MEG current phantom (CTF)

Authors: Francois Tadel, Elizabeth Bock

This tutorial explains how to import and process CTF current phantom recordings. We decided to release this example for testing and cross-validation purposes. With these datasets, we can evaluate the equivalence of various forward models and dipole fitting methods in the case of simple recordings with single dipoles. The recordings are available in two file formats (native and FIF) to cross-validate the file readers available in Brainstorm and MNE. A similar page exists for the Elekta-Neuromag phantom.

License

This tutorial dataset remains a property of its authors: Elizabeth Bock, Francois Tadel and Sylvain Baillet (MEG Lab, McConnell Brain Imaging Center, Montreal Neurological Institute, McGill University, Canada).

If you reference this dataset in your publications, please aknowledge them and cite Brainstorm as indicated on the website. For questions, please contact us through the forum.

CTF current phantom

The CTF current dipole phantom is a spherical container filled with a conducting saline solution which contains a current source and sink. This electric dipole is used to simulate brain sources in a conductive medium. The globe has a 130mm inner diameter and small attachment posts to attach the three CTF head localization coils. The position of this dipole can be adjusted within this globe.

The dipole itself is constructed of two gold spheres about 2 mm in diameter, separated by 9.0 mm center to center. The dipole moment can be calculated by the equation m=I.L, where I is the current flow (in Amperes) and L is the length of the dipole (0.009 meters).

The location of the dipole is recorded relative to the center of the sphere (0,0,0)m, where X is positive toward the nasion, Y is positive toward the left ear and Z is positive toward the top of the head (see the CoordinateSystems tutorial for more details).

Reference

VSM/CTF documentation: PN900-0018, Revision 3.2, 23 November 2006. This document can be found with your full CTF installation at /opt/ctf/docs/Phantom.pdf.

Description of the experiment

Files distributed as part of the CTF phantom tutorial:

Download and installation

Generate anatomy

Access the recordings

Import recordings

Event detection

The sinusoidal signal is generated by the CTF hardware on channel HDAC006. While there are some automatic trigger events generated by the system that can be used for importing, we will have a more precise event average if the events are detected again offline.

Import and average

Noise covariance

Use the empty room recordings.

Source estimation

Compute a forward model and inverse model for a regular grid inside the phantom volume.

Dipole scanning

Scan the for the most significant dipole in the grid of computed dipoles estimate previously.

Dipole fitting with FieldTrip

Perform a non-linear dipole fit with the function ft_dipolefitting from the FieldTrip toolbox.

Results comparison

Condition

Method

Forward model

X

Y

Z

GOF

Nominal location

0

-18

49

mm

200uA

Scanning (5mm)

Single sphere

-1.00

-16.00

44.00

99.80%

Scanning (5mm)

Overlapping spheres

-1.00

-16.00

44.00

99.81%

Scanning (5mm)

OpenMEEG BEM

-1.00

-16.00

44.00

99.76%

Fitting

Single sphere

-1.04

-17.00

43.98

99.95%

Fitting

Overlapping spheres

-1.05

-16.98

44.00

99.95%

CTF software

-1

-17

44

99.95%

MNE software

-0.79

-17.00

43.98

99.9%

20uA

Scanning (5mm)

Single sphere

-1.00

-16.00

44.00

96.94%

Scanning (5mm)

Overlapping spheres

-1.00

-16.00

44.00

96.96%

Scanning (5mm)

OpenMEEG BEM

-1.00

-16.00

44.00

96.90%

Fitting

Single sphere

-1.75

-17.13

44.39

98.25%

Fitting

Overlapping spheres

-1.78

-17.14

44.45

98.25%

CTF software

-1

-17

44

98.38%

MNE software

-1.38

-16.31

44.01

99.1%

The nominal location indicates where the dipole is supposed to be, relative to the center of the sphere. It is measured with rulers with an overall precision of about 5mm. The range of discrepancy we observe between this nominal location and the position of the dipole estimated from the recordings is acceptable.

Advanced

Digitized head points

The head points collected with the Brainstorm digitizer are usually copied to the .ds folders and imported automatically when loading the recordings. We decided not to include them in this example because in the case of this current phantom, there is no ambiguity in the definition of the anatomical fiducials. As this refined registration with the .pos files is not part of the standard CTF workflow, not including it will make it easier to compare the workflow and results with other programs.

For additional testing purposes, the .pos file for the phantom is included in the sample_phantom_ctf.zip package, but you have to add it manually to the recordings. Do not use these points to refine automatically the registration: the fitting algorithm may fail finding the best rotation around the Z axis because the phantom is completely spherical, and the registration is already close to perfection.

Scripting

A script available in the Brainstorm distribution reproduces the different steps of this tutorial:

brainstorm3/toolbox/script/tutorial_phantom_ctf.m

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Tutorials/PhantomCtf (last edited 2018-06-28 12:32:18 by ?MartinCousineau)