fslr: Connecting the FSL Software with R

We present the package fslr, a set of R functions that interface with FSL (FMRIB Software Library), a commonly-used open-source software package for processing and analyzing neuroimaging data. The fslr package performs operations on ‘nifti’ image objects in R using command-line functions from FSL, and returns R objects back to the user. fslr allows users to develop image processing and analysis pipelines based on FSL functionality while interfacing with the functionality provided by R. We present an example of the analysis of structural magnetic resonance images, which demonstrates how R users can leverage the functionality of FSL without switching to shell commands. Glossary of acronyms MRI Magnetic Resonance Imaging/Image FSL FMRIB Software Library PD Proton Density FAST FMRIB’s Automated Segmentation Tool FLAIR Fluid-Attenuated Inversion Recovery FLIRT FMRIB’s Linear Image Registration Tool MS Multiple Sclerosis BET Brain Extraction Tool FMRIB Functional MRI of the Brain Group FNIRT FMRIB’s Nonlinear Image Registration Tool MNI Montreal Neurological Institute

John Muschelli , Elizabeth Sweeney , Martin Lindquist , Ciprian Crainiceanu

CRAN packages used

AnalyzeFMRI, RNiftyReg, fmri, fslr, oro.nifti, ggplot2, ggplot2, mgcv

CRAN Task Views implied by cited packages

MedicalImaging, ChemPhys, Graphics, Phylogenetics, Bayesian, Econometrics, Environmetrics, SocialSciences

Bioconductor packages used



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For attribution, please cite this work as

Muschelli, et al., "The R Journal: fslr: Connecting the FSL Software with R", The R Journal, 2015

BibTeX citation

  author = {Muschelli, John and Sweeney, Elizabeth and Lindquist, Martin and Crainiceanu, Ciprian},
  title = {The R Journal: fslr: Connecting the FSL Software with R},
  journal = {The R Journal},
  year = {2015},
  note = {https://doi.org/10.32614/RJ-2015-013},
  doi = {10.32614/RJ-2015-013},
  volume = {7},
  issue = {1},
  issn = {2073-4859},
  pages = {163-175}