Generate json and yaml files from the BIDS tree, use image03

agt24 commented 1 month ago

A short summary of what you would like to see in the uploader.

Briefly summarizing discussing between @agt24 @ericearl and @hjbockholt on Friday Jun 14, 2024. Additional details to be added later.

The goal is a tool to automate (as much as possible) depositing dataset in OpenNeuro and OpenNeuroPET into the NIMH Data Archive (NDA).

This repo is a fork of code @ericearl had written previously for the DCAN labs that does much of the heavy lifting already (especially with respect to creating manifest files). However, a few modification are needed:

The current tool is focused on fmriresults01 from the NDA data dictionary. We will instead use the image03 datatype from the NDA data dictionary.
The current tool requires the user to create a json and yaml file manual. In the modified version, this information will be extracted from files in the BIDS tree.
Our test case for development will be a recent PET dataset from NIMH https://openneuro.org/datasets/ds004733

Do you have any interest in helping implement the feature?

Yes!

Add any additional information or context about the request here.

No response

ericearl commented 1 month ago

Regarding:

This repo is a fork of code @ericearl had written previously for the DCAN labs that does much of the heavy lifting already

I would like to give credit where credit is due to:

Natalie Alton (who did most of the up-front work with my guidance)
Anders Perrone
Luci Moore
Jacob Lundquist
rae McCollum
Audrey Houghton

Also this way you know not all the bugs and gaps in documentation are my fault. 😄 Go team!

agt24 commented 2 weeks ago

@hjbockholt & @pbbaba Just checking in on this project. Let us know if we can help with getting things started

agt24 commented 6 days ago

@hjbockholt @pbbaba @vdcalhoun Anything we can assist with on this project?

hjbockholt commented 6 days ago

Hi We just met today and plan to have an update on this tomorrow Sorry for the delay we have hi gs in place now for Pooja and I both to didn’t time in this each day going forward

On Thu, Jul 11, 2024 at 14:31 Adam Thomas @.***> wrote:

@hjbockholt https://github.com/hjbockholt @pbbaba https://github.com/pbbaba @vdcalhoun https://github.com/vdcalhoun Anything we can assist with on this project?

— Reply to this email directly, view it on GitHub https://github.com/nimh-dsst/nda-bids-upload/issues/1#issuecomment-2223627460, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAY564RXRACNDZJ6DULCFMLZL3FRVAVCNFSM6AAAAABJK5EGYCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMRTGYZDONBWGA . You are receiving this because you were mentioned.Message ID: @.***>

nimh-dsst / nda-bids-upload