BIDS youtube channel and podcast
Remi Gau
Hey everyone,
Short version:
There is BIDS youtube channel: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw
There is a BIDS podcast: https://anchor.fm/bids-maintenance
We are looking for help to create content and run those.
Now for the longer version
As mentioned at the last BIDS town hall there is now a BIDS youtube channel: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw
Its main goals are to try to:
centralize and curate the videos that already out here into a series of thematic playlist (tutorials, BIDS related tools, presentations of BIDS extensions),
host new original content on many aspects of BIDS and the vibrant community around it.
At the moment, you’ll find 3 “BEP debrief” videos where I had a chat with the leads of the most recently merged BIDS extension (ASL, qMRI, PET) to get their view on the whole process of creating extension to BIDS. Big thank you to Melanie, Martin, Agah, Gilles, Patricia and Henk who readily decided to play along for those.
There should soon be a video “BEP briefing” video with Sylvain Takerkart and Julia Sprenger to introduce the BEP 32 on animal electrophysiology where it’s going and what input they are now looking for from the community.
Gilles and Melanie independently suggested that those videos could be turned into podcast episodes. So now there is also a BIDS podcast: https://anchor.fm/bids-maintenance.
I have some other ideas using the same format, for example chats with:
BIDS apps developers
Users telling us about their experience of using BIDS and how they did managed before
Feedback from PIs about the cost and benefits of switching to BIDS
…
But I really would like to get ideas about where this channel could and should go. So don’t hesitate to get in touch (bids.mainten...@gmail.com) if you:
know of some videos out there that are not listed on the channel,
have ideas for some other videos (like if the BEP you are working on needs a bit of publicity to get more community feedback or if you want to make a series of quick video tutorials on BIDS),
know the basics of video shooting and editing and would like to help
want to help in general with content creation
want to help “host the show”, (would love a co-host who is less dude and less white than me)
are interested in creating a mirror of the channel on bilibili to allow access to the content from countries that can’t connect to youtube
want to create content in other languages or help with sub-titles
@+
Rémi
Rémi Gau
Dr Cyril Pernet
As part of Open NeuroPET, I am creating many datasets - those
will be shared under GDPR (ie user registration)
Datasets do not have licenses but have a DUA
-------- in the BIDS spec ---------
A LICENSE file MAY be provided in
addition to the short specification of the used license in the dataset_description.json "License" field. The "License" field and LICENSE file MUST correspond.
The LICENSE file MUST be either in
ASCII or UTF-8 encoding.
what about
allowing DUA? we all know this is coming ...
-- Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow Neurobiology Research Unit Copenhagen University Hospital, Rigshospitalet Building 8057, Blegdamsvej 9 DK-2100 Copenhagen, Denmark wamc...@gmail.com https://cpernet.github.io/ https://orcid.org/0000-0003-4010-4632
Robert Oostenveld
--
We are all colleagues working together to shape brain imaging for tomorrow, please be respectful, gracious, and patient with your fellow group members.
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Dr Cyril, Pernet
Hi all,
As many of us are moving onto derivatives, I realize that different choices are being made regarding how to describe how a derivative set is being made.
Regardless of that choice, I am thinking we should have principles guiding the json derivatives information - here are a few ideas for the community
- how to describe successive steps that lead to the shared
derivative data (e.g. must have 'step-1', 'step-2', must be in a
{} hierarchy, or whatever else we can agree on)
- how to refer to a specific code located into 'code' which generated the data (1) when located in raw when raw are present (raw and derivative shared); (2 when located in raw which is itself another dataset (derivatives shared separately from raw - although I guess they become the raw folder) (3) when shared/available somewhere else
- if using a 'standard pipeline' (say fmriprep) and wanting to indicate the arguments in should this be a 'code' (a one liner .sh for instance) or we could have a 'arguments' key (my prefered option) like
"GeneratedBy": [ { "Name": "fmriprep", "Version": "1.4.1", "Container": { "Type": "docker", "Tag": "poldracklab/fmriprep:1.4.1", }
"Arguments": "fmriprep --xxx --xx"
},
Cyril
-- Dr Cyril Pernet, PhD, OHBM fellow, SSI fellow Neurobiology Research Unit, Building 8057, Blegdamsvej 9 Copenhagen University Hospital, Rigshospitalet DK-2100 Copenhagen, Denmark
tibor...@gmail.com
Hi Cyril,
There is already a BEP in the pipeline on BIDS provenance:
BIDS Extension Proposal (BEP028): Provenance - Google Doc
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
--
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Dr Cyril, Pernet
yes I know but while it may answer my 'steps' issue (though this
is not what other derivatives are doing and that's a concern), it
doesn't addressed other IMO
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Dr Cyril, Pernet
of of course, NIDM is great but BIDS covers a little more than
MRI :-)
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tibor...@gmail.com
I am not sure I can follow…
Although, BIDS-PROV also covers the particular use case of DICOM conversion (specific for MRI) (1.2.a in the Google Doc), it proposes a framework for provenance for BIDS derivatives in general, regardless of the modality (1.2.b in the Google Doc).
It also specifies file structure, format (JSON-LD), and terms allowing linking data and for a more in-depth provenance for less ‘standard’ workflows.
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
Dr Cyril, Pernet
is not not misleading prov vs common derivatives? i'll try that
way in the next few weeks but seems that others been working on
things separate from that model .. (look at any derivative coming
up with their way to do thing) -- seems like a prblm beyond my
specific questions
tibor...@gmail.com
As far as I can see, it is a generic problem of capturing provenance. Ideally, the same model could be used for any provenance, regardless of the processing stage (preprocessing, modelling, inferencing, sharing) or whether it is within the BIDS ecosystem or not. This would ensure a more efficient linkage and query.
For BIDS derivatives, however, it can potentially be simpler when using ‘standard’ workflow (e.g. a BIDS App).
When I read your mail first, I thought it was BIDS-PROV! The only difference is that BIDS-PROV has a specified set of terms.
Paola Di Maio
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tibor...@gmail.com
Hi Paloa,
There is also a more generic effort to build a data model for neuroimaging.
Please, check out http://nidm.nidash.org and feel free to comment and contribute.
Kind regards,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow
School of Psychology, Faculty of Health and Medical Sciences
University of Surrey, Guildford GU2 7XH
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Paola Di Maio
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yarikoptic
worth announcing on twitter (didn't spot it) and promoting. Whenever reaching 100 subscribers, get a dedicated short name like we got for https://www.youtube.com/c/DataLad .
Remi Gau
> There is BIDS youtube channel: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw
worth announcing on twitter (didn't spot it) and promoting. Whenever reaching 100 subscribers, get a dedicated short name like we got for https://www.youtube.com/c/DataLad .
Actually trying to make it a little more visible from the Starter
Kit angle via this pull request.
https://github.com/bids-standard/bids-starter-kit/pull/263
Also don't hesitate to let us know if there are videos / slides that are not listed.
--
We are all colleagues working together to shape brain imaging for tomorrow, please be respectful, gracious, and patient with your fellow group members.
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Rémi Gau