read_cifti_convert: 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 = c("left", "right"),
  idx = NULL,
  mwall_values = c(NA, NaN),
  verbose = FALSE,
  ...
)

Value

A "xifti" object. See is.xifti.

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 obtain: "left" (left cortex), "right" (right cortex) and/or "subcortical" (subcortex and cerebellum). Can also be "all" (obtain all three brain structures). Default: c("left","right") (cortex only).

If a brain structure is indicated but does not exist in the CIFTI file, a warning will occur 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.