[FieldTrip] Fwd: EEG electrode coordinate system transformation

[Paolo Belardinelli]

Dear Robert,
thank you very much for your answer and support.
We downloaded the ft_electroderealign from the github link you sent us.
We ran the code lines that you inserted in your previous email.
In the resulting interactive topoplot, we were able to rotate and realign
the electrode configuration properly.
However, for some reason, after pushing the 'apply' button, we are still
not able to save the modified configuration and manually close the
interactive window.
As a consequence, when visualizing the new layout, we are still plotting
the old configuration.
Are we missing a step in the interactive GUI or is the subfunction cb_close
not working properly?

Best wishes,

Paolo



On Thu, Oct 22, 2015 at 9:47 PM, Robert Oostenveld <
r.oostenveld at donders.ru.nl> wrote:

> Hi Paolo,
>
> You may want to use ft_electroderealign immediately following the reading
> in. The electrode realign function allows you to rotate and translate (i.e.
> shift) the electrodes. Getting the electrodes properly aligned with the
> axes of the coordinate system will make it easier to make the layout with
> ft_prepare_layout.
>
> I have just made a small change to ft_electroderealign that makes it
> possible to use the function with only electrodes (and no MRI or head
> shape). You should get the latest fieldtrip version (later this evening on
> the FTP) or download
> https://github.com/fieldtrip/fieldtrip/blob/master/ft_electroderealign.m
>
> You can then do
>
> cfg = [];
> cfg.elec = ft_read_sens(‘your localite file’)
> cfg.method = ‘interactive’;
> elec_realigned = ft_electroderealign(cfg)
>
> cfg = [];
> cfg.elec = elec_realigned;
> layout = ft_prepare_layout(cfg);
>
> best regards,
> Robert
>
>
>
>
> On 22 Oct 2015, at 16:55, Paolo Belardinelli <paolo.belardinelli at gmail.com>
> wrote:
>
> Dear all,
>
> we are recording EEG electrode positions using the LOCALITE TMS navigator
> acquisition software. We dispose over MRI data in DICOM format.
> The electrode positions are stored in the (LPS) coordinate system. Unity
> measures are mm.
> We load the electrode positions in Fieldtrip by means of ft_read_sens. We
> use the elec structure to prepare the layout with ft_prepare_layout.
> Attached are the obtained layout (localite_layout) and the layout obtained
> using standard electrode positions (standard_layout).
> Appearantly, besides an inversion of both X and Y axes, we have to deal
> with a Z offset we don't know how to exactly calculate ( a simple inversion
> of axes does not provide correct results, see attached
> inverted_localite_layout).
> Is there a way to address this issue in Fieldtrip or with some
> mathematical manipulation?
>
> Thank you in advance,
>
> Paolo
>
>
>
> --
> --
> Paolo Belardinelli, PhD
> Neurology Department
> University Hospital Tuebingen
> Eberhard Karls University Tuebingen
> Hoppe-Seyler Str. 3
> D-72076 Tuebingen
> Tel: +49 7071 / 29 80478
>
> <standard_layout.jpg><inverted_localite_layout.jpg><localite_layout.jpg>
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-- 
--
Paolo Belardinelli, PhD
Neurology Department
University Hospital Tuebingen
Eberhard Karls University Tuebingen
Hoppe-Seyler Str. 3
D-72076 Tuebingen
Tel: +49 7071 / 29 80478
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