FEM mesh generation

Authors: Takfarinas Medani, Francois Tadel

FEM forward modeling requires the construction of a 3D model of the head tissues. The volume of the head is divided in small geometrical elements with 4 faces (tetrahedrons) or 6 faces (hexahedrons). Each element is associated with a type of biological tissue (e.g. white matter, gray matter, CSF, skull, skin) and electrical conductivity properties.

This page lists the methods integrated with Brainstorm to generate 3D meshes of the head. For a generic introduction to FEM in Brainstorm, refer to the tutorials: Realistic head model: FEM with DUNEuro and FEM median nerve example.

Generate FEM mesh

FEM meshes can be computed from surfaces (as the ones generated for the BEM models) or from MRI volumes (T1w and/or T2w). The methods that are available when using the popup menu Generate FEM mesh depend on the selected inputs.

Surfaces

Select a list of surfaces representing the separation between different tissues (holding the CTRL or SHIFT key), then right-click on any of them. The software Iso2mesh can create a tetrahedral mesh to represent the tissues between these different layers.

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T1 MRI

Right-click on a T1 MRI available in the database. Typically, this is the default MRI volume displayed in green in the subject folder. Methods available: Brain2mesh, SimNIBS3, SimNIBS4, ROAST, FieldTrip.

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T1+T2 MRI

Select the T1+T2 volumes, then right-click on any of them. The different files are identified based on the tags "T1" and "T2" the file names (as displayed in the Brainstorm database explorer). If these identification tags are not found in the file names, the default MRI (in green) is used as the T1, the other as the T2. If none of the is the default MRI, the first selected file is used as the T1, the second is used as the T2. Methods available: Brain2mesh, SimNIBS3, SimNIBS4, ROAST.

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Anatomy folder

If you right-click on the subject folder > Generate FEM mesh, then Brainstorm offers all the possible options, even the ones that are not applicable to this specific subject.

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Iso2mesh

Iso2mesh is a Matlab/Octave-based mesh generation and processing toolbox, available as a Brainstorm plugin.

Brainstorm uses it to generate a FEM tetrahedral mesh from a set of nested surfaces representing the separation between different tissues of the head. For example, these surfaces can be the ones generated for the computation of a BEM forward model. A full example is available in the tutorial Realistic head model: FEM with DUNEuro.

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Options

Examples

Troubleshooting

Brain2mesh

Brain2mesh is a MATLAB/Octave based 3D mesh generation toolbox dedicated to the creation of high-quality multi-layered brain mesh models. This software is developed by the same team developing Iso2mesh and relies heavily on it. Both are available as a Brainstorm plugins. Warning: Requires the Imaging Processing Toolbox.

Brainstorm runs the SPM12 segmentation routine on the T1 or T1+T2 MRI volumes to obtain a 5-tissue classification (white matter, gray matter, CSF, skull and skin), which is then passed to Brain2mesh for 3D meshing. A full example is available in the tutorial FEM tensors estimation. This option runs fast, but does not generate good quality cortex surfaces, which are needed for the full cortically-constrained source estimation pipeline in Brainstorm.

At the moment, Brainstorm can only use the default parameters of Brain2mesh. If you need more options to be available from the interface, please contact us on the user forum.

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Troubleshooting

SimNIBS

SimNIBS software was developed to calculate the electric fields caused by Transcranial Electrical Stimulation (TES) and Transcranial Magnetic Stimulation (TMS). All its software dependencies (CAT12, Netgen, Gmsh, MeshFix) are embedded in the SimNIBS installation, which ensures a high stability and portability. However, it cannot be managed automatically as a plugin by Brainstorm, and needs to be installed manually. See: Download and install SimNIBS. Two versions of SimNIBS are currently supported, that include different segmentation pipelines: SimNIBS 3.x (headreco) and SimNIBS 4.x (charm).

SimNIBS 3: headreco

SimNIBS 3.x includes the pipeline headreco to process T1 or T1+T2 MRI volumes (T1 is required, T2 is recommended) and generate a high-quality tetrahedral FEM mesh. It calls internally CAT12 for tissue segmentation (white matter, gray matter, CSF, skull and scalp), and therefore gives us access to high-quality cortex surfaces and surface-based atlases. The tetrahedral mesh generation is done with Gmsh, Netgen and MeshFix. Depending on your computer performances, this process will take between 2 to 5 hours.

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Options

SimNIBS 4: charm

SimNIBS 4.x includes the pipeline charm to process T1 or T1+T2 MRI volumes (T1 is required, T2 is recommended). This pipeline generates the highest-quality tetrahedral FEM mesh we can get from Brainstorm. It creates segmentations and meshes with more tissues than SimNIBS3/headreco: white matter, gray matter, CSF, compact bone, spongy bone, scalp, eyes, blood and muscle. It also creates high-resolution cortex surfaces registered with the FSAverage template, but it does not generate the full CAT12 output folder anymore. For surface and volume-based atlases, it might be necessary to execute CAT12 from Brainstorm on top of SimNIBS.

Given the high quality of its outputs, SimNIBS/charm is the recommended method for FEM mesh generation in Brainstorm. A full example is available in the tutorial: FEM median nerve example.

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Options

Troubleshooting

ROAST

ROAST is a fully automated, Realistic, vOlumetric Approach to Simulate Transcranial electric stimulation. Open-source and Matlab-based, it is available as a Brainstorm plugin. It calls internally SPM8 for tissue segmentation of the T1 or T1+T2 MRI volumes to obtain a 5-tissue classification (white matter, gray matter, CSF, skull and skin). Then it relies mostly on iso2mesh for generating a tetrahedral mesh.

This option runs fast, but does not generate good quality cortex surfaces, which are needed for the full cortically-constrained source estimation pipeline in Brainstorm.

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Troubleshooting

Fieldtrip

FieldTrip is an open-source Matlab-based toolbox that includes a pipeline dedicated to the generation of hexahedral FEM mesh. It is available as a Brainstorm plugin.

Brainstorm calls the function ft_volumesegment on the T1 MRI volume to obtain a tissue segmentation with 5 layers (white matter, gray matter, CSF, skull and skin), then ft_prepare_mesh_hexa to create a hexahedral mesh.

The mesh generation with the method is simple and fast: it downsamples the tissue classification volume, then converts all the voxels to a hexahedral mesh. The quality of the output is relatively poor: the regular meshing of the voxels makes it inefficient for providing a good representation of the tissues geometry with a limited number of elements.

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Options

Troubleshooting

On the hard drive

Right-click on a FEM mesh > File > View file contents:

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Structure of the FEM mesh files: tess_fem_*.mat

Tutorials/FemMesh (last edited 2023-03-24 13:17:29 by FrancoisTadel)