FSL Anatomical Processing Script

This function calls fsl_anat from FSL

fsl_anat(
  file,
  modality = c("T1", "T2", "PD"),
  outdir = NULL,
  intern = FALSE,
  opts = "",
  verbose = TRUE,
  ...
)

Arguments

file

(character) image to be manipulated, should be full path

modality

(character) Modality of Image to be run

outdir

(character) output directory, if none specified, will default to dirname(file)

intern

(logical) to be passed to system

opts

(character) operations to be passed to fsl_anat

verbose

(logical) print out command before running

...

options passed to checkimg

Value

Result from system command, depends if intern is TRUE or FALSE.