AFNI ReHo — ni_afni_re

Compute regional homogeneity for a given neighbourhood.l,

Usage

ni_afni_re_ho(
  in_file,
  args = NULL,
  chi_sq = NULL,
  ellipsoid = NULL,
  label_set = NULL,
  mask_file = NULL,
  neighborhood = NULL,
  out_file = NULL,
  overwrite = NULL,
  sphere = NULL,
  .cwd = NULL,
  .env = NULL,
  .engine = NULL,
  .profile = NULL,
  dry_run = FALSE,
  echo = interactive()
)

Arguments

in_file: Character; file path. input dataset Required.
args: Character. Additional parameters to the command
chi_sq: Logical. Output the Friedman chi-squared value in addition to the Kendall's W. This option is currently compatible only with the AFNI (BRIK/HEAD) output type; the chi-squared value will be the second sub-brick of the output dataset.
ellipsoid: Character or numeric vector. \ Tuple indicating the x, y, and z radius of an ellipsoid defining the neighbourhood of each voxel. The 'hood is then made according to the following relation: :math:(i/A)^2 + (j/B)^2 + (k/C)^2 \\le 1. which will have approx. :math:V=4 \\pi \\, A B C/3. The impetus for this freedom was for use with data having anisotropic voxel edge lengths.
label_set: Character; file path. a set of ROIs, each labelled with distinct integers. ReHo will then be calculated per ROI.
mask_file: Character; file path. Mask within which ReHo should be calculated voxelwise
neighborhood: Character; one of: "faces", "edges", "vertices". voxels in neighborhood. can be: faces (for voxel and 6 facewise neighbors, only), edges (for voxel and 18 face- and edge-wise neighbors), vertices (for voxel and 26 face-, edge-, and node-wise neighbors).
out_file: Character; file path. Output dataset.
overwrite: Logical. overwrite output file if it already exists
sphere: Numeric. \ For additional voxelwise neighborhood control, the radius R of a desired neighborhood can be put in; R is a floating point number, and must be >1. Examples of the numbers of voxels in a given radius are as follows (you can roughly approximate with the ol' :math:4\\pi\\,R^3/3 thing): * R=2.0 -> V=33 * R=2.3 -> V=57, * R=2.9 -> V=93, * R=3.1 -> V=123, * R=3.9 -> V=251, * R=4.5 -> V=389, * R=6.1 -> V=949, but you can choose most any value.
.cwd: Working directory override.
.env: Named character vector of environment variables.
.engine: Execution engine override.
.profile: Runtime profile override.
dry_run: Logical; preview command without executing.
echo: Logical; echo stdout/stderr in real time.

Value

An ni_result object.