[Eeglablist] eeglablist Digest, Vol 127, Issue 11

Sun May 10 00:34:09 PDT 2015

Hi,

I am a very new user to EEGLab and ERPLab toolbox. I have done practice on
EEG/ERPLab using the sample data given on the website.  I have data
recorded using EGI-128 channel system. Following the same steps when I am
trying to analyse my data I got stucked in following issues:

   ---  Electrode location file which one to use ? I am using HydrocelGSN
net but in the plugins location files GSN128.sfp,  GSN129.sfp and GSN
Hydrocel257.sfp are available. Electrode location file for GSN Hydrocel 128
is absent.

   --- Please clarify  when to use GSN128.sfp and GSN129.sfp ?

   --- How to assign Binlister to the file ?

Thanks & Regards,

Narendra Kumar
Research Scholar
Department of Humanities and Social Sciences
Indian Institute of Technology Ropar
Punjab, India - 140001
Contact No.:- +91-8968945650
Homepage:- https://www.sites.google.com/site/narendraiitrpr/
Social Networking Sites: - Facebook
<https://www.facebook.com/narendra.karna.7>; Researchgate
<https://www.researchgate.net/profile/Narendra_Kumar22/>

On Sun, May 10, 2015 at 12:30 AM, <eeglablist-request at sccn.ucsd.edu> wrote:

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> Today's Topics:
>
>    1. Re: Electrode location.... (Makoto Miyakoshi)
>    2. Re: ICA component rejection (Makoto Miyakoshi)
>    3. Re: Topography plot in component clusters (Makoto Miyakoshi)
>    4. Re: ICA component rejection (Makoto Miyakoshi)
>    5. Re: Regarding PACT (Makoto Miyakoshi)
>
>
> ---------- Forwarded message ----------
> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> To: Gonzalo Rojas Costa <gonzalo.rojas.costa at gmail.com>
> Cc: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Date: Fri, 8 May 2015 12:02:26 -0700
> Subject: Re: [Eeglablist] Electrode location....
> Dear Gonzalo,
>
> Are these channels compatible with 10-20 system? In other words, are they
> Fz, Cz, Pz, etc? If so then you just need to manually enter the channel
> names and 'look up locs' to let EEGLAB read the template locations.
>
> Makoto
>
> On Wed, May 6, 2015 at 2:18 PM, Gonzalo Rojas Costa <
> gonzalo.rojas.costa at gmail.com> wrote:
>
>> Hi:
>>
>> I have a four electrode EEG data file in EDF format.... I loaded
>> successfully in EEGLAB, but I couldn't load the electrode location.... how
>> can I do it?.... I tried to follow the EEGLAB tutorial instructions...
>>
>> Sincerely,
>>
>> Gonzalo Rojas Costa
>>
>> --------------------------------
>> Gonzalo Rojas Costa
>> Advanced Medical Image Processing Laboratory
>> Department of Radiology
>> Clínica las Condes
>> Lo Fontecilla 441, Las Condes, Santiago, Chile.
>> Tel: 56-2-2105170
>> Cel: 56-9-97771785
>> www.clc.cl
>>
>> _______________________________________________
>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
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>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
>
> ---------- Forwarded message ----------
> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> To: Mostafa IR <mostafa.rouzbahani at gmail.com>
> Cc: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Date: Fri, 8 May 2015 12:06:52 -0700
> Subject: Re: [Eeglablist] ICA component rejection
> Dear Mostafa,
>
> First of all, how did you get ICA work on the 5-sec data?
>
> For the example of efficient and flexible group-level IC rejection, see my
> wiki page below.
> http://sccn.ucsd.edu/wiki/Backproject_clustered_ICs
>
> Makoto
>
> On Fri, May 8, 2015 at 12:14 AM, Mostafa IR <mostafa.rouzbahani at gmail.com>
> wrote:
>
>> Hi
>>
>> I want reject bad component after ICA analysis. I read the chapter09 ,
>> Julie Onton
>> Scott Makeig paper and ... . Except eye artifact the others are very hard
>> to distinguish in other hand my data is very large(360 data set each one 5s
>> without any event) and it's hard to reject all of them manually. I try to
>> use MARA  plugins but it need at least 15s of EEG which my data are 5s. Is
>> there any other plugin to help me for bad component rejection
>> automatically?
>>
>> Thank you
>>
>> _______________________________________________
>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
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>>
>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
>
> ---------- Forwarded message ----------
> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> To: Shingo Tokimoto <tokimoto at mejiro.ac.jp>
> Cc: UCSD List EEG <eeglablist at sccn.ucsd.edu>
> Date: Fri, 8 May 2015 14:32:32 -0700
> Subject: Re: [Eeglablist] Topography plot in component clusters
> Dear Shingo,
>
> Ok here is a solution for you based on my guess.
>
> > 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)?
>
> I guess you mean 'to plot *difference* topographies of two experimental
> conditions for a component cluster'. The instruction below is based on this
> assumption.
>
> Case 1: The conditions are all within-subject and with the continuous use
> of an EEG cap.
> Unless each within-subject condition is recorded on different sessions
> (i.e. apply the EEG cap for one session, remove it, and applied it newly
> for the next session), independent components should be shared across the
> conditions. If this is the case, then difference topography is all zero.
> Therefore, *you can't get difference topographies*.
>
> Case 2:  The conditions are between-subject (or within-subject but
> different sessions with different EEG cap application). If this is the
> case, subtraction of IC scalp maps makes sense.
>
> How to do it:
>
> 1. Load your STUDY with group differences (i.e. Case 2 mentioned above)
>
> 2. Use my plugin std_envtopo and show whatever envtopo. This is to
> generate topoall_group under STUDY.cluster(1,X) It looks like this
>
> topoall_group: {{1x14 cell}  {1x17 cell}}
>
> 3. To visualize Group A and Group B in Cluster 5, see my code and result
> example below
>
> https://drive.google.com/open?id=0BzTEovh4TOLiflAwREdrZmxsUTBfVFdjR3AyS0pOV3JONEEtTHpwdndwLU9mVXg3cHlITHc&authuser=0
>
> Let me know if you have any trouble in accessing my Google drive.
>
> Makoto
>
>
>
>
>
> On Tue, May 5, 2015 at 1:23 PM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> wrote:
>
>> Dear Shingo,
>>
>> I don't think it's possible.
>> scalp topo generation is relatively straightforward using pop_topoplot()
>> function. I can help you to do this if you are interested in.
>>
>> Makoto
>>
>> On Thu, Apr 30, 2015 at 3:24 PM, Shingo Tokimoto <tokimoto at mejiro.ac.jp>
>> wrote:
>>
>>> 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
>>> ************************************************
>>>
>>>
>>> _______________________________________________
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>>
>>
>>
>> --
>> Makoto Miyakoshi
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
>
> ---------- Forwarded message ----------
> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> To: Mostafa IR <mostafa.rouzbahani at gmail.com>
> Cc: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Date: Fri, 8 May 2015 14:34:26 -0700
> Subject: Re: [Eeglablist] ICA component rejection
> Dear Mostafa,
>
> > 1)Can I append these 5-sec data together for creating a longer data and
> after that use the ICA?
>
> Yes, for ICA longer the data better the decomposition. If possible, use
> even continuous data.
>
> > 2) If the first question is yes can I separate my data again to 5-sec
> and use the ICA weights of merged data?
>
> Yes. You can actually epoch the data normally after ICA.
>
> Makoto
>
> On Fri, May 8, 2015 at 1:34 PM, Mostafa IR <mostafa.rouzbahani at gmail.com>
> wrote:
>
>> Dear Laura
>> I will be glad to use your plugin and count on your help.
>>
>> Dear Makoto
>> Thanks for your link and your advice. I used to make a big mistake about
>> ICA with neglect of data point rule of thumb.
>> I have a new question. My data is about emotions. In my case the person
>> saw a picture for 5-sec and eeg with 16 channels at 512HZ captured. 10
>> picture with the same content show to the person.
>> 1)Can I append these 5-sec data together for creating a longer data and
>> after that use the ICA?
>> 2) If the first question is yes can I separate my data again to 5-sec and
>> use the ICA weights of merged data?
>>
>> Best Regards
>>
>> On Fri, May 8, 2015 at 23:37 Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
>> wrote:
>>
>>> Dear Mostafa,
>>>
>>> First of all, how did you get ICA work on the 5-sec data?
>>>
>>> For the example of efficient and flexible group-level IC rejection, see
>>> my wiki page below.
>>> http://sccn.ucsd.edu/wiki/Backproject_clustered_ICs
>>>
>>> Makoto
>>>
>>> On Fri, May 8, 2015 at 12:14 AM, Mostafa IR <
>>> mostafa.rouzbahani at gmail.com> wrote:
>>>
>>>> Hi
>>>>
>>>> I want reject bad component after ICA analysis. I read the chapter09 ,
>>>> Julie Onton
>>>> Scott Makeig paper and ... . Except eye artifact the others are very
>>>> hard to distinguish in other hand my data is very large(360 data set each
>>>> one 5s without any event) and it's hard to reject all of them manually. I
>>>> try to use MARA  plugins but it need at least 15s of EEG which my data are
>>>> 5s. Is there any other plugin to help me for bad component rejection
>>>> automatically?
>>>>
>>>> Thank you
>>>>
>>>> _______________________________________________
>>>> Eeglablist page: http://sccn.ucsd.edu/eeglab/eeglabmail.html
>>>> To unsubscribe, send an empty email to
>>>> eeglablist-unsubscribe at sccn.ucsd.edu
>>>> For digest mode, send an email with the subject "set digest mime" to
>>>> eeglablist-request at sccn.ucsd.edu
>>>>
>>>
>>>
>>>
>>> --
>>> Makoto Miyakoshi
>>> Swartz Center for Computational Neuroscience
>>> Institute for Neural Computation, University of California San Diego
>>>
>>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
>
> ---------- Forwarded message ----------
> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> To: "井澤考史" <ko.izawa at gmail.com>
> Cc: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Date: Fri, 8 May 2015 14:50:35 -0700
> Subject: Re: [Eeglablist] Regarding PACT
> Dear Koji,
>
> I tried it but could not replicate the problem. I used Matlab 2014b,
> EEGLAB 13.x, PACT0.17.
>
> From your log,
>
> > pop_eegfiltnew() - performing 425 point bandpass filtering.
>
> This does not make sense to me. Looks like your sampling rate is very low,
> must be around 100Hz? Because the default amplitude frequency cutoff is
> 100Hz (i.e. amplitude of > 100Hz will be analyzed), your sampling rate
> should be much higher than 100Hz.
>
> PACT assumed that the input is ECoG data, which is usually sampled at >=
> 1000Hz. Please try the data with much higher sampling rate (or upsampling
> your data to see if it fixes the problem.)
>
> Makoto
>
>
> On Mon, Apr 27, 2015 at 4:27 PM, 井澤考史 <ko.izawa at gmail.com> wrote:
>
>> Dear EEGLAB and PACT team,
>>
>> I’m trying to learn the PACT by using eeglab_data.set. But I met some
>> errors as follows. Could you provide any opinion to me?
>>
>> My Operation
>> - Loaded dataset.
>> - Launched "Compute PAC” GUI.
>> - No change all parameters value form default and press OK.
>>
>> pop_eegfiltnew() - performing 425 point bandpass filtering.
>> pop_eegfiltnew() - transition band width: 1 Hz
>> pop_eegfiltnew() - passband edge(s): [1 2] Hz
>> pop_eegfiltnew() - cutoff frequency(ies) (-6 dB): [0.5 2.5] Hz
>> pop_eegfiltnew() - filtering the data (zero-phase)
>> firfilt(): |====================| 100%, ETE 00:00
>> Error using pop_eegfiltnew (line 148)
>> Cutoff frequency out of range
>>
>> Error in pac_man (line 181)
>> EEG_highFreqAmp   = pop_eegfiltnew(EEG, hfoAmp(1),   hfoAmp(end));
>>
>> Error in pac_pop_main (line 145)
>> EEG = pac_man(EEG, options{:});
>>
>> Error while evaluating uimenu Callback
>>
>>
>> Best regards,
>> Koji
>>
>>
>> _______________________________________________
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>>
>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
> _______________________________________________
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