Comparison of gradient approximation techniques for optimisation of mutual information in nonrigid registration. - Stefan Klein 001; Marius Staring; Josien P. W. Pluim (Image Processing, 2005)

Nonrigid registration with adaptive content-based filtering of the deformation field. - Marius Staring; Stefan Klein 001; Josien P. W. Pluim (Image Processing, 2005)

Nonrigid registration using a rigidity constraint. - Marius Staring; Stefan Klein 001; Josien P. W. Pluim (Image Processing, 2006)

A Comparison of Acceleration Techniques for Nonrigid Medical Image Registration. - Stefan Klein 001; Marius Staring; Josien P. W. Pluim (WBIR, 2006)

Segmentation of the Prostate in MR Images by Atlas Matching. - Stefan Klein 001; Uulke A. van der Heide; Bas W. Raaymakers; Alexis N. T. J. Kotte; Marius Staring; Josien P. W. Pluim (ISBI, 2007)

Evaluation of Optimization Methods for Nonrigid Medical Image Registration Using Mutual Information and B-Splines. - Stefan Klein 001; Marius Staring; Josien P. W. Pluim (IEEE Trans. Image Process., 2007)

Semi-automatic Reference Standard Construction for Quantitative Evaluation of Lung CT Registration. - Keelin Murphy; Bram van Ginneken; Josien P. W. Pluim; Stefan Klein 001; Marius Staring (MICCAI (2), 2008)

Adaptive local multi-atlas segmentation: application to heart segmentation in chest CT scans. - Eva M. van Rikxoort; Ivana Isgum; Marius Staring; Stefan Klein 001; Bram van Ginneken (Image Processing, 2008)

Cerebellum Segmentation in MRI Using Atlas Registration and Local Multi-Scale Image Descriptors. - Fedde van der Lijn; Marleen de Bruijne; Yoo Young Hoogendam; Stefan Klein 001; Reinhard Hameeteman; Monique M. B. Breteler; Wiro J. Niessen (ISBI, 2009)

GPU Accelerated Alignment of 3-D CTA with 2-D X-Ray Data for Improved Guidance in Coronary Interventions. - Coert Metz; Michiel Schaap; Stefan Klein 001; Annick C. Weustink; Nico Mollet; Carl J. Schultz; Robert Jan van Geuns; Patrick W. Serruys; Theo van Walsum; Wiro J. Niessen (ISBI, 2009)

Iterative Co-linearity Filtering and Parameterization of Fiber Tracts in the Entire Cingulum. - Marius de Groot; Meike W. Vernooij; Stefan Klein 001; Alexander Leemans; Renske de Boer; Aad van der Lugt; Monique M. B. Breteler; Wiro J. Niessen (MICCAI (1), 2009)

Patient Specific 4D Coronary Models from ECG-gated CTA Data for Intra-operative Dynamic Alignment of CTA with X-ray Images. - Coert Metz; Michiel Schaap; Stefan Klein 001; Lisan Neefjes; Ermanno Capuano; Carl J. Schultz; Robert Jan van Geuns; Patrick W. Serruys; Theo van Walsum; Wiro J. Niessen (MICCAI (1), 2009)

Adaptive Stochastic Gradient Descent Optimisation for Image Registration. - Stefan Klein 001; Josien P. W. Pluim; Marius Staring; Max A. Viergever (Int. J. Comput. Vis., 2009)

Registration of Cervical MRI Using Multifeature Mutual Information. - Marius Staring; Uulke A. van der Heide; Stefan Klein 001; Max A. Viergever; Josien P. W. Pluim (IEEE Trans. Medical Imaging, 2009)

Automated carotid artery distensibility measurements from CTA using nonrigid registration. - Reinhard Hameeteman; Sietske Rozie; Coert Metz; Stefan Klein 001; Theo van Walsum; Aad van der Lugt; Wiro J. Niessen (ISBI, 2010)

Early diagnosis of dementia based on intersubject whole-brain dissimilarities. - Stefan Klein 001; Marco Loog; Fedde van der Lijn; Tom den Heijer; Alexander Hammers; Marleen de Bruijne; Aad van der Lugt; Robert P. W. Duin; Monique M. B. Breteler; Wiro J. Niessen (ISBI, 2010)

A patient-specific coronary density estimate. - Rahil Khurram Shahzad; Michiel Schaap; Theo van Walsum; Stefan Klein 001; Annick C. Weustink; Lucas J. van Vliet; Wiro J. Niessen (ISBI, 2010)

Conditional Shape Models for Cardiac Motion Estimation. - Coert Metz; Nora Baka; Hortense A. Kirisli; Michiel Schaap; Theo van Walsum; Stefan Klein 001; Lisan Neefjes; Nico Mollet; Boudewijn P. F. Lelieveldt; Marleen de Bruijne (MICCAI (1), 2010)

Fully automatic cardiac segmentation from 3D CTA data: a multi-atlas based approach. - Hortense A. Kirisli; Michiel Schaap; Stefan Klein 001; Lisan Neefjes; Annick C. Weustink; Theo van Walsum; Wiro J. Niessen (Image Processing, 2010)

Adaptive local multi-atlas segmentation: Application to the heart and the caudate nucleus. - Eva M. van Rikxoort; Ivana Isgum; Yulia Arzhaeva; Marius Staring; Stefan Klein 001; Max A. Viergever; Josien P. W. Pluim; Bram van Ginneken (Medical Image Anal., 2010)

elastix: A Toolbox for Intensity-Based Medical Image Registration. - Stefan Klein 001; Marius Staring; Keelin Murphy; Max A. Viergever; Josien P. W. Pluim (IEEE Trans. Medical Imaging, 2010)

Quantitative comparison of tracking methods for motion analysis in tagged MRI. - Ihor Smal; Noemí Carranza-Herrezuelo; Stefan Klein 001; Wiro J. Niessen; Erik Meijering (ISBI, 2011)

Plaque characterization in ex vivo MRI evaluated by dense 3D correspondence with histology. - Arna van Engelen; Marleen de Bruijne; Stefan Klein 001; Hence J. M. Verhagen; Harald C. Groen; Jolanda J. Wentzel; Aad van der Lugt; Wiro J. Niessen (Computer-Aided Diagnosis, 2011)

Preconditioned Stochastic Gradient Descent Optimisation for Monomodal Image Registration. - Stefan Klein 001; Marius Staring; Patrik Andersson; Josien P. W. Pluim (MICCAI (2), 2011)

Alignment of 4D Coronary CTA with Monoplane X-ray Angiography. - Coert Metz; Michiel Schaap; Stefan Klein 001; Peter R. Rijnbeek; Lisan Neefjes; Nico Mollet; Carl J. Schultz; Patrick W. Serruys; Wiro J. Niessen; Theo van Walsum (AE-CAI, 2011)

Trans-Dimensional MCMC Methods for Fully Automatic Motion Analysis in Tagged MRI. - Ihor Smal; Noemí Carranza-Herrezuelo; Stefan Klein 001; Wiro J. Niessen; Erik Meijering (MICCAI (1), 2011)

Evaluation of optimization methods for intensity-based 2D-3D registration in x-ray guided interventions. - I. M. J. van der Bom; Stefan Klein 001; Marius Staring; R. Homan; Lambertus W. Bartels; Josien P. W. Pluim (Image Processing, 2011)

Multispectral MRI centerline tracking in carotid arteries. - Hui Tang; Theo van Walsum; Robbert S. van Onkelen; Stefan Klein 001; Reinhard Hameeteman; Michiel Schaap; Quirijn J. A. van den Bouwhuijsen; Jacqueline C. M. Witteman; Aad van der Lugt; Lucas J. van Vliet; Wiro J. Niessen (Image Processing, 2011)

Nonrigid registration of dynamic medical imaging data using nD + t B-splines and a groupwise optimization approach. - Coert Metz; Stefan Klein 001; Michiel Schaap; Theo van Walsum; Wiro J. Niessen (Medical Image Anal., 2011)

Semi-automatic construction of reference standards for evaluation of image registration. - Keelin Murphy; Bram van Ginneken; Stefan Klein 001; Marius Staring; Bartjan de Hoop; Max A. Viergever; Josien P. W. Pluim (Medical Image Anal., 2011)

Evaluation of Registration Methods on Thoracic CT: The EMPIRE10 Challenge. - Keelin Murphy; Bram van Ginneken; Joseph M. Reinhardt; Sven Kabus; Kai Ding 003; Xiang Deng; Kunlin Cao; Kaifang Du; Gary E. Christensen; Vincent Garcia; Tom Vercauteren; Nicholas Ayache; et al. (IEEE Trans. Medical Imaging, 2011)

Comparative Evaluation of Regression Methods for 3D-2D Image Registration. - Ana Isabel Rodrigues Gouveia; Coert Metz; Luis Freire; Stefan Klein 001 (ICANN (2), 2012)

Supervised in-vivo plaque characterization incorporating class label uncertainty. - Arna van Engelen; Wiro J. Niessen; Stefan Klein 001; Harald C. Groen; Hence J. M. Verhagen; Jolanda J. Wentzel; Aad van der Lugt; Marleen de Bruijne (ISBI, 2012)

3D-2D image registration by nonlinear regression. - Ana Isabel Rodrigues Gouveia; Coert Metz; Luis Freire; Stefan Klein 001 (ISBI, 2012)

Quantitative imaging biomarkers in neurologic disease: Population study perspective. - Wiro J. Niessen; Henri A. Vrooman; Renske de Boer; Fedde van der Lijn; Hakim C. Achterberg; Marcel Koek; Stefan Klein 001; Aad van der Lugt; Marleen de Bruijne; Mohammad Arfan Ikram; Meike W. Vernooij (ISBI, 2012)

Intracranial aneurysm growth quantification in CTA. - Azadeh Firouzian; Rashindra Manniesing; Coert T. Metz; Stefan Klein 001; Birgitta K. Velthuis; Gabriel J. E. Rinkel; Aad van der Lugt; Wiro J. Niessen (Image Processing, 2012)

Registration of Free-Hand Ultrasound and MRI of Carotid Arteries through Combination of Point-Based and Intensity-Based Algorithms. - Diego D. B. Carvalho; Stefan Klein 001; Zeynettin Akkus; Gerrit L. ten Kate; Hui Tang; Mariana Selwaness; Arend F. L. Schinkel; Johan G. Bosch; Aad van der Lugt; Wiro J. Niessen (WBIR, 2012)

Hierarchical vs. Simultaneous Multiresolution Strategies for Nonrigid Image Registration. - Wei Sun 014; Wiro J. Niessen; Stefan Klein 001 (WBIR, 2012)

Estimating 3D lumen centerlines of carotid arteries in free-hand acquisition ultrasound. - Diego D. B. Carvalho; Stefan Klein 001; Zeynettin Akkus; Gerrit L. ten Kate; Arend F. L. Schinkel; Johan G. Bosch; Aad van der Lugt; Wiro J. Niessen (Int. J. Comput. Assist. Radiol. Surg., 2012)

Cardiac motion-corrected iterative cone-beam CT reconstruction using a semi-automatic minimum cost path-based coronary centerline extraction. - Alfonso A. Isola; Coert Metz; Michiel Schaap; Stefan Klein 001; Michael Grass 001; Wiro J. Niessen (Comput. Medical Imaging Graph., 2012)

Reversible jump MCMC methods for fully automatic motion analysis in tagged MRI. - Ihor Smal; Noemí Carranza-Herrezuelo; Stefan Klein 001; Piotr Wielopolski; Adriaan Moelker; Tirza Springeling; Monique Bernsen; Wiro J. Niessen; Erik Meijering (Medical Image Anal., 2012)

Semiautomatic carotid lumen segmentation for quantification of lumen geometry in multispectral MRI. - Hui Tang; Theo van Walsum; Robbert S. van Onkelen; Reinhard Hameeteman; Stefan Klein 001; Michiel Schaap; Fufa L. Tori; Quirijn J. A. van den Bouwhuijsen; Jacqueline C. M. Witteman; Aad van der Lugt; Lucas J. van Vliet; Wiro J. Niessen (Medical Image Anal., 2012)

Automated measurement of local white matter lesion volume. - Fedde van der Lijn; Benjamin F. J. Verhaaren; Mohammad Arfan Ikram; Stefan Klein 001; Marleen de Bruijne; Henri A. Vrooman; Meike W. Vernooij; Alexander Hammers; Daniel Rueckert; Aad van der Lugt; Monique M. B. Breteler; Wiro J. Niessen (NeuroImage, 2012)

Automated Brain Structure Segmentation Based on Atlas Registration and Appearance Models. - Fedde van der Lijn; Marleen de Bruijne; Stefan Klein 001; Tom den Heijer; Yoo Young Hoogendam; Aad van der Lugt; Monique M. B. Breteler; Wiro J. Niessen (IEEE Trans. Medical Imaging, 2012)

Regression-Based Cardiac Motion Prediction From Single-Phase CTA. - Coert Metz; Nora Baka; Hortense A. Kirisli; Michiel Schaap; Stefan Klein 001; Lisan Neefjes; Nico Mollet; Boudewijn P. F. Lelieveldt; Marleen de Bruijne; Wiro J. Niessen; Theo van Walsum (IEEE Trans. Medical Imaging, 2012)

Validation of a non-rigid registration method for motion compensation in 4D ultrasound of the liver. - Sinara Vijayan; Stefan Klein 001; Erlend Fagertun Hofstad; Frank Lindseth; Brynjulf Ystgaard; Thomas Langø (ISBI, 2013)

Segmentation of 3D Transesophageal Echocardiograms by Multi-cavity Active Shape Model and Gamma Mixture Model. - Alexander Haak; Gonzalo Vegas-Sánchez-Ferrero; Harriët H. Mulder; Hortense A. Kirisli; Nora Baka; Coert Metz; Stefan Klein 001; Ben Ren; Gerard van Burken; Anton F. W. van der Steen; Josien P. W. Pluim; Theo van Walsum; et al. (AE-CAI, 2013)

Groupwise Registration for Correcting Subject Motion and Eddy Current Distortions in Diffusion MRI Using a PCA Based Dissimilarity Metric. - Wyke Huizinga; Coert T. Metz; Dirk H. J. Poot; Meike de Groot; Wiro J. Niessen; Alexander Leemans; Stefan Klein 001 (CDMRI/MMBC@MICCAI, 2013)

Carotid Artery Lumen Segmentation in 3D Free-Hand Ultrasound Images Using Surface Graph Cuts. - Andrés M. Arias Lorza; Diego D. B. Carvalho; Jens Petersen; Anouk C. van Dijk; Aad van der Lugt; Wiro J. Niessen; Stefan Klein 001; Marleen de Bruijne (MICCAI (2), 2013)

Bias correction of maximum likelihood estimation in quantitative MRI. - Dirk H. J. Poot; Gyula Kotek; Wiro J. Niessen; Stefan Klein 001 (Image Processing, 2013)

Fast Parallel Image Registration on CPU and GPU for Diagnostic Classification of Alzheimer's Disease. - Denis P. Shamonin; Esther Bron; Boudewijn P. F. Lelieveldt; Marion Smits; Stefan Klein 001; Marius Staring (Frontiers Neuroinformatics, 2013)

Automatic carotid artery distensibility measurements from CTA using nonrigid registration. - K. Hameeteman; Sietske Rozie; Coert Metz; Rashindra Manniesing; Theo van Walsum; Aad van der Lugt; Wiro J. Niessen; Stefan Klein 001 (Medical Image Anal., 2013)

Improving alignment in Tract-based spatial statistics: Evaluation and optimization of image registration. - Marius de Groot; Meike W. Vernooij; Stefan Klein 001; Mohammad Arfan Ikram; Frans M. Vos; Stephen M. Smith 001; Wiro J. Niessen; Jesper L. R. Andersson (NeuroImage, 2013)

Simultaneous Multiresolution Strategies for Nonrigid Image Registration. - Wei Sun 014; Wiro J. Niessen; Marijn van Stralen; Stefan Klein 001 (IEEE Trans. Image Process., 2013)

Registration of 3D+t Coronary CTA and Monoplane 2D+t X-Ray Angiography. - Coert Metz; Michiel Schaap; Stefan Klein 001; Nora Baka; Lisan Neefjes; Carl J. Schultz; Wiro J. Niessen; Theo van Walsum (IEEE Trans. Medical Imaging, 2013)

Feature Selection Based on SVM Significance Maps for Classification of Dementia. - Esther Bron; Marion Smits; John van Swieten; Wiro J. Niessen; Stefan Klein 001 (MLMI, 2014)

Free-Form Deformation Using Lower-Order B-spline for Nonrigid Image Registration. - Wei Sun 014; Wiro J. Niessen; Stefan Klein 001 (MICCAI (1), 2014)

Atherosclerotic carotid lumen segmentation in combined B-mode and contrast enhanced ultrasound images. - Zeynettin Akkus; Diego D. B. Carvalho; Stefan Klein 001; Stijn C. H. van den Oord; Arend F. L. Schinkel; Nico de Jong; Antonius F. W. van der Steen; Johan G. Bosch (Image Processing, 2014)

Nonrigid motion compensation in B-mode and contrast enhanced ultrasound image sequences of the carotid artery. - Diego D. B. Carvalho; Zeynettin Akkus; Johan G. Bosch; Stijn C. H. van den Oord; Wiro J. Niessen; Stefan Klein 001 (Image Processing, 2014)

Influence of image registration on ADC images computed from free-breathing diffusion MRIs of the abdomen. - Jean-Marie Guyader; Livia Bernardin; Naomi H. M. Douglas; Dirk H. J. Poot; Wiro J. Niessen; Stefan Klein 001 (Image Processing, 2014)

Wavelet based free-form deformations for nonrigid registration. - Wei Sun 014; Wiro J. Niessen; Stefan Klein 001 (Image Processing, 2014)

Fast Multidimensional B-spline Interpolation Using Template Metaprogramming. - Wyke Huizinga; Stefan Klein 001; Dirk H. J. Poot (WBIR, 2014)

Non-rigid Groupwise Image Registration for Motion Compensation in Quantitative MRI. - Wyke Huizinga; Dirk H. J. Poot; Jean-Marie Guyader; Henk Smit; Matthijs van Kranenburg; Robert Jan van Geuns; André Uitterdijk; Heleen M. M. van Beusekom; Bram F. Coolen; Alexander Leemans; Wiro J. Niessen; Stefan Klein 001 (WBIR, 2014)

Randomly Perturbed Free-Form Deformation for Nonrigid Image Registration. - Wei Sun 014; Wiro J. Niessen; Stefan Klein 001 (WBIR, 2014)

Groupwise image registration of multimodal head-and-neck images. - Jean-Marie Guyader; Wyke Huizinga; Valerio Fortunati; Jifke F. Veenland; Margarethus M. Paulides; Wiro J. Niessen; Stefan Klein 001 (ISBI, 2015)

Diffeomorphic image registration with automatic time-step adjustment. - Akshay Pai; Stefan Klein 001; Stefan Sommer; Sune Darkner; Jon Sporring; Mads Nielsen (ISBI, 2015)

XNAT imaging platform for BioMedBridges and CTMM TraIT. - Stefan Klein 001; Erwin Vast; Johan van Soest; Andre Dekker; Marcel Koek; Wiro J. Niessen (J. Clin. Bioinform., 2015)

Feature Selection Based on the SVM Weight Vector for Classification of Dementia. - Esther E. Bron; Marion Smits; Wiro J. Niessen; Stefan Klein 001 (IEEE J. Biomed. Health Informatics, 2015)

Lumen Segmentation and Motion Estimation in B-Mode and Contrast-Enhanced Ultrasound Images of the Carotid Artery in Patients With Atherosclerotic Plaque. - Diego D. B. Carvalho; Zeynettin Akkus; Stijn C. H. van den Oord; Arend F. L. Schinkel; Antonius F. W. van der Steen; Wiro J. Niessen; Johan G. Bosch; Stefan Klein 001 (IEEE Trans. Medical Imaging, 2015)

Detecting Statistically Significant Differences in Quantitative MRI Experiments, Applied to Diffusion Tensor Imaging. - Dirk H. J. Poot; Stefan Klein 001 (IEEE Trans. Medical Imaging, 2015)

The Design of SuperElastix - A Unifying Framework for a Wide Range of Image Registration Methodologies. - Floris F. Berendsen; Kasper Marstal; Stefan Klein 001; Marius Staring (CVPR Workshops, 2016)

Total Correlation-Based Groupwise Image Registration for Quantitative MRI. - Jean-Marie Guyader; Wyke Huizinga; Valerio Fortunati; Dirk H. J. Poot; Matthijs van Kranenburg; Jifke F. Veenland; Margarethus M. Paulides; Wiro J. Niessen; Stefan Klein 001 (CVPR Workshops, 2016)

SimpleElastix: A User-Friendly, Multi-lingual Library for Medical Image Registration. - Kasper Marstal; Floris F. Berendsen; Marius Staring; Stefan Klein 001 (CVPR Workshops, 2016)

The pythagorean averages as group images in efficient groupwise registration. - Mathias Polfliet; Stefan Klein 001; Wyke Huizinga; Johan de Mey; Jef Vandemeulebroucke (ISBI, 2016)

Modeling the brain morphology distribution in the general aging population. - Wyke Huizinga; Dirk H. J. Poot; Gennady V. Roshchupkin; Esther E. Bron; Mohammad Arfan Ikram; Meike W. Vernooij; Daniel Rueckert; Wiro J. Niessen; Stefan Klein 001 (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2016)

Semi-automated registration of pre- and intra-operative liver CT for image-guided interventions. - Gokhan Gunay; Ha Manh Luu; Theo van Walsum; Stefan Klein 001 (Image Processing, 2016)

PCA-based groupwise image registration for quantitative MRI. - Wyke Huizinga; Dirk H. J. Poot; Jean-Marie Guyader; R. Klaassen; Bram F. Coolen; Matthijs van Kranenburg; Robert Jan van Geuns; André Uitterdijk; Mathias Polfliet; Jef Vandemeulebroucke; Alexander Leemans; Wiro J. Niessen; et al. (Medical Image Anal., 2016)

A survey of medical image registration - under review. - Max A. Viergever; J. B. Antoine Maintz; Stefan Klein 001; Keelin Murphy; Marius Staring; Josien P. W. Pluim (Medical Image Anal., 2016)

A Discriminative Event Based Model for Alzheimer's Disease Progression Modeling. - Vikram Venkatraghavan; Esther E. Bron; Wiro J. Niessen; Stefan Klein 001 (IPMI, 2017)

Radiogenomic classification of the 1p/19q status in presumed low-grade gliomas. - Sebastian R. van der Voort; Renske Gahrmann; Martin J. van den Bent; Arnaud J. P. E. Vincent; Wiro J. Niessen; Marion Smits; Stefan Klein 001 (ISBI, 2017)

Parameter Sensitivity Analysis in Medical Image Registration Algorithms Using Polynomial Chaos Expansions. - Gokhan Gunay; Sebastian R. van der Voort; Ha Manh Luu; Adriaan Moelker; Stefan Klein 001 (MICCAI (1), 2017)

Active registration models. - Kasper Marstal; Stefan Klein 001 (Image Processing, 2017)

Laplacian eigenmaps for multimodal groupwise image registration. - Mathias Polfliet; Stefan Klein 001; Wiro J. Niessen; Jef Vandemeulebroucke (Image Processing, 2017)

Registration-by-regression of coronary CTA and X-ray angiography. - Ana Isabel Rodrigues Gouveia; Coert Metz; Luis Freire; Pedro Almeida 001; Stefan Klein 001 (Comput. methods Biomech. Biomed. Eng. Imaging Vis., 2017)

Stochastic optimization with randomized smoothing for image registration. - Wei Sun 014; Dirk H. J. Poot; Ihor Smal; Xuan Yang; Wiro J. Niessen; Stefan Klein 001 (Medical Image Anal., 2017)

Randomly Perturbed B-Splines for Nonrigid Image Registration. - Wei Sun 014; Wiro J. Niessen; Stefan Klein 001 (IEEE Trans. Pattern Anal. Mach. Intell., 2017)

Classification of malignant and benign liver tumors using a radiomics approach. - Martijn P. A. Starmans; Razvan L. Miclea; Sebastian R. van der Voort; Wiro J. Niessen; Maarten G. Thomeer; Stefan Klein 001 (Image Processing, 2018)

Averaged Stochastic Optimization for Medical Image Registration Based on Variance Reduction. - Wei Sun 014; Dirk H. J. Poot; Xuan Yang; Wiro J. Niessen; Stefan Klein 001 (WBIR, 2018)

Local Image Registration Uncertainty Estimation Using Polynomial Chaos Expansions. - Gokhan Gunay; Sebastian R. van der Voort; Ha Manh Luu; Adriaan Moelker; Stefan Klein 001 (WBIR, 2018)

Disease Progression Timeline Estimation for Alzheimer's Disease using Discriminative Event Based Modeling. - Vikram Venkatraghavan; Esther E. Bron; Wiro J. Niessen; Stefan Klein 001; Alzheimer's Disease Neuroimaging Initiative (CoRR, 2018)

Intrasubject multimodal groupwise registration with the conditional template entropy. - Mathias Polfliet; Stefan Klein 001; Wyke Huizinga; Margarethus M. Paulides; Wiro J. Niessen; Jef Vandemeulebroucke (Medical Image Anal., 2018)

A spatio-temporal reference model of the aging brain. - Wyke Huizinga; Dirk H. J. Poot; Meike W. Vernooij; Gennady Roshchupkin; Esther Bron; Mohammad Arfan Ikram; Daniel Rueckert; Wiro J. Niessen; Stefan Klein 001 (NeuroImage, 2018)

Event-Based Modeling with High-Dimensional Imaging Biomarkers for Estimating Spatial Progression of Dementia. - Vikram Venkatraghavan; Florian Dubost; Esther E. Bron; Wiro J. Niessen; Marleen de Bruijne; Stefan Klein 001 (IPMI, 2019)

The Continuous Registration Challenge: Evaluation-as-a-Service for Medical Image Registration Algorithms. - Kasper Marstal; Floris F. Berendsen; Niels Dekker; Marius Staring; Stefan Klein 001 (ISBI, 2019)

Classification Of Prostate Cancer: High Grade Versus Low Grade Using A Radiomics Approach. - Jose M. Castillo T; Martijn P. A. Starmans; Wiro J. Niessen; Ivo Schoots; Stefan Klein 001; Jifke F. Veenland (ISBI, 2019)

Multi-modal Segmentation with Missing MR Sequences Using Pre-trained Fusion Networks. - Karin van Garderen; Marion Smits; Stefan Klein 001 (DART/MIL3ID@MICCAI, 2019)

A Hybrid Deep Learning Framework for Integrated Segmentation and Registration: Evaluation on Longitudinal White Matter Tract Changes. - Bo Li 088; Wiro J. Niessen; Stefan Klein 001; Marius de Groot; Mohammad Arfan Ikram; Meike W. Vernooij; Esther E. Bron (MICCAI (3), 2019)

TADPOLE Challenge: Accurate Alzheimer's Disease Prediction Through Crowdsourced Forecasting of Future Data. - Razvan V. Marinescu; Neil P. Oxtoby; Alexandra L. Young; Esther E. Bron; Arthur W. Toga; Michael W. Weiner; Frederik Barkhof; Nick C. Fox; Polina Golland; Stefan Klein 001; Daniel C. Alexander (PRIME@MICCAI, 2019)

APIR-Net: Autocalibrated Parallel Imaging Reconstruction Using a Neural Network. - Chaoping Zhang; Florian Dubost; Marleen de Bruijne; Stefan Klein 001; Dirk H. J. Poot (MLMIR@MICCAI, 2019)

Towards continuous learning for glioma segmentation with elastic weight consolidation. - Karin van Garderen; Sebastian R. van der Voort; Fatih Incekara; Marion Smits; Stefan Klein 001 (CoRR, 2019)

Disease progression timeline estimation for Alzheimer's disease using discriminative event based modeling. - Vikram Venkatraghavan; Esther E. Bron; Wiro J. Niessen; Stefan Klein 001 (NeuroImage, 2019)

Groupwise Multichannel Image Registration. - Jean-Marie Guyader; Wyke Huizinga; Valerio Fortunati; Dirk H. J. Poot; Jifke F. Veenland; Margarethus M. Paulides; Wiro J. Niessen; Stefan Klein 001 (IEEE J. Biomed. Health Informatics, 2019)

Automatic quantification of hip osteoarthritis from low-quality x-ray images. - Giancarlos Gutiérrez Cervantes; Eveling Castro Gutierrez; Javier Delgado Obando; Victor Paúl Pauca; Stefan Klein 001; Hans Lamecker (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2020)

Atlas-Based Segmentation of the Human Embryo Using Deep Learning with Minimal Supervision. - Wietske A. P. Bastiaansen; Melek Rousian; Régine P. M. Steegers-Theunissen; Wiro J. Niessen; Anton H. J. Koning; Stefan Klein 001 (ASMUS/PIPPI@MICCAI, 2020)

Deep learning-based retinal vessel segmentation with cross-modal evaluation. - Luisa Sánchez Brea; Danilo Andrade De Jesus; Stefan Klein 001; Theo van Walsum (MIDL, 2020)

Towards Segmentation and Spatial Alignment of the Human Embryonic Brain Using Deep Learning for Atlas-Based Registration. - Wietske A. P. Bastiaansen; Melek Rousian; Régine P. M. Steegers-Theunissen; Wiro J. Niessen; Anton H. J. Koning; Stefan Klein 001 (WBIR, 2020)

Analyzing the effect of APOE on Alzheimer's disease progression using an event-based model for stratified populations. - Vikram Venkatraghavan; Stefan Klein 001; Lana Fani; Leontine S. Ham; Henri A. Vrooman; M. Kamran Ikram; Wiro J. Niessen; Esther E. Bron (CoRR, 2020)

WHO 2016 subtyping and automated segmentation of glioma using multi-task deep learning. - Sebastian R. van der Voort; Fatih Incekara; Maarten M. J. Wijnenga; Georgios Kapsas; Renske Gahrmann; Joost W. Schouten; Rishi Nandoe Tewarie; Geert J. Lycklama; Philip C. de Witt Hamer; Roelant S. Eijgelaar; Pim J. French; Hendrikus J. Dubbink; et al. (CoRR, 2020)

Learning unbiased registration and joint segmentation: evaluation on longitudinal diffusion MRI. - Bo Li 088; Wiro J. Niessen; Stefan Klein 001; Mohammad Arfan Ikram; Meike W. Vernooij; Esther E. Bron (CoRR, 2020)

Cross-Cohort Generalizability of Deep and Conventional Machine Learning for MRI-based Diagnosis and Prediction of Alzheimer's Disease. - Esther E. Bron; Stefan Klein 001; Janne M. Papma; Lize C. Jiskoot; Vikram Venkatraghavan; Jara Linders; Pauline Aalten; Peter Paul De Deyn; Geert Jan Biessels; Jurgen A. H. R. Claassen; Huub A. M. Middelkoop; Marion Smits; et al. (CoRR, 2020)

An Efficient Method for Multi-Parameter Mapping in Quantitative MRI Using B-Spline Interpolation. - Willem van Valenberg; Stefan Klein 001; Frans M. Vos; Kirsten Koolstra; Lucas J. van Vliet; Dirk H. J. Poot (IEEE Trans. Medical Imaging, 2020)

Evaluating Glioma Growth Predictions as a Forward Ranking Problem. - Karin A. van Garderen; Sebastian R. van der Voort; Maarten M. J. Wijnenga; Fatih Incekara; Georgios Kapsas; Renske Gahrmann; Ahmad Alafandi; Marion Smits; Stefan Klein 001 (BrainLes@MICCAI (1), 2021)

The Effect of Preprocessing on Convolutional Neural Networks for Medical Image Segmentation. - K. B. de Raad; Karin A. van Garderen; Marion Smits; Sebastian R. van der Voort; Fatih Incekara; Edwin H. G. Oei; Jukka Hirvasniemi; Stefan Klein 001; Martijn P. A. Starmans (ISBI, 2021)

Learning unbiased group-wise registration (LUGR) and joint segmentation: evaluation on longitudinal diffusion MRI. - Bo Li 088; Wiro J. Niessen; Stefan Klein 001; Mohammad Arfan Ikram; Meike W. Vernooij; Esther E. Bron (Image Processing, 2021)

A Review of Generative Adversarial Networks in Cancer Imaging: New Applications, New Solutions. - Richard Osuala; Kaisar Kushibar; Lidia Garrucho; Akis Linardos; Zuzanna Szafranowska; Stefan Klein 001; Ben Glocker; Oliver Díaz; Karim Lekadir (CoRR, 2021)

Reproducible radiomics through automated machine learning validated on twelve clinical applications. - Martijn P. A. Starmans; Sebastian R. van der Voort; Thomas Phil; Milea J. M. Timbergen; Melissa Vos; Guillaume A. Padmos; Wouter Kessels; David Hanff; Dirk J. Grünhagen; Cornelis Verhoef; Stefan Sleijfer; Martin J. van den Bent; et al. (CoRR, 2021)

Differences Between MR Brain Region Segmentation Methods: Impact on Single-Subject Analysis. - Wyke Huizinga; Dirk H. J. Poot; Elisabeth J. Vinke; F. Wenzel; Esther Bron; N. Toussaint; Christian Ledig; Henri A. Vrooman; Mohammad Arfan Ikram; Wiro J. Niessen; Meike W. Vernooij; Stefan Klein 001 (Frontiers Big Data, 2021)

Recurrent inference machines as inverse problem solvers for MR relaxometry. - Emanoel R. Sabidussi; Stefan Klein 001; Matthan W. A. Caan; Shabab Bazrafkan; Arnold J. den Dekker; Jan Sijbers; Wiro J. Niessen; Dirk H. J. Poot (Medical Image Anal., 2021)

Longitudinal diffusion MRI analysis using Segis-Net: A single-step deep-learning framework for simultaneous segmentation and registration. - Bo Li 088; Wiro J. Niessen; Stefan Klein 001; Marius de Groot; Mohammad Arfan Ikram; Meike W. Vernooij; Esther E. Bron (NeuroImage, 2021)

Analyzing the effect of APOE on Alzheimer's disease progression using an event-based model for stratified populations. - Vikram Venkatraghavan; Stefan Klein 001; Lana Fani; Leontine S. Ham; Henri A. Vrooman; M. Kamran Ikram; Wiro J. Niessen; Esther E. Bron (NeuroImage, 2021)

Progression along data-driven disease timelines is predictive of Alzheimer's disease in a population-based cohort. - Vikram Venkatraghavan; Elisabeth J. Vinke; Esther E. Bron; Wiro J. Niessen; Mohammad Arfan Ikram; Stefan Klein 001; Meike W. Vernooij (NeuroImage, 2021)

DeepDicomSort: An Automatic Sorting Algorithm for Brain Magnetic Resonance Imaging Data. - Sebastian R. van der Voort; Marion Smits; Stefan Klein 001 (Neuroinformatics, 2021)

Motion correction in retinal optical coherence tomography imaging using deep learning registration. - Konstantinos Ntatsis; Luisa Sánchez Brea; Danilo Andrade De Jesus; João Barbosa Breda; Theo van Walsum; Edwin Bennink; Stefan Klein 001 (Image Processing, 2022)

Towards a 4D Spatio-Temporal Atlas of the Embryonic and Fetal Brain Using a Deep Learning Approach for Groupwise Image Registration. - Wietske A. P. Bastiaansen; Melek Rousian; Régine P. M. Steegers-Theunissen; Wiro J. Niessen; Anton H. J. Koning; Stefan Klein 001 (WBIR, 2022)

Automatic Segmentation of the Optic Nerve Head Region in Optical Coherence Tomography: A Methodological Review. - Rita Marques; Danilo Andrade De Jesus; João Barbosa Breda; Jan Van Eijgen; Ingeborg Stalmans; Theo van Walsum; Stefan Klein 001; Pedro G. Vaz; Luisa Sánchez Brea (Comput. Methods Programs Biomed., 2022)

Multi-Atlas Segmentation and Spatial Alignment of the Human Embryo in First Trimester 3D Ultrasound. - Wietske A. P. Bastiaansen; Melek Rousian; Régine P. M. Steegers-Theunissen; Wiro J. Niessen; Anton H. J. Koning; Stefan Klein 001 (CoRR, 2022)

Computer-aided diagnosis and prediction in brain disorders. - Vikram Venkatraghavan; Sebastian R. van der Voort; Daniel Bos; Marion Smits; Frederik Barkhof; Wiro J. Niessen; Stefan Klein 001; Esther E. Bron (CoRR, 2022)

Differential Diagnosis and Molecular Stratification of Gastrointestinal Stromal Tumors on CT Images Using a Radiomics Approach. - Martijn P. A. Starmans; Milea J. M. Timbergen; Melissa Vos; Michel Renckens; Dirk J. Grünhagen; Geert J. L. H. van Leenders; Roy S. Dwarkasing; François E. J. A. Willemssen; Wiro J. Niessen; Cornelis Verhoef; Stefan Sleijfer; Jacob J. Visser; et al. (J. Digit. Imaging, 2022)

Time efficiency analysis for undersampled quantitative MRI acquisitions. - Riwaj Byanju; Stefan Klein 001; Alexandra Cristobal-Huerta; Juan Antonio Hernández Tamames; Dirk H. J. Poot (Medical Image Anal., 2022)

Ten years of image analysis and machine learning competitions in dementia. - Esther E. Bron; Stefan Klein 001; Annika Reinke; Janne M. Papma; Lena Maier-Hein; Daniel C. Alexander; Neil P. Oxtoby (NeuroImage, 2022)

Systematic review of reconstruction techniques for accelerated quantitative MRI. - Banafshe Shafieizargar; Riwaj Byanju; Jan Sijbers; Stefan Klein 001; Arnold J. den Dekker; Dirk H. J. Poot (Zenodo, 2022)

An Interpretable Machine Learning Model with Deep Learning-Based Imaging Biomarkers for Diagnosis of Alzheimer's Disease. - Wenjie Kang; Bo Li 088; Janne M. Papma; Lize C. Jiskoot; Peter Paul De Deyn; Geert Jan Biessels; Jurgen A. H. R. Claassen; Huub A. M. Middelkoop; Wiesje M. van der Flier; Inez H. G. B. Ramakers; Stefan Klein 001; Esther E. Bron (ISIC/Care-AI/MedAGI/DeCaF@MICCAI, 2023)

Comparison of different retinal regions-of-interest imaged by OCT for the classification of intermediate AMD. - Danilo Andrade De Jesus; Eric F. Thee; Tim Doekemeijer; Daniel T. Luttikhuizen; Caroline Klaver; Stefan Klein 001; Theo van Walsum; Hans Vingerling; Luisa Sánchez 001 (CoRR, 2023)

Data synthesis and adversarial networks: A review and meta-analysis in cancer imaging. - Richard Osuala; Kaisar Kushibar; Lidia Garrucho; Akis Linardos; Zuzanna Szafranowska; Stefan Klein 001; Ben Glocker; Oliver Díaz; Karim Lekadir (Medical Image Anal., 2023)

dtiRIM: A generalisable deep learning method for diffusion tensor imaging. - Emanoel R. Sabidussi; Stefan Klein 001; Ben Jeurissen; Dirk H. J. Poot (NeuroImage, 2023)

Retinal OCT speckle as a biomarker for glaucoma diagnosis and staging. - Pedro G. Vaz; Luisa Sánchez Brea; Vania Bastos Silva; Jan Van Eijgen; Ingeborg Stalmans; João Cardoso; Theo van Walsum; Stefan Klein 001; João Barbosa Breda; Danilo Andrade De Jesus (Comput. Medical Imaging Graph., 2023)

Evaluating the Fairness of Neural Collapse in Medical Image Classification. - Kaouther Mouheb; Marawan Elbatel; Stefan Klein 001; Esther E. Bron (MICCAI (10), 2024)

qMRI Diffuser: Quantitative T1 Mapping of the Brain Using a Denoising Diffusion Probabilistic Model. - Shishuai Wang; Hua Ma; Juan Antonio Hernández Tamames; Stefan Klein 001; Dirk H. J. Poot (DGM4MICCAI@MICCAI, 2024)

Semi-supervised Three-Dimensional Detection of Congenital Brain Anomalies in First Trimester Ultrasound. - Marcella C. Zijta; Wietske A. P. Bastiaansen; Rene M. H. Wijnen; Régine P. M. Steegers-Theunissen; Bernadette de Bakker; Melek Rousian; Stefan Klein 001 (PIPPI@MICCAI, 2024)

Minimally Interactive Segmentation of Soft-Tissue Tumors on CT and MRI using Deep Learning. - Douwe J. Spaanderman; Martijn P. A. Starmans; Gonnie C. M. van Erp; David F. Hanff; Judith H. Sluijter; Anne-Rose W. Schut; Geert J. L. H. van Leenders; Cornelis Verhoef; Dirk J. Grünhagen; Wiro J. Niessen; Jacob J. Visser; Stefan Klein 001 (CoRR, 2024)

qMRI Diffusor: Quantitative T1 Mapping of the Brain using a Denoising Diffusion Probabilistic Model. - Shishuai Wang; Hua Ma; Juan Antonio Hernández Tamames; Stefan Klein 001; Dirk H. J. Poot (CoRR, 2024)

AI in radiological imaging of soft-tissue and bone tumours: a systematic review evaluating against CLAIM and FUTURE-AI guidelines. - Douwe J. Spaanderman; Matthew Marzetti; Xinyi Wan; Andrew F. Scarsbrook; Philip Robinson; Edwin H. G. Oei; Jacob J. Visser; Robert Hemke; Kirsten van Langevelde; David F. Hanff; Geert J. L. H. van Leenders; Cornelis Verhoef; et al. (CoRR, 2024)

CMAN: Cascaded Multi-scale Spatial Channel Attention-guided Network for large 3D deformable registration of liver CT images. - Xuan Loc Pham; Ha Manh Luu; Theo van Walsum; Hong Son Mai; Stefan Klein 001; Ngoc Ha Le; Trinh Chu Duc (Medical Image Anal., 2024)

The 4D Human Embryonic Brain Atlas. - Wietske A. P. Bastiaansen; Melek Rousian; Anton H. J. Koning; Wiro J. Niessen; Bernadette de Bakker; Régine P. M. Steegers-Theunissen; Stefan Klein 001 (Zenodo, 2024)

Evaluating the Predictive Value of Glioma Growth Models for Low-Grade Glioma After Tumor Resection. - Karin A. van Garderen; Sebastian R. van der Voort; Maarten M. J. Wijnenga; Fatih Incekara; Ahmad Alafandi; Georgios Kapsas; Renske Gahrmann; Joost W. Schouten; Hendrikus J. Dubbink; Arnaud J. P. E. Vincent; Martin J. van den Bent; Pim J. French; et al. (IEEE Trans. Medical Imaging, 2024)

GL-ICNN: An End-To-End Interpretable Convolutional Neural Network for the Diagnosis and Prediction of Alzheimer's Disease. - Wenjie Kang; Lize C. Jiskoot; Peter Paul De Deyn; Geert Jan Biessels; Huiberdina Koek; Jurgen A. H. R. Claassen; Huub A. M. Middelkoop; Wiesje M. van der Flier; Willemijn Jansen; Stefan Klein 001; Esther Bron (ISBI, 2025)

Recurrent inference machine for medical image registration. - Yi Zhang 120; Yidong Zhao; Hui Xue 006; Peter Kellman; Stefan Klein 001; Qian Tao (Medical Image Anal., 2025)

The 4D Human Embryonic Brain Atlas: spatiotemporal atlas generation for rapid anatomical changes using first-trimester ultrasound from the Rotterdam Periconceptional Cohort. - Wietske A. P. Bastiaansen; Melek Rousian; Anton H. J. Koning; Wiro J. Niessen; Bernadette de Bakker; Régine P. M. Steegers-Theunissen; Stefan Klein 001 (CoRR, 2025)

Freehand Ultrafast Doppler Ultrasound Imaging With Optical Tracking Allows for Detailed 3D Reconstruction of Blood Flow in the Human Brain. - Luuk Verhoef; Sadaf Soloukey; Frits Mastik; Bastian S. Generowicz; Eelke M. Bos; Joost W. Schouten; Sebastiaan K. E. Koekkoek; Arnaud J. P. E. Vincent; Stefan Klein 001; Pieter Kruizinga (IEEE Trans. Medical Imaging, 2025)