Massively univariate analysis of face vs house recognition

A permuted Ordinary Least Squares algorithm is run at each voxel in order to determine whether or not it behaves differently under a “face viewing” condition and a “house viewing” condition. We consider the mean image per session and per condition. Otherwise, the observations cannot be exchanged at random because a time dependence exists between observations within a same session (see [1] for more detailed explanations).

The example shows the small differences that exist between Bonferroni-corrected p-values and family-wise corrected p-values obtained from a permutation test combined with a max-type procedure [2]. Bonferroni correction is a bit conservative, as revealed by the presence of a few false negative.

Note

If you are using Nilearn with a version older than 0.9.0, then you should either upgrade your version or import maskers from the input_data module instead of the maskers module.

That is, you should manually replace in the following example all occurrences of:

from nilearn.maskers import NiftiMasker

with:

from nilearn.input_data import NiftiMasker

References

[1] Winkler, A. M. et al. (2014).

Permutation inference for the general linear model. Neuroimage.

[2] Anderson, M. J. & Robinson, J. (2001).

Permutation tests for linear models. Australian & New Zealand Journal of Statistics, 43(1), 75-88. (http://avesbiodiv.mncn.csic.es/estadistica/permut2.pdf)

# Author: Virgile Fritsch, <virgile.fritsch@inria.fr>, Feb. 2014

Load Haxby dataset

from nilearn import datasets, image
haxby_dataset = datasets.fetch_haxby(subjects=[2])

# print basic information on the dataset
print('Mask nifti image (3D) is located at: %s' % haxby_dataset.mask)
print('Functional nifti image (4D) is located at: %s' % haxby_dataset.func[0])

Mask nifti image (3D) is located at: /home/yasmin/nilearn/nilearn_data/haxby2001/mask.nii.gz
Functional nifti image (4D) is located at: /home/yasmin/nilearn/nilearn_data/haxby2001/subj2/bold.nii.gz

Restrict to faces and houses

import numpy as np
import pandas as pd
labels = pd.read_csv(haxby_dataset.session_target[0], sep=" ")
conditions = labels['labels']
categories = conditions.unique()
conditions_encoded = np.zeros_like(conditions)
for c, category in enumerate(categories):
    conditions_encoded[conditions == category] = c
sessions = labels['chunks']
condition_mask = conditions.isin(['face', 'house'])
conditions_encoded = conditions_encoded[condition_mask]

Mask data

mask_filename = haxby_dataset.mask
from nilearn.image import index_img
from nilearn.maskers import NiftiMasker
nifti_masker = NiftiMasker(
    smoothing_fwhm=8,
    mask_img=mask_filename,
    memory='nilearn_cache', memory_level=1)  # cache options
func_filename = haxby_dataset.func[0]
func_reduced = index_img(func_filename,
                         condition_mask)
fmri_masked = nifti_masker.fit_transform(func_reduced)

# We consider the mean image per session and per condition.
# Otherwise, the observations cannot be exchanged at random because
# a time dependence exists between observations within a same session.
n_sessions = np.unique(sessions).size
grouped_fmri_masked = np.empty((2 * n_sessions,  # two conditions per session
                                fmri_masked.shape[1]))
grouped_conditions_encoded = np.empty((2 * n_sessions, 1))

for s in range(n_sessions):
    session_mask = sessions[condition_mask] == s
    session_house_mask = np.logical_and(session_mask,
                                        conditions[condition_mask] == 'house')
    session_face_mask = np.logical_and(session_mask,
                                       conditions[condition_mask] == 'face')
    grouped_fmri_masked[2 * s] = fmri_masked[session_house_mask].mean(0)
    grouped_fmri_masked[2 * s + 1] = fmri_masked[session_face_mask].mean(0)
    grouped_conditions_encoded[2 * s] = conditions_encoded[
        session_house_mask][0]
    grouped_conditions_encoded[2 * s + 1] = conditions_encoded[
        session_face_mask][0]

Perform massively univariate analysis with permuted OLS

We use a two-sided t-test to compute p-values, but we keep trace of the effect sign to add it back at the end and thus observe the signed effect

from nilearn.mass_univariate import permuted_ols
neg_log_pvals, t_scores_original_data, _ = permuted_ols(
    grouped_conditions_encoded, grouped_fmri_masked,
    # + intercept as a covariate by default
    n_perm=10000, two_sided_test=True,
    verbose=1, # display progress bar
    n_jobs=1)  # can be changed to use more CPUs
signed_neg_log_pvals = neg_log_pvals * np.sign(t_scores_original_data)
signed_neg_log_pvals_unmasked = nifti_masker.inverse_transform(
    signed_neg_log_pvals)

[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
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Job #1, processed 2430/10000 permutations (24.30%, 30.408844800642978 seconds remaining)
Job #1, processed 2440/10000 permutations (24.40%, 30.350621305528236 seconds remaining)
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Job #1, processed 2460/10000 permutations (24.60%, 30.33184953239875 seconds remaining)
Job #1, processed 2470/10000 permutations (24.70%, 30.287795452936457 seconds remaining)
Job #1, processed 2480/10000 permutations (24.80%, 30.221402814311364 seconds remaining)
Job #1, processed 2490/10000 permutations (24.90%, 30.1488912708788 seconds remaining)
Job #1, processed 2500/10000 permutations (25.00%, 30.098962783813477 seconds remaining)
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Job #1, processed 2520/10000 permutations (25.20%, 29.991307012618535 seconds remaining)
Job #1, processed 2530/10000 permutations (25.30%, 29.91132531901122 seconds remaining)
Job #1, processed 2540/10000 permutations (25.40%, 29.8327030797643 seconds remaining)
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Job #1, processed 2580/10000 permutations (25.80%, 29.520669371582745 seconds remaining)
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Job #1, processed 2600/10000 permutations (26.00%, 29.368241475178646 seconds remaining)
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Job #1, processed 2620/10000 permutations (26.20%, 29.216886241927405 seconds remaining)
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Job #1, processed 2680/10000 permutations (26.80%, 28.824806587019964 seconds remaining)
Job #1, processed 2690/10000 permutations (26.90%, 28.751567496686178 seconds remaining)
Job #1, processed 2700/10000 permutations (27.00%, 28.678405947155422 seconds remaining)
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Job #1, processed 2720/10000 permutations (27.20%, 28.540130804566775 seconds remaining)
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Job #1, processed 2780/10000 permutations (27.80%, 28.30790392100382 seconds remaining)
Job #1, processed 2790/10000 permutations (27.90%, 28.296302733028234 seconds remaining)
Job #1, processed 2800/10000 permutations (28.00%, 28.287600721631733 seconds remaining)
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Job #1, processed 2850/10000 permutations (28.50%, 28.112703921502096 seconds remaining)
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Job #1, processed 2870/10000 permutations (28.70%, 27.978876181180468 seconds remaining)
Job #1, processed 2880/10000 permutations (28.80%, 27.937681217988334 seconds remaining)
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Job #1, processed 2900/10000 permutations (29.00%, 27.887521242273262 seconds remaining)
Job #1, processed 2910/10000 permutations (29.10%, 27.844384366294364 seconds remaining)
Job #1, processed 2920/10000 permutations (29.20%, 27.774824733603488 seconds remaining)
Job #1, processed 2930/10000 permutations (29.30%, 27.704587151166116 seconds remaining)
Job #1, processed 2940/10000 permutations (29.40%, 27.635053272960945 seconds remaining)
Job #1, processed 2950/10000 permutations (29.50%, 27.648077366715768 seconds remaining)
Job #1, processed 2960/10000 permutations (29.60%, 27.614132906939535 seconds remaining)
Job #1, processed 2970/10000 permutations (29.70%, 27.572357490006517 seconds remaining)
Job #1, processed 2980/10000 permutations (29.80%, 27.529464603270462 seconds remaining)
Job #1, processed 2990/10000 permutations (29.90%, 27.46099143761855 seconds remaining)
Job #1, processed 3000/10000 permutations (30.00%, 27.3910174369812 seconds remaining)
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Job #1, processed 3030/10000 permutations (30.30%, 27.19299020704263 seconds remaining)
Job #1, processed 3040/10000 permutations (30.40%, 27.12605495829331 seconds remaining)
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Job #1, processed 3060/10000 permutations (30.60%, 26.99920239323884 seconds remaining)
Job #1, processed 3070/10000 permutations (30.70%, 26.940301603913696 seconds remaining)
Job #1, processed 3080/10000 permutations (30.80%, 26.876959484893007 seconds remaining)
Job #1, processed 3090/10000 permutations (30.90%, 26.851278494091094 seconds remaining)
Job #1, processed 3100/10000 permutations (31.00%, 26.806803957108524 seconds remaining)
Job #1, processed 3110/10000 permutations (31.10%, 26.793110890403824 seconds remaining)
Job #1, processed 3120/10000 permutations (31.20%, 26.766652143918552 seconds remaining)
Job #1, processed 3130/10000 permutations (31.30%, 26.719847110894545 seconds remaining)
Job #1, processed 3140/10000 permutations (31.40%, 26.723723138213913 seconds remaining)
Job #1, processed 3150/10000 permutations (31.50%, 26.680398297688317 seconds remaining)
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Job #1, processed 3170/10000 permutations (31.70%, 26.632722318360482 seconds remaining)
Job #1, processed 3180/10000 permutations (31.80%, 26.61184658494386 seconds remaining)
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Job #1, processed 3200/10000 permutations (32.00%, 26.577912479639053 seconds remaining)
Job #1, processed 3210/10000 permutations (32.10%, 26.55282615204095 seconds remaining)
Job #1, processed 3220/10000 permutations (32.20%, 26.495294258461232 seconds remaining)
Job #1, processed 3230/10000 permutations (32.30%, 26.46418340508783 seconds remaining)
Job #1, processed 3240/10000 permutations (32.40%, 26.44183744324578 seconds remaining)
Job #1, processed 3250/10000 permutations (32.50%, 26.419086016141453 seconds remaining)
Job #1, processed 3260/10000 permutations (32.60%, 26.380360941214064 seconds remaining)
Job #1, processed 3270/10000 permutations (32.70%, 26.365864352713295 seconds remaining)
Job #1, processed 3280/10000 permutations (32.80%, 26.375350486941453 seconds remaining)
Job #1, processed 3290/10000 permutations (32.90%, 26.314773995825583 seconds remaining)
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Job #1, processed 3310/10000 permutations (33.10%, 26.182599781503132 seconds remaining)
Job #1, processed 3320/10000 permutations (33.20%, 26.11912040538098 seconds remaining)
Job #1, processed 3330/10000 permutations (33.30%, 26.050666502646145 seconds remaining)
Job #1, processed 3340/10000 permutations (33.40%, 25.98328526862367 seconds remaining)
Job #1, processed 3350/10000 permutations (33.50%, 25.914457452830984 seconds remaining)
Job #1, processed 3360/10000 permutations (33.60%, 25.85103686082931 seconds remaining)
Job #1, processed 3370/10000 permutations (33.70%, 25.853700915147 seconds remaining)
Job #1, processed 3380/10000 permutations (33.80%, 25.822858117741244 seconds remaining)
Job #1, processed 3390/10000 permutations (33.90%, 25.789912067683396 seconds remaining)
Job #1, processed 3400/10000 permutations (34.00%, 25.7233465980081 seconds remaining)
Job #1, processed 3410/10000 permutations (34.10%, 25.663867710622526 seconds remaining)
Job #1, processed 3420/10000 permutations (34.20%, 25.668609691642178 seconds remaining)
Job #1, processed 3430/10000 permutations (34.30%, 25.68889215458239 seconds remaining)
Job #1, processed 3440/10000 permutations (34.40%, 25.664296604866202 seconds remaining)
Job #1, processed 3450/10000 permutations (34.50%, 25.642819732859515 seconds remaining)
Job #1, processed 3460/10000 permutations (34.60%, 25.581921340413178 seconds remaining)
Job #1, processed 3470/10000 permutations (34.70%, 25.517214309928736 seconds remaining)
Job #1, processed 3480/10000 permutations (34.80%, 25.50940971812983 seconds remaining)
Job #1, processed 3490/10000 permutations (34.90%, 25.57560982540207 seconds remaining)
Job #1, processed 3500/10000 permutations (35.00%, 25.665590184075494 seconds remaining)
Job #1, processed 3510/10000 permutations (35.10%, 25.74627704022617 seconds remaining)
Job #1, processed 3520/10000 permutations (35.20%, 25.71885671398856 seconds remaining)
Job #1, processed 3530/10000 permutations (35.30%, 25.68753534673632 seconds remaining)
Job #1, processed 3540/10000 permutations (35.40%, 25.62297169502172 seconds remaining)
Job #1, processed 3550/10000 permutations (35.50%, 25.566429517638515 seconds remaining)
Job #1, processed 3560/10000 permutations (35.60%, 25.50874132252811 seconds remaining)
Job #1, processed 3570/10000 permutations (35.70%, 25.466498810370094 seconds remaining)
Job #1, processed 3580/10000 permutations (35.80%, 25.450716614057235 seconds remaining)
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Job #1, processed 3600/10000 permutations (36.00%, 25.364332834879555 seconds remaining)
Job #1, processed 3610/10000 permutations (36.10%, 25.296621203752764 seconds remaining)
Job #1, processed 3620/10000 permutations (36.20%, 25.237984879899418 seconds remaining)
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Job #1, processed 3650/10000 permutations (36.50%, 25.044811189991155 seconds remaining)
Job #1, processed 3660/10000 permutations (36.60%, 24.969205079834317 seconds remaining)
Job #1, processed 3670/10000 permutations (36.70%, 24.923874853742216 seconds remaining)
Job #1, processed 3680/10000 permutations (36.80%, 24.92876493412516 seconds remaining)
Job #1, processed 3690/10000 permutations (36.90%, 24.93273275072982 seconds remaining)
Job #1, processed 3700/10000 permutations (37.00%, 24.90683557536151 seconds remaining)
Job #1, processed 3710/10000 permutations (37.10%, 24.86890429884918 seconds remaining)
Job #1, processed 3720/10000 permutations (37.20%, 24.873147679913426 seconds remaining)
Job #1, processed 3730/10000 permutations (37.30%, 24.824620153565192 seconds remaining)
Job #1, processed 3740/10000 permutations (37.40%, 24.80598479541228 seconds remaining)
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Job #1, processed 3760/10000 permutations (37.60%, 24.73869743752987 seconds remaining)
Job #1, processed 3770/10000 permutations (37.70%, 24.72505921077981 seconds remaining)
Job #1, processed 3780/10000 permutations (37.80%, 24.692863148986984 seconds remaining)
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Job #1, processed 3800/10000 permutations (38.00%, 24.578469577588532 seconds remaining)
Job #1, processed 3810/10000 permutations (38.10%, 24.536245762832518 seconds remaining)
Job #1, processed 3820/10000 permutations (38.20%, 24.50765176343668 seconds remaining)
Job #1, processed 3830/10000 permutations (38.30%, 24.452792940812078 seconds remaining)
Job #1, processed 3840/10000 permutations (38.40%, 24.427514404058456 seconds remaining)
Job #1, processed 3850/10000 permutations (38.50%, 24.37578434758372 seconds remaining)
Job #1, processed 3860/10000 permutations (38.60%, 24.31581071127264 seconds remaining)
Job #1, processed 3870/10000 permutations (38.70%, 24.26207709620473 seconds remaining)
Job #1, processed 3880/10000 permutations (38.80%, 24.2743442869678 seconds remaining)
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Job #1, processed 3900/10000 permutations (39.00%, 24.23468388043917 seconds remaining)
Job #1, processed 3910/10000 permutations (39.10%, 24.21951267908296 seconds remaining)
Job #1, processed 3920/10000 permutations (39.20%, 24.183658872331886 seconds remaining)
Job #1, processed 3930/10000 permutations (39.30%, 24.158941883470572 seconds remaining)
Job #1, processed 3940/10000 permutations (39.40%, 24.1187193672064 seconds remaining)
Job #1, processed 3950/10000 permutations (39.50%, 24.060028112387354 seconds remaining)
Job #1, processed 3960/10000 permutations (39.60%, 24.006666734965158 seconds remaining)
Job #1, processed 3970/10000 permutations (39.70%, 23.947689078016303 seconds remaining)
Job #1, processed 3980/10000 permutations (39.80%, 23.88963007807133 seconds remaining)
Job #1, processed 3990/10000 permutations (39.90%, 23.833816786457724 seconds remaining)
Job #1, processed 4000/10000 permutations (40.00%, 23.775906801223755 seconds remaining)
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Job #1, processed 4050/10000 permutations (40.50%, 23.53086402092451 seconds remaining)
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Job #1, processed 4080/10000 permutations (40.80%, 23.472455903595574 seconds remaining)
Job #1, processed 4090/10000 permutations (40.90%, 23.437545688927614 seconds remaining)
Job #1, processed 4100/10000 permutations (41.00%, 23.400340882743276 seconds remaining)
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Job #1, processed 4120/10000 permutations (41.20%, 23.325793831093794 seconds remaining)
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Job #1, processed 4140/10000 permutations (41.40%, 23.240740423617158 seconds remaining)
Job #1, processed 4150/10000 permutations (41.50%, 23.198083274335747 seconds remaining)
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Job #1, processed 4200/10000 permutations (42.00%, 23.033453805106028 seconds remaining)
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Job #1, processed 4220/10000 permutations (42.20%, 22.969028526007843 seconds remaining)
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Job #1, processed 4240/10000 permutations (42.40%, 22.90392828887364 seconds remaining)
Job #1, processed 4250/10000 permutations (42.50%, 22.86317995015313 seconds remaining)
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Job #1, processed 4290/10000 permutations (42.90%, 22.728402356723528 seconds remaining)
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Job #1, processed 4370/10000 permutations (43.70%, 22.485393652381287 seconds remaining)
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Job #1, processed 4390/10000 permutations (43.90%, 22.420364159386363 seconds remaining)
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Job #1, processed 4580/10000 permutations (45.80%, 21.626235024897817 seconds remaining)
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Job #1, processed 5100/10000 permutations (51.00%, 19.473905030418845 seconds remaining)
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Job #1, processed 5240/10000 permutations (52.40%, 18.89817476636581 seconds remaining)
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Job #1, processed 5270/10000 permutations (52.70%, 18.780483221419622 seconds remaining)
Job #1, processed 5280/10000 permutations (52.80%, 18.748025941126276 seconds remaining)
Job #1, processed 5290/10000 permutations (52.90%, 18.710540537572765 seconds remaining)
Job #1, processed 5300/10000 permutations (53.00%, 18.67310403877834 seconds remaining)
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Job #1, processed 5320/10000 permutations (53.20%, 18.62868798047976 seconds remaining)
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Job #1, processed 5370/10000 permutations (53.70%, 18.42796680736364 seconds remaining)
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Job #1, processed 5390/10000 permutations (53.90%, 18.32862527383723 seconds remaining)
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Job #1, processed 5420/10000 permutations (54.20%, 18.216968062179113 seconds remaining)
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Job #1, processed 5500/10000 permutations (55.00%, 17.891110116785224 seconds remaining)
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Job #1, processed 5690/10000 permutations (56.90%, 17.12146807932058 seconds remaining)
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Job #1, processed 5760/10000 permutations (57.60%, 16.82244650191731 seconds remaining)
Job #1, processed 5770/10000 permutations (57.70%, 16.773870779695294 seconds remaining)
Job #1, processed 5780/10000 permutations (57.80%, 16.725160718376664 seconds remaining)
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Job #1, processed 5870/10000 permutations (58.70%, 16.33064469365082 seconds remaining)
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Job #1, processed 5900/10000 permutations (59.00%, 16.19416037656493 seconds remaining)
Job #1, processed 5910/10000 permutations (59.10%, 16.148197939754944 seconds remaining)
Job #1, processed 5920/10000 permutations (59.20%, 16.10105406915819 seconds remaining)
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Job #1, processed 5950/10000 permutations (59.50%, 15.994694619619546 seconds remaining)
Job #1, processed 5960/10000 permutations (59.60%, 15.961289177004922 seconds remaining)
Job #1, processed 5970/10000 permutations (59.70%, 15.923778789926013 seconds remaining)
Job #1, processed 5980/10000 permutations (59.80%, 15.891952153432332 seconds remaining)
Job #1, processed 5990/10000 permutations (59.90%, 15.843922162891827 seconds remaining)
Job #1, processed 6000/10000 permutations (60.00%, 15.795792897542317 seconds remaining)
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Job #1, processed 6030/10000 permutations (60.30%, 15.684383701131516 seconds remaining)
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Job #1, processed 6050/10000 permutations (60.50%, 15.618663781930593 seconds remaining)
Job #1, processed 6060/10000 permutations (60.60%, 15.592095821997512 seconds remaining)
Job #1, processed 6070/10000 permutations (60.70%, 15.550328666335078 seconds remaining)
Job #1, processed 6080/10000 permutations (60.80%, 15.510019584705958 seconds remaining)
Job #1, processed 6090/10000 permutations (60.90%, 15.465677257046128 seconds remaining)
Job #1, processed 6100/10000 permutations (61.00%, 15.419749599988345 seconds remaining)
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Job #1, processed 6200/10000 permutations (62.00%, 14.969379332757766 seconds remaining)
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Job #1, processed 6220/10000 permutations (62.20%, 14.87590779598886 seconds remaining)
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Job #1, processed 6240/10000 permutations (62.40%, 14.783496416532078 seconds remaining)
Job #1, processed 6250/10000 permutations (62.50%, 14.736993312835693 seconds remaining)
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Job #1, processed 6270/10000 permutations (62.70%, 14.644690852416186 seconds remaining)
Job #1, processed 6280/10000 permutations (62.80%, 14.602113547598483 seconds remaining)
Job #1, processed 6290/10000 permutations (62.90%, 14.566088327732299 seconds remaining)
Job #1, processed 6300/10000 permutations (63.00%, 14.52103995141529 seconds remaining)
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Job #1, processed 6370/10000 permutations (63.70%, 14.227317795461536 seconds remaining)
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Job #1, processed 6390/10000 permutations (63.90%, 14.163054230067653 seconds remaining)
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Job #1, processed 6500/10000 permutations (65.00%, 13.690631206219011 seconds remaining)
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Job #1, processed 6560/10000 permutations (65.60%, 13.4406474886871 seconds remaining)
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Job #1, processed 6610/10000 permutations (66.10%, 13.257241531868388 seconds remaining)
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Job #1, processed 6680/10000 permutations (66.80%, 12.99286761826384 seconds remaining)
Job #1, processed 6690/10000 permutations (66.90%, 12.95610142359997 seconds remaining)
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Job #1, processed 6720/10000 permutations (67.20%, 12.856808364391325 seconds remaining)
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Job #1, processed 6760/10000 permutations (67.60%, 12.693145222917819 seconds remaining)
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Job #1, processed 7000/10000 permutations (70.00%, 11.729338441576276 seconds remaining)
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Job #1, processed 7070/10000 permutations (70.70%, 11.476572409377575 seconds remaining)
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Job #1, processed 7100/10000 permutations (71.00%, 11.355274193723437 seconds remaining)
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Job #1, processed 7240/10000 permutations (72.40%, 10.76014760844615 seconds remaining)
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Job #1, processed 7370/10000 permutations (73.70%, 10.238406590237869 seconds remaining)
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Job #1, processed 7390/10000 permutations (73.90%, 10.153719267761268 seconds remaining)
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[Parallel(n_jobs=1)]: Done   1 out of   1 | elapsed:   38.2s finished

scikit-learn F-scores for comparison

F-test does not allow to observe the effect sign (pure two-sided test)

from sklearn.feature_selection import f_regression
_, pvals_bonferroni = f_regression(
    grouped_fmri_masked,
    grouped_conditions_encoded)  # f_regression implicitly adds intercept
pvals_bonferroni *= fmri_masked.shape[1]
pvals_bonferroni[np.isnan(pvals_bonferroni)] = 1
pvals_bonferroni[pvals_bonferroni > 1] = 1
neg_log_pvals_bonferroni = -np.log10(pvals_bonferroni)
neg_log_pvals_bonferroni_unmasked = nifti_masker.inverse_transform(
    neg_log_pvals_bonferroni)

/home/yasmin/miniconda3/envs/nilearn-dev/lib/python3.10/site-packages/sklearn/utils/validation.py:1141: DataConversionWarning:

A column-vector y was passed when a 1d array was expected. Please change the shape of y to (n_samples, ), for example using ravel().

Visualization

import matplotlib.pyplot as plt
from nilearn.plotting import plot_stat_map, show

# Use the fmri mean image as a surrogate of anatomical data
from nilearn import image
from nilearn.image import get_data

mean_fmri_img = image.mean_img(func_filename)

threshold = -np.log10(0.1)  # 10% corrected

vmax = min(signed_neg_log_pvals.max(),
           neg_log_pvals_bonferroni.max())

# Plot thresholded p-values map corresponding to F-scores
display = plot_stat_map(neg_log_pvals_bonferroni_unmasked, mean_fmri_img,
                        threshold=threshold, cmap=plt.cm.RdBu_r,
                        display_mode='z', cut_coords=[-1, ],
                        vmax=vmax)

neg_log_pvals_bonferroni_data = get_data(neg_log_pvals_bonferroni_unmasked)
n_detections = (neg_log_pvals_bonferroni_data > threshold).sum()
title = ('Negative $\\log_{10}$ p-values'
         '\n(Parametric two-sided F-test'
         '\n+ Bonferroni correction)'
         '\n%d detections') % n_detections

display.title(title, y=1.1)

# Plot permutation p-values map
display = plot_stat_map(signed_neg_log_pvals_unmasked, mean_fmri_img,
                        threshold=threshold, cmap=plt.cm.RdBu_r,
                        display_mode='z', cut_coords=[-1, ],
                        vmax=vmax)

n_detections = (np.abs(signed_neg_log_pvals) > threshold).sum()
title = ('Negative $\\log_{10}$ p-values'
         '\n(Non-parametric two-sided test'
         '\n+ max-type correction)'
         '\n%d detections') % n_detections

display.title(title, y=1.1)

show()

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• 

Estimated memory usage: 949 MB