transform_point_to_template: Calculate template 'MNI' coordinates for points on native...

In beauchamplab/raveio: File-System Toolbox for RAVE Project

Calculate template 'MNI' coordinates for points on native brain

Description

Calculate template 'MNI' coordinates for points on native brain

Usage

transform_point_to_template(
  subject,
  positions,
  space = c("scannerRAS", "tkrRAS"),
  mapping_method = c("volumetric", "surface"),
  flip_hemisphere = FALSE,
  verbose = TRUE,
  project_surface = "pial",
  volumetric_transform = c("auto", "affine", "nonlinear"),
  ...
)

transform_thinfilm_to_mni152(
  subject,
  flip_hemisphere = FALSE,
  interpolator = 0.3,
  n_segments = c(16, 16),
  group_labels = NULL,
  project_surface = "pial",
  volumetric_transform = c("auto", "affine", "nonlinear"),
  template_subject = c("cvs_avg35_inMNI152", "fsaverage", "bert", "MNI152")
)

Arguments

subject	'RAVE' subject
positions	optional matrix of 3 columns, either in scanner or surface space (specified by space); default is missing and will use the electrode localization results (electrodes.csv)
space	if positions is given, which native coordinate system should be used; default is native 'T1' (or 'scannerRAS'); alternative is 'FreeSurfer' surface coordinate (or 'tkrRAS')
mapping_method	whether the mapping is 'volumetric' or 'surface'; default is the former.
flip_hemisphere	whether to flip the hemisphere; default is FALSE
verbose	whether to verbose the mapping progress; default is true
project_surface	for surface mapping only, which surface to project electrodes onto; default is 'pial' surface, other common choices are 'white' for white-matter, or 'smoothwm' for smoothed white matter
volumetric_transform	for volume mapping only, which type of transform to use; default is 'auto' detecting and use non-linear deformation if exists, and fall back to 'affine' transform; other choices are 'affine' or 'nonlinear'
...	ignored
interpolator	whether the transform lean towards volume mapping (interpolator=0) or surface mapping (interpolator=1)
n_segments	positive integers with length of two: resolution of the mapping; default segments the thin-film array into 16 by 16 segments
group_labels	NULL (default) or a character vector indicating the group labels of thin-film electrodes; default assumes that all contacts are from thin-film electrodes.
template_subject	template subject to be mapped to; default is 'cvs_avg35_inMNI152', which is a 'MNI152' template generated by 'FreeSurfer'; other choices are 'fsaverage' and 'bert'

Value

A table of electrode 'MNI' coordinates.

Examples

if(interactive()) {

transform_point_to_template('demo/DemoSubject', mapping_method = "volumetric")

}

beauchamplab/raveio documentation built on March 5, 2025, 11:06 p.m.