Fmriprep- extension of the task flag to support multiple tasks

1

Hi,

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)

i.e.-
-t TASK_ID
should be generalized to handle more than 1 task id.

Thanks!

2

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?

1 Like
3

Hi,
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.

4

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.

5

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.

1 Like
6

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:

7

I would probably try just with:

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

And also page @bpinsard :slight_smile:

1 Like
8

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