[Mne_analysis] Comparing conditions

[Yury Petrov]

> On Oct 6, 2008, at Oct 6, 2008 | 8:59 AM, Daniel Goldenholz wrote:

> - if a dipole were to rotate in a fixed position with a fixed  
> amplitude, what would that do in the subtraction case?

Daniel, you are right, this difference will be lost. But to me it  
seems more reasonable to subtract electrode signals for the two  
conditions first, then localize and do the F statistics on the  
difference signal. So, for example, if a given dipole just changed its  
orientation from inward in cond 1 to outward in cond 2, and you  
subtract averaged potentials for cond 1 from cond 2, then the  
difference will be localized as twice the outward current at the  
dipole location.

> - when subtracting these F statistics, no account is made for  
> temporal relationships. So if I take the subtraction of two  
> different time points from the same source with a sinusoidal signal  
> that are out of phase by 180 degrees, wouldn't this seem like one  
> time point is more "significant" than the other, when in fact you  
> are looking at different phases of the same thing?

Are you talking about comparing steady-state recordings in frequency/ 
phase domain? For regular ERPs the F statistics is calculated for each  
timepoint in the recording, right? Of course, my assumption is that  
one subtracts the conditions for the same timepoints.

> - If the noise is not the same (i.e. when comparing two different  
> sources), what is the meaning of the subtraction? Does it relate to  
> significance of effect, or merely SNR due to anatomy/physics?

You are right. However, most experiments are done by running  
interleaved conditions, each condition for 10 - 20 trials within the  
same run of 15 - 60 minutes long. So the noise covariance should be  
the same for all conditions. Also, in my (little) experience, the  
difference in noise covariance matrices between different EEG  
experiments is not that significant, given that you are using the same  
head and the same net. It is probably even less significant for MEG,  
where the electrode and magnetometer locations are fixed on the  
helmet, and the environmental noise is, generally, better controlled.  
It is important, of course, to multiply the noise covariance matrix by  
2 (or really add the two covariance matrices) when doing F statistics  
on difference signals.

Yury