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%matplotlib inline

3D and 4D niimgs: handling and visualizing

Here we discover how to work with 3D and 4D niimgs.

Downloading tutorial datasets from Internet

Nilearn comes with functions that download public data from Internet

Let's first check where the data is downloaded on our disk:



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from nilearn import datasets
print('Datasets are stored in: %r' % datasets.get_data_dirs())

Let's now retrieve a motor contrast from a localizer experiment



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tmap_filenames = datasets.fetch_localizer_button_task()['tmaps']
print(tmap_filenames)

tmap_filenames is a list of filenames. We need to take the first one



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tmap_filename = tmap_filenames[0]

Visualizing a 3D file

The file contains a 3D volume, we can easily visualize it as a statistical map:



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from nilearn import plotting
plotting.plot_stat_map(tmap_filename)

Visualizing works better with a threshold



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plotting.plot_stat_map(tmap_filename, threshold=3)

Visualizing one volume in a 4D file

We can download resting-state networks from the Smith 2009 study on correspondance between rest and task



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rsn = datasets.fetch_atlas_smith_2009()['rsn10']
print(rsn)

It is a 4D nifti file. We load it into the memory to print its shape.



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from nilearn import image
print(image.load_img(rsn).shape)

We can retrieve the first volume (note that Python indexing starts at 0):



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first_rsn = image.index_img(rsn, 0)
print(first_rsn.shape)

first_rsn is a 3D image.

We can then plot it



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plotting.plot_stat_map(first_rsn)

Looping on all volumes in a 4D file

If we want to plot all the volumes in this 4D file, we can use iter_img to loop on them.

Then we give a few arguments to plot_stat_map in order to have a more compact display.



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for img in image.iter_img(rsn):
    # img is now an in-memory 3D img
    plotting.plot_stat_map(img, threshold=3, display_mode="z", cut_coords=1,
                           colorbar=False)

plotting.show is useful to force the display of figures when running outside IPython



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plotting.show()

To recap, neuroimaging images (niimgs as we call them) come in different flavors:

3D images, containing only one brain volume
4D images, containing multiple brain volumes.

More details about the input formats in nilearn for 3D and 4D images is given in the documentation section: loading_data.

Functions accept either 3D or 4D images, and we need to use on the one hand :func:nilearn.image.index_img or :func:nilearn.image.iter_img to break down 4D images into 3D images, and on the other hand :func:nilearn.image.concat_imgs to group a list of 3D images into a 4D image.