9.1.2. Basic nilearn example: manipulating and looking at data

A simple example showing how to load an existing Nifti file and use basic nilearn functionalities.

# Let us use a Nifti file that is shipped with nilearn
from nilearn.datasets import MNI152_FILE_PATH

# Note that the variable MNI152_FILE_PATH is just a path to a Nifti file
print('Path to MNI152 template: %r' % MNI152_FILE_PATH)

Out:

Path to MNI152 template: '/home/varoquau/dev/nilearn/nilearn/datasets/data/avg152T1_brain.nii.gz'

9.1.2.1. A first step: looking at our data

Let’s quickly plot this file:

from nilearn import plotting
plotting.plot_img(MNI152_FILE_PATH)

Out:

<nilearn.plotting.displays.OrthoSlicer object at 0x7f8bfc7ac700>

This is not a very pretty plot. We just used the simplest possible code. There is a whole section of the documentation on making prettier code.

Exercise: Try plotting one of your own files. In the above, MNI152_FILE_PATH is nothing more than a string with a path pointing to a nifti image. You can replace it with a string pointing to a file on your disk. Note that it should be a 3D volume, and not a 4D volume.

9.1.2.2. Simple image manipulation: smoothing

Let’s use an image-smoothing function from nilearn: nilearn.image.smooth_img

Functions containing ‘img’ can take either a filename or an image as input.

Here we give as inputs the image filename and the smoothing value in mm

from nilearn import image
smooth_anat_img = image.smooth_img(MNI152_FILE_PATH, fwhm=3)

# While we are giving a file name as input, the function returns
# an in-memory object:
smooth_anat_img

Out:

<nibabel.nifti1.Nifti1Image object at 0x7f8c0e747730>

This is an in-memory object. We can pass it to nilearn function, for instance to look at it

plotting.plot_img(smooth_anat_img)

Out:

<nilearn.plotting.displays.OrthoSlicer object at 0x7f8bfc73dc40>

We could also pass it to the smoothing function

more_smooth_anat_img = image.smooth_img(smooth_anat_img, fwhm=3)
plotting.plot_img(more_smooth_anat_img)

Out:

<nilearn.plotting.displays.OrthoSlicer object at 0x7f8bfc6f6f70>

9.1.2.3. Saving results to a file

We can save any in-memory object as follows:

more_smooth_anat_img.to_filename('more_smooth_anat_img.nii.gz')

Finally, calling plotting.show() is necessary to display the figure when running as a script outside IPython

plotting.show()

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To recap, all the nilearn tools can take data as filenames or in-memory objects, and return brain volumes as in-memory objects. These can be passed on to other nilearn tools, or saved to disk.