Improved Optimization for the Robust and Accurate Linear Registration and Motion Correction of Brain Images

By Mark Jenkinson, Peter R. Bannister, M. Brady, Stephen M. Smith. NeuroImage, 2002

12,291 citations recorded by the source corpus.

Subfields: Computer Vision and Pattern Recognition, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/291c9d66cf886ed27d89dc03d42a4612b66ab007

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In Computer Vision and Pattern Recognition

In Radiology, Nuclear Medicine and Imaging

Citations in the corpus

Age-related alterations in white matter microstructure measured by diffusion tensor imaging. (2005, methodology): “This procedure used the 12-parameter affine mutual information cost function transformation procedure in FMRIB's Linear Image Registration Tool (FLIRT) available through the FSL analysis stream [25] [26] [53] [54].”
Three dimensional echo-planar imaging at 7 Tesla (2010, positive): “The following pre-statistics processing was applied; motion correction using MCFLIRT (Jenkinson et al., 2002) nonbrain removal using BET (Smith, 2002); spatial smoothing using a Gaussian kernel of 3 mm FWHM; grand-mean intensity normalization of the entire 4D dataset by a single multiplicative…”
Cortical and Subcortical Contributions to Stop Signal Response Inhibition: Role of the Subthalamic Nucleus (2006, background): “The remaining images were then realigned to compensate for small head movements (Jenkinson et al., 2002).”
Neuronal correlates of altered empathy and social cognition in borderline personality disorder (2011, positive): “…coding for themain effect of cognitive empathy (cognitive empathy vs. physical appearance inference) and emotional empathy (emotional empathy vs. physical appearance inference) were computed for each subject and, after spatial normalization, transformed into standard space (Jenkinson et al., 2002).”
DPABI: Data Processing & Analysis for (Resting-State) Brain Imaging (2016, methodology): “The Jenkinson definition of FD (Jenkinson et al. 2002) was used”
Spatial Topography of Individual-Specific Cortical Networks Predicts Human Cognition, Personality and Emotion (2017, background): “Resting-state fMRI data of GSP and CoRR-HNU were initially pre-processed with the following steps: (i) removal of first 4 frames, (ii) slice time correction with the FSL package (Jenkinson et al., 2002; Smith et al., 2004), (iii) motion correction using rigid body translation and rotation with the F”
ICA-based artifact removal diminishes scan site differences in multi-center resting-state fMRI (2015, methodology): “Boundary-Based Registration (Jenkinson and Smith, 2001; Jenkinson et al., 2002; Greve and Fischl, 2009) was used to register each individual’s echo-planar imaging (EPI) volumes onto their respective high-resolution T1-weighted structural images.”
Methodological considerations on tract-based spatial statistics (TBSS) (2014, methodology): “, 2012), FLIRT (Greve and Fischl, 2009; Jenkinson and Smith, 2001; Jenkinson et al., 2002)) and image masking (FSL, BET (Smith, 2002)).”
Automated Probabilistic Reconstruction of White-Matter Pathways in Health and Disease Using an Atlas of the Underlying Anatomy (2011, methodology): “We registered each individual’s T 1-weighted image to the 1 mm-resolution MNI-152 atlas (Talairach and Tournoux, 1988), using affine registration (Jenkinson et al., 2002).”
An Improved Framework for Confound Regression and Filtering for Control of Motion Artifact in the Preprocessing of Resting-State Functional Connectivity Data (2012, methodology): “These six parameter time series can be condensed to a single vector representing the root mean squared volume-to-volume displacement of all brain voxels (Jenkinson et al., 2002).”
Mapping Human Cortical Areas in vivo Based on Myelin Content as Revealed by T1- and T2-weighted MRI (2011, methodology): “Open Access Publications 2011 Mapping human cortical areas in vivo based on myelin content as revealed by t1- and t2-weighted MRI Matthew F. Glasser Washington University School of Medicine in St. Louis David C. Van Essen Washington University School of Medicine in St. Louis Follow this and…”
EEG correlates of time-varying BOLD functional connectivity (2013, neutral): “Slice-timing and motion coregistration (MCFLIRT (Jenkinson et al., 2002)) were performed with FSL (http://www.fmrib.ox.ac.uk/fsl/), and the following nuisance variables were subsequently regressed out of the data: linear and quadratic trends; low-frequency respiratory volume and heart rate,…”
Statistical harmonization corrects site effects in functional connectivity measurements from multi-site fMRI data (2018, background): “Previous studies have shown that wavelet coherence outperforms Pearson correlation with respect to sensitivity to outliers caused by motion artifact (Huber, 2004; Achard et al., 2006).”
How green is the grass on the other side? Frontopolar cortex and the evidence in favor of alternative courses of action. (2009, positive): “motion correction was applied using rigid body registration to the central volume ( Jenkinson et al., 2002 ); Gaussian spatial smoothing was applied”
Benchmarking of participant‐level confound regression strategies for the control of motion artifact in studies of functional connectivity (2017, methodology): “Confound regression using realignment parameters Time series of six realignment parameters (three translational and three rotational) for each subject were returned by MCFLIRT as part of time series realignment (motion correction).”
DIFFUSION-WEIGHTED IMAGING TRACTOGRAPHY-BASED PARCELLATION OF THE HUMAN PARIETAL CORTEX AND COMPARISON WITH HUMAN AND MACAQUE RESTING STATE FUNCTIONAL CONNECTIVITY (2011, methodology): “Registration of functional images to the skull-stripped structural and a macaque template was done using FLIRT (Jenkinson et al., 2002).”
A Convergent Functional Architecture of the Insula Emerges Across Imaging Modalities (2012, positive): “We used the FSL linear registration tool FLIRT to register each participant's functional time series to the space of their high-resolution structural image, and the high-resolution structural images to the MNI152 template (Jenkinson and Smith, 2001; Jenkinson et al., 2002).”