Note

Go to the end to download the full example code or to run this example in your browser via Binder

Clustering methods to learn a brain parcellation from fMRI#

We use spatially-constrained Ward-clustering, KMeans, Hierarchical KMeans and Recursive Neighbor Agglomeration (ReNA) to create a set of parcels.

In a high dimensional regime, these methods can be interesting to create a ‘compressed’ representation of the data, replacing the data in the fMRI images by mean signals on the parcellation, which can subsequently be used for statistical analysis or machine learning.

Also, these methods can be used to learn functional connectomes and subsequently for classification tasks or to analyze data at a local level.

Download a brain development fMRI dataset and turn it to a data matrix#

We download one subject of the movie watching dataset from Internet

import time

import numpy as np
from matplotlib import patches, ticker

from nilearn import datasets, plotting
from nilearn.image import get_data, index_img, mean_img
from nilearn.regions import Parcellations

dataset = datasets.fetch_development_fmri(n_subjects=1)

# print basic information on the dataset
print(f"First subject functional nifti image (4D) is at: {dataset.func[0]}")

First subject functional nifti image (4D) is at: /home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz

Brain parcellations with Ward Clustering#

Transforming list of images to data matrix and build brain parcellations, all can be done at once using Parcellations object.

# Computing ward for the first time, will be long... This can be seen by
# measuring using time
start = time.time()

# Agglomerative Clustering: ward

# We build parameters of our own for this object. Parameters related to
# masking, caching and defining number of clusters and specific parcellations
# method.
ward = Parcellations(
    method="ward",
    n_parcels=1000,
    standardize=False,
    smoothing_fwhm=2.0,
    memory="nilearn_cache",
    memory_level=1,
    verbose=1,
)
# Call fit on functional dataset: single subject (less samples).
ward.fit(dataset.func)
print(f"Ward agglomeration 1000 clusters: {time.time() - start:.2f}s")

# We compute now ward clustering with 2000 clusters and compare
# time with 1000 clusters. To see the benefits of caching for second time.

# We initialize class again with n_parcels=2000 this time.
start = time.time()
ward = Parcellations(
    method="ward",
    n_parcels=2000,
    standardize=False,
    smoothing_fwhm=2.0,
    memory="nilearn_cache",
    memory_level=1,
    verbose=1,
)
ward.fit(dataset.func)
print(f"Ward agglomeration 2000 clusters: {time.time() - start:.2f}s")

[MultiNiftiMasker.fit] Loading data from [/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz].
[{self.__class__.__name__}.fit] Computing mask
/home/himanshu/Desktop/nilearn_work/nilearn/nilearn/decomposition/_base.py:429: UserWarning: memory_level is currently set to 0 but a Memory object has been provided. Setting memory_level to 1.
  self.masker_.fit(imgs)
[MultiNiftiMasker.transform] Resampling mask
[Parcellations] Loading data
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz')
[MultiNiftiMasker.transform_single_imgs] Smoothing images
[MultiNiftiMasker.transform_single_imgs] Extracting region signals
[MultiNiftiMasker.transform_single_imgs] Cleaning extracted signals
[Parcellations] computing ward
________________________________________________________________________________
[Memory] Calling nilearn.regions.parcellations._estimator_fit...
_estimator_fit(array([[-0.002728, ...,  0.002821],
       ...,
       [-0.001877, ...,  0.003343]]),
AgglomerativeClustering(connectivity=<24256x24256 sparse matrix of type '<class 'numpy.int64'>'
        with 162682 stored elements in COOrdinate format>,
                        memory=Memory(location=nilearn_cache/joblib),
                        n_clusters=1000))
________________________________________________________________________________
[Memory] Calling sklearn.cluster._agglomerative.ward_tree...
ward_tree(array([[-0.002728, ..., -0.001877],
       ...,
       [ 0.002821, ...,  0.003343]]), connectivity=<24256x24256 sparse matrix of type '<class 'numpy.int64'>'
        with 162682 stored elements in COOrdinate format>, n_clusters=1000, return_distance=False)
________________________________________________________ward_tree - 2.5s, 0.0min
____________________________________________________estimator_fit - 2.7s, 0.0min
/home/himanshu/Desktop/nilearn_work/nilearn/nilearn/masking.py:980: UserWarning: Data array used to create a new image contains 64-bit ints. This is likely due to creating the array with numpy and passing `int` as the `dtype`. Many tools such as FSL and SPM cannot deal with int64 in Nifti images, so for compatibility the data has been converted to int32.
  return new_img_like(mask_img, unmasked, affine)
Ward agglomeration 1000 clusters: 11.72s
[MultiNiftiMasker.fit] Loading data from [/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz].
[{self.__class__.__name__}.fit] Computing mask
/home/himanshu/Desktop/nilearn_work/nilearn/nilearn/decomposition/_base.py:429: UserWarning: memory_level is currently set to 0 but a Memory object has been provided. Setting memory_level to 1.
  self.masker_.fit(imgs)
[MultiNiftiMasker.transform] Resampling mask
[Parcellations] Loading data
[Parcellations] computing ward
________________________________________________________________________________
[Memory] Calling nilearn.regions.parcellations._estimator_fit...
_estimator_fit(array([[-0.002728, ...,  0.002821],
       ...,
       [-0.001877, ...,  0.003343]]),
AgglomerativeClustering(connectivity=<24256x24256 sparse matrix of type '<class 'numpy.int64'>'
        with 162682 stored elements in COOrdinate format>,
                        memory=Memory(location=nilearn_cache/joblib),
                        n_clusters=2000))
________________________________________________________________________________
[Memory] Calling sklearn.cluster._agglomerative.ward_tree...
ward_tree(array([[-0.002728, ..., -0.001877],
       ...,
       [ 0.002821, ...,  0.003343]]), connectivity=<24256x24256 sparse matrix of type '<class 'numpy.int64'>'
        with 162682 stored elements in COOrdinate format>, n_clusters=2000, return_distance=False)
________________________________________________________ward_tree - 2.1s, 0.0min
____________________________________________________estimator_fit - 2.3s, 0.0min
/home/himanshu/Desktop/nilearn_work/nilearn/nilearn/masking.py:980: UserWarning: Data array used to create a new image contains 64-bit ints. This is likely due to creating the array with numpy and passing `int` as the `dtype`. Many tools such as FSL and SPM cannot deal with int64 in Nifti images, so for compatibility the data has been converted to int32.
  return new_img_like(mask_img, unmasked, affine)
Ward agglomeration 2000 clusters: 9.47s

Visualize: Brain parcellations (Ward)#

First, we display the parcellations of the brain image stored in attribute labels_img_

ward_labels_img = ward.labels_img_

# Now, ward_labels_img are Nifti1Image object, it can be saved to file
# with the following code:
from pathlib import Path

output_dir = Path.cwd() / "results" / "plot_data_driven_parcellations"
output_dir.mkdir(exist_ok=True, parents=True)
print(f"Output will be saved to: {output_dir}")
ward_labels_img.to_filename(output_dir / "ward_parcellation.nii.gz")


first_plot = plotting.plot_roi(
    ward_labels_img, title="Ward parcellation", display_mode="xz"
)

# Grab cut coordinates from this plot to use as a common for all plots
cut_coords = first_plot.cut_coords

Output will be saved to: /home/himanshu/Desktop/nilearn_work/nilearn/examples/03_connectivity/results/plot_data_driven_parcellations

Compressed representation of Ward clustering#

Second, we illustrate the effect that the clustering has on the signal. We show the original data, and the approximation provided by the clustering by averaging the signal on each parcel.

# Grab number of voxels from attribute mask image (mask_img_).
original_voxels = np.sum(get_data(ward.mask_img_))

# Compute mean over time on the functional image to use the mean
# image for compressed representation comparisons
mean_func_img = mean_img(dataset.func[0])

# Compute common vmin and vmax
vmin = np.min(get_data(mean_func_img))
vmax = np.max(get_data(mean_func_img))

plotting.plot_epi(
    mean_func_img,
    cut_coords=cut_coords,
    title=f"Original ({int(original_voxels)} voxels)",
    vmax=vmax,
    vmin=vmin,
    display_mode="xz",
)

# A reduced dataset can be created by taking the parcel-level average:
# Note that Parcellation objects with any method have the opportunity to
# use a `transform` call that modifies input features. Here it reduces their
# dimension. Note that we `fit` before calling a `transform` so that average
# signals can be created on the brain parcellations with fit call.
fmri_reduced = ward.transform(dataset.func)

# Display the corresponding data compressed
# using the parcellation using parcels=2000.
fmri_compressed = ward.inverse_transform(fmri_reduced)

plotting.plot_epi(
    index_img(fmri_compressed, 0),
    cut_coords=cut_coords,
    title="Ward compressed representation (2000 parcels)",
    vmin=vmin,
    vmax=vmax,
    display_mode="xz",
)
# As you can see below, this approximation is almost good, although there
# are only 2000 parcels, instead of the original 60000 voxels

[Parcellations.wrapped] loading data from Nifti1Image('/home/himanshu/Desktop/nilearn_work/nilearn/examples/03_connectivity/results/plot_data_driven_parcellations/ward_parcellation.nii.gz')
[Parcellations.wrapped] loading data from Nifti1Image(
shape=(50, 59, 50),
affine=array([[   4.,    0.,    0.,  -96.],
       [   0.,    4.,    0., -132.],
       [   0.,    0.,    4.,  -78.],
       [   0.,    0.,    0.,    1.]])
)
________________________________________________________________________________
[Memory] Calling nilearn.maskers.base_masker._filter_and_extract...
_filter_and_extract(<nibabel.nifti1.Nifti1Image object at 0x7214c8861a00>, <nilearn.maskers.nifti_labels_masker._ExtractionFunctor object at 0x7214c80add00>,
{ 'background_label': 0,
  'clean_kwargs': {},
  'detrend': False,
  'dtype': None,
  'high_pass': None,
  'high_variance_confounds': False,
  'keep_masked_labels': True,
  'labels': None,
  'labels_img': <nibabel.nifti1.Nifti1Image object at 0x7214f29e58b0>,
  'low_pass': None,
  'mask_img': <nibabel.nifti1.Nifti1Image object at 0x7214f29e76b0>,
  'reports': True,
  'smoothing_fwhm': 2.0,
  'standardize': False,
  'standardize_confounds': True,
  'strategy': 'mean',
  't_r': None,
  'target_affine': None,
  'target_shape': None}, confounds=None, sample_mask=None, dtype=None, memory=Memory(location=nilearn_cache/joblib), memory_level=1, verbose=1)
[NiftiLabelsMasker.transform_single_imgs] Loading data from Nifti1Image('/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz')
[NiftiLabelsMasker.transform_single_imgs] Smoothing images
[NiftiLabelsMasker.transform_single_imgs] Extracting region signals
[NiftiLabelsMasker.transform_single_imgs] Cleaning extracted signals
_______________________________________________filter_and_extract - 1.6s, 0.0min

<nilearn.plotting.displays._slicers.XZSlicer object at 0x7214c8217830>

Brain parcellations with KMeans Clustering#

We use the same approach as with building parcellations using Ward clustering. But, in the range of a small number of clusters, it is most likely that we want to use standardization. Indeed with standardization and smoothing, the clusters will form as regions.

# class/functions can be used here as they are already imported above.

# This object uses method='kmeans' for KMeans clustering with 10mm smoothing
# and standardization ON
start = time.time()
kmeans = Parcellations(
    method="kmeans",
    n_parcels=50,
    standardize="zscore_sample",
    smoothing_fwhm=10.0,
    memory="nilearn_cache",
    memory_level=1,
    verbose=1,
)
# Call fit on functional dataset: single subject (less samples)
kmeans.fit(dataset.func)
print(f"KMeans clusters: {time.time() - start:.2f}s")

[MultiNiftiMasker.fit] Loading data from [/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz].
[{self.__class__.__name__}.fit] Computing mask
/home/himanshu/Desktop/nilearn_work/nilearn/nilearn/decomposition/_base.py:429: UserWarning: memory_level is currently set to 0 but a Memory object has been provided. Setting memory_level to 1.
  self.masker_.fit(imgs)
[MultiNiftiMasker.transform] Resampling mask
[Parcellations] Loading data
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz')
[MultiNiftiMasker.transform_single_imgs] Smoothing images
[MultiNiftiMasker.transform_single_imgs] Extracting region signals
[MultiNiftiMasker.transform_single_imgs] Cleaning extracted signals
[Parcellations] computing kmeans
________________________________________________________________________________
[Memory] Calling nilearn.regions.parcellations._estimator_fit...
_estimator_fit(array([[-0.002242, ..., -0.008556],
       ...,
       [-0.004365, ...,  0.012342]]),
MiniBatchKMeans(n_clusters=50, n_init=3, random_state=0))
____________________________________________________estimator_fit - 0.8s, 0.0min
KMeans clusters: 13.27s

Visualize: Brain parcellations (KMeans)#

Grab parcellations of brain image stored in attribute labels_img_

kmeans_labels_img = kmeans.labels_img_

display = plotting.plot_roi(
    kmeans_labels_img,
    mean_func_img,
    title="KMeans parcellation",
    display_mode="xz",
)

# kmeans_labels_img is a Nifti1Image object, it can be saved to file with
# the following code:
kmeans_labels_img.to_filename(output_dir / "kmeans_parcellation.nii.gz")

Brain parcellations with Hierarchical KMeans Clustering#

As the number of images from which we try to cluster grows, voxels display more and more specific activity patterns causing KMeans clusters to be very unbalanced with a few big clusters and many voxels left as singletons. Hierarchical Kmeans algorithm is tailored to enforce more balanced clusterings. To do this, Hierarchical Kmeans does a first Kmeans clustering in square root of n_parcels. In a second step, it clusters voxels inside each of these parcels in m pieces with m adapted to the size of the cluster in order to have n balanced clusters in the end.

This object uses method=’hierarchical_kmeans’ for Hierarchical KMeans clustering and 10mm smoothing and standardization to compare with the previous method.

start = time.time()
hkmeans = Parcellations(
    method="hierarchical_kmeans",
    n_parcels=50,
    standardize="zscore_sample",
    smoothing_fwhm=10,
    memory="nilearn_cache",
    memory_level=1,
    verbose=1,
)
# Call fit on functional dataset: single subject (less samples)
hkmeans.fit(dataset.func)

[MultiNiftiMasker.fit] Loading data from [/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz].
[{self.__class__.__name__}.fit] Computing mask
/home/himanshu/Desktop/nilearn_work/nilearn/nilearn/decomposition/_base.py:429: UserWarning: memory_level is currently set to 0 but a Memory object has been provided. Setting memory_level to 1.
  self.masker_.fit(imgs)
[MultiNiftiMasker.transform] Resampling mask
[Parcellations] Loading data
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz')
[MultiNiftiMasker.transform_single_imgs] Smoothing images
[MultiNiftiMasker.transform_single_imgs] Extracting region signals
[MultiNiftiMasker.transform_single_imgs] Cleaning extracted signals
[Parcellations] computing hierarchical_kmeans
________________________________________________________________________________
[Memory] Calling nilearn.regions.parcellations._estimator_fit...
_estimator_fit(array([[-0.002242, ..., -0.008556],
       ...,
       [-0.004365, ...,  0.012342]]),
HierarchicalKMeans(n_clusters=50))
____________________________________________________estimator_fit - 5.3s, 0.1min
/home/himanshu/Desktop/nilearn_work/nilearn/nilearn/masking.py:980: UserWarning: Data array used to create a new image contains 64-bit ints. This is likely due to creating the array with numpy and passing `int` as the `dtype`. Many tools such as FSL and SPM cannot deal with int64 in Nifti images, so for compatibility the data has been converted to int32.
  return new_img_like(mask_img, unmasked, affine)

Parcellations(memory=Memory(location=nilearn_cache/joblib), memory_level=1,
              method='hierarchical_kmeans', smoothing_fwhm=10,
              standardize='zscore_sample')

In a Jupyter environment, please rerun this cell to show the HTML representation or trust the notebook.
On GitHub, the HTML representation is unable to render, please try loading this page with nbviewer.org.

Visualize: Brain parcellations (Hierarchical KMeans)#

Grab parcellations of brain image stored in attribute labels_img_

hkmeans_labels_img = hkmeans.labels_img_

plotting.plot_roi(
    hkmeans_labels_img,
    mean_func_img,
    title="Hierarchical KMeans parcellation",
    display_mode="xz",
    cut_coords=display.cut_coords,
)

# kmeans_labels_img is a :class:`nibabel.nifti1.Nifti1Image` object, it can be
# saved to file with the following code:
hkmeans_labels_img.to_filename(
    output_dir / "hierarchical_kmeans_parcellation.nii.gz"
)

Compare Hierarchical Kmeans clusters with those from Kmeans#

To compare those, we’ll first count how many voxels are contained in each of the 50 clusters for both algorithms and compare those sizes distribution. Hierarchical KMeans should give clusters closer to average (600 here) than KMeans.

First count how many voxels have each label (except 0 which is the background).

_, kmeans_counts = np.unique(get_data(kmeans_labels_img), return_counts=True)

_, hkmeans_counts = np.unique(get_data(hkmeans_labels_img), return_counts=True)

voxel_ratio = np.round(np.sum(kmeans_counts[1:]) / 50)

# If all voxels not in background were balanced between clusters ...

print(f"... each cluster should contain {voxel_ratio} voxels")

... each cluster should contain 485.0 voxels

Let’s plot clusters sizes distributions for both algorithms

You can just skip the plotting code, the important part is the figure

import matplotlib.pyplot as plt

bins = np.concatenate(
    [
        np.linspace(0, 500, 11),
        np.linspace(600, 2000, 15),
        np.linspace(3000, 10000, 8),
    ]
)
fig, axes = plt.subplots(
    nrows=2, sharex=True, gridspec_kw={"height_ratios": [4, 1]}
)
plt.semilogx()
axes[0].hist(kmeans_counts[1:], bins, color="blue")
axes[1].hist(hkmeans_counts[1:], bins, color="green")
axes[0].set_ylim(0, 16)
axes[1].set_ylim(4, 0)
axes[1].xaxis.set_major_formatter(ticker.ScalarFormatter())
axes[1].yaxis.set_label_coords(-0.08, 2)
fig.subplots_adjust(hspace=0)
plt.xlabel("Number of voxels (log)", fontsize=12)
plt.ylabel("Number of clusters", fontsize=12)
handles = [
    patches.Rectangle((0, 0), 1, 1, color=c, ec="k") for c in ["blue", "green"]
]
labels = ["Kmeans", "Hierarchical Kmeans"]
fig.legend(handles, labels, loc=(0.5, 0.8))

<matplotlib.legend.Legend object at 0x7214eff48620>

As we can see, half of the 50 KMeans clusters contain less than 100 voxels whereas three contain several thousands voxels Hierarchical KMeans yield better balanced clusters, with a significant proportion of them containing hundreds to thousands of voxels.

Brain parcellations with ReNA Clustering#

One interesting algorithmic property of ReNA (see References) is that it is very fast for a large number of parcels (notably faster than Ward). As before, the parcellation is done with a Parcellations object. The spatial constraints are implemented inside the Parcellations object.

More about ReNA clustering algorithm in the original paper (Hoyos-Idrobo et al.[3]).

start = time.time()
rena = Parcellations(
    method="rena",
    n_parcels=5000,
    standardize=False,
    smoothing_fwhm=2.0,
    scaling=True,
    memory="nilearn_cache",
    memory_level=1,
    verbose=1,
)

rena.fit_transform(dataset.func)
print(f"ReNA 5000 clusters: {time.time() - start:.2f}s")

[MultiNiftiMasker.fit] Loading data from [/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz].
[{self.__class__.__name__}.fit] Computing mask
/home/himanshu/Desktop/nilearn_work/nilearn/nilearn/decomposition/_base.py:429: UserWarning: memory_level is currently set to 0 but a Memory object has been provided. Setting memory_level to 1.
  self.masker_.fit(imgs)
[MultiNiftiMasker.transform] Resampling mask
[Parcellations] Loading data
[Parcellations] computing rena
________________________________________________________________________________
[Memory] Calling nilearn.regions.parcellations._estimator_fit...
_estimator_fit(array([[-0.002728, ...,  0.002821],
       ...,
       [-0.001877, ...,  0.003343]]),
ReNA(mask_img=<nibabel.nifti1.Nifti1Image object at 0x7214d916d160>,
     memory=Memory(location=nilearn_cache/joblib), n_clusters=5000,
     scaling=True),
'rena')
________________________________________________________________________________
[Memory] Calling nilearn.regions.rena_clustering.recursive_neighbor_agglomeration...
recursive_neighbor_agglomeration(array([[-0.002728, ...,  0.002821],
       ...,
       [-0.001877, ...,  0.003343]]),
<nibabel.nifti1.Nifti1Image object at 0x7214d916d160>, 5000, n_iter=10, threshold=1e-07, verbose=0)
_________________________________recursive_neighbor_agglomeration - 1.4s, 0.0min
____________________________________________________estimator_fit - 1.5s, 0.0min
[Parcellations.wrapped] loading data from Nifti1Image(
shape=(50, 59, 50),
affine=array([[   4.,    0.,    0.,  -96.],
       [   0.,    4.,    0., -132.],
       [   0.,    0.,    4.,  -78.],
       [   0.,    0.,    0.,    1.]])
)
[Parcellations.wrapped] loading data from Nifti1Image(
shape=(50, 59, 50),
affine=array([[   4.,    0.,    0.,  -96.],
       [   0.,    4.,    0., -132.],
       [   0.,    0.,    4.,  -78.],
       [   0.,    0.,    0.,    1.]])
)
________________________________________________________________________________
[Memory] Calling nilearn.maskers.base_masker._filter_and_extract...
_filter_and_extract(<nibabel.nifti1.Nifti1Image object at 0x7214f24cce60>, <nilearn.maskers.nifti_labels_masker._ExtractionFunctor object at 0x7214efe840e0>,
{ 'background_label': 0,
  'clean_kwargs': {},
  'detrend': False,
  'dtype': None,
  'high_pass': None,
  'high_variance_confounds': False,
  'keep_masked_labels': True,
  'labels': None,
  'labels_img': <nibabel.nifti1.Nifti1Image object at 0x7214efe87b30>,
  'low_pass': None,
  'mask_img': <nibabel.nifti1.Nifti1Image object at 0x7214efe85bb0>,
  'reports': True,
  'smoothing_fwhm': 2.0,
  'standardize': False,
  'standardize_confounds': True,
  'strategy': 'mean',
  't_r': None,
  'target_affine': None,
  'target_shape': None}, confounds=None, sample_mask=None, dtype=None, memory=Memory(location=nilearn_cache/joblib), memory_level=1, verbose=1)
[NiftiLabelsMasker.transform_single_imgs] Loading data from Nifti1Image('/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz')
[NiftiLabelsMasker.transform_single_imgs] Smoothing images
[NiftiLabelsMasker.transform_single_imgs] Extracting region signals
[NiftiLabelsMasker.transform_single_imgs] Cleaning extracted signals
_______________________________________________filter_and_extract - 2.1s, 0.0min
ReNA 5000 clusters: 13.89s

Visualize: Brain parcellations (ReNA)#

First, we display the parcellations of the brain image stored in attribute labels_img_

rena_labels_img = rena.labels_img_

# Now, rena_labels_img are Nifti1Image object, it can be saved to file
# with the following code:
rena_labels_img.to_filename(output_dir / "rena_parcellation.nii.gz")

plotting.plot_roi(
    ward_labels_img,
    title="ReNA parcellation",
    display_mode="xz",
    cut_coords=cut_coords,
)

<nilearn.plotting.displays._slicers.XZSlicer object at 0x7214efcb7830>

Compressed representation of ReNA clustering#

We illustrate the effect that the clustering has on the signal. We show the original data, and the approximation provided by the clustering by averaging the signal on each parcel.

We can then compare the results with the compressed representation obtained with Ward.

# Display the original data
plotting.plot_epi(
    mean_func_img,
    cut_coords=cut_coords,
    title=f"Original ({int(original_voxels)} voxels)",
    vmax=vmax,
    vmin=vmin,
    display_mode="xz",
)

# A reduced data can be created by taking the parcel-level average:
# Note that, as many scikit-learn objects, the ``rena`` object exposes
# a transform method that modifies input features. Here it reduces their
# dimension.
# However, the data are in one single large 4D image, we need to use
# index_img to do the split easily:
fmri_reduced_rena = rena.transform(dataset.func)

# Display the corresponding data compression using the parcellation
compressed_img_rena = rena.inverse_transform(fmri_reduced_rena)

plotting.plot_epi(
    index_img(compressed_img_rena, 0),
    cut_coords=cut_coords,
    title="ReNA compressed representation (5000 parcels)",
    vmin=vmin,
    vmax=vmax,
    display_mode="xz",
)

[Parcellations.wrapped] loading data from Nifti1Image('/home/himanshu/Desktop/nilearn_work/nilearn/examples/03_connectivity/results/plot_data_driven_parcellations/rena_parcellation.nii.gz')
[Parcellations.wrapped] loading data from Nifti1Image(
shape=(50, 59, 50),
affine=array([[   4.,    0.,    0.,  -96.],
       [   0.,    4.,    0., -132.],
       [   0.,    0.,    4.,  -78.],
       [   0.,    0.,    0.,    1.]])
)
________________________________________________________________________________
[Memory] Calling nilearn.maskers.base_masker._filter_and_extract...
_filter_and_extract(<nibabel.nifti1.Nifti1Image object at 0x7214c8193c50>, <nilearn.maskers.nifti_labels_masker._ExtractionFunctor object at 0x7214f26b0da0>,
{ 'background_label': 0,
  'clean_kwargs': {},
  'detrend': False,
  'dtype': None,
  'high_pass': None,
  'high_variance_confounds': False,
  'keep_masked_labels': True,
  'labels': None,
  'labels_img': <nibabel.nifti1.Nifti1Image object at 0x7214f2321880>,
  'low_pass': None,
  'mask_img': <nibabel.nifti1.Nifti1Image object at 0x7214f007ab70>,
  'reports': True,
  'smoothing_fwhm': 2.0,
  'standardize': False,
  'standardize_confounds': True,
  'strategy': 'mean',
  't_r': None,
  'target_affine': None,
  'target_shape': None}, confounds=None, sample_mask=None, dtype=None, memory=Memory(location=nilearn_cache/joblib), memory_level=1, verbose=1)
[NiftiLabelsMasker.transform_single_imgs] Loading data from Nifti1Image('/home/himanshu/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz')
[NiftiLabelsMasker.transform_single_imgs] Smoothing images
[NiftiLabelsMasker.transform_single_imgs] Extracting region signals
[NiftiLabelsMasker.transform_single_imgs] Cleaning extracted signals
_______________________________________________filter_and_extract - 2.2s, 0.0min

<nilearn.plotting.displays._slicers.XZSlicer object at 0x7214c890fd70>

Even if the compressed signal is relatively close to the original signal, we can notice that Ward Clustering gives a slightly more accurate compressed representation. However, as said in the previous section, the computation time is reduced which could still make ReNA more relevant than Ward in some cases.

References#

[1]
Bertrand Thirion, Gaël Varoquaux, Elvis Dohmatob, and Jean-Baptiste Poline. Which fmri clustering gives good brain parcellations? Frontiers in Neuroscience, 2014. URL: https://www.frontiersin.org/articles/10.3389/fnins.2014.00167, doi:10.3389/fnins.2014.00167.

[2]
Vincent Michel, Alexandre Gramfort, Gaël Varoquaux, Evelyn Eger, Christine Keribin, and Bertrand Thirion. A supervised clustering approach for fmri-based inference of brain states. Pattern Recognition, 45(6):2041–2049, 2012. Brain Decoding. URL: https://www.sciencedirect.com/science/article/pii/S0031320311001439, doi:https://doi.org/10.1016/j.patcog.2011.04.006.

[3]
Andres Hoyos-Idrobo, Gael Varoquaux, Jonas Kahn, and Bertrand Thirion. Recursive nearest agglomeration (rena): fast clustering for approximation of structured signals. IEEE Trans. Pattern Anal. Mach. Intell., 41(3):669–681, 3 2019. URL: https://doi.org/10.1109/TPAMI.2018.2815524, doi:10.1109/TPAMI.2018.2815524.

Total running time of the script: (1 minutes 24.008 seconds)

Estimated memory usage: 2852 MB

Gallery generated by Sphinx-Gallery

Clustering methods to learn a brain parcellation from fMRI#

See Also#

Download a brain development fMRI dataset and turn it to a data matrix#

Brain parcellations with Ward Clustering#

Visualize: Brain parcellations (Ward)#

Compressed representation of Ward clustering#

Brain parcellations with KMeans Clustering#

Visualize: Brain parcellations (KMeans)#

Brain parcellations with Hierarchical KMeans Clustering#

Visualize: Brain parcellations (Hierarchical KMeans)#

Compare Hierarchical Kmeans clusters with those from Kmeans#

Brain parcellations with ReNA Clustering#

Visualize: Brain parcellations (ReNA)#

Compressed representation of ReNA clustering#

References#