[REF, DOC] Document PAID combination method #264
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- Rename combmode value “ste” to “paid” - Rename variable “ste” to “source_tes” for clarity - Drop PAID support from tedana (because PAID requires smoothed data and multi-echo denoising does not work with smoothed data) but keep it in t2smap workflow.
tsalo
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tsalo
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docs/approach.rst
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| The tedana package also supports another method for optimal combination that | ||
| does not use :math:`T_{2}^*`, known as the parallel-acquired inhomogeneity | ||
| desensitized (PAID) ME-fMRI combination method (`Poser et al., 2006`_). | ||
| This method is not supported in the tedana workflow, however, because |
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Since the t2smap workflow is called as part of the tedana workflow, this is a little confusing, to me.
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We could hypothetically allow users to run tedana without denoising (e.g., --disable-denoising?), which would be the same as the t2smap workflow, but that would mean managing how the combmode and denoising arguments interact (i.e., using paid and denoising should raise a warning and switch paid to t2s automatically).
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Right, sorry, I wasn't thinking quite like that ! I just meant that it is technically in the tedana workflow, but it's not accessible, you're right.
Maybe we could just say something like
This method specifically assumes that noise in the acquired echoes is "isotopic and
homogeneous throughout the image," meaning it should be used on smoothed data.
As we do not recommend performing tedana denoising on smoothed data,
we discourage using PAID within the tedana workflow.
We do, however, make it accessible as an alternative combination method
in the t2smap workflow.
Co-Authored-By: tsalo <tsalo006@fiu.edu>
Codecov Report
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Co-Authored-By: tsalo <tsalo006@fiu.edu>
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Not sure how I "dismissed" your review, but I just added a commit with the requested change. I also think using [skip ci] might have made a mess of things somehow? |
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@tsalo @emdupre - is the protected branch setup to dismiss reviews when there are new commits? That might explain @tsalo question above (#264 (comment))! |
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Yes, sorry, that's how it's set up ! Happy to think about whether that makes sense, but I went ahead and re-approved, for now 😸 |
Closes #210, #214. This was originally part of #247, but has been split off because it is self-contained and should be merged separately.
Changes proposed in this pull request:
combmodevalue “ste” to “paid”stetosource_tesfor clarity