read_xifti2 {ciftiTools}

Read in GIFTI files as a "xifti" object

Description

Read in GIFTI metric or label files as a "xifti" object. May also include surface geometry GIFTI files and perform resampling.

Usage

read_xifti2(
  cortexL = NULL,
  cortexL_mwall = NULL,
  cortexR = NULL,
  cortexR_mwall = NULL,
  mwall_values = c(NA, NaN),
  surfL = NULL,
  surfR = NULL,
  resamp_res = NULL,
  col_names = NULL,
  HCP_32k_auto_mwall = TRUE,
  read_dir = NULL,
  validate = TRUE
)

Arguments

cortexL, cortexL_mwall

Left cortex data and ROI. Each must be a path to a metric or label GIFTI file.

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, or resamp_res must be set.

cortexR, cortexR_mwall

Right cortex data and ROI. Each must be a path to a metric or label GIFTI file.

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, or resamp_res must be set.

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.

surfL, surfR

(Optional) File path(s) to surface GIFTI(s) for the left or right cortex.

resamp_res

Resolution to resample the cortical data and surface to. Default: NULL (do not resample). If provided, the original resolutions of the cortex data and surfaces may differ.

col_names

Names of each measurement/column in the data. Overrides names indicated in the data components.

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.

read_dir

(Optional) Append a directory to all file names in the arguments. If NULL (default), do not modify file names.

validate

Validate that the result is a "xifti" object? Default: TRUE. If FALSE, the result may not be properly formatted if the inputs were invalid.

Value

The "xifti" object containing all the data in the input giftis.

See Also

Other reading: as.xifti(), info_cifti(), load_parc(), load_surf(), read_cifti(), read_surf()