I was looking through the tutorial on noise covariance and came across this option for calculating the matrix for epilepsy data.

Option #1a Compute the noise covariance statistics from blocks of recordings away from the peak of any identified interictal spike, and keep only the diagonal (the variance of the sensors).

I was wondering if by 'keep only the diagonal' it was meant to export the files to matlab and zero all other values? If so, would you zero the non-diagonal values from the NoiseCov variable as well as the FourthMoment?

I apologize if this has gone under the wrong Topic

This indication 'keep only the diagonal' is described in the previous options in the same section. As it was not obvious, I copied the text from the EEG resting state section in the epilepsy section:

This option is available in Brainstorm's advanced options of source computation: select the option "Diagonal noise covariance".

You don't need to modify the noise covariance file explicitly, this is done automatically during the estimation of the sources. When the option "Diagonal noise covariance" is selected, NoiseMethod='diag' in the source estimation function, bst_inverse_linear_2018.m, and in this case, the variable 'FourthMoment' is not used at all: