.. only:: html

    .. note::
        :class: sphx-glr-download-link-note

        Click :ref:`here <sphx_glr_download_auto_examples_03_connectivity_plot_compare_decomposition.py>`     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 <https://hal.inria.fr/hal-00489507/>`_

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(<function compute_multi_brain_mask at 0x7fbf092b7c10>, 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(<function compute_multi_brain_mask at 0x7fbf092b7c10>, 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(<function compute_multi_brain_mask at 0x7fbf092b7c10>, 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 - 0.6s, 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 - 2.0s, 0.0min
    [Parallel(n_jobs=1)]: Done   1 out of   1 | elapsed:    2.1s 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=398764591)
    __________________________________________________________fastica - 2.8s, 0.0min
    [Parallel(n_jobs=1)]: Done   2 out of   2 | 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=924231285)
    __________________________________________________________fastica - 1.5s, 0.0min
    [Parallel(n_jobs=1)]: Done   3 out of   3 | elapsed:    6.4s 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=1478610112)
    __________________________________________________________fastica - 1.3s, 0.0min
    [Parallel(n_jobs=1)]: Done   4 out of   4 | elapsed:    7.7s 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=441365315)
    __________________________________________________________fastica - 2.7s, 0.0min
    [Parallel(n_jobs=1)]: Done   5 out of   5 | elapsed:   10.5s 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=1537364731)
    __________________________________________________________fastica - 2.9s, 0.0min
    [Parallel(n_jobs=1)]: Done   6 out of   6 | elapsed:   13.5s 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)
    __________________________________________________________fastica - 2.9s, 0.0min
    [Parallel(n_jobs=1)]: Done   7 out of   7 | elapsed:   16.4s 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=1491434855)
    __________________________________________________________fastica - 3.0s, 0.1min
    [Parallel(n_jobs=1)]: Done   8 out of   8 | elapsed:   19.5s 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=1819583497)
    __________________________________________________________fastica - 3.3s, 0.1min
    [Parallel(n_jobs=1)]: Done   9 out of   9 | elapsed:   22.8s 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=530702035)
    __________________________________________________________fastica - 2.7s, 0.0min
    [Parallel(n_jobs=1)]: Done  10 out of  10 | elapsed:   25.6s 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,

    <nilearn.plotting.displays.OrthoSlicer object at 0x7fbeff59db20>



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
     <https://hal.archives-ouvertes.fr/hal-01271033/>`_,
     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(<function compute_multi_brain_mask at 0x7fbf092b7c10>, 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(<function compute_multi_brain_mask at 0x7fbf092b7c10>, 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(<function compute_multi_brain_mask at 0x7fbf092b7c10>, 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 - 0.6s, 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 - 1.2s, 0.0min
    [Parallel(n_jobs=1)]: Done   1 out of   1 | elapsed:    1.3s 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 - 5.7s, 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,

    <nilearn.plotting.displays.OrthoSlicer object at 0x7fbefeb338b0>



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 1.06s 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 - 24.6s, 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
    <sphx_glr_auto_examples_03_connectivity_plot_extract_regions_dictlearning_maps.py>`.


.. rst-class:: sphx-glr-timing

   **Total running time of the script:** ( 5 minutes  1.199 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 <plot_compare_decomposition.py>`



  .. container:: sphx-glr-download sphx-glr-download-jupyter

     :download:`Download Jupyter notebook: plot_compare_decomposition.ipynb <plot_compare_decomposition.ipynb>`


.. only:: html

 .. rst-class:: sphx-glr-signature

    `Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_