[Eeglablist] "Frequency Smearing" and ERSP graphs
Makoto Miyakoshi
mmiyakoshi at ucsd.edu
Thu May 7 12:10:24 PDT 2015
Dear Steven,
I agree to the kind and detailed explanation by James.
See slide 21 of this pdf. Sorry I could not point you to this previously. I
was on the conference site and running out of battery in front of my poster.
http://sccn.ucsd.edu/mediawiki/images/1/19/C2_A3_Time-frequencyDecAndAdvancedICAPracticum.pdf
Makoto
On Mon, May 4, 2015 at 12:18 PM, James Jones-Rounds <jj324 at cornell.edu>
wrote:
> 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
>>>
>>> _______________________________________________
>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
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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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>
--
Makoto Miyakoshi
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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