[FieldTrip] Aligning electrodes to template head model

m.goeldi at psychologie.uzh.ch m.goeldi at psychologie.uzh.ch
Thu Sep 17 08:36:34 CEST 2015


Hi Helen

I also had problems using the file GSN-HydroCel-129.sfp electrode locations provided in fieldtrip.
I ended up using the file provided in SPM12 (located in '\spm12\EEGtemplates\egi128_GSN_HydroCel.sfp').
This seems to be the same file (it has the same electrodes) but slightly different locations that fit the headmodel much better.

I hope that helps.
Cheers
Maurice


-----fieldtrip-bounces at science.ru.nl schrieb: -----
An: FieldTrip discussion list <fieldtrip at science.ru.nl>
Von: Helen Wieffering 
Gesendet von: fieldtrip-bounces at science.ru.nl
Datum: 17.09.2015 02:28
Betreff: Re: [FieldTrip] Aligning electrodes to template head model

Hi again, Jia,
I agree- something must be going wrong when I plot the head model, or maybe when I warp the fiducial coordinates from the mri, because the alignment is certainly worse off after I complete all the alignment steps than it was originally! But since all my steps draw from the standard_mri and standard_bem, I'm not sure what the problem could be.

My best success has been simply from interactively aligning the electrodes and verifying it visually. I'm attaching a matlab figure of what it looks like just in case anyone has input - I think it looks accurately aligned, but this is my first time creating a head model in field trip so I have limited experience to draw upon.

As always, thanks for your help.

Best,
Helen Wieffering
Bowdoin College

On Wed, Sep 16, 2015 at 3:50 PM, Helen Wieffering <helen.wieffering at gmail.com> wrote:
Hi Jia,
Thanks so much for taking the time to help me. I'll try what you suggested and see how it goes!

Best,
Helen

On Wed, Sep 16, 2015 at 11:59 AM, Wu, Jia <jia.wu at yale.edu> wrote:
     
 
Helen, 
I ran your code and it seemed to work with the mri and headmodel I have. I looked back at the picture you sent originally. It looks like the electrodes were aligned (before alignment, the tip of the head is facing upwards, after alignment with the mri  provided by the wiki it points to the right), but the headmodel is not plotted correctly. The headmodel needs to be driven from mri. You can double check the headmodel, which is standard_bem in  your code. 
-jia
  
  
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Helen Wieffering [helen.wieffering at gmail.com]
 Sent: Wednesday, September 16, 2015 10:00 AM
 To: FieldTrip discussion list
 Subject: Re: [FieldTrip] Aligning electrodes to template head model
 
 
 
 
 
 
 
 
 
 
 
Hi Jia,
  Thanks so much for getting back to me. If you have a free moment, would you mind looking over my code? I have tried the tutorial steps many times, even having changed the label of the GSN fiducials to 'Nz', 'LPA', 'RPA',  but seem to keep getting the same incorrect  results.
 
 % ALIGN ELECTRODES TO STANDARD_BEM
 
 % read electrode coordinates
 elec = ft_read_sens('GSN-HydroCel-129.sfp');
 
 % convert units to mm to match units of headmodel
 elec = ft_convert_units(elec, 'mm');
 
 % change label of fiducials
 elec.label{1} = 'Nz';
 elec.label{2} = 'LPA'
 elec.label{3} = 'RPA';
 
 % create fiducial structure
 % draw fiducial coordinates from mri
 nas = standard_mri.hdr.fiducial.mri.nas;
 lpa = standard_mri.hdr.fiducial.mri.lpa;
 rpa = standard_mri.hdr.fiducial.mri.rpa;
  
 transm = standard_mri.transform;
  
 nas = ft_warp_apply(transm, nas, 'homogenous');
 lpa = ft_warp_apply(transm, lpa, 'homogenous');
 rpa = ft_warp_apply(transm, rpa, 'homogenous');
 
 % create a structure similar to a template set of electrodes
 fid.chanpos = [nas; lpa; rpa]; % mni-coordinates of fiducials
 fid.label = {'Nz','LPA','RPA'}; % same labels as in elec 
 fid.unit = 'mm'; % same units as mri
  
 % alignment
 cfg = [];
 cfg.method = 'fiducial';            
 cfg.template = fid; % see above
 cfg.elec = elec;
 cfg.fiducial = {'Nz', 'LPA', 'RPA'}; % labels of fiducials in fid and in elec
 elec_aligned = ft_electroderealign(cfg);
 
 % plot to check
 figure;
 ft_plot_mesh(standard_bem.bnd(1), 'edgecolor','none','facealpha',0.8,'facecolor',[0.6 0.6 0.8]); 
 hold on;
 ft_plot_sens(elec_aligned,'style', 'sk');
 
  For reference, the coordinates I get in the structure fid are the following:
 fid = 
 
     chanpos: [3x3 double]
       label: {'Nz'  'LPA'  'RPA'}
        unit: 'mm'
 
 fid.chanpos
 
 ans =
 
     35   -36     0
    118   -35     0
    -82   -35     0
 
 
  If those are different from yours, would you let me know? I'm trying to find out at which step I went wrong. 
  Again, thank you very much!
 
  Best,
  Helen
 
 
 
 
 

       

 
On Mon, Sep 14, 2015 at 11:00 PM, Wu, Jia  <jia.wu at yale.edu> wrote:
  
 
Helen, 

 
What a coincident. I'm also working on source analysis on EEG data using GSN HydroCel 128. I had a post a couple weeks ago about later steps. But I did get the alignment to work. The picture you posted looked like the status before the alignment. So i  suspect that alignment did not happen.  

  
I'm not sure whether you have noticed it, but the fiducial positions in elec location file were called 'FidNz', 'FidT9', 'FidT10', instead of 'Nz','LPA','RPA'  as in the tutorial. So they need to be changed. Then the alignment should work. 

  
best, 
-jia 

 
  
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Helen Wieffering [helen.wieffering at gmail.com]
 Sent: Monday, September 14, 2015 4:46 PM
 To: FieldTrip discussion list
 Subject: [FieldTrip] Aligning electrodes to template head model
 
  
 
 
 
 
 
 
 
Hello all,
 
  I have a quick question on aligning electrodes to the standard_bem headmodel, which I downloaded from the FT server. 
 
  
Namely, are the standard_mri and the standard_bem in the same coordinate system? I assumed this would be so, since one was developed from the other. But when I try to align my electrodes to the standard_bem volume using fiducial positions from the standard_mri,  I get very strange results: (image below and attached)
 
 ÿ
 
 I'm using a GSN HydroCel 128 Cap, and my elec structure contains the fiducial positions relative to the electrodes. 
 I've been following the tutorial at  http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg and would like to follow the steps under 'Automatic Alignment', but as I said: pulling the fiducial positions from the standard_mri seems to not work with the tutorial steps.
  
  Any help is appreciated - thanks in advance!
 
 

  
Helen Wieffering
  
Bowdoin College
            
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[Anhang 'head model.fig' entfernt von Maurice G”ldi/at/UZH]
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