[Eeglablist] "Frequency Smearing" and ERSP graphs
James Jones-Rounds
jj324 at cornell.edu
Mon May 4 12:18:53 PDT 2015
Hi Steven,
I've noticed this "frequency smearing" phenomenon occasionally, too, in my
ERSP graphs, and i believe it has to do with your ERSP settings. The idea
is that the long "vertical" streaks, or "smears" in your graph are the
result of multiple distinct frequency bands being somehow lumped or
averaged together within each time point, leading to the impression that at
a given moment in time, many different frequency bands are all highly
correlated (i.e. all having high power at the same time). This isn't
completely unheard-of, I don't think, but it's also not very likely in most
experimental settings.
If you make sure to put " 'freqs', X " in your ERSP parameters box, where
"X" is a high enough number of distinct frequencies such that EEGLAB
doesn't try to force it's results onto a small number of frequencies, then
you should be able to get rid of that smearing. You might also want to play
with the wavelet cycle parameters. This might work for you, in the ERSP
parameters box:
'cycles', [3 0.8], 'freqs', [5 75], 'nfreqs', 50, 'ntimesout', 100
Hope that helps,
James
On Mon, May 4, 2015 at 3:00 PM, <eeglablist-request at sccn.ucsd.edu> wrote:
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> Today's Topics:
>
> 1. "Frequency Smearing" and ERSP graphs (Steven Pillen)
> 2. Error with Measure Projection (Eddins, Ann)
> 3. Ocular Correction (pop_gratton) in EEGLAB 13_4_4 (Anjali Thapar)
> 4. Computing ERSPs in parallel? (Tom Bullock)
> 5. EOG location (Mostafa IR)
> 6. Topography plot in component clusters (Shingo Tokimoto)
> 7. Porto IV CAN: 4th Cognitive and Affective Neurophysiology
> Summer School (Fernando Ferreira-Santos)
> 8. swrite (Roy Cox)
> 9. Re: Can I manually reorganise the order of trials within set
> files and save them? (Stephen Politzer-Ahles)
> 10. automatic artifact rejection (Son, D.M.E. van)
>
>
> ---------- Forwarded message ----------
> From: Steven Pillen <stevendpillen at gmail.com>
> To: eeglablist <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Sat, 2 May 2015 15:24:54 -0700
> Subject: [Eeglablist] "Frequency Smearing" and ERSP graphs
> Hello, EEGLAB-List.
>
> Here are some ERSP graphs included in a manuscript we submitted to a
> publication:
>
> http://i.imgur.com/KkvAGPA.png
> http://i.imgur.com/iLHeKY9.png
>
> One of the peer reviewers said that the graph showed "frequency smear",
> and we are not entirely sure what that means. Is what you see in these
> images unusual? If there is frequency smearing, what is it, and what can
> we do to correct or account for it?
>
> Thank you,
> Steven Pillen
>
>
> ---------- Forwarded message ----------
> From: "Eddins, Ann" <aeddins at usf.edu>
> To: eeglablist <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Thu, 30 Apr 2015 20:24:05 +0000
> Subject: [Eeglablist] Error with Measure Projection
>
> I’ve just started working with Measure Projection and keep bumping into an
> error related to concatenation and the size of the matrices. It occurs
> whether I try to project ERP, ERSP or Spec. I have precomputed both
> channel and component measures and am wondering if the error is due to a
> precomputing step that might have reduced the size of my dataset for some
> subjects/conditions and not others? The error is as follows:
>
>
>
> Inverting ERP component polarities based on scalp map polarities
>
> Error in concatenating condition. Some conditions for certain subjects
> might be missing.
>
> Dimensions of matrices being concatenated are not consistent.
>
> Undefined variable combinedConditions.
>
>
>
> Error in pr.dipoleAndMeasureOfStudyErp (line 101)
>
> icCombinedErp = cat(2, combinedConditions{:});
>
>
>
> Error in create_mpt_submenu>command_measure_project (line 64)
>
> STUDY.measureProjection.(measureName).object =
> pr.dipoleAndMeasureOfStudyErp(STUDY, ALLEEG);
>
> Error while evaluating uimenu CallbackDoes it matter what pre-processing
> steps have been completed?
>
>
>
> Any suggestions would be welcome!
>
>
>
> Thanks,
>
> Ann
>
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Anjali Thapar <athapar at brynmawr.edu>
> To: <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Thu, 30 Apr 2015 12:16:42 -0400
> Subject: [Eeglablist] Ocular Correction (pop_gratton) in EEGLAB 13_4_4
> Hello All,
>
> I recently updated to EEGLAB 13_4_4 and noticed that the option to use
> Ocular Correction (pop_gratton) to correct blink artifacts is no longer
> available. Has the function been relabeled or moved?
>
> Please advise.
>
> thank you,
> Anjali Thapar
>
>
>
> ---------- Forwarded message ----------
> From: Tom Bullock <thomas.bullock at psych.ucsb.edu>
> To: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Fri, 1 May 2015 09:53:02 -0700
> Subject: [Eeglablist] Computing ERSPs in parallel?
> Hello EEGLAB community,
>
> I'm using the STUDY function to compute ERSPs for a dataset with 18
> subjects and 3 conditions per subject. The ERSPs take a number of hours to
> compute, so I'd like to set up a parfor loop to create the "xxx.datersp"
> files in parallel using our distributed processing network.
>
> This post indicates that it should be possible to set up the parfor loop:
> http://sccn.ucsd.edu/pipermail/eeglablist/2014/008914.html . However I'm
> not sure which of the functions involved in the ERSP computation is the one
> I should attempt to parallelize (std_precomp.m, std_ersp.m or newtimef.m?),
> and which of the for loops I should be editing.
>
> Does anyone have any insight into how to set this up?
>
> Thanks!
>
> Tom
>
> p.s. this is the function I'm currently using to create the ERSPs:
>
> [STUDY ALLEEG] = std_precomp(STUDY, ALLEEG,
> {},'interp','on','recompute','on','ersp','on','erspparams',...
> {'cycles' cycleParam 'nfreqs' 27 'timesout' [0:100:3000] 'freqs' [4 30]
> },'itc','off');
>
> --
> Tom Bullock, PhD
>
> Postdoctoral Researcher, Department of Psychological and Brain Sciences,
> University of California, Santa Barbara, CA 93106-9660
>
> bullock at psych.ucsb.edu
>
> https://labs.psych.ucsb.edu/giesbrecht/barry/Attention_Lab/Tom_Bullock.html
>
> www.linkedin.com/in/tomwbullock
>
>
>
>
> ---------- Forwarded message ----------
> From: Mostafa IR <mostafa.rouzbahani at gmail.com>
> To: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Fri, 1 May 2015 18:23:49 +0430
> Subject: [Eeglablist] EOG location
> Hi everyone
>
> I know my channels location of EEG data and I used the sample location
> folder of EEGLAB to assign the labels. But I couldn't find the EOG channel
> label in these files. I need EOG for my ICA analysis.
> How can I assign for a channel an EOG label?
>
> Best regards
>
>
> ---------- Forwarded message ----------
> From: Shingo Tokimoto <tokimoto at mejiro.ac.jp>
> To: UCSD List EEG <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Fri, 1 May 2015 07:24:44 +0900
> Subject: [Eeglablist] Topography plot in component clusters
> Dear EEGLAB experts,
>
> Is it impossible to plot topographies of two experimental conditions for a
> component cluster as we can do in channel pot (for a time-window)? Thank
> you in advance.
>
> ************************************************
> Shingo Tokimoto, Ph.D.
> in Linguistics and Psychology
> Department of Foreign Languages
> Mejiro University
> 4-31-1, Naka-Ochiai, Shinjuku, Tokyo,
> 161-8539, Japan
> tokimoto at mejiro.ac.jp
> ************************************************
>
>
>
>
>
> ---------- Forwarded message ----------
> From: Fernando Ferreira-Santos <frsantos at fpce.up.pt>
> To: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Thu, 30 Apr 2015 15:34:17 +0000
> Subject: [Eeglablist] Porto IV CAN: 4th Cognitive and Affective
> Neurophysiology Summer School
>
> Dear colleagues,
>
>
>
> The Laboratory of Neuropsychopsysiology of the University of Porto (
> http://www.fpce.up.pt/labpsi/) is pleased to announce the 4th edition of
> the International Cognitive and Affective Neurophysiology Summer School:
> Acquisition, processing, and analysis of EEG signal.
>
>
>
> This summer school is focused on the application of Electroencephalography
> (EEG) and Event Related Potential (ERP) techniques to the study of
> cognitive and affective processes. The course will be fully taught in
> English and is aimed at an introductory level, so no previous experience
> with EEG or ERP is required.
>
>
>
> This event will take place from 7-12 of September 2015 in the lovely city
> of Porto.
>
>
>
> In last year’s edition the course was fully booked and, as such, we
> recommend early registration (course places are attributed by order of
> registration).
>
>
>
> For additional details and instructions on how to register, please consult
> our website (http://www.fpce.up.pt/labpsi/summerschool/).
>
>
>
>
>
> Please feel free to pass this information along to students or researchers
> that may be potentially interested.
>
>
> Thanks you and best wishes,
>
>
> --
> Fernando Ferreira-Santos, PhD
>
> Lecturer
> Laboratory of Neuropsychophysiology
> Faculty of Psychology and Education Sciences
> University of Porto
> Rua Alfredo Allen, 4200-135 Porto (Portugal)
> Tel.: +351 226079700 (ext. 409)
> E-mail: frsantos at fpce.up.pt
> http://www.fpce.up.pt/labpsi/
>
>
> ---------- Forwarded message ----------
> From: Roy Cox <roycox.roycox at gmail.com>
> To: "'eeglablist' (eeglablist at sccn.ucsd.edu)" <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Thu, 30 Apr 2015 10:27:47 -0400
> Subject: [Eeglablist] swrite
> hi,
>
> I'm trying to use the command line to export data into edf format.
>
> I'm calling pop_writeeeg, which calls writeeeg, which finally calls swrite.
>
> But there's no function swrite to be found anywhere. I found a random
> swrite online but this gives me yet another error.
>
> Any ideas how to get this working? I use eeglab 13.4.4b
>
> Roy
>
>
> ---------- Forwarded message ----------
> From: Stephen Politzer-Ahles <spa268 at nyu.edu>
> To: "Carolin Sievers (PSY)" <Carolin.Sievers at uea.ac.uk>
> Cc: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Date: Thu, 30 Apr 2015 16:05:41 +0400
> Subject: Re: [Eeglablist] Can I manually reorganise the order of trials
> within set files and save them?
> Hi Carolin,
>
> Have you tried running this code to see if it actually does re-order your
> events? It should be fairly straightforward to check (i.e., see what the
> event values for the first few trials are before and after running your
> 'list 2' code).
>
> If that doesn't work, I imagine it should be easy to do manually by just
> re-ordering the indices of all the relevant data structures, e.g.:
> order = [2 5 6 1 4 8 9 7 3];
> EEG.data = EEG.data(:,:,order);
> EEG.epoch = EEG.epoch{order};
> % etc...
>
> There may also be built-in functions in EEGLAB or ERPLAB that do this, but
> I'm not aware of any myself.
>
> Best,
> Steve
>
>
>
> Stephen Politzer-Ahles
> New York University, Abu Dhabi
> Neuroscience of Language Lab
> http://www.nyu.edu/projects/politzer-ahles/
>
> On Tue, Apr 28, 2015 at 6:15 PM, Carolin Sievers (PSY) <
> Carolin.Sievers at uea.ac.uk> wrote:
>
>> Hello EEGlab community,
>>
>> I am trying to reorganise the order of trials in my EEG .set files.
>> I was hoping to use the following function:
>> EEG = pop_selectevent( EEG, 'epoch',[]
>> ,'deleteevents','off','deleteepochs','on','invertepochs','off');
>>
>> If I put in parentheses the trials I would like to include, in the
>> order I would like them to be in in a new .set file, will this work?
>>
>> If this is unclear, here some more details:
>> Based on behavioural data, we create two or more sub-sets from one EEG
>> recording. However, within these sub-sets, the order in which stimuli were
>> presented is not the same. Is there a way for me to reorganise the order of
>> trials and save that order in a new .set file? E.g.,
>>
>> List 1
>> EEG = pop_selectevent( EEG, 'epoch',[1:9]
>> ,'deleteevents','off','deleteepochs','on','invertepochs','off');
>>
>> List 2
>> EEG = pop_selectevent( EEG, 'epoch',[2 5 6 1 4 8 9 7 3]
>> ,'deleteevents','off','deleteepochs','on','invertepochs','off');
>>
>> Thank you very much for your help.
>>
>> Best wishes,
>> Carolin
>>
>> _____________
>> Carolin Sievers (PSY)
>> PhD Student
>> School of Psychology
>> LSB 0.109
>> University of East Anglia
>> Norwich, NR47TJ
>>
>> https://www.uea.ac.uk/psychology/people/profile/carolin-sievers
>> Carolin.Sievers at uea.ac.uk
>>
>> _______________________________________________
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>>
>
>
>
> ---------- Forwarded message ----------
> From: "Son, D.M.E. van" <d.m.e.van.son at fsw.leidenuniv.nl>
> To: "'eeglablist at sccn.ucsd.edu'" <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Thu, 30 Apr 2015 08:37:13 +0000
> Subject: [Eeglablist] automatic artifact rejection
> Dear Eeglab members,
>
> Before manually selecting artifacts in my data, I would like to pre-select
> artifacts automatically. I have seen that Eeglab provides an automatic
> epoch rejection toolbox, but specific epoch selection that I would like to
> make, does not seem to be provided.
> e.g.; I would like to remove epochs where the difference between the
> maximum and minimum in an interval of a selectable length, and the
> difference between the maximum and minimum in the epoch itself, exceeds a
> specific value. Also, I’d like to remove epochs wherin the absolute
> difference between two neighboring sampling points exceeds a certain
> value.
>
> Does anyone have an idea if this is possible in Eeglab automatically? Or
> perhaps it is possible that I script this separately?
>
> Many thanks in advance
>
> Dana
>
>
> _______________________________________________
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--
James Jones-Rounds
Laboratory Manager
Human Development EEG and Psychophysiology (HEP) Laboratory,
Department of Human Development,
--------------------------------------------
Cornell University | Ithaca, NY
607-255-9883
eeg at cornell.edu
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