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sccn / EEG-BIDS

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default readme in BIDS dataset after conversion #143

Closed Remi-Gau closed 3 months ago

Remi-Gau commented 2 years ago

hey

We (BIDS maintainers) are trying to see if we can improve the quality of the average README in BIDS dataset. Those tend to be pretty thin and are missing some information we would like to see there even if it cannot be formalized "yet" into the BIDS specification.

Hoping to leverage the bids converters to help to do.

So I am going around the different BIDS converters repo to see if we can start improving the default README they put in a the BIDS dataset.

There is template that is provided in the BIDS starter kit: https://github.com/bids-standard/bids-starter-kit/blob/main/templates/README.MD

Some possible options:

  1. use this template is
  2. use a subset of it
  3. add a link to the template README
  4. something else (a mix of 2 and 3?)

What do you think? I can try to open a PR if you want.

Also let us know if you think that the template README in the starter kit could / should be improved .

Feel free to disregard if you are already using some version of the template README.

arnodelorme commented 2 years ago

This is a worthwhile endeavor. I think this should be formalized in a sidecar file to be useful although as a first step a README file might be useful. Attaching the Fields OpenNeuro uses on their website. It would greatly increase adoption if you use the same. Also OpenNeuro could automatically generate sidecar files since they have that Information in their database.

4 screen captures. The bottom is the one you get when you upload a dataset. Top screen captures are the 3 pop-up entry expanded (species, study type and DX status).

arnodelorme commented 2 years ago

Screen Shot 2022-08-08 at 9 46 55 AM Screen Shot 2022-08-08 at 9 46 49 AM Screen Shot 2022-08-08 at 9 46 42 AM Screen Shot 2022-08-08 at 9 46 20 AM

arnodelorme commented 2 years ago

CCing @robertoostenveld and @sappelhoff (please move the discussion to relevant BIDS channels, although it probably has already occurred there?).

Remi-Gau commented 2 years ago

This is a worthwhile endeavor. I think this should be formalized in a sidecar file to be useful although as a first step a README file might be useful.

If you mean that some of the info in the template README should be formalized as proper field in the dataset_description or in another JSON, I am totally on board with you: also why I was suggesting maybe just pointing the template in the starter kit because we could just update this one as some of those information (hopefully) get more formalized into the spec.

Attaching the Fields OpenNeuro uses on their website. It would greatly increase adoption if you use the same. Also OpenNeuro could automatically generate sidecar files since they have that Information in their database. 4 screen captures. The bottom is the one you get when you upload a dataset. Top screen captures are the 3 pop-up entry expanded (species, study type and DX status).

Good idea: Will add that into the template.

Will cross check what dataset metadata are also required on Neurovault: not for MEEG but may give some ideas as to what type of metadata could be worth adding.

robertoostenveld commented 1 year ago

For reference, https://github.com/fieldtrip/fieldtrip/pull/2286 is how I propose to do it with FieldTrip. It allows the user to specify a multi-line string in their script, and it uses the template README from the starter kit as default.