Getting Started with Electrophysiology

  • Start with 1 element mesh from Monday

  • We made some changes to basis functions:
    • Integration/collocation points to 2 rather than 3
    • TriCubic basis function (move to top)

    • BiCubicLinear Basis function

  • Refine 4x30x16
  • Decrease divisions (maybe to 4)
  • Render lines and .*endo.* nodes (just for reference)
  • Change geometry to BiCubicLinear in nodes form

  • Convert to Cartesian
  • Add 6 empty fields in nodes form for conductivity tensor
  • Recalculate Mesh
  • Calculate conductivity tensor (Mesh > Edit > Tensor Transformation; "update nodes form" in submit tab)

    • This calculation may take a little while (2 or 3 minutes on a fast computer)
    • Produces a tensor like this:
      • 1

        2

        3

        4

        5

        6

  • Make some changes to the nodes form:
    • Add TriCubic field (field 7) that will contain your initial conditions

    • Click "Change list" and Apply value 10.0 to node list .*endo.* of Field 8 Value

  • Recalculate mesh
  • Setup Ionic Model
    • EP_MFHN
    • UG = Field 7
    • Stim Mag = Field 8
    • Tensor11 = Field 1
    • Tensor22 = Field 3
    • Tensor33 = Field 6
    • Tensor21 = Field 2
    • Tensor31 = Field 4
    • Tensor32 = Field 5
  • Send
  • Initialize
  • Calculate Constraints (Fix out of plane...)
  • Reset > Save,reset, and reload

  • Recalculate Mesh
  • Initialize
  • Solve
  • Render Solution (make sure to use 0.0 and 1.0 for Max and Min value)

Potential Gotchas?

  • Must calculate mesh after changing basis functions of fields
  • Maybe memory error with too many frames?
  • Rendering frames is somewhat slow