Note
Click here to download the full example code
Run an image-based meta-analysis (IBMA) workflow
NiMARE provides a plethora of tools for performing meta-analyses on neuroimaging data. Sometimes it’s difficult to know where to start, especially if you’re new to meta-analysis. This tutorial will walk you through using a IBMA workflow function which puts together the fundamental steps of a IBMA meta-analysis.
import os
from pathlib import Path
import matplotlib.pyplot as plt
from nilearn.plotting import plot_stat_map
from nimare.extract import download_nidm_pain
Download data
Load Dataset
from nimare.dataset import Dataset
from nimare.utils import get_resource_path
dset_file = os.path.join(get_resource_path(), "nidm_pain_dset.json")
dset = Dataset(dset_file)
dset.update_path(dset_dir)
Run IBMA Workflow
The fit method of a IBMA workflow class runs the following steps:
Runs a meta-analysis using the specified method (default: Stouffers)
Applies a corrector to the meta-analysis results (default: FDRCorrector, indep)
Generates cluster tables and runs diagnostics on the corrected results (default: Jackknife)
All in one call!
from nimare.workflows.ibma import IBMAWorkflow
workflow = IBMAWorkflow()
result = workflow.fit(dset)
Out:
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/maskers/nifti_masker.py:108: 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.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/_utils/niimg.py:61: UserWarning:
Non-finite values detected. These values will be replaced with zeros.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/reporting/_get_clusters_table.py:339: UserWarning:
Attention: No clusters with stat lower than -1.65
0%| | 0/21 [00:00<?, ?it/s]
0%| | 0/21 [01:52<?, ?it/s]
Plot Results
The fit method of the IBMA workflow class returns a MetaResult object,
where you can access the corrected results of the meta-analysis and diagnostics tables.
Corrected map:
img = result.get_map("z_corr-FDR_method-indep")
plot_stat_map(
img,
cut_coords=4,
display_mode="z",
threshold=1.65, # voxel_thresh p < .05, one-tailed
cmap="RdBu_r",
vmax=4,
)
plt.show()
Out:
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/_utils/niimg.py:61: UserWarning:
Non-finite values detected. These values will be replaced with zeros.
Clusters table
result.tables["z_corr-FDR_method-indep_tab-clust"]
Contribution table
result.tables["z_corr-FDR_method-indep_diag-Jackknife_tab-counts_tail-positive"]
Report
Finally, a NiMARE report is generated from the MetaResult.
from nimare.reports.base import run_reports
# root_dir = Path(os.getcwd()).parents[1] / "docs" / "_build"
# Use the previous root to run the documentation locally.
root_dir = Path(os.getcwd()).parents[1] / "_readthedocs"
html_dir = root_dir / "html" / "auto_examples" / "02_meta-analyses" / "12_plot_ibma_workflow"
html_dir.mkdir(parents=True, exist_ok=True)
run_reports(result, html_dir)
Out:
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/_utils/niimg.py:61: UserWarning:
Non-finite values detected. These values will be replaced with zeros.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/seaborn/axisgrid.py:123: UserWarning:
Tight layout not applied. tight_layout cannot make axes height small enough to accommodate all axes decorations.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/seaborn/axisgrid.py:123: UserWarning:
Tight layout not applied. tight_layout cannot make axes height small enough to accommodate all axes decorations.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/seaborn/axisgrid.py:123: UserWarning:
Tight layout not applied. tight_layout cannot make axes height small enough to accommodate all axes decorations.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/seaborn/axisgrid.py:123: UserWarning:
Tight layout not applied. tight_layout cannot make axes height small enough to accommodate all axes decorations.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/seaborn/axisgrid.py:123: UserWarning:
Tight layout not applied. tight_layout cannot make axes height small enough to accommodate all axes decorations.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/_utils/niimg.py:61: UserWarning:
Non-finite values detected. These values will be replaced with zeros.
/home/docs/checkouts/readthedocs.org/user_builds/nimare/envs/0.2.1/lib/python3.8/site-packages/nilearn/_utils/niimg.py:61: UserWarning:
Non-finite values detected. These values will be replaced with zeros.
Total running time of the script: ( 4 minutes 43.839 seconds)