read_cifti_convert: Read a CIFTI file quickly

In ciftiTools: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

Read a CIFTI file quickly

Description

Read a CIFTI file by exporting it as a single GIFTI using -cifti-convert -to-gifti-ext (read_cifti_flat), and obtaining the brainordinate mapping using -cifti-export-dense-mapping (info_cifti).

Usage

read_cifti_convert(
  cifti_fname,
  surfL_fname = NULL,
  surfR_fname = NULL,
  brainstructures = "existing",
  idx = NULL,
  mwall_values = c(NA, NaN),
  verbose = FALSE,
  ...
)

Arguments

cifti_fname	File path to a CIFTI file (ending in ".d*.nii").
surfL_fname	(Optional) File path to a GIFTI surface geometry file representing the left cortex.
surfR_fname	(Optional) File path to a GIFTI surface geometry file representing the right cortex.
brainstructures	Character vector indicating which brain structure(s) to read in: "left" (left cortex), "right" (right cortex) and/or "subcortical" (subcortex and cerebellum). Can also be "all" (read all three brain structures), or "existing" (read all brain structures in the file). Default: "existing". If a brain structure is indicated but does not exist, a warning will be raised and that brain structure will be skipped.
idx	Numeric vector indicating the data indices (columns) to read. If NULL (default), read in all the data. Must be a subset of the indices present in the file, or an error will occur. For high-resolution CIFTI files, reading in only a subset of the data saves memory, but will be slower than reading in the entire file due to the required intermediate steps.
mwall_values	If the medial wall mask is not present in the CIFTI, infer it from these data values. Default: c(NA, NaN). If NULL, do not attempt to infer the medial wall mask from the data values.
verbose	Should occasional updates be printed? Default: FALSE.
...	Additional arguments to read_cifti_flat.

Value

A "xifti" object. See is.xifti.

ciftiTools documentation built on April 4, 2025, 1:09 a.m.