Note
Go to the end to download the full example code. or to run this example in your browser via Binder
ROI-based decoding analysis in Haxby et al. dataset¶
In this script we reproduce the data analysis conducted by Haxby et al.[1].
Specifically, we look at decoding accuracy for different objects in three different masks: the full ventral stream (mask_vt), the house selective areas (mask_house) and the face selective areas (mask_face), that have been defined via a standard GLM-based analysis.
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
# Fetch data using nilearn dataset fetcher
from nilearn import datasets
from nilearn.plotting import show
Load and prepare the data¶
# by default we fetch 2nd subject data for analysis
haxby_dataset = datasets.fetch_haxby()
func_filename = haxby_dataset.func[0]
# Print basic information on the dataset
print(
"First subject anatomical nifti image (3D) located is "
f"at: {haxby_dataset.anat[0]}"
)
print(
"First subject functional nifti image (4D) is located "
f"at: {func_filename}"
)
# load labels
import pandas as pd
# Load nilearn NiftiMasker, the practical masking and unmasking tool
from nilearn.maskers import NiftiMasker
labels = pd.read_csv(haxby_dataset.session_target[0], sep=" ")
stimuli = labels["labels"]
# identify resting state labels in order to be able to remove them
task_mask = stimuli != "rest"
# find names of remaining active labels
categories = stimuli[task_mask].unique()
# extract tags indicating to which acquisition run a tag belongs
run_labels = labels["chunks"][task_mask]
# apply the task_mask to fMRI data (func_filename)
from nilearn.image import index_img
task_data = index_img(func_filename, task_mask)
[get_dataset_dir] Dataset found in /home/runner/nilearn_data/haxby2001
First subject anatomical nifti image (3D) located is at: /home/runner/nilearn_data/haxby2001/subj2/anat.nii.gz
First subject functional nifti image (4D) is located at: /home/runner/nilearn_data/haxby2001/subj2/bold.nii.gz
Decoding on the different masks¶
The classifier used here is a support vector classifier (svc). We use class:nilearn.decoding.Decoder and specify the classifier.
import numpy as np
# Make a data splitting object for cross validation
from sklearn.model_selection import LeaveOneGroupOut
from nilearn.decoding import Decoder
cv = LeaveOneGroupOut()
We use nilearn.decoding.Decoder
to estimate a baseline.
mask_names = ["mask_vt", "mask_face", "mask_house"]
mask_scores = {}
mask_chance_scores = {}
for mask_name in mask_names:
print(f"Working on {mask_name}")
# For decoding, standardizing is often very important
mask_filename = haxby_dataset[mask_name][0]
masker = NiftiMasker(mask_img=mask_filename, standardize="zscore_sample")
mask_scores[mask_name] = {}
mask_chance_scores[mask_name] = {}
for category in categories:
print(f"Processing {mask_name} {category}")
classification_target = stimuli[task_mask] == category
# Specify the classifier to the decoder object.
# With the decoder we can input the masker directly.
# We are using the svc_l1 here because it is intra subject.
decoder = Decoder(
estimator="svc_l1",
cv=cv,
mask=masker,
scoring="roc_auc",
standardize="zscore_sample",
)
decoder.fit(task_data, classification_target, groups=run_labels)
mask_scores[mask_name][category] = decoder.cv_scores_[1]
mean = np.mean(mask_scores[mask_name][category])
std = np.std(mask_scores[mask_name][category])
print(f"Scores: {mean:1.2f} +- {std:1.2f}")
dummy_classifier = Decoder(
estimator="dummy_classifier",
cv=cv,
mask=masker,
scoring="roc_auc",
standardize="zscore_sample",
)
dummy_classifier.fit(
task_data, classification_target, groups=run_labels
)
mask_chance_scores[mask_name][category] = dummy_classifier.cv_scores_[
1
]
Working on mask_vt
Processing mask_vt scissors
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Scores: 0.92 +- 0.05
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Processing mask_vt face
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Scores: 0.98 +- 0.03
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Processing mask_vt cat
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Scores: 0.96 +- 0.04
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Processing mask_vt shoe
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Scores: 0.92 +- 0.07
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Processing mask_vt house
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Scores: 1.00 +- 0.00
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Processing mask_vt scrambledpix
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Scores: 0.99 +- 0.01
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Processing mask_vt bottle
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Scores: 0.89 +- 0.08
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Processing mask_vt chair
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Scores: 0.93 +- 0.04
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
Working on mask_face
Processing mask_face scissors
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Scores: 0.70 +- 0.16
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Processing mask_face face
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Scores: 0.90 +- 0.06
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Processing mask_face cat
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Scores: 0.76 +- 0.12
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Processing mask_face shoe
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Scores: 0.73 +- 0.17
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Processing mask_face house
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Scores: 0.71 +- 0.16
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Processing mask_face scrambledpix
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Scores: 0.87 +- 0.09
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Processing mask_face bottle
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Scores: 0.68 +- 0.17
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Processing mask_face chair
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Scores: 0.63 +- 0.10
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:797: UserWarning:
After clustering and screening, the decoding model will be trained only on 30 features. Consider raising clustering_percentile or screening_percentile parameters.
Working on mask_house
Processing mask_house scissors
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Scores: 0.83 +- 0.08
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Processing mask_house face
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Scores: 0.90 +- 0.07
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Processing mask_house cat
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Scores: 0.86 +- 0.09
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Processing mask_house shoe
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Scores: 0.82 +- 0.12
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Processing mask_house house
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Scores: 1.00 +- 0.00
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Processing mask_house scrambledpix
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Scores: 0.96 +- 0.05
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Processing mask_house bottle
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Scores: 0.86 +- 0.10
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Processing mask_house chair
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
Scores: 0.90 +- 0.10
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/image/resampling.py:489: UserWarning:
The provided image has no sform in its header. Please check the provided file. Results may not be as expected.
/home/runner/work/nilearn/nilearn/.tox/doc/lib/python3.9/site-packages/nilearn/decoding/decoder.py:775: UserWarning:
Brain mask is smaller than .5% of the size of the standard human brain. This object is probably not tuned to be used on such data.
We make a simple bar plot to summarize the results¶
import matplotlib.pyplot as plt
plt.figure(constrained_layout=True)
tick_position = np.arange(len(categories))
plt.xticks(tick_position, categories, rotation=45)
for color, mask_name in zip("rgb", mask_names):
score_means = [
np.mean(mask_scores[mask_name][category]) for category in categories
]
plt.bar(
tick_position, score_means, label=mask_name, width=0.25, color=color
)
score_chance = [
np.mean(mask_chance_scores[mask_name][category])
for category in categories
]
plt.bar(
tick_position,
score_chance,
width=0.25,
edgecolor="k",
facecolor="none",
)
tick_position = tick_position + 0.2
plt.ylabel("Classification accuracy (AUC score)")
plt.xlabel("Visual stimuli category")
plt.ylim(0.3, 1)
plt.legend(loc="lower right")
plt.title("Category-specific classification accuracy for different masks")
show()
References¶
Total running time of the script: (2 minutes 33.097 seconds)
Estimated memory usage: 1496 MB