## Overview
This project aims to simplify the preparation of accurate electromagnetic head models for EEG forward modeling.
It builds off of the seminal [SimNIBS](http://simnibs.org/) tool the field modelling of transcranial magnetic stimulation (TMS) and transcranial direct current stimulation. Human skin, skull, cerebrospinal fluid, and brain meshing pipelines have been rewritten with Nipype to ease access parallel processing and to allow users to start/stop the workflows. Conductivity tensor mapping from diffusion-weighted imaging is also included.
At present these pipelines depend on interfaces for [Gmsh](http://geuz.org/gmsh/) and [Meshfix](https://code.google.com/p/meshfix/) that can only be found in the enh/conductivity branch of my fork of [Nipype](https://github.com/swederik/nipype).
The reference for the tools found in this repository is:
> **A finite-element reciprocity solution for EEG forward modeling with realistic individual head models**.
E. Ziegler, S.L. Chellappa, G. Gaggioni, J.Q.M. Ly, G. Vandewalle, E. André, C. Geuzaine<sup>1</sup>, C. Phillips<sup>1</sup>
_**NeuroImage**_. Volume 103, December 2014, Pages 542-551, ISSN 1053-8119, [http://dx.doi.org/10.1016/j.neuroimage.2014.08.056](doi:10.1016/j.neuroimage.2014.08.056).
<sup>1</sup> Contributed equally
## Install
To install the package, run:
python setup.py install
Set environment variable FWD_DIR to the root path of the installation directory by placing
export FWD_DIR=/path/to/forward
in your .bashrc or .zshrc file.
## Links
#### Pubmed
http://www.ncbi.nlm.nih.gov/pubmed/25204867
#### ScienceDirect
http://www.sciencedirect.com/science/article/pii/S1053811914007307
#### ORBi (University of Liège)
http://orbi.ulg.ac.be/handle/2268/171896
#### NITRC
http://www.nitrc.org/projects/forward/
## BibTex code
[Direct link to .bib file](https://github.com/CyclotronResearchCentre/forward/raw/master/citation.bib)
@article{Ziegler2014b,
title = "A finite-element reciprocity solution for \{EEG\} forward modeling with realistic individual head models ",
journal = "NeuroImage ",
volume = "103",
number = "0",
pages = "542 - 551",
year = "2014",
note = "",
issn = "1053-8119",
doi = "http://dx.doi.org/10.1016/j.neuroimage.2014.08.056",
url = "http://www.sciencedirect.com/science/article/pii/S1053811914007307",
author = "Erik Ziegler and Sarah L. Chellappa and Giulia Gaggioni and Julien Q.M. Ly and Gilles Vandewalle and Elodie André and Christophe Geuzaine and Christophe Phillips",
keywords = "Electroencephalography",
keywords = "\{EEG\}",
keywords = "Forward model",
keywords = "Diffusion ",
abstract = "Abstract We present a finite element modeling (FEM) implementation for solving the forward problem in electroencephalography (EEG). The solution is based on Helmholtz's principle of reciprocity which allows for dramatically reduced computational time when constructing the leadfield matrix. The approach was validated using a 4-shell spherical model and shown to perform comparably with two current state-of-the-art alternatives (OpenMEEG for boundary element modeling and SimBio for finite element modeling). We applied the method to real human brain \{MRI\} data and created a model with five tissue types: white matter, gray matter, cerebrospinal fluid, skull, and scalp. By calculating conductivity tensors from diffusion-weighted \{MR\} images, we also demonstrate one of the main benefits of FEM: the ability to include anisotropic conductivities within the head model. Root-mean square deviation between the standard leadfield and the leadfield including white-matter anisotropy showed that ignoring the directional conductivity of white matter fiber tracts leads to orientation-specific errors in the forward model. Realistic head models are necessary for precise source localization in individuals. Our approach is fast, accurate, open-source and freely available online. "
}
## References
The citations for these tools are:
**SimNIBS: Simulation of Non-invasive Brain Stimulation**
Windhoff, M., Opitz, A. and Thielscher, A. (2011), Electric field calculations in brain stimulation based on finite elements: An optimized processing pipeline for the generation and usage of accurate individual head models. Human Brain Mapping
**Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities**
C. Geuzaine and J.-F. Remacle. Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities. International Journal for Numerical Methods in Engineering 79(11), pp. 1309-1331, 2009
**GetDP: a General Environment for the Treatment of Discrete Problems**
C. Geuzaine and J.-F. Remacle. Gmsh: a three-dimensional finite element mesh generator with built-in pre- and post-processing facilities. International Journal for Numerical Methods in Engineering 79(11), pp. 1309-1331, 2009
**Meshfix**
M. Attene - A lightweight approach to repairing digitized polygon meshes.
The Visual Computer, 2010. (c) Springer.
**Nipype: Neuroimaging in Python - Pipelines and Interfaces**
Gorgolewski K, Burns CD, Madison C, Clark D, Halchenko YO, Waskom ML, Ghosh SS. (2011). Nipype: a flexible, lightweight and extensible neuroimaging data processing framework in Python. Front. Neuroimform. 5:13.
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该项目旨在简化用于 EEG 正演建模的精确电磁头部模型的准备工作。 它在开创性SimNIBS工具的基础上构建了经颅磁刺激 (TMS) 和经颅直流电刺激的场建模。人体皮肤、头骨、脑脊液和大脑网格化管道已使用 Nipype 重写,以简化访问并行处理并允许用户启动/停止工作流程。还包括来自扩散加权成像的电导率张量映射。 更多详情、使用方法,请下载后阅读README.md文件
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forward-master.zip (73个子文件)
forward-
citation.bib 2KB
LICENSE 18KB
examples
sphere_dipole.py 2KB
almi5_process_diffusion.py 3KB
step4_forward_model.py 3KB
example_compare_leadfields.py 462B
brainsearch.py 857B
example_add_sensors.py 266B
example_almi_SingleImage.py 2KB
step5_iso.py 3KB
sphere_model.py 3KB
step1_process_structural.py 2KB
MAGs.pdf 419KB
step2_process_diffusion.py 3KB
plot_res.py 2KB
RDMs.pdf 420KB
step3_add_electrodes.py 2KB
example_sphere_summary.py 2KB
cost_function_mapping.py 3KB
evaluate_sphere_results.py 8KB
example_draw_electrode_locations.py 790B
searchtest.py 804B
example_rewrite_using_binary_mask.py 502B
example_element_data_math.py 532B
example_FourImageMesh.py 3KB
ForwardSample
TMS007
DTI-MRI_grad_1000_invZ 5KB
plot_res_Simbio.py 2KB
test_analytical.py 301B
rmse_stats.py 766B
setup.py 202B
.gitignore 540B
forward
dipole.py 8KB
simbio
mesh_nodes_elem_to_matlab.py 344B
elem.txt 6.71MB
SphereParameters.par 4KB
elec.txt 2KB
nodes.txt 3.83MB
4shell.v 5.23MB
current.txt 744B
simbio_rdm_mag.py 3KB
testSimBioSphere.m 665B
labels.txt 1.68MB
search.py 3KB
tdcs.py 5KB
electrodes.py 9KB
__init__.py 0B
struct.py 67KB
dti.py 19KB
mesh.py 22KB
analytical.py 4KB
ct.py 9KB
leadfield.py 18KB
sphere.py 6KB
datasets
utils.py 3KB
sample.py 623B
__init__.py 0B
meshmath.py 3KB
README.md 5KB
etc
SphereElectrodeLabels_42.geo 2KB
unity.xfm 160B
icosahedron642.txt 16KB
eeg_forward_sphere.pro 6KB
eeg_leadfield4.m 5KB
icosahedron162.txt 4KB
eeg_forward.pro 7KB
yshift.mat 100B
CC_filterkernel.nii.gz 70B
eeg_leadfield4_prepare.m 3KB
eeg_dipole.pro 7KB
ElectrodeNames.txt 233B
fs2fsl_conform.mat 47B
icosahedron42.txt 918B
fs2fsl_conform_inverse.mat 55B
共 73 条
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- 直接裂开君2024-05-17超级好的资源,很值得参考学习,对我启发很大,支持!
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