Closed
Description
Summary
We should be able to provide T2* maps directly to the workflow, either as a prior or as a complete replacement for the map calculated within the workflow.
Additional Detail
The ability to provide T2* maps should be beneficial in two cases (as far as I can see): (1) when the user has a quantitative T2* map from a separate sequence and (2) for applying a two-stage denoising model that incorporates echo-specific denoising. In the latter case, the workflow would be: (1) run tedana on the minimally preprocessed data, (2) apply echo-specific denoising (e.g., phase regression, aCompCor, tCompCor) to the minimally preprocessed data, and (3) re-run tedana workflow with estimated T2* map, ICA mixing matrix, and component table from Step 1.
Next Steps
- Add tedana workflow argument for T2* map.
- Add CLI parameter for T2* map.
- Check T2* map shape and affine against input data shapes and affines.
- If the T2* map is provided, use that one for optimal combination instead of running
fit_decay
within the workflow.