SMRI Pipeline for Preprocessing Prior to Normalization

SMRI Pipeline for Preprocessing Prior to Normalization

smri_prenormalize(x, gold_standard = NULL, gs_space = NULL,
  probs = c(0, 0.995), non_zero = TRUE,
  interpolator = "lanczosWindowedSinc", brain_mask = NULL,
  gs_interpolator = "genericLabel", num_templates = 15,
  malf_transform = "SyNAggro", outdir = tempdir(), reg_space = "T1",
  brain_extraction_method = c("abp", "malf", "robex", "bet"),
  brain_malf_function = "staple_prob", n_skull_iter = 3,
  brain_threshold = 0.5, verbose = TRUE, remove_negative = TRUE,
  zero_origin = TRUE, reduce = TRUE, cleanup = 1, pad = TRUE, ...)

Arguments

x	List of images
gold_standard	Gold Standard image/filename, if applicable
gs_space	space the Gold Standard is located
probs	passed to winsor for Winsorization
non_zero	Should zeroes be excluded from the calculation of quantiles? Passed to winsor.
interpolator	interpolation passed to reg_to_t1
brain_mask	Brain Mask in reg_space
gs_interpolator	Gold Standard interpolation passed to reg_to_t1
num_templates	Number of templates to use for MALF
malf_transform	type of registration transformation for MALF
outdir	Output directory
reg_space	space to register images to
brain_extraction_method	Brain extraction method, either malf or abp for n4_skull_strip
brain_malf_function	Function to be passed to malf, and subsequently stat_img for brain extraction
n_skull_iter	number of iterations to use n4_skull_strip for skull stripping if brain_extraction_method = "abp".
brain_threshold	Percentage threshold for the brain MALF image to be considered part of the mask
verbose	print diagnostic messages
remove_negative	After reorientation, N4, and registration, any values < 0 are set to 0
zero_origin	Should the origin be set to 0 for the image to be registered to?
reduce	If TRUE, the image size will be reduced using reduce_img.
cleanup	Argument to reduce_img for reducing the images.
pad	should zero padding be done before skull stripping (recommend to TRUE)
...	Additional arguments to MALF

Value

List of the images, brain mask, suffix, and output directory