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| ''Authors: [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani|Takfarinas Medani]], Francois Tadel, Anand Joshi and Richard Leahy'' '''[TUTORIAL UNDER WRITING: NOT READY FOR PUBLIC USE]''' |
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'''[TUTORIAL UNDER REVISION/CORRECTION: NOT READY FOR PUBLIC USE]''' ''Authors: [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani|Takfarinas Medani]], Francois Tadel, Anand Joshi and Richard Leahy'' |
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<<TableOfContents(2,2)>> == Installation == 1. Download the latest version of BrainSuite from http://www.brainsuite.org/download. 1. Install it on your computer by following the instructions in [[http://brainsuite.bmap.ucla.edu/quickstart/installation/|BrainSuite's quick start installation guide]]. 1. Note that you will be using Surface/Volume Registration (SVReg) to do the surface segmentation, so you need to install a compatible [[http://www.mathworks.com/products/compiler/mcr|MATLAB Compiler Runtime]](2015b for BrainSuite 18a). You may ignore any instructions about "Setting up BDP" if you are not planning on using BrainSuite for diffusion imaging. 1. Start BrainSuite (if it is not already open following installation). == Requirement == * You have already followed all the introduction tutorials * You have already generated the FEM mesh as explained here (link to the FEM mesh) * You have a working copy of Brainstorm installed on your computer. * Get the open access reference data set from''' '''here''' link todataset of Ernie / simnibs''' The BrainSuite installation folder must be informed in the Brainstorm preferences: {{https://user-images.githubusercontent.com/6920058/81406567-1c785400-913a-11ea-9048-28c7459af7da.png|image|font-size="10pt"}} == Import data == Onc you have imported the MRI and generated a FEM mesh. == BDP == then right-click on the subject folder > Convert DWI to DTI, select DWI+bvec+bval: {{https://user-images.githubusercontent.com/6920058/81406299-9b20c180-9139-11ea-85ef-25278a78826f.png|image|font-size="10pt"}} Then follow the popup windows by selecting DWI, bval and bval == From diffusion tensor to conductivity tensor == == FEM head model == == Simulated tensors == == References == |
Estimation of brain's tissues anisortopy using Brainsuite Diffusion Pipline
Authors: Takfarinas Medani, Francois Tadel, Anand Joshi and Richard Leahy
[TUTORIAL UNDER WRITING: NOT READY FOR PUBLIC USE]
Describe brainsuite here : here we will describe the process of the brain tissues anisotrpy estimation and the different functions that brainstorm offers.
This tutorial explains how to use Brainsuite to estimate the anisotropy of the brain tissues.
refer to this page
https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite?highlight=%28anand%29
model using the finite element method (FEM). The FEM methods use the realistic volume mesh of the head generated from the segmentation of the MRI. The FEM models provides more accurate results than the spherical forward models, and more realistic geometry and tissue propriety than the BEM methods.
The scope of this page is limited to a basic example (head model with 3 layers), more advanced options for head model generation and forward model options are discussed in the tutorial about FEM mesh generation. We assume that you have already followed the introduction tutorials (or at least the head modeling tutorial), we will not discuss the general principles of forward modeling here.
Contents
Installation
Download the latest version of BrainSuite from http://www.brainsuite.org/download.
Install it on your computer by following the instructions in BrainSuite's quick start installation guide.
Note that you will be using Surface/Volume Registration (SVReg) to do the surface segmentation, so you need to install a compatible MATLAB Compiler Runtime(2015b for BrainSuite 18a). You may ignore any instructions about "Setting up BDP" if you are not planning on using BrainSuite for diffusion imaging.
Start BrainSuite (if it is not already open following installation).
Requirement
- You have already followed all the introduction tutorials
- You have already generated the FEM mesh as explained here (link to the FEM mesh)
- You have a working copy of Brainstorm installed on your computer.
Get the open access reference data set from here link todataset of Ernie / simnibs
The BrainSuite installation folder must be informed in the Brainstorm preferences:
Import data
Onc you have imported the MRI and generated a FEM mesh.
BDP
then right-click on the subject folder > Convert DWI to DTI, select DWI+bvec+bval:
Then follow the popup windows by selecting DWI, bval and bval
From diffusion tensor to conductivity tensor
FEM head model
Simulated tensors