.. 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)
=============================================
First part of this example goes through different options of the
:func:`nilearn.plotting.plot_glass_brain` function (including plotting
negative values).
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.
Retrieve the data
------------------
Nilearn comes with set of functions that download public data from Internet
Let us first see where the data will be downloded and stored on our disk:
.. 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/varoquau/nilearn_data']
Let us now retrieve a motor task contrast map
corresponding to a group one-sample t-test
.. 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 downloded
stat_img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
'/home/varoquau/nilearn_data/neurovault/collection_658/image_10426.nii.gz'
Demo glass brain plotting
--------------------------
.. code-block:: default
from nilearn import plotting
# Whole brain sagittal cuts and map is thresholded at 3
plotting.plot_glass_brain(stat_img, threshold=3)
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_001.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
With a colorbar
.. code-block:: default
plotting.plot_glass_brain(stat_img, threshold=3, colorbar=True)
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_002.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Black background, and only the (x, z) cuts
.. code-block:: default
plotting.plot_glass_brain(stat_img, title='plot_glass_brain',
black_bg=True, display_mode='xz', threshold=3)
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_003.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Plotting the sign of the activation with plot_abs to False
.. code-block:: default
plotting.plot_glass_brain(stat_img, threshold=0, colorbar=True,
plot_abs=False)
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_004.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
The sign of the activation and a colorbar
.. code-block:: default
plotting.plot_glass_brain(stat_img, threshold=3,
colorbar=True, plot_abs=False)
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_005.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Different projections for the left and right hemispheres
---------------------------------------------------------
Hemispheric sagittal cuts
.. code-block:: default
plotting.plot_glass_brain(stat_img,
title='plot_glass_brain with display_mode="lzr"',
black_bg=True, display_mode='lzr', threshold=3)
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_006.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
.. code-block:: default
plotting.plot_glass_brain(stat_img, threshold=0, colorbar=True,
title='plot_glass_brain with display_mode="lyrz"',
plot_abs=False, display_mode='lyrz')
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_007.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Demo glass brain plotting with contours and with fillings
---------------------------------------------------------
To plot maps with contours, we call the plotting function into variable from
which we can use specific display features which are inherited automatically.
In this case, we focus on using add_contours
First, we initialize the plotting function into "display" and first
argument set to None since we want an empty glass brain to plotting the
statistical maps with "add_contours"
.. code-block:: default
display = plotting.plot_glass_brain(None)
# Here, we project statistical maps
display.add_contours(stat_img)
# and a title
display.title('"stat_img" on glass brain without threshold')
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_008.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Plotting with `filled=True` implies contours with fillings. Here, we are not
specifying levels
.. code-block:: default
display = plotting.plot_glass_brain(None)
# Here, we project statistical maps with filled=True
display.add_contours(stat_img, filled=True)
# and a title
display.title('Same map but with fillings in the contours')
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_009.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Here, we input specific level (cut-off) in the statistical map. In other way,
we are thresholding our statistical map
.. code-block:: default
# Here, we set the threshold using parameter called `levels` with value given
# in a list and choosing color to Red.
display = plotting.plot_glass_brain(None)
display.add_contours(stat_img, levels=[3.], colors='r')
display.title('"stat_img" on glass brain with threshold')
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_010.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Plotting with same demonstration but inlcudes now filled=True
.. code-block:: default
display = plotting.plot_glass_brain(None)
display.add_contours(stat_img, filled=True, levels=[3.], colors='r')
display.title('Same demonstration but using fillings inside contours')
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_011.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Plotting with black background, `black_bg` should be set with
`plot_glass_brain`
.. code-block:: default
# We can set black background using black_bg=True
display = plotting.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:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_012.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Black background plotting with filled in contours
.. code-block:: default
display = plotting.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:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_013.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Display contour projections in both hemispheres
-------------------------------------------------
Key argument to vary here is `display_mode` for hemispheric plotting
.. code-block:: default
# Now, display_mode is chosen as 'lr' for both hemispheric plots
display = plotting.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:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_014.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Filled contours in both hemispheric plotting, just by adding filled=True
.. code-block:: default
display = plotting.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:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_015.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
With positive and negative sign of activations with `plot_abs` in
`plot_glass_brain`
.. code-block:: default
# By default parameter `plot_abs` is True and sign of activations can be
# displayed by changing `plot_abs` to False
display = plotting.plot_glass_brain(None, plot_abs=False, display_mode='lzry')
display.add_contours(stat_img)
display.title("Contours with both sign of activations without threshold")
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_016.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Now, adding just filled=True to get positive and negative sign activations
with fillings in the contours
.. code-block:: default
display = plotting.plot_glass_brain(None, plot_abs=False, display_mode='lzry')
display.add_contours(stat_img, filled=True)
display.title("Filled contours with both sign of activations without threshold")
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_017.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Displaying both signs (positive and negative) of activations with threshold
meaning thresholding by adding an argument `levels` in add_contours.
.. code-block:: default
import numpy as np
display = plotting.plot_glass_brain(None, plot_abs=False, display_mode='lzry')
# In 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.
display.add_contours(stat_img, levels=[-2.8, 3.], colors=['b', 'r'],
linewidths=4.)
display.title('Contours with sign of activations with threshold')
.. image:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_018.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
Same display demonstration as above but just adding filled=True to get
fillings inside the contours.
.. code-block:: default
# 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 parametes used as above
display = plotting.plot_glass_brain(None, plot_abs=False, display_mode='lzry')
# Second, we plot negative sign of activation with levels given as negative
# activation value in a list. Upper bound should be kept to -infinity
display.add_contours(stat_img, filled=True, levels=[-np.inf, -2.8],
colors='b')
# Next, within same plotting object we plot positive sign of activation
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:: /auto_examples/01_plotting/images/sphx_glr_plot_demo_glass_brain_extensive_019.png
:alt: plot demo glass brain extensive
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-timing
**Total running time of the script:** ( 0 minutes 14.376 seconds)
.. _sphx_glr_download_auto_examples_01_plotting_plot_demo_glass_brain_extensive.py:
.. only :: html
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:download:`Download Python source code: plot_demo_glass_brain_extensive.py `
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