[FieldTrip] Aligning electrodes to template head model

Wu, Jia jia.wu at yale.edu
Wed Sep 16 17:59:17 CEST 2015

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.
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.


% 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
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'


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!


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

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.


From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Helen Wieffering [helen.wieffering at gmail.com<mailto: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)

[Inline image 1]

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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.fieldtriptoolbox.org_tutorial_headmodel-5Feeg&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=9ehCplyXHP0-m9ayYv1FOg&m=wNRiA8CLR4Y1ZrEaTkTaIoVaUczL5TYuWIx6FyQDphg&s=LjU77qpw8I7LnSHIEQrNIB0R0YLrutfAEtjjOMjBys0&e=> 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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