separate_cifti_files: Separate CIFTI: file names
In ciftiTools: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files

separate_cifti_files

R Documentation

Separate CIFTI: file names

Description

File paths for writing GIFTI and NIFTI files from a CIFTI or "xifti"

Usage

separate_cifti_files(
  bs_present,
  intent = 3006,
  brainstructures = NULL,
  cortexL_fname = NULL,
  cortexR_fname = NULL,
  subcortVol_fname = NULL,
  subcortLabs_fname = NULL,
  ROI_brainstructures = "all",
  ROIcortexL_fname = NULL,
  ROIcortexR_fname = NULL,
  ROIsubcortVol_fname = NULL,
  write_dir = NULL
)

Arguments

`bs_present`	The brain structures actually present in the CIFTI or `"xifti"` object.
`intent`	3002 (default), 3006, or 3007
`brainstructures`	(Optional) character vector indicating a subset of brain structure(s) to write: `"left"` cortex, `"right"` cortex, and/or `"subcortical"` structures. Can also be `"all"` to write out all existing brain structures. Default: `"all"`.
`cortexL_fname`, `cortexR_fname`	(Optional) GIFTI file names (.[func/label].gii) to save the [left/right] cortex data to. dtseries and dscalar files should use "func", whereas dlabel files should use "label". If `NULL` and `write_dir` is provided, defaults to `"[L/R].\[func/label\].gii"`, where * is the file name component of `cifti_fname`.
`subcortVol_fname`, `subcortLabs_fname`	(Optional) NIFTI file names to save the subcortical [volume/labels] to. Provide both or neither. If `NULL` and `write_dir` is provided, defaults to `"[/.labels].nii"`, where is the file name component of `cifti_fname`.
`ROI_brainstructures`	Which ROIs should be obtained? `"all"` (default) to obtain ROIs for each of the `brainstructures`. `NULL` to not obtain any ROIs. This should be a subset of `brainstructures`.
`ROIcortexL_fname`, `ROIcortexR_fname`	(Optional) GIFTI file names (.[func/label].gii) to save the [left/right] cortex ROI to. dtseries and dscalar files should use "func", whereas dlabel files should use "label". If `NULL` and `write_dir` is provided, defaults to `"ROI_[L/R].\[func/label\].gii"`, where * is the file name component of `cifti_fname`. The cortical ROIs typically represent the medial wall mask, with values of 1 for in-ROI (non-medial wall) vertices and 0 for out-of-ROI (medial wall) vertices. Will be written in `write_dir`.
`ROIsubcortVol_fname`	(Optional) NIFTI file names to save the subcortical ROI to. If `NULL` and `write_dir` is provided, defaults to `"ROI.nii"`, where is the file name component of `cifti_fname`. The subcortical ROI typically represents the volumetric mask for the entire subcortical structure, with values of 1 for in-ROI (in subcortex) voxels and 0 for out-of-ROI (not in subcortex) voxels. Will be written in `write_dir`.
`write_dir`	(Optional) A path to an existing directory. If provided, every component in the `"xifti"` will be written to this directory, using automatically-generated names if their `_fname` argument was not provided. Otherwise if `write_dir` is `NULL`, only the components for which their `_fname` was provided will be written.

Details

If write_dir is NULL, only components with provided file names will be written. If write_dir is not NULL, files for all existing brain components will be written to that directory.