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8.1.2. Basic nilearn example: manipulating and looking at data

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8.1.4. A introduction tutorial to fMRI decoding

8.1.3. 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:

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


Datasets are stored in: ['/home/parietal/gvaroqua/nilearn_data']

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

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



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

tmap_filename = tmap_filenames[0] Visualizing a 3D file

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

from nilearn import plotting

Visualizing works better with a threshold

plotting.plot_stat_map(tmap_filename, threshold=3)
../_images/sphx_glr_plot_3d_and_4d_niimg_002.png Visualizing one volume in a 4D file

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

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



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

from nilearn import image


(91, 109, 91, 10)

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

first_rsn = image.index_img(rsn, 0)


(91, 109, 91)

first_rsn is a 3D image.

We can then plot it

../_images/sphx_glr_plot_3d_and_4d_niimg_003.png 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.

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,
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_004.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_005.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_006.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_007.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_008.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_009.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_010.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_011.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_012.png
  • ../_images/sphx_glr_plot_3d_and_4d_niimg_013.png is useful to force the display of figures when running outside IPython

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: Inputing data: file names or image objects.

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

Total running time of the script: ( 0 minutes 5.673 seconds)

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