[Neuroimaging] Planning for data formats - upcoming journal club

Matthew Brett matthew.brett at gmail.com
Wed Nov 17 11:57:54 EST 2021 

Dear all,

There haven't been any responses on the Doodle poll in the last day or
so, so time to call it for the meeting time.

It looks like November 24th at 19:00 - 20:30 UTC is the best date
overall, with 12 green ticks and one orange, so let's go with that.

I'll send out a Zoom invite soon,

Cheers,

Matthew

On Fri, Nov 12, 2021 at 11:45 AM Matthew Brett <matthew.brett at gmail.com> wrote:
>
> Hi,
>
> I've put up a Doodle poll for the journal club, having failed to work
> out how to do the same job in Calendly:
>
> https://doodle.com/poll/5vwkdt7zic2bu3wn
>
> Please do fill in your times there,
>
> Cheers,
>
> Matthew
>
> On Wed, Nov 10, 2021 at 7:22 PM François Rheault
> <Francois.M.Rheault at usherbrooke.ca> wrote:
> >
> > Hi,
> >
> > I would be happy to discuss and collaborate on this! Because of COVID the whole project slowed down quite a bit and I needed help for an external implementation of a prototype. I will try to push everyone involve (yet again) to make sure the project is alive and well!
> >
> > Francois Rheault
> >
> > Université de Sherbrooke
> >
> > ________________________________
> > De : Franco Pestilli <pestilli at utexas.edu>
> > Envoyé : 10 novembre 2021 06:58
> > À : Neuroimaging analysis in Python <neuroimaging at python.org>; François Rheault <Francois.M.Rheault at usherbrooke.ca>
> > Objet : Re: [Neuroimaging] Planning for data formats - upcoming journal club
> >
> > 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
> >
> > 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>
> > >     _______________________________________________
> > >     Neuroimaging mailing list
> > >     Neuroimaging at python.org <mailto:Neuroimaging at python.org>
> > >     https://mail.python.org/mailman/listinfo/neuroimaging
> > >     <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.python.org%2Fmailman%2Flistinfo%2Fneuroimaging&data=04%7C01%7Cg.flandin%40ucl.ac.uk%7C5ed1afff99ca460e7dc008d9a3b04a6c%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C637720800862364927%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=54jpAtVghfeD5eVfeGJvpcGwgn84E5l1rtvk4CXXV6U%3D&reserved=0>
> > >
> > >
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