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AFNI ROIStats

Source: R/wrappers_auto.R
ni_afni_roi_stats.Rd

Display statistics over masked regions

Usage

ni_afni_roi_stats(
  in_file,
  args = NULL,
  debug = NULL,
  format1D = NULL,
  format1DR = NULL,
  mask = NULL,
  mask_f2short = NULL,
  mask_file = NULL,
  nobriklab = NULL,
  nomeanout = NULL,
  num_roi = NULL,
  out_file = NULL,
  quiet = NULL,
  roisel = NULL,
  stat = NULL,
  zerofill = 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

debug

Logical. print debug information

format1D

Logical. Output results in a 1D format that includes commented labels

format1DR

Logical. Output results in a 1D format that includes uncommented labels. May not work optimally with typical 1D functions, but is useful for R functions.

mask

Character; file path. input mask

mask_f2short

Logical. Tells the program to convert a float mask to short integers, by simple rounding.

mask_file

Character; file path. input mask

nobriklab

Logical. Do not print the sub-brick label next to its index

nomeanout

Logical. Do not include the (zero-inclusive) mean among computed stats

num_roi

Integer. Forces the assumption that the mask dataset's ROIs are denoted by 1 to n inclusive. Normally, the program figures out the ROIs on its own. This option is useful if a) you are certain that the mask dataset has no values outside the range [0 n], b) there may be some ROIs missing between [1 n] in the mask data-set and c) you want those columns in the output any-way so the output lines up with the output from other invocations of 3dROIstats.

out_file

Character; file path. output file

quiet

Logical. execute quietly

roisel

Character; file path. Only considers ROIs denoted by values found in the specified file. Note that the order of the ROIs as specified in the file is not preserved. So an SEL.1D of '2 8 20' produces the same output as '8 20 2'

stat

Character or numeric vector. Statistics to compute. Options include: * mean = Compute the mean using only non_zero voxels. Implies the opposite for the mean computed by default. * median = Compute the median of nonzero voxels * mode = Compute the mode of nonzero voxels. (integral valued sets only) * minmax = Compute the min/max of nonzero voxels * sum = Compute the sum using only nonzero voxels. * voxels = Compute the number of nonzero voxels * sigma = Compute the standard deviation of nonzero voxels Statistics that include zero-valued voxels: * zerominmax = Compute the min/max of all voxels. * zerosigma = Compute the standard deviation of all voxels. * zeromedian = Compute the median of all voxels. * zeromode = Compute the mode of all voxels. * summary = Only output a summary line with the grand mean across all briks in the input dataset. This option cannot be used with nomeanout. More that one option can be specified.

zerofill

Character. For ROI labels not found, use the provided string instead of a '0' in the output file. Only active if num_roi is enabled.

.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.