Create command declaring FREESURFER_HOME

Finds the Freesurfer from system environment or getOption("freesurfer.path") for location of Freesurfer functions

get_fs(bin_app = c("bin", "mni/bin", ""))

Arguments

bin_app	Should bin be added to the freesurfer path? All executables are assumed to be in FREESURFER_HOME/bin/. If not, and bin_app = "", they will be assumed to be in FREESURFER_HOME/.

Value

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

Note

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

Examples

if (have_fs()) {
get_fs()
}