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nipreps / fmripost-aroma

Run ICA-AROMA on fMRIPrep derivatives
https://fmripost-aroma.readthedocs.io/
Apache License 2.0
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BIDS App structure #1

Open effigies opened 1 year ago

effigies commented 1 year ago

fmripost-aroma should be a BIDS app of the form:

fmripost-aroma <bids-dir> <out-dir> participant -d <fmriprep-dir> [OPTIONS]

The reason for taking the fmriprep directory as a separate derivative input is to permit the utility to retrieve some data from the raw dataset instead of relying entirely on the fmriprep derivatives. This will become necessary when fMRIPrep supports a minimal mode where only transforms are generated, so we might as well start the CLI where we expect it to end.

We should include the CLI arguments --melodic-dimensionality and --error-on-warnings, corresponding to the fMRIPrep arguments --aroma-melodic-dimensionality and --error-on-aroma-warnings.

geowk commented 3 months ago

Is fmipost-aroma available for use or is it still in the beginning stages of development?

thanks.

-g

tsalo commented 3 months ago

It's still in the beginning stages.

tsalo commented 2 months ago

Given #12, I believe the CLI will need two basic configurations. In the first scenario (the original one above), users have the raw dataset and fMRIPrep derivatives with at least minimal outputs.

fmripost-aroma <bids-dir> <out-dir> participant -d fmriprep=<fmriprep-dir> [OPTIONS]

In the second scenario, users have fMRIPrep derivatives with resampling or full outputs.

fmripost-aroma <fmriprep-dir> <out-dir> participant [OPTIONS]