get.fsl: Create command declaring FSLDIR

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

Create command declaring FSLDIR

Description

Finds the FSLDIR from system environment or getOption("fsl.path") for location of FSL functions

Usage

get.fsl(add_bin = TRUE)

get_fsl(add_bin = TRUE)

Arguments

add_bin

Should bin be added to the fsl path? All executables are assumed to be in FSLDIR/bin/. If not, and add_bin = FALSE, they will be assumed to be in FSLDIR/.

Value

NULL if FSL in path, or bash code for setting up FSL DIR

Note

This will use Sys.getenv("FSLDIR") before getOption("fsl.path"). If the directory is not found for FSL in Sys.getenv("FSLDIR") and getOption("fsl.path"), it will try the default directory /usr/local/fsl.

fslr documentation built on Sept. 10, 2025, 1:06 a.m.