Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Wrapper functions that interface with 'FSL' < http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used 'neuroimaging' software, using system commands. The goal is to be able to interface with 'FSL' completely in R, where you pass R objects of class 'nifti', implemented by package 'oro.nifti', and the function executes an 'FSL' command and returns an R object of class 'nifti' if desired.

Travis-CI build status:

fslr is a port/wrapper of FSL to R.


fslr 2.22.0

  • fixed bug in reverse_rpi_orient_file that was causing ERROR: Could not open file /usr/local/fsl/bin/fslswapdim: 107: [: =: unexpected operator error.
  • added topup to the exports.
  • added fsl_resample.
  • Added fsl_cluster. Removed cluster from exports due to conflicts.
  • added read_xfm for reading transformations.
  • Fixes mid_sagittal_align for flipping.
  • Removed matrixStats as unnecessary dependency.

fslr 2.17.3

  • Added functionality of topup and other DTI-based tools.
  • Tried to get susan to work properly.
  • Need to incorporate fsleyes in the future release.

fslr v1.6.0 (Release date: 2015-12-01)

Major changes

  • Changed default reading/writing to readnii/writenii

fslr v1.5.1 (Release date: 2015-10-20)

Major changes

  • Added readnii and writenii

  • Added ortho_diff

fslr v1.4-4 (Release date: 2015-05-20)

Major Changes

  • Moved functions such as cal_img to oro.nifti package. They are all legacies, such as cal_img still works, but calibrateImage and other camelCase functions have been made default.

  • Fixed fsl_biascorrect.

Reference manual

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2.24.1 by John Muschelli, 2 years ago

Report a bug at https://github.com/muschellij2/fslr/issues

Browse source code at https://github.com/cran/fslr

Authors: John Muschelli [aut, cre]

Documentation:   PDF Manual  

Task views: Medical Image Analysis

GPL-3 license

Imports methods, R.utils, graphics, grDevices, stats, utils

Depends on oro.nifti, neurobase

Suggests knitr, rmarkdown, covr

System requirements: FSL

Imported by neuronorm.

Suggested by freesurfer.

See at CRAN