R: Assemble a '"xifti"' from data

as.xifti {ciftiTools}

R Documentation

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 3-22 (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"