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 fetch_neurovault
documentation for more details.
Warning
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.datasets import fetch_neurovault, load_mni152_brain_mask
from nilearn.image import smooth_img
from nilearn.maskers import NiftiMasker
from nilearn.plotting import plot_stat_map, show
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, timeout=30.0
)
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.
[fetch_neurovault] Dataset found in /home/remi-gau/nilearn_data/neurovault
[fetch_neurovault] Reading local neurovault data.
[fetch_neurovault] Already fetched 1 image
[fetch_neurovault] Already fetched 2 images
[fetch_neurovault] Already fetched 3 images
[fetch_neurovault] Already fetched 4 images
[fetch_neurovault] Already fetched 5 images
[fetch_neurovault] Already fetched 6 images
[fetch_neurovault] Already fetched 7 images
[fetch_neurovault] Already fetched 8 images
[fetch_neurovault] Already fetched 9 images
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[fetch_neurovault] Already fetched 13 images
[fetch_neurovault] Already fetched 14 images
[fetch_neurovault] Already fetched 15 images
[fetch_neurovault] Already fetched 16 images
[fetch_neurovault] Already fetched 17 images
[fetch_neurovault] Already fetched 18 images
[fetch_neurovault] Already fetched 19 images
[fetch_neurovault] Already fetched 20 images
[fetch_neurovault] Already fetched 21 images
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[fetch_neurovault] Already fetched 24 images
[fetch_neurovault] Already fetched 25 images
[fetch_neurovault] Already fetched 26 images
[fetch_neurovault] Already fetched 27 images
[fetch_neurovault] Already fetched 28 images
[fetch_neurovault] Already fetched 29 images
[fetch_neurovault] Already fetched 30 images
[fetch_neurovault] 30 images found on local disk.
[fetch_neurovault] Computing word features.
[fetch_neurovault] Computing word features done; vocabulary size: 1314
Top 10 neurosynth terms from downloaded images:
amygdala
vi
resting state
resting
hippocampus
cerebellar
emotional
hippocampal
lobules
cerebellum
Reshape and mask images¶
import warnings
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, verbose=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:
with warnings.catch_warnings():
warnings.simplefilter("ignore")
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.
[NiftiMasker.fit] Loading mask from <nibabel.nifti1.Nifti1Image object at 0x7587eaa59a80>
[NiftiMasker.fit] Resampling mask
________________________________________________________________________________
[Memory] Calling nilearn.image.resampling.resample_img...
resample_img(<nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, target_affine=None, target_shape=None, copy=False, interpolation='nearest')
_____________________________________________________resample_img - 0.0s, 0.0min
[NiftiMasker.fit] Finished fit
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aa170>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5bd60>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917ab550>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa594e0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917abe50>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5b970>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917a8460>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5af50>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917ab550>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa58b50>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aace0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5afb0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917ab640>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa587c0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aa170>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5bc40>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917a87f0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5bd90>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917abe50>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa58fa0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aaf20>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa58f10>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aacb0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa59120>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917a85b0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa58af0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917a8460>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5baf0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917ab550>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5a920>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aace0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5a1d0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917ab640>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5be50>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aa170>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa58b20>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917a87f0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5ba60>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917abe50>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5b580>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aaf20>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5ace0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.5s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aacb0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa59990>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917a85b0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5b700>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917a8460>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5aa40>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.5s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917ab550>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5be20>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aace0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa59d50>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917ab640>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5af20>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917aa170>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa5a590>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917a87f0>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa58580>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
________________________________________________________________________________
[Memory] Calling nilearn.maskers.nifti_masker.filter_and_mask...
filter_and_mask(<nibabel.nifti1.Nifti1Image object at 0x7587917abe50>, <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>, { 'clean_args': None,
'clean_kwargs': {},
'cmap': 'gray',
'detrend': False,
'dtype': None,
'high_pass': None,
'high_variance_confounds': False,
'low_pass': None,
'reports': True,
'runs': None,
'smoothing_fwhm': None,
'standardize': False,
'standardize_confounds': True,
't_r': None,
'target_affine': None,
'target_shape': None}, memory_level=1, memory=Memory(location=nilearn_cache/joblib), verbose=1, confounds=None, sample_mask=None, copy=True, dtype=None, sklearn_output_config=None)
[NiftiMasker.wrapped] Loading data from <nibabel.nifti1.Nifti1Image object at 0x7587eaa59fc0>
[NiftiMasker.wrapped] Resampling images
[NiftiMasker.wrapped] Extracting region signals
[NiftiMasker.wrapped] Cleaning extracted signals
__________________________________________________filter_and_mask - 0.4s, 0.0min
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, strict=False)
):
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])}"
plot_stat_map(ic_img, threshold=ic_threshold, colorbar=False, title=title)
[NiftiMasker.inverse_transform] Computing image from signals
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([0.166983, ..., 0.22512 ], shape=(235375,)), <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>)
___________________________________________________________unmask - 0.2s, 0.0min
[NiftiMasker.inverse_transform] Computing image from signals
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([0.006767, ..., 0.16057 ], shape=(235375,)), <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>)
___________________________________________________________unmask - 0.2s, 0.0min
[NiftiMasker.inverse_transform] Computing image from signals
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([-0.669131, ..., -1.246227], shape=(235375,)), <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>)
___________________________________________________________unmask - 0.2s, 0.0min
[NiftiMasker.inverse_transform] Computing image from signals
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([ 0.031285, ..., -0.242347], shape=(235375,)), <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>)
___________________________________________________________unmask - 0.2s, 0.0min
[NiftiMasker.inverse_transform] Computing image from signals
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([-0.307528, ..., -0.346196], shape=(235375,)), <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>)
___________________________________________________________unmask - 0.2s, 0.0min
[NiftiMasker.inverse_transform] Computing image from signals
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([0.88318 , ..., 0.359842], shape=(235375,)), <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>)
___________________________________________________________unmask - 0.2s, 0.0min
[NiftiMasker.inverse_transform] Computing image from signals
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([-0.020097, ..., 0.512281], shape=(235375,)), <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>)
___________________________________________________________unmask - 0.2s, 0.0min
[NiftiMasker.inverse_transform] Computing image from signals
________________________________________________________________________________
[Memory] Calling nilearn.masking.unmask...
unmask(array([-0.122086, ..., -0.073002], shape=(235375,)), <nibabel.nifti1.Nifti1Image object at 0x7587917abf10>)
___________________________________________________________unmask - 0.2s, 0.0min
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.
show()
Total running time of the script: (0 minutes 30.581 seconds)
Estimated memory usage: 206 MB
