[Eeglablist] Regarding Simultaneous fMRI-EEG Data

[Joshua Balsters]

Hi Makoto

thanks for your reply! We're using a Philips 3T Acheva, similarly
there's a few preparation scans before data collection starts but i
haven't noticed any impact on the EEG. This may be because I'm only
looking at ERPs at the moment and not oscillatory activity. Do you
have a figure that highlights this so i can compare it with the data
i've been collecting?

Thanks
Josh

2009/9/8 Makoto Miyakoshi <mataothefifth at yahoo.co.jp>:
> Dear Josh,
>
> Our system (Siemens Trio Tim) has additional seven seconds of preparatory
> scan to achieve the steady state. I don't know if the gradient switching
> artifact in the initial part of EEG data is due to the steady state problem
> or subject move.
>
> Would you mind if I asked you to post our communication to the EEGLAB list?
>
> Makoto
>
> --- jhbalsters at gmail.com wrote:
>
>> Dear Makoto
>>
>> I was interested in your comment that discard the first 10 scans for
>> data
>> quality. Do you start the EPI sequence straight away or do you leave
>> 30s
>> before starting the sequence? I'm just wondering if you find that it
>> takes
>> 30s for the EEG data to stabilize to the static field or the gradient
>>
>> switching?
>>
>> Best
>> Josh
>>
>> On Sep 4, 2009 4:28am, Makoto Miyakoshi <mataothefifth at yahoo.co.jp>
>> wrote:
>> > Dear Gaurav,
>>
>>
>>
>> > > I have got similar 3D rendering and SPMmip images but
>>
>> > > your design matrix with contrast, as given in the 'pdf file' you
>> sent
>>
>> > > to me, does not match when giving the contrast values here; can
>> you
>>
>> > > please tell me that how you are giving the no. of volumes to use
>>
>> > > after stabilization of fMRI scanner and contrast parameter.
>>
>>
>>
>> > I discarded first 10 scans (=30seconds duration) to secure data
>> quality.
>>
>> > There are therefore 110 scans. I found it takes while for EEG data
>> to be
>>
>> > stabilized. There is actually seven seconds of preparatory scan
>> that is
>> > not
>>
>> > counted as data, but it seems it is not sufficient. Contrast
>> parameter is
>>
>> > alpha-power time series extracted from one of ICs that represent
>> occipital
>>
>> > alpha. The following is the matlab script prototype I used. Be sure
>> that
>>
>> > you launched EEGLAB and loaded the set file (epoched). I used
>> cycles = 22
>>
>> > at 8-12Hz, which is approximately 3sec. it picks up the highest
>> alpha
>> > power
>>
>> > between 8-12Hz by 0.1Hz step. Note also that the hrf is convolved
>> in the
>>
>> > end (so you need SPM installed).
>>
>>
>>
>> > %%%%%%%%%%%%%%%%%%%%
>>
>>
>>
>> > for n=[11 13 14]; % enter IC numbers
>>
>> > [ersp,itc,powbase,times,freqs,erspboot,itcboot] = newtimef(...
>>
>> > EEG.icaact(n,:),... % data
>>
>> > EEG.pnts,... % frames
>>
>> > [EEG.xmin EEG.xmax]*1000,... % tlimits
>>
>> > EEG.srate,... % srate
>>
>> > 22,... % cycles
>>
>> > 'timesout', 330,...
>>
>> > 'freqs', [8 12],...
>>
>> > 'nfreqs', 41,...
>>
>> > 'plotersp', 'off',...
>>
>> > 'plotitc', 'off',...
>>
>> > 'baseline', NaN);
>>
>> > [power freqn] = max(mean(ersp,2));
>>
>> > disp([num2str(freqs(freqn)) 'Hz selected'])
>>
>> > regressor = ersp(freqn, :);
>>
>> > regressor = resample(regressor, 110, length(regressor));
>>
>> > regressor = conv(regressor, spm_hrf(3));
>>
>> > regressor = regressor(:, [1:110]);
>>
>> > save(['IC' num2str(n)], 'regressor')
>>
>> > end
>>
>>
>>
>> > %%%%%%%%%%%%%%%
>>
>>
>>
>> > > I tried to analyse the eegdata in EEGLab and removed gradient and
>>
>> > > pulse artefacts using the given tools in EEGLab, also tried to
>>
>> > > localize the source using BESA electrode placement design; but I
>> am
>>
>> > > not very much sure about results I am getting, because of two
>>
>> > > reasons, one is the all the parameters I am to give in the
>> software
>>
>> > > are not available to me and I am putting them as given in manual
>> of
>>
>> > > the EEGLab, and the second reason, as being new to this field,
>>
>> > > relating them with biological aspects and brain anatomy.
>>
>>
>>
>> > I have never used BESA plugin, so I don't know anything about it.
>> One of
>>
>> > MEG persons came to me and said the dipole, which was located at
>> left
>>
>> > occipito-temporal area, looks absurd. I don't doubt he is true,
>> because my
>>
>> > data have only 32 channels. My understanding of significance of
>> source
>>
>> > estimation is that it provides spatial information as one of
>> constraint
>>
>> > conditions in interpreting the data, which is not necessarily
>>
>> > physiologically valid given that the current recording condition is
>> far
>>
>> > from ideal. You'll need 128 channels to achieve the spatial Nyquist
>> of a
>>
>> > human head (Srinivasan, 1995).
>>
>>
>>
>> > > I am studying the paper you had sent to me and I will let you
>> know if
>>
>> > > I will be able to implement the idea given in paper.
>>
>>
>>
>> > Great! Please tell me if it works. I also wondered if it is
>> possible to
>>
>> > create a file format converter between EEGLAB and FAST (or SPM8).
>>
>>
>>
>> > > If you also tried for fusion or integration of both
>> simultaneously
>>
>> > > recorded EEG and fMRI data earlier or you know any tool available
>> for
>>
>> > > this purpose, then please let me know.
>>
>>
>>
>> > I also use VisonAnalyzer that came with BrainAmp. I found it
>> convenient to
>>
>> > identify ECG peak manually with it because it has intuitive
>> interactive
>>
>> > interface. I hope the similar interactive interface is implemented
>> in
>>
>> > EEGLAB.
>>
>>
>>
>> > Makoto
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> > --- Gaurav Garg Garg-G at email.ulster.ac.uk> wrote:
>>
>>
>>
>> > > Hello Makoto,
>>
>> > >
>>
>> > > I am doing well here, How is everything with you?
>>
>> > > Its really nice to see your mail. Thankyou very much for sharing
>> your
>>
>> > > analysis results with me and I have also regenerated your results
>>
>> > > here using SPM. I have got similar 3D rendering and SPMmip images
>> but
>>
>> > > your design matrix with contrast, as given in the 'pdf file' you
>> sent
>>
>> > > to me, does not match when giving the contrast values here; can
>> you
>>
>> > > please tell me that how you are giving the no. of volumes to use
>>
>> > > after stabilization of fMRI scanner and contrast parameter.
>>
>> > >
>>
>> > > I tried to analyse the eegdata in EEGLab and removed gradient and
>>
>> > > pulse artefacts using the given tools in EEGLab, also tried to
>>
>> > > localize the source using BESA electrode placement design; but I
>> am
>>
>> > > not very much sure about results I am getting, because of two
>>
>> > > reasons, one is the all the parameters I am to give in the
>> software
>>
>> > > are not available to me and I am putting them as given in manual
>> of
>>
>> > > the EEGLab, and the second reason, as being new to this field,
>>
>> > > relating them with biological aspects and brain anatomy.
>>
>> > >
>>
>> > > I am studying the paper you had sent to me and I will let you
>> know if
>>
>> > > I will be able to implement the idea given in paper.
>>
>> > > If you also tried for fusion or integration of both
>> simultaneously
>>
>> > > recorded EEG and fMRI data earlier or you know any tool available
>> for
>>
>> > > this purpose, then please let me know.
>>
>> > >
>>
>> > > Thanks,
>>
>> > >
>>
>> > > Best Regards
>>
>> > > Gaurav Garg
>>
>> > > =====================================
>>
>> > > Postgraduate Research Scholar
>>
>> > > Room No. MS125
>>
>> > > School of Computing and Intelligent Systems
>>
>> > > University of Ulster
>>
>> > > Magee Campus
>>
>> > > Northland Road
>>
>> > > Derry
>>
>> > > Northern Ireland BT48 7JL
>>
>> > >
>>
>> > > Tel - +442871371207
>>
>> > > ________________________________________
>>
>> > > From: Makoto Miyakoshi [mataothefifth at yahoo.co.jp]
>>
>> > > Sent: 28 August 2009 10:15
>>
>> > > To: Gaurav Garg
>>
>> > > Subject: RE: Regarding Simultaneous fMRI-EEG Data
>>
>> > >
>>
>> > > Hello Gaurav,
>>
>> > >
>>
>> > > How are you doing?
>>
>> > > I recently had chance to analyze the data I shared with you.
>>
>> > > The attached PDF is from one of the best results.
>>
>> > > I used alpha power fluctuation from haku2close as a regressor and
>>
>> > > asked
>>
>> > > negative correlation using SPM5.
>>
>> > > Isn't it great?
>>
>> > >
>>
>> > > About other subjects, I had difficulty in identifying qrs peaks
>> and
>>
>> > > could
>>
>> > > not subtract BCG well. If you have reliable pqr peaks, then you
>> can
>>
>> > > perform
>>
>> > > good BCG remove algorithm such as constraintICA (Leclercq et al.,
>>
>> > > 2009
>>
>> > > Neuroimage) but with no good EKG, I cannot help it.
>>
>> > >
>>
>> > > Makoto
>>
>> > >
>>
>> > >
>>
>> > >
>>
>> > > --- Gaurav Garg Garg-G at email.ulster.ac.uk> wrote:
>>
>> > >
>>
>> > > > Dear Makoto,
>>
>> > > >
>>
>> > > > Thanks for this information about subjects; also it would
>> really be
>>
>> > > > great idea to share your analysis results and findings to me to
>> get
>>
>> > > > good understanding of the facts. I will also let you know if I
>> will
>>
>> > > > find some remarkable things.
>>
>> > > >
>>
>> > > > Thanks,
>>
>> > > >
>>
>> > > > Gaurav
>>
>> > > >
>>
>> > > > ==================================================
>>
>> > > > Gaurav Garg
>>
>> > > >
>>
>> > > > Postgraduate Research Scholar
>>
>> > > > Room No. MS125
>>
>> > > > School of Computing and Intelligent Systems
>>
>> > > > University of Ulster
>>
>> > > > Magee Campus
>>
>> > > > Northland Road
>>
>> > > > Derry
>>
>> > > > Northern Ireland BT48 7JL
>>
>> > > >
>>
>> > > > Tel - +442871371207
>>
>> > > > ________________________________________
>>
>> > > > From: Makoto Miyakoshi [mataothefifth at yahoo.co.jp]
>>
>> > > > Sent: 17 July 2009 03:41
>>
>> > > > To: Gaurav Garg
>>
>> > > > Subject: RE: Regarding Simultaneous fMRI-EEG Data
>>
>> > > >
>>
>> > > > Dear Gaurav,
>>
>> > > >
>>
>> > > > They are healthy young subjects, no history of psycopathology.
>>
>> > > > Haku is a 29 year-old male, right handed.
>>
>> > > > Ojima is a 25 year-old female, right handed.
>>
>> > > > Sawada is a 26 year-old female, right handed.
>>
>> > > >
>>
>> > > > I'm also mining these datasets right now.
>>
>> > > > I'll tell you if I find something interesting.
>>
>> > > >
>>
>> > > > Makoto
>>
>> > > >
>>
>> > > > --- Gaurav Garg Garg-G at email.ulster.ac.uk> wrote:
>>
>> > > >
>>
>> > > > > Dear Makoto,
>>
>> > > > >
>>
>> > > > > I am going through the data, you had, provided to me; and
>> till
>>
>> > > > > everything is going fine.
>>
>> > > > > I have only one query at the time and It would be great, if
>> you
>>
>> > > > could
>>
>> > > > > tell me the condition of test subjects, like this data is
>>
>> > > recorded
>>
>> > > > > from the healthy subjects or for some specific disease
>> related
>>
>> > > > > diagnosis/confirmation purpose.
>>
>> > > > >
>>
>> > > > > Thanks,
>>
>> > > > > Stay in touch,
>>
>> > > > >
>>
>> > > > > Gaurav
>>
>> > > > >
>>
>> > > > > ==================================================
>>
>> > > > > Gaurav Garg
>>
>> > > > >
>>
>> > > > > Postgraduate Research Scholar
>>
>> > > > > Room No. MS125
>>
>> > > > > School of Computing and Intelligent Systems
>>
>> > > > > University of Ulster
>>
>> > > > > Magee Campus
>>
>> > > > > Northland Road
>>
>> > > > > Derry
>>
>> > > > > Northern Ireland BT48 7JL
>>
>> > > > > ________________________________________
>>
>> > > > > From: Makoto Miyakoshi [mataothefifth at yahoo.co.jp]
>>
>> > > > > Sent: 13 July 2009 06:15
>>
>> > > > > To: Gaurav Garg
>>
>> > > > > Subject: RE: Regarding Simultaneous fMRI-EEG Data
>>
>> > > > >
>>
>> > > > > Dear Gaurav,
>>
>> > > > >
>>
>> > > > > Sorry for the slow response.
>>
>> > > > > I've been to Switzerland to visit CERN.
>>
>> > > > >
>>
>> > > > > I'm glad you received the DVD.
>>
>> > > > > If you have any question don't hesitate to ask.
>>
>> > > > >
>>
>> > > > > Makoto
>>
>> > > > >
>>
>> > > > >
>>
>> > > > > --- Gaurav Garg Garg-G at email.ulster.ac.uk> wrote:
>>
>> > > > >
>>
>> > > > > > Dear Makoto,
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > > > Thank you very much!
>>
>> > > > > >
>>
>> > > > > > Today, I have received the EEG-fMRI data DVD, which you
>> have
>>
>> > > sent
>>
>> > > > > to
>>
>> > > > > > me.
>>
>> > > > > >
>>
>> > > > > > I am grateful to you for your efforts, which you had put
>> for
>>
>> > > > > > continuous assistance.
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > > > Please, stay in touch.
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > > > Thanks and Regards
>>
>> > > > > >
>>
>> > > > > > Gaurav Garg
>>
>> > > > > >
>>
>> > > > > > Postgraduate Research Scholar
>>
>> > > > > > Room No. MS125-9
>>
>> > > > > > School of Computing and Intelligent Systems
>>
>> > > > > > University of Ulster
>>
>> > > > > > Magee Campus
>>
>> > > > > > Northland Road
>>
>> > > > > > Derry
>>
>> > > > > > Northern Ireland BT48 7JL
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > > > ________________________________
>>
>> > > > > > From: Gaurav Garg
>>
>> > > > > > Sent: 16 June 2009 12:44
>>
>> > > > > > To: eeglablist at sccn.ucsd.edu
>>
>> > > > > > Subject: Regarding Simultaneous fMRI-EEG Data
>>
>> > > > > >
>>
>> > > > > > Hi,
>>
>> > > > > >
>>
>> > > > > > I am working for some mental degeneration models using
>>
>> > > > Simultaneous
>>
>> > > > > > fMRI-EEG Data Recordings, but I don't have the
>> simultaneously
>>
>> > > > > > captured data available. so, please guide me in this
>> matter,
>>
>> > > that
>>
>> > > > > > where can I get the data.
>>
>> > > > > >
>>
>> > > > > > looking forward for a favourable reply.
>>
>> > > > > >
>>
>> > > > > > Thanks and Regards
>>
>> > > > > > Gaurav Garg
>>
>> > > > > >
>>
>> > > > > >
>>
>> > > > >
>>
>> > > >
>>
>> > >
>>
>>
>>
>> > _______________________________________________
>>
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>>
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>>
>>
>
>



-- 
-- 
Joshua Henk Balsters, PhD
Visiting Research Fellow

Trinity College Institute of Neuroscience
Lloyd Building
Trinity College Dublin
Dublin 2
Ireland

Tel: +353 1 896 1504
http://people.tcd.ie/balsterj