# creating source spaces **URL:** \ **Category:** Mailing List Archive (read-only)\ **Tags:** list-archive\ **Created:** [April 5, 2012, 1:17am UTC](https://mne.discourse.group/t/creating-source-spaces/427 "2012-04-05T01:17:29Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2012, 1:17am UTC](https://mne.discourse.group/t/creating-source-spaces/427/1 "2012-04-05T01:17:29Z")
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](http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20120404/6280846f/attachment.html) ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 5, 2012, 1:36am UTC](https://mne.discourse.group/t/creating-source-spaces/427/2 "2012-04-05T01:36:50Z")
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 ---
**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\ **Post date:** [April 12, 2012, 3:55am UTC](https://mne.discourse.group/t/creating-source-spaces/427/3 "2012-04-12T03:55:47Z")
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