Downloading the Neurosynth database and abstracts from the internet

In this example we will use neurosynth.dataset to download the Neurosynth database (download), as well as the abstracts for all of the articles in the database (download_abstracts). Make sure to use your own email.

In [1]:
import sys
from os.path import abspath, join
sys.path.append(abspath('..'))
import neurosynth
In [2]:
data_dir = '/Users/tsalo/Desktop/ns-dataset/'
email = '[email protected]'
In [3]:
neurosynth.base.dataset.download(data_dir, unpack=True)
Downloading the latest Neurosynth files: https://github.com/neurosynth/neurosynth-data/blob/master/current_data.tar.gz?raw=true bytes: 1
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In [4]:
dset = neurosynth.base.dataset.Dataset(join(data_dir, 'database.txt'))
/Users/tsalo/Documents/tsalo/neurosynth/neurosynth/base/dataset.py:209: FutureWarning: in the future, boolean array-likes will be handled as a boolean array index
  xyz[inds] = self.transformer.apply(s, xyz[inds])
In [5]:
abstracts_df = neurosynth.base.dataset.download_abstracts(dset, path=data_dir, email=email)