as.xifti: Assemble a '"xifti"' from data

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

Assemble a "xifti" from data

Description

Assembles cortical data, subcortical data, and/or surface geometry to form a "xifti". The inputs must be data objects (vectors, matrices or arrays, depending on the argument).

Usage

as.xifti(
  cortexL = NULL,
  cortexL_mwall = NULL,
  cortexR = NULL,
  cortexR_mwall = NULL,
  mwall_values = c(NA, NaN),
  subcortVol = NULL,
  subcortLabs = NULL,
  subcortMask = NULL,
  surfL = NULL,
  surfR = NULL,
  col_names = NULL,
  HCP_32k_auto_mwall = TRUE,
  validate = TRUE
)

as_xifti(
  cortexL = NULL,
  cortexL_mwall = NULL,
  cortexR = NULL,
  cortexR_mwall = NULL,
  mwall_values = c(NA, NaN),
  subcortVol = NULL,
  subcortLabs = NULL,
  subcortMask = NULL,
  surfL = NULL,
  surfR = NULL
)

as.cifti(
  cortexL = NULL,
  cortexL_mwall = NULL,
  cortexR = NULL,
  cortexR_mwall = NULL,
  mwall_values = c(NA, NaN),
  subcortVol = NULL,
  subcortLabs = NULL,
  subcortMask = NULL,
  surfL = NULL,
  surfR = NULL
)

as_cifti(
  cortexL = NULL,
  cortexL_mwall = NULL,
  cortexR = NULL,
  cortexR_mwall = NULL,
  mwall_values = c(NA, NaN),
  subcortVol = NULL,
  subcortLabs = NULL,
  subcortMask = NULL,
  surfL = NULL,
  surfR = NULL
)

Arguments

cortexL, cortexL_mwall	Left cortex data and ROI. Each must be a data matrix or vector. If cortexL_mwall is not provided, cortexL should have data for all vertices on the left cortical surface (V_L \times T data matrix). There will not be a mask for the medial wall. Not providing the medial wall mask is appropriate for ".dlabels.nii" files where the medial wall may have its own label and therefore should not be treated as missing data. If cortexL_mwall is provided, cortexL should either have data for all vertices on the left cortical surface (V_L \times T data matrix, with filler values e.g. 0 or NaN for medial wall vertices), or have data only for non-medial wall vertices ((V_L - mwall_L) \times T data matrix). The medial wall mask will be the 0 values in cortexL_mwall. The medial wall mask should be provided whenever the medial wall should be treated as missing data. Since the unmasked cortices must have the same number of vertices, V_L should match V_R.
cortexR, cortexR_mwall	Right cortex data and ROI. Each must be a data matrix or vector. If cortexR_mwall is not provided, cortexR should have data for all vertices on the right cortical surface (V_R \times T data mre will not be a mask for the medial wall. Not providing the medial wall mask is appropriate for ".dlabels.nii" files where the medial wall may have its own label and therefore should not be treated as missing data. If cortexR_mwall is provided, cortexR should either have data for all vertices on the right cortical surface (V_R \times T data matrix, with filler values e.g. 0 or NaN for medial wall vertices), or have data only for non-medial wall vertices ((V_R - mwall_R) \times T data matrix). The medial wall mask will be the 0 values in cortexR_mwall. The medial wall mask should be provided whenever the medial wall should be treated as missing data. Since the unmasked cortices must have the same number of vertices, V_L should match V_R.
mwall_values	If cortex[L/R]_mwall was not provided, or if it was invalid (i.e. bad length or all TRUE), the medial wall mask will be inferred from rows in cortex[L/R] that are constantly one of these values. Default: c(NA, NaN). If NULL, do not attempt to infer the medial wall from the data values. NULL should be used if NA or NaN are legitimate values that non-medial wall vertices might take on.
subcortVol, subcortLabs, subcortMask	subcortVol represents the data values of the subcortex. It is either a 3D/4D numeric array (i \times j \times k \times T), or a vectorized matrix (V_S voxels by T measurements). If it's vectorized, the voxels should be in spatial order (i index increasing fastest, then j, then k). subcortLabs represents the brainstructure labels of each voxel: see substructure_table. It is either a 3D data array (i \times j \times k) of integer brainstructure indices, or a V_S length vector in spatial order with brainstructure names as factors or integer indices. The indices should be 3-21 (1 and 2 correspond to left and right cortex, respectively) or 1-19 (cortex labels omitted), with 0 representing out-of-mask voxels. subcortMask is logical 3D data array (i \times j \times k) where TRUE values indicate subcortical voxels (in-mask). If it is not provided, the mask will be inferred from voxels with labels 0, NA, or NaN in subcortLabs. If subcortLabs are vectorized and subcortMask is not provided, the mask cannot be inferred so an error will occur.
surfL, surfR	(Optional) Surface geometries for the left or right cortex. Can be a surface GIFTI file path or "surf" object; see make_surf for a full description of valid inputs.
col_names	Names of each measurement/column in the data.
HCP_32k_auto_mwall	If left and/or right cortex data is provided, and the number of vertices matches that of the HCP 32k mesh (29696 on left, and 29716 on right), should the medial wall masks be added to the "xifti" if not provided? Default: TRUE.
validate	Validate that the result is a "xifti"? Default: TRUE. If FALSE, the result may not be properly formatted if the inputs were invalid.

Details

Each data or surface component is optional. Metadata components (cortex[L/R]_mwall, subcortLabs, and subcortMask) will be ignored if its corresponding data component is not provided. If no data or surface components are provided, then the template_xifti will be returned.

If cortical data are provided without a corresponding medial wall mask, or if the provided mask is invalid or empty, then the medial wall will be inferred from data rows that are constantly a value in mwall_values. But if mwall_values is NULL, no attempt to infer the medial wall will be made and the medial wall metadata entry will be NULL.

The total number of grayordinates will be G = (V_L - mwall_L) + (V_R - mwall_R) + V_S: V_L - mwall_L left vertices, V_R - mwall_R right vertices and V_S subcortical voxels. T, the total number of measurements (columns of data), must be the same for each brainstructure.

Value

A "xifti"

See Also

Other reading: info_cifti(), load_parc(), load_surf(), read_cifti(), read_surf(), read_xifti2()

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