interfaces.workbench.cifti¶
CiftiSmooth¶
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]
in_file: (a pathlike object or string representing an existing file)
The input CIFTI file
argument: ``%s``, position: 0
sigma_surf: (a float)
the sigma for the gaussian surface smoothing kernel, in mm
argument: ``%s``, position: 1
sigma_vol: (a float)
the sigma for the gaussian volume smoothing kernel, in mm
argument: ``%s``, position: 2
direction: ('ROW' or 'COLUMN')
which dimension to smooth along, ROW or COLUMN
argument: ``%s``, position: 3
left_surf: (a pathlike object or string representing an existing
file)
Specify the left surface to use
argument: ``-left-surface %s``, position: 5
right_surf: (a pathlike object or string representing an existing
file)
Specify the right surface to use
argument: ``-right-surface %s``, position: 7
[Optional]
out_file: (a pathlike object or string representing a file)
The output CIFTI
argument: ``%s``, position: 4
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.
argument: ``-left-corrected-areas %s``, position: 6
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
argument: ``-right-corrected-areas %s``, position: 8
cerebellum_surf: (a pathlike object or string representing an
existing file)
specify the cerebellum surface to use
argument: ``-cerebellum-surface %s``, position: 9
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
argument: ``cerebellum-corrected-areas %s``, position: 10
requires: cerebellum_surf
cifti_roi: (a pathlike object or string representing an existing
file)
CIFTI file for ROI smoothing
argument: ``-cifti-roi %s``, position: 11
fix_zeros_vol: (a boolean)
treat values of zero in the volume as missing data
argument: ``-fix-zeros-volume``, position: 12
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
args: (a unicode string)
Additional parameters to the command
argument: ``%s``
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', nipype default value: {})
Environment variables
Outputs:
out_file: (a pathlike object or string representing an existing file)
output CIFTI file