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