.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/05_glm_second_level/plot_second_level_association_test.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_05_glm_second_level_plot_second_level_association_test.py: Example of generic design in second-level models ================================================ This example shows the results obtained in a group analysis using a more complex contrast than a one- or two-sample t test. We use the [left button press (auditory cue)] task from the Localizer dataset and seek association between the contrast values and a variate that measures the speed of pseudo-word reading. No confounding variate is included in the model. .. GENERATED FROM PYTHON SOURCE LINES 14-15 At first, we need to load the Localizer contrasts. .. GENERATED FROM PYTHON SOURCE LINES 15-23 .. code-block:: Python from nilearn.datasets import fetch_localizer_contrasts n_samples = 94 localizer_dataset = fetch_localizer_contrasts( ["left button press (auditory cue)"], n_subjects=n_samples, ) .. rst-class:: sphx-glr-script-out .. code-block:: none [fetch_localizer_contrasts] Dataset found in /home/runner/nilearn_data/brainomics_localizer [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d27da3a114a4200190453ab/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d27ebc3114a42001704a18d/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d27f1f0114a42001804603e/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28092e45253a001c3e597f/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d281a531c5b4a001c9ea662/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28295aa26b340018087ef4/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d283473a26b34001609ed88/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d284374114a42001605f4d2/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28590d114a4200160607da/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d285a53114a4200160608be/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d286f35a26b34001908e5c1/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2888ce1c5b4a001b9f789c/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d289b2945253a00193d32ac/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28a00245253a001c3efac9/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28bc0145253a00193d53ab/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28cfd91c5b4a001c9f404d/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28db3ba26b34001808f444/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28f0bc1c5b4a001b9fd7f3/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d28ffc245253a00193d7dac/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2909cd1c5b4a001b9fe6c5/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2919e2114a42001606b46c/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2928bc45253a001b3cf010/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d293a50a26b34001909682a/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d29492fa26b34001709070f/ ... [fetch_localizer_contrasts] ...done. (3 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d295328114a42001606dd9a/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2c37031c5b4a001ca0da2b/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2c442e114a420017071134/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2c5c431c5b4a001da257a5/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2c6c2645253a001c42460f/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2ec286251f0e001604a189/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2ed2875d2cdc001702b4c5/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d341711a667db0017fc816f/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d34294d835aff001958add9/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2ef8925d2cdc001702e0a5/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f0851251f0e0018044fe4/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f26e4a667db0017f72ae9/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f358c251f0e001704a76a/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f41d2835aff001a52da0c/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f5acc835aff0018532004/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f692d835aff00175372e9/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f7456835aff0017537992/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f8881a667db0018f6b634/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2f9552251f0e001605bb64/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2faf785d2cdc0017039bb1/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2fbffd835aff0018535ef5/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2fc225a667db001af6222a/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2fdd77835aff00195494d4/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2fe5d5a667db0017f80f32/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d2ff3ea835aff0018538140/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d301049a667db0019f67ca0/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3021b65d2cdc00190344d6/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d302afe5d2cdc0018030034/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d303ad4835aff001853bca4/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d304f845d2cdc001a032801/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3058cd835aff001853d4c7/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d306f15a667db0018f78b4d/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d307f8b251f0e00190519ca/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d309cb5251f0e001606fe4b/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d30a667251f0e00190534dc/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d30bb07251f0e001705df42/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d30df37251f0e001705fd72/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d30e232a667db0018f7f2a9/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d30f7ec251f0e001805e3cd/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3116dca667db0018f81c29/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d312688251f0e0016079f29/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3134fe5d2cdc001705393d/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3143f9835aff00195630ce/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d315ac0835aff001754e139/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3160bc835aff00195649cf/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d317bb2251f0e001608002e/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d318a6c251f0e001905b6ed/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d31962da667db0017fa303d/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d31abe45d2cdc0019046202/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d31cdeea667db001af75ab9/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d31dc83835aff001956e6c5/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d31fefea667db0018f8ea9f/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d32072b5d2cdc0018043969/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3219b4a667db0018f8ff1f/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3234f3835aff00175590f0/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d323d06251f0e001706f0be/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d324e77251f0e001806e5e7/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d326b70835aff00195762f8/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d32731a5d2cdc001a0472bb/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3286b7251f0e001906427f/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3298815d2cdc001804700c/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d32ab6ea667db0017fb59e8/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d32bb275d2cdc001a049841/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d32d901a667db0018f9684f/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d32e9d3835aff001957cd79/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d32f34f835aff001755ee97/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d3306db5d2cdc001706c36f/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d332373251f0e001609acbd/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) [fetch_localizer_contrasts] Downloading data from https://osf.io/download/5d332b7e835aff001957feec/ ... [fetch_localizer_contrasts] ...done. (2 seconds, 0 min) .. GENERATED FROM PYTHON SOURCE LINES 24-25 Let's print basic information on the dataset. .. GENERATED FROM PYTHON SOURCE LINES 25-30 .. code-block:: Python print( "First contrast nifti image (3D) is located " f"at: {localizer_dataset.cmaps[0]}" ) .. rst-class:: sphx-glr-script-out .. code-block:: none First contrast nifti image (3D) is located at: /home/runner/nilearn_data/brainomics_localizer/brainomics_data/S01/cmaps_LeftAuditoryClick.nii.gz .. GENERATED FROM PYTHON SOURCE LINES 31-32 we also need to load the behavioral variable. .. GENERATED FROM PYTHON SOURCE LINES 32-35 .. code-block:: Python tested_var = localizer_dataset.ext_vars["pseudo"] print(tested_var) .. rst-class:: sphx-glr-script-out .. code-block:: none 0 15.0 1 16.0 2 14.0 3 19.0 4 16.0 ... 89 12.0 90 16.0 91 13.0 92 25.0 93 21.0 Name: pseudo, Length: 94, dtype: float64 .. GENERATED FROM PYTHON SOURCE LINES 36-37 It is worth to do a quality check and remove subjects with missing values. .. GENERATED FROM PYTHON SOURCE LINES 37-47 .. code-block:: Python import numpy as np mask_quality_check = np.where(np.logical_not(np.isnan(tested_var)))[0] n_samples = mask_quality_check.size contrast_map_filenames = [ localizer_dataset.cmaps[i] for i in mask_quality_check ] tested_var = tested_var[mask_quality_check].to_numpy().reshape((-1, 1)) print(f"Actual number of subjects after quality check: {int(n_samples)}") .. rst-class:: sphx-glr-script-out .. code-block:: none Actual number of subjects after quality check: 89 .. GENERATED FROM PYTHON SOURCE LINES 48-52 Estimate second level model --------------------------- We define the input maps and the design matrix for the second level model and fit it. .. GENERATED FROM PYTHON SOURCE LINES 52-59 .. code-block:: Python import pandas as pd design_matrix = pd.DataFrame( np.hstack((tested_var, np.ones_like(tested_var))), columns=["fluency", "intercept"], ) .. GENERATED FROM PYTHON SOURCE LINES 60-61 Fit of the second-level model .. GENERATED FROM PYTHON SOURCE LINES 61-66 .. code-block:: Python from nilearn.glm.second_level import SecondLevelModel model = SecondLevelModel(smoothing_fwhm=5.0, n_jobs=2) model.fit(contrast_map_filenames, design_matrix=design_matrix) .. raw:: html 
Second Level Model
In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook.
On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.


.. GENERATED FROM PYTHON SOURCE LINES 67-69 To estimate the :term:`contrast` is very simple. We can just provide the column name of the design matrix. .. GENERATED FROM PYTHON SOURCE LINES 69-71 .. code-block:: Python z_map = model.compute_contrast("fluency", output_type="z_score") .. GENERATED FROM PYTHON SOURCE LINES 72-73 We compute the fdr-corrected p = 0.05 threshold for these data. .. GENERATED FROM PYTHON SOURCE LINES 73-77 .. code-block:: Python from nilearn.glm import threshold_stats_img _, threshold = threshold_stats_img(z_map, alpha=0.05, height_control="fdr") .. GENERATED FROM PYTHON SOURCE LINES 78-79 Let us plot the second level :term:`contrast` at the computed thresholds. .. GENERATED FROM PYTHON SOURCE LINES 79-94 .. code-block:: Python from nilearn.plotting import plot_stat_map, show cut_coords = [10, -5, 10] plot_stat_map( z_map, threshold=threshold, title="Group-level association between motor activity \n" "and reading fluency (fdr=0.05)", cut_coords=cut_coords, draw_cross=False, ) show() .. image-sg:: /auto_examples/05_glm_second_level/images/sphx_glr_plot_second_level_association_test_001.png :alt: plot second level association test :srcset: /auto_examples/05_glm_second_level/images/sphx_glr_plot_second_level_association_test_001.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 95-97 Computing the (corrected) p-values with parametric test to compare with non parametric test .. GENERATED FROM PYTHON SOURCE LINES 97-106 .. code-block:: Python from nilearn.image import get_data, math_img p_val = model.compute_contrast("fluency", output_type="p_value") n_voxels = np.sum(get_data(model.masker_.mask_img_)) # Correcting the p-values for multiple testing and taking negative logarithm neg_log_pval = math_img( f"-np.log10(np.minimum(1, img * {n_voxels!s}))", img=p_val ) .. rst-class:: sphx-glr-script-out .. code-block:: none :1: RuntimeWarning: divide by zero encountered in log10 .. GENERATED FROM PYTHON SOURCE LINES 107-108 Let us plot the (corrected) negative log p-values for the parametric test .. GENERATED FROM PYTHON SOURCE LINES 108-130 .. code-block:: Python # Since we are plotting negative log p-values and using a threshold equal to 1, # it corresponds to corrected p-values lower than 10%, meaning that there # is less than 10% probability to make a single false discovery # (90% chance that we make no false discoveries at all). # This threshold is much more conservative than the previous one. threshold = 1 title = ( "Group-level association between motor activity and reading: \n" "neg-log of parametric corrected p-values (FWER < 10%)" ) plot_stat_map( neg_log_pval, cut_coords=cut_coords, threshold=threshold, title=title, vmin=threshold, cmap="inferno", draw_cross=False, ) show() .. image-sg:: /auto_examples/05_glm_second_level/images/sphx_glr_plot_second_level_association_test_002.png :alt: plot second level association test :srcset: /auto_examples/05_glm_second_level/images/sphx_glr_plot_second_level_association_test_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out .. code-block:: none /home/runner/work/nilearn/nilearn/examples/05_glm_second_level/plot_second_level_association_test.py:119: UserWarning: Non-finite values detected. These values will be replaced with zeros. plot_stat_map( .. GENERATED FROM PYTHON SOURCE LINES 131-132 Computing the (corrected) negative log p-values with permutation test .. GENERATED FROM PYTHON SOURCE LINES 132-146 .. code-block:: Python from nilearn.glm.second_level import non_parametric_inference neg_log_pvals_permuted_ols_unmasked = non_parametric_inference( contrast_map_filenames, design_matrix=design_matrix, second_level_contrast="fluency", model_intercept=True, n_perm=1000, two_sided_test=False, mask=None, smoothing_fwhm=5.0, n_jobs=2, ) .. GENERATED FROM PYTHON SOURCE LINES 147-148 Let us plot the (corrected) negative log p-values .. GENERATED FROM PYTHON SOURCE LINES 148-167 .. code-block:: Python title = ( "Group-level association between motor activity and reading: \n" "neg-log of non-parametric corrected p-values (FWER < 10%)" ) plot_stat_map( neg_log_pvals_permuted_ols_unmasked, cut_coords=cut_coords, threshold=threshold, title=title, vmin=threshold, cmap="inferno", draw_cross=False, ) show() # The neg-log p-values obtained with non parametric testing are capped at 3 # since the number of permutations is 1e3. # The non parametric test yields a few more discoveries # and is then more powerful than the usual parametric procedure. .. image-sg:: /auto_examples/05_glm_second_level/images/sphx_glr_plot_second_level_association_test_003.png :alt: plot second level association test :srcset: /auto_examples/05_glm_second_level/images/sphx_glr_plot_second_level_association_test_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** (3 minutes 21.686 seconds) **Estimated memory usage:** 108 MB .. _sphx_glr_download_auto_examples_05_glm_second_level_plot_second_level_association_test.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/0.12.0?urlpath=lab/tree/notebooks/auto_examples/05_glm_second_level/plot_second_level_association_test.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_second_level_association_test.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_second_level_association_test.py ` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: plot_second_level_association_test.zip ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_