To get your coordinates into freesurfer space, you need to register them with the T1 image. You could in theory do this with tkmedit, but in my experience, the headpoints interface is broken.

I do the registration (manually) with a custom matlab program, but it requires that you have generated an outer scalp surface. You could do this with watershed, although when I've tried running watershed, the output bem surfaces are not aligned with the input T1 image (with or without -useSRAS flag they come out with the axes mixed up). I use another program for generating the bem surfaces, but it is not very user friendly and won't be released to the public.

If you want the matlab registration program, I can send it to you, but you'll have to find a way to generate the outer scalp surface for each subject.

From: abel cruz vadell abelcruz20001@yahoo.es To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] importing EEG coordinates in free surfer Date: Fri, 23 Feb 2007 10:27:49 +0100 (CET)

Hi everyone

I need to import EEG coordinates (obtained with Polhemus system in ASCII format) in the FreeSurfer workspace. My final aim is characterize small areas of the cortical surface (exactly the regions underlaying my sensors position) with typical parameters of FreeSurfer (cortical thikness,...) .

I have read some papers reporting partial solutions to my needs. All of them used matlab with some exported files of FreeSurfer and registered them with the coordinates of the EEG or MEG analysis. I will like to have an opposite solution: import the file with the coordinates of the EEG into the FreeSufer workspace, maybe using the Load/overlay /registration menu of FreeSurfer or another that you can suggest me.

I guess my coordinates file needs some transformations before import it to the FreeSurfer workspace

thanks in advance

abel

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