A global optimisation method for robust affine registration of brain images

By Mark Jenkinson, Stephen M. Smith. Medical Image Anal., 2001

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View Paper: https://www.semanticscholar.org/paper/7d6365839a069042c79f1cb6471045c61566eaa0

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Citations in the corpus

Task-free MRI Predicts Individual Differences in Brain Activity During Task Performance (2016, unknown): “EMOTION Valance judgments (faces), shape recognition [1] FACES [2] SHAPES [3] FACES-SHAPES”
Disrupted Modularity and Local Connectivity of Brain Functional Networks in Childhood-Onset Schizophrenia (2010, unknown): “FSL’s FLIRT (Jenkinson and Smith, 2001; Jenkinson et al., 2002) was used to register each subject’s functional scans to that subject’s structural scan using a 6 degrees of freedom transformation, and to register the structural scan to MNI stereotactic standard space using a 12 degrees of freedom…”
Semantic reconstruction of continuous language from non-invasive brain recordings (2022, unknown): “55).”
Simple models of human brain functional networks (2012, methodology): “The images were preprocessed on the high-performance NIH Biowulf Linux cluster (http://biowulf.nih.gov), using AFNI (47) and FSL (48, 49) software.”
Tensorial extensions of independent component analysis for multisubject FMRI analysis (2005, methodology): “The data were corrected for subject motion using MCFLIRT (Jenkinson et al., 2002), temporally high-pass filtered (Gaussian-weighted leastsquares straight line fitting, with sigma = 20.0 s) (Marchini and Ripley, 2000), and masked for nonbrain voxels using BET (Smith, 2002).”
ResViT: Residual Vision Transformers for Multimodal Medical Image Synthesis (2021, methodology): “Registration was performed via an afﬁne transformation in FSL [98] based on mutual information.”
Investigations into resting-state connectivity using independent component analysis (2005, unknown): “Data were first motion corrected and coregistered using affine linear registration (Jenkinson & Smith 2001) into a common space defined by the midtransformation of all 10 transformation matrices which take the individual low-resolution datasets to the space of the Montreal Neurological Insitute…”
SynthStrip: skull-stripping for any brain image (2022, unknown): “Similarly, skull-stripping increases the reliability of linear registration (Cox and Jesmanowicz, 1999; Friston et al., 1995; Hoﬀmann et al., 2015; Jenkinson and Smith, 2001; Jiang et al., 1995; Modat et al., 2014; Reuter et al., 2010) by excluding anatomy that deforms non-rigidly, such as the…”
Correlation between motor improvements and altered fMRI activity after rehabilitative therapy. (2002, methodology): “For group analyses, the individual level Z statistic images for all patients and all sessions were registered into standard space using FLIRT (Jenkinson and Smith, 2001).”
Medical image registration: a review (2014, methodology): “…al. 2004; Pluim et al. 2004; Auer et al. 2005; Meyer 2007; Sun et al. 2007; Oliveira and Tavares 2011), the downhill simplex method (Dey et al. 1999; Jenkinson and Smith 2001; Shekhar and Zagrodsky 2002; Shekhar et al. 2004), the Gauss–Newton (Ashburner and Friston 1999), the Levenberg-Marquardt…”
Medical image registration using mutual information (2003, background): “Jenkinson and Smith [47] proposed a scheme for global optimization of MI that combines a fast local”
Probabilistic diffusion tractography with multiple fibre orientations: What can we gain? (2006, methodology): “We then defined primary motor cortex (M1) from a population probability map (taken from Johansen-Berg et al., 2004) thresholded at 30%.”
Tract-based spatial statistics: Voxelwise analysis of multi-subject diffusion data (2006, unknown): “We therefore use FLIRT (Jenkinson and Smith, 2001; Jenkinson et al., 2002) to apply full affine (linear) alignment of each image to the no-diffusionweighting image, using the mutual information cost function.”
Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas (2018, methodology): “14,15 Registration was implemented with a linear affine transformation algorithm using 12 df , trilinear interpolation, and a mutual-information cost function.”
Longitudinal changes in grey and white matter during adolescence (2010, unknown): “The following symmetrical standard-space masks were defined in each hemisphere and registered to the native diffusion space of each subject using FMRIB Linear Image Registration Tool (FLIRT (Jenkinson and Smith, 2001)).”
Neuronal correlates of altered empathy and social cognition in borderline personality disorder (2011, unknown): “Registration to high resolution and standard images was done using FLIRT (Jenkinson and Smith, 2001).”