.. 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_07_advanced_plot_ica_neurovault.py: NeuroVault cross-study ICA maps. ================================ This example shows how to download statistical maps from NeuroVault, label them with NeuroSynth terms, and compute ICA components across all the maps. See :func:`nilearn.datasets.fetch_neurovault` documentation for more details. .. code-block:: default # Author: Ben Cipollini # License: BSD # Ported from code authored by Chris Filo Gorgolewski, Gael Varoquaux # https://github.com/NeuroVault/neurovault_analysis import warnings import numpy as np from scipy import stats from sklearn.decomposition import FastICA from nilearn.datasets import fetch_neurovault from nilearn.image import smooth_img from nilearn.datasets import load_mni152_brain_mask from nilearn.input_data import NiftiMasker from nilearn import plotting Get image and term data ----------------------- .. code-block:: default # Download images # Here by default we only download 80 images to save time, # but for better results I recommend using at least 200. print("Fetching Neurovault images; " "if you haven't downloaded any Neurovault data before " "this will take several minutes.") nv_data = fetch_neurovault(max_images=30, fetch_neurosynth_words=True) images = nv_data['images'] term_weights = nv_data['word_frequencies'] vocabulary = nv_data['vocabulary'] if term_weights is None: term_weights = np.ones((len(images), 2)) vocabulary = np.asarray( ["Neurosynth is down", "Please try again later"]) # Clean and report term scores term_weights[term_weights < 0] = 0 total_scores = np.mean(term_weights, axis=0) print("\nTop 10 neurosynth terms from downloaded images:\n") for term_idx in np.argsort(total_scores)[-10:][::-1]: print(vocabulary[term_idx]) .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Fetching Neurovault images; if you haven't downloaded any Neurovault data before this will take several minutes. Reading local neurovault data. Downloading file: http://neurosynth.org/api/decode/?neurovault=10426 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_658/neurosynth_words_for_image_10426.json Already fetched 1 image Downloading file: http://neurosynth.org/api/decode/?neurovault=32980 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1952/neurosynth_words_for_image_32980.json Already fetched 2 images Downloading file: http://neurosynth.org/api/decode/?neurovault=3041 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_42/neurosynth_words_for_image_3041.json Already fetched 3 images Downloading file: http://neurosynth.org/api/decode/?neurovault=151 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_42/neurosynth_words_for_image_151.json Already fetched 4 images Downloading file: http://neurosynth.org/api/decode/?neurovault=3042 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_98/neurosynth_words_for_image_3042.json Already fetched 5 images Downloading file: http://neurosynth.org/api/decode/?neurovault=2818 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_423/neurosynth_words_for_image_2818.json Already fetched 6 images Downloading file: http://neurosynth.org/api/decode/?neurovault=2834 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_423/neurosynth_words_for_image_2834.json Already fetched 7 images Downloading file: http://neurosynth.org/api/decode/?neurovault=2675 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_413/neurosynth_words_for_image_2675.json Already fetched 8 images Downloading file: http://neurosynth.org/api/decode/?neurovault=2676 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_413/neurosynth_words_for_image_2676.json Already fetched 9 images 9 images found on local disk. Reading server neurovault data. Scroll collections: getting new batch: http://neurovault.org/api/collections/?limit=100&offset=0 Scroll collections: batch size: 100 Scroll images from collection 921: getting new batch: http://neurovault.org/api/collections/921/images/?limit=100&offset=0 Scroll images from collection 921: batch size: 1 On neurovault.org: no image matched query in collection 921 Scroll images from collection 440: getting new batch: http://neurovault.org/api/collections/440/images/?limit=100&offset=0 Scroll images from collection 440: batch size: 2 On neurovault.org: no image matched query in collection 440 Scroll images from collection 496: getting new batch: http://neurovault.org/api/collections/496/images/?limit=100&offset=0 Scroll images from collection 496: batch size: 1 On neurovault.org: no image matched query in collection 496 Scroll images from collection 4008: getting new batch: http://neurovault.org/api/collections/4008/images/?limit=100&offset=0 Scroll images from collection 4008: batch size: 1 Downloading file: https://neurovault.org/media/images/4008/spmT_0001.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_4008/image_65426.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=65426 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_4008/neurosynth_words_for_image_65426.json Already fetched 10 images On neurovault.org: 1 image matched query in collection 4008 Scroll images from collection 4: getting new batch: http://neurovault.org/api/collections/4/images/?limit=100&offset=0 Scroll images from collection 4: batch size: 1 On neurovault.org: no image matched query in collection 4 Scroll images from collection 79: getting new batch: http://neurovault.org/api/collections/79/images/?limit=100&offset=0 Scroll images from collection 79: batch size: 5 Downloading file: https://neurovault.org/media/images/79/neurosynth_spectral_01.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_79/image_11020.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=11020 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_79/neurosynth_words_for_image_11020.json Already fetched 11 images Downloading file: https://neurovault.org/media/images/79/neurosynth_spectral_01_1.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_79/image_11021.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=11021 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_79/neurosynth_words_for_image_11021.json Already fetched 12 images On neurovault.org: 2 images matched query in collection 79 Scroll images from collection 1257: getting new batch: http://neurovault.org/api/collections/1257/images/?limit=100&offset=0 Scroll images from collection 1257: batch size: 100 Downloading file: https://neurovault.org/media/images/1257/abstract_knowledge_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17327.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17327 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17327.json Already fetched 13 images Downloading file: https://neurovault.org/media/images/1257/acoustic_processing_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17328.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17328 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17328.json Already fetched 14 images Downloading file: https://neurovault.org/media/images/1257/action_perception_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17329.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17329 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17329.json Already fetched 15 images Downloading file: https://neurovault.org/media/images/1257/action_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17330.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17330 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17330.json Already fetched 16 images Downloading file: https://neurovault.org/media/images/1257/activation_level_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17331.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17331 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17331.json Already fetched 17 images Downloading file: https://neurovault.org/media/images/1257/activation_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17332.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17332 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17332.json Already fetched 18 images Downloading file: https://neurovault.org/media/images/1257/active_maintenance_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17333.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17333 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17333.json Already fetched 19 images Downloading file: https://neurovault.org/media/images/1257/active_retrieval_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17334.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17334 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17334.json Already fetched 20 images Downloading file: https://neurovault.org/media/images/1257/acuity_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17335.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17335 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17335.json Already fetched 21 images Downloading file: https://neurovault.org/media/images/1257/adaptation_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17336.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17336 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17336.json Already fetched 22 images Downloading file: https://neurovault.org/media/images/1257/adaptive_control_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17337.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17337 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17337.json Already fetched 23 images Downloading file: https://neurovault.org/media/images/1257/addiction_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17338.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17338 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17338.json Already fetched 24 images Downloading file: https://neurovault.org/media/images/1257/affect_perception_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17339.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17339 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17339.json Already fetched 25 images Downloading file: https://neurovault.org/media/images/1257/affect_recognition_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17340.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17340 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17340.json Already fetched 26 images Downloading file: https://neurovault.org/media/images/1257/agency_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17341.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17341 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17341.json Already fetched 27 images Downloading file: https://neurovault.org/media/images/1257/agreeableness_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17342.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17342 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17342.json Already fetched 28 images Downloading file: https://neurovault.org/media/images/1257/altruism_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17343.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17343 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17343.json Already fetched 29 images Downloading file: https://neurovault.org/media/images/1257/altruistic_motivation_regparam.nii.gz Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/image_17344.nii.gz Downloading file: http://neurosynth.org/api/decode/?neurovault=17344 Download succeeded, downloaded to: /home/varoquau/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_17344.json Already fetched 30 images Computing word features. Computing word features done; vocabulary size: 1307 Top 10 neurosynth terms from downloaded images: superior temporal auditory task superior temporale planum temporale planum parietal sound auditory cortex Reshape and mask images ----------------------- .. code-block:: default print("\nReshaping and masking images.\n") with warnings.catch_warnings(): warnings.simplefilter('ignore', UserWarning) warnings.simplefilter('ignore', DeprecationWarning) mask_img = load_mni152_brain_mask() masker = NiftiMasker( mask_img=mask_img, memory='nilearn_cache', memory_level=1) masker = masker.fit() # Images may fail to be transformed, and are of different shapes, # so we need to transform one-by-one and keep track of failures. X = [] is_usable = np.ones((len(images),), dtype=bool) for index, image_path in enumerate(images): # load image and remove nan and inf values. # applying smooth_img to an image with fwhm=None simply cleans up # non-finite values but otherwise doesn't modify the image. image = smooth_img(image_path, fwhm=None) try: X.append(masker.transform(image)) except Exception as e: meta = nv_data['images_meta'][index] print("Failed to mask/reshape image: id: {0}; " "name: '{1}'; collection: {2}; error: {3}".format( meta.get('id'), meta.get('name'), meta.get('collection_id'), e)) is_usable[index] = False # Now reshape list into 2D matrix, and remove failed images from terms X = np.vstack(X) term_weights = term_weights[is_usable, :] .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Reshaping and masking images. Run ICA and map components to terms ----------------------------------- .. code-block:: default print("Running ICA; may take time...") # We use a very small number of components as we have downloaded only 80 # images. For better results, increase the number of images downloaded # and the number of components n_components = 8 fast_ica = FastICA(n_components=n_components, random_state=0) ica_maps = fast_ica.fit_transform(X.T).T term_weights_for_components = np.dot(fast_ica.components_, term_weights) print('Done, plotting results.') .. rst-class:: sphx-glr-script-out Out: .. code-block:: none Running ICA; may take time... Done, plotting results. Generate figures ---------------- .. code-block:: default with warnings.catch_warnings(): warnings.simplefilter('ignore', DeprecationWarning) for index, (ic_map, ic_terms) in enumerate( zip(ica_maps, term_weights_for_components)): if -ic_map.min() > ic_map.max(): # Flip the map's sign for prettiness ic_map = - ic_map ic_terms = - ic_terms ic_threshold = stats.scoreatpercentile(np.abs(ic_map), 90) ic_img = masker.inverse_transform(ic_map) important_terms = vocabulary[np.argsort(ic_terms)[-3:]] title = 'IC%i %s' % (index, ', '.join(important_terms[::-1])) plotting.plot_stat_map( ic_img, threshold=ic_threshold, colorbar=False, title=title) .. rst-class:: sphx-glr-horizontal * .. image:: /auto_examples/07_advanced/images/sphx_glr_plot_ica_neurovault_001.png :alt: plot ica neurovault :class: sphx-glr-multi-img * .. image:: /auto_examples/07_advanced/images/sphx_glr_plot_ica_neurovault_002.png :alt: plot ica neurovault :class: sphx-glr-multi-img * .. image:: /auto_examples/07_advanced/images/sphx_glr_plot_ica_neurovault_003.png :alt: plot ica neurovault :class: sphx-glr-multi-img * .. image:: /auto_examples/07_advanced/images/sphx_glr_plot_ica_neurovault_004.png :alt: plot ica neurovault :class: sphx-glr-multi-img * .. image:: /auto_examples/07_advanced/images/sphx_glr_plot_ica_neurovault_005.png :alt: plot ica neurovault :class: sphx-glr-multi-img * .. image:: /auto_examples/07_advanced/images/sphx_glr_plot_ica_neurovault_006.png :alt: plot ica neurovault :class: sphx-glr-multi-img * .. image:: /auto_examples/07_advanced/images/sphx_glr_plot_ica_neurovault_007.png :alt: plot ica neurovault :class: sphx-glr-multi-img * .. image:: /auto_examples/07_advanced/images/sphx_glr_plot_ica_neurovault_008.png :alt: plot ica neurovault :class: sphx-glr-multi-img As we can see, some of the components capture cognitive or neurological maps, while other capture noise in the database. More data, better filtering, and better cognitive labels would give better maps .. code-block:: default # Done. plotting.show() .. rst-class:: sphx-glr-timing **Total running time of the script:** ( 1 minutes 52.943 seconds) .. _sphx_glr_download_auto_examples_07_advanced_plot_ica_neurovault.py: .. only :: html .. container:: sphx-glr-footer :class: sphx-glr-footer-example .. container:: binder-badge .. image:: https://mybinder.org/badge_logo.svg :target: https://mybinder.org/v2/gh/nilearn/nilearn.github.io/master?filepath=examples/auto_examples/07_advanced/plot_ica_neurovault.ipynb :width: 150 px .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: plot_ica_neurovault.py ` .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: plot_ica_neurovault.ipynb ` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_