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2020 – today
- 2024
- [j24]Hamza Kebiri, Ali Gholipour, Rizhong Lin, Lana Vasung, Camilo Calixto, Zeljka Krsnik, Davood Karimi, Meritxell Bach Cuadra:
Deep learning microstructure estimation of developing brains from diffusion MRI: A newborn and fetal study. Medical Image Anal. 95: 103186 (2024) - [j23]Camilo Calixto, Camilo Jaimes, Matheus D. Soldatelli, Simon K. Warfield, Ali Gholipour, Davood Karimi:
Anatomically constrained tractography of the fetal brain. NeuroImage 297: 120723 (2024) - [c21]Rizhong Lin, Ali Gholipour, Jean-Philippe Thiran, Davood Karimi, Hamza Kebiri, Meritxell Bach Cuadra:
Cross-Age and Cross-Site Domain Shift Impacts on Deep Learning-Based White Matter Fiber Estimation in Newborn and Baby Brains. ISBI 2024: 1-5 - [c20]Haykel Snoussi, Davood Karimi, Onur Afacan, Mustafa Utkur, Ali Gholipour:
Advanced Framework for Fetal Diffusion MRI: Dynamic Distortion and Motion Correction. PIPPI@MICCAI 2024: 35-45 - [c19]Davood Karimi:
An Approach to Building Foundation Models for Brain Image Analysis. MICCAI (12) 2024: 421-431 - [i30]Davood Karimi:
Diffusion MRI with Machine Learning. CoRR abs/2402.00019 (2024) - [i29]Camilo Calixto, Camilo Jaimes, Matheus D. Soldatelli, Simon K. Warfield, Ali Gholipour, Davood Karimi:
Anatomically Constrained Tractography of the Fetal Brain. CoRR abs/2403.02444 (2024) - [i28]Hongwei Bran Li, Fernando Navarro, Ivan Ezhov, Amirhossein Bayat, Dhritiman Das, Florian Kofler, Suprosanna Shit, Diana Waldmannstetter, Johannes C. Paetzold, Xiaobin Hu, Benedikt Wiestler, Lucas Zimmer, Tamaz Amiranashvili, Chinmay Prabhakar, Christoph Berger, Jonas Weidner, Michelle Alonso-Basanta, Arif Rashid, Ujjwal Baid, Wesam Adel, Deniz Alis, Bhakti Baheti, Yingbin Bai, Ishaan Bhat, Sabri Can Cetindag, Wenting Chen, Li Cheng, Prasad Dutande, Lara Dular, Mustafa A. Elattar, Ming Feng, Shengbo Gao, Henkjan Huisman, Weifeng Hu, Shubham Innani, Wei Jiat, Davood Karimi, Hugo J. Kuijf, Jin Tae Kwak, Hoang Long Le, Xiang Lia, Huiyan Lin, Tongliang Liu, Jun Ma, Kai Ma, Ting Ma, Ilkay Öksüz, Robbie Holland, Arlindo L. Oliveira, Jimut Bahan Pal, Xuan Pei, Maoying Qiao, Anindo Saha, Raghavendra Selvan, Linlin Shen, João Lourenço Silva, Ziga Spiclin, Sanjay N. Talbar, Dadong Wang, Wei Wang, Xiong Wang, Yin Wang, Ruiling Xia, Kele Xu, Yanwu Yan, Mert Yergin, Shuang Yu, Lingxi Zeng, YingLin Zhang, Jiachen Zhao, Yefeng Zheng, Martin Zukovec, Richard K. G. Do, Anton S. Becker, Amber L. Simpson, Ender Konukoglu, András Jakab, Spyridon Bakas, Leo Joskowicz, Bjoern H. Menze:
QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge. CoRR abs/2405.18435 (2024) - [i27]Haykel Snoussi, Davood Karimi, Onur Afacan, Mustafa Utkur, Ali Gholipour:
HAITCH: A Framework for Distortion and Motion Correction in Fetal Multi-Shell Diffusion-Weighted MRI. CoRR abs/2406.20042 (2024) - [i26]Weide Liu, Camilo Calixto, Simon K. Warfield, Davood Karimi:
Streamline tractography of the fetal brain in utero with machine learning. CoRR abs/2408.14326 (2024) - [i25]Rizhong Lin, Hamza Kebiri, Ali Gholipour, Yufei Chen, Jean-Philippe Thiran, Davood Karimi, Meritxell Bach Cuadra:
Ground-truth effects in learning-based fiber orientation distribution estimation in neonatal brains. CoRR abs/2409.01195 (2024) - [i24]Davood Karimi, Camilo Calixto, Haykel Snoussi, Maria Camila Cortes-Albornoz, Clemente Velasco-Annis, Caitlin K. Rollins, Camilo Jaimes, Ali Gholipour, Simon K. Warfield:
Detailed delineation of the fetal brain in diffusion MRI via multi-task learning. CoRR abs/2409.06716 (2024) - 2023
- [j22]Davood Karimi, Caitlin K. Rollins, Clemente Velasco-Annis, Abdelhakim Ouaalam, Ali Gholipour:
Learning to segment fetal brain tissue from noisy annotations. Medical Image Anal. 85: 102731 (2023) - [j21]Kelly Payette, Hongwei Bran Li, Priscille de Dumast, Roxane Licandro, Hui Ji, Md Mahfuzur Rahman Siddiquee, Daguang Xu, Andriy Myronenko, Hao Liu, Yuchen Pei, Lisheng Wang, Ying Peng, Juanying Xie, Huiquan Zhang, Guiming Dong, Hao Fu, Guotai Wang, ZunHyan Rieu, Donghyeon Kim, Hyun Gi Kim, Davood Karimi, Ali Gholipour, Helena R. Torres, Bruno Oliveira, João L. Vilaça, Yang Lin, Netanell Avisdris, Ori Ben-Zvi, Dafna Ben-Bashat, Lucas Fidon, Michael Aertsen, Tom Vercauteren, Daniel Sobotka, Georg Langs, Mireia Alenyà, Maria Inmaculada Villanueva, Oscar Camara, Bella Specktor-Fadida, Leo Joskowicz, Liao Weibin, Lv Yi, Xuesong Li, Moona Mazher, Abdul Qayyum, Domenec Puig, Hamza Kebiri, Zelin Zhang, Xinyi Xu, Dan Wu, KuanLun Liao, YiXuan Wu, JinTai Chen, Yunzhi Xu, Li Zhao, Lana Vasung, Bjoern H. Menze, Meritxell Bach Cuadra, András Jakab:
Fetal brain tissue annotation and segmentation challenge results. Medical Image Anal. 88: 102833 (2023) - [j20]Davood Karimi, Ali Gholipour:
Improving Calibration and Out-of-Distribution Detection in Deep Models for Medical Image Segmentation. IEEE Trans. Artif. Intell. 4(2): 383-397 (2023) - [c18]Yihan Wu, Ali Gholipour, Lana Vasung, Davood Karimi:
A Computational Framework for Characterizing Normative Development of Structural Brain Connectivity in the Perinatal Stage. ISBI 2023: 1-5 - [c17]Hamza Kebiri, Ali Gholipour, Rizhong Lin, Lana Vasung, Davood Karimi, Meritxell Bach Cuadra:
Robust Estimation of the Microstructure of the Early Developing Brain Using Deep Learning. MICCAI (7) 2023: 293-303 - [c16]Razieh Faghihpirayesh, Davood Karimi, Deniz Erdogmus, Ali Gholipour:
Automatic brain pose estimation in fetal MRI. Image Processing 2023 - [i23]Hamza Kebiri, Ali Gholipour, Meritxell Bach Cuadra, Davood Karimi:
Direct segmentation of brain white matter tracts in diffusion MRI. CoRR abs/2307.02223 (2023) - [i22]Davood Karimi, Hamza Kebiri, Ali Gholipour:
TBSS++: A novel computational method for Tract-Based Spatial Statistics. CoRR abs/2307.05387 (2023) - [i21]Yihan Wu, Lana Vasung, Camilo Calixto, Ali Gholipour, Davood Karimi:
Characterizing normal perinatal development of the human brain structural connectivity. CoRR abs/2308.11836 (2023) - [i20]Razieh Faghihpirayesh, Davood Karimi, Deniz Erdogmus, Ali Gholipour:
Fetal-BET: Brain Extraction Tool for Fetal MRI. CoRR abs/2310.01523 (2023) - [i19]Rizhong Lin, Ali Gholipour, Jean-Philippe Thiran, Davood Karimi, Hamza Kebiri, Meritxell Bach Cuadra:
Cross-Age and Cross-Site Domain Shift Impacts on Deep Learning-Based White Matter Fiber Estimation in Newborn and Baby Brains. CoRR abs/2312.14773 (2023) - 2022
- [j19]Davood Karimi, Haoran Dou, Ali Gholipour:
Medical Image Segmentation Using Transformer Networks. IEEE Access 10: 29322-29332 (2022) - [j18]Davood Karimi, Ali Gholipour:
Diffusion tensor estimation with transformer neural networks. Artif. Intell. Medicine 130: 102330 (2022) - [j17]Chiara Maffei, Gabriel Girard, Kurt G. Schilling, Dogu Baran Aydogan, Nagesh Adluru, Andrey Zhylka, Ye Wu, Matteo Mancini, Andac Hamamci, Alessia Sarica, Achille Teillac, Steven H. Baete, Davood Karimi, Fang-Cheng Yeh, Mert E. Yildiz, Ali Gholipour, Yann Bihan-Poudec, Bassem Hiba, Andrea Quattrone, Aldo Quattrone, Tommy Boshkovski, Nikola Stikov, Pew-Thian Yap, Alberto De Luca, Josien P. W. Pluim, Alexander Leemans, Vivek Prabhakaran, Barbara B. Bendlin, Andrew L. Alexander, Bennett A. Landman, Erick Jorge Canales-Rodríguez, Muhamed Barakovic, Jonathan Rafael-Patino, Thomas Yu, Gaëtan Rensonnet, Simona Schiavi, Alessandro Daducci, Marco Pizzolato, Elda Fischi Gomez, Jean-Philippe Thiran, George Dai, Giorgia Grisot, Nikola Lazovski, Santi Puch, Marc Ramos, Paulo Rodrigues, Vesna Prckovska, Robert Jones, Julia Lehman, Suzanne N. Haber, Anastasia Yendiki:
Insights from the IronTract challenge: Optimal methods for mapping brain pathways from multi-shell diffusion MRI. NeuroImage 257: 119327 (2022) - [c15]Razieh Faghihpirayesh, Davood Karimi, Deniz Erdogmus, Ali Gholipour:
Deep Learning Framework for Real-Time Fetal Brain Segmentation in MRI. PIPPI@MICCAI 2022: 60-70 - [c14]Davood Karimi, Ali Gholipour:
Atlas-Powered Deep Learning (ADL) - Application to Diffusion Weighted MRI. MICCAI (1) 2022: 123-132 - [i18]Davood Karimi, Ali Gholipour:
Diffusion Tensor Estimation with Transformer Neural Networks. CoRR abs/2201.05701 (2022) - [i17]Davood Karimi, Caitlin K. Rollins, Clemente Velasco-Annis, Abdelhakim Ouaalam, Ali Gholipour:
Learning to segment fetal brain tissue from noisy annotations. CoRR abs/2203.14962 (2022) - [i16]Kelly Payette, Hongwei Li, Priscille de Dumast, Roxane Licandro, Hui Ji, Md Mahfuzur Rahman Siddiquee, Daguang Xu, Andriy Myronenko, Hao Liu, Yuchen Pei, Lisheng Wang, Ying Peng, Juanying Xie, Huiquan Zhang, Guiming Dong, Hao Fu, Guotai Wang, ZunHyan Rieu, Donghyeon Kim, Hyun Gi Kim, Davood Karimi, Ali Gholipour, Helena R. Torres, Bruno Oliveira, João L. Vilaça, Yang Lin, Netanell Avisdris, Ori Ben-Zvi, Dafna Ben-Bashat, Lucas Fidon, Michael Aertsen, Tom Vercauteren, Daniel Sobotka, Georg Langs, Mireia Alenyà, Maria Inmaculada Villanueva, Oscar Camara, Bella Specktor-Fadida, Leo Joskowicz, Weibin Liao, Lv Yi, Xuesong Li, Moona Mazher, Abdul Qayyum, Domenec Puig, Hamza Kebiri, Zelin Zhang, Xinyi Xu, Dan Wu, KuanLun Liao, YiXuan Wu, JinTai Chen, Yunzhi Xu, Li Zhao, Lana Vasung, Bjoern H. Menze, Meritxell Bach Cuadra, András Jakab:
Fetal Brain Tissue Annotation and Segmentation Challenge Results. CoRR abs/2204.09573 (2022) - [i15]Razieh Faghihpirayesh, Davood Karimi, Deniz Erdogmus, Ali Gholipour:
Deep Learning Framework for Real-time Fetal Brain Segmentation in MRI. CoRR abs/2205.01675 (2022) - [i14]Davood Karimi, Ali Gholipour:
Atlas-powered deep learning (ADL) - application to diffusion weighted MRI. CoRR abs/2205.03210 (2022) - [i13]Arvind Balachandrasekaran, Davood Karimi, Camilo Jaimes, Ali Gholipour:
Subject-specific quantitative susceptibility mapping using patch based deep image priors. CoRR abs/2210.06471 (2022) - 2021
- [j16]Davood Karimi, Simon K. Warfield, Ali Gholipour:
Transfer learning in medical image segmentation: New insights from analysis of the dynamics of model parameters and learned representations. Artif. Intell. Medicine 116: 102078 (2021) - [j15]Davood Karimi, Lana Vasung, Camilo Jaimes, Fedel Machado-Rivas, Shadab Khan, Simon K. Warfield, Ali Gholipour:
A machine learning-based method for estimating the number and orientations of major fascicles in diffusion-weighted magnetic resonance imaging. Medical Image Anal. 72: 102129 (2021) - [j14]Davood Karimi, Lana Vasung, Camilo Jaimes, Fedel Machado-Rivas, Simon K. Warfield, Ali Gholipour:
Learning to estimate the fiber orientation distribution function from diffusion-weighted MRI. NeuroImage 239: 118316 (2021) - [j13]Davood Karimi, Camilo Jaimes, Fedel Machado-Rivas, Lana Vasung, Shadab Khan, Simon K. Warfield, Ali Gholipour:
Deep learning-based parameter estimation in fetal diffusion-weighted MRI. NeuroImage 243: 118482 (2021) - [j12]Haoran Dou, Davood Karimi, Caitlin K. Rollins, Cynthia M. Ortinau, Lana Vasung, Clemente Velasco-Annis, Abdelhakim Ouaalam, Xin Yang, Dong Ni, Ali Gholipour:
A Deep Attentive Convolutional Neural Network for Automatic Cortical Plate Segmentation in Fetal MRI. IEEE Trans. Medical Imaging 40(4): 1123-1133 (2021) - [c13]Davood Karimi, Rabab Ward:
Interpolation of CT Projections by Exploiting Their Self-Similarity and Smoothness. ICIP 2021: 165-169 - [c12]Davood Karimi, Serge Vasylechko, Ali Gholipour:
Convolution-Free Medical Image Segmentation Using Transformers. MICCAI (1) 2021: 78-88 - [c11]Davood Karimi, Lana Vasung, Fedel Machado-Rivas, Camilo Jaimes, Shadab Khan, Ali Gholipour:
Accurate Parameter Estimation in Fetal Diffusion-Weighted MRI - Learning from Fetal and Newborn Data. MICCAI (7) 2021: 487-496 - [i12]Davood Karimi, Serge Vasylechko, Ali Gholipour:
Convolution-Free Medical Image Segmentation using Transformers. CoRR abs/2102.13645 (2021) - [i11]Davood Karimi, Rabab K. Ward:
Interpolation of CT Projections by Exploiting Their Self-Similarity and Smoothness. CoRR abs/2103.03968 (2021) - [i10]Golnoosh Samei, Davood Karimi, Claudia Kesch, Septimiu E. Salcudean:
Automatic Segmentation of the Prostate on 3D Trans-rectal Ultrasound Images using Statistical Shape Models and Convolutional Neural Networks. CoRR abs/2106.09662 (2021) - [i9]Davood Karimi, Simon K. Warfield, Ali Gholipour:
Calibrated Diffusion Tensor Estimation. CoRR abs/2111.10847 (2021) - 2020
- [j11]Davood Karimi, Haoran Dou, Simon K. Warfield, Ali Gholipour:
Deep learning with noisy labels: Exploring techniques and remedies in medical image analysis. Medical Image Anal. 65: 101759 (2020) - [j10]Davood Karimi, Guy Nir, Ladan Fazli, Peter C. Black, Larry Goldenberg, Septimiu E. Salcudean:
Deep Learning-Based Gleason Grading of Prostate Cancer From Histopathology Images - Role of Multiscale Decision Aggregation and Data Augmentation. IEEE J. Biomed. Health Informatics 24(5): 1413-1426 (2020) - [j9]Davood Karimi, Septimiu E. Salcudean:
Reducing the Hausdorff Distance in Medical Image Segmentation With Convolutional Neural Networks. IEEE Trans. Medical Imaging 39(2): 499-513 (2020) - [c10]Davood Karimi, Jurriaan M. Peters, Abdelhakim Ouaalam, Sanjay P. Prabhu, Mustafa Sahin, Darcy A. Krueger, Alexander Kolevzon, Charis Eng, Simon K. Warfield, Ali Gholipour:
Learning to Detect Brain Lesions from Noisy Annotations. ISBI 2020: 1910-1914 - [i8]Davood Karimi, Ali Gholipour:
Improving Calibration and Out-of-Distribution Detection in Medical Image Segmentation with Convolutional Neural Networks. CoRR abs/2004.06569 (2020) - [i7]Haoran Dou, Davood Karimi, Caitlin K. Rollins, Cynthia M. Ortinau, Lana Vasung, Clemente Velasco-Annis, Abdelhakim Ouaalam, Xin Yang, Dong Ni, Ali Gholipour:
A Deep Attentive Convolutional Neural Network for Automatic Cortical Plate Segmentation in Fetal MRI. CoRR abs/2004.12847 (2020) - [i6]Davood Karimi, Simon K. Warfield, Ali Gholipour:
Critical Assessment of Transfer Learning for Medical Image Segmentation with Fully Convolutional Neural Networks. CoRR abs/2006.00356 (2020) - [i5]Davood Karimi, Lana Vasung, Camilo Jaimes, Fedel Machado-Rivas, Shadab Khan, Simon K. Warfield, Ali Gholipour:
A machine learning-based method for estimating the number and orientations of major fascicles in diffusion-weighted magnetic resonance imaging. CoRR abs/2006.11117 (2020)
2010 – 2019
- 2019
- [j8]Davood Karimi, Qi Zeng, Prateek Mathur, Apeksha Avinash, Sara Mahdavi, Ingrid Spadinger, Purang Abolmaesumi, Septimiu E. Salcudean:
Accurate and robust deep learning-based segmentation of the prostate clinical target volume in ultrasound images. Medical Image Anal. 57: 186-196 (2019) - [c9]Qi Zeng, Davood Karimi, Emily H. T. Pang, Shahed K. Mohammed, Caitlin Schneider, Mohammad Honarvar, Septimiu E. Salcudean:
Liver Segmentation in Magnetic Resonance Imaging via Mean Shape Fitting with Fully Convolutional Neural Networks. MICCAI (2) 2019: 246-254 - [i4]Davood Karimi, Golnoosh Samei, Yanan Shao, Tim Salcudean:
A deep learning-based method for prostate segmentation in T2-weighted magnetic resonance imaging. CoRR abs/1901.09462 (2019) - [i3]Davood Karimi, Septimiu E. Salcudean:
Reducing the Hausdorff Distance in Medical Image Segmentation with Convolutional Neural Networks. CoRR abs/1904.10030 (2019) - [i2]Davood Karimi, Haoran Dou, Simon K. Warfield, Ali Gholipour:
Deep learning with noisy labels: exploring techniques and remedies in medical image analysis. CoRR abs/1912.02911 (2019) - [i1]Davood Karimi:
Sparse and redundant signal representations for x-ray computed tomography. CoRR abs/1912.03379 (2019) - 2018
- [j7]Qi Zeng, Golnoosh Samei, Davood Karimi, Claudia Kesch, Seyedeh Sara Mahdavi, Purang Abolmaesumi, Septimiu E. Salcudean:
Prostate segmentation in transrectal ultrasound using magnetic resonance imaging priors. Int. J. Comput. Assist. Radiol. Surg. 13(6): 749-757 (2018) - [j6]Davood Karimi, Golnoosh Samei, Claudia Kesch, Guy Nir, Septimiu E. Salcudean:
Prostate segmentation in MRI using a convolutional neural network architecture and training strategy based on statistical shape models. Int. J. Comput. Assist. Radiol. Surg. 13(8): 1211-1219 (2018) - [j5]Guy Nir, Soheil Hor, Davood Karimi, Ladan Fazli, Brian F. Skinnider, Peyman Tavassoli, Dmitry Turbin, Carlos F. Villamil, Gang Wang, R. Storey Wilson, Kenneth A. Iczkowski, M. Scott Lucia, Peter C. Black, Purang Abolmaesumi, S. Larry Goldenberg, Septimiu E. Salcudean:
Automatic grading of prostate cancer in digitized histopathology images: Learning from multiple experts. Medical Image Anal. 50: 167-180 (2018) - [c8]Davood Karimi, Qi Zeng, Prateek Mathur, Apeksha Avinash, Sara Mahdavi, Ingrid Spadinger, Purang Abolmaesumi, Septimiu E. Salcudean:
Accurate and Robust Segmentation of the Clinical Target Volume for Prostate Brachytherapy. MICCAI (4) 2018: 531-539 - 2017
- [c7]Davood Karimi, Rabab K. Ward:
Image reconstruction in computed tomography using variance-reduced stochastic gradient descent. ISBI 2017: 543-547 - [c6]Davood Karimi, Dan Ruan:
Synergistic Combination of Learned and Hand-Crafted Features for Prostate Lesion Classification in Multiparametric Magnetic Resonance Imaging. MICCAI (3) 2017: 391-398 - 2016
- [j4]Davood Karimi, Pierre Deman, Rabab K. Ward, Nancy L. Ford:
A sinogram denoising algorithm for low-dose computed tomography. BMC Medical Imaging 16: 11 (2016) - [j3]Davood Karimi, Rabab K. Ward:
Patch-based models and algorithms for image processing: a review of the basic principles and methods, and their application in computed tomography. Int. J. Comput. Assist. Radiol. Surg. 11(10): 1765-1777 (2016) - [j2]Davood Karimi, Rabab K. Ward:
A denoising algorithm for projection measurements in cone-beam computed tomography. Comput. Biol. Medicine 69: 71-82 (2016) - [j1]Davood Karimi, Rabab K. Ward:
On the computational implementation of forward and back-projection operations for cone-beam computed tomography. Medical Biol. Eng. Comput. 54(8): 1193-1204 (2016) - [c5]Davood Karimi, Rabab K. Ward:
Sinogram smoothing and interpolation via alternating projections onto the slope and curvature constraints. Image Processing 2016: 97840M - [c4]Davood Karimi, Rabab K. Ward:
A novel structured dictionary for fast processing of 3D medical images, with application to computed tomography restoration and denoising. Image Processing 2016: 97840N - 2015
- [c3]Davood Karimi, Rabab K. Ward, Nancy L. Ford:
Angular upsampling of projection measurements in 3D computed tomography using a sparsity prior. ICIP 2015: 3363-3367 - 2013
- [c2]Cameron A. MacGregor, Davood Karimi, Ali Azarbarzin, Zahra Moussavi:
Statistical analysis of tracheal breath sounds during wakefulness for screening obstructive sleep apnea. EMBC 2013: 4549-4552 - 2012
- [c1]Ehsan Shams, Davood Karimi, Zahra Moussavi:
Bispectral analysis of tracheal breath sounds for Obstructive Sleep Apnea. EMBC 2012: 37-40
Coauthor Index
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