[FieldTrip] No mtmconvol on data with partial nans

[Tzvetomir]

Dear Stephen,

you could also apply the nanconv() function of B.Kraus, available on  
Matlab's fileexchange.

(http://www.mathworks.com/matlabcentral/fileexchange/41961-nanconv)

I'm doing my own wavelet processing for the reason that part of my 
epochs are filled with nan's due to experimental design.

But fieldtrip website remains a huge source of infos, tips and solutions 
where to look for :)

all the best,

Tzvetomir

On 2016-05-25 10:08 PM, Stephen Whitmarsh wrote:
> As a follow-up: I guess the best solution in the case would then be to 
> make my TFR, and replace those values with nans based on the sample 
> number from the time-series artifact detection.
>
> Cheers,
> Stephen
>
> On 25 May 2016 at 15:58, Stephen Whitmarsh 
> <stephen.whitmarsh at gmail.com <mailto:stephen.whitmarsh at gmail.com>> wrote:
>
>     Hi Jim!
>
>     Thanks. Ofcourse, that's the problem. However, method = 'wavelet',
>     and method = 'tfr' give the same problem. I'm afraid I'll end up
>     writing my own code, cutting up data and using an FFT :-/
>
>     Thank again,
>
>     Stephen
>
>     On 25 May 2016 at 15:34, Herring, J.D. (Jim)
>     <j.herring at donders.ru.nl <mailto:j.herring at donders.ru.nl>> wrote:
>
>         Hi Stephen,
>
>         As far as I know this is expected as mtmconvol is actually
>         multiplying the fft of the entire trial with the fft of your
>         tapered windows. Perhaps it will work of you use one of the
>         methods that actually uses convolution in the time domain
>         rather than multiplication in the frequency domain.
>
>         Best,
>
>         Jim
>
>
>
>         > On 25 May 2016, at 15:29, Stephen Whitmarsh
>         <stephen.whitmarsh at gmail.com
>         <mailto:stephen.whitmarsh at gmail.com>> wrote:
>         >
>         > Hi FieldTrippers,
>         >
>         > I hope someone can help me with the following.
>         >
>         > My problem is that I like to maintain my original
>         rpt/chan/time/freq size after artefact rejection based on the
>         time series data, i.e. to have the same dimensions of the TFR
>         as if I did not reject data. This is for reasons of
>         bookkeeping between different types of channels that are
>         processed differently throughout my analysis.
>         >
>         > What works well is to detect artifacts in the data and
>         replace those intervals with nans using ft_rejectartifact,
>         with cfg.reject = 'nan'. So far this is perfect for the
>         approach I had in mind.
>         >
>         > However, ft_freqanalysis (method = 'mtmconvol') outputs
>         whole trials as nans whenever a (small) period has nans. What
>         I would need - and in fact expect - is that only those
>         time/frequency windows that have (one or more) nan values will
>         output nan, while the rest should merrily go round giving
>         power values. After all, the data is there.
>         >
>         > It is unclear to me whether this is expected behaviour or
>         not. I might be making a mistake but some simple tests
>         replicated this behaviour.
>         >
>         > Is there a solution that still allows me to end up with a
>         rpt/chan/time/freq representation of the same size as when i
>         would not have rejected artifacts?
>         >
>         > The only other FieldTrip-like option I can think of is to
>         use ft_rejectartifact with method = 'partial', do the
>         freqanalysis on trial parts, and somehow glue the separate
>         trial parts together again afterwards. But I really don't want
>         to go in that direction.
>         >
>         > In the end I'm afraid I don't understand the core of
>         ft_specest_mtmconvol enough to see where I could hack it. I
>         hope some of you might be able to help.
>         >
>         > Best wishes,
>         > Stephen
>         >
>         >
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-- 
__________________________________________________

Tzvetomir Tzvetanov, PhD
(赐为)

Associate Professor
Vision Research Laboratory, School of Life Sciences,
CAS Key Laboratory of Brain Function and Disease,
University of Science & Technology of China
Hefei, Anhui 230027, P.R.China
http://vision.ustc.edu.cn/
Email: tzvetan at ustc.edu.cn


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