.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/01_plotting/plot_demo_glass_brain_extensive.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_01_plotting_plot_demo_glass_brain_extensive.py: Glass brain plotting in nilearn (all options) ============================================= The first part of this example goes through different options of the :func:`~nilearn.plotting.plot_glass_brain` function (including plotting negative values). The second part goes through same options but selected of the same glass brain function but plotting is seen with contours. See :ref:`plotting` for more plotting functionalities and :ref:`Section 4.3 ` for more details about display objects in Nilearn. Also, see :func:`nilearn.datasets.fetch_neurovault_motor_task` for details about the plotting data and associated meta-data. .. GENERATED FROM PYTHON SOURCE LINES 22-29 Retrieve the data ------------------ Nilearn comes with set of functions that download public data from Internet Let us first see where the data will be downloaded and stored on our disk: .. GENERATED FROM PYTHON SOURCE LINES 29-32 .. code-block:: default from nilearn import datasets print('Datasets shipped with nilearn are stored in: %r' % datasets.get_data_dirs()) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Datasets shipped with nilearn are stored in: ['/home/nicolas/nilearn_data'] .. GENERATED FROM PYTHON SOURCE LINES 33-35 Let us now retrieve a motor task contrast map  corresponding to a group one-sample t-test .. GENERATED FROM PYTHON SOURCE LINES 35-41 .. code-block:: default motor_images = datasets.fetch_neurovault_motor_task() stat_img = motor_images.images[0] # stat_img is just the name of the file that we downloaded stat_img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none '/home/nicolas/nilearn_data/neurovault/collection_658/image_10426.nii.gz' .. GENERATED FROM PYTHON SOURCE LINES 42-51 Demo glass brain plotting -------------------------- By default, :func:`~nilearn.plotting.plot_glass_brain` uses a display mode called 'ortho' which results in three projections. It is equivalent to specify ``display_mode='ortho'`` in :func:`~nilearn.plotting.plot_glass_brain`. Note that depending on the value of ``display_mode``, different display objects are returned. Here, a :class:`~nilearn.plotting.displays.OrthoProjector` is returned. .. GENERATED FROM PYTHON SOURCE LINES 51-59 .. code-block:: default from nilearn import plotting from nilearn.plotting import plot_glass_brain # Whole brain sagittal cuts and map is thresholded at 3 plot_glass_brain(stat_img, threshold=3) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_001.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_001.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 60-62 The same figure, with a colorbar, can be produced by setting ``colorbar=True``. .. GENERATED FROM PYTHON SOURCE LINES 62-66 .. code-block:: default plot_glass_brain(stat_img, threshold=3, colorbar=True) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_002.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_002.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 67-70 Here, we show how to set a black background, and we only view sagittal and axial projections by setting ``display_mode='xz'``, which returns a :class:`~nilearn.plotting.displays.XZProjector`. .. GENERATED FROM PYTHON SOURCE LINES 70-77 .. code-block:: default plot_glass_brain( stat_img, title='plot_glass_brain', black_bg=True, display_mode='xz', threshold=3 ) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_003.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_003.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 78-82 We can also plot the sign of the activation by setting ``plot_abs=False``. Additionally, we only visualize coronal and axial projections by setting ``display_mode='yz'`` which returns a :class:`~nilearn.plotting.displays.YZProjector`. .. GENERATED FROM PYTHON SOURCE LINES 82-88 .. code-block:: default plot_glass_brain( stat_img, threshold=0, colorbar=True, plot_abs=False, display_mode='yz' ) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_004.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_004.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 89-91 Setting ``plot_abs=True`` and ``display_mode='yx'`` (returns a :class:`~nilearn.plotting.displays.YXProjector`). .. GENERATED FROM PYTHON SOURCE LINES 91-97 .. code-block:: default plot_glass_brain( stat_img, threshold=3, colorbar=True, plot_abs=False, display_mode='yx' ) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_005.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_005.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 98-107 Different projections for the left and right hemispheres --------------------------------------------------------- In the previous section we saw a few projection modes, which are controlled by setting the argument ``display_mode`` of :func:`~nilearn.plotting.plot_glass_brain`. In this section, we will show some additional possibilities. For example, setting ``display_mode='lzr'`` enables an hemispheric sagittal view. The display object returned is then a :class:`~nilearn.plotting.displays.LZRProjector`. .. GENERATED FROM PYTHON SOURCE LINES 107-114 .. code-block:: default plot_glass_brain( stat_img, title='plot_glass_brain with display_mode="lzr"', black_bg=True, display_mode='lzr', threshold=3 ) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_006.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_006.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 115-117 ``display_mode='lyrz'`` returns a :class:`~nilearn.plotting.displays.LYRZProjector` object. .. GENERATED FROM PYTHON SOURCE LINES 117-125 .. code-block:: default plot_glass_brain( stat_img, threshold=0, colorbar=True, title='plot_glass_brain with display_mode="lyrz"', plot_abs=False, display_mode='lyrz' ) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_007.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_007.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 126-133 If you are only interested in single projections, you can set ``display_mode`` to 'x' (returns a :class:`~nilearn.plotting.displays.XProjector`), 'y' (returns a :class:`~nilearn.plotting.displays.YProjector`), 'z' (returns a :class:`~nilearn.plotting.displays.ZProjector`), 'l' (returns a :class:`~nilearn.plotting.displays.LProjector`), or 'r' (returns a :class:`~nilearn.plotting.displays.RProjector`). .. GENERATED FROM PYTHON SOURCE LINES 133-140 .. code-block:: default plot_glass_brain( stat_img, threshold=0, colorbar=True, title='display_mode="x"', plot_abs=False, display_mode='x' ) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_008.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_008.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none .. GENERATED FROM PYTHON SOURCE LINES 141-156 Demo glass brain plotting with contours and with fillings --------------------------------------------------------- The display objects returned by :func:`~nilearn.plotting.plot_glass_brain` all inherit from the :class:`~nilearn.plotting.displays.OrthoProjector` and enable further customisation of the figures. In this example, we focus on using methods :meth:`~nilearn.plotting.displays.OrthoProjector.add_contours` and :meth:`~nilearn.plotting.displays.OrthoProjector.title`. First, we save the display object (here a :class:`~nilearn.plotting.displays.LZRYProjector`) into a variable named ``display``. Note that we set the first argument to ``None`` since we want an empty glass brain to plot the statistical maps with :meth:`~nilearn.plotting.displays.OrthoProjector.add_contours`. .. GENERATED FROM PYTHON SOURCE LINES 156-164 .. code-block:: default display = plot_glass_brain(None, display_mode='lzry') # Here, we project statistical maps display.add_contours(stat_img) # and add a title display.title('"stat_img" on glass brain without threshold') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_009.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_009.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 165-167 We can fill the contours by setting ``filled=True``. Note that we are not specifying levels here .. GENERATED FROM PYTHON SOURCE LINES 167-175 .. code-block:: default display = plot_glass_brain(None, display_mode='lzry') # Here, we project statistical maps with filled=True display.add_contours(stat_img, filled=True) # and add a title display.title('Same map but with fillings in the contours') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_010.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_010.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 176-182 Here, we input a specific level (cut-off) in the statistical map. In other words, we are thresholding our statistical map. We set the threshold using a parameter of method :meth:`~nilearn.plotting.displays.OrthoProjector.add_contours` called ``levels`` which value is given as a list and we choose the color to be red. .. GENERATED FROM PYTHON SOURCE LINES 182-188 .. code-block:: default display = plot_glass_brain(None, display_mode='lzry') display.add_contours(stat_img, levels=[3.], colors='r') display.title('"stat_img" on glass brain with threshold') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_011.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_011.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 189-191 Plotting with same demonstration but fill the contours (by setting ``filled=True``). .. GENERATED FROM PYTHON SOURCE LINES 191-197 .. code-block:: default display = plot_glass_brain(None, display_mode='lzry') display.add_contours(stat_img, filled=True, levels=[3.], colors='r') display.title('Same demonstration but using fillings inside contours') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_012.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_012.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 198-200 Plotting with black background, ``black_bg`` should be set to ``True`` through :func:`~nilearn.plotting.plot_glass_brain`. .. GENERATED FROM PYTHON SOURCE LINES 200-207 .. code-block:: default # We can set black background using black_bg=True display = plot_glass_brain(None, black_bg=True) display.add_contours(stat_img, levels=[3.], colors='g') display.title('"stat_img" on glass brain with black background') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_013.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_013.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 208-209 Black background plotting with filled in contours. .. GENERATED FROM PYTHON SOURCE LINES 209-215 .. code-block:: default display = plot_glass_brain(None, black_bg=True) display.add_contours(stat_img, filled=True, levels=[3.], colors='g') display.title('Glass brain with black background and filled in contours') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_014.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_014.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 216-222 Display contour projections in both hemispheres ------------------------------------------------- The key argument to vary here is ``display_mode`` for hemispheric plotting. Here, we set ``display_mode='lr'`` for both hemispheric plots. Note that a :class:`~nilearn.plotting.displays.LRProjector` is returned. .. GENERATED FROM PYTHON SOURCE LINES 222-228 .. code-block:: default display = plot_glass_brain(None, display_mode='lr') display.add_contours(stat_img, levels=[3.], colors='r') display.title('"stat_img" on glass brain only "l" "r" hemispheres') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_015.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_015.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 229-230 Filled contours in both hemispheric plotting, by adding ``filled=True``. .. GENERATED FROM PYTHON SOURCE LINES 230-236 .. code-block:: default display = plot_glass_brain(None, display_mode='lr') display.add_contours(stat_img, filled=True, levels=[3.], colors='r') display.title('Filled contours on glass brain only "l" "r" hemispheres') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_016.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_016.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 237-244 With positive and negative signs of activations with ``plot_abs`` in :func:`~nilearn.plotting.plot_glass_brain`. By default parameter ``plot_abs`` is ``True`` and sign of activations can be displayed by changing ``plot_abs`` to ``False``. Note that we also specify ``display_mode='lyr'`` which returns a :class:`~nilearn.plotting.displays.LYRProjector` display object. .. GENERATED FROM PYTHON SOURCE LINES 244-250 .. code-block:: default display = plot_glass_brain(None, plot_abs=False, display_mode='lyr') display.add_contours(stat_img) display.title("Contours with both sign of activations without threshold") .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_017.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_017.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 251-253 Now, adding ``filled=True`` to get positive and negative sign activations with fillings in the contours. .. GENERATED FROM PYTHON SOURCE LINES 253-261 .. code-block:: default display = plot_glass_brain(None, plot_abs=False, display_mode='lyr') display.add_contours(stat_img, filled=True) display.title( "Filled contours with both sign of activations without threshold" ) .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_018.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_018.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 262-272 Displaying both signs (positive and negative) of activations with threshold meaning thresholding by adding an argument ``levels`` in method :meth:`~nilearn.plotting.displays.OrthoProjector.add_contours`. We give two values through the argument ``levels`` which corresponds to the thresholds of the contour we want to draw: One is positive and the other one is negative. We give a list of ``colors`` as argument to associate a different color to each contour. Additionally, we also choose to plot contours with thick line widths. For ``linewidths``, one value would be enough so that same value is used for both contours. .. GENERATED FROM PYTHON SOURCE LINES 272-281 .. code-block:: default import numpy as np display = plot_glass_brain(None, plot_abs=False, display_mode='lzry') display.add_contours( stat_img, levels=[-2.8, 3.], colors=['b', 'r'], linewidths=4. ) display.title('Contours with sign of activations with threshold') .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_019.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_019.png :class: sphx-glr-single-img .. GENERATED FROM PYTHON SOURCE LINES 282-292 Same display demonstration as above but adding ``filled=True`` to get fillings inside the contours. Unlike in previous plot, here we specify each sign at a time. We call negative values display first followed by positive values display. First, we fetch our display object with same parameters used as above. Then, we plot negative sign of activation with levels given as negative activation value in a list. Upper bound should be kept to -infinity. Next, using the same display object, we plot positive sign of activation. .. GENERATED FROM PYTHON SOURCE LINES 292-303 .. code-block:: default display = plot_glass_brain(None, plot_abs=False, display_mode='lzry') display.add_contours( stat_img, filled=True, levels=[-np.inf, -2.8], colors='b' ) display.add_contours( stat_img, filled=True, levels=[3.], colors='r' ) display.title('Now same plotting but with filled contours') # Finally, displaying them plotting.show() .. image-sg:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_020.png :alt: plot demo glass brain extensive :srcset: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_020.png :class: sphx-glr-single-img .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 0 minutes 27.856 seconds) **Estimated memory usage:** 9 MB .. _sphx_glr_download_auto_examples_01_plotting_plot_demo_glass_brain_extensive.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/01_plotting/plot_demo_glass_brain_extensive.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_demo_glass_brain_extensive.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_demo_glass_brain_extensive.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_