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In [1]:



    


%matplotlib inline

5 - Graph Analysis (Group)

If this tutorial we are going to use an fMRI autism dataset.

Load data





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import warnings
warnings.simplefilter(action='ignore', category=FutureWarning)



    











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import numpy as np
np.set_printoptions(threshold=np.nan)



    











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fmri = np.load('data/autism_fmri_ts.npy')
labels = np.load('data/autism_labels.npy')



    











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num_subjects = len(fmri)
num_samples, num_rois = np.shape(fmri[0])

Compute the connectivity





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conn_mtx = np.zeros((num_subjects, num_rois, num_rois))



    











In [7]:



    


for subj in range(num_subjects):
    print("Processing subject {0}".format(subj + 1))
    
    fmri_ts = fmri[subj]
    conn_mtx[subj, ...] = np.corrcoef(fmri_ts.T)



    


















    






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/opt/py36/lib/python3.6/site-packages/numpy/lib/function_base.py:3183: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[:, None]
/opt/py36/lib/python3.6/site-packages/numpy/lib/function_base.py:3184: RuntimeWarning: invalid value encountered in true_divide
  c /= stddev[None, :]










    






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np.save('data/autism_fmri_conn_mtx.npy', conn_mtx)

Filter connectivity matrices





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thres_conn_mtx = np.zeros_like(conn_mtx)



    











In [10]:



    


from dyconnmap.graphs import threshold_eco



    











In [11]:



    


for subj in range(num_subjects):
    print("Processing subject {0}".format(subj + 1))
    
    subj_conn_mtx = np.abs(conn_mtx[subj])
    _, CIJtree, _  = threshold_eco(subj_conn_mtx)
    
    thres_conn_mtx[subj] = CIJtree



    


















    






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In [12]:



    


np.save('data/autism_fmri_thres_conn_mtx.npy', thres_conn_mtx)



    











In [ ]:

Content source: makism/dyfunconn

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