FSL Command Wrapper — fslcmd • fslr

This function calls fsl command passed to func

fslcmd(
  func,
  file,
  outfile = NULL,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  samefile = FALSE,
  opts_after_outfile = FALSE,
  frontopts = "",
  no.outfile = FALSE,
  trim_front = FALSE,
  run = TRUE,
  ...
)

Arguments

func: (character) FSL function
file: (character) image to be manipulated
outfile: (character) resultant image name (optional)
retimg: (logical) return image of class nifti
reorient: (logical) If retimg, should file be reoriented when read in? Passed to readnii.
intern: (logical) to be passed to system
opts: (character) operations to be passed to func
verbose: (logical) print out command before running
samefile: (logical) is the output the same file?
opts_after_outfile: (logical) should opts come after the outfile in the FSL command?
frontopts: (character) options/character to put in before filename
no.outfile: (logical) is there an output file in the arguments of the FSL function?
trim_front: trim the whitespace from the front of the command.
run: (logical) Should the command just be printed (if FALSE)?
...: additional arguments passed to readnii.

Value

If retimg then object of class nifti. Otherwise, Result from system command, depends if intern is TRUE or FALSE.