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Python MapNode.terminal_output方法代码示例

本文整理汇总了Python中nipype.MapNode.terminal_output方法的典型用法代码示例。如果您正苦于以下问题:Python MapNode.terminal_output方法的具体用法?Python MapNode.terminal_output怎么用?Python MapNode.terminal_output使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在nipype.MapNode的用法示例。


在下文中一共展示了MapNode.terminal_output方法的1个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: create_workflow

# 需要导入模块: from nipype import MapNode [as 别名]
# 或者: from nipype.MapNode import terminal_output [as 别名]

#.........这里部分代码省略.........
    bandpass = Node(Function(input_names=['files', 'lowpass_freq',
                                          'highpass_freq', 'fs'],
                             output_names=['out_files'],
                             function=bandpass_filter,
                             imports=imports),
                    name='bandpass_unsmooth')
    bandpass.inputs.fs = 1. / TR
    bandpass.inputs.highpass_freq = highpass_freq
    bandpass.inputs.lowpass_freq = lowpass_freq
    wf.connect(filter2, 'out_res', bandpass, 'files')

    """Smooth the functional data using
    :class:`nipype.interfaces.fsl.IsotropicSmooth`.
    """

    smooth = MapNode(interface=fsl.IsotropicSmooth(), name="smooth", iterfield=["in_file"])
    smooth.inputs.fwhm = vol_fwhm

    wf.connect(bandpass, 'out_files', smooth, 'in_file')

    collector = Node(Merge(2), name='collect_streams')
    wf.connect(smooth, 'out_file', collector, 'in1')
    wf.connect(bandpass, 'out_files', collector, 'in2')

    """
    Transform the remaining images. First to anatomical and then to target
    """

    warpall = MapNode(ants.ApplyTransforms(), iterfield=['input_image'],
                      name='warpall')
    warpall.inputs.input_image_type = 3
    warpall.inputs.interpolation = 'Linear'
    warpall.inputs.invert_transform_flags = [False, False]
    warpall.terminal_output = 'file'
    warpall.inputs.reference_image = target_file
    warpall.inputs.args = '--float'
    warpall.inputs.num_threads = 2
    warpall.plugin_args = {'sbatch_args': '-c%d' % 2}

    # transform to target
    wf.connect(collector, 'out', warpall, 'input_image')
    wf.connect(registration, 'outputspec.transforms', warpall, 'transforms')

    mask_target = Node(fsl.ImageMaths(op_string='-bin'), name='target_mask')

    wf.connect(registration, 'outputspec.anat2target', mask_target, 'in_file')

    maskts = MapNode(fsl.ApplyMask(), iterfield=['in_file'], name='ts_masker')
    wf.connect(warpall, 'output_image', maskts, 'in_file')
    wf.connect(mask_target, 'out_file', maskts, 'mask_file')

    # map to surface
    # extract aparc+aseg ROIs
    # extract subcortical ROIs
    # extract target space ROIs
    # combine subcortical and cortical rois into a single cifti file

    #######
    # Convert aparc to subject functional space

    # Sample the average time series in aparc ROIs
    sampleaparc = MapNode(freesurfer.SegStats(default_color_table=True),
                          iterfield=['in_file', 'summary_file',
                                     'avgwf_txt_file'],
                          name='aparc_ts')
    sampleaparc.inputs.segment_id = ([8] + list(range(10, 14)) + [17, 18, 26, 47] +
开发者ID:Gilles86,项目名称:nipype,代码行数:70,代码来源:rsfmri_vol_surface_preprocessing_nipy.py


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