Multi-Atlas Label Fusion

Takes in an input file and template images with a set of template structures and creates a label fusion

malf(
  infile,
  template.images,
  template.structs,
  inverted = FALSE,
  keep_images = FALSE,
  outfiles = NULL,
  outfile = NULL,
  retimg = TRUE,
  func = "mode",
  ties.method = "first",
  keep_regs = FALSE,
  outprefix = NULL,
  interpolator = "NearestNeighbor",
  typeofTransform = "SyN",
  verbose = TRUE,
  ...
)

Arguments

infile	Input Image file
template.images	Template Images to register to infile
template.structs	Template gold standards to apply registration into infile space
inverted	Should the MALF be inverted (infile to template then use inverse transforms)
keep_images	Keep the template.structs in infile space
outfiles	Output filenames for template.structs in infile space
outfile	Fused output filename
retimg	Return Image to user using readnii
func	function to combine labels. See stat_img.
ties.method	If func = "mode", then this is passed to stat_img.
keep_regs	Keep list of registrations. If TRUE, then remove.warp = FALSE in registration
outprefix	passed to registration if keep_regs = TRUE
interpolator	interpolation done for antsApplyTransforms
typeofTransform	type of transformed used, passed to antsRegistration
verbose	Print diagnostic output
...	Arguments to be passed to malf_registration, which really are options for registration

Value

The output filename or the nifti image or list of registrations and output file