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1. Standardized Assessment of Automatic Segmentation of White Matter Hyperintensities and Results of the WMH Segmentation Challenge

Author

Kuijf, Hugo J., Biesbroek, J. Matthijs, de Bresser, Jeroen, Heinen, Rutger, Andermatt, Simon, Bento, Mariana, Berseth, Matt, Belyaev, Mikhail, Cardoso, M. Jorge, Casamitjana, Adrià, Collins, D. Louis, Dadar, Mahsa, Georgiou, Achilleas, Ghafoorian, Mohsen, Jin, Dakai, Khademi, April, Knight, Jesse, Li, Hongwei, Lladó, Xavier, Luna, Miguel, Mahmood, Qaiser, McKinley, Richard, Mehrtash, Alireza, Ourselin, Sébastien, Park, Bo-yong, Park, Hyunjin, Park, Sang Hyun, Pezold, Simon, Puybareau, Elodie, Rittner, Leticia, Sudre, Carole H., Valverde, Sergi, Vilaplana, Verónica, Wiest, Roland, Xu, Yongchao, Xu, Ziyue, Zeng, Guodong, Zhang, Jianguo, Zheng, Guoyan, Chen, Christopher, van der Flier, Wiesje, Barkhof, Frederik, Viergever, Max A., and Biessels, Geert Jan

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR images, which is a laborious procedure. Automatic WMH segmentation methods exist, but a standardized comparison of the performance of such methods is lacking. We organized a scientific challenge, in which developers could evaluate their method on a standardized multi-center/-scanner image dataset, giving an objective comparison: the WMH Segmentation Challenge (https://wmh.isi.uu.nl/). Sixty T1+FLAIR images from three MR scanners were released with manual WMH segmentations for training. A test set of 110 images from five MR scanners was used for evaluation. Segmentation methods had to be containerized and submitted to the challenge organizers. Five evaluation metrics were used to rank the methods: (1) Dice similarity coefficient, (2) modified Hausdorff distance (95th percentile), (3) absolute log-transformed volume difference, (4) sensitivity for detecting individual lesions, and (5) F1-score for individual lesions. Additionally, methods were ranked on their inter-scanner robustness. Twenty participants submitted their method for evaluation. This paper provides a detailed analysis of the results. In brief, there is a cluster of four methods that rank significantly better than the other methods, with one clear winner. The inter-scanner robustness ranking shows that not all methods generalize to unseen scanners. The challenge remains open for future submissions and provides a public platform for method evaluation., Comment: Accepted for publication in IEEE Transactions on Medical Imaging

Published
2019
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2. Identifying the Best Machine Learning Algorithms for Brain Tumor Segmentation, Progression Assessment, and Overall Survival Prediction in the BRATS Challenge

Author

Bakas, Spyridon, Reyes, Mauricio, Jakab, Andras, Bauer, Stefan, Rempfler, Markus, Crimi, Alessandro, Shinohara, Russell Takeshi, Berger, Christoph, Ha, Sung Min, Rozycki, Martin, Prastawa, Marcel, Alberts, Esther, Lipkova, Jana, Freymann, John, Kirby, Justin, Bilello, Michel, Fathallah-Shaykh, Hassan, Wiest, Roland, Kirschke, Jan, Wiestler, Benedikt, Colen, Rivka, Kotrotsou, Aikaterini, Lamontagne, Pamela, Marcus, Daniel, Milchenko, Mikhail, Nazeri, Arash, Weber, Marc-Andre, Mahajan, Abhishek, Baid, Ujjwal, Gerstner, Elizabeth, Kwon, Dongjin, Acharya, Gagan, Agarwal, Manu, Alam, Mahbubul, Albiol, Alberto, Albiol, Antonio, Albiol, Francisco J., Alex, Varghese, Allinson, Nigel, Amorim, Pedro H. A., Amrutkar, Abhijit, Anand, Ganesh, Andermatt, Simon, Arbel, Tal, Arbelaez, Pablo, Avery, Aaron, Azmat, Muneeza, B., Pranjal, Bai, W, Banerjee, Subhashis, Barth, Bill, Batchelder, Thomas, Batmanghelich, Kayhan, Battistella, Enzo, Beers, Andrew, Belyaev, Mikhail, Bendszus, Martin, Benson, Eze, Bernal, Jose, Bharath, Halandur Nagaraja, Biros, George, Bisdas, Sotirios, Brown, James, Cabezas, Mariano, Cao, Shilei, Cardoso, Jorge M., Carver, Eric N, Casamitjana, Adrià, Castillo, Laura Silvana, Catà, Marcel, Cattin, Philippe, Cerigues, Albert, Chagas, Vinicius S., Chandra, Siddhartha, Chang, Yi-Ju, Chang, Shiyu, Chang, Ken, Chazalon, Joseph, Chen, Shengcong, Chen, Wei, Chen, Jefferson W, Chen, Zhaolin, Cheng, Kun, Choudhury, Ahana Roy, Chylla, Roger, Clérigues, Albert, Colleman, Steven, Colmeiro, Ramiro German Rodriguez, Combalia, Marc, Costa, Anthony, Cui, Xiaomeng, Dai, Zhenzhen, Dai, Lutao, Daza, Laura Alexandra, Deutsch, Eric, Ding, Changxing, Dong, Chao, Dong, Shidu, Dudzik, Wojciech, Eaton-Rosen, Zach, Egan, Gary, Escudero, Guilherme, Estienne, Théo, Everson, Richard, Fabrizio, Jonathan, Fan, Yong, Fang, Longwei, Feng, Xue, Ferrante, Enzo, Fidon, Lucas, Fischer, Martin, French, Andrew P., Fridman, Naomi, Fu, Huan, Fuentes, David, Gao, Yaozong, Gates, Evan, Gering, David, Gholami, Amir, Gierke, Willi, Glocker, Ben, Gong, Mingming, González-Villá, Sandra, Grosges, T., Guan, Yuanfang, Guo, Sheng, Gupta, Sudeep, Han, Woo-Sup, Han, Il Song, Harmuth, Konstantin, He, Huiguang, Hernández-Sabaté, Aura, Herrmann, Evelyn, Himthani, Naveen, Hsu, Winston, Hsu, Cheyu, Hu, Xiaojun, Hu, Xiaobin, Hu, Yan, Hu, Yifan, Hua, Rui, Huang, Teng-Yi, Huang, Weilin, Van Huffel, Sabine, Huo, Quan, HV, Vivek, Iftekharuddin, Khan M., Isensee, Fabian, Islam, Mobarakol, Jackson, Aaron S., Jambawalikar, Sachin R., Jesson, Andrew, Jian, Weijian, Jin, Peter, Jose, V Jeya Maria, Jungo, Alain, Kainz, B, Kamnitsas, Konstantinos, Kao, Po-Yu, Karnawat, Ayush, Kellermeier, Thomas, Kermi, Adel, Keutzer, Kurt, Khadir, Mohamed Tarek, Khened, Mahendra, Kickingereder, Philipp, Kim, Geena, King, Nik, Knapp, Haley, Knecht, Urspeter, Kohli, Lisa, Kong, Deren, Kong, Xiangmao, Koppers, Simon, Kori, Avinash, Krishnamurthi, Ganapathy, Krivov, Egor, Kumar, Piyush, Kushibar, Kaisar, Lachinov, Dmitrii, Lambrou, Tryphon, Lee, Joon, Lee, Chengen, Lee, Yuehchou, Lee, M, Lefkovits, Szidonia, Lefkovits, Laszlo, Levitt, James, Li, Tengfei, Li, Hongwei, Li, Wenqi, Li, Hongyang, Li, Xiaochuan, Li, Yuexiang, Li, Heng, Li, Zhenye, Li, Xiaoyu, Li, Zeju, Li, XiaoGang, Lin, Zheng-Shen, Lin, Fengming, Lio, Pietro, Liu, Chang, Liu, Boqiang, Liu, Xiang, Liu, Mingyuan, Liu, Ju, Liu, Luyan, Llado, Xavier, Lopez, Marc Moreno, Lorenzo, Pablo Ribalta, Lu, Zhentai, Luo, Lin, Luo, Zhigang, Ma, Jun, Ma, Kai, Mackie, Thomas, Madabushi, Anant, Mahmoudi, Issam, Maier-Hein, Klaus H., Maji, Pradipta, Mammen, CP, Mang, Andreas, Manjunath, B. S., Marcinkiewicz, Michal, McDonagh, S, McKenna, Stephen, McKinley, Richard, Mehl, Miriam, Mehta, Sachin, Mehta, Raghav, Meier, Raphael, Meinel, Christoph, Merhof, Dorit, Meyer, Craig, Miller, Robert, Mitra, Sushmita, Moiyadi, Aliasgar, Molina-Garcia, David, Monteiro, Miguel A. B., Mrukwa, Grzegorz, Myronenko, Andriy, Nalepa, Jakub, Ngo, Thuyen, Nie, Dong, Ning, Holly, Niu, Chen, Nuechterlein, Nicholas K, Oermann, Eric, Oliveira, Arlindo, Oliveira, Diego D. C., Oliver, Arnau, Osman, Alexander F. I., Ou, Yu-Nian, Ourselin, Sebastien, Paragios, Nikos, Park, Moo Sung, Paschke, Brad, Pauloski, J. Gregory, Pawar, Kamlesh, Pawlowski, Nick, Pei, Linmin, Peng, Suting, Pereira, Silvio M., Perez-Beteta, Julian, Perez-Garcia, Victor M., Pezold, Simon, Pham, Bao, Phophalia, Ashish, Piella, Gemma, Pillai, G. N., Piraud, Marie, Pisov, Maxim, Popli, Anmol, Pound, Michael P., Pourreza, Reza, Prasanna, Prateek, Prkovska, Vesna, Pridmore, Tony P., Puch, Santi, Puybareau, Élodie, Qian, Buyue, Qiao, Xu, Rajchl, Martin, Rane, Swapnil, Rebsamen, Michael, Ren, Hongliang, Ren, Xuhua, Revanuru, Karthik, Rezaei, Mina, Rippel, Oliver, Rivera, Luis Carlos, Robert, Charlotte, Rosen, Bruce, Rueckert, Daniel, Safwan, Mohammed, Salem, Mostafa, Salvi, Joaquim, Sanchez, Irina, Sánchez, Irina, Santos, Heitor M., Sartor, Emmett, Schellingerhout, Dawid, Scheufele, Klaudius, Scott, Matthew R., Scussel, Artur A., Sedlar, Sara, Serrano-Rubio, Juan Pablo, Shah, N. Jon, Shah, Nameetha, Shaikh, Mazhar, Shankar, B. Uma, Shboul, Zeina, Shen, Haipeng, Shen, Dinggang, Shen, Linlin, Shen, Haocheng, Shenoy, Varun, Shi, Feng, Shin, Hyung Eun, Shu, Hai, Sima, Diana, Sinclair, M, Smedby, Orjan, Snyder, James M., Soltaninejad, Mohammadreza, Song, Guidong, Soni, Mehul, Stawiaski, Jean, Subramanian, Shashank, Sun, Li, Sun, Roger, Sun, Jiawei, Sun, Kay, Sun, Yu, Sun, Guoxia, Sun, Shuang, Suter, Yannick R, Szilagyi, Laszlo, Talbar, Sanjay, Tao, Dacheng, Teng, Zhongzhao, Thakur, Siddhesh, Thakur, Meenakshi H, Tharakan, Sameer, Tiwari, Pallavi, Tochon, Guillaume, Tran, Tuan, Tsai, Yuhsiang M., Tseng, Kuan-Lun, Tuan, Tran Anh, Turlapov, Vadim, Tustison, Nicholas, Vakalopoulou, Maria, Valverde, Sergi, Vanguri, Rami, Vasiliev, Evgeny, Ventura, Jonathan, Vera, Luis, Vercauteren, Tom, Verrastro, C. A., Vidyaratne, Lasitha, Vilaplana, Veronica, Vivekanandan, Ajeet, Wang, Guotai, Wang, Qian, Wang, Chiatse J., Wang, Weichung, Wang, Duo, Wang, Ruixuan, Wang, Yuanyuan, Wang, Chunliang, Wen, Ning, Wen, Xin, Weninger, Leon, Wick, Wolfgang, Wu, Shaocheng, Wu, Qiang, Wu, Yihong, Xia, Yong, Xu, Yanwu, Xu, Xiaowen, Xu, Peiyuan, Yang, Tsai-Ling, Yang, Xiaoping, Yang, Hao-Yu, Yang, Junlin, Yang, Haojin, Yang, Guang, Yao, Hongdou, Ye, Xujiong, Yin, Changchang, Young-Moxon, Brett, Yu, Jinhua, Yue, Xiangyu, Zhang, Songtao, Zhang, Angela, Zhang, Kun, Zhang, Xuejie, Zhang, Lichi, Zhang, Xiaoyue, Zhang, Yazhuo, Zhang, Lei, Zhang, Jianguo, Zhang, Xiang, Zhang, Tianhao, Zhao, Sicheng, Zhao, Yu, Zhao, Xiaomei, Zhao, Liang, Zheng, Yefeng, Zhong, Liming, Zhou, Chenhong, Zhou, Xiaobing, Zhou, Fan, Zhu, Hongtu, Zhu, Jin, Zhuge, Ying, Zong, Weiwei, Kalpathy-Cramer, Jayashree, Farahani, Keyvan, Davatzikos, Christos, van Leemput, Koen, and Menze, Bjoern

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence, Computer Science - Machine Learning, Statistics - Machine Learning
Abstract

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset., Comment: The International Multimodal Brain Tumor Segmentation (BraTS) Challenge

Published
2018

4. Spinal Cord Gray Matter-White Matter Segmentation on Magnetic Resonance AMIRA Images with MD-GRU

Author

Horvath, Antal, Tsagkas, Charidimos, Andermatt, Simon, Pezold, Simon, Parmar, Katrin, and Cattin, Philippe

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

The small butterfly shaped structure of spinal cord (SC) gray matter (GM) is challenging to image and to delinate from its surrounding white matter (WM). Segmenting GM is up to a point a trade-off between accuracy and precision. We propose a new pipeline for GM-WM magnetic resonance (MR) image acquisition and segmentation. We report superior results as compared to the ones recently reported in the SC GM segmentation challenge and show even better results using the averaged magnetization inversion recovery acquisitions (AMIRA) sequence. Scan-rescan experiments with the AMIRA sequence show high reproducibility in terms of Dice coefficient, Hausdorff distance and relative standard deviation. We use a recurrent neural network (RNN) with multi-dimensional gated recurrent units (MD-GRU) to train segmentation models on the AMIRA dataset of 855 slices. We added a generalized dice loss to the cross entropy loss that MD-GRU uses and were able to improve the results., Comment: MICCAI 2018 CSI workshop, 12 pages, 7 figures, 3 tables

Published
2018

5. Pathology Segmentation using Distributional Differences to Images of Healthy Origin

Author

Andermatt, Simon, Horváth, Antal, Pezold, Simon, and Cattin, Philippe

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

Fully supervised segmentation methods require a large training cohort of already segmented images, providing information at the pixel level of each image. We present a method to automatically segment and model pathologies in medical images, trained solely on data labelled on the image level as either healthy or containing a visual defect. We base our method on CycleGAN, an image-to-image translation technique, to translate images between the domains of healthy and pathological images. We extend the core idea with two key contributions. Implementing the generators as residual generators allows us to explicitly model the segmentation of the pathology. Realizing the translation from the healthy to the pathological domain using a variational autoencoder allows us to specify one representation of the pathology, as this transformation is otherwise not unique. Our model hence not only allows us to create pixelwise semantic segmentations, it is also able to create inpaintings for the segmentations to render the pathological image healthy. Furthermore, we can draw new unseen pathology samples from this model based on the distribution in the data. We show quantitatively, that our method is able to segment pathologies with a surprising accuracy being only slightly inferior to a state-of-the-art fully supervised method, although the latter has per-pixel rather than per-image training information. Moreover, we show qualitative results of both the segmentations and inpaintings. Our findings motivate further research into weakly-supervised segmentation using image level annotations, allowing for faster and cheaper acquisition of training data without a large sacrifice in segmentation accuracy.

Published
2018
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6. Multi-dimensional Gated Recurrent Units for Automated Anatomical Landmark Localization

Author

Andermatt, Simon, Pezold, Simon, Amann, Michael, and Cattin, Philippe C.

Subjects
Computer Science - Computer Vision and Pattern Recognition
Abstract

We present an automated method for localizing an anatomical landmark in three-dimensional medical images. The method combines two recurrent neural networks in a coarse-to-fine approach: The first network determines a candidate neighborhood by analyzing the complete given image volume. The second network localizes the actual landmark precisely and accurately in the candidate neighborhood. Both networks take advantage of multi-dimensional gated recurrent units in their main layers, which allow for high model complexity with a comparatively small set of parameters. We localize the medullopontine sulcus in 3D magnetic resonance images of the head and neck. We show that the proposed approach outperforms similar localization techniques both in terms of mean distance in millimeters and voxels w.r.t. manual labelings of the data. With a mean localization error of 1.7 mm, the proposed approach performs on par with neurological experts, as we demonstrate in an interrater comparison., Comment: 8 pages, 3 figures, 1 table

Published
2017

7. Gamma Source Location Learning from Synthetic Multi-pinhole Collimator Data

Author

von Niederhäusern, Peter A., Seppi, Carlo, Pezold, Simon, Nicolas, Guillaume, Gkoumas, Spyridon, Haerle, Stephan K., Cattin, Philippe C., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Knoll, Florian, editor, Maier, Andreas, editor, Rueckert, Daniel, editor, and Ye, Jong Chul, editor

Published
2019
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8. Spinal Cord Gray Matter-White Matter Segmentation on Magnetic Resonance AMIRA Images with MD-GRU

Author

Horváth, Antal, Tsagkas, Charidimos, Andermatt, Simon, Pezold, Simon, Parmar, Katrin, Cattin, Philippe, Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Zheng, Guoyan, editor, Belavy, Daniel, editor, Cai, Yunliang, editor, and Li, Shuo, editor

Published
2019
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9. Pathology Segmentation Using Distributional Differences to Images of Healthy Origin

Author

Andermatt, Simon, Horváth, Antal, Pezold, Simon, Cattin, Philippe, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Crimi, Alessandro, editor, Bakas, Spyridon, editor, Kuijf, Hugo, editor, Keyvan, Farahani, editor, Reyes, Mauricio, editor, and van Walsum, Theo, editor

Published
2019
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10. Adaptive Graph Diffusion Regularisation for Discontinuity Preserving Image Registration

Author

Sandkühler, Robin, Jud, Christoph, Pezold, Simon, Cattin, Philippe C., Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Klein, Stefan, editor, Staring, Marius, editor, Durrleman, Stanley, editor, and Sommer, Stefan, editor

Published
2018
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11. Automated Segmentation of Multiple Sclerosis Lesions Using Multi-dimensional Gated Recurrent Units

Author

Andermatt, Simon, Pezold, Simon, Cattin, Philippe C., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Crimi, Alessandro, editor, Bakas, Spyridon, editor, Kuijf, Hugo, editor, Menze, Bjoern, editor, and Reyes, Mauricio, editor

Published
2018
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12. High Order Slice Interpolation for Medical Images

Author

Horváth, Antal, Pezold, Simon, Weigel, Matthias, Parmar, Katrin, Cattin, Philippe, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Tsaftaris, Sotirios A., editor, Gooya, Ali, editor, Frangi, Alejandro F., editor, and Prince, Jerry L., editor

Published
2017
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13. Model-Driven 3-D Regularisation for Robust Segmentation of the Refractive Corneal Surfaces in Spiral OCT Scans

Author

Wagner, Joerg, Pezold, Simon, Cattin, Philippe C., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Cardoso, M. Jorge, editor, Arbel, Tal, editor, Melbourne, Andrew, editor, Bogunovic, Hrvoje, editor, Moeskops, Pim, editor, Chen, Xinjian, editor, Schwartz, Ernst, editor, Garvin, Mona, editor, Robinson, Emma, editor, Trucco, Emanuele, editor, Ebner, Michael, editor, Xu, Yanwu, editor, Makropoulos, Antonios, editor, Desjardin, Adrien, editor, and Vercauteren, Tom, editor

Published
2017
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14. Compressed Sensing on Multi-pinhole Collimator SPECT Camera for Sentinel Lymph Node Biopsy

Author

Seppi, Carlo, Nahum, Uri, von Niederhäusern, Peter A., Pezold, Simon, Rissi, Michael, Haerle, Stephan K., Cattin, Philippe C., Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Descoteaux, Maxime, editor, Maier-Hein, Lena, editor, Franz, Alfred, editor, Jannin, Pierre, editor, Collins, D. Louis, editor, and Duchesne, Simon, editor

Published
2017
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16. Variational Segmentation of the White and Gray Matter in the Spinal Cord Using a Shape Prior

Author

Horváth, Antal, Pezold, Simon, Weigel, Matthias, Parmar, Katrin, Bieri, Oliver, Cattin, Philippe, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Yao, Jianhua, editor, Vrtovec, Tomaž, editor, Zheng, Guoyan, editor, Frangi, Alejandro, editor, Glocker, Ben, editor, and Li, Shuo, editor

Published
2016
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17. Multi-dimensional Gated Recurrent Units for the Segmentation of Biomedical 3D-Data

Author

Andermatt, Simon, Pezold, Simon, Cattin, Philippe, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Carneiro, Gustavo, editor, Mateus, Diana, editor, Peter, Loïc, editor, Bradley, Andrew, editor, Tavares, João Manuel R. S., editor, Belagiannis, Vasileios, editor, Papa, João Paulo, editor, Nascimento, Jacinto C., editor, Loog, Marco, editor, Lu, Zhi, editor, Cardoso, Jaime S., editor, and Cornebise, Julien, editor

Published
2016
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18. Automatic, Robust, and Globally Optimal Segmentation of Tubular Structures

Author

Pezold, Simon, Horváth, Antal, Fundana, Ketut, Tsagkas, Charidimos, Andělová, Michaela, Weier, Katrin, Amann, Michael, Cattin, Philippe C., Hutchison, David, Editorial Board Member, Kanade, Takeo, Editorial Board Member, Kittler, Josef, Editorial Board Member, Kleinberg, Jon M., Editorial Board Member, Mattern, Friedemann, Editorial Board Member, Mitchell, John C., Editorial Board Member, Naor, Moni, Editorial Board Member, Pandu Rangan, C., Editorial Board Member, Terzopoulos, Demetri, Editorial Board Member, Tygar, Doug, Editorial Board Member, Weikum, Gerhard, Series Editor, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Ourselin, Sebastien, editor, Joskowicz, Leo, editor, Sabuncu, Mert R., editor, Unal, Gozde, editor, and Wells, William, editor

Published
2016
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23. Direct Calibration of a Laser Ablation System in the Projective Voltage Space

Author

Schneider, Adrian, Pezold, Simon, Baek, Kyung-won, Marinov, Dilyan, Cattin, Philippe C., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Navab, Nassir, editor, Hornegger, Joachim, editor, Wells, William M., editor, and Frangi, Alejandro, editor

Published
2015
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24. Augmented Reality Assisted Brain Tumor Extraction in Mice

Author

Schneider, Adrian, Thalmann, Peter, Pezold, Simon, Hieber, Simone E., Cattin, Philippe C., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, De Paolis, Lucio Tommaso, editor, and Mongelli, Antonio, editor

Published
2015
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26. Augmented Reality Assisted Laparoscopic Partial Nephrectomy

Author

Schneider, Adrian, Pezold, Simon, Sauer, Andreas, Ebbing, Jan, Wyler, Stephen, Rosenthal, Rachel, Cattin, Philippe C., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Golland, Polina, editor, Hata, Nobuhiko, editor, Barillot, Christian, editor, Hornegger, Joachim, editor, and Howe, Robert, editor

Published
2014
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27. Landmark-Based Surgical Navigation

Author

Schneider, Adrian, Baumberger, Christian, Griessen, Mathias, Pezold, Simon, Beinemann, Jörg, Jürgens, Philipp, Cattin, Philippe C., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Erdt, Marius, editor, Linguraru, Marius George, editor, Oyarzun Laura, Cristina, editor, Shekhar, Raj, editor, Wesarg, Stefan, editor, González Ballester, Miguel Angel, editor, and Drechsler, Klaus, editor

Published
2014
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28. Correction to: Gamma Source Location Learning from Synthetic Multi-pinhole Collimator Data

Author

von Niederhäusern, Peter A., Seppi, Carlo, Pezold, Simon, Nicolas, Guillaume, Gkoumas, Spyridon, Haerle, Stephan K., Cattin, Philippe C., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Knoll, Florian, editor, Maier, Andreas, editor, Rueckert, Daniel, editor, and Ye, Jong Chul, editor

Published
2019
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32. Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis

Author

Tsagkas, Charidimos, primary, Huck-Horvath, Antal, additional, Cagol, Alessandro, additional, Haas, Tanja, additional, Barakovic, Muhamed, additional, Amann, Michael, additional, Ruberte, Esther, additional, Melie-Garcia, Lester, additional, Weigel, Matthias, additional, Pezold, Simon, additional, Schlaeger, Regina, additional, Kuhle, Jens, additional, Sprenger, Till, additional, Kappos, Ludwig, additional, Bieri, Oliver, additional, Cattin, Philippe, additional, Granziera, Cristina, additional, and Parmar, Katrin, additional

Published
2022
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36. Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis.

Author

Tsagkas, Charidimos, Huck-Horvath, Antal, Cagol, Alessandro, Haas, Tanja, Barakovic, Muhamed, Amann, Michael, Ruberte, Esther, Melie-Garcia, Lester, Weigel, Matthias, Pezold, Simon, Schlaeger, Regina, Kuhle, Jens, Sprenger, Till, Kappos, Ludwig, Bieri, Oliver, Cattin, Philippe, Granziera, Cristina, and Parmar, Katrin

Subjects
SPINAL cord, CERVICAL cord, MULTIPLE sclerosis, SUPERIOR colliculus, GRAY matter (Nerve tissue), WHITE matter (Nerve tissue)
Abstract

Background: Spinal cord (SC) gray and white matter pathology plays a central role in multiple sclerosis (MS). Objective: We aimed to investigate the extent, pattern, and clinical relevance of SC gray and white matter atrophy in vivo. Methods: 39 relapsing–remitting patients (RRMS), 40 progressive MS patients (PMS), and 24 healthy controls (HC) were imaged at 3T using the averaged magnetization inversion recovery acquisitions sequence. Total and lesional cervical gray and white matter, and posterior (SCPH) and anterior horn (SCAH) areas were automatically quantified. Clinical assessment included the expanded disability status scale, timed 25-foot walk test, nine-hole peg test, and the 12-item MS walking scale. Results: PMS patients had significantly reduced cervical SCAH — but not SCPH — areas compared with HC and RRMS (both p < 0.001). In RRMS and PMS, the cervical SCAH areas increased significantly less in the region of cervical SC enlargement compared with HC (all p < 0.001). This reduction was more pronounced in PMS compared with RRMS (both p < 0.001). In PMS, a lower cervical SCAH area was the most important magnetic resonance imaging (MRI)-variable for higher disability scores. Conclusion: MS patients show clinically relevant cervical SCAH atrophy, which is more pronounced in PMS and at the level of cervical SC enlargement. [ABSTRACT FROM AUTHOR]

Published
2023
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40. sj-docx-2-msj-10.1177_13524585221139152 – Supplemental material for Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis

Author

Tsagkas, Charidimos, Huck-Horvath, Antal, Cagol, Alessandro, Haas, Tanja, Barakovic, Muhamed, Amann, Michael, Ruberte, Esther, Melie-Garcia, Lester, Weigel, Matthias, Pezold, Simon, Schlaeger, Regina, Kuhle, Jens, Sprenger, Till, Kappos, Ludwig, Bieri, Oliver, Cattin, Philippe, Granziera, Cristina, and Parmar, Katrin

Subjects
FOS: Clinical medicine, 111702 Aged Health Care, FOS: Health sciences, 110904 Neurology and Neuromuscular Diseases
Abstract

Supplemental material, sj-docx-2-msj-10.1177_13524585221139152 for Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis by Charidimos Tsagkas, Antal Huck-Horvath, Alessandro Cagol, Tanja Haas, Muhamed Barakovic, Michael Amann, Esther Ruberte, Lester Melie-Garcia, Matthias Weigel, Simon Pezold, Regina Schlaeger, Jens Kuhle, Till Sprenger, Ludwig Kappos, Oliver Bieri, Philippe Cattin, Cristina Granziera and Katrin Parmar in Multiple Sclerosis Journal

Published
2022
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41. sj-docx-7-msj-10.1177_13524585221139152 – Supplemental material for Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis

Author

Tsagkas, Charidimos, Huck-Horvath, Antal, Cagol, Alessandro, Haas, Tanja, Barakovic, Muhamed, Amann, Michael, Ruberte, Esther, Melie-Garcia, Lester, Weigel, Matthias, Pezold, Simon, Schlaeger, Regina, Kuhle, Jens, Sprenger, Till, Kappos, Ludwig, Bieri, Oliver, Cattin, Philippe, Granziera, Cristina, and Parmar, Katrin

Subjects
FOS: Clinical medicine, 111702 Aged Health Care, FOS: Health sciences, 110904 Neurology and Neuromuscular Diseases
Abstract

Supplemental material, sj-docx-7-msj-10.1177_13524585221139152 for Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis by Charidimos Tsagkas, Antal Huck-Horvath, Alessandro Cagol, Tanja Haas, Muhamed Barakovic, Michael Amann, Esther Ruberte, Lester Melie-Garcia, Matthias Weigel, Simon Pezold, Regina Schlaeger, Jens Kuhle, Till Sprenger, Ludwig Kappos, Oliver Bieri, Philippe Cattin, Cristina Granziera and Katrin Parmar in Multiple Sclerosis Journal

Published
2022
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42. sj-docx-1-msj-10.1177_13524585221139152 – Supplemental material for Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis

Author

Tsagkas, Charidimos, Huck-Horvath, Antal, Cagol, Alessandro, Haas, Tanja, Barakovic, Muhamed, Amann, Michael, Ruberte, Esther, Melie-Garcia, Lester, Weigel, Matthias, Pezold, Simon, Schlaeger, Regina, Kuhle, Jens, Sprenger, Till, Kappos, Ludwig, Bieri, Oliver, Cattin, Philippe, Granziera, Cristina, and Parmar, Katrin

Subjects
FOS: Clinical medicine, 111702 Aged Health Care, FOS: Health sciences, 110904 Neurology and Neuromuscular Diseases
Abstract

Supplemental material, sj-docx-1-msj-10.1177_13524585221139152 for Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis by Charidimos Tsagkas, Antal Huck-Horvath, Alessandro Cagol, Tanja Haas, Muhamed Barakovic, Michael Amann, Esther Ruberte, Lester Melie-Garcia, Matthias Weigel, Simon Pezold, Regina Schlaeger, Jens Kuhle, Till Sprenger, Ludwig Kappos, Oliver Bieri, Philippe Cattin, Cristina Granziera and Katrin Parmar in Multiple Sclerosis Journal

Published
2022
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43. sj-docx-6-msj-10.1177_13524585221139152 – Supplemental material for Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis

Author

Tsagkas, Charidimos, Huck-Horvath, Antal, Cagol, Alessandro, Haas, Tanja, Barakovic, Muhamed, Amann, Michael, Ruberte, Esther, Melie-Garcia, Lester, Weigel, Matthias, Pezold, Simon, Schlaeger, Regina, Kuhle, Jens, Sprenger, Till, Kappos, Ludwig, Bieri, Oliver, Cattin, Philippe, Granziera, Cristina, and Parmar, Katrin

Subjects
FOS: Clinical medicine, 111702 Aged Health Care, FOS: Health sciences, 110904 Neurology and Neuromuscular Diseases
Abstract

Supplemental material, sj-docx-6-msj-10.1177_13524585221139152 for Anterior horn atrophy in the cervical spinal cord: A new biomarker in progressive multiple sclerosis by Charidimos Tsagkas, Antal Huck-Horvath, Alessandro Cagol, Tanja Haas, Muhamed Barakovic, Michael Amann, Esther Ruberte, Lester Melie-Garcia, Matthias Weigel, Simon Pezold, Regina Schlaeger, Jens Kuhle, Till Sprenger, Ludwig Kappos, Oliver Bieri, Philippe Cattin, Cristina Granziera and Katrin Parmar in Multiple Sclerosis Journal

Published
2022
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45. Landmark-Based Surgical Navigation

Author

Schneider, Adrian, primary, Baumberger, Christian, additional, Griessen, Mathias, additional, Pezold, Simon, additional, Beinemann, Jörg, additional, Jürgens, Philipp, additional, and Cattin, Philippe C., additional

Published
2014
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47. Classification of multiple sclerosis based on patterns of CNS regional atrophy covariance

Author

Tsagkas, Charidimos, primary, Parmar, Katrin, additional, Pezold, Simon, additional, Barro, Christian, additional, Chakravarty, Mallar M., additional, Gaetano, Laura, additional, Naegelin, Yvonne, additional, Amann, Michael, additional, Papadopoulou, Athina, additional, Wuerfel, Jens, additional, Kappos, Ludwig, additional, Kuhle, Jens, additional, Sprenger, Till, additional, Granziera, Cristina, additional, and Magon, Stefano, additional

Published
2021
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48. Improving Accuracy of Brainstem MRI Volumetry: Effects of Age and Sex, and Normalization Strategies

Author

Sander, Laura, primary, Horvath, Antal, additional, Pezold, Simon, additional, Andermatt, Simon, additional, Amann, Michael, additional, Sinnecker, Tim, additional, Wendebourg, Maria J., additional, Kesenheimer, Eva, additional, Yaldizli, Özgür, additional, Kappos, Ludwig, additional, Granziera, Cristina, additional, Wuerfel, Jens, additional, Cattin, Philippe, additional, and Schlaeger, Regina, additional

Published
2020
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50. Medulla Oblongata Atrophy in Early Stage Multiple Sclerosis (4278)

Author

Sander, Laura, primary, Horvath, Antal, additional, Pezold, Simon, additional, Amann, Michael, additional, Andermatt, Simon, additional, Yaldizli, Oezguer, additional, Wuerfel, Jens, additional, Kappos, Ludwig, additional, Granziera, Cristina, additional, Gobbi, Claudio, additional, Kuhle, Jens, additional, Cattin, Philippe, additional, and Schlaeger, Regina, additional

Published
2020
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