We can start with the Freesurfer one and check implementation difficulty for the other ones (functional networks, etc.).
Still need to figure out some things regarding how to manage software dependencies and containers, etc.
One idea would be for extractors to be scripts that are not Nipoppy-aware, so the inputs are just paths to files/directories that are pipeline outputs. But the outputs would have to follow some standard (e.g. subjects/session labelling). Then we could have a Boutiques descriptor (e.g. freesurfer-extractor.json) for it, and the extractor workflow would loop over subjects/sessions who completed the pipeline, run the extractor script for all of them, then potentially aggregate them into a single file (or not).
We can start with the Freesurfer one and check implementation difficulty for the other ones (functional networks, etc.).
Still need to figure out some things regarding how to manage software dependencies and containers, etc.
One idea would be for extractors to be scripts that are not Nipoppy-aware, so the inputs are just paths to files/directories that are pipeline outputs. But the outputs would have to follow some standard (e.g. subjects/session labelling). Then we could have a Boutiques descriptor (e.g.
freesurfer-extractor.json) for it, and the extractor workflow would loop over subjects/sessions who completed the pipeline, run the extractor script for all of them, then potentially aggregate them into a single file (or not).