smri_prenormalize: SMRI Pipeline for Preprocessing Prior to Normalization
In neuroconductor/smri.process: Processing of Structural Magnetic Resonance Imaging

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, ...)

`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