[FieldTrip] baseline normalizing

[mubeen afzal]

Hi Jan,

Thanks for this added info. This (ft_channelnormalise) appears like a good function for my power analysis because it provides the perchannel vs across channel added option. I have not been sure in brainstorm whether the baseline values being used as input to z-transform was derived from all channels or per respective channel.  I think 'all channels' will be more appropriate as I am looking at abrupt discharges which dont necessarily channel by channel follow the resting state baseline rhythm variation. For example frontal regions have more faster lower amplitude but the discharges of my interest have higher amplitude frontally. Makes it tricky.

I see however there is no segment definition input in this function for baseline selection which makes preproc_standardize good. My understanding was that baseline for transforming is always better selected 'out of' the segment to be analysed. I will test and try and see both functions.

Regards,
Mubeen

________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) <jan.schoffelen at donders.ru.nl>
Sent: Sunday, March 28, 2021 5:23 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] baseline normalizing

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/<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Freference%2Fft_preproc_standardize%2F&data=04%7C01%7C%7C50500c0f02d049d45c2308d8f1f84540%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637525396099670134%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ts%2Fb%2BIy0goudTeiglpck7bhc0c7HaKmwMmAVUlsqR34%3D&reserved=0> 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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