.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.workbench.cifti
==========================


.. _nipype.interfaces.workbench.cifti.CiftiSmooth:


.. index:: CiftiSmooth

CiftiSmooth
-----------

`Link to code <file:///build/nipype-1.1.9/nipype/interfaces/workbench/cifti.py#L105>`__

Wraps the executable command ``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'

Inputs::

        [Mandatory]
        direction: (u'ROW' or u'COLUMN')
                which dimension to smooth along, ROW or COLUMN
                argument: ``%s``, position: 3
        left_surf: (an existing file name)
                Specify the left surface to use
                argument: ``-left-surface %s``, position: 5
        sigma_surf: (a float)
                the sigma for the gaussian surface smoothing kernel, in mm
                argument: ``%s``, position: 1
        in_file: (an existing file name)
                The input CIFTI file
                argument: ``%s``, position: 0
        sigma_vol: (a float)
                the sigma for the gaussian volume smoothing kernel, in mm
                argument: ``%s``, position: 2
        right_surf: (an existing file name)
                Specify the right surface to use
                argument: ``-right-surface %s``, position: 7

        [Optional]
        out_file: (a file name)
                The output CIFTI
                argument: ``%s``, position: 4
        cerebellum_corrected_areas: (an existing file name)
                vertex areas (as a metric) to use instead of computing them from the
                cerebellum surface
                argument: ``cerebellum-corrected-areas %s``, position: 10
                requires: cerebellum_surf
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        fix_zeros_vol: (a boolean)
                treat values of zero in the volume as missing data
                argument: ``-fix-zeros-volume``, position: 12
        left_corrected_areas: (an existing file name)
                vertex areas (as a metric) to use instead of computing them from the
                left surface.
                argument: ``-left-corrected-areas %s``, position: 6
        environ: (a dictionary with keys which are a newbytes or None or a
                  newstr or None and with values which are a newbytes or None or a
                  newstr or None, nipype default value: {})
                Environment variables
        fix_zeros_surf: (a boolean)
                treat values of zero on the surface as missing data
                argument: ``-fix-zeros-surface``, position: 13
        merged_volume: (a boolean)
                smooth across subcortical structure boundaries
                argument: ``-merged-volume``, position: 14
        right_corrected_areas: (an existing file name)
                vertex areas (as a metric) to use instead of computing them from the
                right surface
                argument: ``-right-corrected-areas %s``, position: 8
        cifti_roi: (an existing file name)
                CIFTI file for ROI smoothing
                argument: ``-cifti-roi %s``, position: 11
        cerebellum_surf: (an existing file name)
                specify the cerebellum surface to use
                argument: ``-cerebellum-surface %s``, position: 9

Outputs::

        out_file: (an existing file name)
                output CIFTI file
