As lateralization is known to occur also in PD patients and might be expected in transgenic PD models as well, we propose that MR-derived asymmetry ratios in the striatum might be a useful tool for in vivo phenotyping of animal models of PD.}, keywords = {Animals, Corpus Striatum, Disease Models, Animal, Female, Magnetic Resonance Imaging, Oxidopamine, Parkinsonian Disorders, Positron-Emission Tomography, Rats, Rats, Wistar, Reproducibility of Results, Sensitivity and Specificity}, issn = {1352-8661}, doi = {10.1007/s10334-010-0198-7}, author = {N. Van Camp and Vreys, Ruth and Koen Van Laere and E. Lauwers and Dirk Beque and Marleen Verhoye and Casteels, Cindy and Alfons Verbruggen and Zeger Debyser and Luc Mortelmans and Jan Sijbers and Johan Nuyts and Veerle Baekelandt and Annemie Van Der Linden} } @article {jbatenbuBalsjsijbersKubelMidgleyHernandezKaiserEncinaCoronadoTendeloo2009, title = {3D imaging of nanomaterials by discrete tomography}, journal = {Ultramicroscopy}, volume = {109}, year = {2009}, pages = {730-740}, doi = {10.1016/j.ultramic.2009.01.009}, author = {Kees Joost Batenburg and Sara Bals and Jan Sijbers and C. Kubel and P.A. Midgley and J.C. Hernandez and U. Kaiser and E.R. Encina and E.A. Coronado and Van Tendeloo, Gustaaf} } @article {1375, title = {Diffusion tensor imaging in a rat model of Parkinson{\textquoteright}s disease after lesioning of the nigrostriatal tract.}, journal = {NMR in biomedicine}, volume = {22}, year = {2009}, month = {2009 Aug}, pages = {697-706}, abstract = {Parkinson{\textquoteright}s disease (PD) is characterised by degeneration of the nigrostrial connection causing dramatic changes in the dopaminergic pathway underlying clinical pathology. Till now, no MRI tools were available to follow up any specific PD-related neurodegeneration. However, recently, diffusion tensor imaging (DTI) has received considerable attention as a new and potential in vivo diagnostic tool for various neurodegenerative diseases. To assess this in PD, we performed DTI in the acute 6-hydroxydopamine (6-OHDA) rat model of PD to evaluate diffusion properties in the degenerating nigrostriatal pathway and its connecting structures. Injection of a neurotoxin in the striatum causes retrograde neurodegeneration of the nigrostriatal tract, and selective degeneration of nigral neurons. The advantage of this model is that the lesion size is well controllable by the injected dose of the toxin. The degree of functional impairment was evaluated in vivo using the amphetamine rotation test and microPET imaging of the dopamine transporter (DAT). Despite a nearly complete lesion of the nigrostriatal tract, DTI changes were limited to the ipsilateral substantia nigra (SN). In this study we demonstrate, using voxel-based statistics (VBS), an increase in fractional anisotropy (FA), whereas all eigenvalues were significantly decreased. VBS enabled us to visualise neurodegeneration of a cluster of neurons but failed to detect degeneration of more diffuse microstructures such as the nigrostriatal fibres or the dopaminergic endings in the striatum. VBS without a priori information proved to be better than manual segmentation of brain structures as it does not suffer from volume averaging and is not susceptible to erroneous segmentations of brain regions that show very little contrast on MRI images such as SN.}, keywords = {Animals, Behavior, Animal, Diffusion Magnetic Resonance Imaging, Disease Models, Animal, Female, Imaging, Three-Dimensional, Immunohistochemistry, Parkinson Disease, Positron-Emission Tomography, Rats, Rats, Wistar, Substantia Nigra}, issn = {1099-1492}, doi = {10.1002/nbm.1381}, author = {N. Van Camp and Ines Blockx and Marleen Verhoye and Casteels, Cindy and Coun, Frea and Alexander Leemans and Jan Sijbers and Veerle Baekelandt and Koen Van Laere and Annemie Van Der Linden} } @article {HufkensCeulemanspscheund2009, title = {Ecotones in vegetation ecology: methodology and definitions revisited}, journal = {Ecological Research}, volume = {24}, year = {2009}, pages = {977-986}, author = {Koen Hufkens and Reinhart Ceulemans and Paul Scheunders} } @article {1266, title = {Imaging of voids due to deformation in alloy steel using micro-focus X-ray beam}, journal = {Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms}, volume = {267}, year = {2009}, month = {10/2009}, pages = {3488 - 3490}, issn = {0168583X}, doi = {10.1016/j.nimb.2009.07.005}, author = {Gupta, C. and Elke Van de Casteele and Chakravartty, J.K.} } @inproceedings {1297, title = {Three-dimensional monitoring of physical weathering in limestone with X-ray computed microtomography (micro-CT)}, booktitle = {12th Euroseminar on Microscopy Applied to Building Materials (EMABM)}, year = {2009}, author = {Boone, M.A. and De Kock, T. and Dewanckele, J. and Cnudde, Veerle and Boone, M.N. and Van Loo, D. and Elke Van de Casteele and De Schutter, G. and Jacobs, P.} } @article {HufkenspscheundCeulemans2009, title = {Validation of the sigmoid wave curve fitting algorithm on a forest-tundra ecotone in the Northwest Territories, Canada}, journal = {Ecological Informatics}, volume = {4}, year = {2009}, pages = {1-7}, author = {Koen Hufkens and Paul Scheunders and Reinhart Ceulemans} } @article {HufkensCeulemanspscheund2008, title = {Estimating the ecotone width in patchy ecotones using a sigmoid wave approach}, journal = {Ecological Informatics}, volume = {3}, year = {2008}, pages = {97-104}, author = {Koen Hufkens and Reinhart Ceulemans and Paul Scheunders} } @inproceedings {1295, title = {Evaluation of conservation treatments for archeological waterlogged wooden artifacts}, booktitle = {9th International Conference on NDT of Art}, year = {2008}, author = {Bugani, Simone and Cloetens, Peter and Colombini, Maria Perla and Giachi, Gianna and Janssens, Koen and Modugno, Francesca and Morselli, Luciano and Elke Van de Casteele} } @article {1265, title = {Investigating morphological changes in treated vs. untreated stone building materials by x-ray micro-CT}, journal = {Analytical and Bioanalytical Chemistry}, volume = {391}, year = {2008}, month = {6/2008}, pages = {1343 - 1350}, issn = {1618-2642}, doi = {10.1007/s00216-008-1946-7}, author = {Bugani, Simone and Camaiti, Mara and Morselli, Luciano and Elke Van de Casteele and Janssens, Koen} } @article {KempeneersZarco-TejadaNorthsdbackerDelalieuxSepulcre-CantoMoralesAardtSagardoyCoppinpscheund2008, title = {Model inversion for chlorophyll estimation in open canopies from hyperspectral imagery}, journal = {International Journal of Remote Sensing}, volume = {29}, number = {17}, year = {2008}, pages = {5093-5111}, author = {Pieter Kempeneers and P.J. Zarco-Tejada and P.R.J. North and Steve De Backer and Stephanie Delalieux and G. Sepulcre-Canto and F. Morales and Jan van Aardt and Ruth Sagardoy and P. Coppin and Paul Scheunders} } @article {sdbackerCornelissenLemeireNuydensMeertSchelkenspscheund2008, title = {Mosiacing of Fibered Fluorescence Microscopy Video}, journal = {Lecture notes in Computer Science}, volume = {5259}, year = {2008}, month = {October}, pages = {915-923}, author = {Steve De Backer and F. Cornelissen and J. Lemeire and R. Nuydens and T. Meert and P. Schelkens and Paul Scheunders} } @inproceedings {1294, title = {X-ray computed tomography as a non-destructive tool for stone conservation}, booktitle = {9th International Conference on NDT of Art}, year = {2008}, author = {Bugani, Simone and Camaiti, Mara and Morselli, Luciano and Elke Van de Casteele and Cloetens, Peter and Janssens, Koen} } @inproceedings {wvheckealeemansBrabanderLaridonClaeysCeulemansGoethemParizeljsijbers2007, title = {Diffusion Tensor Fiber Tracking Reveals Probst Bundles in Patients with Agenesis of the Corpus Callosum}, booktitle = {32nd Congress of the Europea Society of NeuroRadiolog}, year = {2007}, pages = {135}, author = {Wim Van Hecke and Alexander Leemans and N. De Brabander and A. Laridon and K. Claeys and B. Ceulemans and J. Van Goethem and Paul M Parizel and Jan Sijbers} } @article {1264, title = {Investigation on porosity changes of Lecce stone due to conservation treatments by means of x-ray nano- and improved micro-computed tomography: preliminary results}, journal = {X-Ray Spectrometry}, volume = {36}, year = {2007}, month = {09/2007}, pages = {316 - 320}, issn = {00498246}, doi = {10.1002/(ISSN)1097-453910.1002/xrs.v36:510.1002/xrs.976}, author = {Bugani, Simone and Camaiti, Mara and Morselli, Luciano and Elke Van de Casteele and Janssens, Koen} } @inproceedings {1293, title = {X-ray microtomography as a non-destructive tool for stone characterization in a conservation study}, booktitle = {4th ICNDT Hellenic Society}, year = {2007}, author = {Elke Van de Casteele and Bugani, Simone and Camaiti, Mara and Morselli, Luciano and Janssens, Koen} } @inproceedings {KempeneerssdbackerZarco-TejadaDelalieuxSepulcre-Cant{\'o}MoralesSagardoyAardtCoppinpscheund2006, title = {Chlorophyll retrieval from canopy reflectance over orchards using hyperspectral techniques}, booktitle = {2nd International Symposium on Recent Advances in Quantitative Remote Sensing, 25-29 September 2006, Torrent (Valencia), Spain}, year = {2006}, author = {Pieter Kempeneers and Steve De Backer and P.J. Zarco-Tejada and Stephanie Delalieux and G. Sepulcre-Cant{\'o} and F. Morales and Ruth Sagardoy and Jan van Aardt and P. Coppin and Paul Scheunders} } @inproceedings {wvheckealeemansBrabanderLaridonCeulemansJParizel2006, title = {Diffusion tensor fiber tracking in patients with agenesis of the corpus callosum}, booktitle = {23rd Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology}, year = {2006}, pages = {34-35}, address = {Warsaw, Poland}, author = {Wim Van Hecke and Alexander Leemans and N. De Brabander and A. Laridon and B. Ceulemans and Jan Sijbers and Paul M Parizel} } @inproceedings {NagelsVandervlietwvheckeEngelborghshoogheCrasParizelDeyn2006, title = {fMRI during PASAT and PVSAT in mild MS, moderate MS and normal volunteers.}, booktitle = {22nd Congress of the European Committee for}, year = {2006}, address = {Madrid, Spain}, author = {Guy Nagels and Everhard Vandervliet and Wim Van Hecke and Sebastiaan Engelborghs and M.B. D hooghe and P. Cras and Paul M Parizel and P.P. De Deyn} } @conference {1300, title = {Investigation on Lecce stone porosity by means of micro and nano X-ray tomography}, year = {2006}, author = {Bugani, Simone and Camaiti, Mara and Morselli, Luciano and Janssens, Koen and Elke Van de Casteele} } @inproceedings {KempeneerssdbackerTejadaDelalieuxCantoIribasAardtCoppinpscheund2006, title = {Stress detection in orchards with hyperspectral remote sensing data}, booktitle = {SPIE Remote Sensing, Stockholm, Sweden, september 11-14}, volume = {6359}, number = {38}, year = {2006}, month = {September}, author = {Pieter Kempeneers and Steve De Backer and P J Zarco Tejada and Stephanie Delalieux and G Sepulcre Canto and F Morales Iribas and Jan van Aardt and P. Coppin and Paul Scheunders} } @inproceedings {CampBlockxCamonVeramverhoyealeemansMartinezjsijbersPlanasavdlinde2006, title = {White and grey matters changes in a rat model for Huntington{\textquoteright}s disease discerned with in vivo DTI}, booktitle = {23rd Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology}, year = {2006}, pages = {210-211}, address = {Warsaw, Poland}, author = {N. Van Camp and Ines Blockx and L. Camon and N. de Vera and Marleen Verhoye and Alexander Leemans and E. Martinez and Jan Sijbers and A. Planas and Annemie Van Der Linden} } @inproceedings {sdbackerKempeneersDebruynpscheund2004, title = {Classification of Dune Vegetation from Remotely Sensed Hyperspectral Images}, booktitle = {Image Analysis and Recognition Proc. of International Conference on Image Analysis and Recognition}, series = {Lecture Notes in Computer Science}, year = {2004}, pages = {497-503}, publisher = {Springer}, organization = {Springer}, address = {Porto, Portugal}, author = {Steve De Backer and Pieter Kempeneers and W. Debruyn and Paul Scheunders}, editor = {A. Campilho and M. Kamel} } @article {CuytjsijbersVerdonkdvandyck2004, title = {Region and Contour Identification of Physical Objects}, journal = {Applied Numerical Analysis Computational Mathematics}, volume = {1}, number = {3}, year = {2004}, pages = {343-352}, doi = {10.1002/anac.200410002}, author = {A. Cuyt and Jan Sijbers and B. Verdonk and Dirk Van Dyck} } @inproceedings {KempeneerssdbackerDelalieuxSterckxDebruynCoppinpscheund2004, title = {Upscaling of spectroradiometer data for stress detection in orchards with remote sensing}, booktitle = {SPIE Remote Sensing, Gran Canaria, 13-16 september}, volume = {127}, year = {2004}, pages = {37-45}, publisher = {SPIE}, organization = {SPIE}, address = {Maspalomas, Spain}, author = {Pieter Kempeneers and Steve De Backer and Stephanie Delalieux and S Sterckx and W. Debruyn and P. Coppin and Paul Scheunders}, editor = {Manfred Owe, Guido D{\textquoteright}Urso, Ben T. Gouweleeuw, Anne M. Jochum} } @article {HungpscheundPhamSuColeman2004, title = {Using Intelligent Optimization Techniques in the K-means Algorithm for Multispectral Image Classification}, journal = {International Journal of Fuzzy Systems}, volume = {6}, number = {3}, year = {2004}, pages = {107-117}, author = {C.C. Hung and Paul Scheunders and M. Pham and M.C. Su and T. Coleman} } @inproceedings {SterckxCoppinsdbackerDebruynKempeneersMeulemanNackaertsReusenpscheund2003, title = {Information extraction techniques for monitoring of stress symptoms in orchards}, booktitle = {Proc. Earsel 2003, Imaging Spectroscopy workshop Oberpfaffenhofen}, year = {2003}, pages = {278-283}, author = {S Sterckx and P. Coppin and Steve De Backer and W. Debruyn and Pieter Kempeneers and K. Meuleman and K. Nackaerts and I. Reusen and Paul Scheunders} } @inproceedings {MeulemanCoppinsdbackerDebruynNackaertspscheundStercks2003, title = {Optimal hyperspectral indicators for stress detection in orchards}, booktitle = {Proc. Earsel 2003, Imaging Spectroscopy workshop Oberpfaffenhofen}, year = {2003}, pages = {534-541}, author = {K. Meuleman and P. Coppin and Steve De Backer and W. Debruyn and K. Nackaerts and Paul Scheunders and S Sterckx} } @inbook {pscheund2003, title = {A wavelet representation of multispectral images; in: Frontiers of Remote Sensing Information Processing}, year = {2003}, pages = {197-224}, publisher = {World Scientific}, organization = {World Scientific}, chapter = {9}, author = {Paul Scheunders}, editor = {C.H. Chen} } @inproceedings {jsijbersCeulemansdvandyck2002, title = {Algorithm for the computation of 3D Fourier descriptors}, booktitle = {16th International Conference on Pattern Recognition}, year = {2002}, month = {August}, pages = {790-793}, address = {Quebec, Canada}, author = {Jan Sijbers and T. Ceulemans and Dirk Van Dyck} } @inproceedings {mverhoyeMichielsjsijbersEelenPeetersAudekerkeDHoogheDeynavdlinde2000, title = {Changes during pentetrazol-induced epilepsy in rat recorded by simultaneous EEG/MRI at 7T}, booktitle = {SPIE Medical Imaging}, volume = {3978}, year = {2000}, month = {February}, pages = {485-493}, address = {San Diego, USA}, author = {Marleen Verhoye and I. Michiels and Jan Sijbers and J. Eelen and Ron R Peeters and Johan Van Audekerke and R. Dhooghe and P.P. De Deyn and Annemie Van Der Linden}, editor = {Chin-Tu Chen, Anne V. Clough} } @article {KooyReyniersmverhoyejsijbersCrasOostraWillemsavdlinde1999, title = {Neuroanatomy of the fragile X knockout mouse brain studied using in vivo high resolution Magnetic Resonance Imaging (MRI)}, journal = {European Journal of Human Genetics}, volume = {7}, year = {1999}, pages = {526-532}, author = {R.F. Kooy and E. Reyniers and Marleen Verhoye and Jan Sijbers and P. Cras and B. A. Oostra and P. J. Willems and Annemie Van Der Linden} } @inproceedings {HungColemanpscheund1998, title = {The genetic algorithm approach and K-means clustering: their role in unsupervised training in image classification}, booktitle = {Proc. IASTED International Conf. On Computer Graphics and Imaging , Halifax, Canada, june 1-3}, year = {1998}, pages = {103-106}, author = {C.C. Hung and T. Coleman and Paul Scheunders} } @inproceedings {HungColemanpscheund1998, title = {Using genetic differential competitive learning for unsupervised training in multispectral image classification systems}, booktitle = {Proceedings IEEE International Conference on Systems, Man, and Cybernetics , San Diego, California, October 11-14}, year = {1998}, pages = {4482-4485}, author = {C.C. Hung and T. Coleman and Paul Scheunders} } @inproceedings {mverhoyejsijberspscheunddvandyckReyniersKooyWillemsCrasOostraavdlinde1997, title = {In vivo assessment of cerebellum volume in transgenic fragile X knockout mice using MTI microscopy at 7T}, booktitle = {Proceedings of the European Society for Magnetic Resonance in Medicine and Biology: 14th annual meeting}, volume = {2}, number = {2}, year = {1997}, month = {September}, pages = {45-46}, address = {Brussels, Belgium}, author = {Marleen Verhoye and Jan Sijbers and Paul Scheunders and Dirk Van Dyck and E. Reyniers and R.F. Kooy and P. J. Willems and P. Cras and B. A. Oostra and Annemie Van Der Linden} } @inproceedings {KooyReyniersmverhoyejsijbersFransenCampCrasOostraavdlindeWillems1997, title = {MRI as a tool to study brain structure from mouse models of mental retardation}, booktitle = {Abstracts of the 8th international workshop on Fragile X syndrome and X-linked mental retardation}, year = {1997}, month = {August}, address = {Picton, Ontario, Canada}, author = {R.F. Kooy and E. Reyniers and Marleen Verhoye and Jan Sijbers and Erik Fransen and C. Van Camp and P. Cras and B. A. Oostra and Annemie Van Der Linden and P. J. Willems} } @inproceedings {mverhoyeavdlindejsijberspscheunddvandyckReyniersKooyWillemsCrasOostra1996, title = {High resolution MRI study of the cerebellum of mice as a function of age, in a mouse model for fragile X mental retardation}, booktitle = {Proceedings of the European Society for Magnetic Resonance in Medicine and Biology}, volume = {2}, number = {2}, year = {1996}, month = {September}, pages = {168}, address = {Prague, Czech Republic}, author = {Marleen Verhoye and Annemie Van Der Linden and Jan Sijbers and Paul Scheunders and Dirk Van Dyck and E. Reyniers and R.F. Kooy and P. J. Willems and P. Cras and B. A. Oostra} } @inproceedings {jsijberseramanAudekerkeMalflietLindenVerhoyeCloeck1993, title = {The construction of a gradient set}, booktitle = {4th Meeting of the FGWO/FRSM Contact Group Biomedical MR}, year = {1993}, pages = {5}, address = {Louvain-la-Neuve, Belgium}, author = {Jan Sijbers and Erik Raman and Johan Van Audekerke and W. Malfliet and Annemie Van Der Linden and Marleen Verhoye and C. Cloeck} }