= MEG current phantom (Elekta-Neuromag) =
''Authors: Ken Taylor, John Mosher''

This tutorial explains how to import and process Elekta-Neuromag 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 [[Tutorials/PhantomCtf|CTF phantom]].

<<TableOfContents(3,2)>>

== License ==
This  tutorial  dataset remains a  property of its authors: Ken Taylor, John Mosher (Epilepsy Center, Cleveland Clinic Neurological Institute, Cleveland, OH USA).

If  you reference this dataset in your publications, please acknowledge them and cite Brainstorm as indicated on the [[http://neuroimage.usc.edu/brainstorm/CiteBrainstorm|website]]. For questions, please contact us through the forum.

== The phantom ==
A current phantom is provided with the Elekta Neuromag for checking the system performance. It contains 32 artificial dipoles and four fixed head-position indicator coils. The phantom is based on the mathematical fact that an equilateral triangular line current produces equivalent magnetic field distribution to that of a tangential current dipole in a spherical conductor, provided that the vertex of the triangle and the origin of the conducting sphere coincide. For a detailed description of how the phantom works, see [[http://neuroimage.usc.edu/paperspdf/1985_IlmoniemHamKnuu_ForwardInversModel.pdf|here]].

The phantom dipoles are energized using an internal signal generator which also feeds the HPI coils. An external multiplexer box is used to connect the signal to the individual dipoles. Only one dipole can be activated at a time. 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).

Use of the phantom is shown below. Note that the uncovered version is the phantom that came with the Neuromag-122, which explicitly shows the wiring. The covered version uses the same principle but somewhat different dipole locations. Further details are available in Section 7.2 of the User's Manual.

 . {{attachment:phantom.gif||height="366",width="632"}}

==== References ====
R.J. Ilmoniemi, M.S. Hämäläinen, and J. Knuutila, The Forward and Inverse Problems in the Spherical Model. In: Biomagnetism: Applications and Theory, eds. H. Weinberg, G. Stroink, T. Katil, Pergamon Press, 1985.

Elekta Neuromag System Hardware User's Manual, Revision G, September 2005.

== Description of the experiment ==
[To do]

== Download and installation ==
 * '''Requirements''':  You have followed the introduction tutorials and Brainstorm is installed.
 * Go to the [[http://neuroimage.usc.edu/bst/download.php|Download]] page of this website, and download the file: '''sample_phantom_elekta.zip'''
 * Unzip   it in a folder that is not in any of the Brainstorm folders (program   folder or database folder)
 * Start Brainstorm (Matlab scripts or stand-alone version)

Select the menu File > Create new protocol. Name it '''TutorialPhantomElekta''' and select the options:

 * '''No, use individual anatomy''',
 * '''No, use one channel file per acquisition run (MEG)'''.

== Generate anatomy ==
 * In the Matlab command window: type "'''generate_phantom''''''_elekta'''".

This creates a new subject '''Kojak_Sphere''' (so named after the 70's TV show) and generates the "anatomy" for this device: one volume and a few surfaces representing the geometry of the phantom. <<BR>><<BR>>

 . {{attachment:kojak_anat.gif||height="247",width="630"}} <<BR>><<BR>>

 * You can display the MRI and surfaces as presented in the introduction tutorials. <<BR>><<BR>> {{attachment:MRIandSurface.gif||height="427",width="630"}}

== Access the recordings ==
We can now review one of the raw kojak data sets. These have been generated by sequentially activating each of the 32 phantom dipoles in a single raw file.

 * Switch to the '''functional data''' view by clicking the second button under the protocol name.

 * Right-click on the subject folder > '''Review raw file'''.

 * Select the '''200nA''' source.

 * Click '''Event channel''', select '''STI201''', and hit '''OK'''.

Close the figure and double click the link to raw file to open a list of the events. At this point, you may wish to rename your groups so that the ordering remains convenient. To do this, click group 1, click '''Events''' > '''Rename group''', and rename it to '''01'''. Repeat this for 2 - 9.

This step, and others like it, can also be performed by importing the data into '''MATLAB''', running the following code below, and then exporting the data back into Brainstorm:

 . {{attachment:kojak_matlab1.gif||height="122",width="500"}}

Some other triggers are generated by the neuromag system which are unnecessary so we will delete them:


 * Trim away the singleton events by clicking on '''256 (x1)''', shift clicking on '''7936 (x1)''' and pressing the '''delete''' key.

There is also a switching transient in the phantom generator which should be removed:

 * Remove the first event from dipole '''01''' by clicking on it, clicking on the '''first''' time instant, and pressing the '''delete''' key.

Events should now appear as per the image below on the right: <<BR>>

 . {{attachment:editing_events.gif||height="444",width="630"}}

__'''Note:'''__''' '''Make sure to save the modifications that you make before proceeding. If you hit the grey X to close all figures and clear memory, you will be prompted to save modifications, and you should click '''Yes'''.

== Importing the dipole events ==
Right click on '''Link to raw file''' and click '''Import in database'''

 * Uncheck '''Apply SSP/ICA projectors''' (we will use noise covariance to stabilize the data)
 * Check '''Remove DC offset''', set the time range from -100 to -10ms
 * Resample the recordings to '''100Hz''' (change from 1000Hz)
 * Do __not__ create separate folders
 * Click '''Import'''<<BR>><<BR>> {{attachment:kojak_dipole_import.gif||height="306",width="630"}} <<BR>><<BR>>

== Noise covariance ==
With the epochs loaded, we can now calculate the noise covariance from  the prestims. To do this, '''select all 32 dipoles''' (click the first then  shift click the last), then right click, '''Noise covariance''' > '''Compute  from recordings'''. Uncheck '''MEG MAG''' and hit '''OK'''. <<BR>><<BR>>

 . {{attachment:kojak_noise_covariance.gif||height="216",width="630"}} <<BR>><<BR>>

Average all of the epochs by '''selecting all 32 '''again, dragging them to  the process box, clicking '''RUN'''. Next click the cog, and select '''Average''' > '''Average files'''. Group the files '''By trial group (folder  average)''', and select '''Arithmetic average: mean(x)''', and click "'''Run'''". <<BR>><<BR>>

 . {{attachment:kojak_average.gif||height="420",width="630"}}

== Head modelling ==
To compute the head model, right click on the '''kojak_all_200nA  '''file and select '''Compute head model'''.

 * Source space: select '''MRI volume'''
 * Forward modeling methods: '''Single sphere'''<<BR>><<BR>> {{attachment:kojak_head_model.gif||height="233",width="630"}}

 . <<BR>>

A figure opens showing a sphere fit to the phantom, however we can see that the location is a little off. In this case we alread know where the center of the sphere should be, so we adjust it manually:

 * Click the '''Edit sphere properties''' button in the top toolbar.
 * Change the center location to '''[ 0 0 0 ] '''and hit OK.

The center of the sphere shifts to the correct position. Click the '''OK '''button next to the edit sphere properties button to perform the MRI/surface interpolation. A window appears allowing adjustment of the volume source grid.

 * Select '''Regular grid (isotropic) '''with '''Grid resolution 2.5mm'''

This results in an around 56K grid point, which is sufficient.<<BR>><<BR>>

 . {{attachment:kojak_sphere.gif||height="335",width="630"}}

 . <<BR>>

== Dipole source estimation ==
 * Right click the Single sphere (volume) and select '''Compute sources [2016] '''
 * Method: '''Dipole modeling'''
 * Source model: Dipole orientations '''Unconstrained'''

For the sensor selection you can choose to use either the gradiometers or the magnetometers, in this case we select '''both'''.

Click '''Show details '''if the noise covariance regularization is hidden.

 * Select '''Regularize noise covariance: 0.1'''
 * Ignore the other settings, and click '''OK'''

== Dipole scanning ==
Select the set of 32 averages and drop them into the process box again. Switch to '''process sources  '''and click the '''cog''' in the pipeline editor. Select '''Sources '''> '''Dipole Scanning [BETTER]'''. Set the process options to look at 60ms only by changing the '''Time window''' to '''60ms - 60ms''', and clicking '''Run'''.

Next we should average all the dipole fits together. To do this, we can expand the tree of average files and select '''Avg: 01 (19 files) | dipole scan '''through''' ''''''Avg: 32 (20 files) | dipole scan''', then right click and select '''Merge dipoles'''. Alternatively, we can set Matlab to the study directory and use ''FILES = dir('dipoles_fit*'); new = dipoles_merge({FILES.name}).''