TypeError: 'bool' object is not iterable

[JohannesWiesner]

Summary

When trying to run nimare.extract.fetch_neurosynth("../data", unpack=True) I get:

INFO:nimare.extract.utils:Dataset created in ../data/neurosynth
Traceback (most recent call last):

  File ~/micromamba/envs/csp_wiesner_johannes/lib/python3.8/site-packages/spyder_kernels/py3compat.py:356 in compat_exec
    exec(code, globals, locals)

  File ~/work/projects/project_hcp/code/analysis_neurosynth.py:12
    nimare.extract.fetch_neurosynth("../data", unpack=True)

  File ~/micromamba/envs/csp_wiesner_johannes/lib/python3.8/site-packages/nimare/extract/extract.py:191 in fetch_neurosynth
    found_databases = _fetch_database(kwargs, URL, data_dir, overwrite=overwrite)

  File ~/micromamba/envs/csp_wiesner_johannes/lib/python3.8/site-packages/nimare/extract/extract.py:74 in _fetch_database
    if not _find_entities(coordinates_file, search_pairs, log=log):

  File ~/micromamba/envs/csp_wiesner_johannes/lib/python3.8/site-packages/nimare/extract/extract.py:42 in _find_entities
    search_pairs = [[f"{k}-{v_i}" for v_i in v] for k, v in search_pairs.items()]

  File ~/micromamba/envs/csp_wiesner_johannes/lib/python3.8/site-packages/nimare/extract/extract.py:42 in <listcomp>
    search_pairs = [[f"{k}-{v_i}" for v_i in v] for k, v in search_pairs.items()]

TypeError: 'bool' object is not iterable

Additional details

• NiMARE version: 0.1.1

What were you trying to do?

Following this code section:

https://neurostars.org/t/is-there-any-way-to-pull-unthresholded-images-from-neurosynth/19431/2?u=johanneswiesner

What did you expect to happen?

Successful download of neurosynth database

What actually happened?

Download failed.

[JohannesWiesner]

I use Ubuntu and installed NiMARE into an exisiting conda environement, but could also be reproduced on a Windows machine with a fresh conda environment (i.e. conda create -n test pip + pip install nimare)

[JohannesWiesner]

Seems to work though with nimare.extract.fetch_neurosynth(path="."):

INFO:nimare.extract.utils:Dataset created in /home/johannes.wiesner/.nimare/neurosynth
INFO:nimare.extract.extract:Searching for any feature files matching the following criteria: [('path-.', 'data-neurosynth', 'version-7')]
Downloading data-neurosynth_version-7_coordinates.tsv.gz
Downloading data-neurosynth_version-7_metadata.tsv.gz
Downloading data-neurosynth_version-7_vocab-LDA100_keys.tsv
Downloading data-neurosynth_version-7_vocab-LDA100_metadata.json
Downloading data-neurosynth_version-7_vocab-LDA100_source-abstract_type-weight_features.npz
Downloading data-neurosynth_version-7_vocab-LDA100_vocabulary.txt
Downloading data-neurosynth_version-7_vocab-LDA200_keys.tsv
Downloading data-neurosynth_version-7_vocab-LDA200_metadata.json
Downloading data-neurosynth_version-7_vocab-LDA200_source-abstract_type-weight_features.npz
Downloading data-neurosynth_version-7_vocab-LDA200_vocabulary.txt
Downloading data-neurosynth_version-7_vocab-LDA400_keys.tsv
Downloading data-neurosynth_version-7_vocab-LDA400_metadata.json
Downloading data-neurosynth_version-7_vocab-LDA400_source-abstract_type-weight_features.npz
Downloading data-neurosynth_version-7_vocab-LDA400_vocabulary.txt
Downloading data-neurosynth_version-7_vocab-LDA50_keys.tsv
Downloading data-neurosynth_version-7_vocab-LDA50_metadata.json
Downloading data-neurosynth_version-7_vocab-LDA50_source-abstract_type-weight_features.npz
Downloading data-neurosynth_version-7_vocab-LDA50_vocabulary.txt
Downloading data-neurosynth_version-7_vocab-terms_source-abstract_type-tfidf_features.npz
Downloading data-neurosynth_version-7_vocab-terms_vocabulary.txt

I think this is might be a string-parsing bug that appears when you set path to some other string than "."

[JulioAPeraza]

I think this issue comes from the unpack argument. In that call (nimare.extract.fetch_neurosynth("../data", unpack=True)), the parameter is interpreted as a kwargs and then passed to _fetch_database.

Starting in version 0.0.10 we are using a new format for fetching Neurosynth and NeuroQuery databases. The parameters url and unpack were removed, and we changed the parameter path to data_dir.

You would find an example with the new format here: https://nimare.readthedocs.io/en/stable/auto_examples/01_datasets/02_download_neurosynth.html#download-neurosynth

[jdkent]

Closing this issue for now, let us know if we did not answer your question fully and I'll reopen, thanks!