.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/07_advanced/plot_localizer_simple_analysis.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. or to run this example in your browser via Binder .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_07_advanced_plot_localizer_simple_analysis.py: Massively univariate analysis of a calculation task from the Localizer dataset ============================================================================== This example shows how to use the Localizer dataset in a basic analysis. A standard Anova is performed (massively univariate F-test) and the resulting Bonferroni-corrected p-values are plotted. We use a calculation task and 20 subjects out of the 94 available. The Localizer dataset contains many contrasts and subject-related variates. The user can refer to the `plot_localizer_mass_univariate_methods.py` example to see how to use these. .. GENERATED FROM PYTHON SOURCE LINES 14-21 .. code-block:: Python from nilearn._utils.helpers import check_matplotlib check_matplotlib() import matplotlib.pyplot as plt .. GENERATED FROM PYTHON SOURCE LINES 22-28 .. code-block:: Python import numpy as np from nilearn import datasets from nilearn.image import get_data from nilearn.maskers import NiftiMasker .. GENERATED FROM PYTHON SOURCE LINES 29-30 Load Localizer contrast .. GENERATED FROM PYTHON SOURCE LINES 30-36 .. code-block:: Python n_samples = 20 localizer_dataset = datasets.fetch_localizer_calculation_task( n_subjects=n_samples ) tested_var = np.ones((n_samples, 1)) .. rst-class:: sphx-glr-script-out .. code-block:: none [fetch_localizer_calculation_task] Dataset found in /home/runner/nilearn_data/brainomics_localizer .. GENERATED FROM PYTHON SOURCE LINES 37-38 Mask data .. GENERATED FROM PYTHON SOURCE LINES 38-44 .. code-block:: Python nifti_masker = NiftiMasker( smoothing_fwhm=5, memory="nilearn_cache", memory_level=1, verbose=1 ) cmap_filenames = localizer_dataset.cmaps fmri_masked = nifti_masker.fit_transform(cmap_filenames) .. rst-class:: sphx-glr-script-out .. code-block:: none \[NiftiMasker.wrapped] Loading data from ['/home/runner/nilearn_data/brainomics_ localizer/brainomics_data/S01/cmaps_Auditory&VisualCalculation.nii.gz', '/home/r unner/nilearn_data/brainomics_localizer/brainomics_data/S02/cmaps_Auditory&Visua lCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics _data/S03/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/b rainomics_localizer/brainomics_data/S04/cmaps_Auditory&VisualCalculation.nii.gz' , '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S05/cmaps_Audi tory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/ brainomics_data/S06/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nile arn_data/brainomics_localizer/brainomics_data/S07/cmaps_Auditory&VisualCalculati on.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S08/ cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_ localizer/brainomics_data/S09/cmaps_Auditory&VisualCalculation.nii.gz', '/home/r unner/nilearn_data/brainomics_localizer/brainomics_data/S10/cmaps_Auditory&Visua lCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics _data/S11/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/b rainomics_localizer/brainomics_data/S12/cmaps_Auditory&VisualCalculation.nii.gz' , '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S13/cmaps_Audi tory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/ brainomics_data/S14/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nile arn_data/brainomics_localizer/brainomics_data/S15/cmaps_Auditory&VisualCalculati on.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S16/ cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_ localizer/brainomics_data/S17/cmaps_Auditory&VisualCalculation.nii.gz', '/home/r unner/nilearn_data/brainomics_localizer/brainomics_data/S18/cmaps_Auditory&Visua lCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics _data/S19/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/b rainomics_localizer/brainomics_data/S20/cmaps_Auditory&VisualCalculation.nii.gz' ] \[NiftiMasker.wrapped] Computing mask ________________________________________________________________________________ [Memory] Calling nilearn.masking.compute_background_mask... compute_background_mask([ '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S01/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S02/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S03/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S04/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S05/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S06/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data..., verbose=0) __________________________________________compute_background_mask - 0.1s, 0.0min \[NiftiMasker.wrapped] Resampling mask ________________________________________________________________________________ [Memory] Calling nilearn.image.resampling.resample_img... resample_img(, target_affine=None, target_shape=None, copy=False, interpolation='nearest') _____________________________________________________resample_img - 0.0s, 0.0min \[NiftiMasker.wrapped] Finished fit /home/runner/work/nilearn/nilearn/examples/07_advanced/plot_localizer_simple_analysis.py:42: FutureWarning: boolean values for 'standardize' will be deprecated in nilearn 0.15.0. Use 'zscore_sample' instead of 'True' or use 'None' instead of 'False'. ________________________________________________________________________________ [Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask... filter_and_mask([ '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S01/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S02/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S03/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S04/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S05/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data/brainomics_localizer/brainomics_data/S06/cmaps_Auditory&VisualCalculation.nii.gz', '/home/runner/nilearn_data..., , { 'clean_args': None, 'clean_kwargs': {}, 'cmap': 'gray', 'detrend': False, 'dtype': None, 'high_pass': None, 'high_variance_confounds': False, 'low_pass': None, 'reports': True, 'runs': None, 'smoothing_fwhm': 5, 'standardize': False, 'standardize_confounds': True, 't_r': None, 'target_affine': None, 'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None) \[NiftiMasker.wrapped] Loading data from \[NiftiMasker.wrapped] Smoothing images \[NiftiMasker.wrapped] Extracting region signals \[NiftiMasker.wrapped] Cleaning extracted signals __________________________________________________filter_and_mask - 0.3s, 0.0min .. GENERATED FROM PYTHON SOURCE LINES 45-46 Anova (parametric F-scores) .. GENERATED FROM PYTHON SOURCE LINES 46-58 .. code-block:: Python from sklearn.feature_selection import f_regression # Center=False is used to not remove intercept _, pvals_anova = f_regression(fmri_masked, tested_var.ravel(), center=False) pvals_anova *= fmri_masked.shape[1] pvals_anova[np.isnan(pvals_anova)] = 1 pvals_anova[pvals_anova > 1] = 1 neg_log_pvals_anova = -np.log10(pvals_anova) neg_log_pvals_anova_unmasked = nifti_masker.inverse_transform( neg_log_pvals_anova ) .. rst-class:: sphx-glr-script-out .. code-block:: none \[NiftiMasker.inverse_transform] Computing image from signals ________________________________________________________________________________ [Memory] Calling nilearn.masking.unmask... unmask(array([-0., ..., -0.]), ) ___________________________________________________________unmask - 0.0s, 0.0min .. GENERATED FROM PYTHON SOURCE LINES 59-60 Visualization .. GENERATED FROM PYTHON SOURCE LINES 60-89 .. code-block:: Python from nilearn.plotting import plot_stat_map, show # Various plotting parameters plotted_slice = 45 threshold = -np.log10(0.1) # 10% corrected masked_pvals = np.ma.masked_less( get_data(neg_log_pvals_anova_unmasked), threshold ) title = ( "Negative $\\log_{10}$ p-values" "\n(Parametric + Bonferroni correction)" f"\n{(~masked_pvals.mask).sum()} detections" ) # Plot Anova p-values display = plot_stat_map( neg_log_pvals_anova_unmasked, threshold=threshold, display_mode="z", cut_coords=[plotted_slice], figure=plt.figure(figsize=(5, 6), facecolor="w"), cmap="inferno", vmin=threshold, title=title, ) show() .. image-sg:: /auto_examples/07_advanced/images/sphx_glr_plot_localizer_simple_analysis_001.png :alt: plot localizer simple analysis :srcset: /auto_examples/07_advanced/images/sphx_glr_plot_localizer_simple_analysis_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 2.837 seconds) **Estimated memory usage:** 110 MB .. _sphx_glr_download_auto_examples_07_advanced_plot_localizer_simple_analysis.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/nilearn/nilearn/0.14.0rc0?urlpath=lab/tree/notebooks/auto_examples/07_advanced/plot_localizer_simple_analysis.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_localizer_simple_analysis.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_localizer_simple_analysis.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_localizer_simple_analysis.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_