Towards better brain models using current injections

PHYSX PGR Conference

Matthew Walker

Your brain

…it’s complicated

How complicated?

  • 100 billion neurons
  • Each with 10,000 synapses
  • More connections than there are stars in our galaxy!*
  • Electrical activity is happening constantly

*https://medicine.yale.edu/lab/colon_ramos/overview/

How do we measure it?

  • Electroenphalography (EEG)

How do we measure it?

  • Electroenphalography (EEG)
  • Localise the source of electrical activity by modelling the brain with Finite Element Methods
  • FEM is a numerical method to solve boundary value problems
  • We need realistic head models for accuracy

Realistic head models



  • MRI (magnetic resonance imaging) scans
  • CT (computerised tomography) scans

Realistic head models

  • MRI gives us detailed images of the head
  • Segment into separate tissues and build FEM mesh using ISO2MESH toolbox
  • Now we need some conductivities for each layer
  • But we can’t just use the population average*

*McCann et al 2019 - Variation in Reported Human Head Tissue Electrical Conductivity Values

Electrical Impedance Tomography

  • An imaging method to estimate the conductivity distribution within the head
  • Place electrodes on the scalp
  • Inject currents through one electrode, extract through another
  • Measure the electrical potential on the other electrodes
  • We use FEM to simulate how the current propagates (similar to EEG)
  • Split into a forward problem and an inverse problem

Forward Problem

  • Simulate how the current moves through the model
  • Involves solving a LARGE system of simultaneous equations \[\boldsymbol{A} \boldsymbol{u}=\boldsymbol{b}\]
  • Where the number of equations is equal to the number of nodes in the mesh

Inverse Problem

  • Lots of forward problems
  • An optimisation method to find the forward problem closest to the measurements

Desmos graphical calculator

Our problem

  • EIT is very computationally expensive
  • Which makes it prohibitive
  • In practice, only scalp and skull estimates are feasible (but not skull bone marrow)

Our solution: Reduced Order Modelling

  • Designed for the solution of partial differential equations in parameterized systems
  • Our EIT problem fits perfectly
  • It reduces the dimensionality of the forward problem!

Reduced Order Modelling

  • The aim: to construct a reduced basis space.
  • A space where we can find an approximation to a forward problem for any point in parameter space \(\mathscr{P}\).
  • We build it by orthonormalising forward problem solutions at points \(\mathscr{P}_1, \mathscr{P}_2, ...\)
  • These are called the reduced basis functions and make up our reduced basis space.

  • Each new solution is projected onto these basis vectors to capture additional information.
  • Iterate until the reduced basis space is sufficient to approximate our forward problems to low errors.

Reduced Order Modelling

Results

Conclusions

  • With some training time, we’re able to solve the EIT forward and inverse problems instantly.

  • Now we can include those conductivities in subject-specific head models

What’s next?

  • Refining the framework

  • Testing with real EIT and EEG data

  • Applications to transcranial direct current stimulation

Thanks for listening

  • These slides are here: https://matthew-walker.net/slides/PGRCon/PGRCon.html

Acknowledgements

  • Leandro Beltrachini - Supervisor

  • Jack Atkinson - For presentation advice

Bonus content

EIT formulation

\[\nabla\cdot(\sigma\nabla u)=0 \ \ \ \textrm{in }\Omega\\ \sigma\frac{\partial u}{\partial \textbf{n}} = \langle\sigma\nabla u,\textbf{n}\rangle=0 \ \ \ \textrm{on }\partial\Omega \backslash \cup^L_{l=1} e_l \\ u + z_l\sigma\frac{\partial u}{\partial \textbf{n}} = U_l \ \ \ \textrm{for } l=1,...,L \\ \int_{e_l}\sigma\frac{\partial u}{\partial \textbf{n}} d(\partial \Omega) = I_l \ \ \ \textrm{on } e_l \]

Variational Formulation

\[B((u,U),(v,V)) = \int_{\Omega} \sigma \nabla u \cdot \nabla v d \Omega \\ + \sum^L_{l=1} \frac{1}{z_l} \int_{e_l}(u-U_l)(v-V_l)d(\partial \Omega)\]

Ritz-Galerkin Discritization

\[\begin{gather} \begin{pmatrix} \boldsymbol A & - \boldsymbol B \\ - \boldsymbol B^T & \boldsymbol C\end{pmatrix} \begin{pmatrix}\boldsymbol \alpha \\ \boldsymbol \beta\end{pmatrix} = \begin{pmatrix}\boldsymbol 0 \\ \boldsymbol I \end{pmatrix} \label{CEM_sys} \end{gather}\]