[FieldTrip] positions of Neuromag sensors rotated

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Thu Feb 27 09:58:27 CET 2020

Dear Jo,

Have you plotted the 2 headshapes in a single figure, and likewise for the gradiometers? In other words, which of the 4 objects is off in terms of expected location in space?
Have you checked for the problematic subject, whether the order of the landmark-clicking in the polhemus procedure was consistent with how the coordinate system is defined?

Best wishes,

On 19 Feb 2020, at 15:15, joachim.lange at med.uni-duesseldorf.de<mailto:joachim.lange at med.uni-duesseldorf.de> wrote:

Dear Fieldtrippers,
I’m not sure whether my problem is a Fieldtrip or a Neuromag problem, but maybe someone can help me here.

I’ve recorded MEG data with a Neuromag system and the headshape and hpi coils using the polhemus system. When I read the headshape and the sensor locations from the fif-file and plot them using Fieldtrip, the plots look as expected, i.e., the “headshape” and the hpi coils are located within the MEG sensors / helmet (see attached example figures S1_1 and S1_2 from different angles). For one subject, however, the sensors from the hdr.grad-file seem rotated and it even looks like the “headshape” is partly outside the MEG sensors / helmet (see attached figures S2_1 and S2_2).
I have no idea what is going wrong here and/or how I could correct the apparently wrong positions. Any help would be much appreciated.

Ps: the simple FT-code:

hdr = ft_read_header(‘subject.fif’);
headshape = ft_read_headshape(‘subject.fif’);
ft_plot_sens(hdr.grad, 'style', 'b.', 'coil', 'false');
ft_plot_mesh(headshape.pos(1:4,:),'vertexsize',20,'vertexcolor','r'); %HPI coils
ft_plot_mesh(headshape.pos(5:end,:),'vertexsize',20,'vertexcolor','k'); %”manual” headshape
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