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| Detection, localization and labeling of SEEG depth electrodes is a vital step in studying brain activity. This tutorial can be considered as a precursor to the [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity | Epileptogenicity]] tutorial. | Detection, localization and labeling of SEEG depth electrodes is a vital step in studying brain activity. This tutorial can be considered as a precursor to the [[https://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity|Epileptogenicity]] tutorial. |
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| * '''CT2MRIREG''': If you are running Brainstorm from the MATLAB environment, for the coregistration between CT and MRI volumes, you need to have the ct2mrireg Anatomy plugin installed on your computer, as a [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|Brainstorm plugin]]. | * '''SPM''': If you are running Brainstorm from the MATLAB environment, you need to have the SPM12 toolbox installed on your computer, as a [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|Brainstorm plugin]] or a custom installation. <<BR>>With the stand-alone compiled version of Brainstorm: all the needed SPM scripts have been compiled and included in the executable. * '''CT2MRIREG''': If you are running Brainstorm from the MATLAB environment, for the coregistration between pre-implantation MRI and post-implantation CT volumes, you need to have the '''ct2mrireg''' plugin installed on your computer, as a [[https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins|Brainstorm plugin]]. It can be found under the menu '''Plugins > Anatomy > ct2mrireg'''. |
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| * Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page of this website, and download the file: '''tutorial_seeg_contact_localization.zip''' * Unzip it in a folder that is not in any of the Brainstorm folders (program folder or database folder) |
* Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page of this website, and download the file: '''tutorial_seeg_contact_localization.zip'''. * Unzip it in a folder that is not in any of the Brainstorm folders (program folder or database folder). |
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| * Select the menu File > Create new protocol. Name it "'''TutorialSeegImplantation'''" and select the options: <<BR>>"'''No, use individual anatomy'''",<<BR>>"'''No, use one channel file per acquisition run'''". | * Select the menu '''File > Create new protocol'''. Name it "'''TutorialSeegImplantation'''" and select the options: <<BR>>"'''No, use individual anatomy'''",<<BR>>"'''No, use one channel file per acquisition run'''". == Import the anatomy == === Pre-implantation MRI === * Right-click on the TutorialSeegImplantation folder > '''New subject''' > '''Subject01'''.<<BR>>Keep the default options you defined for the protocol. * Switch to the "anatomy" view of the protocol. * Right-click on the subject node > '''Import MRI''':<<BR>>Set the file format: "All MRI file (subject space)"<<BR>>Select: '''tutorial_epimap_bids/sub-01/ses-preimp/anat/sub-01_ses-preimp_T1w.nii.gz''' * Do you want to apply the transformation to the MRI file? '''YES''' * The MRI viewer opens automatically. The positions of all the anatomical fiducials are already defined, they were read from the .json file located in the same folder. * Click on "[[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#MNI_normalization|Click here to compute MNI normalization]]", option "'''maff8'''". It does affine registration using SPM mutual information algorithm. <<BR>><<BR>> {{attachment:mni_transformation.gif}} * Click on [Save] to close the MRI viewer. * Rename the new file: '''T1pre'''. <<BR>><<BR>> {{attachment:import_t1pre.gif}} |
iEEG Contact Localization (UNDER CONSTRUCTION)
Authors: Chinmay Chinara, Takfarinas Medani.
Detection, localization and labeling of SEEG depth electrodes is a vital step in studying brain activity. This tutorial can be considered as a precursor to the Epileptogenicity tutorial.
NOT FOR CLINICAL USE:
The performance characteristics of the methods and software implementation presented in this tutorial have not been certified as medical devices and should be used for research purposes only.
Download and installation
Requirements: You have already followed all the introduction tutorials and you have a working copy of Brainstorm installed on your computer.
SPM: If you are running Brainstorm from the MATLAB environment, you need to have the SPM12 toolbox installed on your computer, as a Brainstorm plugin or a custom installation.
With the stand-alone compiled version of Brainstorm: all the needed SPM scripts have been compiled and included in the executable.CT2MRIREG: If you are running Brainstorm from the MATLAB environment, for the coregistration between pre-implantation MRI and post-implantation CT volumes, you need to have the ct2mrireg plugin installed on your computer, as a Brainstorm plugin. It can be found under the menu Plugins > Anatomy > ct2mrireg.
Download the dataset:
Go to the Download page of this website, and download the file: tutorial_seeg_contact_localization.zip.
- Unzip it in a folder that is not in any of the Brainstorm folders (program folder or database folder).
Brainstorm:
- Start Brainstorm (MATLAB scripts or stand-alone version).
Select the menu File > Create new protocol. Name it "TutorialSeegImplantation" and select the options:
"No, use individual anatomy",
"No, use one channel file per acquisition run".
Import the anatomy
Pre-implantation MRI
Right-click on the TutorialSeegImplantation folder > New subject > Subject01.
Keep the default options you defined for the protocol.- Switch to the "anatomy" view of the protocol.
Right-click on the subject node > Import MRI:
Set the file format: "All MRI file (subject space)"
Select: tutorial_epimap_bids/sub-01/ses-preimp/anat/sub-01_ses-preimp_T1w.nii.gzDo you want to apply the transformation to the MRI file? YES
- The MRI viewer opens automatically. The positions of all the anatomical fiducials are already defined, they were read from the .json file located in the same folder.
Click on "Click here to compute MNI normalization", option "maff8". It does affine registration using SPM mutual information algorithm.
![[ATTACH]](/moin_static198/brainstorm1/img/attach.png "[ATTACH]")
- Click on [Save] to close the MRI viewer.
Rename the new file: T1pre.
![[ATTACH]](/brainstorm/Tutorials/IeegContactLocalization?action=AttachFile&do=upload_form&ticket=006826d66a.9792f211245d6def5b90cd4bd821168d76474855&target=mni_transformation.gif "[ATTACH]"){kind=small}
![[ATTACH]](/brainstorm/Tutorials/IeegContactLocalization?action=AttachFile&do=upload_form&ticket=006826d66a.9792f211245d6def5b90cd4bd821168d76474855&target=import_t1pre.gif "[ATTACH]"){kind=small}