.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/04_glm_first_level/plot_design_matrix.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note Click :ref:`here ` 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_04_glm_first_level_plot_design_matrix.py: Examples of design matrices =========================== Three examples of design matrices specification and computation for first-level fMRI data analysis (event-related design, block design, FIR design). This examples requires matplotlib. .. GENERATED FROM PYTHON SOURCE LINES 11-17 .. code-block:: default try: import matplotlib.pyplot as plt except ImportError: raise RuntimeError("This script needs the matplotlib library") .. GENERATED FROM PYTHON SOURCE LINES 18-21 Define parameters ---------------------------------- At first, we define parameters related to the images acquisition. .. GENERATED FROM PYTHON SOURCE LINES 21-26 .. code-block:: default import numpy as np tr = 1.0 # repetition time is 1 second n_scans = 128 # the acquisition comprises 128 scans frame_times = np.arange(n_scans) * tr # here are the corresponding frame times .. GENERATED FROM PYTHON SOURCE LINES 27-28 Then we define parameters related to the experimental design. .. GENERATED FROM PYTHON SOURCE LINES 28-40 .. code-block:: default # these are the types of the different trials conditions = ['c0', 'c0', 'c0', 'c1', 'c1', 'c1', 'c3', 'c3', 'c3'] duration = [1., 1., 1., 1., 1., 1., 1., 1., 1.] # these are the corresponding onset times onsets = [30., 70., 100., 10., 30., 90., 30., 40., 60.] # Next, we simulate 6 motion parameters jointly observed with fMRI acquisitions motion = np.cumsum(np.random.randn(n_scans, 6), 0) # The 6 parameters correspond to three translations and three # rotations describing rigid body motion add_reg_names = ['tx', 'ty', 'tz', 'rx', 'ry', 'rz'] .. GENERATED FROM PYTHON SOURCE LINES 41-45 Create design matrices ------------------------------------- The same parameters allow us to obtain a variety of design matrices. We first create an events object. .. GENERATED FROM PYTHON SOURCE LINES 45-49 .. code-block:: default import pandas as pd events = pd.DataFrame({'trial_type': conditions, 'onset': onsets, 'duration': duration}) .. GENERATED FROM PYTHON SOURCE LINES 50-52 We sample the events into a design matrix, also including additional regressors. .. GENERATED FROM PYTHON SOURCE LINES 52-58 .. code-block:: default hrf_model = 'glover' from nilearn.glm.first_level import make_first_level_design_matrix X1 = make_first_level_design_matrix( frame_times, events, drift_model='polynomial', drift_order=3, add_regs=motion, add_reg_names=add_reg_names, hrf_model=hrf_model) .. GENERATED FROM PYTHON SOURCE LINES 59-62 Now we compute a block design matrix. We add duration to create the blocks. For this we first define an event structure that includes the duration parameter. .. GENERATED FROM PYTHON SOURCE LINES 62-66 .. code-block:: default duration = 7. * np.ones(len(conditions)) events = pd.DataFrame({'trial_type': conditions, 'onset': onsets, 'duration': duration}) .. GENERATED FROM PYTHON SOURCE LINES 67-68 Then we sample the design matrix. .. GENERATED FROM PYTHON SOURCE LINES 68-72 .. code-block:: default X2 = make_first_level_design_matrix(frame_times, events, drift_model='polynomial', drift_order=3, hrf_model=hrf_model) .. GENERATED FROM PYTHON SOURCE LINES 73-74 Finally we compute a FIR model .. GENERATED FROM PYTHON SOURCE LINES 74-81 .. code-block:: default events = pd.DataFrame({'trial_type': conditions, 'onset': onsets, 'duration': duration}) hrf_model = 'FIR' X3 = make_first_level_design_matrix(frame_times, events, hrf_model='fir', drift_model='polynomial', drift_order=3, fir_delays=np.arange(1, 6)) .. GENERATED FROM PYTHON SOURCE LINES 82-83 Here are the three designs side by side. .. GENERATED FROM PYTHON SOURCE LINES 83-92 .. code-block:: default from nilearn.plotting import plot_design_matrix fig, (ax1, ax2, ax3) = plt.subplots(figsize=(10, 6), nrows=1, ncols=3) plot_design_matrix(X1, ax=ax1) ax1.set_title('Event-related design matrix', fontsize=12) plot_design_matrix(X2, ax=ax2) ax2.set_title('Block design matrix', fontsize=12) plot_design_matrix(X3, ax=ax3) ax3.set_title('FIR design matrix', fontsize=12) .. image-sg:: /auto_examples/04_glm_first_level/images/sphx_glr_plot_design_matrix_001.png :alt: Event-related design matrix, Block design matrix, FIR design matrix :srcset: /auto_examples/04_glm_first_level/images/sphx_glr_plot_design_matrix_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Text(0.5, 1.1753015208063937, 'FIR design matrix') .. GENERATED FROM PYTHON SOURCE LINES 93-94 Let's improve the layout and show the result. .. GENERATED FROM PYTHON SOURCE LINES 94-96 .. code-block:: default plt.subplots_adjust(left=0.08, top=0.9, bottom=0.21, right=0.96, wspace=0.3) plt.show() .. image-sg:: /auto_examples/04_glm_first_level/images/sphx_glr_plot_design_matrix_002.png :alt: plot design matrix :srcset: /auto_examples/04_glm_first_level/images/sphx_glr_plot_design_matrix_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 4.543 seconds) **Estimated memory usage:** 9 MB .. _sphx_glr_download_auto_examples_04_glm_first_level_plot_design_matrix.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/nilearn/nilearn.github.io/main?filepath=examples/auto_examples/04_glm_first_level/plot_design_matrix.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_design_matrix.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_design_matrix.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_