[FieldTrip] baseline normalizing

[Schoffelen, J.M. (Jan Mathijs)]

Just one addition to Tzvetan’s reply, just for future reference:

ft_preproc_standardize is a rather ‘low-level’ function, and not recommended unless you know what you’re doing.
For your purpose you probably want to use ft_channelnormalise or ft_denoise_prewhiten. Which of the two depends on what you think is happening in Brainstorm. Note that the former (i.e. ft_channelnormalise) only scales the data (and the resulting power spectra if you proceed with spectral analysis), so it is not  really clear what you intend to achieve.

Best wishes,
Jan-Mathijs

On 28 Mar 2021, at 15:52, mubeen afzal <mubafzal at hotmail.com<mailto:mubafzal at hotmail.com>> wrote:

Ahh perfect Tzvetan. Thanks  alot for the quick reply. This function is good to transform the time series data.

Regards,
Mubeen

________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>> on behalf of Tzvetan Popov <tzvetan.popov at uni-konstanz.de<mailto:tzvetan.popov at uni-konstanz.de>>
Sent: Sunday, March 28, 2021 10:48 AM
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] baseline normalizing

Dear Mubeen,
The function you intend to use requires time dimension. What you provide is only power spectrum.
You could use https://www.fieldtriptoolbox.org/reference/ft_preproc_standardize/ prior to your freqanalysis if standardized z-scores is what you need.

Good luck,
Tzvetan


Am 3/28/21 um 07:16 schrieb mubeen afzal <mubafzal at hotmail.com<mailto:mubafzal at hotmail.com>>:



Hi all,

In brainstorm there is option of baseline normalizing (zscore or db or other methods) the timeseries epochs/trials of interest before frequency analysis allowing visual comparisons and further frequency analysis of the normalized epochs

The normalization function function [freq] = ft_freqbaseline(cfg, freq) doesnt allow normalizing a freq output dimord structure with chan_freq derived using 'mtmfft' method

I get this error message -

"the call to "ft_freqanalysis" took 1 seconds
the input is freq data with 21 channels, 191 frequencybins and no timebins
Error using ft_freqbaseline (line 146)
unsupported data dimensions: chan_freq"

Is there a way around this?

Thanks all.

Mubeen
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