seg_normalize: Spatially Normalize SMRI data and Tissue Segmentation

In neuroconductor/smri.process: Processing of Structural Magnetic Resonance Imaging

Description

Spatially Normalize SMRI data and Tissue Segmentation, note T1 is required

Usage

seg_normalize(prenormalize, template = c("none", "Eve", "MNI"),
  norm_outdir = prenormalize$outdir, verbose = TRUE,
  typeofTransform = "SyN", segment_typeofTransform = typeofTransform,
  interpolator = "lanczosWindowedSinc",
  dis_interpolator = "genericLabel",
  malf_interpolator = "genericLabel", copy_origin = TRUE,
  force_registration = FALSE, ...)

Arguments

prenormalize	list from smri_prenormalize
template	Resampling to 1x1x1 (template = none) or Template to register to - either MNI or Eve template
norm_outdir	Output directory of spatially normalized data. The output directory of the segmentation images will still be specified in prenormalize$outdir
verbose	print diagnostic messages
typeofTransform	Transformation to use for registration, passed to registration
segment_typeofTransform	Transformation to use for malf segmentation
interpolator	Interpolation done, passed to registration for continuous data
dis_interpolator	Interpolation done, passed to registration for discrete data
malf_interpolator	interpolator for MALF procedure, passed to t1_segment
copy_origin	Copy image origin from image being registered, using antsCopyOrigin
force_registration	Should the MALF registrations be re-run if they already exist?
...	arguments passed to t1_segment

Value

List of images, suffix, brain mask, gold standard, and registration if applicable

neuroconductor/smri.process documentation built on Sept. 29, 2020, 2:32 p.m.