8.3.4. Voxel-Based Morphometry on Oasis dataset with Space-Net prior

Predicting age from gray-matter concentration maps from OASIS dataset. Note that age is a continuous variable, we use the regressor here, and not the classification object.

See also the SpaceNet documentation: SpaceNet: decoding with spatial structure for better maps.

# Authors: DOHMATOB Elvis
#          FRITSCH Virgile Load the Oasis VBM dataset

import numpy as np
from nilearn import datasets
n_subjects = 200  # increase this number if you have more RAM on your box
dataset_files = datasets.fetch_oasis_vbm(n_subjects=n_subjects)
age = dataset_files.ext_vars['age'].astype(float)
age = np.array(age)
gm_imgs = np.array(dataset_files.gray_matter_maps)

# Split data into training set and test set
from sklearn.utils import check_random_state
from sklearn.cross_validation import train_test_split
rng = check_random_state(42)
gm_imgs_train, gm_imgs_test, age_train, age_test = train_test_split(
    gm_imgs, age, train_size=.6, random_state=rng)

# Sort test data for better visualization (trend, etc.)
perm = np.argsort(age_test)[::-1]
age_test = age_test[perm]
gm_imgs_test = gm_imgs_test[perm] Fit the SpaceNet and predict with it

from nilearn.decoding import SpaceNetRegressor

# To save time (because these are anat images with many voxels), we include
# only the 5-percent voxels most correlated with the age variable to fit.
# Also, we set memory_level=2 so that more of the intermediate computations
# are cached. Also, you may pass and n_jobs=<some_high_value> to the
# SpaceNetRegressor class, to take advantage of a multi-core system.
# Also, here we use a graph-net penalty but more beautiful results can be
# obtained using the TV-l1 penalty, at the expense of longer runtimes.
decoder = SpaceNetRegressor(memory="nilearn_cache", penalty="graph-net",
                            screening_percentile=5., memory_level=2)
decoder.fit(gm_imgs_train, age_train)  # fit
coef_img = decoder.coef_img_
y_pred = decoder.predict(gm_imgs_test).ravel()  # predict
mse = np.mean(np.abs(age_test - y_pred))
print('Mean square error (MSE) on the predicted age: %.2f' % mse)


[NiftiMasker.fit] Loading data from [/home/kamalakar/nilearn_data/oasis1/OAS1_0003_MR1/mwrc1OAS1_0003_MR1_mpr_anon_fslswapdim_bet.nii.gz, /home/kamalakar/nilearn_data/oasis1/OAS1_0086_MR1/mwrc1OAS1_0086_MR1_mpr_anon_fslswapdim_bet.nii.g
[NiftiMasker.fit] Computing the mask
[NiftiMasker.fit] Resampling mask
Time Elapsed: 13.7437 seconds, 0 minutes.
Mean square error (MSE) on the predicted age: 12.49

Visualize the resulting maps

from nilearn.plotting import plot_stat_map
# weights map
background_img = gm_imgs[0]
plot_stat_map(coef_img, background_img, title="graph-net weights",
              display_mode="z", cut_coords=1)
../../_images/sphx_glr_plot_oasis_vbm_space_net_001.png Visualize the quality of predictions

import matplotlib.pyplot as plt
plt.suptitle("graph-net: Mean Absolute Error %.2f years" % mse)
linewidth = 3
ax1 = plt.subplot('211')
ax1.plot(age_test, label="True age", linewidth=linewidth)
ax1.plot(y_pred, '--', c="g", label="Predicted age", linewidth=linewidth)
ax2 = plt.subplot("212")
ax2.plot(age_test - y_pred, label="True age - predicted age",


Total running time of the script: ( 0 minutes 15.685 seconds)

Generated by Sphinx-Gallery