[Neuroimaging] Planning for data formats - upcoming journal club

[Franco Pestilli]

Hi Matthew,

I would love to participate, this would synergize with our efforts of
defining BIDS for Connectivity Derivatives: https://osf.io/t4nxy/
And the tractography file format was one of interests we were
discussing @fFrançois
Rheault <Francois.M.Rheault at usherbrooke.ca>

Cheers
Franco

On Wed, Nov 10, 2021 at 5:42 AM Guillaume Flandin <g.flandin at ucl.ac.uk>
wrote:

> Hi All,
>
> Also interested in attending, time permitting. There has been many
> discussions on this topic over the years across several platforms - one
> of them is captured in Anderson's document but I could also remember
> this one:
>   https://github.com/bids-standard/bids-specification/issues/197
> Compression was also discussed in the early days of BIDS but it seems it
> was a group email exchange with no public archive.
>
> Best,
> Guillaume.
>
> On 09/11/2021 18:32, Ariel Rokem wrote:
> > ⚠ Caution: External sender
> >
> >
> > Hi Matthew and all,
> >
> > Sounds interesting! At some point, we might want to discuss Francois
> > Rheault's (and others') efforts to update the formats for tractography
> > data (https://github.com/frheault/tractography_file_format/).
> >
> > Thanks for organizing!
> > Ariel
> > On Tue, Nov 9, 2021 at 3:32 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
> >
> >     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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.ascom.2015.06.004&data=04%7C01%7Cg.flandin%40ucl.ac.uk%7C5ed1afff99ca460e7dc008d9a3b04a6c%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637720800862344941%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=Z%2FHoOKl4tljjjzQ5IWnHjwMH65eunYlTNIdbIK6CTXI%3D&reserved=0
> >.
> >     (https://www.sciencedirect.com/science/article/pii/S2213133715000645
> >     <
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2213133715000645&data=04%7C01%7Cg.flandin%40ucl.ac.uk%7C5ed1afff99ca460e7dc008d9a3b04a6c%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637720800862354932%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ialaMuABzvWaOXvlBj0KcpzRYYmXrjyLvW8Lm2CnoHc%3D&reserved=0
> >)
> >
> >     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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcyrille.rossant.net%2Fmoving-away-hdf5%2F&data=04%7C01%7Cg.flandin%40ucl.ac.uk%7C5ed1afff99ca460e7dc008d9a3b04a6c%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637720800862354932%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=afzzkSku7KmL1XetF6NaTsmxDDQ8LR5ebFe0q1oov5c%3D&reserved=0
> >
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