BET statistics

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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


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  • person_outline Stephen Smith <>

Publication for Brain Extraction Tool

BET in pipelines

PMCID: 5954149
PMID: 29765059
DOI: 10.1038/s41598-018-25245-7

[…] 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 […]

PMCID: 5278114
PMID: 28154795
DOI: 10.1016/j.nicl.2017.01.007

[…] ()., the imaging processing steps were performed using fsl 5 (fmrib's software library, first, non-brain tissue was removed from the 3d t1-weighted images using the brain extraction tool (), and grey and white matter segmentation was performed using fast (). to construct each individual's functional brain network, the automated anatomical labeling (aal) atlas […]

PMCID: 5504468
PMID: 28744192
DOI: 10.3389/fnins.2017.00394

[…] with the ac-pc midpoint providing the origin, the ac-pc line forming the y-axis, and a midline forming the z-axis. the x-axis ran left to right. skull stripping was performed using the automated brain extraction tool (bet; smith, ) provided as a part of the fmrib software library (fsl,; smith et al., ). fractional intensity threshold was determined […]

PMCID: 5661170
PMID: 29118724
DOI: 10.3389/fpsyt.2017.00205

[…] eddy-current, and head-motion correction, fa calculation and whole-brain deterministic dti fiber tractography (). first, the non-brain tissues of the images were deleted by employing the brain extraction tool (). second, the head motion and eddy current distortions were corrected through registering the dw images to the b0 image with an affine transformation (). after correction, six […]

PMCID: 5056177
PMID: 27777556
DOI: 10.3389/fnbeh.2016.00194

[…] (university of oxford, uk) to correct for eddy currents and head motion. after two acquisitions being averaged, the averaged images were masked to remove the skull and non-brain tissue using the fsl brain extraction tool (bet) (). afterward, the fractional anisotropy (fa) was calculated using the diffusion tensor analysis toolkit (fdt; )., the whole cerebral cortex was parcellated into 90 areas […]

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BET in publications

PMCID: 5945627
PMID: 29748588
DOI: 10.1038/s41598-018-25757-2

[…] 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 […]

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

[…] 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. […]

PMCID: 5940845
PMID: 29740105
DOI: 10.1038/s41598-018-25705-0

[…] 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 […]

PMCID: 5954324
PMID: 29780611
DOI: 10.1177/2055217318773540

[…] 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, […]

PMCID: 5932175
PMID: 29755401
DOI: 10.3389/fneur.2018.00279

[…] for preprocessing image intensity, non-uniformity correction was estimated and applied to all t1 images within a subject-specific brain mask using n4itk (). the brain masks were created using fsl’s brain extraction tool () with robust brain center estimation and a fractional intensity threshold of 0.2. for each patient, we co-registered the structural preprocessed t1-weighted image to the mean […]

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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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