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The reconstruction of cortical surfaces is a prerequisite for quantitative analyses of the cerebral cortex in magnetic resonance imaging (MRI). Existing segmentation-based methods separate the surface registration from the surface…

Image and Video Processing · Electrical Eng. & Systems 2024-03-05 Fabian Bongratz , Anne-Marie Rickmann , Christian Wachinger

The reconstruction of cortical surfaces from brain magnetic resonance imaging (MRI) scans is essential for quantitative analyses of cortical thickness and sulcal morphology. Although traditional and deep learning-based algorithmic pipelines…

Computer Vision and Pattern Recognition · Computer Science 2022-03-21 Fabian Bongratz , Anne-Marie Rickmann , Sebastian Pölsterl , Christian Wachinger

The study of neurodegenerative diseases relies on the reconstruction and analysis of the brain cortex from magnetic resonance imaging (MRI). Traditional frameworks for this task like FreeSurfer demand lengthy runtimes, while its accelerated…

Image and Video Processing · Electrical Eng. & Systems 2020-10-23 Rodrigo Santa Cruz , Leo Lebrat , Pierrick Bourgeat , Clinton Fookes , Jurgen Fripp , Olivier Salvado

Magnetic resonance imaging (MRI) is a crucial medical imaging modality. However, long acquisition times remain a significant challenge, leading to increased costs, and reduced patient comfort. Recent studies have shown the potential of…

Computer Vision and Pattern Recognition · Computer Science 2025-07-30 Amirmohammad Shamaei , Alexander Stebner , Salome , Bosshart , Johanna Ospel , Gouri Ginde , Mariana Bento , Roberto Souza

Accurate cortical surface reconstruction from magnetic resonance imaging (MRI) data is crucial for reliable neuroanatomical analyses. Current methods have to contend with complex cortical geometries, strict topological requirements, and…

Image and Video Processing · Electrical Eng. & Systems 2025-10-22 Kaveh Moradkhani , R Jarrett Rushmore , Sylvain Bouix

Cortical surface reconstruction (CSR) from MRI is key to investigating brain structure and function. While recent deep learning approaches have significantly improved the speed of CSR, a substantial amount of runtime is still needed to map…

Image and Video Processing · Electrical Eng. & Systems 2023-12-12 Xiaoyang Chen , Junjie Zhao , Siyuan Liu , Sahar Ahmad , Pew-Thian Yap

Predicting future brain state from a baseline magnetic resonance image (MRI) is a central challenge in neuroimaging and has important implications for studying neurodegenerative diseases such as Alzheimer's disease (AD). Most existing…

Computer Vision and Pattern Recognition · Computer Science 2026-05-28 Ali Farki , Elaheh Moradi , Deepika Koundal , Jussi Tohka

The reconstruction of cerebral cortex surfaces from brain MRI scans is instrumental for the analysis of brain morphology and the detection of cortical thinning in neurodegenerative diseases like Alzheimer's disease (AD). Moreover, for a…

Neurons and Cognition · Quantitative Biology 2022-10-05 Anne-Marie Rickmann , Fabian Bongratz , Sebastian Pölsterl , Ignacio Sarasua , Christian Wachinger

To achieve fast, robust, and accurate reconstruction of the human cortical surfaces from 3D magnetic resonance images (MRIs), we develop a novel deep learning-based framework, referred to as SurfNN, to reconstruct simultaneously both inner…

Image and Video Processing · Electrical Eng. & Systems 2023-03-07 Hao Zheng , Hongming Li , Yong Fan

Cortical surface reconstruction (CSR) from magnetic resonance imaging (MRI) is fundamental to neuroimage analysis, enabling morphological studies of the cerebral cortex and functional brain mapping. Recent advances in learning-based CSR…

Computer Vision and Pattern Recognition · Computer Science 2025-09-19 Patrick Madlindl , Fabian Bongratz , Christian Wachinger

Magnetic Resonance Imaging (MRI) is a non-invasive diagnostic and radiotherapy (RT) planning tool, offering detailed insights into the anatomy of the human body. The extensive scan time is stressful for patients, who must remain motionless…

Image and Video Processing · Electrical Eng. & Systems 2023-11-23 Shahinur Alam , Jinsoo Uh , Alexander Dresner , Chia-ho Hua , Khaled Khairy

Deep learning-based 3-dimensional (3D) shape reconstruction from 2-dimensional (2D) magnetic resonance imaging (MRI) has become increasingly important in medical disease diagnosis, treatment planning, and computational modeling. This review…

Machine Learning · Computer Science 2025-10-03 Emma McMillian , Abhirup Banerjee , Alfonso Bueno-Orovio

Surface analysis of the cortex is ubiquitous in human neuroimaging with MRI, e.g., for cortical registration, parcellation, or thickness estimation. The convoluted cortical geometry requires isotropic scans (e.g., 1mm MPRAGEs) and good…

Image and Video Processing · Electrical Eng. & Systems 2023-05-04 Karthik Gopinath , Douglas N. Greve , Sudeshna Das , Steve Arnold , Colin Magdamo , Juan Eugenio Iglesias

Dynamic magnetic resonance imaging (MRI) plays an indispensable role in cardiac diagnosis. To enable fast imaging, the k-space data can be undersampled but the image reconstruction poses a great challenge of high-dimensional processing.…

Image and Video Processing · Electrical Eng. & Systems 2024-10-03 Zi Wang , Min Xiao , Yirong Zhou , Chengyan Wang , Naiming Wu , Yi Li , Yiwen Gong , Shufu Chang , Yinyin Chen , Liuhong Zhu , Jianjun Zhou , Congbo Cai , He Wang , Di Guo , Guang Yang , Xiaobo Qu

Magnetic resonance imaging (MRI) reconstruction is a fundamental task aimed at recovering high-quality images from undersampled or low-quality MRI data. This process enhances diagnostic accuracy and optimizes clinical applications. In…

Image and Video Processing · Electrical Eng. & Systems 2025-03-11 Xiaoyan Kui , Zijie Fan , Zexin Ji , Qinsong Li , Chengtao Liu , Weixin Si , Beiji Zou

High spatiotemporal resolution dynamic magnetic resonance imaging (MRI) is a powerful clinical tool for imaging moving structures as well as to reveal and quantify other physical and physiological dynamics. The low speed of MRI necessitates…

Image and Video Processing · Electrical Eng. & Systems 2019-10-14 Yuhua Chen , Jaime L. Shaw , Yibin Xie , Debiao Li , Anthony G. Christodoulou

The cerebral cortex performs higher-order brain functions and is thus implicated in a range of cognitive disorders. Current analysis of cortical variation is typically performed by fitting surface mesh models to inner and outer cortical…

Image and Video Processing · Electrical Eng. & Systems 2020-10-06 Samuel Budd , Prachi Patkee , Ana Baburamani , Mary Rutherford , Emma C. Robinson , Bernhard Kainz

Multimodal MRI offers complementary multi-scale information to characterize the brain structure. However, it remains challenging to effectively integrate multimodal MRI while achieving neuroscience interpretability. Here we propose to use…

Neurons and Cognition · Quantitative Biology 2025-12-15 Chengzhi Xia , Jianwei Chen , Yixuan Jiang , Qi Yan , Chao Li

Surface-based analysis of the cerebral cortex is ubiquitous in human neuroimaging with MRI. It is crucial for cortical registration, parcellation, and thickness estimation. Traditionally, these analyses require high-resolution, isotropic…

Image and Video Processing · Electrical Eng. & Systems 2024-09-09 Karthik Gopinath , Douglas N. Greve , Colin Magdamo , Steve Arnold , Sudeshna Das , Oula Puonti , Juan Eugenio Iglesias

Segmentation of Multiple Sclerosis (MS) lesions in longitudinal brain MR scans is performed for monitoring the progression of MS lesions. We hypothesize that the spatio-temporal cues in longitudinal data can aid the segmentation algorithm.…

Image and Video Processing · Electrical Eng. & Systems 2020-09-29 Stefan Denner , Ashkan Khakzar , Moiz Sajid , Mahdi Saleh , Ziga Spiclin , Seong Tae Kim , Nassir Navab
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