Note
Click here to download the full example code or to run this example in your browser via Binder
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 nilearn.datasets.fetch_neurovault
documentation for more details.
Note
If you are using Nilearn with a version older than 0.9.0,
then you should either upgrade your version or import maskers
from the input_data module instead of the maskers module.
That is, you should manually replace in the following example all occurrences of:
from nilearn.maskers import NiftiMasker
with:
from nilearn.input_data import NiftiMasker
# 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.maskers import NiftiMasker
from nilearn import plotting
Get image and term data#
# 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])
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=2675
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_413/neurosynth_words_for_image_2675.json
Already fetched 1 image
Downloading file: http://neurosynth.org/api/decode/?neurovault=2676
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_413/neurosynth_words_for_image_2676.json
Already fetched 2 images
Downloading file: http://neurosynth.org/api/decode/?neurovault=151
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_42/neurosynth_words_for_image_151.json
Already fetched 3 images
Downloading file: http://neurosynth.org/api/decode/?neurovault=3041
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_42/neurosynth_words_for_image_3041.json
Already fetched 4 images
Downloading file: http://neurosynth.org/api/decode/?neurovault=32980
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_1952/neurosynth_words_for_image_32980.json
Already fetched 5 images
Downloading file: http://neurosynth.org/api/decode/?neurovault=3042
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_98/neurosynth_words_for_image_3042.json
Already fetched 6 images
Downloading file: http://neurosynth.org/api/decode/?neurovault=10426
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_658/neurosynth_words_for_image_10426.json
Already fetched 7 images
Downloading file: http://neurosynth.org/api/decode/?neurovault=2818
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_423/neurosynth_words_for_image_2818.json
Already fetched 8 images
Downloading file: http://neurosynth.org/api/decode/?neurovault=2834
Download succeeded, downloaded to: /home/alexis/nilearn_data/neurovault/collection_423/neurosynth_words_for_image_2834.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/alexis/nilearn_data/neurovault/collection_4008/image_65426.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=65426
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_79/image_11020.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=11020
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_79/image_11021.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=11021
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17327.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17327
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17328.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17328
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17329.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17329
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17330.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17330
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17331.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17331
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17332.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17332
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17333.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17333
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17334.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17334
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17335.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17335
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17336.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17336
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17337.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17337
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17338.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17338
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17339.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17339
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17340.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17340
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17341.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17341
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17342.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17342
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17343.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17343
Download succeeded, downloaded to: /home/alexis/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/alexis/nilearn_data/neurovault/collection_1257/image_17344.nii.gz
Downloading file: http://neurosynth.org/api/decode/?neurovault=17344
Download succeeded, downloaded to: /home/alexis/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
planum temporale
temporale
planum
superior
anterior insula
parietal
posterior superior
Reshape and mask images#
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, :]
Reshaping and masking images.
Run ICA and map components to terms#
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.')
Running ICA; may take time...
/home/alexis/miniconda3/envs/nilearn/lib/python3.10/site-packages/sklearn/decomposition/_fastica.py:488: FutureWarning:
From version 1.3 whiten='unit-variance' will be used by default.
Done, plotting results.
Generate figures#
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)
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
# Done.
plotting.show()
Total running time of the script: ( 2 minutes 16.535 seconds)
Estimated memory usage: 187 MB
