9.8.10. Advanced decoding using scikit learn

This tutorial opens the box of decoding pipelines to bridge integrated functionalities provided by the nilearn.decoding.Decoder object with more advanced usecases. It reproduces basic examples functionalities with direct calls to scikit-learn function and gives pointers to more advanced objects. If some concepts seem unclear, please refer to the documentation on decoding and in particular to the advanced section. As in many other examples, we perform decoding of the visual category of a stimuli on Haxby 2001 dataset, focusing on distinguishing two categories : face and cat images.

  • J.V. Haxby et al. “Distributed and Overlapping Representations of Faces and Objects in Ventral Temporal Cortex”, Science vol 293 (2001), p 2425.-2430. Retrieve and load the fMRI data from the Haxby study First download the data

# The :func:`nilearn.datasets.fetch_haxby` function will download the
# Haxby dataset composed of fmri images in a Niimg, a spatial mask and a text
# document with label of each image
from nilearn import datasets
haxby_dataset = datasets.fetch_haxby()
mask_filename = haxby_dataset.mask_vt[0]
fmri_filename = haxby_dataset.func[0]
# Loading the behavioral labels
import pandas as pd
behavioral = pd.read_csv(haxby_dataset.session_target[0], delimiter=' ')
labels chunks
0 rest 0
1 rest 0
2 rest 0
3 rest 0
4 rest 0
... ... ...
1447 rest 11
1448 rest 11
1449 rest 11
1450 rest 11
1451 rest 11

1452 rows × 2 columns

We keep only a images from a pair of conditions(cats versus faces). Performing decoding with scikit-learn

# Importing a classifier
# ........................
# We can import many predictive models from scikit-learn that can be used in a
# decoding pipelines. They are all used with the same `fit()` and `predict()`
# functions. Let's define a `Support Vector Classifier <http://scikit-learn.org/stable/modules/svm.html >`_ (or SVC).
from sklearn.svm import SVC
svc = SVC() Masking the data

To use a scikit-learn estimator on brain images, you should first mask the data using a nilearn.input_data.NiftiMasker to extract only the voxels inside the mask of interest, and transform 4D input fMRI data to 2D arrays(shape=(n_timepoints, n_voxels)) that estimators can work on.

from nilearn.input_data import NiftiMasker
masker = NiftiMasker(mask_img=mask_filename, sessions=session_label,
                     smoothing_fwhm=4, standardize=True,
                     memory="nilearn_cache", memory_level=1)
fmri_masked = masker.fit_transform(fmri_niimgs)


/home/nicolas/GitRepos/nilearn-fork/nilearn/_utils/helpers.py:145: FutureWarning: The parameter "sessions" will be removed in 0.9.0 release of Nilearn. Please use the parameter "runs" instead.
  return func(*args, **kwargs) Cross-validation with scikit-learn

To train and test the model in a meaningful way we use cross-validation with the function sklearn.model_selection.cross_val_score that computes for you the score for the different folds of cross-validation.

from sklearn.model_selection import cross_val_score
cv_scores = cross_val_score(svc, fmri_masked, conditions, cv=5)

# Here `cv=5` stipulates a 5-fold cross-validation Tuning cross-validation parameters

You can change many parameters of the cross_validation here, for example:

  • use a different cross - validation scheme, for example LeaveOneGroupOut()

  • speed up the computation by using n_jobs = -1, which will spread the computation equally across all processors.

  • use a different scoring function, as a keyword or imported from scikit-learn : scoring = ‘roc_auc’

from sklearn.model_selection import LeaveOneGroupOut
cv = LeaveOneGroupOut()
cv_scores = cross_val_score(svc, fmri_masked, conditions, cv=cv,
                            scoring='roc_auc', groups=session_label, n_jobs=-1)
print("SVC accuracy: {:.3f}".format(cv_scores.mean()))


SVC accuracy: 0.858 Measuring the chance level

sklearn.dummy.DummyClassifier (purely random) estimators are the simplest way to measure prediction performance at chance. A more controlled way, but slower, is to do permutation testing on the labels, with sklearn.model_selection.permutation_test_score. Dummy estimator

from sklearn.dummy import DummyClassifier
null_cv_scores = cross_val_score(
    DummyClassifier(), fmri_masked, conditions, cv=cv, groups=session_label)

print("Dummy accuracy: {:.3f}".format(null_cv_scores.mean()))


Dummy accuracy: 0.500 Permutation test

from sklearn.model_selection import permutation_test_score
null_cv_scores = permutation_test_score(
    svc, fmri_masked, conditions, cv=cv, groups=session_label)[1]
print("Permutation test score: {:.3f}".format(null_cv_scores.mean()))


Permutation test score: 0.502 Decoding without a mask: Anova-SVM in scikit-lean

We can also implement feature selection before decoding as a scikit-learn pipeline`(:class:`sklearn.pipeline.Pipeline). For this, we need to import the sklearn.feature_selection module and use sklearn.feature_selection.f_classif, a simple F-score based feature selection (a.k.a. Anova),

from sklearn.pipeline import Pipeline
from sklearn.feature_selection import SelectPercentile, f_classif
from sklearn.model_selection import cross_validate
from sklearn.svm import LinearSVC
feature_selection = SelectPercentile(f_classif, percentile=10)
anova_svc = Pipeline([('anova', feature_selection), ('svc', LinearSVC())])
# We can use our ``anova_svc`` object exactly as we were using our ``svc``
# object previously.
# As we want to investigate our model, we use sklearn `cross_validate` function
# with `return_estimator = True` instead of cross_val_score, to save the estimator

fitted_pipeline = cross_validate(anova_svc, fmri_masked, conditions,
                                 cv=cv, groups=session_label, return_estimator=True)
    "ANOVA+SVC test score: {:.3f}".format(fitted_pipeline["test_score"].mean()))


ANOVA+SVC test score: 0.801 Visualize the ANOVA + SVC’s discriminating weights

# retrieve the pipeline fitted on the first cross-validation fold and its SVC
# coefficients
first_pipeline = fitted_pipeline["estimator"][0]
svc_coef = first_pipeline.named_steps['svc'].coef_
print("After feature selection, the SVC is trained only on {} features".format(

# We invert the feature selection step to put these coefs in the right 2D place
full_coef = first_pipeline.named_steps['anova'].inverse_transform(svc_coef)

print("After inverting feature selection, we have {} features back".format(

# We apply the inverse of masking on these to make a 4D image that we can plot
from nilearn.plotting import plot_stat_map
weight_img = masker.inverse_transform(full_coef)
plot_stat_map(weight_img, title='Anova+SVC weights')
plot advanced decoding scikit


After feature selection, the SVC is trained only on 47 features
After inverting feature selection, we have 464 features back

<nilearn.plotting.displays.OrthoSlicer object at 0x7fc02301faf0> Going further with scikit-learn Changing the prediction engine

To change the prediction engine, we just need to import it and use in our pipeline instead of the SVC. We can try Fisher’s Linear Discriminant Analysis (LDA)

# Construct the new estimator object and use it in a new pipeline after anova

from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
feature_selection = SelectPercentile(f_classif, percentile=10)
lda = LinearDiscriminantAnalysis()
anova_lda = Pipeline([('anova', feature_selection), ('LDA', lda)])

# Recompute the cross-validation score:
import numpy as np
cv_scores = cross_val_score(anova_lda, fmri_masked,
                            conditions, cv=cv, verbose=1, groups=session_label)
classification_accuracy = np.mean(cv_scores)
n_conditions = len(set(conditions))  # number of target classes
print("ANOVA + LDA classification accuracy: %.4f / Chance Level: %.4f" %
      (classification_accuracy, 1. / n_conditions))


[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
[Parallel(n_jobs=1)]: Done  12 out of  12 | elapsed:    0.2s finished
ANOVA + LDA classification accuracy: 0.8009 / Chance Level: 0.5000 Changing the feature selection

Let’s say that you want a more sophisticated feature selection, for example a Recursive Feature Elimination(RFE) before a svc. We follows the same principle.

# Import it and define your fancy objects
from sklearn.feature_selection import RFE
svc = SVC()
rfe = RFE(SVC(kernel='linear', C=1.), 50, step=0.25)

# Create a new pipeline, composing the two classifiers `rfe` and `svc`

rfe_svc = Pipeline([('rfe', rfe), ('svc', svc)])

# Recompute the cross-validation score
# cv_scores = cross_val_score(rfe_svc, fmri_masked, target, cv=cv, n_jobs=-1, verbose=1)
# But, be aware that this can take * A WHILE * ...


/home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/sklearn/utils/validation.py:70: FutureWarning: Pass n_features_to_select=50 as keyword args. From version 1.0 (renaming of 0.25) passing these as positional arguments will result in an error
  warnings.warn(f"Pass {args_msg} as keyword args. From version "

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