More plotting tools from nilearn#
In this example, we show how to use some plotting options available with plotting functions of nilearn. These techniques are essential for visualizing brain image analysis results.
Plotting functions of Nilearn, such as
plot_stat_map, have a few useful parameters
which control what type of display object will be
returned, as well as how many cuts will be shown for example.
As we will see in the first part of this example, depending on the values of
cut_coords, plotting functions return
different display objects, all subclasses of
These objects implement various methods to interact with the figures. In the
second part of this example, we show how to use these methods to further
customize the figures obtained with plotting functions. More precisely, we
will show how to use
add_markers, all essential
in visualizing regions of interest images, or mask images overlaying on
subject specific anatomical / EPI image.
display_mode is used to draw brain slices along given
specific directions, where directions can be one of ‘ortho’,
‘tiled’, ‘mosaic’, ‘x’, ‘y’, ‘z’, ‘yx’, ‘xz’, ‘yz’. Whereas parameter
cut_coords is used to specify a limited number of slices to visualize
along given specific slice direction.
cut_coords can also be used to draw the specific cuts in
the slices by giving its particular coordinates in MNI space
accordingly with particular slice direction. This helps us point to the
activation specific location of the brain slices.
See Plotting brain images for more details.
First, we retrieve data from nilearn provided (general-purpose) datasets#
from nilearn import datasets # haxby dataset to have anatomical image, EPI images and masks haxby_dataset = datasets.fetch_haxby() haxby_anat_filename = haxby_dataset.anat haxby_mask_filename = haxby_dataset.mask_vt haxby_func_filename = haxby_dataset.func # example motor activation image distributed with nilearn stat_img = datasets.load_sample_motor_activation_image()
Now, we show from here how to visualize the retrieved datasets using plotting tools from nilearn.
from nilearn import plotting
Visualizing in - ‘sagittal’, ‘coronal’ and ‘axial’ with given coordinates#
The first argument
stat_img is a path to the filename of a contrast map.
The optional argument
display_mode is given as a string ‘ortho’ to
visualize the map in three specific directions xyz. Because of this, the
plotting function returns a
object. The optional
cut_coords argument is specified here as a list of
integers representing coordinates of each slice in the order [x, y, z].
By default the
colorbar argument is set to
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7fd1efd03850>
Visualizing in - single view ‘axial’ with number of cuts=5#
For axial visualization, we set
display_mode='z'. As a
plot_stat_map returns a
cut_coords is provided here as an integer (5) rather than
a list, which implies that the number of cuts in the slices should be 5
maximum. Note that the coordinates used to cut the slices are selected
<nilearn.plotting.displays._slicers.ZSlicer object at 0x7fd1ed44a510>
Visualizing in - single view ‘sagittal’ with only two slices#
For sagittal visualization, we set
display_mode='x' which returns a
Additionally, we provide the coordinates of the slices as a list of
<nilearn.plotting.displays._slicers.XSlicer object at 0x7fd1cf12ccd0>
Visualizing in - ‘coronal’ view with single cut#
For coronal view, we set
display_mode='y' which returns a
cut_coords is provided as an integer (1), and the coordinates are,
again, selected automatically.
<nilearn.plotting.displays._slicers.YSlicer object at 0x7fd1f2689f90>
Visualizing without a colorbar on the right side#
colorbar should be set to
False to show plots without
a colorbar on the right side.
<nilearn.plotting.displays._slicers.ZSlicer object at 0x7fd1c371fa90>
Visualize in - two views ‘sagittal’ and ‘axial’ with given coordinates#
In order to visualize both sagittal and axial views, we set
display_mode='xz', where ‘x’ stands for sagittal and ‘z’ for axial view.
plot_stat_map thus returns a
Finally, the argument
cut_coords should match with the input number of
views (two here). It is provided as a list of integers here to select the
slices to be displayed.
<nilearn.plotting.displays._slicers.XZSlicer object at 0x7fd1c4002010>
Changing the views to ‘coronal’, ‘sagittal’ views with coordinates#
Similarly, we can set
display_mode='yx' for combining a coronal with a
sagittal view, which will return a
The coordinates will be assigned in the order of direction as [x, y, z].
<nilearn.plotting.displays._slicers.YXSlicer object at 0x7fd1efd55fd0>
Now, views are changed to ‘coronal’ and ‘axial’ views with coordinates#
We can set
display_mode='yz' to combine a coronal with an axial
view, which will return a
<nilearn.plotting.displays._slicers.YZSlicer object at 0x7fd1f22a4450>
Visualizing three views in 2x2 fashion#
<nilearn.plotting.displays._slicers.TiledSlicer object at 0x7fd1fbaa15d0>
Visualizing three views along multiple rows and columns#
If we set
display_mode='mosaic', we can easily combine sagittal,
coronal, and axial views with different rows and columns. In this
plot_stat_map returns a
In addition, we show here the default option
<nilearn.plotting.displays._slicers.MosaicSlicer object at 0x7fd1efc8d550>
Now, changing the number of slices along columns#
Here, we still set
display_mode='mosaic', but we set the number of
slices to be the same across views. In this case, we can specify it as
an integer, i.e.
<nilearn.plotting.displays._slicers.MosaicSlicer object at 0x7fd1f000f5d0>
Now, another way of limiting the number of slices along rows and columns#
It can be the case that we want to display a different number of cuts in
each view. In this situation, we still set
we specify the number of slices as a tuple of length 3.
<nilearn.plotting.displays._slicers.MosaicSlicer object at 0x7fd1f27a2410>
Demonstrating various display features#
In this second part, we demonstrate how to interact with the obtained figures. More precisely, we will show how to use specific methods of the display objects which can be helpful in projecting brain imaging results for further interpretation.
Showing how to use add_edges#
Now let us see how to use the method
add_edges for checking
coregistration by overlaying anatomical image as edges (red) on top of
mean functional image (background), both being of same subject.
We then use the
method. The first argument is the anatomical image and, by default,
edges will be displayed in red (‘r’). To choose a different color, use
How to use add_contours#
As before, we call the
plot_anat function with a
background image as first argument, in this case the mean fMRI
image, and argument
cut_coords as a list for manual cuts with coordinates
pointing at masked brain regions.
We then use the
method of the display object returned by
plot_anat. We provide the path to a mask image
from the Haxby dataset as the first argument, and we provide
a list of values to select particular levels in the contour to display.
We also specify
colors='r' to display edges in red (See function
contour to use more options).
Here, we plot the outline of the mask (in blue) with color fillings using
the same method
By default, no color fillings will be shown using
add_contours. To see
contours with color fillings, use argument
filled=True. Here, contour
colors are changed to blue ‘b’, and we specify
alpha=0.7 to set the
transparency of the fillings.
contourf to use more options (given
filled should be
Plotting seeds using add_markers#
The coordinates of the seed regions should be specified as the first
argument, and second argument
marker_color is used to denote the
color of the sphere (in this case yellow ‘y’). The third argument
marker_size is used to control the size of the sphere.
It is possible to alter the default annotations of plots, using the
annotate of the
display objects. For example, we can add a scale bar at the bottom
right of each view:
Further configuration can be achieved by setting
scale_* keyword args.
For instance, we can change the
mm, or use a different
scale bar size.
Saving plots to file#
Finally, we can save a plot to file in two different ways:
First, we can save the contrast maps plotted with the function
nilearn.plotting.plot_stat_map using the built-in parameter
output_file. We provide the filename and the file extension as
a string (supported extensions are .png, .pdf, .svg).
A second way to save plots is by using the method
savefig of the display
Total running time of the script: (0 minutes 35.136 seconds)
Estimated memory usage: 914 MB