[Neuroimaging] Planning for data formats - upcoming journal club

Anderson M. Winkler andersonwinkler at gmail.com
Tue Nov 9 08:47:02 EST 2021

Hi Matthew, hi all,

I put some thinking on this a few years ago and concluded that HDF5 would
be ideal. The blog post you link was already up and I didn't feel deterred
by it, despite the interesting insights.

At the time I put online a document for discussion (
and as a starting point, made a mapping to how we'd store NIFTI as HDF5 (

At the end, I had to focus on other things, including career (and country)
moves, and couldn't spend time and effort on this, despite the fact that
the needs from then continue very much the same as today (if not perhaps
even more needed now than then...).

I'd be happy to participate in any effort you or others may lead towards



On Tue, Nov 9, 2021 at 8:24 AM KEVEEN RODRIGUEZ ZAPATA <
keveen.rodriguez at udea.edu.co> wrote:

> Hello, thanks for the initiative Matthew, I would like to be part of the
> schedule.
> On Tue, 9 Nov 2021 at 6:32 AM Matthew Brett <matthew.brett at gmail.com>
> wrote:
>> Hi,
>> Summary:  we are planning to do a journal club to discuss new
>> neuroimaging data formats.  Please let me (Matthew) know if you want
>> to be included in the scheduling for the journal club.  Of course,
>> once we've got a time, anyone can join the journal club Zoom.
>> Detail:
>> As part of the Chan-Zuckerberg grant work, we are thinking about new
>> formats for using and sharing neuroimaging data.
>> As you can see in the grant documents:
>> https://github.com/matthew-brett/czi-nibabel
>> we've been thinking about HDF5, but further research (e.g. [1]) has
>> given us some pause for reflection.  Meanwhile, the astronomy
>> community has done some serious thinking about this, and written this
>> up in a paper proposing a new astronomy format:
>> Greenfield, M. Droettboom, E. Bray,
>> ASDF: A new data format for astronomy,
>> Astronomy and Computing,
>> Volume 12,
>> 2015,
>> Pages 240-251,
>> ISSN 2213-1337,
>> https://doi.org/10.1016/j.ascom.2015.06.004.
>> (https://www.sciencedirect.com/science/article/pii/S2213133715000645)
>> Both the discussion and the format seem like a very good starting
>> point for our own thinking about data formats, so we'd like to have a
>> journal club to discuss it.
>> I (Matthew) am going to organize this via Calendly, and I've made a
>> Caldendly account for Nipy-related stuff, but, if you want to have a
>> say in when we do the journal club, please let me know so I can add
>> you to that account.  I'll publish the Calendly link in a day or so.
>> Cheers,
>> Matthew
>> [1] https://cyrille.rossant.net/moving-away-hdf5/
>> _______________________________________________
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>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
> --
> Keveen Rodríguez Zapata
> B.Eng. Bioengineer
> Msc. Student in Biomedical Sciences: Neuroscience and Bsc. Computer Science
> Universidad de Antioquia
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