[Neuroimaging] Planning for data formats - upcoming journal club
Dimitri Papadopoulos Orfanos
dimitri.papadopoulos at cea.fr
Tue Nov 9 11:51:01 EST 2021
Hi,
I do not know how much the community has embraced the ISMRM Raw Data
Format (ISMRMRD). It is based on HDF5 so it might be useful to hear from
them and have a look at their format:
https://ismrmrd.github.io
Best,
Dimitri Papadopoulos
Le 09/11/2021 à 15:16, JB Poline a écrit :
> Hi,
>
> Another thing that could be useful would be to have a look at the NWB
> folks experience - they have gone through quite a few pain points - we
> ask one of the developer to give a little talk / summary of their experience
>
> I'd be interested as well
> Cheers
> JB
>
> On Tue, Nov 9, 2021 at 8:48 AM Anderson M. Winkler
> <andersonwinkler at gmail.com <mailto:andersonwinkler at gmail.com>> wrote:
>
> 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
> (https://docs.google.com/document/d/1s5DX4YPS680mc3Rb9msLetrjlPcDhaw835Um-jJb-Dw/edit?usp=sharing
> <https://docs.google.com/document/d/1s5DX4YPS680mc3Rb9msLetrjlPcDhaw835Um-jJb-Dw/edit?usp=sharing>)
> and as a starting point, made a mapping to how we'd store NIFTI as
> HDF5
> (https://docs.google.com/document/d/1hL27J2wNqHj27aX3VrCY8ajHyIBYtgYVmNmSoZZC8aA/edit?usp=sharing
> <https://docs.google.com/document/d/1hL27J2wNqHj27aX3VrCY8ajHyIBYtgYVmNmSoZZC8aA/edit?usp=sharing>).
>
> 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 this.
>
> Cheers,
>
> Anderson
>
>
> On Tue, Nov 9, 2021 at 8:24 AM KEVEEN RODRIGUEZ ZAPATA
> <keveen.rodriguez at udea.edu.co <mailto: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 <mailto: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
> <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://doi.org/10.1016/j.ascom.2015.06.004>.
> (https://www.sciencedirect.com/science/article/pii/S2213133715000645
> <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/
> <https://cyrille.rossant.net/moving-away-hdf5/>
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> --
>
> Keveen Rodríguez Zapata
> B.Eng. Bioengineer
> Msc. Student in Biomedical Sciences: Neuroscience and Bsc.
> Computer Science
> GRUNECO
> Universidad de Antioquia
>
> <http://www.biomaterialesudea.com.co>
>
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