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enh: wb cifti-smoothing
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‎nipype/interfaces/workbench/__init__.py

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# vi: set ft=python sts=4 ts=4 sw=4 et:
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from .metric import MetricResample
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from .cifti import CiftiSmooth

‎nipype/interfaces/workbench/cifti.py

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# -*- coding: utf-8 -*-
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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"""This module provides interfaces for workbench CIFTI commands"""
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from __future__ import (print_function, division, unicode_literals,
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absolute_import)
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import os
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from ..base import (TraitedSpec, File, traits, CommandLineInputSpec)
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from .base import WBCommand
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from ... import logging
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iflogger = logging.getLogger('nipype.interface')
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class CiftiSmoothInputSpec(CommandLineInputSpec):
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in_file = File(
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exists=True,
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mandatory=True,
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argstr="%s",
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position=0,
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desc="The input CIFTI file")
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sigma_surf = traits.Float(
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mandatory=True,
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argstr="%s",
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position=1,
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desc="the sigma for the gaussian surface smoothing kernel, in mm")
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sigma_vol = traits.Float(
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mandatory=True,
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argstr="%s",
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position=2,
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desc="the sigma for the gaussian volume smoothing kernel, in mm")
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direction = traits.Enum(
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"ROW",
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"COLUMN",
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mandatory=True,
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argstr="%s",
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position=3,
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desc="which dimension to smooth along, ROW or COLUMN")
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out_file = File(
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name_source=["in_file"],
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name_template="smoothed_%s.nii",
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keep_extension=True,
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argstr="%s",
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position=4,
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desc="The output CIFTI")
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left_surf = File(
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exists=True,
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mandatory=True,
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position=5,
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argstr="-left-surface %s",
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desc="Specify the left surface to use")
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left_corrected_areas = File(
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exists=True,
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position=6,
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argstr="-left-corrected-areas %s",
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desc="vertex areas (as a metric) to use instead of computing them from "
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"the left surface.")
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right_surf = File(
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exists=True,
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mandatory=True,
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position=7,
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argstr="-right-surface %s",
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desc="Specify the right surface to use")
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right_corrected_areas = File(
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exists=True,
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position=8,
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argstr="-right-corrected-areas %s",
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desc="vertex areas (as a metric) to use instead of computing them from "
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"the right surface")
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cerebellum_surf = File(
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exists=True,
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position=9,
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argstr="-cerebellum-surface %s",
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desc="specify the cerebellum surface to use")
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cerebellum_corrected_areas = File(
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exists=True,
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position=10,
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requires=["cerebellum_surf"],
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argstr="cerebellum-corrected-areas %s",
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desc="vertex areas (as a metric) to use instead of computing them from "
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"the cerebellum surface")
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cifti_roi = File(
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exists=True,
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position=11,
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argstr="-cifti-roi %s",
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desc="CIFTI file for ROI smoothing")
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fix_zeros_vol = traits.Bool(
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position=12,
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argstr="-fix-zeros-volume",
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desc="treat values of zero in the volume as missing data")
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fix_zeros_surf = traits.Bool(
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position=13,
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argstr="-fix-zeros-surface",
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desc="treat values of zero on the surface as missing data")
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merged_volume = traits.Bool(
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position=14,
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argstr="-merged-volume",
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desc="smooth across subcortical structure boundaries")
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class CiftiSmoothOutputSpec(TraitedSpec):
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out_file = File(exists=True, desc="output CIFTI file")
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class CiftiSmooth(WBCommand):
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"""
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Smooth a CIFTI file
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The input cifti file must have a brain models mapping on the chosen
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dimension, columns for .dtseries, and either for .dconn. By default,
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data in different structures is smoothed independently (i.e., "parcel
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constrained" smoothing), so volume structures that touch do not smooth
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across this boundary. Specify ``merged_volume`` to ignore these
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boundaries. Surface smoothing uses the ``GEO_GAUSS_AREA`` smoothing method.
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The ``*_corrected_areas`` options are intended for when it is unavoidable
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to smooth on group average surfaces, it is only an approximate correction
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for the reduction of structure in a group average surface. It is better
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to smooth the data on individuals before averaging, when feasible.
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The ``fix_zeros_*`` options will treat values of zero as lack of data, and
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not use that value when generating the smoothed values, but will fill
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zeros with extrapolated values. The ROI should have a brain models
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mapping along columns, exactly matching the mapping of the chosen
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direction in the input file. Data outside the ROI is ignored.
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>>> from nipype.interfaces.workbench import CiftiSmooth
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>>> smooth = CiftiSmooth()
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>>> smooth.inputs.in_file = 'sub-01_task-rest.dtseries.nii'
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>>> smooth.inputs.sigma_surf = 4
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>>> smooth.inputs.sigma_vol = 4
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>>> smooth.inputs.direction = 'COLUMN'
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>>> smooth.inputs.right_surf = 'sub-01.R.midthickness.32k_fs_LR.surf.gii'
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>>> smooth.inputs.left_surf = 'sub-01.L.midthickness.32k_fs_LR.surf.gii'
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>>> smooth.cmdline
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'wb_command -cifti-smoothing sub-01_task-rest.dtseries.nii 4.0 4.0 COLUMN \
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smoothed_sub-01_task-rest.dtseries.nii \
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-left-surface sub-01.L.midthickness.32k_fs_LR.surf.gii \
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-right-surface sub-01.R.midthickness.32k_fs_LR.surf.gii'
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"""
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input_spec = CiftiSmoothInputSpec
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output_spec = CiftiSmoothOutputSpec
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_cmd = 'wb_command -cifti-smoothing'

‎nipype/interfaces/workbench/tests/test_auto_CiftiSmooth.py

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# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
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from __future__ import unicode_literals
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from ..cifti import CiftiSmooth
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def test_CiftiSmooth_inputs():
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input_map = dict(
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args=dict(argstr='%s', ),
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cerebellum_corrected_areas=dict(
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argstr='cerebellum-corrected-areas %s',
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position=10,
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requires=['cerebellum_surf'],
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),
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cerebellum_surf=dict(
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argstr='-cerebellum-surface %s',
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position=9,
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),
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cifti_roi=dict(
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argstr='-cifti-roi %s',
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position=11,
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),
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direction=dict(
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argstr='%s',
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mandatory=True,
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position=3,
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),
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environ=dict(
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nohash=True,
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usedefault=True,
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),
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fix_zeros_surf=dict(
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argstr='-fix-zeros-surface',
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position=13,
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),
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fix_zeros_vol=dict(
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argstr='-fix-zeros-volume',
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position=12,
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),
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in_file=dict(
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argstr='%s',
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mandatory=True,
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position=0,
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),
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left_corrected_areas=dict(
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argstr='-left-corrected-areas %s',
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position=6,
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),
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left_surf=dict(
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argstr='-left-surface %s',
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mandatory=True,
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position=5,
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),
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merged_volume=dict(
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argstr='-merged-volume',
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position=14,
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),
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out_file=dict(
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argstr='%s',
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keep_extension=True,
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name_source=['in_file'],
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name_template='smoothed_%s.nii',
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position=4,
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),
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right_corrected_areas=dict(
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argstr='-right-corrected-areas %s',
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position=8,
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),
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right_surf=dict(
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argstr='-right-surface %s',
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mandatory=True,
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position=7,
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),
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sigma_surf=dict(
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argstr='%s',
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mandatory=True,
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position=1,
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),
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sigma_vol=dict(
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argstr='%s',
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mandatory=True,
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position=2,
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),
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)
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inputs = CiftiSmooth.input_spec()
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for key, metadata in list(input_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(inputs.traits()[key], metakey) == value
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def test_CiftiSmooth_outputs():
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output_map = dict(out_file=dict(), )
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outputs = CiftiSmooth.output_spec()
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for key, metadata in list(output_map.items()):
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for metakey, value in list(metadata.items()):
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assert getattr(outputs.traits()[key], metakey) == value

‎nipype/testing/data/sub-01.L.midthickness.32k_fs_LR.surf.gii

Whitespace-only changes.

‎nipype/testing/data/sub-01.R.midthickness.32k_fs_LR.surf.gii

Whitespace-only changes.

‎nipype/testing/data/sub-01_task-rest.dtseries.nii

Whitespace-only changes.

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