[FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields
haiteng.jiang at gmail.com
Sun Jul 7 20:17:58 CEST 2013
I am not clear about what's ft_denoise_synthetic doing. However , I
don't have such problem when I use . The reason you get
'mismatching number of channels' probably because you specify cfg.channel
='MEG' instead of including all channels. My FT code is something like
cfg = ;
cfg.dataset = dataset;
cfg.trialdef.eventtype = '';
cfg.trialdef.eventvalue = ;
cfg.continuous = 'yes';
cfg.trialdef.prestim = ;
cfg.trialdef.poststim = ;
cfg = ft_definetrial(cfg);
trl = cfg.trl;
cfg.demean = 'yes';
cfg.gradient = 'G3BR';
In my pipeline , the grad changes into NAN only after I run I ICA to
remove artifacts . I replace this grad with previous good gradient
information and assume it is fine for the latter source reconstruction.
Hope this helps.
> Message: 2
> Date: Fri, 5 Jul 2013 09:38:55 +0200
> From: Alexander Backus <a.backus at donders.ru.nl>
> To: fieldtrip at science.ru.nl
> Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in
> grad fields
> CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to
> covert to 3rd order gradient, it replaces the values in data.grad.chanpos
> and data.grad.chanori with NaNs.
> I assume this is done because they are no longer valid.
> When digging into the low-level code I found something about mismatching
> number of channels.
> Anyway, when I want to subsequently covert to planar gradient (does this
> actually makes sense?) or create a source model, I need these grad values.
> I have two questions:
> 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why
> are NaNs inserted in the grad subfields?
> 2) Can I still use the data for planar gradient conversion or source
> modeling by using the earlier stored old gradient info (pre
> ft_denoise_synthetic) or is this ill-advised and is there a more wise
> course of action?
> Thanks in advance,
> Alexander Backus
Neuronal Oscillations Group
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Donders Centre for Cognitive Neuroimaging
6525 EN Nijmegen
Tel.: +31 (0)243668291
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