change participant-label to participant_label

[yibeichan]

Hi this is related to #184
i checked that most BIDS Apps here (https://bids-website.readthedocs.io/en/latest/tools/bids-apps.html) uses --participant_label. for those which use --participant-label (e.g., fmriprep) also support --participant_label. so maybe it's better for us to use --participant_label

[tsalo]

Hm... fMRIPrep mostly only supports dashes in its CLI parameters, so --participant_label is a bit of a one-off. With QSIPrep and QSIRecon (and probably XCP-D in the future) we only support --participant-label. so this might be something we need to configure on an app-by-app basis. @mattcieslak @tientong98 WDYT?

[mattcieslak]

yes, we'll have to configure it somehow. Maybe in the yaml?

[yibeichan]

we can either specify it if-else for certain bids-apps in the code, or add --participant_label or --participant-label specification somewhere in yaml?

[satra]

it's called --subject-label and only includes ids not sub- : https://bids-standard.github.io/execution-spec/inputs.html#reserved-arguments

i think we need a bids app validator for its input specs. many of those apps were created during a sprint and never updated afterwards. it may be useful to bring this up to the bids spec folks.

[yibeichan]

Hi hi, just wanna follow up on this issue, what would be our solution?

[tien-tong]

Hi @yibeichan, because different BIDS apps have different flags for this, so we think the best way is to add participant-selection-flag to the config yaml file, and babs-init will use that to write the apptainer run cmd. I can work on this in a bit.

[yibeichan]

@tientong98 thank you! if you're gonna work on this, we can close this current PR