fast: FSL FAST

Description

This function calls fast from FSL

Usage

fast(
  file,
  outfile = NULL,
  bias_correct = TRUE,
  retimg = TRUE,
  reorient = FALSE,
  intern = FALSE,
  opts = "",
  type = c("T1", "T2", "PD"),
  out_type = c("seg", "mixeltype", "pve_0", "pve_1", "pve_2", "pveseg"),
  verbose = TRUE,
  all_images = FALSE,
  ...
)
fast_all(..., all_images = TRUE)
fast_nobias_all(..., bias_correct = FALSE, all_images = FALSE)
fsl_fast(..., outfile = tempfile(fileext = ".nii.gz"), retimg = FALSE)
fslfast(...)
fsl_fast_nobias(
  ...,
  bias_correct = FALSE,
  outfile = tempfile(fileext = ".nii.gz"),
  retimg = FALSE
)
fast_nobias(..., bias_correct = FALSE)
fslfast_nobias(..., bias_correct = FALSE)

Value

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

Arguments

file: (character) image to be manipulated
outfile: (character) resultant image name (optional)
bias_correct: (logical) if FALSE, then "--nobias" is passed to FAST. Additional options can be sent using opts, but this is the most commonly one changed.
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 fast
type: type of image T1, T2, or PD.
out_type: (character) Suffix to grab from outfile. For example, output filename is paste0(outfile, "_", out_type)
verbose: (logical) print out command before running
all_images: If retimg
...: additional arguments passed to readnii.