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| = iEEG Contact Localization (UNDER CONSTRUCTION) = ''Authors: Chinmay Chinara, Takfarinas Medani, Anand Joshi.'' 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. __'''NOT FOR CLINICAL USE'''__:<<BR>>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. <<TableOfContents(3,2)>> == 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 [[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'''. * '''Download the dataset''': * Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page of this website, and download the file: '''tutorial_seeg_implantation.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: <<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_seeg_implantation/preMRI.nii''' * Do you want to apply the transformation to the MRI file? '''YES''' * The MRI viewer opens automatically. * Click on "[[http://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#MNI_normalization|Click here to compute MNI normalization]]", option "'''maff8'''". This method is embedded in Brainstorm and does not require the installation of SPM12. However, it requires the automatic download of the file SPM12 Tissue Probability Maps. If you do not have access to internet, see the instructions on the [[https://neuroimage.usc.edu/brainstorm/Installation#No_internet_access|Installation]] page. It is based on an affine co-registration with the MNI ICBM152 template from the SPM software, described in the following article: Ashburner J, Friston KJ, [[http://www.ncbi.nlm.nih.gov/pubmed/15955494|Unified segmentation]], NeuroImage 2005.. <<BR>><<BR>> {{attachment:1.png}} {{attachment:2.png}} * Click on '''Save''' to close the MRI viewer. * Rename the new file: '''preMRI'''. <<BR>><<BR>> {{attachment:3.png}} === Post-implantation CT === * The pre-implantation MRI will be used as the anatomical reference for this subject. We will now import a second scan done after the SEEG implantation, on which we can see the SEEG contacts. In this dataset, the post-implantation volume is a CT scan (contacts hypersignal appear in white). * Right-click on the subject node > '''Import CT''':<<BR>>Select: '''tutorial_seeg_implantation/postCT.nii''' * Follow steps [[https://neuroimage.usc.edu/brainstorm/Tutorials/ImportAnatomy#Import_CT|here]] to complete the process on importing a CT. * The MRI viewer opens automatically, showing the post-implantation CT volume as a colored layer on top of the previous volume. Adjust the transparency and amplitude threshold of this layer in the section '''Data options''' of the '''Surface '''tab, adjust its [[Tutorials/Colormaps|colormap]] with the popup menu of the figure. Use this display to validate that the coregistration of the two volume is correct, all the parts of the head must align well. <<BR>><<BR>> {{attachment:4.png}} * Rename the new file: '''postCT'''.<<BR>><<BR>> {{attachment:5.png}} === Generate isoSurface === This creates a thresholded mesh from the CT to separate the contacts out from rest of the CT. This allows the user to better see and localize the electrodes and its contacts. * Right click on '''postCT > CT segmentation > Generate threshold mesh from CT'''.<<BR>><<BR>> {{attachment:6.png}} * This will bring the '''Generate isosurface''' window. This window shows 4 things in the '''Hounsfield Unit (HU)''', the Background level, the White level, the Max Intensity and the '''Set isoValue''' fields. The first 3 values are calculated automatically from the histogram of the CT and is displayed for reference. This is to help the user to decide on what to set the isoValue for getting a good thresholded mesh. Another way is to refer to the [[https://en.wikipedia.org/wiki/Hounsfield_scale|Wiki]]. The editable isoValue field shows an estimated best guess value based on mean of White Level and Max Intensity. Just let that value be and press '''OK'''.<<BR>><<BR>> {{attachment:7.png}} * An isosurface is generated showing the contact as blobs overlayed on the 3D MRI slices. The '''Thresh''' slider under '''Surface options''' can be used to fine tune and regenerate mesh with different isoValues.<<BR>><<BR>> {{attachment:8.png}} |
Please not the this tutorial is not anymore availabe. Please visit the section for the more updated contents: [[https://neuroimage.usc.edu/brainstorm/Tutorials#Stereo-electroencephalography_.28sEEG.29_analysis|Stereo-electroencephalography (sEEG) analysis]] |
Please not the this tutorial is not anymore availabe. Please visit the section for the more updated contents: Stereo-electroencephalography (sEEG) analysis