nipype.interfaces.workbench.cifti module

This module provides interfaces for workbench CIFTI commands

CiftiSmooth

Link to code

Bases: WBCommand

Wrapped executable: wb_command -cifti-smoothing.

Smooth a CIFTI file

The input cifti file must have a brain models mapping on the chosen dimension, columns for .dtseries, and either for .dconn. By default, data in different structures is smoothed independently (i.e., “parcel constrained” smoothing), so volume structures that touch do not smooth across this boundary. Specify merged_volume to ignore these boundaries. Surface smoothing uses the GEO_GAUSS_AREA smoothing method.

The *_corrected_areas options are intended for when it is unavoidable to smooth on group average surfaces, it is only an approximate correction for the reduction of structure in a group average surface. It is better to smooth the data on individuals before averaging, when feasible.

The fix_zeros_* options will treat values of zero as lack of data, and not use that value when generating the smoothed values, but will fill zeros with extrapolated values. The ROI should have a brain models mapping along columns, exactly matching the mapping of the chosen direction in the input file. Data outside the ROI is ignored.

>>> from nipype.interfaces.workbench import CiftiSmooth
>>> smooth = CiftiSmooth()
>>> smooth.inputs.in_file = 'sub-01_task-rest.dtseries.nii'
>>> smooth.inputs.sigma_surf = 4
>>> smooth.inputs.sigma_vol = 4
>>> smooth.inputs.direction = 'COLUMN'
>>> smooth.inputs.right_surf = 'sub-01.R.midthickness.32k_fs_LR.surf.gii'
>>> smooth.inputs.left_surf = 'sub-01.L.midthickness.32k_fs_LR.surf.gii'
>>> smooth.cmdline
'wb_command -cifti-smoothing sub-01_task-rest.dtseries.nii 4.0 4.0 COLUMN     smoothed_sub-01_task-rest.dtseries.nii     -left-surface sub-01.L.midthickness.32k_fs_LR.surf.gii     -right-surface sub-01.R.midthickness.32k_fs_LR.surf.gii'
Mandatory Inputs:

  • direction (‘ROW’ or ‘COLUMN’) – Which dimension to smooth along, ROW or COLUMN. Maps to a command-line argument: %s (position: 3).

  • in_file (a pathlike object or string representing an existing file) – The input CIFTI file. Maps to a command-line argument: %s (position: 0).

  • left_surf (a pathlike object or string representing an existing file) – Specify the left surface to use. Maps to a command-line argument: -left-surface %s (position: 5).

  • right_surf (a pathlike object or string representing an existing file) – Specify the right surface to use. Maps to a command-line argument: -right-surface %s (position: 7).

  • sigma_surf (a float) – The sigma for the gaussian surface smoothing kernel, in mm. Maps to a command-line argument: %s (position: 1).

  • sigma_vol (a float) – The sigma for the gaussian volume smoothing kernel, in mm. Maps to a command-line argument: %s (position: 2).

Optional Inputs:

  • args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

  • cerebellum_corrected_areas (a pathlike object or string representing an existing file) – Vertex areas (as a metric) to use instead of computing them from the cerebellum surface. Maps to a command-line argument: cerebellum-corrected-areas %s (position: 10). Requires inputs: cerebellum_surf.

  • cerebellum_surf (a pathlike object or string representing an existing file) – Specify the cerebellum surface to use. Maps to a command-line argument: -cerebellum-surface %s (position: 9).

  • cifti_roi (a pathlike object or string representing an existing file) – CIFTI file for ROI smoothing. Maps to a command-line argument: -cifti-roi %s (position: 11).

  • environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value: {})

  • fix_zeros_surf (a boolean) – Treat values of zero on the surface as missing data. Maps to a command-line argument: -fix-zeros-surface (position: 13).

  • fix_zeros_vol (a boolean) – Treat values of zero in the volume as missing data. Maps to a command-line argument: -fix-zeros-volume (position: 12).

  • left_corrected_areas (a pathlike object or string representing an existing file) – Vertex areas (as a metric) to use instead of computing them from the left surface. Maps to a command-line argument: -left-corrected-areas %s (position: 6).

  • merged_volume (a boolean) – Smooth across subcortical structure boundaries. Maps to a command-line argument: -merged-volume (position: 14).

  • out_file (a pathlike object or string representing a file) – The output CIFTI. Maps to a command-line argument: %s (position: 4).

  • right_corrected_areas (a pathlike object or string representing an existing file) – Vertex areas (as a metric) to use instead of computing them from the right surface. Maps to a command-line argument: -right-corrected-areas %s (position: 8).

Outputs:

out_file (a pathlike object or string representing an existing file) – Output CIFTI file.