FSL Command Wrapper

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.