fslcmd {fslr}

FSL Command Wrapper

Description

This function calls fsl command passed to func

Usage

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.