In [1]:

    

import nibabel as nib
import numpy as np


    

In [2]:

    

from scipy.ndimage.measurements import label
from scipy.ndimage.morphology import generate_binary_structure


    

In [78]:

    

sim_img = image.load_img('/Users/dlurie/Dropbox/Projects/avalanche/avalanche/data/simdata_c1-c5_noise.nii.gz')


    

In [79]:

    

sim_data = sim_img.get_data()


    

In [80]:

    

sim_data.shape


    

    
Out[80]:





(10, 10, 10, 20)

In [81]:

    

labels = label(sim_data)


    

In [82]:

    

labels[0].max()


    

    
Out[82]:





15

In [83]:

    

affine = np.diag([1, 1, 1, 1])
labels_img = nib.Nifti1Image(labels[0], affine)


    

In [84]:

    

labels_img.to_filename('/Users/dlurie/Dropbox/Projects/avalanche/avalanche/data/simdata_c1-c5_labels_default.nii.gz')


    

In [3]:

    

struct_44 = generate_binary_structure(4,4)


    

In [109]:

    

labels_44 = label(sim_data, structure=struct_44)


    

In [110]:

    

labels_44[0].max()


    

    
Out[110]:





10

In [111]:

    

labels_44_img = nib.Nifti1Image(labels_44[0], affine)


    

In [112]:

    

labels_44_img.to_filename('/Users/dlurie/Dropbox/Projects/avalanche/avalanche/data/simdata_c1-c5_labels_44.nii.gz')


    

In [4]:

    

struct_43 = generate_binary_structure(4,3)


    

In [94]:

    

labels_43 = label(sim_data, structure=struct_43)


    

In [95]:

    

labels_43[0].max()


    

    
Out[95]:





10

In [96]:

    

labels_43_img = nib.Nifti1Image(labels_43[0], affine)


    

In [97]:

    

labels_43_img.to_filename('/Users/dlurie/Dropbox/Projects/avalanche/avalanche/data/simdata_c1-c5_labels_43.nii.gz')


    

In [98]:

    

struct_42 = generate_binary_structure(4,2)


    

In [99]:

    

labels_42 = label(sim_data, structure=struct_42)


    

In [100]:

    

labels_42[0].max()


    

    
Out[100]:





12

In [101]:

    

labels_42_img = nib.Nifti1Image(labels_42[0], affine)


    

In [102]:

    

labels_42_img.to_filename('/Users/dlurie/Dropbox/Projects/avalanche/avalanche/data/simdata_c1-c5_labels_42.nii.gz')


    

In [103]:

    

struct_41 = generate_binary_structure(4,1)


    

In [104]:

    

labels_41 = label(sim_data, structure=struct_41)


    

In [105]:

    

labels_41[0].max()


    

    
Out[105]:





15

In [106]:

    

labels_41_img = nib.Nifti1Image(labels_41[0], affine)


    

In [107]:

    

labels_41_img.to_filename('/Users/dlurie/Dropbox/Projects/avalanche/avalanche/data/simdata_c1-c5_labels_41.nii.gz')