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ciftiTools (version 0.3.1)

smooth_cifti: Smooth a CIFTI

Description

Smooth CIFTI data. This uses the -cifti-smoothing command from Connectome Workbench.

Usage

smooth_cifti(
  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
)
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

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 default very inflated 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.

Value

The cifti_target_fname, invisibly

Connectome Workbench Requirement

This function uses a system wrapper for the 'wb_command' executable. The user must first download and install the Connectome Workbench, available from https://www.humanconnectome.org/software/get-connectome-workbench .

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 inflated surfaces included in "ciftiTools" will be used.