[Mne_analysis] creating source spaces

[dgw]

Jeff Eriksen wrote:
> I have a few misc questions regarding MNE:
> 
> What is meant by "the traditional method for cortical surface 
> decimation"? How is it different from the —ico icosahedral method?

I am unsure of the exact algorithm used, but essentially, it just 
decimates by picking points every X mm, so if you put 1 you get the full 
FreeSurfer surface picking other numbers subsamples to try to fit the 
inter-vertex distance specified. If downsampling, I strongly suggest 
using the --ico method as this has huge benefits for group analysis.
> 
> I have previously run FreeSurfer and have all the surfaces. I am trying 
> to do the coordinate frame alignment by following section 7.16 in the 
> manual (v2.7, Dec 2009). I there a way to see the points I choose for 
> the 3 fiducials so I know I have them right?

If you mean the points on the head surface you select, No. But in 
practice that would be an extremely tedious way of fitting (speaking 
from experience). Additionally, why only use three points, when we have 
so much more data. It is very easy to do a quick fit of that (It does 
not need to be perfect). Then visualize the digitized points and use the 
iterative fitting procedure to refine the fit (if you want to play 
around manually, the arrows are available for manual tuning).
> 
> Once I have the transformation the way I like it, how do I associate it 
> with my EEG data? 
Well, you save the MRI set, and that is pretty much it MNE will 
automatically, pick up the most recently created transformation matrix 
from that step (you can also manually select).


> I can create FIF files with raw EEG data OK, but not 
> sure what to do with them.
Not sure, what you are referring to here. You may want to take a step 
back and run through the MNE tutorial with the tutorial dataset as many 
of these steps (and the subsequent steps) are explained/walked through 
in that. Even though your data may be EEG only, all the steps should be 
very similar.

D

> 
> Thanks,
> -Jeff
> 
> 
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