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| [[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]] 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. |
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| == Installation == | == Requirement == * You have already followed all the introduction tutorials * You have a working copy of Brainstorm installed on your computer == Brainsuite Installation == |
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| 1. The BrainSuite installation folder should be informed in the Brainstorm preferences | |
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| == 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''' |
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| The BrainSuite installation folder should be informed in the Brainstorm preferences: | ---- /!\ '''Edit conflict - other version:''' ---- |
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| {{https://user-images.githubusercontent.com/6920058/81406567-1c785400-913a-11ea-9048-28c7459af7da.png|image}} | ---- /!\ '''Edit conflict - other version:''' ---- {{attachment:brainsuiteInstalation.JPG||height="250",width="650"}} |
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| == 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. |
---- /!\ '''Edit conflict - your version:''' ---- {{attachment:brainsuiteInstalation.JPG||height="250",width="650"}} ---- /!\ '''End of edit conflict''' ---- ---- /!\ '''Edit conflict - your version:''' ---- {{attachment:brainsuiteInstalation.JPG||height="250",width="650"}} ---- /!\ '''End of edit conflict''' ---- == 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 [[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]] 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. |
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| 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. | 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. |
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| 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. | {{attachment:mri.JPG||height="100",width="250"}} === Diffusion tensor generation (DTI) from DWI === Right-click on the subject and then select the item "Convert DWI to DTI". ---- /!\ '''Edit conflict - other version:''' ---- ---- /!\ '''Edit conflict - other version:''' ---- Then follow the popup windows by selecting the DWI, bval, and bval. 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). ---- /!\ '''Edit conflict - your version:''' ---- Then follow the popup windows by selecting the DWI, bval, and bval. 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). ---- /!\ '''End of edit conflict''' ---- ---- /!\ '''Edit conflict - your version:''' ---- Then follow the popup windows by selecting the DWI, bval, and bval. 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). ---- /!\ '''End of edit conflict''' ---- In this step, Brainstorm calls the Brainsuite internally, and the diffusion tensors are computed. 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"}} === Conductivity tensor generation from DTI === The Effective Medium Approach is applied to convert the diffusion tensors to the conductivity tensors. 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). ---- /!\ '''Edit conflict - other version:''' ---- ---- /!\ '''Edit conflict - other version:''' ---- 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. ---- /!\ '''Edit conflict - your version:''' ---- 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. ---- /!\ '''End of edit conflict''' ---- ---- /!\ '''Edit conflict - your version:''' ---- 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. ---- /!\ '''End of edit conflict''' ---- |
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| 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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| ---- /!\ '''Edit conflict - other version:''' ---- | |
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| ---- /!\ '''Edit conflict - other version:''' ---- Brainstorm will load the available tissue in the FEM head model and the following windows appear. |
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| Brainstorm will load the avialbale tissue in the FEM head model and the following windows appears. | Select the WM anisotropy and kee all the other tissues as isotropic. |
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| Select the WM anisotropy and kee all the oher 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. |
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| 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 structure. [explain how it is organized and how to use it outside brainstorm ] |
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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 ] | ---- /!\ '''Edit conflict - your version:''' ---- 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 ] ---- /!\ '''End of edit conflict''' ---- ---- /!\ '''Edit conflict - your version:''' ---- 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 ] ---- /!\ '''End of edit conflict''' ---- |
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| 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. | ---- /!\ '''Edit conflict - other version:''' ---- ---- /!\ '''Edit conflict - other version:''' ---- 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. ---- /!\ '''Edit conflict - your version:''' ---- 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. ---- /!\ '''End of edit conflict''' ---- ---- /!\ '''Edit conflict - your version:''' ---- 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. ---- /!\ '''End of edit conflict''' ---- |
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
- 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
![/!\](/moin_static198/brainstorm1/img/alert.png "/!\"){kind=small}
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![[ATTACH]](/brainstorm/Tutorials/FemTensors?action=AttachFile&do=upload_form&ticket=006738f0c4.c457ea445f14255bc3d681d81f7a0fbb791cec17&target=brainsuiteInstalation.JPG "[ATTACH]"){kind=small}
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End of edit conflict
Edit conflict - your version:
End of edit conflict
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,
![[ATTACH]](/brainstorm/Tutorials/FemTensors?action=AttachFile&do=upload_form&ticket=006738f0c4.c457ea445f14255bc3d681d81f7a0fbb791cec17&target=vierMriFolder.JPG "[ATTACH]"){kind=small}
The second file is the DWI and should contain at least three files
![[ATTACH]](/brainstorm/Tutorials/FemTensors?action=AttachFile&do=upload_form&ticket=006738f0c4.c457ea445f14255bc3d681d81f7a0fbb791cec17&target=vierDWIFolder.JPG "[ATTACH]"){kind=small}
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
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.
![[ATTACH]](/brainstorm/Tutorials/FemTensors?action=AttachFile&do=upload_form&ticket=006738f0c4.c457ea445f14255bc3d681d81f7a0fbb791cec17&target=mri.JPG "[ATTACH]"){kind=small}
Diffusion tensor generation (DTI) from DWI
Right-click on the subject and then select the item "Convert DWI to DTI".
Edit conflict - other version:
Edit conflict - other version:
Then follow the popup windows by selecting the DWI, bval, and bval. 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).
Edit conflict - your version:
Then follow the popup windows by selecting the DWI, bval, and bval. 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).
End of edit conflict
Edit conflict - your version:
Then follow the popup windows by selecting the DWI, bval, and bval. 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).
End of edit conflict
In this step, Brainstorm calls the Brainsuite internally, and the diffusion tensors are computed. 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.
![[ATTACH]](/brainstorm/Tutorials/FemTensors?action=AttachFile&do=upload_form&ticket=006738f0c4.c457ea445f14255bc3d681d81f7a0fbb791cec17&target=mriAndDTI-EIG.JPG "[ATTACH]"){kind=small}
Conductivity tensor generation from DTI
The Effective Medium Approach is applied to convert the diffusion tensors to the conductivity tensors. 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).
Edit conflict - other version:
Edit conflict - other version:
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.
Edit conflict - your version:
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.
End of edit conflict
Edit conflict - your version:
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.
End of edit conflict
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,
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Edit conflict - other version:
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 ]
Edit conflict - your version:
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 ]
End of edit conflict
Edit conflict - your version:
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 ]
End of edit conflict
Display the tensors
Artificial/simulated conductivity tensors
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Edit conflict - other version:
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.
Edit conflict - your version:
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.
End of edit conflict
Edit conflict - your version:
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.
End of edit conflict
Two approaches are integrated within Brainstorm. Either the