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.
import sys
from os.path import abspath, join
sys.path.append(abspath('..'))
import neurosynth
data_dir = '/Users/tsalo/Desktop/ns-dataset/'
email = '[email protected]'
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 8192 [819200.00%]16384 [1638400.00%]24576 [2457600.00%]32768 [3276800.00%]40960 [4096000.00%]49152 [4915200.00%]57344 [5734400.00%]65536 [6553600.00%]73728 [7372800.00%]81920 [8192000.00%]90112 [9011200.00%]98304 [9830400.00%]106496 [10649600.00%]114688 [11468800.00%]122880 [12288000.00%]131072 [13107200.00%]139264 [13926400.00%]147456 [14745600.00%]155648 [15564800.00%]163840 [16384000.00%]172032 [17203200.00%]180224 [18022400.00%]188416 [18841600.00%]196608 [19660800.00%]204800 [20480000.00%]212992 [21299200.00%]221184 [22118400.00%]229376 [22937600.00%]237568 [23756800.00%]245760 [24576000.00%]253952 [25395200.00%]262144 [26214400.00%]270336 [27033600.00%]278528 [27852800.00%]286720 [28672000.00%]294912 [29491200.00%]303104 [30310400.00%]311296 [31129600.00%]319488 [31948800.00%]327680 [32768000.00%]335872 [33587200.00%]344064 [34406400.00%]352256 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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])
abstracts_df = neurosynth.base.dataset.download_abstracts(dset, path=data_dir, email=email)