This repository has the key functions needed for the MDEIT reconstruction pipeline. It expands on existing code for the forward modelling in the Magnetic-EIT repository. A prior understanding of how to use EIDORS and COMSOL Multiphysics (with MATLAB via LiveLink) is required.
The code provided includes sample data and geometry to enable reconstruction of four resistive perturbations in a realistic human head phantom. The scripts provided contain more information on their functionality.
Instructions:
- Install EIDORS. Installation instructions and software documentation can be found on the EIDORS website.
- Install COMSOL Multiphysics - requires a license.
- The geometry for the human head phantom can be found in the CAD folder.
- The forward is ran using the running_forward script. If using a magnetometer system with gradiometers, the forward must then be converted using the convert_forward_magnetometers script.
- The MDEIT Jacobian can be computed using the jacobian_calculation script. This will compute the Jacobian for the x-, y- and z-axis. The full Jacobian can be computed with the jacobian_full script, and requires the sensor norms.
- Image reconstruction is done with the reconstructing_MDEIT script, and visualisation of the reconstructions (and target images) with the visualising_recons script.
A custom colormap, some pre-computed forward solutions, Jacobian, hexahedral meshes, etc. are provided as an example. The Jacobian, hexahedral mesh, and sample data can be found here.
For any questions or issues, please contact florencia.alperovich.17@ucl.ac.uk