Get the neighbors of target voxels

neighbors.py

"""
Get the neighbors of target voxels
"""

import numpy as np
from nilearn import datasets
from nilearn import input_data
from sklearn.feature_extraction import image

### Load nyu_rest dataset #####################################################
nyu_dataset = datasets.fetch_nyu_rest(n_subjects=1)
nifti_masker = input_data.NiftiMasker(memory='nilearn_cache',
                                      mask_strategy='epi', memory_level=1,
                                      standardize=False)
func_filename = nyu_dataset.func[0]
fmri_masked = nifti_masker.fit_transform(func_filename)
mask = nifti_masker.mask_img_.get_data().astype(np.bool)
roi = mask[mask > 0]  # but could be any niimg

# Compute connectivity matrix: which voxel is connected to which
shape = mask.shape
connectivity = image.grid_to_graph(n_x=shape[0], n_y=shape[1],
                                   n_z=shape[2], mask=mask)
neighbors = connectivity.tolil().rows
# whant the neighbors only within a given roi ?
neighbors_within_roi = [neighbors[i] for i in range(mask.sum()) if roi[i]]
# then you can extract signals etc