[Eeglablist] eeglablist Digest, Vol 100, Issue 28
Makoto Miyakoshi
mmiyakoshi at ucsd.edu
Mon Feb 25 11:41:20 PST 2013
Dear Neelam,
>there is 3-4 file export option. but which one of my use...???
If you are thinking about exporting the channel EEG data, well... it
depends on what system you want to use to import those data, so I can't say
for sure. If you will import them using matlab-based application, then you
want to save them as .mat file, don't you?
Makoto
2013/2/23 neelam sharma <sharma21neelam at gmail.com>
> Dear Makoto
>
> Thank you very much for your reply. Sorry but my 2nd question exactly was,
> how i get corrected eeg data after component removal in txt or csv format
> ?? there is 3-4 file export option. but which one of my use...???
>
>
> On Sat, Feb 23, 2013 at 3:43 AM, Makoto Miyakoshi <mmiyakoshi at ucsd.edu>wrote:
>
>> Dear Neelam,
>>
>> > 1. Is it neccesary to extract data epochs & why ??
>>
>> If your experimental design is to examine event-related potential, yes
>> you should. There is no why because this is tautological.
>>
>> > 2. After running ICA how can i get eeg data back..??
>>
>> Yes. Running ICA actually generates additional data and does not change
>> your channel EEG.
>>
>> > 3. why are these function disable. specially Tools>Reject data using
>> ICA> *Reject data (all method)* & Tools>* reject data epoch> reject data
>> (all method) *
>> bold letter function are disable.
>>
>> This is because you are analyzing continuous data. Epoc rejection
>> requires epoch statistics. So no epoch, no epoch rejection.
>>
>> Makoto
>>
>>
>> 2013/2/21 neelam sharma <sharma21neelam at gmail.com>
>>
>>> Dear all
>>>
>>> I have 14 channel eeg recorded data from emotiv epoc. It is continuous
>>> data in edf format using Test bench and I want to remove artifact from it
>>> using ICA. I follow A12 Quick Tutorial Rejection & chapter 09- decomposing
>>> data using ICA from wiki tutorial.
>>> I am using eeglab v 12.0.1.0.b. some function are disable during
>>> analysis of data. like Automatic epoch rejection, reject data epochs etc.
>>> And after running ICA only one function is enable i.e Tools>Reject Data
>>> using ICA> Reject component by maps.
>>> when i am rejecting component and run second ICA. data gets reduced.
>>>
>>> so kindly answer the following questions & suggest me easy way for data
>>> analysis of continuous eeg as soon as possible.
>>>
>>> 1. Is it neccesary to extract data epochs & why ??
>>> 2. After running ICA how can i get eeg data back..??
>>> 3. why are these function disable. specially Tools>Reject data using
>>> ICA> *Reject data (all method)* & Tools>* reject data epoch> reject
>>> data (all method) *
>>> bold letter function are disable.
>>>
>>> Regards
>>> Neelam Sharma
>>>
>>>
>>> On Wed, Feb 20, 2013 at 11:19 PM, <eeglablist-request at sccn.ucsd.edu>wrote:
>>>
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>>>> Today's Topics:
>>>>
>>>> 1. Standardize electrodes montage for group analysis
>>>> (Iman M.Rezazadeh)
>>>> 2. Re: running ICA a second time (Tarik S Bel-Bahar)
>>>> 3. Re: Standardize electrodes montage for group analysis
>>>> (Chadwick Boulay)
>>>>
>>>>
>>>> ----------------------------------------------------------------------
>>>>
>>>> Message: 1
>>>> Date: Tue, 19 Feb 2013 16:47:08 -0800
>>>> From: "Iman M.Rezazadeh" <irezazadeh at ucdavis.edu>
>>>> Subject: [Eeglablist] Standardize electrodes montage for group
>>>> analysis
>>>> To: <eeglablist at sccn.ucsd.edu>
>>>> Message-ID: <00e501ce0f03$d0364860$70a2d920$@ucdavis.edu>
>>>> Content-Type: text/plain; charset="utf-8"
>>>>
>>>> Dear all,
>>>>
>>>> Since each subject has its own head diameter thus electrode placement
>>>> over the head might be slightly different !
>>>>
>>>> Thus, do you have any idea how to standardize the electrode
>>>> configuration from different subjects for within or btw group comparison!
>>>>
>>>> I am using spline interpolation to convert my 128 channel data to 81
>>>> channel. However the new coordinates are still slightly different from
>>>> subject to subject!
>>>>
>>>>
>>>>
>>>> Any thought???
>>>>
>>>>
>>>>
>>>> Iman M.Rezazadeh, PhD
>>>>
>>>> Postdoctoral Research Fellow
>>>>
>>>> Center for Mind and Brain
>>>>
>>>> University of California, Davis
>>>>
>>>> <http://www.linkedin.com/pub/iman-m-rezazadeh/10/859/840>
>>>> www.linkedin.com/pub/iman-m-rezazadeh/10/859/840
>>>>
>>>> <http://mindbrain.ucdavis.edu/people/imanmr>
>>>> http://mindbrain.ucdavis.edu/people/imanmr
>>>>
>>>> email : <mailto:irezazadeh at ucdavis.edu> irezazadeh at ucdavis.edu
>>>>
>>>> Tel: 530-297-4444
>>>>
>>>> Cell:310-490-1808
>>>>
>>>> Skype: Imanmr
>>>>
>>>> ????? ???? ???????
>>>>
>>>> ???????
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -- The information contained in this message is intended only for the
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>>>> ------------------------------
>>>>
>>>> Message: 2
>>>> Date: Tue, 19 Feb 2013 20:01:03 -0500
>>>> From: Tarik S Bel-Bahar <tarikbelbahar at gmail.com>
>>>> Subject: Re: [Eeglablist] running ICA a second time
>>>> To: Veerle ROSS <veerle.ross at uhasselt.be>
>>>> Cc: "eeglablist at sccn.ucsd.edu" <eeglablist at sccn.ucsd.edu>
>>>> Message-ID:
>>>> <CABCAK+hyJeONgdRHVx==
>>>> ReN3EM+55YnaNevnY7jpaO3U5EXMqQ at mail.gmail.com>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> Greetings Ross:
>>>>
>>>> Some brief responses to your questions below, I hope they are helpful.
>>>> I've
>>>> numbered the responses according to your questions.
>>>>
>>>> 0. if you have note please search eeglab list archives where you will
>>>> definitely find some past discussions.
>>>> PLease read through the articles about cleaning with eeglab, which you
>>>> can
>>>> easily find on Google Scholar.
>>>> Check out the eeglab tutorial and wiki, particular guidelines.
>>>>
>>>> 1a. You can use PCA (see post within last 2 months on this subject
>>>> based on
>>>> a "should I PCA and if so what is best method")
>>>> Reducing by PCA may decrease the "validity" or "truthfullness" of your
>>>> ICs.
>>>> Check Joseph Dien's PCA toolkit for some principled methods to do PCA.
>>>>
>>>> 1c. You should find similar ICs after 2 ICAs, as the second ICA
>>>> decomposition. The ones in the second ICA should be cleaner and more
>>>> accurate.
>>>> Some people just publish their first ICA results, as it is not always
>>>> the
>>>> case that you gain much from a second ICA.
>>>>
>>>> 2a. I assume you have properly cleaned your data before the first ICA.
>>>> My recommendation is, if you want to do a second ICA, first consider
>>>> doing
>>>> what eeglab documentation recommend:
>>>> after your first ICA, then do artifactual epoch rejection using
>>>> ICA-based
>>>> rejection, then do a second ICA.
>>>>
>>>> 2b. it's not clear what your question is, perhaps there is a word
>>>> missing
>>>> in your question.
>>>> You could remove noisy or blink or other artifactual components if you
>>>> want
>>>> to, go ahead
>>>> and do a second ICA, and compare the results to doing it via the method
>>>> suggested in the response to 2a above.
>>>>
>>>> also:
>>>> Check out the the ADJUST plugin (amongst others for a variety of
>>>> cleaning
>>>> techniques).
>>>> &
>>>> Note there are least three camps:
>>>> a. those who use ICA just to deblink or otherwise clean their data, and
>>>> then they reconstruct the EEG and do their analyses outside of ICA
>>>> space.
>>>> [ergo, ICA is a cleaning tool]
>>>> b. those who use ICA to get ICs that reflect brain dynamics and (often)
>>>> established ERP components, they do their analyses on ICs [ergo, ICA
>>>> gives
>>>> real brain dynamics]
>>>> c. those who use PCA (with or without ICA) to decompose ERPs into
>>>> spatial
>>>> (and/or) temporal components, they do their analyses on PCs
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>>>> ------------------------------
>>>>
>>>> Message: 3
>>>> Date: Wed, 20 Feb 2013 11:36:14 +0900
>>>> From: Chadwick Boulay <boulay at bme.bio.keio.ac.jp>
>>>> Subject: Re: [Eeglablist] Standardize electrodes montage for group
>>>> analysis
>>>> To: eeglablist at sccn.ucsd.edu, "Iman M.Rezazadeh"
>>>> <irezazadeh at ucdavis.edu>
>>>> Message-ID: <5124369E.7000804 at bme.bio.keio.ac.jp>
>>>> Content-Type: text/plain; charset="iso-8859-1"
>>>>
>>>> I think the assumption is that if brain A is 10% larger than brain B
>>>> then the cortical region normally associated with C3 is 10% further from
>>>> the midline in brain A than it is in brain B. Thus, if you are using
>>>> differently-sized caps (with different electrode spacing) for
>>>> differently-sized heads then you may assume that C3 from subject A
>>>> represents approximately the same patch of brain as C3 from subject B.
>>>> The precise coordinates of C3 don't matter.
>>>>
>>>> Of course the above assumption is false not only because the head shapes
>>>> vary but also because the relative skull conductance and brain
>>>> curvatures vary. While having super-accurate coordinates might help
>>>> overcome the problem of head shape, it won't help with the other
>>>> problems. If you have anatomical MR images for each subject and you are
>>>> able to coregister your electrode positions with the MRI then you may be
>>>> able to use ICA+NFT+DIPFIT to identify subject-specific neurobiological
>>>> 'sources'. You may then use some component-clustering algorithm to
>>>> figure out which component from each subject represents a particular
>>>> patch of brain then do your between subject/group comparisons on those
>>>> components' activations. (Notice that I skipped over the
>>>> skull-conductance problem.)
>>>>
>>>> If you need to identify precise (not necessarily accurate) brain regions
>>>> associated with your task then the above method might be for you.
>>>> However, if you REALLY need to identify brain sources accurately then
>>>> you might be better off going with fMRI or EEG-fMRI if time-resolution
>>>> is important.
>>>>
>>>> If you don't need to report specific brain regions then I'd just stick
>>>> with averaging across electrodes with the same name.
>>>>
>>>> On 2/20/2013 9:47 AM, Iman M.Rezazadeh wrote:
>>>> >
>>>> > Dear all,
>>>> >
>>>> > Since each subject has its own head diameter thus electrode placement
>>>> > over the head might be slightly different !
>>>> >
>>>> > Thus, do you have any idea how to standardize the electrode
>>>> > configuration from different subjects for within or btw group
>>>> comparison!
>>>> >
>>>> > I am using spline interpolation to convert my 128 channel data to 81
>>>> > channel. However the new coordinates are still slightly different from
>>>> > subject to subject!
>>>> >
>>>> > Any thought???
>>>> >
>>>> > Iman M.Rezazadeh, PhD
>>>> >
>>>> > Postdoctoral Research Fellow
>>>> >
>>>> > Center for Mind and Brain
>>>> >
>>>> > University of California, Davis
>>>> >
>>>> > www.linkedin.com/pub/iman-m-rezazadeh/10/859/840
>>>> > <http://www.linkedin.com/pub/iman-m-rezazadeh/10/859/840>
>>>> >
>>>> > http://mindbrain.ucdavis.edu/people/imanmr
>>>> >
>>>> > email : irezazadeh at ucdavis.edu <mailto:irezazadeh at ucdavis.edu>
>>>> >
>>>> > Tel: 530-297-4444
>>>> >
>>>> > Cell:310-490-1808
>>>> >
>>>> > Skype: Imanmr
>>>> >
>>>> > ????? ???? ???????
>>>> >
>>>> > ??*?*????
>>>> >
>>>> > /-- The information contained in this message is intended only for the
>>>> > recipient, and may be a confidential communication or may otherwise be
>>>> > privileged and confidential and protected from disclosure. If the
>>>> > reader of this message is not the intended recipient, or an employee
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>>>> > please immediately notify us by replying to the message and then
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>>>> >
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>>
>>
>>
>> --
>> Makoto Miyakoshi
>> JSPS Postdoctral Fellow for Research Abroad
>> Swartz Center for Computational Neuroscience
>> Institute for Neural Computation, University of California San Diego
>>
>
>
--
Makoto Miyakoshi
JSPS Postdoctral Fellow for Research Abroad
Swartz Center for Computational Neuroscience
Institute for Neural Computation, University of California San Diego
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