Fast robust automated brain extraction
TLDR
An automated method for segmenting magnetic resonance head images into brain and non‐brain has been developed and described and examples of results and the results of extensive quantitative testing against “gold‐standard” hand segmentations, and two other popular automated methods.Abstract:
An automated method for segmenting magnetic resonance head images into brain and non-brain has been developed. It is very robust and accurate and has been tested on thousands of data sets from a wide variety of scanners and taken with a wide variety of MR sequences. The method, Brain Extraction Tool (BET), uses a deformable model that evolves to fit the brain's surface by the application of a set of locally adaptive model forces. The method is very fast and requires no preregistration or other pre-processing before being applied. We describe the new method and give examples of results and the results of extensive quantitative testing against "gold-standard" hand segmentations, and two other popular automated methods.read more
Citations
More filters
Journal ArticleDOI
Advances in functional and structural MR image analysis and implementation as FSL.
Stephen M. Smith,Mark Jenkinson,Mark W. Woolrich,Mark W. Woolrich,Christian F. Beckmann,Behrens Tej.,Heidi Johansen-Berg,Peter R. Bannister,M De Luca,Ivana Drobnjak,D E Flitney,Rami K. Niazy,J Saunders,J Vickers,Yongyue Zhang,N. De Stefano,J M Brady,Paul M. Matthews +17 more
TL;DR: A review of the research carried out by the Analysis Group at the Oxford Centre for Functional MRI of the Brain (FMRIB) on the development of new methodologies for the analysis of both structural and functional magnetic resonance imaging data.
Journal ArticleDOI
Tract-based spatial statistics: voxelwise analysis of multi-subject diffusion data.
Stephen M. Smith,Mark Jenkinson,Heidi Johansen-Berg,Daniel Rueckert,Thomas E. Nichols,Clare E. Mackay,Kate E. Watkins,Olga Ciccarelli,M Z Cader,Paul M. Matthews,Timothy E.J. Behrens +10 more
TL;DR: TBSS aims to improve the sensitivity, objectivity and interpretability of analysis of multi-subject diffusion imaging studies by solving the question of how to align FA images from multiple subjects in a way that allows for valid conclusions to be drawn from the subsequent voxelwise analysis.
Journal ArticleDOI
Consistent resting-state networks across healthy subjects
Jessica S. Damoiseaux,Serge A.R.B. Rombouts,Frederik Barkhof,Philip Scheltens,Cornelis J. Stam,Stephen M. Smith,Christian F. Beckmann +6 more
TL;DR: Findings show that the baseline activity of the brain is consistent across subjects exhibiting significant temporal dynamics, with percentage BOLD signal change comparable with the signal changes found in task-related experiments.
Journal ArticleDOI
The minimal preprocessing pipelines for the Human Connectome Project.
Matthew F. Glasser,Stamatios N. Sotiropoulos,J. Anthony Wilson,Timothy S. Coalson,Bruce Fischl,Jesper L. R. Andersson,Junqian Xu,Saâd Jbabdi,Matthew A. Webster,Jonathan R. Polimeni,David C. Van Essen,Mark Jenkinson +11 more
TL;DR: The minimal preprocessing pipelines for structural, functional, and diffusion MRI that were developed by the HCP to accomplish many low level tasks, including spatial artifact/distortion removal, surface generation, cross-modal registration, and alignment to standard space are described.
Journal ArticleDOI
Investigations into resting-state connectivity using independent component analysis
TL;DR: A probabilistic independent component analysis approach, optimized for the analysis of fMRI data, is reviewed and it is demonstrated that this is an effective and robust tool for the identification of low-frequency resting-state patterns from data acquired at various different spatial and temporal resolutions.
References
More filters
Journal ArticleDOI
Snakes : Active Contour Models
TL;DR: This work uses snakes for interactive interpretation, in which user-imposed constraint forces guide the snake near features of interest, and uses scale-space continuation to enlarge the capture region surrounding a feature.
Journal ArticleDOI
Cortical surface-based analysis. I. Segmentation and surface reconstruction
TL;DR: A set of automated procedures for obtaining accurate reconstructions of the cortical surface are described, which have been applied to data from more than 100 subjects, requiring little or no manual intervention.
Journal ArticleDOI
A global optimisation method for robust affine registration of brain images
Mark Jenkinson,Stephen M. Smith +1 more
TL;DR: It is demonstrated that the use of local optimisation methods together with the standard multi-resolution approach is not sufficient to reliably find the global minimum, so a global optimisation method is proposed that is specifically tailored to this form of registration.
Journal ArticleDOI
Segmentation of brain MR images through a hidden Markov random field model and the expectation-maximization algorithm
TL;DR: The authors propose a novel hidden Markov random field (HMRF) model, which is a stochastic process generated by a MRF whose state sequence cannot be observed directly but which can be indirectly estimated through observations.
Journal ArticleDOI
Accurate, Robust, and Automated Longitudinal and Cross-Sectional Brain Change Analysis
Stephen M. Smith,Yongyue Zhang,Mark Jenkinson,Jacqueline T. Chen,Paul M. Matthews,Antonio Federico,Nicola De Stefano +6 more
TL;DR: Improvements to this method are described, and an extension of SIENA is extended to a new method for cross-sectional (single time point) analysis, which provides easy manual review of their output by the automatic production of summary images.
Related Papers (5)
Advances in functional and structural MR image analysis and implementation as FSL.
A global optimisation method for robust affine registration of brain images
Mark Jenkinson,Stephen M. Smith +1 more