BEP Proposal: Atlas specification

[jdkent]

Your idea

EDIT

github draft for current discussion: https://github.com/PESTILLILAB/bids-specification/blob/bep038/src/atlas.md

the google doc draft (deprecated in favor of the github draft) : https://docs.google.com/document/d/1RxW4cARr3-EiBEcXjLpSIVidvnUSHE7yJCUY91i5TfM/edit?usp=sharing

[PeerHerholz]

We currently aim to organize a meeting to further discuss the atlas-related BEP developments in #1379.

[CPernet]

yo, count me in

[PeerHerholz]

Hi @bids-standard/maintainers,

as we aim to share our draft with the community to receive and integrate feedback soon, we would like to ask if it would be possible to move our BEP to the next stage. More specifically, this refers to step 5 of the BEP development guide, ie making the BEP official and obtaining a number. We followed and conducted steps 1-3 and would now like to access if the requirements for step 4 were fulfilled and if not, what would be missing to achieve this.

We are aware of the current status concerning the two atlas-related BEPs and one of our team (myself) will attend the next maintainers meeting to discuss if the outlined procedure is feasible. However, based on the so-far positive nature of the received feedback on this matter we nevertheless already wanted to ask regarding the further steps.

If you have any questions, please don't hesitate to ask.
We're looking forward to working with you on this.

Best, Peer

[PeerHerholz]

Hi everyone,

I just wanted to follow up on my earlier message: would it be possible to evaluate if the requirements for step 4 were fulfilled and if not, indicate what we would need to do to achieve this?

It would be great to hear from you.

Best, Peer

[CPernet]

@effigies you were there at the steering group meeting, and while we are still a little unsure of some specific aspects, I cannot see any reasons not to move on stage 4 - IMO +1

[sappelhoff]

reposted from other thread:

Hi @PeerHerholz, thanks for the patience -- I am not sure I'm the correct person to judge this, but to obtain a number you may open a PR to the bids-website repo by editing these files. We can then discuss in that PR and potentially approve and merge it, and then you'll have the official number :-)

• https://github.com/bids-standard/bids-website/tree/gh-pages/_bep_collection
• https://github.com/bids-standard/bids-website/blob/gh-pages/_data/beps.yml

[PeerHerholz]

Hi @sappelhoff,

thanks for getting back to us and the information. We opened a respective PR here.

Looking forward to the discussion!

Cheers, Peer

[PeerHerholz]

Hello @bids-standard/maintainers, @bids-standard/steering & everyone,

I hope you're doing fine.

We (@jdkent, @dorahermes, @francopestilli, @dlevitas, @poldrack, @CPernet, @melanieganz, @mnoergaard, @mathesong, @bendhouseart, @MaxvandenBoom and others) continued to work on BEP038 - Atlases. We would like to finalize Step 9 of the BEP development process: Incorporate the feedback and strive for consensus. . Thus, I thought about creating a dedicated issue within which we can track what is still needed in order to do so.

If y'all could have a look at the draft again and share your thoughts re the current status and if something/what definitely still needs to be addressed, that would be great! I'll start a list below and will keep editing it based on your comments.

Needs to be addressed

• PR [SCHEMA][ENH] Remove atlas entity and replace it with seg in prep of BEP038 #1579
• Electrophysiology example/pointer
• "atlas" as "DatasetType", ie no modality tag(s)
• outline differences and files of BEP17

Would be cool to address but not necessary

Thanks so much again for all your help and effort, we highly appreciated it.

[melanieganz]

Thanks @PeerHerholz! And please check out the atlas PR and voice your opinions, so we ensure to address all concerns before moving forward.

[PeerHerholz]

Thanks @melanieganz! I/we keep monitoring the PR closely but so far we haven't noticed any major issues concerning the BEP. IMHO it's better to see what the PR leads to and then adapt the BEP respectively as this would greatly enhance adaptation and streamline the process (I think for the BEP this would most likely mean smaller changes, ie changing some definitions and naming patterns).

[PeerHerholz]

Hi everyone,

given that #1579 was merged, I think we can proceed with finalizing the draft.

Could I please ask everyone, the moderators/leads (@eduff, @jdkent) and contributors (@dorahermes, @francopestilli, @dlevitas, @poldrack, @CPernet, @melanieganz, @mnoergaard, @mathesong, @bendhouseart, @MaxvandenBoom, @dlevitas) to have another look at the BEP and indicate problems that should be addressed before we're moving forward (except the ones listed above)?

Thank you very much for your continued supported, we highly appreciate it.

Cheers, Peer

[CPernet]

• PR [SCHEMA][ENH] Remove atlas entity and replace it with seg in prep of BEP038 #1579
• Electrophysiology example --> given the scope, we said no need of that - correct?
• "atlas" as "DatasetType", ie no modality tag(s) --> I still think we need to constrain a little more the _*map.[ext] proposal but also we should move along with it to progress

[PeerHerholz]

Thx for the reply and comments @CPernet!

Electrophysiology example --> given the scope, we said no need of that - correct?

Sure thing, we can remove it for the time being and add one if needed.

"atlas" as "DatasetType", ie no modality tag(s) --> I still think we need to constrain a little more the _*map.[ext] proposal but also we should move along with it to progress

I'm actually not sure if #1602 applies here, ie for atlases, or did you mean PET-related things more generally? However, I agree that we should try to move forward.