fslr: An R Package Interfacing with FSL for Neuroimaging Analysis

A HopStat and Jump Away

I use a set of neuroimaging tools, but my language of choice is R. FSL, which is from the University of Oxford’s Functional MRI of the Brain (FMRIB), and stands for FMRIB Software Library, is one tool I commonly use. I wrote some wrapper functions into an R package called fslr and wanted to discuss some of the functions.

FSL – what is it?

FSL is has a command line interface with shell-type syntax as well as a GUI (which I generally don’t use). It has a lot of functions that are good for general imaging purposes – fslstats and fslmaths have loads of functionality. Using FSL during your pipeline is fine, but I don’t like switching between shell and R too much in an analysis and like to have scripts that don’t jump around too much, so I created fslr.

One of the main problems I…

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