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Multimodal surface matching with higher-order smoothness constraints

Emma C. Robinson, Kara Garcia, Matthew F. Glasser, Zhengdao Chen, Timothy S. Coalson, Antonios Makropoulos, Jelena Bozek, Robert Wright, Andreas Schuh, Matthew Webster, Jana Hutter, Anthony Price (+11 others)
2018 NeuroImage  
The Multimodal Surface Matching (MSM) tool is a flexible, spherical registration approach that enables accurate registration of surfaces based on a variety of different features.  ...  In brain imaging, accurate alignment of cortical surfaces is fundamental to the statistical sensitivity and spatial localisation of group studies, and cortical surface-based alignment has generally been  ...  The Multimodal Surface Matching (MSM) tool is a flexible, spherical registration approach that enables accurate registration of surfaces based on a variety of different features.  ... 
doi:10.1016/j.neuroimage.2017.10.037 pmid:29100940 pmcid:PMC5991912 fatcat:dhrkgap4zbbe3cudmyy6ajvcme

MSM: A new flexible framework for Multimodal Surface Matching

Emma C. Robinson, Saad Jbabdi, Matthew F. Glasser, Jesper Andersson, Gregory C. Burgess, Michael P. Harms, Stephen M. Smith, David C. Van Essen, Mark Jenkinson
2014 NeuroImage  
In this paper we demonstrate the utility of a new Multimodal Surface Matching (MSM) algorithm capable of driving alignment using a wide variety of descriptors of brain architecture, function and connectivity  ...  We compare the results with two state of the art surface registration methods that use geometric features: FreeSurfer and Spherical Demons.  ...  The framework is implemented using a fast, mul-tiresolution, discrete optimisation scheme, which offers significant speed-ups relative to the widely-used FreeSurfer surface registration method, while not  ... 
doi:10.1016/j.neuroimage.2014.05.069 pmid:24939340 pmcid:PMC4190319 fatcat:4zrkee5ttjb2jcndhq2rxts56i

Multimodal Surface Matching with Higher-Order Smoothness Constraints [article]

Emma Claire Robinson, Kara Garcia, Matthew F. Glasser, Zhengdao Chen, Timothy S. Coalson, Antonios Makropoulos, Jelena Bozek, Robert Wright, Andreas Schuh, Matthew Webster, Jana Hutter, Anthony Price (+11 others)
2017 bioRxiv   pre-print
The Multimodal Surface Matching (MSM) tool is a flexible, spherical registration approach that enables accurate registration of surfaces based on a variety of different features.  ...  In brain imaging, accurate alignment of cortical surfaces is fundamental to the statistical sensitivity and spatial localisation of group studies; and cortical surface-based alignment has generally been  ...  The Multimodal Surface Matching (MSM) tool is a flexible, spherical registration approach that enables accurate registration of surfaces based on a variety of different features.  ... 
doi:10.1101/178962 fatcat:h5lnr6h4wzbyxitdckyr74qlka

Benchmarking Geometric Deep Learning for Cortical Segmentation and Neurodevelopmental Phenotype Prediction [article]

Abdulah Fawaz, Logan Zane John Williams, Amir Alansary, Cher Bass, Karthik Gopinath, Mariana Da Silva, Simon Dahan, Christopher L Adamson, Bonnie Alexander, Deanne Thompson, Gareth Ball, Christian Desrosiers (+4 others)
2021 bioRxiv   pre-print
Several recent studies have explored the potential for using these techniques to analyse and segment the cortical surface.  ...  This paper benchmarks a collection of geometric and traditional deep learning models on phenotype prediction and segmentation of sphericalised neonatal cortical surface data, from the publicly available  ...  All registrations were performed using Multimodal Surface Matching (MSM) (Robinson et al., 2014 (Robinson et al., , 2018) ) driven by sulcal depth as the sole feature.  ... 
doi:10.1101/2021.12.01.470730 fatcat:szpev7wqenax7mds53ncg5stte

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning [article]

Alessa Hering, Lasse Hansen, Tony C. W. Mok, Albert C. S. Chung, Hanna Siebert, Stephanie Häger, Annkristin Lange, Sven Kuckertz, Stefan Heldmann, Wei Shao, Sulaiman Vesal, Mirabela Rusu (+37 others)
2021 arXiv   pre-print
We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration.  ...  Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed.  ...  feature extraction, using an nnUNet, and a very fast and accurate conventional optimisation.  ... 
arXiv:2112.04489v2 fatcat:4hunhsm75bdkxipdwmngsdafjy

A Survey of Methods for 3D Histology Reconstruction

Jonas Pichat, Juan Eugenio Iglesias, Tarek Yousry, Sébastien Ourselin, Marc Modat
2018 Medical Image Analysis  
It is thereby possible to recover the original topology of histology and lost relationships, gain insight into what affects the signals used to construct medical images (and characterising them), or build  ...  This paper reviews almost three decades of methods for 3D reconstruction from serial sections, used in the study of many different types of tissue.  ...  Smriti Patodia, from UCL Institute of Neurology (Department of Neuropathology), for her comments on Section 2 and the images used in Figures  ... 
doi:10.1016/j.media.2018.02.004 pmid:29502034 fatcat:ta5hlvqjpzenxhltfwh6p4mhqq

Modelling the Neuroanatomical Progression of Alzheimer's Disease and Posterior Cortical Atrophy [article]

Razvan V. Marinescu
2020 arXiv   pre-print
My first contribution is a study on the progression of Posterior Cortical Atrophy, using models already developed: the Event-based Model (EBM) and the Differential Equation Model (DEM).  ...  In this work I developed novel models of disease progression and applied them to estimate the progression of Alzheimer's disease and Posterior Cortical atrophy, a rare neurodegenerative syndrome causing  ...  He has always encouraged me to pursue interesting ideas and supported me in developing them.  ... 
arXiv:2003.04805v1 fatcat:a5gmy75lvnfnhbtvztqoxikukm

The developing Human Connectome Project (dHCP) automated resting-state functional processing framework for newborn infants

Sean P. Fitzgibbon, Samuel J. Harrison, Mark Jenkinson, Luke Baxter, Emma C. Robinson, Matteo Bastiani, Jelena Bozek, Vyacheslav Karolis, Lucilio Cordero Grande, Anthony N. Price, Emer Hughes, Antonios Makropoulos (+15 others)
2020 NeuroImage  
We provide a detailed description and evaluation of the pipeline which includes integrated slice-to-volume motion correction and dynamic susceptibility distortion correction, a robust multimodal registration  ...  This is being achieved through the acquisition of multi-modal MRI data from over 1000 in- and ex-utero subjects combined with the development of optimised pre-processing pipelines.  ...  Mark Chiew for advice on multi-band artefacts, and Assoc. Prof. Kenneth Pope for assistance with the neonatal HRF.  ... 
doi:10.1016/j.neuroimage.2020.117303 pmid:32866666 pmcid:PMC7762845 fatcat:f2xibrg5snfczhvwe2rruhd5cm

SynthSeg: Domain Randomisation for Segmentation of Brain Scans of any Contrast and Resolution [article]

Benjamin Billot, Douglas N. Greve, Oula Puonti, Axel Thielscher, Koen Van Leemput, Bruce Fischl, Adrian V. Dalca, Juan Eugenio Iglesias
2021 arXiv   pre-print
Finally, we demonstrate the generalisability of SynthSeg by applying it to cardiac MRI and CT segmentation.  ...  Despite advances in data augmentation and transfer learning, convolutional neural networks (CNNs) difficultly generalise to unseen domains.  ...  thus do not solve While these networks obtain fast and accurate segmen- the general lack of generalisation of neural networks.  ... 
arXiv:2107.09559v2 fatcat:lxppdyslkffg7hxggk3ztcs73m

EEG and MEG Data Analysis in SPM8

Vladimir Litvak, Jérémie Mattout, Stefan Kiebel, Christophe Phillips, Richard Henson, James Kilner, Gareth Barnes, Robert Oostenveld, Jean Daunizeau, Guillaume Flandin, Will Penny, Karl Friston
2011 Computational Intelligence and Neuroscience  
based on the general linear model, with correction for multiple comparisons using random field theory; (ii) Bayesian M/EEG source reconstruction, including support for group studies, simultaneous EEG and  ...  SPM8 is integrated with the FieldTrip toolbox , making it possible for users to combine a variety of standard analysis methods with new schemes implemented in SPM and build custom analysis tools using  ...  The authors would like to thank all their colleagues and SPM coauthors who have contributed directly and indirectly to the software described in this paper.  ... 
doi:10.1155/2011/852961 pmid:21437221 pmcid:PMC3061292 fatcat:fpvvw7yr2vey5ic2kuqxi6axfe

3D shape matching and registration : a probabilistic perspective [article]

Pengdong Xiao, University, The Australian National, University, The Australian National
2018
Dense correspondence is a key area in computer vision and medical image analysis. It has applications in registration and shape analysis.  ...  In this thesis, we use belief propagation to perform the probabilistic inference for 3D shape matching.  ...  [83] present a rigid body registration approach based on an active surface model, which can be used for surface-to-3D images and surface-to-surface registration.  ... 
doi:10.25911/5d5155d7a4031 fatcat:3r7wqgpxhrhu5nmq3a5kqjiqba

Modeling & Analysis

2003 NeuroImage  
This anomaly has lead to the use of computer-based tools that create 2D cortical surfaces, which can be inflated, flattened, and overlaid with functional activation data.  ...  This review provides a discussion of two freely available cortical surface modeling packages that have gained wide use in the field of neuroimaging: FreeSurfer [1, 2] and SureFit [3].  ...  We parameterize hippocampus surfaces using spherical harmonic (SPHARM) expansions [1]. Using more SPHARM coefficients leads to a more detailed surface reconstruction ( Figure 1 ).  ... 
doi:10.1016/s1053-8119(05)70006-9 fatcat:zff2suxcofbxvetfrwfwcxi3zm

The developing Human Connectome Project (dHCP) automated resting-state functional processing framework for newborn infants [article]

Sean Patrick Fitzgibbon, Samuel J Harrison, Mark Jenkinson, Luke Baxter, Emma Claire Robinson, Matteo Bastiani, Jelena Bozek, Vyacheslav Karolis, Lucilio Cordero Grande, Anthony N Price, Emer Hughes, Antonios Makropoulos (+15 others)
2019 bioRxiv   pre-print
We provide a detailed description and evaluation of the pipeline which includes integrated slice-to-volume motion correction and dynamic susceptibility distortion correction, a robust multimodal registration  ...  This is being achieved through the acquisition of multi-modal MRI data from over 1000 in- and ex-utero subjects combined with the development of optimised pre-processing pipelines.  ...  Acknowledgements We are grateful to Dr Mark Chiew for advice on multi-band artefacts, and Assoc. Prof. Kenneth Pope for assistance with the neonatal HRF.  ... 
doi:10.1101/766030 fatcat:j6xg3n7lfjhrrfujmpqf7juv54

Spatiotemporal organization of human sensorimotor beta burst activity [article]

Catharina Zich, Andrew J Quinn, James J Bonaiuto, George O'Neill, Lydia C Mardell, Nick S Ward, Sven Bestmann
2022 bioRxiv   pre-print
These burst events have been linked to a range of sensory and motor processes, but their precise spatial, spectral, and temporal structure remains unclear.  ...  Finally, our results suggest that sensorimotor beta bursts occurring before and after a movement share the same generator but can be distinguished by their anatomical, spectral and spatiotemporal characteristics  ...  Subject-specific head-casts optimise co-registration and reduce head movements, and thereby significantly improve the signal to noise ratio.  ... 
doi:10.1101/2022.05.19.492617 fatcat:3veme77rnzc5leffwjjw5drabm

Causal inference in the multisensory brain [article]

Yinan Cao, Christopher Summerfield, Hame Park, Bruno L. Giordano, Christoph Kayser
2018 bioRxiv   pre-print
association cortices, thereby framing multisensory integration in the generalised context of adaptive behaviour.  ...  The brain could solve this challenge using a hierarchical principle, by deriving rapidly a fused sensory estimate for computational expediency and, later and if required, filtering out irrelevant signals  ...  association cortices, thereby framing multisensory integration in the generalised context of adaptive behaviour.  ... 
doi:10.1101/500413 fatcat:qpsiyomeezfk5ft5ja3zhmsrp4
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