[FieldTrip] positions of Neuromag sensors rotated

Fri Mar 6 13:37:18 CET 2020

Dear Jo,

Thanks for the update. It’s always nice to hear back from people, although in your case it’s a pity to hear that it might be something unresolvable. I am surprised though that the discrepancy is so big. So, if I understand you well, it could be that the position between the subject and the polhemus’ reference point was not fixed over time, and specifically that it changed between the timewindow in which the ‘landmark clicking’ took place, in order to establish a coordinate system relative to the subject’s head, and the timewindow in which the scalp surface was sampled along with the HPI coil positions. Couldn’t this be easily verified by looking up the LPA/RPA/nasion points in the polhemus file? (at least, in our Polhemus procedure this information is available).

Best wishes,
JM

> On 6 Mar 2020, at 08:28, joachim.lange at med.uni-duesseldorf.de wrote:
> 
> Hi Jan-Mathijs,
> Just a brief update: I got feedback from other researchers who experienced similar problems. In their case the problem was that the reference point of the polhemus system (which is fixed at "glasses") had moved somehow during the measurement resulting in a rotated coordinate system. Have to check whether this is really the problem for me as well, but given the very similar problems it's pretty likely. That would mean that there is actually no solution for the problem ...
> Thanks for your help anyway,
> Jo
> 
> Date: Fri, 28 Feb 2020 09:18:32 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] positions of Neuromag sensors rotated
> Message-ID: <91D47250-8461-48E9-A60A-02E2E5F3C93B at donders.ru.nl>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Jo,
> Is there another way in which you can check the  coregistration information in the fif-file? E.g. in the Elekta,  apologies, Megin software? If I recall well, but I am no expert here, there may be various coordinate systems defined in the fif-files, and it could be that something went wrong there.
> 
> Best wishes,
> JM
> 
> 
> On 28 Feb 2020, at 09:41, joachim.lange at med.uni-duesseldorf.de<mailto:joachim.lange at med.uni-duesseldorf.de> wrote:
> 
> Dear JM ;)
> Thanks for your reply and the suggestions. I had done the plotting you suggested and it's the MEG sensors of the problematic subject that are off. I also had a second look at the landmarks (and the other polhemus recordings in the "headshape" variable) but couldn't find anything suspicious.
> Best,
> Jo
> 
> 
> Date: Thu, 27 Feb 2020 08:58:27 +0000
> From: "Schoffelen, J.M. (Jan Mathijs)" <jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
> Subject: Re: [FieldTrip] positions of Neuromag sensors rotated
> Message-ID: <65A8AC04-6811-404A-B470-96893F76D805 at donders.ru.nl<mailto:65A8AC04-6811-404A-B470-96893F76D805 at donders.ru.nl>>
> Content-Type: text/plain; charset="utf-8"
> 
> 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,
> JM
> 
> On 19 Feb 2020, at 15:15, joachim.lange at med.uni<mailto:joachim.lange at med.uni>-
> duesseldorf.de<http://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.
> Thanks,
> Jo
> 
> Ps: the simple FT-code:
> 
> hdr = ft_read_header(‘subject.fif’);
> headshape = ft_read_headshape(‘subject.fif’); figure; 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
> <S1_1.tif><S1_2.tif><S2_1.tif><S2_2.tif>___________________________
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> https://doi.org/10.1371/journal.pcbi.1002202
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