3D Localization methods for intracranial electrodes

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

Questions?

Email

bowens@mnepilepsy.net