Stefan Klein

Summary

Affiliation: Erasmus MC
Country: The Netherlands

Publications

  1. ncbi request reprint Preconditioned stochastic gradient descent optimisation for monomodal image registration
    Stefan Klein
    Biomedical Imaging Group Rotterdam, Erasmus MC, Rotterdam, The Netherlands
    Med Image Comput Comput Assist Interv 14:549-56. 2011
  2. doi request reprint elastix: a toolbox for intensity-based medical image registration
    Stefan Klein
    University Medical Center Utrecht, Image Sciences Institute, 3508 GA Utrecht, The Netherlands
    IEEE Trans Med Imaging 29:196-205. 2010
  3. ncbi request reprint Conditional shape models for cardiac motion estimation
    Coert Metz
    Dept of Rad and Med Informatics, Erasmus MC, Rotterdam, The Netherlands
    Med Image Comput Comput Assist Interv 13:452-9. 2010
  4. ncbi request reprint Automated aortic calcium scoring on low-dose chest computed tomography
    Ivana Isgum
    Image Sciences Institute, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
    Med Phys 37:714-23. 2010
  5. doi request reprint Adaptive local multi-atlas segmentation: application to the heart and the caudate nucleus
    Eva M van Rikxoort
    Image Sciences Institute, University Medical Center Utrecht, The Netherlands
    Med Image Anal 14:39-49. 2010
  6. doi request reprint Automated brain structure segmentation based on atlas registration and appearance models
    Fedde van der Lijn
    Departments of Medical Informatics and Radiology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
    IEEE Trans Med Imaging 31:276-86. 2012
  7. doi request reprint Delayed gadolinium-enhanced MRI of the meniscus (dGEMRIM) in patients with knee osteoarthritis: relation with meniscal degeneration on conventional MRI, reproducibility, and correlation with dGEMRIC
    Jasper van Tiel
    Department of Orthopaedic Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
    Eur Radiol 24:2261-70. 2014
  8. doi request reprint Changes in normal-appearing white matter precede development of white matter lesions
    Marius de Groot
    Department of Radiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
    Stroke 44:1037-42. 2013
  9. doi request reprint Image subtraction facilitates assessment of volume and density change in ground-glass opacities in chest CT
    Marius Staring
    Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
    Invest Radiol 44:61-6. 2009
  10. ncbi request reprint Multiparametric computer-aided differential diagnosis of Alzheimer's disease and frontotemporal dementia using structural and advanced MRI
    Esther E Bron
    Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology and Nuclear Medicine, Erasmus MC, Office Na2502, P O Box 2040, 3000 CA, Rotterdam, The Netherlands
    Eur Radiol . 2016

Detail Information

Publications45

  1. ncbi request reprint Preconditioned stochastic gradient descent optimisation for monomodal image registration
    Stefan Klein
    Biomedical Imaging Group Rotterdam, Erasmus MC, Rotterdam, The Netherlands
    Med Image Comput Comput Assist Interv 14:549-56. 2011
    ..The method is validated on 3D fMRI time-series and 3D CT chest follow-up scans. The experimental results show that the preconditioning strategy improves the rate of convergence...
  2. doi request reprint elastix: a toolbox for intensity-based medical image registration
    Stefan Klein
    University Medical Center Utrecht, Image Sciences Institute, 3508 GA Utrecht, The Netherlands
    IEEE Trans Med Imaging 29:196-205. 2010
    ..The usage of elastix for comparing different registration methods is illustrated with three example experiments, in which individual components of the registration method are varied...
  3. ncbi request reprint Conditional shape models for cardiac motion estimation
    Coert Metz
    Dept of Rad and Med Informatics, Erasmus MC, Rotterdam, The Netherlands
    Med Image Comput Comput Assist Interv 13:452-9. 2010
    ..The prediction of motion from shape information is thus relevant for this purpose. Evaluation of the accuracy of the predicted motion was performed using CTA scans of 50 patients, showing an average accuracy of 1.1 mm...
  4. ncbi request reprint Automated aortic calcium scoring on low-dose chest computed tomography
    Ivana Isgum
    Image Sciences Institute, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
    Med Phys 37:714-23. 2010
    ..The authors developed and evaluated a computer-aided system for automatic detection and quantification of aortic calcifications in low-dose noncontrast-enhanced chest CT...
  5. doi request reprint Adaptive local multi-atlas segmentation: application to the heart and the caudate nucleus
    Eva M van Rikxoort
    Image Sciences Institute, University Medical Center Utrecht, The Netherlands
    Med Image Anal 14:39-49. 2010
    ..In addition, AMAS was applied to an online segmentation challenge for delineation of the caudate nucleus in brain MRI scans where it achieved the best score of all results submitted to date...
  6. doi request reprint Automated brain structure segmentation based on atlas registration and appearance models
    Fedde van der Lijn
    Departments of Medical Informatics and Radiology, Erasmus MC, 3000 CA Rotterdam, The Netherlands
    IEEE Trans Med Imaging 31:276-86. 2012
    ..95 for the cerebellum, and 0.87 for the hippocampus. This was comparable to or better than the other methods, whereas the proposed technique is more widely applicable and robust...
  7. doi request reprint Delayed gadolinium-enhanced MRI of the meniscus (dGEMRIM) in patients with knee osteoarthritis: relation with meniscal degeneration on conventional MRI, reproducibility, and correlation with dGEMRIC
    Jasper van Tiel
    Department of Orthopaedic Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
    Eur Radiol 24:2261-70. 2014
    ....
  8. doi request reprint Changes in normal-appearing white matter precede development of white matter lesions
    Marius de Groot
    Department of Radiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
    Stroke 44:1037-42. 2013
    ..We therefore investigated whether development of WML is preceded by quantifiable changes in normal-appearing white matter (NAWM)...
  9. doi request reprint Image subtraction facilitates assessment of volume and density change in ground-glass opacities in chest CT
    Marius Staring
    Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
    Invest Radiol 44:61-6. 2009
    ..To study the impact of image subtraction of registered images on the detection of change in pulmonary ground-glass nodules identified on chest CT...
  10. ncbi request reprint Multiparametric computer-aided differential diagnosis of Alzheimer's disease and frontotemporal dementia using structural and advanced MRI
    Esther E Bron
    Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology and Nuclear Medicine, Erasmus MC, Office Na2502, P O Box 2040, 3000 CA, Rotterdam, The Netherlands
    Eur Radiol . 2016
    ..To investigate the added diagnostic value of arterial spin labelling (ASL) and diffusion tensor imaging (DTI) to structural MRI for computer-aided classification of Alzheimer's disease (AD), frontotemporal dementia (FTD), and controls...
  11. doi request reprint Joint intensity-and-point based registration of free-hand B-mode ultrasound and MRI of the carotid artery
    Diego D B Carvalho
    Department of Radiology and Department of Medical Informatics, Biomedical Imaging Group Rotterdam, Erasmus MC, Rotterdam 3015 CE, The Netherlands
    Med Phys 41:052904. 2014
    ..To introduce a semiautomatic algorithm to perform the registration of free-hand B-Mode ultrasound (US) and magnetic resonance imaging (MRI) of the carotid artery...
  12. ncbi request reprint Carotid artery lumen segmentation in 3D free-hand ultrasound images using surface graph cuts
    Andrés M Arias Lorza
    Department of Radiology, Erasmus MC, The Netherlands
    Med Image Comput Comput Assist Interv 16:542-9. 2013
    ..Our method successfully segmented the lumen in all cases. We obtained an average dice overlap with respect to a manual segmentation of 84% for healthy volunteers. For the patient data, we obtained a dice overlap of 66.7%...
  13. ncbi request reprint A rigidity penalty term for nonrigid registration
    Marius Staring
    University Medical Center Utrecht, Image Sciences Institute, Q0S 459, P O Box 85500, 3508 GA Utrecht, The Netherlands
    Med Phys 34:4098-108. 2007
    ..The results show that nonrigid registration using the proposed rigidity penalty term is capable of nonrigidly aligning images, while keeping user-defined structures locally rigid...
  14. ncbi request reprint Patient specific 4D coronary models from ECG-gated CTA data for intra-operative dynamic alignment of CTA with X-ray images
    Coert T Metz
    Dept of Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
    Med Image Comput Comput Assist Interv 12:369-76. 2009
    ..Improvement of registration robustness by using the 2D+t/3D+t registration is successfully demonstrated by comparison of the actual X-ray cardiac phase with the automatically determined best matching phase in the 4D coronary model...
  15. ncbi request reprint Automatic segmentation of the prostate in 3D MR images by atlas matching using localized mutual information
    Stefan Klein
    Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
    Med Phys 35:1407-17. 2008
    ..87. The segmentation quality is especially good at the prostate-rectum interface, where the segmentation error remains below 1 mm in 50% of the cases and below 1.5 mm in 75% of the cases...
  16. pmc Atherosclerotic plaque component segmentation in combined carotid MRI and CTA data incorporating class label uncertainty
    Arna van Engelen
    Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
    PLoS ONE 9:e94840. 2014
    ....
  17. doi request reprint Semiautomatic carotid lumen segmentation for quantification of lumen geometry in multispectral MRI
    Hui Tang
    Biomedical Imaging Group Rotterdam, Departments of Radiology and Medical Informatics, Erasmus MC, Rotterdam, The Netherlands
    Med Image Anal 16:1202-15. 2012
    ..This demonstrates that the automated method can be used for replacing manual centerline annotation and manual contour drawing for lumen segmentation in MRIs data prior to quantifying the carotid bifurcation geometry...
  18. pmc Structural and functional brain abnormalities place phenocopy frontotemporal dementia (FTD) in the FTD spectrum
    Rebecca M E Steketee
    Department of Radiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
    Neuroimage Clin 11:595-605. 2016
    ..We aimed to identify abnormalities in gray matter (GM) volume and perfusion in phFTD and to assess whether phFTD belongs to the FTD spectrum. We compared phFTD patients with both healthy controls and bvFTD patients...
  19. doi request reprint No Difference on Quantitative Magnetic Resonance Imaging in Patellofemoral Cartilage Composition Between Patients With Patellofemoral Pain and Healthy Controls
    Rianne A van der Heijden
    Department of General Practice, Erasmus MC, University Medical Center, Rotterdam, The Netherlands Department of Radiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
    Am J Sports Med 44:1172-8. 2016
    ..To date, there is no conclusive evidence for an association between cartilage defects and PFP. Nowadays, advanced quantitative magnetic resonance imaging (MRI) techniques enable estimation of cartilage composition...
  20. doi request reprint Determinants of carotid atherosclerotic plaque burden in a stroke-free population
    Mariana Selwaness
    Department of Epidemiology, MC, Rotterdam, The Netherlands
    Atherosclerosis 255:186-192. 2016
    ..In a large stroke-free population, we sought to identify cardiovascular risk factors and carotid plaque components associated with carotid plaque burden, lumen volume and stenosis...
  21. pmc Early-stage differentiation between presenile Alzheimer's disease and frontotemporal dementia using arterial spin labeling MRI
    Rebecca M E Steketee
    Department of Radiology, Erasmus MC University Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
    Eur Radiol 26:244-53. 2016
    ....
  22. pmc Automated segmentation of atherosclerotic histology based on pattern classification
    Arna van Engelen
    Biomedical Imaging Group Rotterdam, Department of Medical Informatics and Radiology, Erasmus Medical Centre, Rotterdam, Netherlands
    J Pathol Inform 4:S3. 2013
    ..Histology sections provide accurate information on atherosclerotic plaque composition, and are used in various applications. To our knowledge, no automated systems for plaque component segmentation in histology sections currently exist...
  23. doi request reprint Registration of cervical MRI using multifeature mutual information
    Marius Staring
    University Medical Center Utrecht, Image Sciences Institute, Utrecht, The Netherlands
    IEEE Trans Med Imaging 28:1412-21. 2009
    ..76 to 0.77 for the rectum (p = 2 x 10(-4)). The registration error is improved at important tissue interfaces, such as that of the bladder with the CTV, and the interface of the rectum with the uterus and cervix...
  24. ncbi request reprint Iterative co-linearity filtering and parameterization of fiber tracts in the entire cingulum
    Marius de Groot
    Biomedical Imaging Group Rotterdam, Department of Radiology, Erasmus MC, Rotterdam, The Netherlands
    Med Image Comput Comput Assist Interv 12:853-60. 2009
    ..Our asymmetry analysis shows a higher fractional anisotropy in the left anterior part of the cingulum compared to the right side, and the opposite effect in the posterior part...
  25. doi request reprint Fully automated carotid plaque segmentation in combined contrast-enhanced and B-mode ultrasound
    Zeynettin Akkus
    Department of Biomedical Engineering, Thoraxcenter, Erasmus MC, Rotterdam, The Netherlands
    Ultrasound Med Biol 41:517-31. 2015
    ..To the best of our knowledge, this is the first method to perform fully automatic carotid plaque segmentation using combined BMUS and CEUS...
  26. doi request reprint Improving alignment in Tract-based spatial statistics: evaluation and optimization of image registration
    Marius de Groot
    Department of Radiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
    Neuroimage 76:400-11. 2013
    ..At optimal parameters, both algorithms outperformed the registration of TBSS, showing feasibility of adopting such approaches in TBSS. This was further confirmed in the example experiment...
  27. doi request reprint Estimating 3D lumen centerlines of carotid arteries in free-hand acquisition ultrasound
    Diego D B Carvalho
    Department of Radiology and Med Informatics, Biomedical Imaging Group Rotterdam, Erasmus MC, Rotterdam, The Netherlands
    Int J Comput Assist Radiol Surg 7:207-15. 2012
    ..Challenging aspects here are speckle noise in US images, artifacts, and the lack of contrast in the direction orthogonal to the US beam direction...
  28. ncbi request reprint Evaluation of optimization methods for nonrigid medical image registration using mutual information and B-splines
    Stefan Klein
    University Medical Center Utrecht, Image Sciences Institute, 3508 GA Utrecht, The Netherlands
    IEEE Trans Image Process 16:2879-90. 2007
    ..From the other methods the quasi-Newton and the nonlinear conjugate gradient method achieve a slightly higher precision, at the price of larger computation times...
  29. doi request reprint A survey of medical image registration - under review
    Max A Viergever
    Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands Electronic address
    Med Image Anal 33:140-4. 2016
    ..It may be concluded that the field of medical image registration has evolved, but still is in need of further development in various aspects. ..
  30. doi request reprint T1 mapping in the rat myocardium at 7 tesla using a modified CINE inversion recovery sequence
    Henk Smit
    Departments of Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
    J Magn Reson Imaging 39:901-10. 2014
    ..To evaluate the reproducibility and sensitivity of the modified CINE inversion recovery (mCINE-IR) acquisition on rats for measuring the myocardial T1 at 7 Tesla...
  31. doi request reprint Automated measurement of local white matter lesion volume
    Fedde van der Lijn
    Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands
    Neuroimage 59:3901-8. 2012
    ..But the proposed method can localize the region of association with greater precision than techniques that distinguish between periventricular and subcortical lesions only...
  32. doi request reprint Multi-feature-based plaque characterization in ex vivo MRI trained by registration to 3D histology
    Arna van Engelen
    Biomedical Imaging Group Rotterdam, Department of Medical Informatics, Erasmus, MC, Rotterdam, The Netherlands
    Phys Med Biol 57:241-56. 2012
    ..05). Although 2D registration or selection of three slices from the 3D set slightly decreased accuracy, these differences were non-significant...
  33. doi request reprint Automated Registration of Freehand B-Mode Ultrasound and Magnetic Resonance Imaging of the Carotid Arteries Based on Geometric Features
    Diego D B Carvalho
    Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus MC, Rotterdam, The Netherlands
    Ultrasound Med Biol 43:273-285. 2017
    ..We conclude that the proposed method can robustly and accurately register US and MR images of the carotid artery, allowing multimodal analysis of the carotid plaque to improve plaque assessment...
  34. doi request reprint Stochastic optimization with randomized smoothing for image registration
    Wei Sun
    Biomedical Imaging Group Rotterdam, Departments of Radiology and Medical Informatics, Erasmus MC, Rotterdam, The Netherlands Laboratory of Neuro Imaging LONI, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Los Angeles, USA Electronic address
    Med Image Anal 35:146-158. 2017
    ..Experiments on synthetic images, cell images, public CT lung data, and public MR brain data demonstrate the effectiveness of the novel RS technique in terms of registration accuracy and robustness...
  35. pmc Delayed gadolinium-enhanced MRI of cartilage (dGEMRIC) shows no change in cartilage structural composition after viscosupplementation in patients with early-stage knee osteoarthritis
    Jasper van Tiel
    Department of Orthopedic Surgery, Erasmus MC, University Medical Center, Rotterdam, The Netherlands Department of Radiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
    PLoS ONE 8:e79785. 2013
    ..The aim of this study was to assess whether improvement in cartilage structural composition is detected using dGEMRIC 14 weeks after 3 weekly injections with HA in patients with early-stage knee OA...
  36. doi request reprint Evaluation of registration methods on thoracic CT: the EMPIRE10 challenge
    Keelin Murphy
    Image Sciences Institute, University Medical Center, Utrecht, The Netherlands
    IEEE Trans Med Imaging 30:1901-20. 2011
    ..This paper details the organization of the challenge, the data and evaluation methods and the outcome of the initial launch with 20 algorithms. The gain in knowledge and future work are discussed...
  37. pmc Real-time decoding of brain responses to visuospatial attention using 7T fMRI
    Patrik Andersson
    Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
    PLoS ONE 6:e27638. 2011
    ..ECoG data recorded from one epilepsy patient showed that local changes in gamma-power can be used to separate the three classes...
  38. ncbi request reprint Trans-dimensional MCMC methods for fully automatic motion analysis in tagged MRI
    Ihor Smal
    Biomedical Imaging Group Rotterdam, Department of Medical Informatics, Erasmus MC University Medical Center, Rotterdam, The Netherlands
    Med Image Comput Comput Assist Interv 14:573-80. 2011
    ....
  39. doi request reprint Influence of image registration on apparent diffusion coefficient images computed from free-breathing diffusion MR images of the abdomen
    Jean Marie Guyader
    Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus MC University Medical Center Rotterdam, The Netherlands
    J Magn Reson Imaging 42:315-30. 2015
    ..To evaluate the influence of image registration on apparent diffusion coefficient (ADC) images obtained from abdominal free-breathing diffusion-weighted MR images (DW-MRIs)...
  40. pmc Multiple Sparse Representations Classification
    Esben Plenge
    Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus University Medical Center, Rotterdam, The Netherlands
    PLoS ONE 10:e0131968. 2015
    ..The results show that mSRC outperforms SRC and the other reference methods. In addition, we present an extensive evaluation of the effect of the main mSRC parameters: patch size, dictionary size, and sparsity level. ..
  41. pmc Standardized evaluation of algorithms for computer-aided diagnosis of dementia based on structural MRI: the CADDementia challenge
    Esther E Bron
    Biomedical Imaging Group Rotterdam, Department of Medical Informatics, Erasmus MC, Rotterdam, The Netherlands Biomedical Imaging Group Rotterdam, Department of Radiology, Erasmus MC, Rotterdam, The Netherlands Electronic address
    Neuroimage 111:562-79. 2015
    ..The challenge is open for new submissions via the web-based framework: http://caddementia.grand-challenge.org. ..
  42. doi request reprint Diagnostic classification of arterial spin labeling and structural MRI in presenile early stage dementia
    Esther E Bron
    Departments of Medical Informatics and Radiology, Biomedical Imaging Group Rotterdam, Erasmus MC University Medical Center Rotterdam, The Netherlands
    Hum Brain Mapp 35:4916-31. 2014
    ..However, our findings indicated only little added diagnostic value when combining ASL with the structural MRI data (AUC = 91%), which did not significantly improve over accuracy of structural MRI atrophy marker by itself...
  43. pmc Image registration improves human knee cartilage T1 mapping with delayed gadolinium-enhanced MRI of cartilage (dGEMRIC)
    Esther E Bron
    Biomedical Imaging Group Rotterdam, Departments of Medical Informatics and Radiology, Erasmus MC, P O Box 2040, 3000, CA, Rotterdam, The Netherlands
    Eur Radiol 23:246-52. 2013
    ....
  44. ncbi request reprint Nonrigid registration with tissue-dependent filtering of the deformation field
    Marius Staring
    Image Sciences Institute, University Medical Center Utrecht, PO Box 85500, 3508 GA, Room Q0S 459, Utrecht, The Netherlands
    Phys Med Biol 52:6879-92. 2007
    ..The results show that tissue-dependent filtering of the deformation field leads to improved registration results: tumour volumes and vessel widths are preserved rather than affected...
  45. pmc Facilitating tumor functional assessment by spatially relating 3D tumor histology and in vivo MRI: image registration approach
    Lejla Alic
    Biomedical Imaging Group Rotterdam, Department of Radiology and Medical Informatics, Erasmus Medical Center, Rotterdam, The Netherlands
    PLoS ONE 6:e22835. 2011
    ..However, registration is complicated by deformations during pathological processing, and differences in scale and information content...