How to wrap a Python script

This is a minimal pure python interface. As you can see all you need to do is to do is to define inputs, outputs, _run_interface() (not run()), and _list_outputs.

from nipype.interfaces.base import BaseInterface, \
    BaseInterfaceInputSpec, traits, File, TraitedSpec
from nipype.utils.filemanip import split_filename

import nibabel as nb
import numpy as np
import os

class SimpleThresholdInputSpec(BaseInterfaceInputSpec):
    volume = File(exists=True, desc='volume to be thresholded', mandatory=True)
    threshold = traits.Float(desc='everything below this value will be set to zero',

class SimpleThresholdOutputSpec(TraitedSpec):
    thresholded_volume = File(exists=True, desc="thresholded volume")

class SimpleThreshold(BaseInterface):
    input_spec = SimpleThresholdInputSpec
    output_spec = SimpleThresholdOutputSpec

    def _run_interface(self, runtime):
        fname = self.inputs.volume
        img = nb.load(fname)
        data = np.array(img.get_data())

        active_map = data > self.inputs.threshold

        thresholded_map = np.zeros(data.shape)
        thresholded_map[active_map] = data[active_map]

        new_img = nb.Nifti1Image(thresholded_map, img.affine, img.header)
        _, base, _ = split_filename(fname), base + '_thresholded.nii')

        return runtime

    def _list_outputs(self):
        outputs = self._outputs().get()
        fname = self.inputs.volume
        _, base, _ = split_filename(fname)
        outputs["thresholded_volume"] = os.path.abspath(base + '_thresholded.nii')
        return outputs