Note
Click here to download the full example code or to run this example in your browser via Binder
Deriving spatial maps from group fMRI data using ICA and Dictionary Learning#
Various approaches exist to derive spatial maps or networks from group fmr data. The methods extract distributed brain regions that exhibit similar BOLD fluctuations over time. Decomposition methods allow for generation of many independent maps simultaneously without the need to provide a priori information (e.g. seeds or priors.)
This example will apply two popular decomposition methods, ICA and Dictionary learning, to fMRI data measured while children and young adults watch movies. The resulting maps will be visualized using atlas plotting tools.
CanICA is an ICA method for group-level analysis of fMRI data. Compared to other strategies, it brings a well-controlled group model, as well as a thresholding algorithm controlling for specificity and sensitivity with an explicit model of the signal. The reference paper is:
G. Varoquaux et al. “A group model for stable multi-subject ICA on fMRI datasets”, NeuroImage Vol 51 (2010), p. 288-299 preprint
Load brain development fmri dataset#
from nilearn import datasets
rest_dataset = datasets.fetch_development_fmri(n_subjects=30)
func_filenames = rest_dataset.func # list of 4D nifti files for each subject
# print basic information on the dataset
print('First functional nifti image (4D) is at: %s' %
rest_dataset.func[0]) # 4D data
Downloading data from https://osf.io/download/5c8ff3e14712b400183b7097/ ...
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First functional nifti image (4D) is at: /home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
Apply CanICA on the data#
We use “whole-brain-template” as a strategy to compute the mask, as this leads to slightly faster and more reproducible results. However, the images need to be in MNI template space.
from nilearn.decomposition import CanICA
canica = CanICA(n_components=20,
memory="nilearn_cache", memory_level=2,
verbose=10,
mask_strategy='whole-brain-template',
random_state=0)
canica.fit(func_filenames)
# Retrieve the independent components in brain space. Directly
# accessible through attribute `components_img_`.
canica_components_img = canica.components_img_
# components_img is a Nifti Image object, and can be saved to a file with
# the following line:
canica_components_img.to_filename('canica_resting_state.nii.gz')
[MultiNiftiMasker.fit] Loading data from [/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar124_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar125_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar126_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar127_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar128_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar001_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar002_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar003_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar004_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar005_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar006_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar007_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar008_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar009_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar010_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar011_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar012_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar013_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar014_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar015_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar016_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar017_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar018_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar019_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar020_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar021_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar022_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar023_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar024_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz]
[MultiNiftiMasker.fit] Computing mask
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/joblib/memory.py:632: UserWarning:
Cannot inspect object functools.partial(<function compute_multi_brain_mask at 0x7ff8fd620d30>, mask_type='whole-brain'), ignore list will not work.
Template whole-brain mask computation
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/joblib/memory.py:810: UserWarning:
Cannot inspect object functools.partial(<function compute_multi_brain_mask at 0x7ff8fd620d30>, mask_type='whole-brain'), ignore list will not work.
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/joblib/memory.py:632: UserWarning:
Cannot inspect object functools.partial(<function compute_multi_brain_mask at 0x7ff8fd620d30>, mask_type='whole-brain'), ignore list will not work.
[MultiNiftiMasker.transform] Resampling mask
[CanICA] Loading data
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar124_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar125_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar126_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar127_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar128_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar001_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar002_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar003_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar004_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar005_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar006_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar007_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar008_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar009_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar010_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar011_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar012_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar013_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar014_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar015_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar016_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar017_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar018_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar019_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar020_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar021_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar022_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar023_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar024_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
________________________________________________________________________________
[Memory] Calling sklearn.utils.extmath.randomized_svd...
randomized_svd(array([[0.003659, ..., 0.013254],
...,
[0.012477, ..., 0.002881]]), n_components=20, transpose=True, random_state=0, n_iter=3)
___________________________________________________randomized_svd - 1.0s, 0.0min
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=209652396)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 1.3s, 0.0min
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 1.4s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=398764591)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 1.1s, 0.0min
[Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 2.5s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=924231285)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 1.0s, 0.0min
[Parallel(n_jobs=1)]: Done 3 out of 3 | elapsed: 3.5s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=1478610112)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 1.4s, 0.0min
[Parallel(n_jobs=1)]: Done 4 out of 4 | elapsed: 4.9s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=441365315)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 0.7s, 0.0min
[Parallel(n_jobs=1)]: Done 5 out of 5 | elapsed: 5.6s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=1537364731)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 0.9s, 0.0min
[Parallel(n_jobs=1)]: Done 6 out of 6 | elapsed: 6.5s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=192771779)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 1.2s, 0.0min
[Parallel(n_jobs=1)]: Done 7 out of 7 | elapsed: 7.8s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=1491434855)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 0.9s, 0.0min
[Parallel(n_jobs=1)]: Done 8 out of 8 | elapsed: 8.8s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=1819583497)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 1.2s, 0.0min
[Parallel(n_jobs=1)]: Done 9 out of 9 | elapsed: 10.0s remaining: 0.0s
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.004071, ..., 0.000497],
...,
[ 0.005856, ..., -0.004765]]), whiten=True, fun='cube', random_state=530702035)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 1.2s, 0.0min
[Parallel(n_jobs=1)]: Done 10 out of 10 | elapsed: 11.2s finished
To visualize we plot the outline of all components on one figure
from nilearn.plotting import plot_prob_atlas
# Plot all ICA components together
plot_prob_atlas(canica_components_img, title='All ICA components')
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/numpy/ma/core.py:2826: UserWarning:
Warning: converting a masked element to nan.
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/nilearn/plotting/displays/_axes.py:71: UserWarning:
linewidths is ignored by contourf
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/nilearn/plotting/displays/_axes.py:71: UserWarning:
No contour levels were found within the data range.
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff8f28f7ca0>
Finally, we plot the map for each ICA component separately
from nilearn.image import iter_img
from nilearn.plotting import plot_stat_map, show
for i, cur_img in enumerate(iter_img(canica_components_img)):
plot_stat_map(cur_img, display_mode="z", title="IC %d" % i,
cut_coords=1, colorbar=False)
Compare CanICA to dictionary learning#
Dictionary learning is a sparsity based decomposition method for extracting spatial maps. It extracts maps that are naturally sparse and usually cleaner than ICA. Here, we will compare networks built with CanICA to networks built with Dictionary learning.
Arthur Mensch et al. Compressed online dictionary learning for fast resting-state fMRI decomposition, ISBI 2016, Lecture Notes in Computer Science
Create a dictionary learning estimator
from nilearn.decomposition import DictLearning
dict_learning = DictLearning(n_components=20,
memory="nilearn_cache", memory_level=2,
verbose=1,
random_state=0,
n_epochs=1,
mask_strategy='whole-brain-template')
print('[Example] Fitting dicitonary learning model')
dict_learning.fit(func_filenames)
print('[Example] Saving results')
# Grab extracted components umasked back to Nifti image.
# Note: For older versions, less than 0.4.1. components_img_
# is not implemented. See Note section above for details.
dictlearning_components_img = dict_learning.components_img_
dictlearning_components_img.to_filename('dictionary_learning_resting_state.nii.gz')
[Example] Fitting dicitonary learning model
[MultiNiftiMasker.fit] Loading data from [/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar124_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar125_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar126_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar127_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar128_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar001_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar002_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar003_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar004_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar005_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar006_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar007_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar008_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar009_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar010_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar011_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar012_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar013_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar014_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar015_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar016_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar017_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar018_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar019_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar020_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar021_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar022_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar023_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz,
/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar024_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz]
[MultiNiftiMasker.fit] Computing mask
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/joblib/memory.py:632: UserWarning:
Cannot inspect object functools.partial(<function compute_multi_brain_mask at 0x7ff8fd620d30>, mask_type='whole-brain'), ignore list will not work.
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/joblib/memory.py:810: UserWarning:
Cannot inspect object functools.partial(<function compute_multi_brain_mask at 0x7ff8fd620d30>, mask_type='whole-brain'), ignore list will not work.
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/joblib/memory.py:632: UserWarning:
Cannot inspect object functools.partial(<function compute_multi_brain_mask at 0x7ff8fd620d30>, mask_type='whole-brain'), ignore list will not work.
[MultiNiftiMasker.transform] Resampling mask
[DictLearning] Loading data
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar124_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar125_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar126_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar127_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar128_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar001_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar002_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar003_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar004_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar005_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar006_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar007_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar008_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar009_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar010_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar011_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar012_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar013_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar014_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar015_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar016_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar017_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar018_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar019_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar020_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar021_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar022_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar023_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
[MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/alexis/nilearn_data/development_fmri/development_fmri/sub-pixar024_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
[DictLearning] Learning initial components
________________________________________________________________________________
[Memory] Calling sklearn.utils.extmath.randomized_svd...
randomized_svd(array([[-0.001315, ..., 0.004387],
...,
[ 0.011243, ..., 0.004194]]), n_components=20, transpose=True, random_state=0, n_iter=3)
___________________________________________________randomized_svd - 2.2s, 0.0min
[Parallel(n_jobs=1)]: Using backend SequentialBackend with 1 concurrent workers.
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._fastica.fastica...
fastica(array([[ 0.00289 , ..., -0.002135],
...,
[ 0.005107, ..., -0.012507]]), whiten=True, fun='cube', random_state=209652396)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:304: FutureWarning:
From version 1.3 whiten=True should be specified as whiten='arbitrary-variance' (its current behaviour). This behavior is deprecated in 1.1 and will raise ValueError in 1.3.
__________________________________________________________fastica - 2.9s, 0.0min
[Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 2.9s finished
[DictLearning] Computing initial loadings
________________________________________________________________________________
[Memory] Calling nilearn.decomposition.dict_learning._compute_loadings...
_compute_loadings(array([[-0.001057, ..., -0.00525 ],
...,
[-0.000299, ..., 0.001863]]),
array([[-0.624512, ..., 5.338654],
...,
[ 0.779528, ..., 0.745343]]))
_________________________________________________compute_loadings - 0.4s, 0.0min
[DictLearning] Learning dictionary
________________________________________________________________________________
[Memory] Calling sklearn.decomposition._dict_learning.dict_learning_online...
dict_learning_online(array([[-0.624512, ..., 0.779528],
...,
[ 5.338654, ..., 0.745343]]),
20, alpha=10, n_iter=1090, batch_size=20, method='cd', dict_init=array([[-0.141934, ..., 0.100905],
...,
[-0.016547, ..., -0.117455]]), verbose=0, random_state=0, return_code=True, shuffle=True, n_jobs=1)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_dict_learning.py:732: FutureWarning:
'n_iter' is deprecated in version 1.1 and will be removed in version 1.3. Use 'max_iter' instead.
_____________________________________________dict_learning_online - 6.9s, 0.1min
[Example] Saving results
Visualize the results
First plot all DictLearning components together
plot_prob_atlas(dictlearning_components_img,
title='All DictLearning components')
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/nilearn/plotting/displays/_axes.py:71: UserWarning:
linewidths is ignored by contourf
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/nilearn/plotting/displays/_axes.py:71: UserWarning:
No contour levels were found within the data range.
<nilearn.plotting.displays._slicers.OrthoSlicer object at 0x7ff90794c700>
One plot of each component
for i, cur_img in enumerate(iter_img(dictlearning_components_img)):
plot_stat_map(cur_img, display_mode="z", title="Comp %d" % i,
cut_coords=1, colorbar=False)
Estimate explained variance per component and plot using matplotlib
The fitted object dict_learning can be used to calculate the score per component
scores = dict_learning.score(func_filenames, per_component=True)
# Plot the scores
import numpy as np
from matplotlib import pyplot as plt
from matplotlib.ticker import FormatStrFormatter
plt.figure(figsize=(4, 4))
positions = np.arange(len(scores))
plt.barh(positions, scores)
plt.ylabel('Component #', size=12)
plt.xlabel('Explained variance', size=12)
plt.yticks(np.arange(20))
plt.gca().xaxis.set_major_formatter(FormatStrFormatter('%.3f'))
plt.tight_layout()
show()
________________________________________________________________________________
[Memory] Calling nilearn.decomposition.base.explained_variance...
explained_variance(array([[-6.245714e-01, ..., 5.338591e+00],
...,
[-6.892003e-15, ..., -4.273528e-16]]),
array([[-0. , ..., 0.018368],
...,
[ 0. , ..., 0. ]]), per_component=True)
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/nilearn/decomposition/base.py:502: UserWarning:
Persisting input arguments took 1.91s to run.
If this happens often in your code, it can cause performance problems
(results will be correct in all cases).
The reason for this is probably some large input arguments for a wrapped
function (e.g. large strings).
THIS IS A JOBLIB ISSUE. If you can, kindly provide the joblib's team with an
example so that they can fix the problem.
______________________________________________explained_variance - 45.9s, 0.8min
Note
To see how to extract subject-level timeseries’ from regions created using Dictionary learning, see example Regions extraction using dictionary learning and functional connectomes.
Total running time of the script: ( 6 minutes 41.415 seconds)
Estimated memory usage: 2596 MB
