The purpose of this page is just to serve as todo or scratch pad for the development project and to list and share some ideas.

After making changes to the code and/or documentation, this page should remain on the website as a reminder of what was done and how it was done. However, there is no guarantee that this page is updated in the end to reflect the final state of the project

So chances are that this page is considerably outdated and irrelevant. The notes here might not reflect the current state of the code, and you should not use this as serious documentation.

How to create a volumetric current density

Upon reviewing this page on the website, it seems to me that this project is not going to happen. Although the FieldTrip code base might be used (in combination with other code), the released code will not be extended to specifically facilitate this.

Introduction

What is the tutorial about

This is relevant for TMS tDCS ….

Background

What is TMS/tDCS

Why we need current densities

Overview about the methods which are used

Procedure

A set of logical steps describing the pipeline, in MATLAB, FieldTrip code or also from somewhere else (e.g., FreeSurfer)

Examples with code/command lines instructions

@Cristiano

  • segment inner skull from CT
  • segment the outer brain from the MRI
  • project the electrodes from CT onto inner skull (CT space)

  • superimpose two surfaces (electrodes are expressed in brain coordinates afterwards) This is done in SPM by coregistration of the CT to MRI images. This automatically gives the transfer matrix from CT to MRI coordinates (and hence you also have the electrodes expressed in MRI coordinates)

  • check the surface does not contain self intersections
  • mesh the brain triangulation with Tetgen
  • assign conductivity to nodes -> elements

@Arno

  • convert mesh pnt and tri into a structure readable by Tetgen (.poly and .nodes)
  • run Tetgen
  • collect result (.node, .ele, (maybe .faces))

@All

  • write wfmesh/elec/parameters/cond on disk
  • run SimBio solver

Alternatively (interactive)

  • write .mat files : elec/wfmesh/cond
  • write a SciRun schematic
  • run SciRun
  • collect solution and save it in a .mat file

@Robert

  • discuss next steps

Questions

Is the output of SimBio/SciRun the stiffness matrix (profiles of current in the head)? (input: current, output: spatial current density)

Summary

General conclusions

Suggested readings

Other FT documentation pages