FSL FAST

This function calls fast from FSL

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)

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.

Value

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

Note

Functions with underscores have different defaults and will return an output filename, so to be used for piping