[FieldTrip] positions of Neuromag sensors rotated

Fri Feb 28 10:18:32 CET 2020

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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Message: 6
Date: Thu, 27 Feb 2020 09:25:17 +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] Possible bug in mtmconvol padding option
Message-ID: <6E10027C-7D87-49CB-A159-72C16BBB1D4B at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"

Hi Mireia,

There was a typo in my pseudo-code, the value to be used for cfg.pad would
of course be 1.
Best,
JM

On 27 Feb 2020, at 09:29, Schoffelen, J.M. (Jan Mathijs)
<jan.schoffelen at donders.ru.nl<mailto:jan.schoffelen at donders.ru.nl>>
wrote:

Hi Mireia,

Indeed the cfg.pad parameter operates on the full epoch length, not on the
sliding window length. This is per design, and it is not a bug.

Although I don’t fully understand the deeper reason of why you want to do
what you want to do, one way to get there would be to handcraft your own
procedure, and create the TFRs in a computationally inefficient for-loop. This
would require a lot of data bookkeeping on your end.

Procedurally:

for k = 1:the-number-of-time-point-onto-which-you-want-to-estimate-your-
tfr

 cfg = [];
 cfg.latency = timepoint(k)+[-0.25 0.25-1./data.fsample];
 tmpdata = ft_selectdata(cfg, data);

 cfg = [];
 cfg.pad = 0.5;
 cfg.method = ‘mtmfft’;
 cfg….
 tmpfreq(k) = ft_freqanalysis(cfg, tmpdata);

end

freq = tmpfreq(1);
freq.powspctrm = cat( 3-or-4-depending-on-whether-you-did-
cfg.keeptrials=‘yes’-previously, tmpfreq.powspctrm);
freq.time = timepoint;
freq.dimord = (‘rpt_)chan_freq_time’;

Sounds like an overkill to me, though.

Best wishes, and good luck,

Jan-Mathijs

PS: Please feel free to suggest an update to the help-section of the
ft_freqanalysis function, to explain better the cfg.pad parameter. We look
forward to a PR!

On 24 Feb 2020, at 18:17, TORRALBA CUELLO, MIREIA
<mireia.torralba at upf.edu<mailto:mireia.torralba at upf.edu>> wrote:

Hi,
I am a Fieldtrip user and I came across this error

ft_error('the specified padding is too short');

when calculating power spectrum using this code:

cfg=[];
   cfg.method='mtmconvol';
   cfg.foi=2:1:40;
   cfg.t_ftimwin=0.5*ones(length(cfg.foi),1);
   cfg.pad=1;
cfg.taper='hanning';
fLast=ft_freqanalysis(cfg,dataLast);

As I see it, the padding should work in each of my time windows (0.5 seconds
length each) and therefore the error should not appear, but when I
inspected which is the segment padded by the function I saw
that what is being padded to 1 is the whole segment. I think this is not right,
as what I would like is to increase my frequency resolution by padding each
of the timewindows where I calculate the spectrum. The problem I have is
that I want to use as a baseline another segment which has 0.5 seconds
length, and as the frequency extracted by mtmconvol depends on the length
of the segment, I am getting different frequency resolutions for the baseline
and the target data.

Can anyone help me?
Thanks and best regards.

Mireia

Mireia Torralba Cuello
Multisensory Research Group
Center for Brain and Cognition, Universitat Pompeu Fabra
Address: Edifici Mercè Rodoreda 24.313
       c\ Ramon Trias Fargas, 25-27
       08005 Barcelona
http://www.mrg.upf.edu<http://www.mrg.upf.edu/>
Tel +34 935422745

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