[Neuroimaging] ANN: openneuro-py, a new app for downloading OpenNeuro datasets

[Christopher Markiewicz]

Hi all,

FWIW almost all public datasets have been pushed to GitHub and can be accessed via datalad (exceptions being tracked on these issues: https://github.com/OpenNeuroOrg/openneuro/issues/1741 and https://github.com/OpenNeuroOrg/openneuro/issues/1743).

    datalad install https://github.com/OpenNeuroDatasets/ds00WXYZ.git

Datalad makes it pretty straightforward to download only the portions of the data you want.

This isn't to deprecate Richard's tool. There are some things only doable through the API at present (uploading, accessing private data) and I would also find a Python interface much more comprehensible and hackable. Just want to make it clear that in many cases you can bypass the website and API altogether.

Best,
Chris

________________________________________
From: Neuroimaging <neuroimaging-bounces+markiewicz=stanford.edu at python.org> on behalf of Aldo Camargo <aldo.camargo at gmail.com>
Sent: Tuesday, December 15, 2020 9:45 AM
To: Neuroimaging analysis in Python
Subject: Re: [Neuroimaging] ANN: openneuro-py, a new app for downloading OpenNeuro datasets

Hi Richard,

Very interesting application. One question, which dataset can be downloaded?

Thanks a lot,

Aldo

On Mon, Dec 14, 2020 at 2:24 PM Eleftherios Garyfallidis <garyfallidis at gmail.com<mailto:garyfallidis at gmail.com>> wrote:
Hi Richard,
Thank you for sharing.
Best,
Eleftherios

On Mon, Dec 14, 2020 at 1:33 PM Richard Höchenberger <richard.hoechenberger at gmail.com<mailto:richard.hoechenberger at gmail.com>> wrote:
Hello all,

many of you may know https://openneuro.org, the platform for sharing neuroimaging and electrophysiological data.

I was experiencing a little bit of trouble downloading datasets with the official openneuro-cli application, so I started my own app, named openneuro-py.

openneuro-py is a command line tool that allows one to retrieve OpenNeuro datasets. You can restrict downloading to only a subset of files or directories, or exclude specific items from the download if you wish. Interrupted downloads may be resumed at a later time.

You can find installation and usage instructions, and of course the source code, at https://github.com/hoechenberger/openneuro-py

This project is literally just two days old, so there are probably bugs and missing features. However, I think it could already be of use to some of you. I'd love to hear your feedback! Either open an issue on the GitHub page, or drop me an email. And if you feel like contributing – go ahead, that would be awesome!

Enjoy,
and stay healthy!

   Richard

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