.. only:: html .. note:: :class: sphx-glr-download-link-note Click :ref:`here ` to download the full example code or to run this example in your browser via Binder .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_03_connectivity_plot_compare_decomposition.py: 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 :term:`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, :term:`ICA` and Dictionary Learning, to :term:`fMRI` data measured while children and young adults watch movies. The resulting maps will be visualized using atlas plotting tools. :term:`CanICA` is an :term:`ICA` method for group-level analysis of :term:`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 ----------------------------------- .. code-block:: default 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 .. rst-class:: sphx-glr-script-out Out: .. code-block:: none First functional nifti image (4D) is at: /home/nicolas/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 :term:`MNI` template space. .. code-block:: default 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') .. rst-class:: sphx-glr-script-out Out: .. code-block:: none [MultiNiftiMasker.fit] Loading data from [/home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar124_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar125_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar126_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar127_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar128_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar001_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar002_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar003_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar004_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar005_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar006_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar007_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar008_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar009_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar010_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar011_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar012_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar013_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar014_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar015_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar016_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar017_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar018_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar019_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar020_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar021_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar022_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar023_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar024_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz] [MultiNiftiMasker.fit] Computing mask /home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/joblib/memory.py:614: UserWarning: Cannot inspect object functools.partial(, mask_type='whole-brain'), ignore list will not work. return hashing.hash(filter_args(self.func, self.ignore, args, kwargs), Template whole-brain mask computation /home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/joblib/memory.py:792: UserWarning: Cannot inspect object functools.partial(, mask_type='whole-brain'), ignore list will not work. argument_dict = filter_args(self.func, self.ignore, /home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/joblib/memory.py:614: UserWarning: Cannot inspect object functools.partial(, mask_type='whole-brain'), ignore list will not work. return hashing.hash(filter_args(self.func, self.ignore, args, kwargs), [MultiNiftiMasker.transform] Resampling mask [CanICA] Loading data [MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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) __________________________________________________________fastica - 2.8s, 0.0min [Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 2.8s 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=398764591) __________________________________________________________fastica - 4.3s, 0.1min [Parallel(n_jobs=1)]: Done 2 out of 2 | elapsed: 7.1s 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) __________________________________________________________fastica - 2.5s, 0.0min [Parallel(n_jobs=1)]: Done 3 out of 3 | elapsed: 9.7s 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) __________________________________________________________fastica - 1.7s, 0.0min [Parallel(n_jobs=1)]: Done 4 out of 4 | elapsed: 11.4s 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=441365315) __________________________________________________________fastica - 2.9s, 0.0min [Parallel(n_jobs=1)]: Done 5 out of 5 | elapsed: 14.3s 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) __________________________________________________________fastica - 2.9s, 0.0min [Parallel(n_jobs=1)]: Done 6 out of 6 | elapsed: 17.2s 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) __________________________________________________________fastica - 3.5s, 0.1min [Parallel(n_jobs=1)]: Done 7 out of 7 | elapsed: 20.7s 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) __________________________________________________________fastica - 2.5s, 0.0min [Parallel(n_jobs=1)]: Done 8 out of 8 | elapsed: 23.3s 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) __________________________________________________________fastica - 3.9s, 0.1min [Parallel(n_jobs=1)]: Done 9 out of 9 | elapsed: 27.2s 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) __________________________________________________________fastica - 2.9s, 0.0min [Parallel(n_jobs=1)]: Done 10 out of 10 | elapsed: 30.2s finished /home/nicolas/GitRepos/nilearn-fork/nilearn/image/image.py:1106: FutureWarning: The parameter "sessions" will be removed in 0.9.0 release of Nilearn. Please use the parameter "runs" instead. data = signal.clean( To visualize we plot the outline of all components on one figure .. code-block:: default from nilearn.plotting import plot_prob_atlas # Plot all ICA components together plot_prob_atlas(canica_components_img, title='All ICA components') .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_001.png :alt: plot compare decomposition :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays.py:101: UserWarning: No contour levels were found within the data range. im = getattr(ax, type)(data_2d.copy(), /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays.py:101: UserWarning: linewidths is ignored by contourf im = getattr(ax, type)(data_2d.copy(), /home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/numpy/ma/core.py:2825: UserWarning: Warning: converting a masked element to nan. _data = np.array(data, dtype=dtype, copy=copy, Finally, we plot the map for each :term:`ICA` component separately .. code-block:: default 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) .. rst-class:: sphx-glr-horizontal * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_002.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_003.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_004.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_005.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_006.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_007.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_008.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_009.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_010.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_011.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_012.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_013.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_014.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_015.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_016.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_017.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_018.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_019.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_020.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_021.png :alt: plot compare decomposition :class: sphx-glr-multi-img 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 :term:`ICA`. Here, we will compare networks built with :term:`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 .. code-block:: default 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') .. rst-class:: sphx-glr-script-out Out: .. code-block:: none [Example] Fitting dicitonary learning model [MultiNiftiMasker.fit] Loading data from [/home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar124_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar125_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar126_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar127_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar128_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar001_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar002_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar003_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar004_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar005_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar006_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar007_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar008_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar009_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar010_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar011_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar012_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar013_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar014_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar015_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar016_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar017_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar018_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar019_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar020_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar021_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar022_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar023_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz, /home/nicolas/nilearn_data/development_fmri/development_fmri/sub-pixar024_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz] [MultiNiftiMasker.fit] Computing mask /home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/joblib/memory.py:614: UserWarning: Cannot inspect object functools.partial(, mask_type='whole-brain'), ignore list will not work. return hashing.hash(filter_args(self.func, self.ignore, args, kwargs), /home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/joblib/memory.py:792: UserWarning: Cannot inspect object functools.partial(, mask_type='whole-brain'), ignore list will not work. argument_dict = filter_args(self.func, self.ignore, /home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/joblib/memory.py:614: UserWarning: Cannot inspect object functools.partial(, mask_type='whole-brain'), ignore list will not work. return hashing.hash(filter_args(self.func, self.ignore, args, kwargs), [MultiNiftiMasker.transform] Resampling mask [DictLearning] Loading data [MultiNiftiMasker.transform_single_imgs] Loading data from Nifti1Image('/home/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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/nicolas/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 - 0.9s, 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) __________________________________________________________fastica - 1.8s, 0.0min [Parallel(n_jobs=1)]: Done 1 out of 1 | elapsed: 1.8s finished [DictLearning] Computing initial loadings ________________________________________________________________________________ [Memory] Calling nilearn.decomposition.dict_learning._compute_loadings... _compute_loadings(array([[ 0.002908, ..., -0.001032], ..., [-0.001924, ..., 0.002546]]), array([[-0.624512, ..., 5.338654], ..., [ 0.779528, ..., 0.745343]])) _________________________________________________compute_loadings - 0.2s, 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([[-0.149264, ..., -0.15276 ], ..., [-0.419212, ..., 0.168289]]), verbose=0, random_state=0, return_code=True, shuffle=True, n_jobs=1) _____________________________________________dict_learning_online - 8.2s, 0.1min /home/nicolas/GitRepos/nilearn-fork/nilearn/image/image.py:1106: FutureWarning: The parameter "sessions" will be removed in 0.9.0 release of Nilearn. Please use the parameter "runs" instead. data = signal.clean( [Example] Saving results Visualize the results First plot all DictLearning components together .. code-block:: default plot_prob_atlas(dictlearning_components_img, title='All DictLearning components') .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_022.png :alt: plot compare decomposition :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays.py:101: UserWarning: linewidths is ignored by contourf im = getattr(ax, type)(data_2d.copy(), /home/nicolas/GitRepos/nilearn-fork/nilearn/plotting/displays.py:101: UserWarning: No contour levels were found within the data range. im = getattr(ax, type)(data_2d.copy(), /home/nicolas/anaconda3/envs/nilearn/lib/python3.8/site-packages/numpy/ma/core.py:2825: UserWarning: Warning: converting a masked element to nan. _data = np.array(data, dtype=dtype, copy=copy, One plot of each component .. code-block:: default 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) .. rst-class:: sphx-glr-horizontal * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_023.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_024.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_025.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_026.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_027.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_028.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_029.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_030.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_031.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_032.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_033.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_034.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_035.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_036.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_037.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_038.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_039.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_040.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_041.png :alt: plot compare decomposition :class: sphx-glr-multi-img * .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_042.png :alt: plot compare decomposition :class: sphx-glr-multi-img Estimate explained variance per component and plot using matplotlib The fitted object `dict_learning` can be used to calculate the score per component .. code-block:: default 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() .. image:: /auto_examples/03_connectivity/images/sphx_glr_plot_compare_decomposition_043.png :alt: plot compare decomposition :class: sphx-glr-single-img .. rst-class:: sphx-glr-script-out Out: .. code-block:: none ________________________________________________________________________________ [Memory] Calling nilearn.decomposition.base.explained_variance... explained_variance(array([[-6.245714e-01, ..., 5.338591e+00], ..., [-6.058495e-15, ..., 8.672042e-17]]), array([[ 0., ..., 0.], ..., [-0., ..., 0.]]), per_component=True) /home/nicolas/GitRepos/nilearn-fork/nilearn/decomposition/base.py:507: UserWarning: Persisting input arguments took 1.07s 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. return self._cache(explained_variance)(data, self.components_, ______________________________________________explained_variance - 21.8s, 0.4min .. note:: To see how to extract subject-level timeseries' from regions created using Dictionary Learning, see :ref:`example Regions extraction using Dictionary Learning and functional connectomes `. .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 5 minutes 18.818 seconds) .. _sphx_glr_download_auto_examples_03_connectivity_plot_compare_decomposition.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: binder-badge .. image:: images/binder_badge_logo.svg :target: https://mybinder.org/v2/gh/nilearn/nilearn.github.io/main?filepath=examples/auto_examples/03_connectivity/plot_compare_decomposition.ipynb :alt: Launch binder :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_compare_decomposition.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_compare_decomposition.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_