Tractometry explanation

[36000]

Updates tractometry explanation using resources put together for neurohackademy, converted to RST
Additionally updates GradientTable instantiation calls to not generate warnings anymore.

[Copilot]

Pull Request Overview

This PR updates the tractometry explanation documentation by converting resources from neurohackademy to RST format and updating GradientTable instantiation calls to use explicit keyword arguments to prevent deprecation warnings.

• Replaces the old pipeline documentation with comprehensive tractometry explanations including model fitting, tractography, bundle recognition, and tract profiling
• Updates all GradientTable instantiation calls throughout the codebase to use explicit bvals and bvecs keyword arguments
• Adds ecosystem table and resources overview to help users understand the broader tractometry toolchain

Reviewed Changes

Copilot reviewed 11 out of 43 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
docs/source/explanations/tractometry_pipeline.rst	Removed old pipeline overview with simple flowchart
docs/source/explanations/index.rst	Complete rewrite with detailed tractometry explanations, visualizations, and ecosystem overview
examples/howto_examples/plot_stages_of_tractometry.py	Updated gradient_table call to use explicit keyword arguments
CHANGES.rst	Added changelog entry for version 2.1
AFQ/utils/testing.py	Updated gradient_table calls to use explicit keyword arguments
AFQ/utils/models.py	Updated gradient_table call to use explicit keyword arguments
AFQ/tests/test_fixes.py	Updated gradient_table call to use explicit keyword arguments
AFQ/tests/test_dti.py	Updated gradient_table call to use explicit keyword arguments
AFQ/tests/test_dki.py	Updated gradient_table call to use explicit keyword arguments
AFQ/registration.py	Updated gradient_table call and removed legacy parameter handling
AFQ/models/csd.py	Updated gradient_table call to use explicit keyword arguments

[36000]

@arokem this is ready for review/merge, Its mostly just adding the talk I gave on pyAFQ to our documentation on the explanations page.

[arokem]

The content looks great! I wonder if we shouldn't take this as an opportunity to handle references a bit better? There are a lot of (useful!) references here, but it would be hard for a reader to find some of these, I think. DIPY now uses https://sphinxcontrib-bibtex.readthedocs.io/en/latest/usage.html, which should help.

[36000]

@arokem a lot of these citations are from your slides and im not familiar with them. what does Behrens 2013 refer to?

is it this?
Chapter 19 - MR Diffusion Tractography
Timothy E.J. Behrens

[36000]

Also, is descoteaux 2014 supposed to be this?
https://scholar.google.com/citations?view_op=view_citation&hl=en&user=ohzG9ScAAAAJ&cstart=300&pagesize=100&sortby=pubdate&citation_for_view=ohzG9ScAAAAJ:fPk4N6BV_jEC

[36000]

We are already using bibtex, so i will just add the references I know to that system.