[FieldTrip] Align electrods to headmodel with method 'interactiv'

[Steinmann, Iris]

Hi Debora,

I tried to do so before, but I ended up with the following error:

Do you want to change the anatomical labels for the axes [Y, n]? Y
What is the anatomical label for the positive X-axis [r, l, a, p, s, i]? r
What is the anatomical label for the positive Y-axis [r, l, a, p, s, i]? a
What is the anatomical label for the positive Z-axis [r, l, a, p, s, i]? s
Is the origin of the coordinate system at the a(nterior commissure), i(nterauricular), n(ot a landmark)? n
Undefined function or variable 'template'.

Error in ft_electroderealign (line 244)
  for j=1:length(template)
Error in eeg_beamforming (line 107)
    elec_aligned = ft_electroderealign(cfg);

I prepared now a template following this instruction: http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel
In this example the template is only used for  the cfg.method = ‘fiducial’ but not for the ‘interactiv’ option.
Anyhow I additionally specified the template together with the ‘interactiv’ method like this:

cfg = [];
cfg.method    = 'interactive';
cfg.elec      = elec;
cfg.headshape = vol.bnd(1);

cfg.template = elec_mni;
elec_new = ft_electroderealign(cfg);


now it works!

Thanks!

Iris


From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Debora Desideri
Sent: Mittwoch, 17. Februar 2016 11:20
To: FieldTrip discussion list
Subject: Re: [FieldTrip] Align electrods to headmodel with method 'interactiv'

Dear Iris,
you should press Y and specify the coordinate system following the questions that will appear on the command window (you will be asked to specify whether your coordinate sytsem is ras or lps and so on and where the origin of the coordinate system is located). afterwards, the GUI will display the electrodes and the head of the subject as well. You should then be able to align the electrode by simply applying translation/rotation or whatever you need make the electrode fit on the head surface.
In case you want to use the methiod 'fiducials', you should have recorded together with the elctrode positions some anatomical landmarks that you can easily find in the MRI of the subject. If you did not record such landmarks during the acquisition of the electrode positions, than I guess your only option is to use the method 'interactive'
Hope this helps!
Best,
Debora

On Tue, Feb 16, 2016 at 6:07 PM, Steinmann, Iris <iris.steinmann at med.uni-goettingen.de<mailto:iris.steinmann at med.uni-goettingen.de>> wrote:
Hi FieldTripper,

I want to do source reconstruction with my EEG data and try to align my electrodes to the headmodel (calculated with my own MR data)
(following this description: http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel)

I run the ft_electroderealign function with the following options:

cfg = [];
cfg.method    = 'interactive';
cfg.elec      = elec;
cfg.headshape = vol.bnd(1);
elec_new = ft_electroderealign(cfg);

But all I get is a figure showing a coordinate system with my electrodepositions. The scull saved in vol.bnd(1) is not plotted.
(I attached a jpg of the figure).
The MATLAB panel asked me: "Do you want to change the anatomical labels for the axes [Y, n]? "
If I say 'no', I get the following error:

Undefined function or variable 'template'.
Error in ft_electroderealign (line 244)
  for j=1:length(template)

I tried the ft_electroderealign function with the cfg.method = 'fiducials', but ended up with the same figure and the same question in
the MATLAB panel.

Would be great if someone could help me to figure out what's going wrong here and how I can align my electrodes to the headmodel.

Thanks!

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--

Debora Desideri, PhD Student
BNP Lab - Neurology Department
University Hospital Tübingen
Eberhard Karls University Tübingen
Hoppe-Seyler Str. 3
D-72076 Tübingen
Tel: +49 7071/29 80478

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