Note
Go to the end to download the full example code. or to run this example in your browser via Binder
Computing a connectome with sparse inverse covariance¶
This example constructs a functional connectome using the sparse inverse covariance.
We use the MSDL atlas
of functional regions in movie watching, and the
NiftiMapsMasker
to extract time series.
Note that the inverse covariance (or precision) contains values that can be linked to negated partial correlations, so we negated it for display.
As the MSDL atlas comes with (x, y, z) MNI coordinates for the different regions, we can visualize the matrix as a graph of interaction in a brain. To avoid having too dense a graph, we represent only the 20% edges with the highest values.
Note
If you are using Nilearn with a version older than 0.9.0
,
then you should either upgrade your version or import maskers
from the input_data
module instead of the maskers
module.
That is, you should manually replace in the following example all occurrences of:
from nilearn.maskers import NiftiMasker
with:
from nilearn.input_data import NiftiMasker
Retrieve the atlas and the data¶
from nilearn.datasets import fetch_atlas_msdl, fetch_development_fmri
atlas = fetch_atlas_msdl()
# Loading atlas image stored in 'maps'
atlas_filename = atlas["maps"]
# Loading atlas data stored in 'labels'
labels = atlas["labels"]
# Loading the functional datasets
data = fetch_development_fmri(n_subjects=1)
# print basic information on the dataset
print(f"First subject functional nifti images (4D) are at: {data.func[0]}")
[fetch_atlas_msdl] Dataset found in /home/runner/nilearn_data/msdl_atlas
[fetch_development_fmri] Dataset found in
/home/runner/nilearn_data/development_fmri
[fetch_development_fmri] Dataset found in
/home/runner/nilearn_data/development_fmri/development_fmri
[fetch_development_fmri] Dataset found in
/home/runner/nilearn_data/development_fmri/development_fmri
First subject functional nifti images (4D) are at: /home/runner/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
Extract time series¶
from nilearn.maskers import NiftiMapsMasker
masker = NiftiMapsMasker(
maps_img=atlas_filename,
standardize="zscore_sample",
standardize_confounds=True,
memory="nilearn_cache",
verbose=1,
)
time_series = masker.fit_transform(data.func[0], confounds=data.confounds)
[NiftiMapsMasker.wrapped] Loading regions from
'/home/runner/nilearn_data/msdl_atlas/MSDL_rois/msdl_rois.nii'
[NiftiMapsMasker.wrapped] Resampling regions
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/sklearn/utils/_set_output.py:273: UserWarning: memory_level is currently set to 0 but a Memory object has been provided. Setting memory_level to 1.
data_to_wrap = f(self, X, *args, **kwargs)
[NiftiMapsMasker.wrapped] Finished fit
________________________________________________________________________________
[Memory] Calling nilearn.maskers.base_masker.filter_and_extract...
filter_and_extract('/home/runner/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz',
<nilearn.maskers.nifti_maps_masker._ExtractionFunctor object at 0x7fd081bedb80>, { 'allow_overlap': True,
'clean_args': None,
'clean_kwargs': {},
'cmap': 'CMRmap_r',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'keep_masked_maps': True,
'low_pass': None,
'maps_img': '/home/runner/nilearn_data/msdl_atlas/MSDL_rois/msdl_rois.nii',
'mask_img': None,
'reports': True,
'smoothing_fwhm': None,
'standardize': 'zscore_sample',
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, confounds=[ '/home/runner/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_desc-reducedConfounds_regressors.tsv'], sample_mask=None, dtype=None, memory=Memory(location=nilearn_cache/joblib), memory_level=1, verbose=1)
[NiftiMapsMasker.wrapped] Loading data from
'/home/runner/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-p
ixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'
[NiftiMapsMasker.wrapped] Extracting region signals
[NiftiMapsMasker.wrapped] Cleaning extracted signals
_______________________________________________filter_and_extract - 1.3s, 0.0min
Compute the sparse inverse covariance¶
from sklearn.covariance import GraphicalLassoCV
estimator = GraphicalLassoCV()
estimator.fit(time_series)
Display the connectome matrix¶
from nilearn.plotting import (
plot_connectome,
plot_matrix,
show,
view_connectome,
)
# Display the covariance
# The covariance can be found at estimator.covariance_
plot_matrix(
estimator.covariance_,
labels=labels,
figure=(9, 7),
vmax=1,
vmin=-1,
title="Covariance",
)

<matplotlib.image.AxesImage object at 0x7fd081a8bd30>
And now display the corresponding graph¶
coords = atlas.region_coords
plot_connectome(estimator.covariance_, coords, title="Covariance")

<nilearn.plotting.displays._projectors.OrthoProjector object at 0x7fd05e179160>
Display the sparse inverse covariance¶
we negate it to get partial correlations
plot_matrix(
-estimator.precision_,
labels=labels,
figure=(9, 7),
vmax=1,
vmin=-1,
title="Sparse inverse covariance",
)

<matplotlib.image.AxesImage object at 0x7fd059fe0a30>
And now display the corresponding graph¶
plot_connectome(
-estimator.precision_, coords, title="Sparse inverse covariance"
)
show()

3D visualization in a web browser¶
An alternative to plot_connectome
is to use
view_connectome
that gives more interactive
visualizations in a web browser. See 3D Plots of connectomes
for more details.
view = view_connectome(-estimator.precision_, coords)
# In a Jupyter notebook, if ``view`` is the output of a cell, it will
# be displayed below the cell
view
# uncomment this to open the plot in a web browser:
# view.open_in_browser()
Total running time of the script: (0 minutes 14.712 seconds)
Estimated memory usage: 1283 MB