FSL statistics

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Protocols

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FSL specifications

Information


Unique identifier OMICS_20572
Name FSL
Alternative name FMRIB Software Library
Software type Framework/Library
Interface Command line interface, Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C#, C++
License Other
Computer skills Advanced
Version 5.0
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/FMRIB_Software_Library

Subtools


  • Atlases
  • Atlasquery
  • BASIL
  • BayCEST
  • BET
  • BIANCA
  • Cluster
  • Dual Regression
  • eddy
  • FABBER
  • FAST
  • FDR
  • FDT
  • FEAT
  • FIRST
  • FLIRT
  • FLOBS
  • FNIRT
  • fsl_anat
  • FSL-VBM
  • FSLeyes
  • FSLUTILS
  • FSLView
  • FUGUE
  • GLM
  • MCFLIRT
  • MELODIC
  • Miscvis
  • MIST
  • Mm
  • MSM
  • POSSUM
  • randomize
  • SIENA
  • SIENAX
  • SUSAN
  • TBSS
  • topup
  • VERBENA

Versioning


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Publications for FMRIB Software Library

library_books

FSL.

2012 Neuroimage
PMID: 21979382
DOI: 10.1016/j.neuroimage.2011.09.015

FSL in pipelines

 (26)
2018
PMCID: 5902293
PMID: 29620625
DOI: 10.1097/MD.0000000000010134

[…] were corrected using an affine transformation of each diffusion-weighted image to the nondiffusion-weighted (b = 0) image as reference volume. the brain mask was estimated using the bet command of fmrib software library. thus, images of fa were generated for each subject by applying an fmrib58_fa template. individual fa images were registered to the fa template in the mni standard space. […]

2018
PMCID: 5954149
PMID: 29765059
DOI: 10.1038/s41598-018-25245-7

[…] maturation on their term-equivalent age mri., dti data were transferred to an offline workstation for further image processing and analysis. we pre-processed all images using fsl 5.0 software of fmrib software library (analysis group, fmrib, oxford, uk) and dtistudio 3.0.2 of mri studio (johns hopkins university, baltimore, md). briefly, we converted raw dti dicom data into analyze format […]

2017
PMCID: 5278114
PMID: 28154795
DOI: 10.1016/j.nicl.2017.01.007

[…] and (2) by defining overlap if the tumor spread across > 50% of all voxels within the aal hub area., preprocessing of the fmri data was performed using standard fsl procedures () included in melodic (), which included discarding the first 5 volumes, motion correction, spatial smoothing (6 mm full width at half maximum gaussian kernel), and high-pass filtering (100 s cut-off). following […]

2017
PMCID: 5504468
PMID: 28744192
DOI: 10.3389/fnins.2017.00394

[…] 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, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/; smith et al., ). fractional intensity threshold was determined for all mri data., using the mricron software package (rorden et […]

2017
PMCID: 5655281
PMID: 29113386
DOI: 10.18632/oncotarget.18111

[…] into nifti format during this step. the dcm2nii tool embedded in mricron accomplished this task., 2) estimating the brain mask: this step yielded the brain mask by using the bet command of fsl (fmrib software library v5.0) []. the brain mask was required for the subsequent processing steps. here, the b0 image without diffusion weighting was used for the estimation., 3) cropping the raw […]


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FSL in publications

 (1794)
PMCID: 5954098
PMID: 29765024
DOI: 10.1038/s41467-018-04268-8

[…] in the same way as described for sample s259. the only differences in analyses were found in their preprocessing. for example, the human connectome project utilizes a combination of the fsl tools topup and eddy in order to correct for eddy currents, head motion, and epi distortions simultaneously. these tools represent an updated version of the eddy_correct tool used for the s259 sample […]

PMCID: 5953411
PMID: 27133575
DOI: 10.1016/j.neuroscience.2016.04.034

[…] time (pre- vs. post-training), as well as the between-subject factor group (training vs. control)., a voxel-wise whole-volume fmri analysis of the ppi (, ) was performed for the transfer runs using feat. preprocessing steps consisted of those employed for the functional localizer (see above). modest spatial filtering with a fwhm = 5 mm was applied to allow for better registration () […]

PMCID: 5953409
PMID: 28214578
DOI: 10.1016/j.neuroscience.2017.02.010

[…] to report whether they used those strategies and how effective they felt each strategy was on a 5-point likert scale., bold fmri data for each subject were analyzed off-line using tools from the fmrib software library (http://www.fmrib.ox.ac.uk/fsl). pre-processing of the images included, motion correction spatial smoothing using a gaussian kernel of 5-mm full width at half maximum (fwhm), […]

PMCID: 5915574
PMID: 29307608
DOI: 10.1016/j.neuroimage.2017.12.098

[…] of interests (roi) in each subject for a given roi atlas. the mean time series of each roi is obtained by averaging all the time series within a roi. to parcellate the brain, we use two data-driven atlases; power atlas () which is constructed of 264 non-neighboring cortical and sub-cortical rois and each rois has 81 voxels (is case of 2 mm isotropic volumes) and gordon atlas () […]

PMCID: 5946463
PMID: 29751782
DOI: 10.1186/s12883-018-1065-9

[…] brain parenchyma volumes were measured on t1w gradient echo images by using the cross-sectional version of the siena (structural image evaluation using normalization of atrophy) software, named sienax (part of fsl 4.0: http://www.fmrib.ox.ac.uk/fsl/), a previously described method to estimate global brain volume normalized for head size []. mri analysis allowed for normalized brain volume […]


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FSL institution(s)
FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, UK

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