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3D Localization methods for intracranial electrodes
Brian Owens, REEG/EPT, CNIM, CLTM, CMEG
MN Epilepsy Group | mnepilepsy.org
Disclosures
None
About me
Minnesota Epilepsy Group – Present
EEG Supervisor
MSI/MEG lab
Epilepsy Surgery
Neuronavigation
Purpose
Location of intracranial electrodes is essential for planning of resection of epileptogenic zone.
Locations of electrodes can be saved and used for surgical decision making at a later time, especially for SEEG.
Removes the guess work.
GoalShare with you the workflow of our pipeline for localizing grid/SEEG electrodes.
Familiarize you with various methods and software platforms used for localization.
THEN
Now
Imaging
Pre-contrast T1 MRI 1mm contiguous slices (no spaces, non-overlapping)
Whole head
No gantry tilt
Axial or sagittal plane
CT volume scan (post implantation) 1mm contiguous slices (no spaces, non-overlapping)
Whole head
No gantry tilt
Axial or sagittal plane
DICOM
Digital Imaging and Communications in Medicine
Unlike EEG, DICOM is standard for storing and transmitting medical images
May have a .dcm file extension or no file extension at all
Contain header information with patient info, modality, scanner type, position, etc.
CT Electrodes are hyperintense on CT compared to the tissue
Makes it easy to segment
Grid electrodes on bone windowed CT
MRI & CT Coregistration
CT overlay on MRI
Types of software
Open-source
Academic
Commercial
Imaging software
Neurophysiology softwareFreeSurfer
3 Applications discussed
Neuronavigation (Brainlab)
CURRY (Compumedics)
Brainstorm (Open-source)
Neuro-navigation
Neuronavigationaka IGS
Image-guided surgery is the general term used for any surgical procedure where the surgeon utilizes tracked surgical instruments in conjunction with preoperative or intraoperative images in order to indirectly guide the procedure
Neuronavigation Brainlab
Medtronic Stealth
How Neuronavigation works
CT fusion with MRI
Cerebrum segmentation
Threshold segmentation
Threshold adjustment
Tight thresholding
3D Grid
3D grid overlay on cortex
Brain shift
Brain shift
Not a problem for SEEG
Can be up to a centimeter
Mostly lateral shift
Must be taken into consideration
Multiple data sets and objects
Neuro-navigation with grid and MEG
Benefits of neuronavigationintegration
Help guide surgery
Integration of several different image sets (fMRI, DTI, ECOG)
Draw and/or threshold objects or ROIs
CURRY (Compumedics)
Commercial
Expensive
FDA Cleared
Courses offered
Some tutorials and documentation
Analysis of MEG/EEG, ECOG, SEEG
DICOM supported
Neurophysiology, source localization software for MEG/EEG data
Grid/SEEG Planning
Can be used to plan grid place
Can be used to plan SEEG depths and contact positions
Grid Planning Create virtual grids
Create virtual depths
Electrode size
Electrode spacing
SEEG Planning
CURRY 7 Import CT and MRI from DICOM
Automatic co-registration of CT to MR
Import ECOG data
Importing ECOG data
EDF or EDF+
European Data Format
Always export in system reference
Many native file types for EEG data
Xltek (.erd)
Nihon Kohden (.eeg)
EGI (.raw)
Nicolet (.eeg)
Telefactor (.dat)
Stellate (.sig)
Coregistering MRI & CT
Import MRI from DICOM
Import CT from DICOM
Define landmarks
Autodetect – volume-based coregistration
BEM Cortex
CT Segmentation
Voxel mesh
Click electrodes in the order that correspond to your ECOG data
Threshold segmented electrodes in 3D
Channels selected in 3D and saved
Localize
Screenshots of electrode positions
Can be put into a slide show
Physician can look at them anywhere without software
Use of a macro will save time for screenshots
Integration of ECOG
ECOG data and electrode positions
Single moving dipole
Mesial temp seizure
CURRY Overview
Commercially available
Company support
Training courses available
User manual and tutorials
Specific tutorial for intracranial electrode localization
Imports straight from DICOM
Create BEM Cortex model quickly
Brainstormhttp://neuroimage.usc.edu/brainstorm/
AboutBrainstorm Brainstorm is a collaborative,
open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and animal electrophysiology.
Brainstorm
Academic software
Free/Open source/GPL
Collaborative
Analysis of MEG, EEG, fNIRS, ECoG, SEEG
Matlab version and standalone version (MCR)
Platform-independent (Windows, Mac, Linux)
DICOM not supported (must convert to NIfTI)
Many online tutorials
Online forum
Courses now offered for epilepsy analyses
Brainstorm Requirements
With Matlab
Matlab version >= R2007b (7.5)
Optional: Signal Processing Toolbox
Without Matlab
Operating system: Windows: Any version
Linux: Ubuntu 14.04+, RedHat 6.x+, Debian 7.x, SUSE 11.3+
MacOS: 10.9.5 (Mavericks), 10.10 (Yosemite)
NIFTI File Format
Formally a format called ANALYZE 7.5
Neuroimaging Informatics Technology Initiative
Standard in neuroimaging community
DICOM is a large format and is focused towards clinical and communication use
Initial focus for NIFTI is for fMRI and secondary for neuroscience research
Extracting the cortex
First you need the anatomy of the subject which must include at least three files: an MRI volume, the envelope of the cortex and the head surface of the head.
Brainstorm cannot extract the cortex envelope from the MRI, you have to run this operation with an external program of your choice.
The results of the MRI segmentation obtained with the following programs can be automatically imported: FreeSurfer, BrainSuite, BainVISA and CIVET.
3D modeling of the cortex
Freesurfer
• Automated
• Command line
• Linux or mac
• Takes hours
BrainSuite
• Faster
• Sometimes errors
• GUI
Freesurfer
Freesurfer.net
Download
Register for a license key
Follow install instructions
Navigate to your DICOM folder
Run the recon-all command
Go home, come back in the morning.
What Freesurfer does
Running FreeSurfer
Freesurfer tutorial & download
http://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer
http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall
BrainSuite
What BrainSuitedoes?
Extract inner and outer surfaces of the cortex
Segment and label gray and white matter structures
Analyze diffusion imaging data (DTI)
GUI interface
Running BrainSuite File>Open Volume…
BrainSuite Check scan
Cortical Surface Extraction
Import anatomy
Freesurfer folder
Fiducial points
Coordinate systems
Naison (NAS)
Pre-auricular (LPA, RPA)
Talairach coordinates Anterior commissure (AC)
Posterior commissure (PC)
Interhemispheric point (IH)
Convert CT from DICOM to NIfTI with MRIcroGL
Place all the DICOM images you wish to convert into a folder
Drag and drop one of the images onto dcm2nii.
Windows/Mac/Linux
Import CT Convert CT to Nifti first!
MRIcroGL (DICOM to Nifti)
Drag and drop GUI (EASY!)
Import CT to Brainstorm
Transform & register/resample
Register on default MRI
Import ECOG data
Edit channel file
Overlay on default MRI (MRI Viewer)
Electrode positions
Select electrode positions from MRI Viewer (right click)
3D overlay
Import EEG data
ECoG/SEEG displays
Brainstormsummary
Free
Academic, not FDA cleared
Big learning curve
Requires other software resources to work
Lots of online resources Tutorials
Forum
Videos
Conclusion
3D intracranial images proved crucial information during invasive evaluations
Commercial software expensive, requires training and time, built to perform specific tasks, a little more user friendly
Academic software free but can have a big learning curve, time consuming, not as user friendly
Neuronavigation may not be accessible, limited to imaging only but useful during surgery
References
Scarabin, Jean-Marie. (2012) Stereotaxy and Epilepsy Surgery.Montrouge, France: Editions John Libbey Eurotext
Taimouri V et al. (2014). Electrode localization for planning surgical resection of the epileptogenic zone in pediatric epilepsy. International Journal of Computer Assisted Radiological Surgery, 9(1)99-105. doi: 10.1007/s11548-013-0915-6
François Tadel, Sylvain Baillet, John C. Mosher, Dimitrios Pantazis, Richard M. Leahy.(2011) Brainstorm: A User-Friendly Application for MEG/EEG Analysis Volume 2011, Computational Intelligence and Neuroscience, doi: 10.1155/2011/879716
Data analysis was performed with Brainstorm (Tadel et al. 2011), which is documented and freely available for download online under the GNU general public license (http://neuroimage.usc.edu/brainstorm).
Neuroimaging Informatics Technology Initiative (2005 April 11)https://nifti.nimh.nih.gov/background
Application links
Brainlab | http://brainlab.com
CURRY | http://compumedicsneuroscan.com
Brainstorm | http://neuroimage.usc.edu/brainstorm
Freesurfer | http://www.freesurfer.net
Brainsuite | http://brainsuite.org/
MRIcroGL | http://www.mccauslandcenter.sc.edu/mricrogl
