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BET specifications


Unique identifier OMICS_16354
Name BET
Alternative name Brain Extraction Tool
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Stephen Smith

Publication for Brain Extraction Tool

BET citations


Postnatal Microstructural Developmental Trajectory of Corpus Callosum Subregions and Relationship to Clinical Factors in Very Preterm Infants

Sci Rep
PMCID: 5954149
PMID: 29765059
DOI: 10.1038/s41598-018-25245-7
call_split See protocol

[…] , MD, radial diffusivity [RD], and axial diffusivity [AD; L1 – lamda1]). Figure  illustrates examples of FA color maps at each of the four postmenstrual age time points. Last, in FSL, we employed the Brain Extraction Tool to perform brain extraction and BEDPOSTX (Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques) to run probabilistic tractography and model for crossing […]


Altered attentional control over the salience network in complex regional pain syndrome

Sci Rep
PMCID: 5945627
PMID: 29748588
DOI: 10.1038/s41598-018-25757-2
call_split See protocol

[…] e Library tools (FSL, The standard preprocessing steps consisted of motion correction using multi-resolution rigid body co-registration, brain extraction using the FSL Brain Extraction Tool (BET), spatial smoothing with a Gaussian kernel of full width at half maximum of 5 mm, and high-pass filtering at 0.01 Hz. Functional image data of each individual was first co-r […]


Axonal chronic injury in treatment naïve HIV+ adults with asymptomatic neurocognitive impairment and its relationship with clinical variables and cognitive status

PMCID: 5943991
PMID: 29747571
DOI: 10.1186/s12883-018-1069-5
call_split See protocol

[…] ddy currents and head movements and deformations using eddy current correction within FDT. Then, brain mask extraction was performed on one of the no-diffusion-weighting (b = 0) images by running the Brain Extraction Tool in FSL. Finally, the diffusion tensor model was computed using DTIFIT within FDT for whole brain volumes to generate tensor-derived maps, including FA, MD, AD, and RD. TBSS-proce […]


Distributed representation of pelvic floor muscles in human motor cortex

Sci Rep
PMCID: 5940845
PMID: 29740105
DOI: 10.1038/s41598-018-25705-0
call_split See protocol

[…] For participants in both groups, we preprocessed each participant’s fMRI data using the FMRIB Expert Analysis Tool (FEAT,, which included skull extraction using the brain extraction tool (BET) in FSL (FMRIB Software Library), slice timing correction, motion correction, and spatial smoothing using a Gaussian kernel with full-width half-maximum of 5 mm and nonlinea […]


Distant from input: Evidence of regions within the default mode network supporting perceptually decoupled and conceptually guided cognition

PMCID: 5883322
PMID: 29339310
DOI: 10.1016/j.neuroimage.2018.01.017

[…] All imaging data were pre-processed using a standard pipeline and analysed via FMRIB Software Library (FSL Version 6.0). Images were skull-stripped using a brain extraction tool [BET (),]. The first five volumes (10s) of each scan were removed to minimize the effects of magnetic saturation, and slice-timing correction with Fourier space time-series phase […]


Myelin status is associated with change in functional mobility following slope walking in people with multiple sclerosis

PMCID: 5954324
PMID: 29780611
DOI: 10.1177/2055217318773540
call_split See protocol

[…] igher myelin content.For each participant, two region of interest (ROI) masks were generated using the FMRIB Software Library v5.0 (): NAWM ROI mask procedure: T1 images were skull stripped using the Brain Extraction Tool and then segmented into three categories, gray matter, white matter, and cerebrospinal fluid (CSF), using FMRIB's Automated Segmentation Tool. After visual inspection, the segmen […]

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BET institution(s)
Oxford Centre for Functional Magnetic Resonance Imaging of the Brain, Department of Clinical Neurology, Oxford University, John Radcliffe Hospital, Headington, Oxford, UK
BET funding source(s)
This work was supported by the FMRIB Centre from the UK Medical Research Council.

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