Note

Go to the end 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

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
    )
  • plot ica neurovault
  • plot ica neurovault
  • plot ica neurovault
  • plot ica neurovault
  • plot ica neurovault
  • plot ica neurovault
  • plot ica neurovault
  • plot ica neurovault

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: (1 minutes 4.498 seconds)

Estimated memory usage: 378 MB

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