[TUTORIAL UNDER CONSTRUCTION: NOT READY FOR PUBLIC USE]


FEM tensors estimation with BrainSuite

Authors: Takfarinas Medani, Francois Tadel, Anand Joshi and Richard Leahy

In this tutorial, we describe the estimation of realistic conductivity tensors of living brain tissues using the BrainSuite software. These results are used in FEM forward modeling, as described in the tutorials: FEM with DUNEuro and FEM median nerve example.

The realistic tensors are estimated from the Diffusion-Weighted Images (DWI): Brainstorm calls the BrainSuite software to compute the diffusion tensors on each brain MRI voxel (DTI), then Effective Medium Approach (EMA) is applied to estimate the conductivity tensors for each element of a tetrahedral FEM mesh. This is particularly interesting for the modeling the anisotropy of the white matter.

BrainSuite is also used for other purposes in Brainstorm, particularly the T1 MRI segmentation, as documented in this tutorial: MRI segmentation: BrainSuite.

Download and installation

Requirements

Install Brainsuite

  1. Download the latest version of BrainSuite from http://forums.brainsuite.org/download/.

  2. Install it on your computer by following the instructions in BrainSuite's quick start installation guide.

  3. You will be using BrainSuite Diffusion Pipeline (BDP), so you need to install a compatible MATLAB Runtime (2019b for BrainSuite 21a).

  4. In Brainstorm, menu File > Edit preferences > Enter the BrainSuite installation folder:

    brainsuiteInstall.gif

Download the dataset

Import the anatomy

T1 MRI

Diffusion imaging

This computes the This requires BrainSuite to be installed on your computer, with the bdp program available in the system path.

FEM mesh

The FEM approach requires a segmentation of the head volume in different tissues, represented as hexahedral or tetrahedral 3D meshes. The methods available within Brainstorm are listed in the tutorial FEM mesh generation.

Here we illustrate only the use of Brain2mesh: this is not the most accurate solution for MRI segmentation but it is probably the fastest solution to obtain a tetrahedral mesh of the head with 5 tissues (gray matter, white matter, CSF, skull, skin). For more accurate results, we recommend using SimNIBS with T1+T2, as illustrated in the tutorial FEM median nerve example.

FEM conductivity tensors

Once the FEM mesh and the DTI tensors are available in the Brainstorm database, the next step is to compute the conductivity tensor for each of the FEM mesh element.

Visualization

Advanced

Simulated conductivity tensors [TODO]

When the DWI is not available, or to evaluate the effect of the conductivity change on the head model, artificial conductivities can be used using the third option "Simulated".

Two approaches are integrated within Brainstorm: Wang's constraint or Wolters's volume constraint. The common feature between these methods is the ratio between the transversal and longitudinal conductivity ratio.

A common example is the skull anisotropy simulation, where the longitudinal conductivity can be higher than the transversal conductivity, the ratio can vary from 2 to 10 [ref].

Keep all the tissue as isotropic, except the skull, we use a ratio of 0.1 and select the volume constraint. The following figures show the results of this example.

Users can reach this option by following this tutorial and select the third method in this panel. [ATTACH]

"eigenvalues parallel (longitudinal) and perpendicular (transverse) to the fiber directions" for 1:10 anisotropy (transverse:longitudinal)

[ATTACH] [ATTACH]

Additional documentation

Articles

Tutorials/FemTensors (last edited 2021-08-17 16:01:17 by FrancoisTadel)