Note
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Basic Atlas plotting¶
Plot the regions of a reference atlas (Harvard-Oxford and Juelich atlases).
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(f"Atlas ROIs are located at: {atlas_ho_filename}")
print(f"Atlas ROIs are located at: {atlas_ju_filename}")
[get_dataset_dir] Dataset found in /home/remi/nilearn_data/fsl
[get_dataset_dir] Dataset found in /home/remi/nilearn_data/fsl
Atlas ROIs are located at: /home/remi/nilearn_data/fsl/data/atlases/HarvardOxford/HarvardOxford-cort-maxprob-thr25-2mm.nii.gz
Atlas ROIs are located at: /home/remi/nilearn_data/fsl/data/atlases/Juelich/Juelich-maxprob-thr0-1mm.nii.gz
Visualizing the Harvard-Oxford atlas¶
from nilearn import plotting
plotting.plot_roi(atlas_ho_filename, title="Harvard Oxford atlas")
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x740cfb0abb80>
Visualizing the Juelich atlas¶
plotting.plot_roi(atlas_ju_filename, title="Juelich atlas")
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x740d1d6c5c10>
Visualizing the Harvard-Oxford atlas with contours¶
plotting.plot_roi(
atlas_ho_filename,
view_type="contours",
title="Harvard Oxford atlas in contours",
)
plotting.show()
/home/remi/github/nilearn/nilearn_doc_build/.tox/doc/lib/python3.9/site-packages/nilearn/plotting/displays/_axes.py:74: UserWarning: No contour levels were found within the data range.
im = getattr(ax, type)(
Visualizing the Juelich atlas with contours¶
plotting.plot_roi(
atlas_ju_filename, view_type="contours", title="Juelich atlas in contours"
)
plotting.show()
Total running time of the script: (1 minutes 6.377 seconds)
Estimated memory usage: 256 MB
