[FieldTrip] Inquiry regarding "cfg.rotate" (Petar Atanasov)
Harris, Alison
Alison.Harris at ClaremontMcKenna.edu
Thu Aug 3 19:33:37 CEST 2023
Hi Bence and Petar,
How are you specifying the "layout" parameter in your cfg file for ft_topoplotER?
Before I run ft_topoplotER, I first set the path to the "biosemi128.lay" layout file in the Fieldtrip templates folder and call "ft_prepare_layout":
layoutFile = '~/Documents/MATLAB/fieldtrip/template/layout/biosemi128.lay'; % Path to the Biosemi 128 layout in the fieldtrip folder (shown for a Mac)
layoutcfg = [];
layoutcfg.layout = layoutFile;
layout = ft_prepare_layout(layoutcfg,data);
Then when I run ft_topoplotER, I specify the layout as part of my cfg variable for the topographic plotting:
cfg.layout = layout;
I haven't noticed any issues with the orientation of the electrodes using this approach, at least for my own Biosemi 128-channel data. Let me know whether it works for you!
Best wishes,
Alison
--
Alison Harris, PhD
Ostby-Cook Associate Professor of Psychology & George R. Roberts Fellow
Claremont McKenna College
850 Columbia Avenue
Claremont, CA 91711
Phone: (909) 607-9397
Email: aharris at cmc.edu
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-----Original Message-----
From: fieldtrip <fieldtrip-bounces at science.ru.nl> On Behalf Of Bence Szaszkó via fieldtrip
Sent: Thursday, August 3, 2023 9:03 AM
To: fieldtrip at science.ru.nl
Cc: Bence Szaszkó <bence.szaszko at univie.ac.at>
Subject: Re: [FieldTrip] Inquiry regarding "cfg.rotate" (Petar Atanasov)
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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> 2. Re: mtmconvol with hanning window (Jochem Rieger)
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> ----------------------------------------------------------------------
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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
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> 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.ou
> tlook.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
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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
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>>
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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
> Web:
> https://urldefense.com/v3/__https://uol.de/en/applied-neurocognitive-p
> sychology__;!!HJOPV4FYYWzcc1jazlU!-UMNRq4rK2lyaAG8yIA6-u8wPh3_Ic4bONsC
> zmSVBYJvI7KL-OF49B7YMouv8_fdUNpmkV9OETzEF9L3eX1WFqiwLBLSsuSroRqJ$
> github:
> https://urldefense.com/v3/__https://github.com/ANCPLabOldenburg__;!!HJ
> OPV4FYYWzcc1jazlU!-UMNRq4rK2lyaAG8yIA6-u8wPh3_Ic4bONsCzmSVBYJvI7KL-OF4
> 9B7YMouv8_fdUNpmkV9OETzEF9L3eX1WFqiwLBLSsvYGzS6g$
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