Update boilerplate

[araikes]

The current boilerplate needs to be updated to reflect various updates, upgrades, and better wording/clarity. This can serve a bit as a running list of recommendations/needs. To start with:

1. Ensure templateflow usage is documented and cited.
2. Ensure that MNI space is cited appropriately.
3. Ensure that Freesurfer is cited relevantly.
4. Ensure that ANTs is cited relevantly.
5. Include more verbose denoising descriptions and robust citation.
6. Update resampling statement regarding eddy
7. Include missing RRIDs (like MRtrix)

I'm sure there are more to be included. @mattcieslak has further list, I'm sure.

[araikes]

More:

1. Reorder descriptions for TOPUP and Eddy since TOPUP runs first
2. Describe mask creation for DWI
3. Conditionalize the comment about treating bvals < 100 as a b=0, so that is present when relevant.
4. Describe image-level quality metrics that are saved (like NDC), which are separate from the timeseries.