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Update docs based on Scott's feedback #478

Merged
merged 9 commits into from
Nov 1, 2024
Merged

Update docs based on Scott's feedback #478

merged 9 commits into from
Nov 1, 2024

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harisorgn and others added 5 commits October 30, 2024 15:36
Looks like this replicates their dynamics now. Includes all the weights from their paper and splits the striatum into the three groups instead of wherever we got that one striatum block from.
@agchesebro
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Parkinson's tutorial no longer goes to infinity, but the cortical inhibitory neurons do act as a massive damped oscillator:

image

Since we need a plot or two for the end of the tutorial I'm going to just make a couple recipes to replicate some of the figures from the paper. They never show the x portion of the oscillators - just the y and the power spectrum, so you don't see that huge initial oscillation.

@harisorgn
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I'm going to just make a couple recipes

If these plots are something specific to the paper and our API covers the data that is plotted then you don't have to add a recipe, just make a figure on the tutorial. If it's something more general then recipe would be better.

@agchesebro
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The Parkinson's tutorial using Jansen-Rit models is significantly redone and ready for review @harisorgn. A couple important notes:

  • Scott will discuss some illustration ideas with Annabel tomorrow to see if we can get a nice circuit diagram to start off the tutorial, potentially from a GUI layout pic. That's what the "NEED FIGURE HERE" text is for lol.
  • I wound up not needing any new recipes - just a new dispatch of powerspectrum for neural masses. So no breaking changes or additional documentation there.
  • I realize that the simulations don't match the figures entirely in the paper even if you use their parameters. The dynamics are roughly similar though, and I've avoided direct comparisons with the figures but incorporated just the concepts. Why don't they match? Well the paper uses a forward Euler solver with a medium dt, so.......
  • The dynamics do have a marked shift between the Parkinson's and healthy parameter regimes that are roughly what we expect too, so it still works as a nice intro tutorial I think.

@harisorgn
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Thanks Anthony, looks good!

Well the paper uses a forward Euler solver with a medium dt, so.......

You can try matching the solver to see if this is the only difference like
sol = solve(prob, Euler(); dt = 0.1)

@harisorgn harisorgn merged commit 2e9e578 into master Nov 1, 2024
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@harisorgn harisorgn deleted the ho/docs_feedback branch November 1, 2024 11:35
@agchesebro agchesebro restored the ho/docs_feedback branch November 1, 2024 12:33
david-hofmann pushed a commit that referenced this pull request Nov 11, 2024
* update Getting Started text

* change title and fix link in parkinsons

* add seed and update plot in resting_state

* remove outdated phrase

* Fix the Parkinson's circuit to match Liu et al. 2020

Looks like this replicates their dynamics now. Includes all the weights from their paper and splits the striatum into the three groups instead of wherever we got that one striatum block from.

* Prettify the introduction

* Fix Jansen-Rit docstring to show defaults

* Add dispatch of powerspectrum for neural masses

* Overhaul of Parkinson's JR tutorial

This has some pretty significant changes that should address nearly all the points

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Co-authored-by: agchesebro <[email protected]>
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2 participants