[Neuroimaging] Planning for data formats - upcoming journal club

Wed Nov 10 12:58:45 EST 2021

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/<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fosf.io%2Ft4nxy%2F&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003298394%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qmDirnQP0F%2Fc%2FOM5ZITqlgzN5zaWJaKjIiuOuPB9Mlc%3D&reserved=0>
And the tractography file format was one of interests we were discussing @fFrançois Rheault<mailto: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<mailto: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<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fbids-standard%2Fbids-specification%2Fissues%2F197&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003308352%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=tHToRUy%2FTrrBcDRKqxbGMx9KHkwe%2Fbg%2Bhk2GIbHZ%2Fbw%3D&reserved=0>
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/<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffrheault%2Ftractography_file_format%2F&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003318307%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=bolUzcycQNb7emSbSzBvIkjVMFDAqOFVQTLNm7r9%2FLM%3D&reserved=0>).
>
> 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>
> <mailto: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://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmatthew-brett%2Fczi-nibabel&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003318307%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=pCwR8VSQXtWIMF2W%2FkjfVizZtTJgipgMlnK9rVPccsw%3D&reserved=0>
>
>     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://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.ascom.2015.06.004&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003328274%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=BMvjxilr8lMMbG4QXssocMRewEPx139LnIEbZ7Lj44Q%3D&reserved=0>
>     <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://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1016%2Fj.ascom.2015.06.004&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003328274%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=BMvjxilr8lMMbG4QXssocMRewEPx139LnIEbZ7Lj44Q%3D&reserved=0>>.
>     (https://www.sciencedirect.com/science/article/pii/S2213133715000645<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2213133715000645&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003338226%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rnjWdOv%2FwsLjtkmEUl3QaGxFVH15IDcL4pTIlwaMByY%3D&reserved=0>
>     <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<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.sciencedirect.com%2Fscience%2Farticle%2Fpii%2FS2213133715000645&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003338226%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=rnjWdOv%2FwsLjtkmEUl3QaGxFVH15IDcL4pTIlwaMByY%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://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcyrille.rossant.net%2Fmoving-away-hdf5%2F&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003348180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qWAeVEf7CIeI4ZlraXsA2ofwITbi0qUW%2BwVA9PZzoIk%3D&reserved=0>
>     <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<https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcyrille.rossant.net%2Fmoving-away-hdf5%2F&data=04%7C01%7CFrancois.M.Rheault%40usherbrooke.ca%7Cb2d16bcb5824410b659608d9a449d6aa%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637721461003348180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qWAeVEf7CIeI4ZlraXsA2ofwITbi0qUW%2BwVA9PZzoIk%3D&reserved=0>>
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