R: Smooth CIFTI data

smooth_cifti {ciftiTools}

R Documentation

Smooth CIFTI data

Description

Spatially smooth the metric data of a CIFTI file or "xifti" object.

Usage

smooth_cifti(
  x,
  cifti_target_fname = NULL,
  surf_FWHM = 5,
  vol_FWHM = 3,
  surfL_fname = NULL,
  surfR_fname = NULL,
  cerebellum_fname = NULL,
  subcortical_zeroes_as_NA = FALSE,
  cortical_zeroes_as_NA = FALSE,
  subcortical_merged = FALSE
)

smoothCIfTI(
  x,
  cifti_target_fname = NULL,
  surf_FWHM = 5,
  vol_FWHM = 5,
  surfL_fname = NULL,
  surfR_fname = NULL,
  cerebellum_fname = NULL,
  subcortical_zeroes_as_NA = FALSE,
  cortical_zeroes_as_NA = FALSE,
  subcortical_merged = FALSE
)

smoothcii(
  x,
  cifti_target_fname = NULL,
  surf_FWHM = 5,
  vol_FWHM = 5,
  surfL_fname = NULL,
  surfR_fname = NULL,
  cerebellum_fname = NULL,
  subcortical_zeroes_as_NA = FALSE,
  cortical_zeroes_as_NA = FALSE,
  subcortical_merged = FALSE
)

smooth_xifti(
  x,
  cifti_target_fname = NULL,
  surf_FWHM = 5,
  vol_FWHM = 5,
  surfL_fname = NULL,
  surfR_fname = NULL,
  cerebellum_fname = NULL,
  subcortical_zeroes_as_NA = FALSE,
  cortical_zeroes_as_NA = FALSE,
  subcortical_merged = FALSE
)

Arguments

`x`	The CIFTI file name or `"xifti"` object to smooth.
`cifti_target_fname`	File name for the smoothed CIFTI. If `NULL`, will be written to "smoothed.d*.nii" in the current working directory if `x` was a CIFTI file, and in a temporary directory if `x` was a `"xifti"` object.
`surf_FWHM`, `vol_FWHM`	The full width at half maximum (FWHM) parameter for the gaussian surface or volume smoothing kernel, in mm. Default: `5` for cortex (surface) and `3` for subcortex (volume).
`surfL_fname`, `surfR_fname`	(Required if the corresponding cortex is present) Surface GIFTI files for the left and right cortical surfaces. If not provided, the surfaces in `x` are used, but if those are also not present, the default surfaces will be used.
`cerebellum_fname`	(Optional) Surface GIFTI file for the cerebellar surface
`subcortical_zeroes_as_NA`, `cortical_zeroes_as_NA`	Should zero-values in the subcortical volume or cortex be treated as NA? Default: `FALSE`.
`subcortical_merged`	Smooth across subcortical structure boundaries? Default: `FALSE`.

Details

If the CIFTI is a ".dlabel" file (intent 3007), then it will be converted to a ".dscalar" file because the values will no longer be integer indices. Unless the label values were ordinal, this is probably not desired so a warning will be printed.

Can accept a "xifti" object as well as a path to a CIFTI-file.

Surfaces are required for each hemisphere in the CIFTI. If they are not provided, the default inflated surfaces will be used.

Conversion for sigma: \sigma \times 2 \times \sqrt(2 \times \log(2)) = FWHM

Value

The cifti_target_fname, invisibly, if x was a CIFTI file name. A "xifti" object if x was a "xifti" object.

Connectome Workbench

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