separate_cifti: Separate a CIFTI file

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

Separate a CIFTI file

Description

Separate a CIFTI file into GIFTI files for the cortical data and NIFTI files for the subcortical data and labels. ROIs can also be written to indicate the medial wall mask (cortex) and volume mask (subcortex). This uses the Connectome Workbench command -cifti-separate.

Usage

separate_cifti(
  cifti_fname,
  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
)

separateCIfTI(
  cifti_fname,
  brainstructures = "all",
  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
)

separatecii(
  cifti_fname,
  brainstructures = "all",
  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

cifti_fname	File path to a CIFTI file (ending in ".d*.nii").
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

Time unit, start, and step (dtseries files) will not be written to the GIFTI/NIFTIs. Column names (dscalar files) will not be written to the GIFTIs, as well as label names and colors (dlabel files). (Haven't checked the NIFTIs yet.)

ROI/medial wall behavior: If there are 32k vertices in the left cortex with 3k representing the medial wall, then both cortexL_fname and ROIcortexL_fname will have 32k entries, 3k of which having a value of 0 indicating the medial wall. The non-medial wall entries will have the data values in cortexL_fname and a value of 1 in ROIcortexL_fname. Thus, exporting ROIcortexL_fname is vital if the data values include 0, because 0-valued non-medial wall vertices and medial wall vertices cannot be distinguished from one another within cortexL_fname alone.

Value

A named character vector with the file paths to the written NIFTI and GIFTI files

Connectome Workbench

This function interfaces with the "-cifti-separate" Workbench command.

See Also

Other writing: write_cifti(), write_metric_gifti(), write_subcort_nifti(), write_surf_gifti(), write_xifti2()

ciftiTools documentation built on Oct. 4, 2024, 1:12 a.m.