Multiple documentation updates

[handwerkerd]

Closes #683. Closes #898. Closes #900. Closes #942

This will be a PR to address many of the open issues regarding documentation. As I address more, I'll update this initial message. Others are welcome to work on documentation issues/gap and add to this PR.

Changes proposed in this pull request:

• Adds a reference to fmrwhy in multi-echo.rst (Add fmrwhy to multi-echo resources #683)
• Cleaned up text on distortion correction and spatial normalization in multi-echo.rst (follow-up to Add recommendations for distortion correction #896)
• Edited text on the adaptive mask in approach.rst and added "Why are there so few voxels in my mask?" to faq.rst (Improve documentation on masking options #898)
• Edited text and replaced static figures in outputs.rst ica-components-report. Also linking to the new interactive demo from OHBM2023. (Re-do interactive reports demo in documentation #942)
  • In making the above edits, I also added text on how to interpret each of the report figures. This might also address Listing standards on inspecting components and reclassification #915 but I'm not (yet) going to close it with this PR, pending feedback from others about whether we would include more information elsewhere to fully address Listing standards on inspecting components and reclassification #915.
• Added info about non-steady state volumes to a note in the initial "Multi-echo data" section of approach.rst and as a issue to look for when looking at time series in the reports in outputs.rst "individual-component-view" (Mention dropping non-steady-state volumes in documentation #900)

[codecov]

Codecov Report

Patch and project coverage have no change.

Comparison is base (d11f021) 89.00% compared to head (fb39d0d) 89.00%.

Additional details and impacted files

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  Coverage   89.00%   89.00%           
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  Files          27       27           
  Lines        3411     3411           
  Branches      622      622           
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  Hits         3036     3036           
  Misses        227      227           
  Partials      148      148           

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[tsalo]

@all-contributors please add @handwerkerd for code.

[allcontributors]

@tsalo

I've put up a pull request to add @handwerkerd! 🎉

[handwerkerd]

I think I've included all the open low-hanging-fruit documentation open issues. There are a few others that might take a bit more work and are sufficiently separate from the rest of these. It would be good to get reviews from both people who know what's happening under the hood and people who can see if I'm explaining things clearly. While you're reading, also keep an eye out for other simple things that could be written more clearly or have added info. @tsalo @eurunuela @dowdlelt @n-reddy @NaomiGaggi @marco7877

You can view the rendered documentation for this PR at: https://tedana--948.org.readthedocs.build/en/948/

[tsalo]

There might be a small typo, but LGTM otherwise.

[dowdlelt]

I can't recall - is the original input mask still used as the mask for the final data (even if the ICA is run on a reduced mask due to drop out).

[handwerkerd]

All voxels with at least 1 good echo are included. The revised text clarifies this.

[dowdlelt]

github is being finicky...I approve pending typo corrections

[dowdlelt]

I abused my powers to fix a typo, because honestly it feels like kind of insane to point at a typo, say I approve, get that dismissed, then approve again. I approve!