[Neuroimaging] Planning for data formats - upcoming journal club
fangqq at gmail.com
Wed Nov 24 01:04:31 EST 2021
Dear list, just want to share this offline self-intro to Matt, following
the thread of data format discussions - I look forward to the journal
club discussions tomorrow.
-------- Forwarded Message --------
Subject: Fwd: data formats
Date: Thu, 11 Nov 2021 15:03:17 -0500
From: Qianqian Fang <q.fang at northeastern.edu>
To: matthew.brett at gmail.com
CC: Guillaume Flandin <g.flandin at ucl.ac.uk>
Guillaume forwarded me a thread of discussions
regarding an upcoming journal club on data formats. I tried to register
to the mailing list but it has not been approved (the list is moderated).
just a quick self-introduction - I recently received a U24 award
(NeuroJSON, http://neurojson.org) from the NIH on developing JSON-based
universal data exchange formats (with NoSQL db support) for the broad
neuroimaging community. Robert Oostenveld (BIDS), Guilaume Flandin (SPM)
and a few other project leads (freesurfer, brainstorm, homer ...) are in
You can find more info about the NeuroJSON project on our websites and a
poster at fNIRS2021)
http://neurojson.org (partially completed)
the idea behind is very simple - we want to make data human-readable,
universally parsable with minimal overhead, scalable, and flexible for
future extensions. We have been developing 1-to-1 mapping specifications
to mirror neuroimaging data files to JSON (JNIfTI
etc); the JSON serialization of complex data is based on a lightweight
annotation specification called JData
- supporting N-D strongly-typed binary arrays
trees, graphs, etc. Ultimately, we will map all BIDS folder structure to
a JSON tree and optionally push to a NoSQL db (mongodb, couchdb ...) for
scalability and dissemination.
We currently have lightweight parsers/writers to process JData-styled
for Python (pyjdata <https://pypi.org/project/jdata/> and pybj
<https://pypi.org/project/bjdata/>), MATLAB/Octave (jsonlab
(jsdata <https://github.com/fangq/jsdata/blob/master/jdata.js>) and C/C++.
I'd love to participate this discussion, either as part of the journal
club, or schedule a separate meeting, and present our project
let me know if you are interested.
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