[Mne_analysis] BabySQUID dipole fit

[Matti Hamalainen]

Hi Alex,


On Aug 3, 2012, at 2:23 AM, Alexander Hunold wrote:

> Analyzing MEG and EEG data from spontaneous recordings of epileptic patients with BabySQUID1, I ran into 3 issues with the dipole fit procedure. 
> 1)      Preprocessing – Noise covariance estimate
> From my understanding this matrix shall reflect the interdependencies of different channels with respect to the recorded noise / background activity. Is that correct?
> 
The noise covariance gives estimates of the variances of Gaussian noise of the measurement channels (on the diagonal) and the covariances between channels (in the off-diagonal elements).
> Based on this assumption I would calculate the noise covariance matrix on a recording segment without epileptic activity. Would that make sense? Would it be more appropriate to derive the noise covariance matrix from the entire recording?
> 
> 

If the epileptic activity is infrequent, you can even use the entire recording. Be sure to include a long enough data segment to make the covariance matrix well behaved.

> 2)      EEG source localization
> Which unit range does MNE expect as EEG input? When I enable EEG data for source localization (current density estimate, dipole fit), I receive unrealistically strong sources in a very deep location. I assume this is due to a scaling issue.
> 

The EEG data in the fif files should be in volts. 
> 
> 3)      Bdip content
> I would like to display the confidence ellipsoid to a dipole fitted by MNE and saved in bdip format. From my understanding the ellipsoid semi-axis parameters are stored in the error matrix. Reading this into a 5x5 matrix in Matlab, I am not able to determine which values correspond to the axis. Here an example of an error matrix: 
> E = [-7.8358e-39 0 0 0 0; 0 1.9263e-38 0 3.3224e-31 7.2643e-42; 3.8519e-34 4.2782e+09 0 1.3004e-41 3.4159; 0 -1.1768e-19 2.2510e-41 1.4324e-16 -3.3895e+38; 3.8519e-34 4.2782e+09 0 1.4324e-16 -3.3895e+38
> 
> 

MNE does not calculate the confidence intervals for dipoles. Therefore, the error matrix will contain invalid data. There is a field called "errors_computed" in the bdip structure, set to zero to indicate that the error estimates have not been computed.

- Matti




---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu
mhamalainen at partners.org






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