Fmriprep- extension of the task flag to support multiple tasks


I think it would be very useful if there will be an option to specify multiple tasks (not all tasks as in the default… but multiple)

should be generalized to handle more than 1 task id.


Hi. The issues page is a better place to make feature suggestions. I agree this would be useful. Would you have any time and interest in submitting a patch?

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Sorry- you are right.

Unfortunately I’m quite overloaded these days, but I’d love to find some time for contribution- probably in about 4-5 months from now (if time will allow beforehand- it would be great).
Many many thanks for anyone involved in the development- will do my best to find the time for contribution as soon as possible.

Hello! Any chance there’s support for this now? Or does the --task-id flag still only handle one task?

I checked GitHub to see if this feature was listed as an issue, but couldn’t find anything. I can submit one if not.

I think you should be able to do that with the --bids-filters argument. We probably should deprecate --task-id and other ad-hoc selectors (except for the participant ID).

Otherwise, if the community considers that keeping --task-id would be interesting, your offer for improving --task-id will be definitely welcome.

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Oooh!! I didn’t see the new --bids-filter-file flag!! I love this new feature!! Sorry about that! That is exactly what I’m looking to do! Thank you!

In which case, I think it would make sense to deprecate --task-id in future versions (but definitely low priority).

If I wanted to preprocess only two tasks without a session label and a fieldmap (labeled run-01). Can I pass a .json file that looks something like this?

    "t1w": {
        "datatype": "anat",
        "suffix": "T1w"
    "bold": {
        "datatype": "func",
        "task": ["task1", "task2"],
        "suffix": "bold"
    "fmap": {
        "datatype": "fmap",
        "run": "01",

Thanks for your help!

Update: That didn’t work (:laughing:). I can’t find any documentation about adding a “task” field in the .json file :frowning:

I would probably try just with:

  "bold": {"task": ["task1", "task2"]}

And also page @bpinsard :slight_smile:

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Looks like that works (so far)! Thanks so much!