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_data/haxby2001/mask.nii.gz
Functional nifti image (4D) is located at: /home/yasmin/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 2420/10000 permutations (24.20%, 28.987584009643427 seconds remaining)
Job #1, processed 2430/10000 permutations (24.30%, 28.92496593793233 seconds remaining)
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Job #1, processed 2470/10000 permutations (24.70%, 28.636653862501447 seconds remaining)
Job #1, processed 2480/10000 permutations (24.80%, 28.575380509899507 seconds remaining)
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Job #1, processed 2500/10000 permutations (25.00%, 28.441984176635742 seconds remaining)
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Job #1, processed 2520/10000 permutations (25.20%, 28.32084111561851 seconds remaining)
Job #1, processed 2530/10000 permutations (25.30%, 28.252878167412497 seconds remaining)
Job #1, processed 2540/10000 permutations (25.40%, 28.250466609564356 seconds remaining)
Job #1, processed 2550/10000 permutations (25.50%, 28.20571803579143 seconds remaining)
Job #1, processed 2560/10000 permutations (25.60%, 28.179589949548244 seconds remaining)
Job #1, processed 2570/10000 permutations (25.70%, 28.116749400758557 seconds remaining)
Job #1, processed 2580/10000 permutations (25.80%, 28.080608622972356 seconds remaining)
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Job #1, processed 2600/10000 permutations (26.00%, 28.16631584901076 seconds remaining)
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Job #1, processed 2620/10000 permutations (26.20%, 28.434212770170838 seconds remaining)
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Job #1, processed 2680/10000 permutations (26.80%, 28.190540740739056 seconds remaining)
Job #1, processed 2690/10000 permutations (26.90%, 28.127065878375312 seconds remaining)
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Job #1, processed 2720/10000 permutations (27.20%, 27.91736238844254 seconds remaining)
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Job #1, processed 2780/10000 permutations (27.80%, 27.6460145308817 seconds remaining)
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Job #1, processed 2800/10000 permutations (28.00%, 27.657209873199466 seconds remaining)
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Job #1, processed 2820/10000 permutations (28.20%, 27.61274432966895 seconds remaining)
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Job #1, processed 2870/10000 permutations (28.70%, 27.39494738761556 seconds remaining)
Job #1, processed 2880/10000 permutations (28.80%, 27.333215415477753 seconds remaining)
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Job #1, processed 2900/10000 permutations (29.00%, 27.203468026786013 seconds remaining)
Job #1, processed 2910/10000 permutations (29.10%, 27.133452017282703 seconds remaining)
Job #1, processed 2920/10000 permutations (29.20%, 27.071678187749157 seconds remaining)
Job #1, processed 2930/10000 permutations (29.30%, 27.00831647619046 seconds remaining)
Job #1, processed 2940/10000 permutations (29.40%, 26.959548098700385 seconds remaining)
Job #1, processed 2950/10000 permutations (29.50%, 26.91118317943508 seconds remaining)
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Job #1, processed 2970/10000 permutations (29.70%, 26.845938207324505 seconds remaining)
Job #1, processed 2980/10000 permutations (29.80%, 26.838588290566566 seconds remaining)
Job #1, processed 2990/10000 permutations (29.90%, 26.83448727712982 seconds remaining)
Job #1, processed 3000/10000 permutations (30.00%, 26.892871856689453 seconds remaining)
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Job #1, processed 3030/10000 permutations (30.30%, 26.91224194831974 seconds remaining)
Job #1, processed 3040/10000 permutations (30.40%, 26.896557042473237 seconds remaining)
Job #1, processed 3050/10000 permutations (30.50%, 26.884760082745164 seconds remaining)
Job #1, processed 3060/10000 permutations (30.60%, 26.900648389766417 seconds remaining)
Job #1, processed 3070/10000 permutations (30.70%, 26.91085027794108 seconds remaining)
Job #1, processed 3080/10000 permutations (30.80%, 26.938918027010832 seconds remaining)
Job #1, processed 3090/10000 permutations (30.90%, 27.087190141184042 seconds remaining)
Job #1, processed 3100/10000 permutations (31.00%, 27.100085504593384 seconds remaining)
Job #1, processed 3110/10000 permutations (31.10%, 27.083769670253403 seconds remaining)
Job #1, processed 3120/10000 permutations (31.20%, 27.042161207932693 seconds remaining)
Job #1, processed 3130/10000 permutations (31.30%, 26.98578139920585 seconds remaining)
Job #1, processed 3140/10000 permutations (31.40%, 26.924755330298353 seconds remaining)
Job #1, processed 3150/10000 permutations (31.50%, 26.87010752587091 seconds remaining)
Job #1, processed 3160/10000 permutations (31.60%, 26.81096768681007 seconds remaining)
Job #1, processed 3170/10000 permutations (31.70%, 26.793917370895482 seconds remaining)
Job #1, processed 3180/10000 permutations (31.80%, 26.768176138775907 seconds remaining)
Job #1, processed 3190/10000 permutations (31.90%, 26.739347654450274 seconds remaining)
Job #1, processed 3200/10000 permutations (32.00%, 26.77292510867119 seconds remaining)
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Job #1, processed 3220/10000 permutations (32.20%, 26.76624658833379 seconds remaining)
Job #1, processed 3230/10000 permutations (32.30%, 26.72352380058714 seconds remaining)
Job #1, processed 3240/10000 permutations (32.40%, 26.650502599315878 seconds remaining)
Job #1, processed 3250/10000 permutations (32.50%, 26.579653611549965 seconds remaining)
Job #1, processed 3260/10000 permutations (32.60%, 26.537678515252892 seconds remaining)
Job #1, processed 3270/10000 permutations (32.70%, 26.477798153501034 seconds remaining)
Job #1, processed 3280/10000 permutations (32.80%, 26.42023672708651 seconds remaining)
Job #1, processed 3290/10000 permutations (32.90%, 26.356986048736104 seconds remaining)
Job #1, processed 3300/10000 permutations (33.00%, 26.295400836250998 seconds remaining)
Job #1, processed 3310/10000 permutations (33.10%, 26.231346685720716 seconds remaining)
Job #1, processed 3320/10000 permutations (33.20%, 26.179267843085597 seconds remaining)
Job #1, processed 3330/10000 permutations (33.30%, 26.159183288121728 seconds remaining)
Job #1, processed 3340/10000 permutations (33.40%, 26.175647838386944 seconds remaining)
Job #1, processed 3350/10000 permutations (33.50%, 26.1611795176321 seconds remaining)
Job #1, processed 3360/10000 permutations (33.60%, 26.12703704266321 seconds remaining)
Job #1, processed 3370/10000 permutations (33.70%, 26.06208983373217 seconds remaining)
Job #1, processed 3380/10000 permutations (33.80%, 26.094476273779335 seconds remaining)
Job #1, processed 3390/10000 permutations (33.90%, 26.047122857563615 seconds remaining)
Job #1, processed 3400/10000 permutations (34.00%, 26.005345218321857 seconds remaining)
Job #1, processed 3410/10000 permutations (34.10%, 25.951297987940723 seconds remaining)
Job #1, processed 3420/10000 permutations (34.20%, 25.89155874893679 seconds remaining)
Job #1, processed 3430/10000 permutations (34.30%, 25.852602100233298 seconds remaining)
Job #1, processed 3440/10000 permutations (34.40%, 25.79728290646575 seconds remaining)
Job #1, processed 3450/10000 permutations (34.50%, 25.739860147669695 seconds remaining)
Job #1, processed 3460/10000 permutations (34.60%, 25.72613463374232 seconds remaining)
Job #1, processed 3470/10000 permutations (34.70%, 25.672971634081527 seconds remaining)
Job #1, processed 3480/10000 permutations (34.80%, 25.62747406137401 seconds remaining)
Job #1, processed 3490/10000 permutations (34.90%, 25.57680258914871 seconds remaining)
Job #1, processed 3500/10000 permutations (35.00%, 25.526010819843837 seconds remaining)
Job #1, processed 3510/10000 permutations (35.10%, 25.492595396150552 seconds remaining)
Job #1, processed 3520/10000 permutations (35.20%, 25.436054495247923 seconds remaining)
Job #1, processed 3530/10000 permutations (35.30%, 25.44964248803115 seconds remaining)
Job #1, processed 3540/10000 permutations (35.40%, 25.407496904922745 seconds remaining)
Job #1, processed 3550/10000 permutations (35.50%, 25.385845033215805 seconds remaining)
Job #1, processed 3560/10000 permutations (35.60%, 25.372896285539262 seconds remaining)
Job #1, processed 3570/10000 permutations (35.70%, 25.354849460078217 seconds remaining)
Job #1, processed 3580/10000 permutations (35.80%, 25.331375295223474 seconds remaining)
Job #1, processed 3590/10000 permutations (35.90%, 25.29230974245204 seconds remaining)
Job #1, processed 3600/10000 permutations (36.00%, 25.318096584743923 seconds remaining)
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Job #1, processed 3620/10000 permutations (36.20%, 25.239168993017287 seconds remaining)
Job #1, processed 3630/10000 permutations (36.30%, 25.18517752784015 seconds remaining)
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Job #1, processed 3650/10000 permutations (36.50%, 25.11179740134984 seconds remaining)
Job #1, processed 3660/10000 permutations (36.60%, 25.04700652627997 seconds remaining)
Job #1, processed 3670/10000 permutations (36.70%, 24.992078298443992 seconds remaining)
Job #1, processed 3680/10000 permutations (36.80%, 24.934305310249332 seconds remaining)
Job #1, processed 3690/10000 permutations (36.90%, 24.878672657943355 seconds remaining)
Job #1, processed 3700/10000 permutations (37.00%, 24.857977557826686 seconds remaining)
Job #1, processed 3710/10000 permutations (37.10%, 24.819127141947373 seconds remaining)
Job #1, processed 3720/10000 permutations (37.20%, 24.764571953845277 seconds remaining)
Job #1, processed 3730/10000 permutations (37.30%, 24.71528157663729 seconds remaining)
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Job #1, processed 3750/10000 permutations (37.50%, 24.616130987803142 seconds remaining)
Job #1, processed 3760/10000 permutations (37.60%, 24.578641617551764 seconds remaining)
Job #1, processed 3770/10000 permutations (37.70%, 24.52828136552866 seconds remaining)
Job #1, processed 3780/10000 permutations (37.80%, 24.482555376789563 seconds remaining)
Job #1, processed 3790/10000 permutations (37.90%, 24.42866706281979 seconds remaining)
Job #1, processed 3800/10000 permutations (38.00%, 24.38035757918107 seconds remaining)
Job #1, processed 3810/10000 permutations (38.10%, 24.32780508294193 seconds remaining)
Job #1, processed 3820/10000 permutations (38.20%, 24.290036650852382 seconds remaining)
Job #1, processed 3830/10000 permutations (38.30%, 24.24948447864921 seconds remaining)
Job #1, processed 3840/10000 permutations (38.40%, 24.20046745737394 seconds remaining)
Job #1, processed 3850/10000 permutations (38.50%, 24.156808664272358 seconds remaining)
Job #1, processed 3860/10000 permutations (38.60%, 24.102763886278773 seconds remaining)
Job #1, processed 3870/10000 permutations (38.70%, 24.036193619094767 seconds remaining)
Job #1, processed 3880/10000 permutations (38.80%, 23.98138912682681 seconds remaining)
Job #1, processed 3890/10000 permutations (38.90%, 23.95325484802913 seconds remaining)
Job #1, processed 3900/10000 permutations (39.00%, 23.92546113943442 seconds remaining)
Job #1, processed 3910/10000 permutations (39.10%, 23.876092639420644 seconds remaining)
Job #1, processed 3920/10000 permutations (39.20%, 23.823191467596555 seconds remaining)
Job #1, processed 3930/10000 permutations (39.30%, 23.777214876568046 seconds remaining)
Job #1, processed 3940/10000 permutations (39.40%, 23.729689665857308 seconds remaining)
Job #1, processed 3950/10000 permutations (39.50%, 23.75220244745665 seconds remaining)
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Job #1, processed 3970/10000 permutations (39.70%, 23.71330602283141 seconds remaining)
Job #1, processed 3980/10000 permutations (39.80%, 23.67073114912714 seconds remaining)
Job #1, processed 3990/10000 permutations (39.90%, 23.630396238843304 seconds remaining)
Job #1, processed 4000/10000 permutations (40.00%, 23.58368182182312 seconds remaining)
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Job #1, processed 4040/10000 permutations (40.40%, 23.390745599671167 seconds remaining)
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Job #1, processed 4070/10000 permutations (40.70%, 23.224773135759317 seconds remaining)
Job #1, processed 4080/10000 permutations (40.80%, 23.179933650820868 seconds remaining)
Job #1, processed 4090/10000 permutations (40.90%, 23.126661910987426 seconds remaining)
Job #1, processed 4100/10000 permutations (41.00%, 23.07026139701285 seconds remaining)
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Job #1, processed 4120/10000 permutations (41.20%, 22.96545144886646 seconds remaining)
Job #1, processed 4130/10000 permutations (41.30%, 22.904445024148608 seconds remaining)
Job #1, processed 4140/10000 permutations (41.40%, 22.850141218894922 seconds remaining)
Job #1, processed 4150/10000 permutations (41.50%, 22.798004486474646 seconds remaining)
Job #1, processed 4160/10000 permutations (41.60%, 22.75009362055705 seconds remaining)
Job #1, processed 4170/10000 permutations (41.70%, 22.69539460518377 seconds remaining)
Job #1, processed 4180/10000 permutations (41.80%, 22.64948797682256 seconds remaining)
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Job #1, processed 4200/10000 permutations (42.00%, 22.545291900634766 seconds remaining)
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Job #1, processed 4220/10000 permutations (42.20%, 22.451587472481748 seconds remaining)
Job #1, processed 4230/10000 permutations (42.30%, 22.399610337354332 seconds remaining)
Job #1, processed 4240/10000 permutations (42.40%, 22.339739205702298 seconds remaining)
Job #1, processed 4250/10000 permutations (42.50%, 22.271810419419232 seconds remaining)
Job #1, processed 4260/10000 permutations (42.60%, 22.209217503596918 seconds remaining)
Job #1, processed 4270/10000 permutations (42.70%, 22.157092833128132 seconds remaining)
Job #1, processed 4280/10000 permutations (42.80%, 22.106611294167067 seconds remaining)
Job #1, processed 4290/10000 permutations (42.90%, 22.105932862052832 seconds remaining)
Job #1, processed 4300/10000 permutations (43.00%, 22.06375586154849 seconds remaining)
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Job #1, processed 4360/10000 permutations (43.60%, 21.91141426891362 seconds remaining)
Job #1, processed 4370/10000 permutations (43.70%, 21.882835172679385 seconds remaining)
Job #1, processed 4380/10000 permutations (43.80%, 21.849228558475026 seconds remaining)
Job #1, processed 4390/10000 permutations (43.90%, 21.832534822624748 seconds remaining)
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Job #1, processed 4470/10000 permutations (44.70%, 21.663093632499642 seconds remaining)
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Job #1, processed 4690/10000 permutations (46.90%, 21.142452999981227 seconds remaining)
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Job #1, processed 5140/10000 permutations (51.40%, 19.19469201425634 seconds remaining)
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Job #1, processed 5240/10000 permutations (52.40%, 18.721594246289204 seconds remaining)
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Job #1, processed 5270/10000 permutations (52.70%, 18.591872606603197 seconds remaining)
Job #1, processed 5280/10000 permutations (52.80%, 18.554834575364087 seconds remaining)
Job #1, processed 5290/10000 permutations (52.90%, 18.526282238825058 seconds remaining)
Job #1, processed 5300/10000 permutations (53.00%, 18.490223434736144 seconds remaining)
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Job #1, processed 5320/10000 permutations (53.20%, 18.40775538387155 seconds remaining)
Job #1, processed 5330/10000 permutations (53.30%, 18.360845552823783 seconds remaining)
Job #1, processed 5340/10000 permutations (53.40%, 18.31308394603515 seconds remaining)
Job #1, processed 5350/10000 permutations (53.50%, 18.267942667007446 seconds remaining)
Job #1, processed 5360/10000 permutations (53.60%, 18.237959484555827 seconds remaining)
Job #1, processed 5370/10000 permutations (53.70%, 18.19727171821523 seconds remaining)
Job #1, processed 5380/10000 permutations (53.80%, 18.15707843454354 seconds remaining)
Job #1, processed 5390/10000 permutations (53.90%, 18.115719781957 seconds remaining)
Job #1, processed 5400/10000 permutations (54.00%, 18.07141853261877 seconds remaining)
Job #1, processed 5410/10000 permutations (54.10%, 18.07424533036632 seconds remaining)
Job #1, processed 5420/10000 permutations (54.20%, 18.077214880623057 seconds remaining)
Job #1, processed 5430/10000 permutations (54.30%, 18.03119574989403 seconds remaining)
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Job #1, processed 5480/10000 permutations (54.80%, 17.77520783278194 seconds remaining)
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Job #1, processed 5500/10000 permutations (55.00%, 17.66991545937278 seconds remaining)
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Job #1, processed 5580/10000 permutations (55.80%, 17.26197575753735 seconds remaining)
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Job #1, processed 5600/10000 permutations (56.00%, 17.16357604094914 seconds remaining)
Job #1, processed 5610/10000 permutations (56.10%, 17.11216158025405 seconds remaining)
Job #1, processed 5620/10000 permutations (56.20%, 17.05976421043966 seconds remaining)
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Job #1, processed 5670/10000 permutations (56.70%, 16.837134945750023 seconds remaining)
Job #1, processed 5680/10000 permutations (56.80%, 16.787107984784626 seconds remaining)
Job #1, processed 5690/10000 permutations (56.90%, 16.740300665421312 seconds remaining)
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Job #1, processed 5710/10000 permutations (57.10%, 16.638380405990546 seconds remaining)
Job #1, processed 5720/10000 permutations (57.20%, 16.58627158611804 seconds remaining)
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Job #1, processed 5760/10000 permutations (57.60%, 16.387591335508557 seconds remaining)
Job #1, processed 5770/10000 permutations (57.70%, 16.338409190781192 seconds remaining)
Job #1, processed 5780/10000 permutations (57.80%, 16.289175685301785 seconds remaining)
Job #1, processed 5790/10000 permutations (57.90%, 16.239034112871003 seconds remaining)
Job #1, processed 5800/10000 permutations (58.00%, 16.187036152543694 seconds remaining)
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Job #1, processed 5820/10000 permutations (58.20%, 16.0941663304555 seconds remaining)
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Job #1, processed 5840/10000 permutations (58.40%, 15.992673495044448 seconds remaining)
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Job #1, processed 5870/10000 permutations (58.70%, 15.841331264635567 seconds remaining)
Job #1, processed 5880/10000 permutations (58.80%, 15.79265539662368 seconds remaining)
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Job #1, processed 5900/10000 permutations (59.00%, 15.70299229783527 seconds remaining)
Job #1, processed 5910/10000 permutations (59.10%, 15.678242730206845 seconds remaining)
Job #1, processed 5920/10000 permutations (59.20%, 15.66200385544751 seconds remaining)
Job #1, processed 5930/10000 permutations (59.30%, 15.64496625052737 seconds remaining)
Job #1, processed 5940/10000 permutations (59.40%, 15.619202518302583 seconds remaining)
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Job #1, processed 5960/10000 permutations (59.60%, 15.561837631584012 seconds remaining)
Job #1, processed 5970/10000 permutations (59.70%, 15.561505535339789 seconds remaining)
Job #1, processed 5980/10000 permutations (59.80%, 15.517130701836937 seconds remaining)
Job #1, processed 5990/10000 permutations (59.90%, 15.470356907390793 seconds remaining)
Job #1, processed 6000/10000 permutations (60.00%, 15.42608086268107 seconds remaining)
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Job #1, processed 6030/10000 permutations (60.30%, 15.295334061975307 seconds remaining)
Job #1, processed 6040/10000 permutations (60.40%, 15.251070641523956 seconds remaining)
Job #1, processed 6050/10000 permutations (60.50%, 15.206157430144382 seconds remaining)
Job #1, processed 6060/10000 permutations (60.60%, 15.161193373179671 seconds remaining)
Job #1, processed 6070/10000 permutations (60.70%, 15.116864887847145 seconds remaining)
Job #1, processed 6080/10000 permutations (60.80%, 15.08134293242505 seconds remaining)
Job #1, processed 6090/10000 permutations (60.90%, 15.041395919076328 seconds remaining)
Job #1, processed 6100/10000 permutations (61.00%, 15.001909873524651 seconds remaining)
Job #1, processed 6110/10000 permutations (61.10%, 14.961331113855888 seconds remaining)
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Job #1, processed 6140/10000 permutations (61.40%, 14.852535789098336 seconds remaining)
Job #1, processed 6150/10000 permutations (61.50%, 14.819796420694367 seconds remaining)
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Job #1, processed 6170/10000 permutations (61.70%, 14.742026893594081 seconds remaining)
Job #1, processed 6180/10000 permutations (61.80%, 14.706070661544802 seconds remaining)
Job #1, processed 6190/10000 permutations (61.90%, 14.673124673100782 seconds remaining)
Job #1, processed 6200/10000 permutations (62.00%, 14.642561635663432 seconds remaining)
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Job #1, processed 6220/10000 permutations (62.20%, 14.591117514674684 seconds remaining)
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Job #1, processed 6240/10000 permutations (62.40%, 14.516673247019451 seconds remaining)
Job #1, processed 6250/10000 permutations (62.50%, 14.46792197227478 seconds remaining)
Job #1, processed 6260/10000 permutations (62.60%, 14.423367413469016 seconds remaining)
Job #1, processed 6270/10000 permutations (62.70%, 14.37762941698138 seconds remaining)
Job #1, processed 6280/10000 permutations (62.80%, 14.334642507468061 seconds remaining)
Job #1, processed 6290/10000 permutations (62.90%, 14.290867805480957 seconds remaining)
Job #1, processed 6300/10000 permutations (63.00%, 14.245776778175719 seconds remaining)
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Job #1, processed 6320/10000 permutations (63.20%, 14.158999086935307 seconds remaining)
Job #1, processed 6330/10000 permutations (63.30%, 14.115170571476362 seconds remaining)
Job #1, processed 6340/10000 permutations (63.40%, 14.071007642084117 seconds remaining)
Job #1, processed 6350/10000 permutations (63.50%, 14.027207337026521 seconds remaining)
Job #1, processed 6360/10000 permutations (63.60%, 13.983104392417571 seconds remaining)
Job #1, processed 6370/10000 permutations (63.70%, 13.937213480753277 seconds remaining)
Job #1, processed 6380/10000 permutations (63.80%, 13.899509640696657 seconds remaining)
Job #1, processed 6390/10000 permutations (63.90%, 13.859102592781676 seconds remaining)
Job #1, processed 6400/10000 permutations (64.00%, 13.823063492774963 seconds remaining)
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Job #1, processed 6490/10000 permutations (64.90%, 13.51763229487673 seconds remaining)
Job #1, processed 6500/10000 permutations (65.00%, 13.481511317766628 seconds remaining)
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Job #1, processed 6520/10000 permutations (65.20%, 13.39981922342733 seconds remaining)
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Job #1, processed 6560/10000 permutations (65.60%, 13.23865360457723 seconds remaining)
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Job #1, processed 6580/10000 permutations (65.80%, 13.156636815665344 seconds remaining)
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Job #1, processed 6600/10000 permutations (66.00%, 13.083878856716733 seconds remaining)
Job #1, processed 6610/10000 permutations (66.10%, 13.048021473430111 seconds remaining)
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Job #1, processed 6680/10000 permutations (66.80%, 12.83258603575701 seconds remaining)
Job #1, processed 6690/10000 permutations (66.90%, 12.800967647712145 seconds remaining)
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Job #1, processed 6720/10000 permutations (67.20%, 12.682525725591749 seconds remaining)
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Job #1, processed 6760/10000 permutations (67.60%, 12.510483970303511 seconds remaining)
Job #1, processed 6770/10000 permutations (67.70%, 12.467741305930222 seconds remaining)
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Job #1, processed 6800/10000 permutations (68.00%, 12.338168200324564 seconds remaining)
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Job #1, processed 7000/10000 permutations (70.00%, 11.571245057242256 seconds remaining)
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Job #1, processed 7070/10000 permutations (70.70%, 11.272763625904389 seconds remaining)
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Job #1, processed 7100/10000 permutations (71.00%, 11.145926438586812 seconds remaining)
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Job #1, processed 7120/10000 permutations (71.20%, 11.060939585224965 seconds remaining)
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Job #1, processed 7150/10000 permutations (71.50%, 10.972400750313605 seconds remaining)
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Job #1, processed 7170/10000 permutations (71.70%, 10.894603118071826 seconds remaining)
Job #1, processed 7180/10000 permutations (71.80%, 10.854739562382607 seconds remaining)
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Job #1, processed 7200/10000 permutations (72.00%, 10.779984063572353 seconds remaining)
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Job #1, processed 7240/10000 permutations (72.40%, 10.620166235865806 seconds remaining)
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Job #1, processed 7270/10000 permutations (72.70%, 10.493793549859046 seconds remaining)
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Job #1, processed 7290/10000 permutations (72.90%, 10.40950760134944 seconds remaining)
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Job #1, processed 7370/10000 permutations (73.70%, 10.112000427220211 seconds remaining)
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Job #1, processed 7390/10000 permutations (73.90%, 10.036945666608691 seconds remaining)
Job #1, processed 7400/10000 permutations (74.00%, 10.005027326377663 seconds remaining)
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Job #1, processed 7500/10000 permutations (75.00%, 9.632915337880451 seconds remaining)
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Job #1, processed 8000/10000 permutations (80.00%, 7.707551181316376 seconds remaining)
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Job #1, processed 8100/10000 permutations (81.00%, 7.319729033811592 seconds remaining)
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[Parallel(n_jobs=1)]: Done   1 out of   1 | elapsed:   39.4s 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:1107: 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()

• 
• 

Estimated memory usage: 1008 MB