= 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||