Query neuroimaging meta-analysis datasets using coord2study

Demonstrates fetching NiMARE datasets and finding studies related to specific MNI coordinates.

1. Import Required Libraries We start by importing the necessary libraries.

from coord2region.coord2study import prepare_datasets, get_studies_for_coordinate
from coord2region.paths import get_working_directory

2. Prepare the NIDM-Pain Dataset

We use prepare_datasets to load a cached deduplicated dataset or download and create one if necessary. For speed, we only include the NIDM-Pain dataset in this example.

working_dir = get_working_directory("coord2region_full")
dataset = prepare_datasets(data_dir=working_dir, sources=["nidm_pain","neurosynth","neuroquery"])
datasets = {"Combined": dataset}

print(f"Loaded dataset with {len(dataset.ids)} studies")

3. Query Studies for an MNI Coordinate

We specify an MNI coordinate to find studies reporting activation at that location.

mni_coord = [48,-38, -24]  # Example coordinate in MNI space

study_results = get_studies_for_coordinate(datasets, coord=mni_coord,radius=2, email="snesmaeili@gmail.com")

# Display results
print(f"\nFound {len(study_results)} studies for MNI coordinate {mni_coord}:\n")
for study in study_results[:5]:  # Show only first 5 studies for brevity
    print(f"Study ID: {study['id']}")
    print(f"Source: {study['source']}")
    print(f"Title: {study.get('title', 'No title available')}")
    print("-" * 40)

4. Extract and Display Study Metadata

If available, we can retrieve additional metadata such as abstracts using PubMed.

for study in study_results[:3]:  # Limit to first 3 studies
    print(f"Study ID: {study['id']}")
    print(f"Title: {study.get('title', 'No title available')}")
    if "abstract" in study:
        print(f"Abstract: {study['abstract'][:300]}...")  # Show only first 300 characters
    print("=" * 60)

5. Summary

In this tutorial, we: - Prepared the NIDM-Pain dataset using prepare_datasets - Queried studies reporting activation at a given MNI coordinate - Extracted study titles and abstracts from the results

This functionality is useful for meta-analysis research, allowing users to explore which brain regions are consistently activated across multiple studies.