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Add ability to provide T2* map as input #407

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@tsalo

Description

@tsalo

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

  1. Add tedana workflow argument for T2* map.
  2. Add CLI parameter for T2* map.
  3. Check T2* map shape and affine against input data shapes and affines.
  4. If the T2* map is provided, use that one for optimal combination instead of running fit_decay within the workflow.

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