Todo for thesis repository

To do:

Ch6: 
Methods: limit discussion of roots
Results: SD curve -> limit interpretation
Results: optimised -> mostly to Ch7
Results: limit mention of roots
Discussion: limit discussion of electrode position etc.
Figures: remove variation in position
- optimal position to spinal cord only
- SD curves more limited?

Ch7:
Figures:
- Basic montages and targets
- SD curves at midline
- Variation in electrode position
- Activation thresholds
- SD curves at optimal: selectivity
- Point of AP generation
-> identify mechanism and ideal positions

?figure: activation as fctn of position for each target - flip 180, then transpose
Combine w selectivity: region where threshold < threshold for any other
-> measure total area of selectivity
then SD curve within this region

Selectivity figure:
Take min of all OTHER structures at each point
Subtract TARGET from this at each point
If >0: thTARGET < thOTHERS -> selective
If <0: thOTHERS < thTARGET -> off-target

Figures

---

Sync to repo
Set up on GPU: can access remotely and write
?Contact Digitimer re. faster stimulation for bursts

- Solver: 
		References
		RESULTS: error measures and values
- Coupling:
		References

- Variational: 
		References
- Nrrd: 
		References
		Tables
- Waveforms: 
		References

- Main intro:
	Epidemiology: incidence & prevalence
	References

- Conclusion: draft

- Acknowledgements
- Abbreviations

- Theory intro: write
	Add introduction: overall motivation, biophysics & modelling
	Fields: equation describing fields, voltage and current controlled stimulation, mono vs. bipolar (location of return), boundary conditions for each
	Interface: charge transfer, models, ?boundary conditions; ?use for macroelectrodes
	Biophysics: cables, HH; influence of extracellular stimulation; double-cable myelinated models
	Approximations: derivation of activating function and weaknesses; other metrics
	Optimisation: capturing clinical intent; individualised models for neuromodulation
	?circuit diagrams

- Mechanism: draft + get results
- Validation: draft + get results

Qs:
- Active voice - we or I?
- Combine models and solver?
- Separate coupling and optimisation?
- Toolbox as chapter or appendix?
- Variational forms with solver or appendix?

Biophys methods
Biophys discussion
Figures: solver, biophys
- List all -> collect -> place
Results: solver, biophys

Toolbox chapter outline
Overall intro
Combine solver, models

More detail on solver implementation?
Function spaces, degree of approximation, assembly, etc.?

Finish methods
Add solver figures
	New figures
	?time dependent
	Composite figures
Write solver results
	Analytical
	Numerical
	Application
Write solver discussion
Revise patient specific chapter
?combine

Coupling figures
Coupling intro
Coupling methods
Coupling results
Coupling discussion
?Combine with optimisation

?toolbox to standalone chapter

Revise rotated intro
Alter refs in intro etc.
Write overall intro
Add to physical framework

Outline application chapters

Basic equations
Add annotations

- New chapters
- Detailed outlines
- Revisit outlines:
	- optimisation
	- nrrdosurgery
	- mechanism
	- validation
	- conclusion
- Subheadings in introductions?
- ?appendix on biophysical parameters, incl conductivities etc.
- ?derivations to ch2 rather than appendix

- Quotes for chapter headings

- Theory outline
- Revise patient-specific
- Collate content for
	- Solver
	- Trajectories
- Plan missing content
- Intro outline

- Full text:
	- theory
	- patient specific
	- solver
	- coupling
	- optimisation
	- toolbox
	- mechanism
	- validation
	- conclusion

- Populate chapters with outlines: sections & subsections
- List todos for each chapter
- Set up projects & priorities: based on results etc.
- List planned derived works & prioritise
- Planned timeline for work

- List planned appendices: electrodynamics, FEM, biophysics, optimisation, control theory, etc.; neurophysiology, anatomy, pathology, rehabilitation, etc.; NRRDosurgery documentation, phrenic nerve device details, etc.

- ?page break between short & detailed ToC
- ?short (one page) intro (not listed in ToC) at beginning of each section outlining contents of section
- ?short outline before intro - outline overall contents
