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 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

import numpy as np
from scipy import stats
from sklearn.decomposition import FastICA

from nilearn import plotting
from nilearn.datasets import fetch_neurovault, load_mni152_brain_mask
from nilearn.image import smooth_img
from nilearn.maskers import NiftiMasker

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.
[get_dataset_dir] Dataset found in /home/runner/nilearn_data/neurovault
[fetch_neurovault] Reading local neurovault data.
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=3042
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_98/neurosynth_words_for_image_30
42.json
[fetch_neurovault] Already fetched 1 image
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=2834
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_423/neurosynth_words_for_image_2
834.json
[fetch_neurovault] Already fetched 2 images
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=2818
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_423/neurosynth_words_for_image_2
818.json
[fetch_neurovault] Already fetched 3 images
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=2676
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_413/neurosynth_words_for_image_2
676.json
[fetch_neurovault] Already fetched 4 images
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=2675
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_413/neurosynth_words_for_image_2
675.json
[fetch_neurovault] Already fetched 5 images
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=3041
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_42/neurosynth_words_for_image_30
41.json
[fetch_neurovault] Already fetched 6 images
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=151
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_42/neurosynth_words_for_image_15
1.json
[fetch_neurovault] Already fetched 7 images
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=32980
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1952/neurosynth_words_for_image_
32980.json
[fetch_neurovault] Already fetched 8 images
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=10426
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_658/neurosynth_words_for_image_1
0426.json
[fetch_neurovault] Already fetched 9 images
[fetch_neurovault] 9 images found on local disk.
[memory_usage] Reading server neurovault data.
[<module>] Scroll collections: getting new batch:
https://neurovault.org/api/collections/?limit=100&offset=0
[<module>] Scroll collections: batch size: 100
[fetch_neurovault] Scroll images from collection 921: getting new batch:
https://neurovault.org/api/collections/921/images/?limit=100&offset=0
[fetch_neurovault] Scroll images from collection 921: batch size: 1
[fetch_neurovault] On neurovault.org: no image matched query in collection 921
[fetch_neurovault] Scroll images from collection 440: getting new batch:
https://neurovault.org/api/collections/440/images/?limit=100&offset=0
[fetch_neurovault] Scroll images from collection 440: batch size: 2
[fetch_neurovault] On neurovault.org: no image matched query in collection 440
[fetch_neurovault] Scroll images from collection 496: getting new batch:
https://neurovault.org/api/collections/496/images/?limit=100&offset=0
[fetch_neurovault] Scroll images from collection 496: batch size: 1
[fetch_neurovault] On neurovault.org: no image matched query in collection 496
[fetch_neurovault] Scroll images from collection 4008: getting new batch:
https://neurovault.org/api/collections/4008/images/?limit=100&offset=0
[fetch_neurovault] Scroll images from collection 4008: batch size: 1
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/4008/spmT_0001.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_4008/image_65426.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=65426
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_4008/neurosynth_words_for_image_
65426.json
[fetch_neurovault] Already fetched 10 images
[fetch_neurovault] On neurovault.org: 1 image matched query in collection 4008
[fetch_neurovault] Scroll images from collection 4: getting new batch:
https://neurovault.org/api/collections/4/images/?limit=100&offset=0
[fetch_neurovault] Scroll images from collection 4: batch size: 1
[fetch_neurovault] On neurovault.org: no image matched query in collection 4
[fetch_neurovault] Scroll images from collection 79: getting new batch:
https://neurovault.org/api/collections/79/images/?limit=100&offset=0
[fetch_neurovault] Scroll images from collection 79: batch size: 5
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/79/neurosynth_spectral_01.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_79/image_11020.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=11020
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_79/neurosynth_words_for_image_11
020.json
[fetch_neurovault] Already fetched 11 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/79/neurosynth_spectral_01_1.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_79/image_11021.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=11021
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_79/neurosynth_words_for_image_11
021.json
[fetch_neurovault] Already fetched 12 images
[fetch_neurovault] On neurovault.org: 2 images matched query in collection 79
[fetch_neurovault] Scroll images from collection 1257: getting new batch:
https://neurovault.org/api/collections/1257/images/?limit=100&offset=0
[fetch_neurovault] Scroll images from collection 1257: batch size: 100
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/abstract_knowledge_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17327.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17327
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17327.json
[fetch_neurovault] Already fetched 13 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/acoustic_processing_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17328.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17328
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17328.json
[fetch_neurovault] Already fetched 14 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/action_perception_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17329.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17329
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17329.json
[fetch_neurovault] Already fetched 15 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/action_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17330.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17330
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17330.json
[fetch_neurovault] Already fetched 16 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/activation_level_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17331.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17331
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17331.json
[fetch_neurovault] Already fetched 17 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/activation_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17332.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17332
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17332.json
[fetch_neurovault] Already fetched 18 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/active_maintenance_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17333.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17333
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17333.json
[fetch_neurovault] Already fetched 19 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/active_retrieval_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17334.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17334
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17334.json
[fetch_neurovault] Already fetched 20 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/acuity_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17335.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17335
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17335.json
[fetch_neurovault] Already fetched 21 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/adaptation_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17336.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17336
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17336.json
[fetch_neurovault] Already fetched 22 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/adaptive_control_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17337.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17337
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17337.json
[fetch_neurovault] Already fetched 23 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/addiction_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17338.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17338
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17338.json
[fetch_neurovault] Already fetched 24 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/affect_perception_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17339.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17339
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17339.json
[fetch_neurovault] Already fetched 25 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/affect_recognition_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17340.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17340
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17340.json
[fetch_neurovault] Already fetched 26 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/agency_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17341.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17341
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17341.json
[fetch_neurovault] Already fetched 27 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/agreeableness_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17342.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17342
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17342.json
[fetch_neurovault] Already fetched 28 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/altruism_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17343.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17343
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17343.json
[fetch_neurovault] Already fetched 29 images
[fetch_neurovault] Downloading file:
http://neurovault.org/media/images/1257/altruistic_motivation_regparam.nii.gz
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/image_17344.nii.gz
[fetch_neurovault] Downloading file:
https://neurosynth.org/api/decode/?neurovault=17344
[fetch_neurovault] Download succeeded, downloaded to:
/home/runner/nilearn_data/neurovault/collection_1257/neurosynth_words_for_image_
17344.json
[fetch_neurovault] Already fetched 30 images
[neurosynth_words_vectorized] Computing word features.
[neurosynth_words_vectorized] 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")

mask_img = load_mni152_brain_mask(resolution=2)
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(
            f"Failed to mask/reshape image: id: {meta.get('id')}; "
            f"name: '{meta.get('name')}'; "
            f"collection: {meta.get('collection_id')}; error: {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.

/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling images
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/maskers/nifti_masker.py:114: UserWarning:

imgs are being resampled to the mask_img resolution. This process is memory intensive. You might want to provide a target_affine that is equal to the affine of the imgs or resample the mask beforehand to save memory and computation time.

[NiftiMasker.wrapped] Resampling 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...
Done, plotting results.

Generate figures

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 = f"IC{int(index)}  {', '.join(important_terms[::-1])}"

    plotting.plot_stat_map(
        ic_img, threshold=ic_threshold, colorbar=False, title=title
    )

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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()

Estimated memory usage: 269 MB