seg_normalize: Spatially Normalize SMRI data and Tissue Segmentation

Description Usage Arguments Value

View source: R/seg_normalize.R

Description

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

Usage

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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.