smooth_cifti: Smooth CIFTI data

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

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.

See Also

Other manipulating xifti: add_surf(), apply_parc(), apply_xifti(), combine_xifti(), convert_xifti(), impute_xifti(), merge_xifti(), move_to_mwall(), move_to_submask(), newdata_xifti(), remap_cifti(), remove_xifti(), resample_cifti(), resample_cifti_from_template(), scale_xifti(), select_xifti(), set_names_xifti(), transform_xifti()

Other common: is.cifti(), read_cifti(), resample_cifti(), view_xifti(), write_cifti()

mandymejia/ciftiTools documentation built on Feb. 1, 2025, 7:57 p.m.