9.2.3. Basic Atlas plotting

Plot the regions of a reference atlas (Harvard-Oxford and Juelich atlases).

9.2.3.1. Retrieving the atlas data

from nilearn import datasets

dataset_ho = datasets.fetch_atlas_harvard_oxford('cort-maxprob-thr25-2mm')
dataset_ju = datasets.fetch_atlas_juelich('maxprob-thr0-1mm')

atlas_ho_filename = dataset_ho.filename
atlas_ju_filename = dataset_ju.filename

print('Atlas ROIs are located at: %s' % atlas_ho_filename)
print('Atlas ROIs are located at: %s' % atlas_ju_filename)

Out:

Atlas ROIs are located at: /home/nicolas/nilearn_data/fsl/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr25-2mm.nii.gz
Atlas ROIs are located at: /home/nicolas/nilearn_data/fsl/data/atlases/Juelich/Juelich-maxprob-thr0-1mm.nii.gz

9.2.3.2. Visualizing the Harvard-Oxford atlas

from nilearn import plotting

plotting.plot_roi(atlas_ho_filename, title="Harvard Oxford atlas")

Out:

<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7fa52d39ab80>

9.2.3.3. Visualizing the Juelich atlas

plotting.plot_roi(atlas_ju_filename, title="Juelich atlas")

Out:

<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7fa52d2e1820>

9.2.3.4. Visualizing the Harvard-Oxford atlas with contours

plotting.plot_roi(atlas_ho_filename, view_type='contours',
                  title="Harvard Oxford atlas in contours")
plotting.show()

Out:

/home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays/_axes.py:71: UserWarning: No contour levels were found within the data range.
  im = getattr(ax, type)(data_2d.copy(),

9.2.3.5. Visualizing the Juelich atlas with contours

plotting.plot_roi(atlas_ju_filename, view_type='contours',
                  title="Juelich atlas in contours")
plotting.show()

Out:

/home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays/_axes.py:71: UserWarning: No contour levels were found within the data range.
  im = getattr(ax, type)(data_2d.copy(),

Estimated memory usage: 138 MB