read_cifti_separate: Read a CIFTI file with optional resampling

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

Read a CIFTI file with optional resampling

Description

Read a CIFTI file by writing each component into a GIFTI and NIFTI file (separate_cifti), optionally resampling the GIFTIs, (resample_gifti), and then reading each separated component into R (make_xifti). Surfaces can also be provided; they will be resampled along with the CIFTI for viewing.

Usage

read_cifti_separate(
  cifti_fname,
  surfL_fname = NULL,
  surfR_fname = NULL,
  brainstructures = c("left", "right"),
  idx = NULL,
  resamp_res = NULL,
  resamp_method = c("barycentric", "adaptive"),
  areaL_original_fname = NULL,
  areaR_original_fname = NULL,
  mwall_values = c(NA, NaN),
  verbose = TRUE
)

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.
resamp_res	(Optional) Target resolution for resampling (number of cortical surface vertices per hemisphere). If NULL (default) or FALSE, do not perform resampling.
resamp_method	"barycentric" (default) or "adaptive" resampling for the metric or label data. These options correspond to the Workbench command options "BARYCENTRIC" and "ADAP_BARY_AREA", respectively. While adaptive resampling is recommended for metric or label data, it requires that area[L/R]_original_fname be provided. Note that surfaces will resampled using barycentric resampling regardless of resamp_method, because barycentric resampling rather than adaptive resampling is recommended for surface data.
areaL_original_fname, areaR_original_fname	File paths to the surfaces to use for vertex area correction during adaptive resampling. (Only used if resampling with the adaptive method.) area[L/R]_original_fname should match the current resolution of the data. For resampling: the Workbench command for adaptive resampling requires the target surfaces for area correction too. But to make the workflow easier, ciftiTools will resample area[L/R]_original_fname with the barycentric method and use that for the target area. For remapping: area[L/R]_target_fname must be directly provided.
mwall_values	If the medial wall locations are not indicated in the CIFTI, use these values to infer the medial wall mask. Default: c(NA, NaN). If NULL, do not attempt to infer the medial wall.
verbose	Should occasional updates be printed? Default: TRUE.

Details

The subcortical component (NIFTI) is not resampled.

Value

A "xifti" object. See is.xifti.

mandymejia/ciftiTools documentation built on Feb. 28, 2024, 11:20 a.m.