utils.py

import os
import os.path as op
import nibabel as nib
import numpy as np
import nipype.interfaces.fsl as fsl
from nilearn.datasets import load_mni152_brain_mask

def make_sphere(x, y, z, output_dir):

    mask = load_mni152_brain_mask()
    mask_img = mask.get_data()
    xyz_img = np.dot(np.linalg.inv(mask.affine), [x, y, z, 1]).astype(int)

    tmp_mask_img = mask_img * 0
    tmp_mask_img[xyz_img[0],xyz_img[1],xyz_img[2]] = 1
    tmp_roi_img = nib.Nifti1Image(tmp_mask_img, mask.affine, mask.header)

    tmp_roi_fn = op.join(output_dir, '{x}_{y}_{z}.nii.gz'.format(x=x, y=y, z=z))
    nib.save(tmp_roi_img, tmp_roi_fn)

    di = fsl.maths.DilateImage(in_file = tmp_roi_fn,
                               operation = "mean",
                               kernel_shape = "sphere",
                               kernel_size = 4,
                               out_file = tmp_roi_fn)
    #di.run()