antsMotionCalculation: antsMotionCalculation

In stnava/ANTsR: ANTs in R: Quantification Tools for Biomedical Images

antsMotionCalculation

Description

Correct 4D time-series data for motion.

Usage

antsMotionCalculation(
  img,
  mask = NULL,
  fixed = NULL,
  moreaccurate = 1,
  txtype = "Affine",
  framewise = 1,
  verbose = FALSE,
  num_threads = 1,
  seed = NULL,
  ...
)

Arguments

img	antsImage, usually 4D.
mask	mask for image (3D). If not provided, estimated from data.
fixed	Fixed image to register all timepoints to. If not provided, mean image is used.
moreaccurate	strategy desired for motion correction. One of 0 (test) 1 (high-res only), 2 (multi-level inter-subject), 3 (FIXME), or a special method for intraSubjectBOLD.
txtype	Type of transform. One of "Affine", "Rigid", or "SyN".
framewise	Calculate framewise displacement?
verbose	enables verbose output.
num_threads	will execute Sys.setenv(ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS = num_threads) before running to attempt a more reproducible result. See https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues for discussion. If NULL, will not set anything.
seed	will execute Sys.setenv(ANTS_RANDOM_SEED = seed) before running to attempt a more reproducible result. See https://github.com/ANTsX/ANTs/wiki/antsRegistration-reproducibility-issues for discussion. If NULL, will not set anything.
...	additional argument to .motion_correction

Value

List containing:

moco_img

Motion corrected time-series image.

moco_params

Data frame of translation parameters.

moco_avg_img

Average motion-corrected image.

moco_mask

Mask used to calculate framewise displacement.

tsDisplacement

Time-series displacement image.

fd

Time-series mean and max displacements.

dvars

DVARS, derivative of frame-wise intensity changes.

Author(s)

Benjamin M. Kandel

stnava/ANTsR documentation built on April 13, 2025, 4:10 a.m.