preprocess_mri_across: Preprocess MRI acros visits

In neuroconductor/extrantsr: Extra Functions to Build on the 'ANTsR' Package

Description

This function performs preprocessing and registration across visits and within visits

Usage

preprocess_mri_across(
  baseline_files,
  followup_files,
  baseline_outfiles,
  followup_outfiles,
  retimg = FALSE,
  maskfile = NULL,
  correct = TRUE,
  correction = "N4",
  skull_strip = TRUE,
  bet.opts = "-B -f 0.1 -v",
  betcmd = "bet",
  within.transform = "Rigid",
  within.interpolator = "LanczosWindowedSinc",
  across.transform = within.transform,
  across.interpolator = within.interpolator,
  verbose = TRUE,
  ...
)

Arguments

baseline_files	filename of baseline images
followup_files	filename of followup images
baseline_outfiles	output filenames for baseline images
followup_outfiles	output filenames for followup images
retimg	(logical) return list of images of class nifti
maskfile	Filename (or nifti object) of binary mask for baseline image. If filename exists, skull stripping will be done by masking it. If it does not, then skull stripping will get one from the baseline image
correct	Perform bias field correction
correction	(character) N3 or N4 correction?
skull_strip	do Skull stripping with FSL BET
bet.opts	Options to pass to fslbet
betcmd	Command to pass to fslbet
within.transform	Transformation for within-visit registration
within.interpolator	Interpolator for within-visit registration
across.transform	Transformation for across-visit registration
across.interpolator	Interpolator for across-visit registration
verbose	print diagnostic outputs
...	arguments to preprocess_mri_within and ants_regwrite

Value

list of objects from preprocess_mri_within and registration

neuroconductor/extrantsr documentation built on Sept. 28, 2020, 11:31 a.m.