[TUTORIAL UNDER DEVELOPMENT: NOT READY FOR PUBLIC USE]
This page will explain the differents options available within brainstorm to generate the FEM mesh.
Describe meshGeneration here.
SimNIBS Installation
Please follow the instructions on this webapge (new brainstom page that explain how to generate the head model is under development)
in order to do the SimNibs software shoud be installed in your computer.
Iso2Mesh Installation
If iso2mesh is not installed in your computer, Brainstrom will download the last release from this webpage and install it when it'is needed. However, you can also download the iso2mesh from the github and add it to your matlab path.
Brain2Mesh Installation [TODO]
Brainsuite Installation [TODO]
FEM surfaces / Volume generation
Volume mesh generation from Brainstorm
The most modern software that are used to generate the volume mesh head model are integrated within brainstorm with an easy graphical interface to use call these tools.
Right click on the subject and then "Generate FEM Mesh"
![[ATTACH]](/brainstorm/Tutorials/FemMesh?action=AttachFile&do=upload_form&ticket=006656c2b0.46c2c3faa8102be7358850dcf181c2abb9683ff0&target=menuGenerateFemMesh.PNG "[ATTACH]"){kind=small}
The available options are :
![[ATTACH]](/brainstorm/Tutorials/FemMesh?action=AttachFile&do=upload_form&ticket=006656c2b0.46c2c3faa8102be7358850dcf181c2abb9683ff0&target=FemMeshMethods.PNG "[ATTACH]"){kind=small}
"Iso2mesh" : This option merges the brainstorm surfaces available on the subject and then generarte the tetrahedral mesh.
"Brain2Mesh" : This options uses the MRIs available on the subjects, then it calls the SPM segmentation of the volume into 5 tissus (white, gray, scf, skull and skin). After that it converts into a tetrahedral mesh.
"SimNibs" : The recommended option, it calls the headreco {ref} and generate a FEM head model
"FieldTrip" : (in progress) "Roast" : (in progress)
"headreco" :
https://simnibs.github.io/simnibs/build/html/documentation/command_line/headreco.html
This function is part of the SimNibs software:
https://simnibs.github.io/simnibs/build/html/index.html
headreco
The headreco function is fully integrated to brainstorm. With this option, brainstorm can reconstructs a tetrahedral head mesh from T1- and T2-weighted structural MR images. It runs also with only a T1w image, but it will achieve more reliable skull segmentations when a T2w image is supplied.
Surface mesh generation from volume mesh
Volume generation from surface files
In this part you can generate your FEM mesh from surfaces that you can get fron the segmentation software (brainSuite, FreeSurfer ....).
This process will
- merge the surfaces,
- check the self intersecting
- fixe the size of the mesh
- generate the volum mesh
- visual checking ...
- TODO : may be we can add some mesh auqlity measures ??
Volume generation from T1/T2 MRI data
You can also generate your own FEM head model and then load it to brainstorm. However the automatic head model generation from from imaging techniques are not accurate and most of the time visual checking are needed and manual correction are required.
==> this depends lagely on the quality of the T1/T2 MRI image(https://simnibs.github.io/simnibs/build/html/tutorial/head_meshing.html).
This step is based on the "roast" toolbox (link to roast : https://github.com/andypotatohy/roast
) that we adapted for the MEEG forward computation. If you want to generate your own FEM head model from an MRI, you will need to download these file (link), then run the bst process as explained here.
- f there is a MRI file with the string "T2" in the subject anatomy folder, it will use it
- Otherwise, if you select explicitly two MRI files with CTRL+Click, it will use the first one as the T1 and the second one as the T2 (this needs to be documented in the tutorial)
FEM Head model generation with SimNibs
This method used the SimNibs software. So to call this process, you need to download and install the SimNibs software, the process of the installation is explained in the SimNibs webpage : https://simnibs.github.io/simnibs/build/html/installation/simnibs_installer.html.
When you have installed SimNibs, Brainstorm can call the main function used for the mesh generation frm the main graphical interface. Depemding on your computer performances, this process will take between 2 to 5 hours. We highly recommend to close all other running process and application on our computer in order to speed this process.
- Explain here the main steps with screenshots :
1- Create new subject within the current protocole
2- Load the T1 of the subject to the brainstorm database.
3- Associate a T2 mri to the subject if it's available (this is better for csf/skull/scalp segmentation)
4- Right click on the subject, select the "Generate FEM mesh"
- Select "SIMNIBS", and choose "Tetrahedral element" and keep the other options to the default value.
5- When this process is finished, a new node will appear in the data base, which hase he name "FEM xxxV, (simNibs, yLayers)". This is the FEM mesh model generated from the T1.
FEM Head model template
- Load the FEM volumic mesh (template created from ICBM T1 MRI using SimNibs)
- Load the surface mesh (template created also from ICBM using ICBM ) and then generates the volume mesh (either tetra or hexa) by calling the tetgen process cia iso2mesh toolbox (if hexa are desired, the tetra mesh will be converted to hexa ... )
https://github.com/brainstorm-tools/brainstorm3/issues/185#issuecomment-576749612
Head model based on the level set approach
TODO and Validate