nipreps / fmripost-aroma

Run ICA-AROMA on fMRIPrep derivatives
https://fmripost-aroma.readthedocs.io/
Apache License 2.0
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Infer the slice timing reference from fMRIPrep derivatives #60

Open tsalo opened 2 months ago

tsalo commented 2 months ago

We can either grab StartTime from the preprocessed BOLD file's sidecar or find the config.toml file from the fMRIPrep run and grab the config.workflow.slice_time_ref value.

Also, we might need to either patch in the selected reference as config.workflow.slice_time_ref or modify fmriprep.workflows.bold.stc.init_bold_stc_wf to accept the slice time reference as a parameter.

tsalo commented 1 month ago

If we want to support minimal derivatives, then we need to grab the slice_time_ref from the config file. However, I also think that limits the generalizability of the fMRIPost workflow. I think we want these fMRIPost workflows to theoretically work on any BIDS-compliant derivatives dataset with the right outputs, and the config file is a Nipreps-specific creation.

effigies commented 1 month ago

If you're doing minimal derivatives, you need to run the STC yourself, so you can give end-users the choice or make it for them.