Differences between revisions 11 and 27 (spanning 16 versions)

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

The realistic tensors are estimated from the Diffusion-Weighted Images (DWI). For this purpose, Brainstorm calls internally the BrainSuite Diffusion Pipeline to compute the diffusion tensors on each brain voxel. Afterward, the Effective Medium Approach is applied to convert the diffusion tensors to the conductivity tensors. The following section shows the users how to do it from the graphical interface.

Only the NIfTI is supported. All the diffusion data, including the DWI file and direction and the value of the gradient files, respectively the *.nii, the *.bval and the *.bvec are required. Ideally, these files should have the same name and saved in the same folder.

Contents

Requirement
Brainsuite Installation
Dataset
Realistic condctivity tensors
Artificial/simulated conductivity tensors
References

Requirement

You have already followed all the introduction tutorials
You have a working copy of Brainstorm installed on your computer

Brainsuite 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).
The BrainSuite installation folder should be informed in the Brainstorm preferences

Dataset

In this tutorial, we use the Brainsuite dataset example available on the Brainsuite tutorial webpage

http://brainsuite.org/tutorials/. The T1w of the subject can be download from this link BrainSuiteTutorialSVReg_Sept16.zip. The DWI from this link DWI_Feb15.zip

The first link contains the T1 MRI, with the name '2523412.nii.gz'. as in this figure,

The second file is the DWI and should contain at least three files

Where the *.bval is a text file that contains the value of the gradient, and the *.bvec is also a text file that contains the orientation of the gradient. The nii.gz file is the NifTi file of the DWI where the images are stored.

Realistic condctivity tensors

Load the T1 MRI data to brainstorm

First, you need to create a new subject in your protocol, let call it the 'BrainSuiteSubject'. Then import the T1 MRI of the subject and set the fiducials points as explained in the previous tutorial.

The T1 MRI is required since all the BDP uses the T1 space for its computation. Furthermore, this is required since it will be used to align the tensors to the FEM mesh later.

Diffusion tensor generation (DTI) from DWI

In this step, Brainstorm calls the Brainsuite internally, and the diffusion tensors are computed.

Right-click on the subject and then select the item "Convert DWI to DTI". Then follow the popup windows by selecting the DWI, bval, and bval files. If these files are in the same folder, Brainstorm will detect them automatically, otherwise, the user will be asked to browse the files one by one (as it's the case in this tutorial).

At the end of this process, a new node will appear in the Brainstorm database with the name 'DTI-EIT'. This name refers to, DTI: diffusion tensors images, and EIG for eigenvalue, since the eigenvalues and eigenvectors are computed at voxel and stored in Brainstorm database.

If you check the structure of the file DTI-EIG, by right click -> File and then 'Display file contents', the following figure is displayed.

The size of the matrix is 128x256x256x12, where the first 3 values are the same as the size of the T1 MRI and 12 corresponds to the 3 eigenvectors components (9) and eigenvalues (3)

Conductivity tensor generation from DTI

The Effective Medium Approach is applied to convert the diffusion tensors to the conductivity tensors.

FEM mesh head model

This step requires the FEM mesh of the head model. You can generate the FEM head model from the MRI as explained on this page (add link).

For the following, we used the SimNibs FEM mesh generation. The following figure shows the FEM mesh obtained from using the T1 MRI.

Note that this mesh is obtained only from the T1, the use of the T2 is highly recommended if it's available.

Computation of FEM mesh tensors

Once the FEM mesh and the DTI tensors are available in the Brainstorm database, the next step for the FEM tensors can be performed by the following:

- Right-click on the FEM mesh - Compute FEM tensors

Brainstorm checks the available tissues in the FEM head model and displays the following panel

This panel lists the tissues available in the FEM head model and assigns a default value of the conductivity for each compartment. Users can change these values to their own if needed.

DTI values can be used to generate conductivity tensors for the white matter (and in some cases for the grey matter). Please, note that the DWI can be used only for the brain tissues and not for the outers compartments (skull and skin)

In this tutorial (and in most cases) we select the white matter. Select the anisotropy button for the white matter and then these additional options appear asking for the method to use.

The available methods are:

- Effective Medium approach (EMA)

- Effective Medium approach with volume constraints (EMA + VC)

- Simulated or the artificial anisotropy

Only the twos first methods require the DTI. More information about these methods can be found on these references [][] and in our main paper [link]

In this tutorial, we use the method "EMA + VC", where the final tensors are constrained to fits the volume of the isotropic tensor volume.

Visulation of FEM mesh tensors

FEM mesh tensors

In the case where the user wants to use generate isotropic tensors, then the DTI is not required.

In the case where more than one FEM head model is in the database, the highlighted one in the green color will be used.

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',

Brainstorm will load the available tissue in the FEM head model and the following windows appear.

Select the WM anisotropy and kee all the other tissues as isotropic.

The process of conversion from DWI to Conductivity tensors uses the EMA, furthermore, brainstorm proposes 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 structure. [explain how it is organized and how to use it outside brainstorm ]

Brainstorm will load the available tissue in the FEM head model and the following windows appear.

Select the WM anisotropy and kee all the other tissues as isotropic.

The process will take around 10 min, and then the FEM tensors are computed and stored in the FEM structure. [explain how it is organized and how to use it outside brainstorm ]

Artificial/simulated conductivity tensors

In the case where the DWI is not available, or the users desire to evaluate the effect of the conductivity change on the model, the artificial conductivity can be used.

Two approaches are integrated within Brainstorm. Either the

-  ⇤ ← Revision 11 as of 2020-06-20 03:13:00 → 
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+   ← Revision 27 as of 2020-08-25 03:03:14 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
+## page was renamed from brainsuiteBDP
-Line 2:
+Line 3:
-= Estimation of brain's tissues anisortopy using Brainsuite Diffusion Pipline =
+= FEM tensors estimation with BrainSuite =
-Line 13:
+Line 14:
-[[https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite?highlight=(anand)|https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite?highlight=%28anand%29]]
+[[https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite?highlight=(Anand)|https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite?highlight=%28anand%29]]
-Line 15:
+Line 16:
---(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 realistic tensors are estimated from the Diffusion-Weighted Images (DWI). For this purpose, Brainstorm calls internally the BrainSuite Diffusion Pipeline to compute the diffusion tensors on each brain voxel. Afterward, the Effective Medium Approach is applied to convert the diffusion tensors to the conductivity tensors. The following section shows the users how to do it from the graphical interface.
-Line 17:
+Line 18:
---(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.)--
+Only the NIfTI is supported. All the diffusion data, including the DWI file and direction and the value of the gradient files, respectively the *.nii, the *.bval and the *.bvec are required. Ideally, these files should have the same name and saved in the same folder.
-Line 21:
+Line 22:
-== Installation ==
+== Requirement ==
 * You have already followed all the introduction tutorials
 * You have a working copy of Brainstorm installed on your computer

== Brainsuite Installation ==
-Line 24:
+Line 29:
-. 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).
+. 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).
 1. The BrainSuite installation folder should be informed in the Brainstorm preferences
-Line 27:
+Line 33:
-== Requirement ==
+{{attachment:brainsuiteInstalation.JPG||height="250",width="650"}}
-Line 29:
+Line 35:
- * 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'''
+----
== Dataset ==
In this tutorial, we use the Brainsuite dataset example available on the Brainsuite tutorial webpage
-Line 34:
+Line 39:
-The BrainSuite installation folder must be informed in the Brainstorm preferences:
+http://brainsuite.org/tutorials/. The T1w of the subject can be download from this link  [[http://brainsuite.org/WebTutorialData/BrainSuiteTutorialSVReg_Sept16.zip|BrainSuiteTutorialSVReg_Sept16.zip]]. The DWI from this link  [[http://brainsuite.org/WebTutorialData/DWI_Feb15.zip|DWI_Feb15.zip]]
-Line 36:
+Line 41:
-{{https://user-images.githubusercontent.com/6920058/81406567-1c785400-913a-11ea-9048-28c7459af7da.png|image|font-size="10pt"}}
+The first link contains the T1 MRI, with the name '2523412.nii.gz'. as in this figure,

{{attachment:vierMriFolder.JPG||height="130",width="580"}}

The second file is the DWI and should contain at least three files

{{attachment:vierDWIFolder.JPG||height="150",width="580"}}

Where the *.bval is a text file that contains the value of the gradient, and the *.bvec is also a text file that contains the orientation of the gradient. The nii.gz file is the NifTi file of the DWI where the images are stored.

== Realistic condctivity tensors ==
=== Load the T1 MRI data to brainstorm ===
First, you need to create a new subject in your protocol, let call it the 'BrainSuiteSubject'. Then import the T1 MRI of the subject and set the fiducials points as explained in the previous tutorial.

The T1 MRI is required since all the BDP uses the T1 space for its computation. Furthermore, this is required since it will be used to align the tensors to the FEM mesh later.

{{attachment:mri.JPG||height="100",width="250"}}

=== Diffusion tensor generation (DTI) from DWI ===
In this step, Brainstorm calls the Brainsuite internally, and the diffusion tensors are computed.

Right-click on the subject and then select the item "Convert DWI to DTI". Then follow the popup windows by selecting the DWI, bval, and bval files. If these files are in the same folder, Brainstorm will detect them automatically, otherwise, the user will be asked to browse the files one by one (as it's the case in this tutorial).

At the end of this process, a new node will appear in the Brainstorm database with the name 'DTI-EIT'. This name refers to, DTI: diffusion tensors images, and EIG for eigenvalue, since the eigenvalues and eigenvectors are computed at voxel and stored in Brainstorm database.

{{attachment:mriAndDTI-EIG.JPG||height="100",width="250"}}

If you check the structure of the file DTI-EIG, by right click -> File and then 'Display file contents', the following figure is displayed.

{{attachment:EIG-hardDisc.JPG||height="200",width="450"}}

The size of the matrix is 128x256x256x12, where the first 3 values are the same as the size of the T1 MRI and 12 corresponds to the 3 eigenvectors components (9) and eigenvalues (3)

=== Conductivity tensor generation from DTI ===
The Effective Medium Approach is applied to convert the diffusion tensors to the conductivity tensors.

==== FEM mesh head model ====
This step requires the FEM mesh of the head model. You can generate the FEM head model from the MRI as explained on this page (add link).

For the following, we used the SimNibs FEM mesh generation. The following figure shows the FEM mesh obtained from using the T1 MRI.

{{attachment:Mri&femMeshView.JPG|Mri&femMeshView.JPG|height="300",width="260"}} {{attachment:femMeshView.JPG||height="300",width="280"}}

Note that this mesh is obtained only from the T1, the use of the T2 is highly recommended if it's available.

==== Computation of FEM mesh tensors ====
Once the FEM mesh and the DTI tensors are available in the Brainstorm database, the next step for the FEM tensors can be performed by the following:

- Right-click on the FEM mesh - Compute FEM tensors

{{attachment:menuGenerateFemTensors.png||height="280",width="250"}}

Brainstorm checks the available tissues in the FEM head model and displays the following panel

{{attachment:FEMConductivitiesIsoPanel.JPG||height="250",width="250"}}

This panel lists the tissues available in the FEM head model and assigns a default value of the conductivity for each compartment. Users can change these values to their own if needed.

DTI values can be used to generate conductivity tensors for the white matter (and in some cases for the grey matter). Please, note that the DWI can be used only for the brain tissues and not for the outers compartments (skull and skin)

In this tutorial (and in most cases) we select the white matter. Select the anisotropy button for the white matter and then these additional options appear asking for the method to use.

{{attachment:FEMConductivitiesAnisoPanel.JPG||height="300",width="250"}}

The available methods are: 

- Effective Medium approach (EMA) 

- Effective Medium approach with volume constraints  (EMA + VC)

- Simulated or the artificial anisotropy

Only the twos first methods require the DTI. More information about these methods can be found on these references [][] and in our main paper [link] 

In this tutorial, we use the method "EMA + VC", where the final tensors are constrained to fits the volume of the isotropic tensor volume. 

==== Visulation of FEM mesh tensors ====
-Line 40:
+Line 121:
-== Import data ==
Onc you have imported the MRI and generated a FEM mesh.
+==== FEM mesh tensors ====
-Line 43:
+Line 123:
-== BDP ==
+In the case where the user wants to use generate isotropic tensors, then the DTI is not required.
-Line 45:
+Line 125:
+In the case where more than one FEM head model is in the database, the highlighted one in the green color will be used.
-Line 46:
+Line 127:
+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)
-Line 47:
+Line 129:
-then right-click on the subject folder > Convert DWI to DTI, select DWI+bvec+bval:
+When this is done, then right-click on the subject -> 'Convert DWI to DTI',
-Line 49:
+Line 131:
-{{https://user-images.githubusercontent.com/6920058/81406299-9b20c180-9139-11ea-85ef-25278a78826f.png|image|font-size="10pt"}}
+Brainstorm will load the available tissue in the FEM head model and the following windows appear.
-Line 51:
+Line 133:
-Then follow the popup windows by selecting DWI, bval and bval
+Select the WM anisotropy and kee all the other tissues as isotropic.
-Line 53:
+Line 135:
-== From diffusion tensor to conductivity tensor ==
== FEM head model ==
== Simulated tensors ==
+The process of conversion from DWI to Conductivity tensors uses the EMA, furthermore, brainstorm proposes 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 structure. [explain how it is organized and how to use it outside brainstorm ]

Brainstorm will load the available tissue in the FEM head model and the following windows appear.

Select the WM anisotropy and kee all the other tissues as isotropic.

The process of conversion from DWI to Conductivity tensors uses the EMA, furthermore, brainstorm proposes 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 structure. [explain how it is organized and how to use it outside brainstorm ]

== Artificial/simulated conductivity tensors ==
In the case where the DWI is not available, or the users desire to evaluate the effect of the conductivity change on the model, the artificial conductivity can be used.

Two approaches are integrated within Brainstorm. Either the

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