write_subcort_nifti

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Write subcortical data to NIFTI files

Write subcortical data to NIFTI files representing the data values, subcortical structure labels, and volumetric mask. The input formats of subcortVol, subcortLabs, and subcortMask correspond to the data structures of xifti$data$subcort, xifti$meta$subcort$labels , and xifti$meta$subcort$mask respectively. subcortVol and subcortLabs should be vectorized, so if they are volumes consider using RNifti::writeNIfTI.

Usage
write_subcort_nifti(
  subcortVol,
  subcortLabs,
  subcortMask,
  trans_mat = NULL,
  subcortVol_fname,
  subcortLabs_fname,
  ROIsubcortVol_fname = NULL,
  fill = 0,
  wb_path = NULL
)
Arguments
subcortVol

A vectorized data matrix: V voxels by T measurements

subcortLabs

Numeric (0 and 3-21) or factor vector corresponding to subcortical structure labels. See substructure_table.

subcortMask

Logical volumetric mask. Values of 0 represent out-of-mask voxels (not subcortical), and values of 1 represent in-mask voxels (subcortical),

trans_mat

The TransformationMatrixIJKtoXYZ, or equivalently the desired sform matrix (srow_x, srow_y and srow_z) to write. If NULL, do not write it (all zeroes).

subcortVol_fname, subcortLabs_fname, ROIsubcortVol_fname

File path to a NIFTI to save the corresponding data. ROIsubcortVol_fname is optional but the rest is required.

fill

Values to use for out-of-mask voxels. Default: 0.

wb_path

(Optional) Path to Connectome Workbench folder or executable. If not provided, should be set with ciftiTools.setOption("wb_path", "path/to/workbench").

Details

All file path arguments are required except ROIsubcortVol_fname. If not provided, the volumetric mask will not be written. (It's redundant with the 0 values in subcortLabs_fname because valid labels have positive indexes.)

Value

Named character vector with the "subcortVol", "subcortLabs", and "ROIsubcortVol" file names (if written)

Aliases
  • write_subcort_nifti
Documentation reproduced from package ciftiTools, version 0.1.6.0, License: GPL-3

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