Download and convert the Neurosynth database

Download and convert the Neurosynth database (with abstracts) for analysis with NiMARE.

Note

This will likely change as we work to shift database querying to a remote database, rather than handling it locally with NiMARE.

Start with the necessary imports

import os

from neurosynth.base.dataset import download

import nimare

Download Neurosynth

out_dir = os.path.abspath('../example_data/')
if not os.path.isdir(out_dir):
    os.mkdir(out_dir)

if not os.path.isfile(os.path.join(out_dir, 'database.txt')):
    download(out_dir, unpack=True)

Convert Neurosynth database to NiMARE dataset file

dset = nimare.io.convert_neurosynth_to_dataset(
    os.path.join(out_dir, 'database.txt'),
    os.path.join(out_dir, 'features.txt'))
dset.save(os.path.join(out_dir, 'neurosynth_dataset.pkl.gz'))

Add article abstracts to dataset

dset = nimare.extract.download_abstracts(dset, 'tsalo006@fiu.edu')
dset.save(os.path.join(out_dir, 'neurosynth_nimare_with_abstracts.pkl.gz'))