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Add ability to denoise data using existing component table #334

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tsalo opened this issue Jun 8, 2019 · 7 comments · Fixed by #508
Closed
1 of 2 tasks

Add ability to denoise data using existing component table #334

tsalo opened this issue Jun 8, 2019 · 7 comments · Fixed by #508
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enhancement issues describing possible enhancements to the project

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@tsalo
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tsalo commented Jun 8, 2019

Summary

We currently support manual identification of accepted components (and could easily extend to rejected components) using comma-separated lists of components. However, additional decision trees (e.g., AROMA) could easily operate by overwriting the original component table with updated classifications. We should be able to simply run tedana with a component table (which may have updated classifications) without a separate list of classifications.

Additional Detail

This will impact our internal logic regarding component tables, the mixing matrix, and manacc (and possibly a future manrej). It could also be a separate post-tedana workflow, if needed.

Next Steps

  • Vote on whether to implement this as a post-tedana workflow or within tedana.
  • Add new workflow or adjust tedana workflow.
@tsalo tsalo added the enhancement issues describing possible enhancements to the project label Jun 8, 2019
@jbteves
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jbteves commented Jun 8, 2019

My intuition is that you would want it to be a post-tedana operation since I would assume you at least want the PCA denoising and optimal combination before you run AROMA. That could be wrong, though, since I don't work with other ICA routines.

@dowdlelt
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I imagine a post-tedana workflow where you provide it with the table and tedana output directory, and it creates a new output directory, applying the new classifications, regenerating the denoised data, noise component timeseries for inspection, etc.

@emdupre
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emdupre commented Jun 19, 2019

I like the idea of incorporating it into tedana in that it'd be great to be able to just update the classification table instead of providing a list to manacc. I personally find using manual classification really clunky right now, and I'd prefer to let users supply a new table.

Not a strong preference, since there are other ways we could update manacc, but just my 2c !

@emdupre
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emdupre commented Nov 8, 2019

Is this related to #407 or #344 ?

@tsalo
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tsalo commented Nov 8, 2019

More #407 than #344. #407 should make it possible to denoise data the exact same way as the original denoising using the existing workflow. In its current form, even with a mixing matrix and component table provided, T2* estimation and optimal combination will still be performed from scratch. Both are deterministic, so in practice this isn't a problem, but still...

@stale
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stale bot commented Feb 6, 2020

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions to tedana:tada: !

@stale stale bot added the stale label Feb 6, 2020
@stale stale bot closed this as completed Feb 13, 2020
@tsalo
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tsalo commented Feb 21, 2020

I think this should have been closed by #508 🤦‍♂

@tsalo tsalo linked a pull request Feb 21, 2020 that will close this issue
@tsalo tsalo removed the stale label Feb 21, 2020
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