## Glossary of Acronyms and Abbreviations

AVW | Analyze file format
BET | Brain Extraction Tool - segments brain from non-brain in structural and functional data
COPE | Contrast of Parameter Estimates
DOF | Degrees Of Freedom, the number of independent pieces of information that go into the estimate of a parameter
EV | Explanatory Variable, an effect (e.g. type of stimulation, confound) that is included in a general linear model
FAST | FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction
FE | Fixed Effects. FE variance is the within-session across-time variances estimated in first-level analyses
FEAT | FMRI Expert Analysis Tool - for preprocessing and statistical analysis of FMRI data
FILM | FMRIB's Improved Linear Model - for GLM-based analysis of first level (time series) data with prewhitening
FIR | Finite Impulse Response, a discrete, fixed duration resonse to an impulse
FLAME | FMRIB's Local Analysis of Mixed Effects - for higher level analyses of multiple subjects/sessions
FLIRT | FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration
FMRIB | Oxford Centre for Functional Magnetic Resonance Imaging of the Brain
FSL | FMRIB Software Library - a collection of functional and structural brain image analysis tools
FUGUE | FMRIB's Utility for Geometrically Unwarping EPIs - Unwarps geometric distortion in EPI images using B0 field maps
FWHM | Full Width between Half Maximum values of a function
GLM | General Linear Model (more properly referred to as just "linear model")
GRF | Gaussian Random Field. GRF theory is used in various thresholding techniques
GUI | Graphical User Interface - lets users interact with tools using a "point and click" approach rather than typing text into a command line.
HRF | Haemodynamic Response Function, describes the delayed, blurred haemodynamic response that occurs in response to a stimulus
ICA | Independent Component Analysis
MCFLIRT | Motion Correction using FMRIB's Linear Image Registration Tool
MCMC | Markov Chain Monte Carlo, a sampling technique
ME | Mixed Effects. ME variance is the sum of "fixed-effects" variance and "random-effects" variance
MELODIC | Multivariate Exploratory Linear Optimized Decomposition into Independent Components - PICA-based model-free analysis of FMRI data
MNI | Montreal Neurological Institute. The MNI152 template is a standard-space average of 152 brains
OLS | Ordinary Least Squares, a technique for calculating the parameters in a regression equation that minimizes the sum of the squares of the error terms
PE | Parameter Estimate, an estimate of how strongly an EV fits the data at each voxel
PICA | Probabilistic Independent Component Analysis
RE | Random Effects. RE variance is the "true" cross-session variances of first-level parameter estimates
SIENA | Structural brain change analysis - for estimating brain atrophy (stands for: Structural Image Evaluation, using Normalisation, of Atrophy)
SUSAN | nonlinear noise reduction (stands for: Smallest Univalue Segment Assimilating Nucleus)
TBSS | Tract-Based Spatial Statistics - a method for carrying out voxelwise comparisons of diffusion data across subjects
TR | Repetition Time - time between scanning succesive brain volumes