[Eeglablist] RELICA download available?

James Jones-Rounds jj324 at cornell.edu
Mon Dec 7 12:12:59 PST 2015


Specifically, the method was first published by Makeig, Delorme, and
company, in 2014, here:


"Neuroimage. 2014 Dec;103:391-400. doi: 10.1016/j.neuroimage.2014.09.010.
Epub 2014 Sep 16.
RELICA: a method for estimating the reliability of independent components.
Artoni F1, Menicucci D2, Delorme A3, Makeig S4, Micera S5."

Thanks! I really think this is a game-changer in ensuring reproducible
component-space results, and would like to begin implementing this method
as soon as possible.

James


On Mon, Dec 7, 2015 at 3:00 PM, <eeglablist-request at sccn.ucsd.edu> wrote:

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> Today's Topics:
>
>    1. Re: Average Reference after measuring 128 Ch using one of the
>       128 channels as reference (Cz)? (Ernesto Gonzalez Trejo)
>    2. RELICA download available? (James Jones-Rounds)
>    3. t2circ (Buz?s P?ter)
>    4. Re: Error while precomputing STUDY: NaN values in
>       cluster.sets (Tarik S Bel-Bahar)
>    5. Re: Electrolyte gel question (Tarik S Bel-Bahar)
>    6. Re: Time- frequency analysis (Makoto Miyakoshi)
>
>
> ---------- Forwarded message ----------
> From: Ernesto Gonzalez Trejo <gonzalez at snn-unit.de>
> To: <mmiyakoshi at ucsd.edu>
> Cc: eeglablist <eeglablist at sccn.ucsd.edu>
> Date: Fri, 4 Dec 2015 10:33:03 +0100
> Subject: Re: [Eeglablist] Average Reference after measuring 128 Ch using
> one of the 128 channels as reference (Cz)?
> Dear Makoto,
>
> thanks again for your answer. Still:
>
> > If you have reference channel in your data, the recorded signal is (ref
> chan)
> > - (ref chan) = 0, so it should be flat. You want to remove this flat
> channel,
> > of course.
>
> As i mentioned on the previous emails, the reference channel in the
> recorded
> signal is NOT zero, due to the manufacturer (g.tec) settings (since there
> are no
> dedicated reference electrodes, the channel chosen as a reference will be
> measured against Ground and not against itself, in order not to lose the
> channel).  That's why i was not sure if this channel should be used within
> the
> averaging or if EEGLAB ignores it for the calculation of AR.
>
> It seems then, that EEGLAB ignores the reference channel (since
> theoretically
> should be 0) so from now on i will remove it pre-AR, and afterwards i will
> write
> the inverted mean of all electrodes into the reference channel (as it
> should be
> (ref chan-ref chan)-(average of all channels)).
>
> Thanks,
>
> Ernesto
>
>
>
>
> > On December 2, 2015 at 7:19 PM Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> wrote:
> >
> > Dear Ernesto,
> >
> > > Should I remove the reference channel from my data (select>
> > If you have reference channel in your data, the recorded signal is (ref
> chan)
> > - (ref chan) = 0, so it should be flat. You want to remove this flat
> channel,
> > of course.
> >
> > After average referencing, you may want to discard *any* one channel to
> make
> > the data full-ranked.
> >
> > Makoto
> >
> > On Wed, Dec 2, 2015 at 3:11 AM, Ernesto Gonzalez Trejo <
> gonzalez at snn-unit.de>
> > wrote:
> >
> > > Dear Makoto,
> > >
> > >  thank you for your answer.
> > >
> > >  There is no problem when importing the data and setting Cz (ch 30) as
> > > reference
> > >  when i set the channel locations. But i don't know if it is valid for
> > > EEGLAB if
> > >  i assign one of my existing 128 channels as reference (by
> edit->channel
> > >  locations->set reference-> Channel Indices 1:128, Reference Cz).
> There is
> > > no
> > >  exclusive reference channel appended at the end. Is this refrence
> > > assignment
> > >  only a label? does it matter when computing the average reference?
> > >
> > >  I can "synthesize" my question as follows: Should I remove the
> reference
> > > channel
> > >  from my data (select>
> > >
> > > > On December 1, 2015 at 9:17 PM Makoto Miyakoshi <mmiyakoshi at ucsd.edu
> >
> > > > wrote:
> > > >
> > > > Dear Ernesto,
> > > > > i have a brief question
> > > >
> > > > I thought it was quite long, which is why I did not understand the
> > > > question.Let me start from here: What's the problem of importing the
> data
> > > > and
> > > > apply average reference?
> > > > REST is a good solution but I've never been used it myself. Does
> REST has
> > > > Matlab code? If it's available I'd love to try it out.
> > > > Another approach is Nima Bigdely-Shamlo's PREP. It'll do
> conscientious
> > > > channel
> > > > cleaning before average
> > > > referencing.
> http://journal.frontiersin.org/article/10.3389/fninf.2015.00016/abstract
> > >
> > > > Makoto
> > > > On Thu, Nov 26, 2015 at 7:14 AM, Ernesto Gonzalez Trejo
> > > > <gonzalez at snn-unit.de>
> > > > wrote:
> > > > > Hi everyone,
> > > > >
> > > > > i have a brief question regarding a correct average referencing in
> > > > > EEGLAB,
> > > > > that until now i've been unable to solve. I've read the EEGLAB
> tutorial
> > > > > and
> > > > > also searched for some answers in the EEGLAB list but until now i
> didn't
> > > > > find one that helps me solve the problem.
> > > > >
> > > > > I am doing EEG measurements with 128 Channels, using the channel
> in the
> > > > > position Cz as reference(ch. 30 in my cap). During the
> acquisition, the
> > > > > amplifier properties have Cz set as reference for all electrodes,
> and
> > > > > the
> > > > > Cz electrode is then measured then against the ground.
> Additionally, two
> > > > > more channels (63-64) are on the earlobes and are usually discarded
> > > > > since
> > > > > i'm not using them as reference or for data analysis.
> > > > >
> > > > > Given the nature of the measurement I consider the average
> reference the
> > > > > way
> > > > > to go in order to represent better the brain activity.
> > > > >
> > > > > The acquisition is done through SIMULINK and saved into a MAT
> file, for
> > > > > post-processing in MATLAB. (The output is a 128xL matrix, where L
> is the
> > > > > length of the measurement in samples).
> > > > >
> > > > > The problem i have is that i can't seem to indicate correctly to
> EEGLAB
> > > > > that
> > > > > the reference used in my measurement is also part of the channels.
> When
> > > > > i
> > > > > import the mat file, i cannot give explicitely the channel (as
> stated on
> > > > > the
> > > > > import window's help:
> > > > >
> > > > > "Ref. channel indices or mode" - [edit box] current reference.
> This edit
> > > > > box
> > > > >  cannot be edited. To change data reference, use menu
> > > > >  Tools > Re-reference calling function pop_reref(). The reference
> > > > >  can be a string, 'common' indicating an unknow common reference,
> > > > >  'averef' indicating average reference, or an array of integer
> > > > >  containing the indices of the reference channels."
> > > > >
> > > > > Then, after I import the data without a reference, I select the
> channel
> > > > > locations (using a self-made loc file for the cap i use). Here,
> each one
> > > > > of
> > > > > the 128 channels has a label (10-10 system names for electrodes
> 1-64 and
> > > > > just the electrode number for 65-128). Once loaded, i click on "Set
> > > > > Reference" and write 1:128 as channel indices and Cz as
> "Reference".
> > > > > (Channel 30 has the label Cz and was the reference in the
> measurement).
> > > > > After the locations are set, i remove channels 63 and 64, since i
> don't
> > > > > want
> > > > > to use them for AR.
> > > > >
> > > > > So far, so good. After this i can just go and compute the average
> > > > > reference
> > > > > using the tools from EEGLAB. I wanted to validate the results so i
> kept
> > > > > doing some tests, and i realized that if i clicked on
> tools-rereference
> > > > > and
> > > > > then to "add current reference channel back to the data", the
> error :
> > > > >
> > > > > "There are no Reference channel defined, add it using the channel
> > > > > location
> > > > > editor"
> > > > >
> > > > > appeared, although in the main EEGLAB window the Reference is
> stated to
> > > > > be
> > > > > Cz and Channel locations as "Yes".
> > > > >
> > > > > Question 1:
> > > > >
> > > > > Could it be that i am giving the Reference wrong in the channel
> > > > > locations?
> > > > > After reading the tutorials i only got that the reference is
> usually
> > > > > given
> > > > > as an extra channel, which is appended to the locations. In this
> case,
> > > > > it is
> > > > > not an extra channel, but channel 30 of 128. Is it wrong then, to
> input
> > > > > this
> > > > > channel as i did in the channel locations?
> > > > >
> > > > > Question 2:
> > > > >
> > > > > Since i wanted to see how exactly the average referencing was
> working, I
> > > > > checked also the reref.m function from EEGLAB and tried to run it
> > > > > standalone
> > > > > as follows:
> > > > >
> > > > > output=reref(eeg,30,'exclude',[63 64],'keepref','on');,
> > > > >
> > > > > where i am only interesed on the average-referenced EEG (output)
> and i
> > > > > give
> > > > > a 128xL matrix (my EEG measurement), I indicate my reference was
> the
> > > > > channel
> > > > > (row) 30, and i exclude the earlobes (63 64).
> > > > >
> > > > > The output is however very different to the one i obtain with the
> method
> > > > > explained above in EEGLAB.
> > > > >
> > > > > In order to obtain the (mostly) same result as in EEGLAB i have to
> input
> > > > > the
> > > > > following:
> > > > >
> > > > > output=reref(eeg,30,'exclude',[30 63 64],'keepref','on');
> > > > >
> > > > > So, what exactly am i doing wrong here? I am probably specifying
> the
> > > > > reference in a wrong way. How should one manage such a reference
> system
> > > > > within EEGLAB or in the reref function? As i understand the
> calculation
> > > > > of
> > > > > average referencing, i should NOT use the values of the reference
> to
> > > > > calculate the mean of all electrodes, which would be afterwards
> > > > > subtracted
> > > > > from each one. And if i wanted to see the signal of Cz post-AR, i
> would
> > > > > have
> > > > > it by inverting the mean of all electrodes. If so, then the right
> way to
> > > > > go
> > > > > here would be to exclude also the channel 30 in the reref
> function. Is
> > > > > that
> > > > > right?
> > > > >
> > > > > I am using currently EEGLAB v13.4.4b on MATLAB R2013a
> > > > >
> > > > > Thanks in advance!
> > > > >
> > > > > EG
> > > > >
> > > > > _______________________________________________
> > > > >  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: James Jones-Rounds <jj324 at cornell.edu>
> To: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Cc: Jihoon Lim <jl2382 at cornell.edu>
> Date: Fri, 4 Dec 2015 11:16:53 -0500
> Subject: [Eeglablist] RELICA download available?
> Hello all,
>
> Is a downloadable version of the RELICA toolbox, featured in this article:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330719/ (Callan DE, Durantin
> G, Terzibas C. Classification of single-trial auditory events using
> dry-wireless EEG during real and motion simulated flight. Frontiers in
> Systems Neuroscience. 2015) available yet?
>
> Thank you!
>
> James
>
> --
> 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
>
>
> ---------- Forwarded message ----------
> From: "Buzás Péter" <peter.buzas at aok.pte.hu>
> To: <eeglablist at sccn.ucsd.edu>
> Cc:
> Date: Fri, 4 Dec 2015 15:39:23 +0100
> Subject: [Eeglablist] t2circ
> Dear EEGLabListers,
>
> is anyone aware of an implementation of theT_square_circ test integrated in
> the EEGLab workflow? I mean the statistical test described by Victor and
> Mast ("A new statistic for steady-state evoked potentials",
> Electroencephalography and clinical Neurophvsiology, 1991, 78:378-388).
>
> As a novice to EEGLab, I would really appreciate your help.
>
> Peter Buzas
>
>
>
>
> ---------- Forwarded message ----------
> From: Tarik S Bel-Bahar <tarikbelbahar at gmail.com>
> To: Nikola Vukovic <vukovicnikola at gmail.com>
> Cc: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Date: Thu, 3 Dec 2015 23:51:29 -0500
> Subject: Re: [Eeglablist] Error while precomputing STUDY: NaN values in
> cluster.sets
> Thanks very much Nikola for sharing your experiences. So the workaround is
> manual but effective!
> This is close to what I remember, it was definitely an issue of missing or
> mismatched ICs, which I could not fully resolve.
> Will try to followup if I find anything useful.
> Respectfully,tarik
>
> On Wed, Dec 2, 2015 at 1:18 PM, Nikola Vukovic <vukovicnikola at gmail.com>
> wrote:
>
>> So I was playing some more with the STUDY files, and I found the
>> solution! For some reason, the ICA matrices were not copied correctly from
>> the continuous subject-level dataset into the separate epoched sets -
>> despite the fact that loading the latter in eeglab shows the ICA as
>> present, and even allows the components to be plotted. The solution for me
>> was to manually copy the ICA weights from the non-NaN epoched sets to the
>> problematic ones. Having done that, it seems to work now - I was able to
>> precluster the STUDY components without the error message.
>> Hope this helps someone with a similar issue...
>> N
>>
>>
>> On Wed, Dec 2, 2015 at 12:33 PM, Sebastian Grissmann <
>> sebastian.grissmann at lead.uni-tuebingen.de> wrote:
>>
>>>
>>> Hi there,
>>>
>>> I had the same issue twice.
>>>
>>> The only (suboptimal) solution I found
>>> was to remove the subjects with NaN values.
>>>
>>> Best,
>>> Sebastian
>>>
>>>
>>>
>>> Quoting Nikola Vukovic <vukovicnikola at gmail.com>:
>>>
>>> Hi Tarik,
>>>>
>>>> Indeed this seems to be a long standing bug - it has stalled my analysis
>>>> for two weeks now... I have found one similar post on Bugzilla a couple
>>>> of
>>>> years ago, but it was not resolved, and so I posted it again there (
>>>> https://sccn.ucsd.edu/bugzilla/show_bug.cgi?id=1822), but it hasn't
>>>> been
>>>> looked at by the admins...
>>>>
>>>> As for EEGLab not knowing which dataset belongs to which subject, it
>>>> must
>>>> be due to some non-obvious field. At study creation, I tag all datasets
>>>> with subject and condition information, like this:
>>>> { 'index' 1 'load' '/EEG/RF01/Epoched/RF01_S 1.set' 'subject' 'RF01'
>>>> 'condition' 'IAllo' }
>>>>
>>>> N
>>>>
>>>> On Tue, Dec 1, 2015 at 5:45 AM, Tarik S Bel-Bahar <
>>>> tarikbelbahar at gmail.com>
>>>> wrote:
>>>>
>>>> Greetings,
>>>>>
>>>>> I've seen this several times, and it's led to a lot of wasted time. I'm
>>>>> sure others have come across it before,  perhaps it was already
>>>>> mentioned
>>>>> it on eeglablist posts, did you check?.
>>>>>
>>>>> This issue sounds like a bug, if so it should be reported to the EEGLAB
>>>>> bugzilla.
>>>>>
>>>>> I believe that the problem is that eeglab is looking for exactly
>>>>> matching
>>>>> ICs across datasets that it considers to be coming from one ID or
>>>>> subject.
>>>>> I would also check if there is not some special information (such as
>>>>> ID or
>>>>> group) that is being read incorrectly and affecting how STUDY thinks
>>>>> about
>>>>> organizing the ICs.
>>>>>
>>>>> Try uploading a small study of short datasets with the ICs, which
>>>>> replicates the problem when STUDY is set up.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Nov 25, 2015 at 10:41 AM, Akshay Maggu <
>>>>> akshaymaggu86 at gmail.com>
>>>>> wrote:
>>>>>
>>>>> Hi Nikola,
>>>>>>
>>>>>> I am facing the same issue. All pre-processing steps carefully
>>>>>> followed
>>>>>> and ICAs done for all subjects. But still this 'Na' error (
>>>>>> https://www.dropbox.com/s/sw6xvujbalidg24/error_preclustering.JPG?dl=0
>>>>>> )
>>>>>> pops up saying that some of the datasets have ICA decompositions
>>>>>> missing.
>>>>>>
>>>>>> Let's see what experts on the list have to say about it.
>>>>>>
>>>>>> Akshay
>>>>>>
>>>>>> On Tue, Nov 24, 2015 at 7:33 AM, Nikola Vukovic <
>>>>>> vukovicnikola at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>> Dear EEGLAB list
>>>>>>>
>>>>>>> I would be very grateful is someone could help me out with an error
>>>>>>> I've
>>>>>>> been getting. When I try to precluster components in a given STUDY
>>>>>>> (it
>>>>>>> happens for several study files), I get the following error:
>>>>>>>
>>>>>>> FOR CLUSTERING, YOU MAY ONLY USE DIPOLE OR SCALP MAP CLUSTERING.
>>>>>>> This is
>>>>>>> because some datasets do not have ICA pairs. Look for NaN values in
>>>>>>> STUDY.cluster(1).sets which indicate missing datasets. Each column
>>>>>>> in this
>>>>>>> array indicate datasets with common ICA decompositions.
>>>>>>>
>>>>>>> Looking inside the cluster(1).sets, I can indeed find some NaN
>>>>>>> fields, suggesting not all files have associated ICA decomposition data.
>>>>>>> This, however, is puzzling because I made sure to do ICA on each subject's
>>>>>>> dataset *before* epoching, meaning that all sets for individual conditions
>>>>>>> share the same weights for a subject. After getting this error I even tried
>>>>>>> to copy the weights (EEG.icawinv + EEG.icasphere + EEG.icaweights +
>>>>>>> EEG.icachansind) from the unepoched set to all the epoched ones.
>>>>>>>
>>>>>>> Did anyone have this error too, and how could it be solved?
>>>>>>>
>>>>>>> Thanks for any help,
>>>>>>>
>>>>>>> Nikola
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> 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
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Akshay Raj Maggu,
>>>>>> PhD Candidate,
>>>>>> Laboratory for Language, Learning and the Brain,
>>>>>> Department of Linguistics and Modern Languages,
>>>>>> The Chinese University of Hong Kong,
>>>>>> Hong Kong.
>>>>>> Webpage: http://www.cuhk.edu.hk/lin/new/people/students/maggu/
>>>>>> *Save trees.. Save life! Please don't print this email unless you
>>>>>> really
>>>>>> need to.....*
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>
>>>
>>> --
>>> Sebastian Grissmann (Mag. rer. nat)
>>> PhD student
>>>
>>> LEAD Graduate School
>>> University of Tübingen
>>> Gartenstrasse 29 (1st floor)
>>> 72074 Tübingen
>>> Germany
>>> Phone  +49 7071 29-73579
>>>
>>> www.lead.uni-tuebingen.de
>>>
>>>
>>> _______________________________________________
>>> 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
>>>
>>
>>
>> _______________________________________________
>> 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
>>
>
>
>
> ---------- Forwarded message ----------
> From: Tarik S Bel-Bahar <tarikbelbahar at gmail.com>
> To: Pamela Leigh Stevenson <pamela.stevenson at unb.ca>
> Cc: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
> Date: Fri, 4 Dec 2015 00:20:19 -0500
> Subject: Re: [Eeglablist] Electrolyte gel question
> Hello Pamela, it sounds like there used to be no bubbles! Try moving to
> another gel from another manufacturer, unless the eeg manufactuer has
> specified that the bubble gel is the only one that should be used with
> their EEG system/trodes. I've not seen bubbles in most gels. try contacting
> other RAs or labs. Try Elefix, Redux used with EGI systems. We also like
> Abralyte distributed by brain products with "grit" in it that helps with
> reducing impedances, it might be manufactured by easycap. All gels you try
> will likely wash out of your caps/trodes easily. Although unlikely, there
> may be some bits in your caps/trodes that don't like other gels besides the
> one you have. all the best.
>
>
> On Tue, Dec 1, 2015 at 5:29 PM, Pamela Leigh Stevenson <
> pamela.stevenson at unb.ca> wrote:
>
>> Hello everyone!
>>
>>
>> I would like to get your advice on an issue related to electrolyte gel:
>>
>>
>> We ordered some electrolyte gel this summer and noticed that it arrived
>> full of bubbles. We contacted the company to let them know and they send us
>> some replacement gel. Unfortunately, the replacement gel has just as many
>> bubbles as the original batch. We sought advice on how to decrease the
>> amount of bubbles from the company who makes the gel, but nothing they
>> suggested has helped. This has made data collection much more difficult (in
>> terms of reducing electrode impedance).
>>
>>
>> Have any of you experienced this? If so, have you been able to reduce the
>> amount of bubbles in the gel? Can anyone suggest a brand of gel that you
>> have had a good experience with?
>>
>>
>> Thank you for your advice/suggestions!
>>
>> Pam
>>
>>
>> _______________________________________________
>> 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
>>
>
>
>
> ---------- Forwarded message ----------
> From: Makoto Miyakoshi <mmiyakoshi at ucsd.edu>
> To: Leonardo Lion <llionname at gmail.com>
> Cc: EEGLAB List <eeglablist at sccn.ucsd.edu>
> Date: Mon, 7 Dec 2015 11:32:52 -0800
> Subject: Re: [Eeglablist] Time- frequency analysis
> Dear Leonardo,
>
> I haven't tested the time-frequency baseline parameters myself so I'm
> afraid I'm not so much of your help.
>
> > 1- For me, in order to select the baseline, I try first (with code)
> applying several values (a few ms before or after 0), and best on the
> worthy plot, I determine the suitable baseline. Is considered a good way to
> select the baseline?
>
> No I don't think so. It seems as if you are cherry picking. Use the most
> reasonable and a priori definition of baseline and stick to it unless you
> have clear reason not to do so.
>
> > 2-Now, without code, when I use the eeglab, 0 is the value that is
> selected by default in the time-frequency dialog (pop_newtimef()). In the
> case of my continuous data, when I change select values for my baseline,
> e.g., [0 300] or [-400 -200], I get the folllwing error message:
> There are no sample points found in the default baseline. This may happen
> even though data time limits overlap with the baseline period (because of
> the time-freq. window width). Either disable the baseline, change the
> baseline limits.
>
> Sorry but I have no idea about this. If you like please post it to EEGLAB
> Bugzilla
> https://sccn.ucsd.edu/bugzilla/
>
> > a- My major aim is to know when to select any of the options of
> drop-down list (Use divisive baseline (DIV) as selecting them keep change
> the dB into e.g., STD, Use standard deviation (STD), Use single trial DIV
> baseline, and single trial baseline) because when I change the default
> option that produces dB unit, it will be change into STD.
>
> If you don't know which one to use because you don't know what they do,
> use the default. If you know the differences but still not sure which one
> to use, make a decision. If you can't, use the default.
>
> > Is the STD (or any of the left 3 choice in drop-down list) produces dB
> unit? In the 2 attached plots, I highlighted both default option and STD
> option results where the dB changed to STD.
>
> No, if the unit is STD it probably means X times deviant from the baseline
> STD.
>
> > b- When to select each of Use divisive baseline (DIV),Use standard
> deviation (STD), Use single trial DIV baseline, and Use single trial STD
> baseline?
>
> The developer's implicit recommendation would be to use the default... I
> would take so.
>
> Makoto
>
>
>
> On Fri, Dec 4, 2015 at 7:39 PM, Leonardo Lion <llionname at gmail.com> wrote:
>
>> Dear Makoto and the list,
>>
>> Thanks a lot for your explanation and help. In fact, I still have some
>> issues about this particular topic.
>>
>> 1- For me, in order to select the baseline, I try first (with code)
>> applying several values (a few ms before or after 0), and best on the
>> worthy plot, I determine the suitable baseline. Is considered a good way to
>> select the baseline?
>>
>> 2-Now, without code, when I use the eeglab, 0 is the value that is
>> selected by default in the time-frequency dialog (pop_newtimef()). In
>> the case of my continuous data, when I change select values for my
>> baseline, e.g., [0 300] or [-400 -200], I get the folllwing error message:
>>
>> There are no sample points found in the default baseline. This may happen
>> even though data time limits overlap with the baseline period (because of
>> the time-freq. window width). Either disable the baseline, change the
>> baseline limits.
>>
>>
>>
>> How to solve this matter?
>>
>> 3-
>>
>> For baseline, when to select the option "Use standard deviation (STD)",
>>> "Single trial DIV baseline", and "Single trial STD baseline"?  When we
>>> change from one to another, does that change the dB unit or not, knowing
>>> that the default option "Use divisive baseline" produces bar column in dB.
>>> However, this bar color will be changed (e.g., std.) when we change the
>>> option into "Use Single trial STD baseline".
>>>
>>> I believe the difference is how to take the baseline. It's my guess but
>>> sounds like the default is the std of the baseline period after averaging,
>>> while the 'single trial' option calculates it at single trials (I don't
>>> know exactly how). The dB unit will be the same, but the baseline values
>>> would be different since they are differently calculated.
>>>
>>>
>> a- My major aim is to know when to select any of the options of drop-down
>> list (Use divisive baseline (DIV) as selecting them keep change the dB into
>> e.g., STD, Use standard deviation (STD), Use single trial DIV baseline, and
>> single trial baseline) because when I change the default option that
>> produces dB unit, it will be change into STD. Is the STD (or any of the
>> left 3 choice in drop-down list) produces dB unit? In the 2 attached plots,
>> I highlighted both default option and STD option results where the dB
>> changed to STD.
>>
>> b- When to select each of Use divisive baseline (DIV),Use standard
>> deviation (STD), Use single trial DIV baseline, and Use single trial STD
>> baseline?
>>
>>
>> Kind regards,
>> Leonardo
>>
>>
>>
>> Makoto
>>>
>>> On Thu, Dec 3, 2015 at 9:42 AM, Leonardo Lion <llionname at gmail.com>
>>> wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> My question is about applying ht e Time- frequency analysis on my
>>>> continuous dataset (I don't have any epoch in the data).
>>>>
>>>> In the EEGLAB, under the "Time-frequency transforms" option, there is a
>>>> parameter called "Sub-epoch time limits". In the help of this parameter was
>>>> written that "sub epochs may be extracted (note that this function aims at
>>>> plotting data epochs not continuous data). You may select the new epoch
>>>> limits in this edit box".
>>>>
>>>>
>>>> 1- Does that mean, I can't do time-frequency analysis using
>>>> "Time-frequency transforms" of EEGLAB because I don't have epochs in my
>>>> data)? Is this could be a limitation of Time-frequency transforms (only
>>>> dealing withe epoch data rather than continuous one)?
>>>>
>>>> 2- In same "Time-frequency transforms" option, what is the meaning of
>>>> the word "log" that we find it in both "Log spaced" and "log power"
>>>> parameters?
>>>>
>>>> 3- For baseline, when to select the option "Use standard deviation
>>>> (STD)", "Single trial DIV baseline", and "Single trial STD baseline"?  When
>>>> we change from one to another, does that change the dB unit or not, knowing
>>>> that the default option "Use divisive baseline" produces bar column in dB.
>>>> However, this bar color will be changed (e.g., std.) when we change the
>>>> option into "Use Single trial STD baseline".
>>>>
>>>>
>>>> Kind regards,
>>>> Leonardo
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>
>
> --
> Makoto Miyakoshi
> Swartz Center for Computational Neuroscience
> Institute for Neural Computation, University of California San Diego
>
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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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