9.8.4. Functional connectivity predicts age group

This example compares different kinds of functional connectivity between regions of interest : correlation, partial correlation, and tangent space embedding.

The resulting connectivity coefficients can be used to discriminate children from adults. In general, the tangent space embedding outperforms the standard correlations: see Dadi et al 2019 for a careful study.

9.8.4.1. Load brain development fMRI dataset and MSDL atlas

We study only 60 subjects from the dataset, to save computation time.

from nilearn import datasets

development_dataset = datasets.fetch_development_fmri(n_subjects=60)

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We use probabilistic regions of interest (ROIs) from the MSDL atlas.

from nilearn.input_data import NiftiMapsMasker

msdl_data = datasets.fetch_atlas_msdl()
msdl_coords = msdl_data.region_coords

masker = NiftiMapsMasker(
    msdl_data.maps, resampling_target="data", t_r=2, detrend=True,
    low_pass=.1, high_pass=.01, memory='nilearn_cache', memory_level=1).fit()
masked_data = [masker.transform(func, confounds) for
               (func, confounds) in zip(
                   development_dataset.func, development_dataset.confounds)]

Out:

/usr/lib/python3/dist-packages/numpy/lib/npyio.py:2358: VisibleDeprecationWarning: Reading unicode strings without specifying the encoding argument is deprecated. Set the encoding, use None for the system default.
  output = genfromtxt(fname, **kwargs)

9.8.4.2. What kind of connectivity is most powerful for classification?

we will use connectivity matrices as features to distinguish children from adults. We use cross-validation and measure classification accuracy to compare the different kinds of connectivity matrices.

# prepare the classification pipeline
from sklearn.pipeline import Pipeline
from nilearn.connectome import ConnectivityMeasure
from sklearn.svm import LinearSVC
from sklearn.dummy import DummyClassifier
from sklearn.model_selection import GridSearchCV

kinds = ['correlation', 'partial correlation', 'tangent']

pipe = Pipeline(
    [('connectivity', ConnectivityMeasure(vectorize=True)),
     ('classifier', GridSearchCV(LinearSVC(), {'C': [.1, 1., 10.]}, cv=5))])

param_grid = [
    {'classifier': [DummyClassifier('most_frequent')]},
    {'connectivity__kind': kinds}
]

Out:

/home/varoquau/dev/scikit-learn/sklearn/utils/validation.py:68: FutureWarning: Pass strategy=most_frequent as keyword args. From version 0.25 passing these as positional arguments will result in an error
  warnings.warn("Pass {} as keyword args. From version 0.25 "

We use random splits of the subjects into training/testing sets. StratifiedShuffleSplit allows preserving the proportion of children in the test set.

from sklearn.model_selection import GridSearchCV, StratifiedShuffleSplit
from sklearn.preprocessing import LabelEncoder

groups = [pheno['Child_Adult'] for pheno in development_dataset.phenotypic]
classes = LabelEncoder().fit_transform(groups)

cv = StratifiedShuffleSplit(n_splits=30, random_state=0, test_size=10)
gs = GridSearchCV(pipe, param_grid, scoring='accuracy', cv=cv, verbose=1,
                  refit=False, n_jobs=8)
gs.fit(masked_data, classes)
mean_scores = gs.cv_results_['mean_test_score']
scores_std = gs.cv_results_['std_test_score']

Out:

Fitting 30 folds for each of 4 candidates, totalling 120 fits

display the results

from matplotlib import pyplot as plt

plt.figure(figsize=(6, 4))
positions = [.1, .2, .3, .4]
plt.barh(positions, mean_scores, align='center', height=.05, xerr=scores_std)
yticks = ['dummy'] + list(gs.cv_results_['param_connectivity__kind'].data[1:])
yticks = [t.replace(' ', '\n') for t in yticks]
plt.yticks(positions, yticks)
plt.xlabel('Classification accuracy')
plt.gca().grid(True)
plt.gca().set_axisbelow(True)
plt.tight_layout()

This is a small example to showcase nilearn features. In practice such comparisons need to be performed on much larger cohorts and several datasets. Dadi et al 2019 Showed that across many cohorts and clinical questions, the tangent kind should be preferred.

plt.show()