[Neuroimaging] Planning for data formats - upcoming journal club

Anderson M. Winkler andersonwinkler at gmail.com
Tue Nov 9 11:46:40 EST 2021

Hi Matthew,

Good point. It would probably be a good idea to start a fresh one, more
focused on what is more current (BIDS, for example, came a long way since
2016). Maybe include a link in the new doc to that old discussion so it
doesn't get lost and we don't necessarily reiterate the same arguments --
and also think about addressing concerns where they existed. I think I
received further feedback at the time, I'll dig up my email this afternoon
and if I find I'll add to the old doc.

It's good to revisit this topic!

Thanks thanks!



On Tue, Nov 9, 2021 at 11:21 AM Matthew Brett <matthew.brett at gmail.com>

> Hi,
> On Tue, Nov 9, 2021 at 4:12 PM Satrajit Ghosh <satra at mit.edu> wrote:
> >
> > hi matthew,
> >
> > that paper is a great place to start. is there a document that you have
> where we can add thoughts/pointers to things that have been developed or
> reevaluated between 2015 and now ?
> I haven't got that far yet.  Anderson - I wonder whether your doc is
> good place for that?  Or do we need another one, less focused on HDF5?
> > quick clarification: is the scope of the discussion limited to certain
> types of data (e.g, MRI, transforms - i think this was in the czi proposal)
> or broadly speaking all things neuroimaging (e.g.
> MEG/EEG/Microscopy/Genetics/Surfaces) or even more general (e.g. nd-arrays,
> trees, graphs )?
> Certainly surfaces - these are on the CZI proposal - but I was - at
> the moment - thinking of MRI / CT / PET / transforms.  I haven't
> checked out the BIDS spec in detail - but I had naively imagined
> something that would be compatible with that, and cover the same sort
> of ground - if that proves interesting and necessary.
> For example - I could imagine a version of the nice YaML / binary ASDF
> format for neuroimaging data, that would have the advantage of being
> easily human-readable, being a single file to make copying and sharing
> easier, and allowing formal validation against a JSON schema.  But
> that's really way ahead of where I am now, personally - I've got lots
> of reading and listening to do.
> Cheers,
> Matthew
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://mail.python.org/pipermail/neuroimaging/attachments/20211109/43f31499/attachment.html>

More information about the Neuroimaging mailing list