matlab based dataset template generator?

INT-NIT / BEP032tools

Software tools supporting the BIDS Extension Proposal (BEP) dedicated to adding support for electrophysiological data recorded in animal models (BEP032)

MIT License

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matlab based dataset template generator? #119

Open Remi-Gau opened 2 years ago

Remi-Gau commented 2 years ago

I have no idea how many people in animal ephys tend to use Matlab rather than python, but using bids-matlab I should be able to create something equivalent to the template generator you have in python.

Let me know if that is something potentially interesting.

SylvainTakerkart commented 2 years ago

Hi Rémi, I believe there's a good amount of matlab users out there... But at the moment, we don't have any direct contacts with some that have expressed an interest in BIDS-ephys, and we're lacking man-power to try to drag them to BIDS... This would clearly be a good addition to the BIDS-ephys ecosystem to help in that regard, but in the middle of everything else, I'm just wondering what kind of priority we should give to this project... @Remi-Gau , do you know of any potential users that would be interested in the short term? @JuliaSprenger WDYT?

JuliaSprenger commented 2 years ago

Hi @Remi-Gau ! Yes, I think there's definitely some matlab users still around in the community. I didn't look into bids-matlab yet, so I can't estimate how time intense it is to extend it to a new modality. If it's designed to be extended in a simple fashion, then we should definitely go for it.

Remi-Gau commented 2 years ago

Well I am pretty much the lead maintainer of bids matlab so...

If it is a matter of creating a small script to generate template datasets, no specific change to bids matlab is required and I can do that fairly quickly.

Adapting to ephys:

in "strict" mode bids-matlab works with the BIDS schema so ephys data will only be indexed if I do a small tweak to the JSON version of the schema hosted in the bids-matlab repo (most likely in a separate branch).
in "tolerant" mode bids matlab can index any file as long as it follows the BIDS filenaming conventions:
- this-would_be-indexed_because-hyphens_and-underscores_are-in_where-they_should.be
- this_file_would_be.skipped

Remi-Gau commented 2 years ago

Getting some sort of draft for a dataset template generator for Matlab: https://github.com/Remi-Gau/bids-matlab/blob/ephys_ds_generator/examples/ephys_templates.ipynb

Should work in the bids-matlab binder too: https://mybinder.org/v2/gh/Remi-Gau/bids-matlab/ephys_ds_generator?labpath=examples%2Fephys_templates.ipynb

Required me to start drafting the BIDS schema for ephys: nothing big for now. https://github.com/Remi-Gau/bids-matlab/blob/ephys_ds_generator/bids-specification/src/schema/rules/datatypes/ephys.yaml