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Name

FSL - The FMRIB Software Library

Byline

FMRIB, Oxford University

Description

The FMRIB Software Library (FSL) is a collection of functional and structural brain image analysis tools. FSL is completely self-contained. Most of the tools can be run both from the unix command line and as GUIs (easy to use "point-and-click" graphical user interfaces) in unix. You do not need any other software in order to use FSL. However, if you have MEDx, you can configure it to seamlessly access the FSL GUIs. MEDx is a GUI-driven commercial image analysis and display package, available from Sensor Systems. The latest version of MEDx (3.4) comes with a previous FSL release (1.2a) built in.

LIST OF TOOLS IN FSL

STRUCTURAL TOOLS

BET - Brain Extraction Tool - segments brain from non-brain in structural and functional data.
SUSAN - Nonlinear noise reduction.
FAST - FMRIB's Automated Segmentation Tool - brain segmentation (into different tissue types) and bias field correction.
FLIRT - FMRIB's Linear Image Registration Tool - linear inter- and intra-modal registration.
FUGUE - Unwarps distortion in EPI images using B0 field maps.
SIENA - Structural brain change analysis, for estimating brain atrophy.

(BET, FLIRT and FUGUE are also used in FMRI analysis)

FUNCTIONAL TOOLS

FEAT - Advanced FMRI analysis with easy-to-use yet powerful GUI. Includes all necessary preprocesing, model-based and semi-model-free statistical analysis, automatic registration to structural and/or standard space, and fixed- and random-effects group statistics.
MCFLIRT - FMRI motion correction.
MELODIC - ICA-based model-free analysis of FMRI (and other 4D) data.

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