/2023_invitro

Primary LanguageR

NOTES on the research project "Electric field simulations for in-vitro TMS experiments"

Preparations

  1. Install the latest version of R and RStudio: https://posit.co/download/rstudio-desktop/
  2. Open RStudio and install ProjectTemplate library by typing this in the console: install.packages('ProjectTemplate')
  3. Download this github repository to a desired location on your notebook/computer.

Variables

  • bt_width: width of brain tissue in mm.
    • range: from 2.66 to 4.88 mm
    • 31 unique values (but due to surface smoothing slight differences occur)
  • bt_depth: depth of brain tissue in mm.
    • range: from 2.1 to 3.84 mm
    • 31 unique values (but due to surface smoothing slight differences occur)
  • bt_height: height of brain tissue in mm.
    • value ranges from 0.15 mm to 0.4 mm with a step size of 0.05 mm.
    • 6 unique values
  • liquid_height: height of the liquid in the Petri dish in mm.
    • 10 mm: petri dish is full with liquid
    • 2.16: 2 mm + brain tissue height of 0.15 mm + 0.01 mm (10 micron) liquid on the top of the brain tissue
  • coil_distance:
    • value ranges from -3 to 3 mm with a step size of 1 mm.
    • 6 unique values
    • if value is positive: distance between the top (lid) of the Petri dish and the TMS coil in mm. This is stimulating "from the top".
    • if value is negative: distance between the bottom of the Petri dish and the TMS coil in mm. This is stimulating "from below".
  • mso: maximum stimulator intensity in percentage
    • value ranges from 1% MSO (lowest possible intensity) to 100% MSO (heighest possible intensity).
    • 100 unique values
  • EF_min: minimum electric field.
  • EF_mean: mean electric field.
  • EF_median: median electric field.
  • EF_robust_max98: 98th percentile of electric field.
  • EF_robust_max99: 99th percentile of electric field.

Electric field values

Electric field values are extracted from the volume compartment of the entire brain tissue and are given in V/m (equivalent to mV/mm).

Usage

  1. Open RStudio.
  2. File > open project, select file "invitro.Rproj".
  3. File > open file, go to "src" folder, and select file "get_efield_value.R".
  4. In "get_efield_value.R", define the desired stimulation parameters (e.g., intensity, brain tissue size, etc.).
  5. You can execute lines by pressing strg + enter.
  6. Results will be shown in the console window and in "results" variable that you can find in Environment > Global environment.

Useful link(s)