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| = Estimation of brain's tissues anisortopy using Brainsuite Diffusion Pipline = | ## page was renamed from brainsuite = FEM tensors estimation with BrainSuite = ''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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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=(anand)|https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite?highlight=%28anand%29]] <<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 BrainSuite Diffusion Pipeline(BDP), so you need to install a compatible [[http://www.mathworks.com/products/compiler/mcr|MATLAB Compiler Runtime]](last version). 1. Start BrainSuite to check if the installation (It's not required to open BrainSuite to run this tutorial). == Requirement == * You have already followed all the introduction tutorials * You have already generated the FEM mesh as explained here (link to the FEM mesh tutorial) * 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 should be informed in the Brainstorm preferences: {{https://user-images.githubusercontent.com/6920058/81406567-1c785400-913a-11ea-9048-28c7459af7da.png|image}} == Import data == Onc you have imported the MRI and generated a FEM mesh. You can call the process to generate the FEM tensors. In the folowing, both the realistic tensors from the DWI and the artificial tensors will be generated. == Realistic condctivity tensors == The realistic tensors are estimated from the Diffusion Weighted Images (DWI). For this purpose, Brainstorm calls internally the BrainSuite Diffusion Pipline to compute the diffusion tensors on each brain voxel. Afterwards, the Effective Medium Appeach is applied to convert the diffusion tensors to the conductivity tensors. The following section shows to the users how to do it from the graphical intefrace. Only the NIfTI are supported. All the diffusion data, inclusing the DWI file and direction and the value of the gradient files , respectively the the *.nii, the *.bval and the *.bvec are required. Ideally these files should have the same name and saved in the same folder. The FEM head model to use for tensors should be selected and highlighted with the green color (double click on the FEM mesh node to select it) When this is done, then right-click on the subject > Convert DWI to DTI, Then follow the popup windows by selecting DWI, bval and bval. If these files are in the same folder, Brainstorm will detect them automatiquely, otherwise user will be asked to browse the files one by one. |
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| '''[TUTORIAL UNDER REVISION/CORRECTION: NOT READY FOR PUBLIC USE]''' | Brainstorm will load the avialbale tissue in the FEM head model and the following windows appears. |
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| ''Authors: [[https://neuroimage.usc.edu/brainstorm/AboutUs/tmedani|Takfarinas Medani]], Juan Garcia-Prieto, Francois Tadel, Sophie Schrader, Christian Engwer, Carsten Wolters, John Mosher and Richard Leahy'' | Select the WM anisotropy and kee all the oher tissues as isotropic. |
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| This tutorial explains how to use Brainsuite to estimate the anisotropy of the brain tissues. | The process of conversion from DWI to Conductivity tensors use the EMA, furthermore, brainstorm propose the option to use the adaptative EMA with the volume constraint option [ref]. In this example we select the EMA with the VC. |
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| --()-- | The process will take around 10 min, and then the FEM tensors are computed and stored in the FEM strucutre. [explain how it is organised and how to use it outside brainstorm ] |
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| --(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.)-- | === Display the tensors === == Artificial/simulated conductivity tensors == In the case where the DWI is not available, or the users desire to evaluates the effect of the conductivity change on the model, the artificial conductivity can be use. |
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| --(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.)-- | Two approaches are integrated within Brainstorm. Either the == References == |
FEM tensors estimation with BrainSuite
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
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 BrainSuite Diffusion Pipeline(BDP), so you need to install a compatible MATLAB Compiler Runtime(last version).
Start BrainSuite to check if the installation (It's not required to open BrainSuite to run this tutorial).
Requirement
- You have already followed all the introduction tutorials
- You have already generated the FEM mesh as explained here (link to the FEM mesh tutorial)
- 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 should be informed in the Brainstorm preferences:
Import data
Onc you have imported the MRI and generated a FEM mesh. You can call the process to generate the FEM tensors. In the folowing, both the realistic tensors from the DWI and the artificial tensors will be generated.
Realistic condctivity tensors
The realistic tensors are estimated from the Diffusion Weighted Images (DWI). For this purpose, Brainstorm calls internally the BrainSuite Diffusion Pipline to compute the diffusion tensors on each brain voxel. Afterwards, the Effective Medium Appeach is applied to convert the diffusion tensors to the conductivity tensors. The following section shows to the users how to do it from the graphical intefrace.
Only the NIfTI are supported. All the diffusion data, inclusing the DWI file and direction and the value of the gradient files , respectively the the *.nii, the *.bval and the *.bvec are required. Ideally these files should have the same name and saved in the same folder.
The FEM head model to use for tensors should be selected and highlighted with the green color (double click on the FEM mesh node to select it)
When this is done, then right-click on the subject > Convert DWI to DTI,
Then follow the popup windows by selecting DWI, bval and bval. If these files are in the same folder, Brainstorm will detect them automatiquely, otherwise user will be asked to browse the files one by one.
Brainstorm will load the avialbale tissue in the FEM head model and the following windows appears.
Select the WM anisotropy and kee all the oher tissues as isotropic.
The process of conversion from DWI to Conductivity tensors use the EMA, furthermore, brainstorm propose the option to use the adaptative EMA with the volume constraint option [ref]. In this example we select the EMA with the VC.
The process will take around 10 min, and then the FEM tensors are computed and stored in the FEM strucutre. [explain how it is organised and how to use it outside brainstorm ]
Display the tensors
Artificial/simulated conductivity tensors
In the case where the DWI is not available, or the users desire to evaluates the effect of the conductivity change on the model, the artificial conductivity can be use.
Two approaches are integrated within Brainstorm. Either the