Publications

1 Reyes M., Meier R., Pereira S., Silva C., Dahlweid FM., von Teng-Kobligk H., Summers R., and Wiest R. On the interpretability of artificial intelligence in radiology: Challenges and opportunities. Radiology: Artificial Intelligence, 2(3):e190043, 2020.
2 Bjoern Menze, Fabian Isensee, Roland Wiest, Bene Wiestler, Klaus Maier-Hein, Mauricio Reyes, and Spyridon Bakas. Analyzing magnetic resonance imaging data from glioma patients using deep learning. Computerized Medical Imaging and Graphics, page 101828, 2020.
3 Balsiger F., Jungo A., Scheidegger O., Carlier P., Reyes M., and Marty B. Spatially regularized parametric map reconstruction for fast magnetic resonance fingerprinting. Medical Image Analysis, 64:101741, August 2020.
4 Suter Y., Knecht U., Alao M., Valenzuela W., Hewer E., Schucht P., Wiest R., and Reyes M. Radiomics for glioblastoma survival analysis in pre-operative mri: Exploring feature robustness, class boundaries, and machine learning techniques. Cancer Imaging, 20(2):1–13, June 2020.
5 Michael Rebsamen, Christian Rummel, Mauricio Reyes, Roland Wiest, and Richard McKinley. Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation. Human brain mapping, 41(17):4804–4814, 2020.
6 Zongxin-Jin B., De Stefano P., Petroulia V., Rummel C., Kiefer C., Reyes M., Schindler K., van Mierlo P., Seeck M., and Wiest R. Diagnosis of epilepsy after first seizure. introducing the swiss first study. Clinical and Translational Neuroscience, 4(2):2514183X20939448, 2020.
7 Ermi¸s E., Jungo A., Poel R., Blatti-Moreno M., Meier R., Knecht U., Aebersold D., Fix M., Manser P., Reyes M., and Herrmann E. Fully automated brain resection cavity delineation for radiation target volume definition in glioblastoma patients using deep learning. Radiation oncology, 15:1–10, 2020.
8 Hu X., Luo W., Hu J., Guo S., Huang W., Scott M., Wiest R., Dahlweid M., and Reyes M. Brain segnet: 3d local refinement network for brain lesion segmentation. BMC Medical Imaging, 20(1):17, 2020.
9 Jungo A., Balsiger F., and Reyes M. Analyzing the quality and challenges of uncertainty estimations for brain tumor segmentation. Frontiers in Neuroscience, 14:282, 2020.
10 McKinley R., Wepfer R., Grunder L., Aschwanden F., Fischer T., Friedli C., Muri R., Rummel C., Verma R.K., Weisstanner C., Wiestler B., Berger C., Eichinger P., Muhlau M., Reyes M., Salmen A., Chan A., Wiest R., and Wagner F. Automatic detection of lesion load change in multiple sclerosis using convolutional neural networks with segmentation confidence. NeuroImage: Clinical, 25:102104, 2020.
11 Rebsamen M., Suter Y., Wiest R., Reyes M., and Rummel C. Brain morphometry estimation: From hours to seconds using deep learning. Frontiers in Neurology, 11:244, 2020.
12 Barros N., Meier R., Pletscher M., Stettler S., Knecht U., Reyes M., Gralla J., Wiest R., and Slotboom J. Analysis of metabolic abnormalities in high-grade glioma using mrsi and convex nmf. NMR in Biomedicine, 32(8):e4109, August 2019.
13 Bozorgtabar B., Mahapatra D., von Teng-Kobligk H., Pollinger A., Ebner L., Thiran JP., and Reyes M. Informative sample generation using class aware generative adversarial networks for classification of chest xrays. Computer Vision and Image Understanding, 184:57–65, 2019.
14 Meier R., Lux P., Jung S., Fischer U., Gralla J., Reyes M., Wiest R., McKinley R., and Kaesmacher J. Neural network–derived perfusion maps for the assessment of lesions in patients with acute ischemic stroke. Radiology: Artificial Intelligence, 1(5):e190019, 2019.
15 Pinto A., Mckinley R., Alves V., Wiest R., Silva C., and Reyes M. Stroke lesion outcome prediction based on mri imaging combined with clinical information. Frontiers in Neurology, 9:1060, 2018.
16 Balsiger F., Steindel C., Arn M., Wagner B., Grunder L., El-Koussy M., Valenzuela W., Reyes M., and Scheidegger O. Segmentation of peripheral nerves from magnetic resonance neurography: A fully-automatic, deep learning-based approach. Frontiers in Neurology, 9:777, 2018.
17 Habegger S., Wiest R., Weder B., Mordasini P., Gralla J., Haeni L., Jung S., Reyes M., and McKinley R. Relating acute lesion loads to chronic outcome in ischemic stroke–an exploratory comparison of mismatch patterns and predictive modeling. Frontiers in Neurology, 9:737, 2018.
18 Winzeck S., Hakim A., McKinley R., Pinto J., Alves V., Silva C., Pisov M., Krivov E., Belyaev M., Monteiro M., Oliveira A., Choi Y., Paik M., Kwon Y., Lee H., Kim B., Won J-H, Islam M., Ren H., Robben D., Suetens P., Gong E., Niu Y., Xu J., Pauly J., Lucas C., Heinrich M., Rivera L., Castillo L., Daza L., Beers A., Arbelaezs P., Maier O., Chang K., Brown J., Kalpathy-Cramer J., Zaharchuk G., Wiest R., and Reyes M. Isles 2016 and 2017-benchmarking ischemic stroke lesion outcome prediction based on multispectral mri. Frontiers in Neurology, 9:679, 2018.
19 Pereira S., Meier R., McKinley R., Wiest R., Alves V., Silva C., and Reyes M. Enhancing interpretability of automatically extracted machine learning features: application to a rbm-random forest system on brain lesion segmentation. Med Image Anal, 44:228–244, Feb 2018.
20 Barros N., Meier R., Pletscher M., Stettler S., Knecht U., Herrmann E., Schucht P., Reyes M., Gralla J., Wiest R., and Slotboom J. On the relation between mr spectroscopy features and the distance to mri-visible solid tumor in gbm patients. Magn Reson Med, Jun 2018.
21 Chandran V., Reyes M., and Zysset P. A novel registration-based methodology for prediction of trabecular bone fabric from clinical qct: A comprehensive analysis. PLOS ONE, 12(11):1–23, 11 2017.
22 Gerber N., Reyes M., Barazzetti L., Kjer H., Vera S., Stauber M., Mistrik P., Ceresa M., Mangado N., Wimmer W., Stark T., Paulsen R., Weber S., Caversaccio M., and Ballester-Gonzalez M. A multiscale imaging and modelling dataset of the human inner ear. Nature Scientific Data, 4:170132 EP –, 09 2017.
23 Meier R., Porz N., Knecht U., Loosli T., Schucht P., Beck J., Slotboom J., Wiest R., and Reyes M. Automatic estimation of extent of resection and residual tumor volume of patients with glioblastoma. Journal of Neurosurgery, pages 1–9, 2017.
24 Kellner-Weldon F., Stippich C., Wiest R., Lehmann V., Meier R., Beck J., Schucht P., Raabe A., Reyes M., and Bink A. Comparison of perioperative automated versus manual two-dimensional tumor analysis in glioblastoma patients. Eur J Radiol, 95:75–81, Oct 2017.
25 Lu P., Barazzetti L., Chandran V., Gavaghan K., Weber S., Gerber N., and Reyes M. Highly accurate facial nerve segmentation refinement from cbct/ct imaging using a super resolution classification approach. IEEE Transactions on Biomedical Engineering, PPs(99):1–1, 2017.
26 Porz N., Habegger S., Meier R., Verma R.K., Jilch A., Fichtner J., Knecht U., Radina C., Schucht P., Ju¨rgen B., Raabe A., Slotboom J., Reyes M., and Wiest R. Fully automated enhanced tumor compartmentalization: Man vs. machine reloaded. PLoS ONE, 11(11):1–16, 11 2016.
27 Maier O., Menze B., Wiest R., Handels H., and Reyes M. ISLES 2015 - A public evaluation benchmark for ischemic stroke lesion segmentation from multispectral MRI. Medical Image Analysis, 35:250–269, aug 2016.
28 McKinley R., Haeni L., Gralla J., El-Koussy M., Bauer S., Arnold M., Fischer U., Jung S., Mattmann K., Reyes M., and Wiest R. Fully automated stroke tissue estimation using random forest classifiers (faster). Journal of Cerebral Blood Flow and Metabolism, 37(8):2728–2741, August 2017.
29 Meier R., Knecht U., Loosli T., Bauer S., Slotboom J., Wiest R., and Reyes M. Clinical evaluation of a fully-automatic segmentation method for longitudinal brain tumor volumetry. Nature Scientific Reports, 6(23376), 2016.
30 Valenzuela W., Ferguson S., Ignasiak D., Diserens G., Haeni L., Wiest R., Vermathen P., Boesch C., and Reyes M. Fisico: Fast image segmentation correction. PLoS ONE, 11(5):1–17, 05 2016.
31 Seif M., Mani L., Lu H., Boesch C., Reyes M., Vogt B., and Vermathen P. Diffusion tensor imaging of the human kidney: Does image registration permit scanning without respiratory triggering? J Magn Reson Imaging, 44(2):327–334, Feb 2016.
32 Taghizadeh E., Reyes M., Zysset P., Latypova A., Terrier A., and Buchler P. Biomechanical role of bone anisotropy estimated on clinical ct scans by image registration. Ann Biomed Eng, Jan 2016.
33 Rios-Velazquez E., Meier R., Dunn W., Alexander B., Wiest R., Bauer S., Gutmann D., Reyes M., and Aerts H. Fully automatic gbm segmentation in the tcga-gbm dataset: Prognosis and correlation with vasari features. Nature Scientific Reports, 5(16822), November 2015.
34 Menze B., Reyes M., and Van Leemput K. The multimodal brain tumor image segmentation benchmark (brats). IEEE Trans Med Imaging, 34(10), Oct 2015.
35 Cerrolaza J.J., Reyes M., Summers R.M., Gonz´alez-Ballester M.A., and Linguraru M.G. Automatic multi-resolution shape modeling of multi-organ structures. Medical Image Analysis, 25(1):11–21, April 2015.
36 V. Chappuis, O. Engel, K. Shahim, M. Reyes, C. Katsaros, and D. Buser. Soft tissue alterations in esthetic postextraction sites: A 3-dimensional analysis. Journal of Dental Research, 94(9 suppl):187S–193S, 2015.
37 Seif M., Lu H., Boesch C., Reyes M., and Vermathen P. Image registration for triggered and non-triggered dti of the human kidney: Reduced variability of diffusion parameter estimation. J Magn Reson Imaging, 41(5):1228–1235, Jun 2014.
38 Porz N., Bauer S., Pica A., Schucht P., Beck J., Verma R.K., Slotboom J., Reyes M., and Wiest R. Multi-modal glioblastoma segmentation: Man versus machine. PLoS ONE, 9(5):e96873, May 2014.
39 Bonaretti S., Seiler C., Boichon C., Reyes M., and Buechler P. Image-based vs. mesh-based statistical appearance models of the human femur: Implications for finite element simulations. Medical Engineering & Physics, 36(12):1626 – 1635, 2014.
40 Bou-Sleiman H., Paul L., Nolte L.P., and Reyes M. Comparative evaluation of pelvic allograft selection methods. Annals of Biomedical Engineering, 41(5):931–938, May 2013.
41 Oliveira-Santos T., Baumberger C., Constantinescu M., Olariu R., Nolte L.P., Alaraibi S., and Reyes M. 3d face reconstruction from 2d pictures: First results of a web-based computer aided system for aesthetic procedures. Annals of Biomedical Engineering, 41(5):952–966, May 2013.
42 Lu H., Beisteiner R., Nolte L.P., and Reyes M. Hierarchical segmentation-assisted multimodal registration for mr brain images. Computerized Medical Imaging and Graphics, 37(3):234–244, April 2013.
43 Bauer S., Lu H., May C., Nolte L.P., Buechler P., and Reyes M. Integrated segmentation of brain tumor images for radiotherapy and neurosurgery. International Journal of Imaging Systems and Technology, 23(1):59–63, March 2013.
44 Bou Sleiman H., Iizuka T., Nolte L.P., and Reyes M. Population-based design of mandibular fixation plates with bone quality and morphology considerations. Annals of Biomedical Engineering, 41(2):377–384, February 2013.
45 Bauer S., Wiest R., Nolte L.P., and Reyes M. A survey of mri-based medical image analysis for brain tumor studies. Physics in Medicine and Biology, 58(13):R97, 2013.
46 Chappuis V., Engel O., Reyes. M., Shahim K., Nolte L.P., and Buser D. Ridge alterations post-extraction in the esthetic zone a 3d analysis with cbct. Journal of Dental Research, 92(12 suppl):195S–201S, 2013.
47 Kim B.R., Oh K.M., Cevidanes L.H.S., Park J.E., Sim H.S., Seo S.K., Reyes M., Kim Y.J., and Park Y.H. Analysis of 3d soft tissue changes after 1-and 2-jaw orthognathic surgery in mandibular prognathism patients. Journal of Oral and Maxillofacial Surgery, 71(1):151–161, January 2013.
48 Seiler C., Pennec X., Nolte L.P., and Reyes M. Capturing the multiscale anatomical shape variability with polyaffine transformation trees. Medical Image Analysis, 16(7):1371–1384, October 2012.
49 Bauer S., Ritacco L.E., Boesch C., Nolte L.P., and Reyes M. Automatic scan planning for magnetic resonance imaging of the knee joint. Annals of Biomedical Engineering, 40(9):2033–2042, September 2012.
50 Blanc R., Seiler C., Sz´ekely G., Nolte L.P., and Reyes M. Statistical model based shape prediction from a combination of direct observations and various surrogates. application to orthopaedic research. Medical Image Analysis, 16(6):1156–1166, August 2012.
51 Seiler C., Gazdhar A., Reyes M., Benneker L.M., Geiser T., Siebenrock K.A., and Gantenbein-Ritter B. Time-lapse microscopy and classification of 2d human mesenchymal stem cells based on cell shape picks up myogenic from osteogenic and adipogenic differentiation. Journal of Tissue Engineering and Regenerative Medicine, page In Press, July 2012.
52 Ritacco L.E., Seiler C., Farfalli G.L., Nolte L., Reyes M., Muscolo D.L., and Tinao L.A. Validity of an automatic measure protocol in distal femur for allograft selection from a three-dimensional virtual bone bank system. Cell Tissue Bank, 1:1–8, Apr 2012.
53 de Heras Ciechomski P., Constantinescu M., Garcia J., Olariu R., Dindoyal I., Le Huu S., and Reyes M. Development and implementation of a web-enabled 3d consultation tool for breast augmentation surgery based on 3d-image reconstruction of 2d pictures. Journal of Medical Internet Research, 14(1):e21, 2012.
54 Lu H., Nolte L.P., and Reyes M. Interest points localization for brain image using landmark-annotated atlas. International Journal of Imaging Systems and Technology, 22(2):145–152, 2012.
55 Schulz A.P, Reimers N. Nils, Wipf F., Vallotton M., Bonaretti S., Kozic N., Reyes M., and Kienast B.J. Evidence based development of a novel lateral fibula plate (variax fibula) using a real ct bone data based optimization process during device development. Open Orthop J, 6:1–7, January 2012.
56 Kim Y.J., Oh K.M., Hong J.S., Lee J.H., Kim H.M., Reyes M., Cevidanes L.H.S., and Park Y.H. Do patients treated with bimaxillary surgery have more stable condylar positions than those who have undergone single-jaw surgery? Journal of Oral and Maxillofacial Surgery, 70(9):2143–52, September 2011.
57 Bauer S., May C., Dionysiou D., Stamatakos G., Buechler P., and Reyes M. Multi-scale modeling for image analysis of brain tumor studies. IEEE Trans Biomed Eng, 59(1):25–29, Aug 2011.
58 Ju¨rgens P., Klug C., Krol Z., Beinemann J., Kim H., Reyes M., Guevara-Rojas G., Zeilhofer H. F, Ewers R., and Schicho K. Navigation-guided harvesting of autologous iliac crest graft for mandibular reconstruction. J Oral Maxillofac Surg, 69(11):2915–2923, May 2011.
59 Bou Sleiman H., Ritacco L.E., Aponte-Tinao L., Muscolo D.L., Nolte L.P., and Reyes M. Allograft selection for transepiphyseal tumor resection around the knee using three-dimensional surface registration. Annals of Biomedical Engineering, 39(6):1720–7, March 2011.
60 Marias K., Dionysiou D., Sakkalis V., Graf N., Bohle RM, Coveney PV, Wan S., Folarin A., Bu¨chler P., Reyes M., et al. Clinically driven design of multi-scale cancer models: the contracancrum project paradigm. Interface Focus, 1(3):450–461, 2011.
61 Kim H., Ju¨rgens P., Weber S., Nolte L.P., and Reyes M. A new soft-tissue simulation strategy for cranio-maxillofacial surgery using facial muscle template model. Progress in Biophysics and Molecular Biology. Special Issue on Soft Tissue Modelling, 103(2-3):284–291, December 2010.
62 Tucker S., Cevidanes L., Styner M., Kim H., Reyes M., Proffit W., and Turvey T. Comparison of actual surgical outcomes and 3-dimensional surgical simulations. J Oral Maxillofac Surg, 68(10):2412–2421, Oct 2010.
63 Kozic N., Weber S., Bu¨chler P., Lutz C., Reimers N., Gonz´alez Ballester MA., and Reyes M. Optimisation of orthopaedic implant design using statistical shape space analysis based on level sets. Medical Image Analysis, 14(3):265–275, June 2010.
64 Cevidanes L., Tucker S., Styner M., Kim H., Chapuis J., Reyes M., Proffit W., Turvey T., and Jaskolka M. Three-dimensional surgical simulation. American Journal of Orthodontics and Dentofacial Orthopedics, 138(3):361 – 371, 2010.
65 Kozic N., Weber S., Gonz´alez-Ballester M.A., Abdo G., Rufenacht D.A., Ferguson S., and Reyes M. Automated cement segmentation in vertebroplasty. Comput Aided Surg, 15(1-3):49–55, 2010.
66 Reyes M., Malandain G., Koulibaly P.M., Gonz´alez-Ballester M.A., and Darcourt J. Model-based respiratory motion compensation for emission tomography image reconstruction. Physics in Medicine and Biology, 52(12):3579–3600, June 2007.
67 Linguraru M.G., Vercauteren T., Reyes M., Gonz´alez-Ballester M.A., and Ayache N. Segmentation propagation from deformable atlases for brain mapping and analysis. Brain Research Journal, 1(4):269–287, 2007.
68 Reyes M., Gonz´alez-Ballester M.A., and Linguraru M.G. Statistical bone shape analysis for image free surgery. Acta Universitatis Cibiniensis, Technical Series, Vol, LV:121–129, 2007.
69 Malandain G. and Reyes M. La tomographie en mouvement. Pour la science, 338:132–137, December 2005.
70 Reyes M. and Pereda J. Reconstrucci´on virtual de la mano de un embri´on humano, evaluaci´on experimental. Teor´ıa y Metodolog´ıas. Cl´ınica y Ciencia magazine, 1(2), 2001.