[FieldTrip] Inquiry regarding "cfg.rotate" (Petar Atanasov)

Bence Szaszkó bence.szaszko at univie.ac.at
Thu Aug 3 18:02:31 CEST 2023 

Dear Petar,

I had the same issue with my data. I am using a Biosemi128 system, and 
cfg.rotate never really did anything to my data (maybe it is a placebo 
argument ;)). My positions were based on data.elec.elecpos and 
data.elec.label and in my case, X and Y from the XYZ coordinates (so 
column 1 and 2) were switched when I compared them to the ones provided 
by the manufacturer.

Maybe a similar approach will solve your problem as well? You can try 
cfg.placebo again alternatively :))

Cheers,
Bence

---
Bence Szaszkó, BSc MA MSc
University Assistant (prae doc)

Vienna Doctoral School CoBeNe
PhD Representative

University of Vienna
Faculty of Psychology
Department of Cognition, Emotion, and Methods in Psychology

Liebiggasse 5
A-1010 Wien/Vienna
Austria

e-mail: bence.szaszko at univie.ac.at

Am 02.08.2023 12:00, schrieb fieldtrip-request at science.ru.nl:
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>    1. Re: fieldtrip Digest, Vol 153, Issue 1 (Petar Atanasov)
>    2. Re: mtmconvol with hanning window (Jochem Rieger)
> 
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> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 1 Aug 2023 10:13:19 +0000
> From: Petar Atanasov <PAtanasov at uclan.ac.uk>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] fieldtrip Digest, Vol 153, Issue 1
> Message-ID:
> 	<VI1PR03MB2895B1F5AD8B0DB0D60899A6F20AA at VI1PR03MB2895.eurprd03.prod.outlook.com>
> 
> Content-Type: text/plain; charset="windows-1252"
> 
> Good morning,
> Thank you for the suggestion, I have now tried using 270 instead of
> -90 with cfg.rotate and the issue still persists.
> Kind regards,
> 
> Petar Atanasov
> 
> ________________________________
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> fieldtrip-request at science.ru.nl <fieldtrip-request at science.ru.nl>
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>    1. Inquiry regarding "cfg.rotate" (Petar Atanasov)
>    2. Re: Inquiry regarding "cfg.rotate" (Tom Marshall)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Tue, 1 Aug 2023 07:30:00 +0000
> From: Petar Atanasov <PAtanasov at uclan.ac.uk>
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Subject: [FieldTrip] Inquiry regarding "cfg.rotate"
> Message-ID:
> 
> <VI1PR03MB2895CE5460B423241F88E4CEF205A at VI1PR03MB2895.eurprd03.prod.outlook.com>
> 
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Good evening,
> I am currently analysing some co-registered eye-tracking and
> electroencephalography fixation-related potential (FRP) data.
> I am using MATLAB 2022b but I have also replicated the issue with 
> MATLAB 2020b.
> For the pre-processing of the data, I have used EEGLAB 2023.0 as well
> as the EYE-EEG 0.99 and Unfold.
> 
> I have been trying to plot topographies and waveforms via the
> "ft_multiplotER" and the "ft_topoplotER" functions, such that my
> frontal electrodes are at the top of the image and the occipital
> electrodes are at the bottom of the image.
> However, when I plot the data both with the default as well as with
> "-90" or "90" degree rotation via "cfg.rotate", my images always show
> frontal electrodes on the right and occipital electrodes on the left.
> 
> When I plot the channel locations with the same coordinates in EEGLAB
> I get the images with the correct orientation for all electrodes.
> 
> Can you please advice on how I may be able to rotate my images
> correctly and why is it that "cfg.rotate" may not be working as
> expected?
> 
> I am happy to provide further information as needed.
> Thank you in advance for your feedback and assistance with my inquiry.
> Kind regards,
> 
> Petar Atanasov
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> ------------------------------
> 
> Message: 2
> Date: Tue, 1 Aug 2023 08:50:44 +0000
> From: Tom Marshall <tom.marshall at psy.ox.ac.uk>
> To: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] Inquiry regarding "cfg.rotate"
> Message-ID: <5DF104D5-14E8-41F4-A58A-620A2DF6CC75 at psy.ox.ac.uk>
> Content-Type: text/plain; charset="utf-8"
> 
> Hi Petar,
> 
> If you replace ‘-90’ with ‘270’, does that produce the rotation you 
> want?
> 
> Just a hunch, based on Robert’s suggestion in
> https://urldefense.com/v3/__https://eur01.safelinks.protection.outlook.com/?url=https*3A*2F*2Furldefense.com*2Fv3*2F__https*3A*2F*2Fgithub.com*2Ffieldtrip*2Ffieldtrip*2Fissues*2F1674__*3B!!HJOPV4FYYWzcc1jazlU!60QKCY0R3GJgesY3D65R61rkvsPCyUDVpHSnavjhWSDCpQ2Vu-BW3lZhV1WPd6hmlTyBG01GQtvtkIb4n2sca54o-uJkN7VJ*24&data=05*7C01*7Cpatanasov*40uclan.ac.uk*7Cd770fb746c5240beed0608db92769b60*7Cebf69982036b4cc4b2027aeb194c5065*7C0*7C0*7C638264810352946528*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C&sdata=LZCZUOEaZJ4h0qqI4ebvFewBCE8dJ3uPnhTBZfjTrnY*3D&reserved=0__;JSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!HJOPV4FYYWzcc1jazlU!8iTHHIwQdSFfHeM4kISO2yK0F6SHSGWcyQuoRnsy-cp-IzOyAJyWoFoY1zdweZTiwvPn_qyO3DQLvEZgjgPdt3-M53U$
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> .
> 
> Best,
> Tom
> 
> 
> From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Petar
> Atanasov via fieldtrip <fieldtrip at science.ru.nl>
> Reply to: FieldTrip discussion list <fieldtrip at science.ru.nl>
> Date: Tuesday, 1 August 2023 at 09:19
> To: "fieldtrip at science.ru.nl" <fieldtrip at science.ru.nl>
> Cc: Petar Atanasov <PAtanasov at uclan.ac.uk>
> Subject: [FieldTrip] Inquiry regarding "cfg.rotate"
> 
> Good evening,
> I am currently analysing some co-registered eye-tracking and
> electroencephalography fixation-related potential (FRP) data.
> I am using MATLAB 2022b but I have also replicated the issue with 
> MATLAB 2020b.
> For the pre-processing of the data, I have used EEGLAB 2023.0 as well
> as the EYE-EEG 0.99 and Unfold.
> 
> I have been trying to plot topographies and waveforms via the
> "ft_multiplotER" and the "ft_topoplotER" functions, such that my
> frontal electrodes are at the top of the image and the occipital
> electrodes are at the bottom of the image.
> However, when I plot the data both with the default as well as with
> "-90" or "90" degree rotation via "cfg.rotate", my images always show
> frontal electrodes on the right and occipital electrodes on the left.
> 
> When I plot the channel locations with the same coordinates in EEGLAB
> I get the images with the correct orientation for all electrodes.
> 
> Can you please advice on how I may be able to rotate my images
> correctly and why is it that "cfg.rotate" may not be working as
> expected?
> 
> I am happy to provide further information as needed.
> Thank you in advance for your feedback and assistance with my inquiry.
> Kind regards,
> 
> Petar Atanasov
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> Message: 2
> Date: Mon, 31 Jul 2023 16:32:28 +0200
> From: Jochem Rieger <jochem.rieger at uni-oldenburg.de>
> To: "Weisholtz, Daniel S.,MD via fieldtrip" <fieldtrip at science.ru.nl>
> Subject: Re: [FieldTrip] mtmconvol with hanning window
> Message-ID: <596f1ab4-03b0-40c2-92c8-a37597aac43a at uni-oldenburg.de>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
> 
> Hi Dan,
> 
> think of short term fft as windowing with a rectangular window. This 
> has
> rather bad frequency resolution (wide central lobe, many side lobes in
> the amplitude spectrum). It produces "veridical" values for the
> amplitude estimate over the analysis  interval (your window length)
> 
> The other methods underestimate the amplitudes systematically. If you
> are only interested in relative amplitudes (most cases) that doesn't
> matter.
> 
> The Hanning window improves the cross talk and is typically applied
> once  the whole intervall and then an FFT is calculated to get the
> amplitude spectrum. The cost for that improvement is that the amplitude
> estimate are biased towards the center of the window and the amplitude
> values are underestimated.
> 
> Multitaper analysis applies multiple orthogonal windows and obtains by
> that approach multilple amplitude spectra, which are then combined for
> the final estimate. Approach reduces the noise in the amplitude
> spectrum  lets  you trade-off frequency resolution against noise.
> 
> When you write multiple sliding windows you likely refer to the Welch
> method which applies multiple shorter and partly overlapping tapers to
> the analysis interval and then combines those correlated amplitude
> estimates. This method reduces the noise in the amplitude spectrum. In
> principle, you could use different types of windows.
> 
> Hope that helps,
> 
>      Jochem
> 
> 
> On 27.07.23 18:43, Weisholtz, Daniel S.,MD via fieldtrip wrote:
>> 
>> ACHTUNG!Diese E-Mail kommt von Extern! WARNING! This email originated
>> off-campus.
>> 
>> Dear FieldTrip community,
>> 
>> I understand that using the hanning window with this function will
>> make this function use a single sliding taper window rather than
>> multitaper. Does that make this analysis equivalent to a short-time
>> fft analysis? If you do this, will FieldTrip ignore the tapsmofrq
>> parameter?
>> 
>> Thanks for your help!
>> 
>> Best,
>> Dan
>> 
>> The information in this e-mail is intended only for the person to whom
>> it is addressed.  If you believe this e-mail was sent to you in error
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> 
> --
> Jochem Rieger
> Prof. Dr. rer. nat. habil.
> Applied Neurocognitive Psychology
> DFG Center for Open and Reproducible Neuroscience Tools
> NFDI sections ELSA and metadata
> 
> Carl-von-Ossietzky University Oldenburg
> Phone: +49 (0)441 798 4533
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