[FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields
moh3nalimoradi at gmail.com
Wed Jul 10 12:12:01 CEST 2013
I am mohsen alimoradi, MSc student of artificial intelligence
in Qazvin Azad University. *
**I am working on the Biomag 2012 analysis competition.**
I have downloaded a .zip file from
<ftp://ftp.fcdonders.nl/pub/biomag2012/>** ** I have extracted the
content and I am interested in the second objective,** the one
related to long-term memory representations (folder data2).** ** I
was able to load the 2 mat files into Matlab workspace.** ** I was
also able to use FieldTrip functions on tutorial code.** ** How
could I use FieldTrip on this data? If there are more ways, which one
would be the fastest/easiest?** ** Thanks a lot*
On Tue, Jul 9, 2013 at 9:16 PM, Alexander Backus <a.backus at donders.ru.nl>wrote:
> Thanks for your answer Haiteng.
> To share our findings on this topic:
> After some more debugging, we realized that it could indeed be the ICA
> function that inserts NaNs into the grad info.
> It seems ft_denoise_synthetic only changes the grad info for some
> reference channels...
> We now use Haiteng's trick of replacing the post-ICA grad info, with the
> post-denoise grad info, however, it feels somewhat dangerous to perform
> such "dirty" fixes, since that grad info is probably removed for a certain
> reason. We are oblivious to its impact subsequent steps like planar
> transform and source reconstruction.
> In addition, we dug up the following page on the FieldTrip wiki which
> explains the denoising.
> On Sun, Jul 7, 2013 at 8:17 PM, Haiteng Jiang <haiteng.jiang at gmail.com>wrote:
>> Hi Alexander,
>> 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
>> % reading
>> cfg = ;
>> cfg.dataset = dataset;
>> cfg.trialdef.eventtype = '';
>> cfg.trialdef.eventvalue = ;
>> cfg.continuous = 'yes';
>> cfg.channel= 'all';
>> cfg.trialdef.prestim = ;
>> cfg.trialdef.poststim = ;
>> cfg = ft_definetrial(cfg);
>> trl = cfg.trl;
>> cfg.detrend ='yes';
>> cfg.demean = 'yes';
>> data= ft_preprocessing(cfg);
>> cfg.gradient = 'G3BR';
>> data= ft_denoise_synthetic(cfg,data);
>> 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
>>> 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
>> Haiteng Jiang
>> PhD candidate
>> Neuronal Oscillations Group
>> Donders Institute for Brain, Cognition and Behaviour
>> Centre for Cognitive Neuroimaging
>> Radboud University Nijmegen
>> Visiting address
>> Room 2.32
>> Donders Centre for Cognitive Neuroimaging
>> Kapittelweg 29
>> 6525 EN Nijmegen
>> the Netherlands
>> Tel.: +31 (0)243668291
>> Web: https://sites.google.com/site/haitengjiang/
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
> Alexander R. Backus, MSc
> PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen
> Memory and Space Research Group
> P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands
> Telephone: +31(0)24 36 10754
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
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