creating source spaces

✉️ Mailing List Archive (read-only)
1

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 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?

Once I have the transformation the way I like it, how do I associate it with my EEG data? I can create FIF files with raw EEG data OK, but not sure what to do with them.

Thanks,
-Jeff

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20120404/6280846f/attachment.html

2

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

3

Thanks for the answers so far, please see below

Jeff Eriksen wrote:

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).

Let me be more explicit here. I have used mne_edf2fif to put my EEG data
into a FIF file, let's call it EEG-FIF. I can visulaize it OK with
mne_browse_raw. I have previously run FreeSurfer to get all the surfaces.
I then run mne_analyze where I load the inflated surface, digitizer data,
the scalp surface, and then run the alignment procedure. I can save using
"Save MRI", and "Save default", but when I try to use "Save", which I
thought I could use to save the alignment into a FIF file with EEG data, I
cannot get my EEG-FIF file to appear in the file list, and hence cannot go
any further.

Not sure what you mean by "save the MRI set" above.

Thanks for any further suggestions of what I am missing here.

-Jeff