<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On 21 November 2013 21:46, <span dir="ltr"><<a href="mailto:fieldtrip-request@science.ru.nl" target="_blank">fieldtrip-request@science.ru.nl</a>></span> wrote:<br>
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Today's Topics:<br>
<br>
1. Re: Motor beta activity - DICS solution more noisy than<br>
sensor data? (Eelke Spaak)<br>
2. Re: Motor beta activity - DICS solution more noisy than<br>
sensor data? (Cristiano Micheli)<br>
3. Re: Motor beta activity - DICS solution more noisy than<br>
sensor data? (Stan van Pelt)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 21 Nov 2013 18:27:43 +0100<br>
From: Eelke Spaak <<a href="mailto:eelke.spaak@donders.ru.nl">eelke.spaak@donders.ru.nl</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] Motor beta activity - DICS solution more<br>
noisy than sensor data?<br>
Message-ID:<br>
<CABPNLUr577Rq=<a href="mailto:zBvahNkAp9rO9LTRimRWR09GbeC3vfEv1sXHg@mail.gmail.com">zBvahNkAp9rO9LTRimRWR09GbeC3vfEv1sXHg@mail.gmail.com</a>><br>
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<br>
Thanks for the input Vit?ria. Are you using Fourier input to<br>
sourceanalysis, or 'powandcsd'? I'm wondering whether the csd computation<br>
inside sourceanalysis might be to blame. Will investigate this tomorrow :)<br>
<br>
Eelke<br>
On Nov 21, 2013 6:01 PM, "Vitoria Piai" <<a href="mailto:v.piai.research@gmail.com">v.piai.research@gmail.com</a>> wrote:<br>
<br>
> Hi all, Eelke,<br>
><br>
> Maybe adding to Eelke's remark, although I'm not working with motor beta<br>
> activity and lateralised index.<br>
> I'm also using DICS and my very clear, focal sensor-level effects all of a<br>
> sudden become localised to the whole brain or a whole hemisphere!<br>
> I happen to have heard from Jan-Mathijs that there may something going on<br>
> at the moment, but at least for now, Eelke, I don't think this error is<br>
> unique to our data (and I was actually going to post my incompatible<br>
> sensor-source results here soon, so now it's less work for me :)<br>
><br>
> Looking forward to hearing your updates,<br>
> (I'm interrupting my source-level analyses for the time to get a better<br>
> feeling for the sensor-level data first)<br>
> Vit?ria<br>
><br>
> On 21-11-2013 17:36, Eelke Spaak wrote:<br>
><br>
>> Fellow FieldTrippers,<br>
>><br>
>> Currently I am looking at a contrast for left- versus right-hand index<br>
>> finger button presses. As expected, on sensor level (combined planar<br>
>> gradient, grand average) I see a clear lateralisation in beta band<br>
>> power starting at least 0.5s before the button press (see<br>
>> <a href="https://db.tt/Rtch3Qjy" target="_blank">https://db.tt/Rtch3Qjy</a>). Both 'blobs' are significant; there is<br>
>> clearly more beta power ipsilateral to the response hand. I would<br>
>> prefer to do further analyses on source level, so I attempt to<br>
>> reconstruct the sources for this effect using DICS beamformer (common<br>
>> filter, applied to both conditions separately; fixedori and realfilter<br>
>> = 'yes'). The grand average results for this (again contrast left vs<br>
>> right response hand) are shown at <a href="https://db.tt/IBQZG0d8" target="_blank">https://db.tt/IBQZG0d8</a> . (Ignore the<br>
>> R/L-flip, this is radiological convention.)<br>
>><br>
>> As you can see, the source level solution is much more blurry than on<br>
>> sensor level. This picture is without using any regularisation (lambda<br>
>> parameter), the results are even worse when I use lambda = '5%'. The<br>
>> negative blob (right hand higher power than left) becomes 'marginally<br>
>> significant' on source level (p ~ 0.06) where it was p < 0.001 on<br>
>> sensor level. The positive blob is nowhere near significant. Also, the<br>
>> individual results are much less topographically consistent on source<br>
>> than on sensor level (explaining the worse statistics).<br>
>><br>
>> I have checked the segmentation of my MRIs, the 'gray' seems to be<br>
>> nicely within the head all the time. Also, I have manually verified<br>
>> the alignment of headmodel, sourcemodel, and gradiometer information<br>
>> for all subjects.<br>
>><br>
>> As a final note, the above sensor-level plot was taken from a 'slice'<br>
>> out of a planar-gradient time-frequency analysis (mtmconvol). The<br>
>> ingredient for the beamformer was an mtmfft fourier spectrum on the<br>
>> axial gradiometer data, obtained for just the time-frequency range of<br>
>> interest (subselect toilim [-0.5 0], mtmfft foi = 23, tapsmofrq = 7).<br>
>> When I compute condition-averaged power based on these fourier spectra<br>
>> and look at the contrast, the results are again as expected:<br>
>> <a href="https://db.tt/n2P3UKcQ" target="_blank">https://db.tt/n2P3UKcQ</a> (of course less localised because of axial<br>
>> gradient vs planar). The freq structures underlying this contrast are<br>
>> exactly the same as those going into ft_sourceanalysis, so the problem<br>
>> must be in the source analysis step (and/or in the preparation of the<br>
>> geometric information, although these seem fine by visual inspection).<br>
>><br>
>> Does anyone have any idea that might explain these seemingly<br>
>> contradictory results? I would have expected demixing to improve<br>
>> signal-to-noise ratio, rather than worsen it.<br>
>><br>
>> Thanks!<br>
>> Best,<br>
>> Eelke<br>
>> _______________________________________________<br>
>> fieldtrip mailing list<br>
>> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
>> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
>><br>
><br>
><br>
> --<br>
> Vit?ria Piai<br>
> PhD Candidate<br>
> Donders Institute for Brain, Cognition and Behaviour<br>
> Centre for Cognition, Radboud University Nijmegen<br>
> Montessorilaan 3, B.01.05<br>
> 6525 HR Nijmegen<br>
> The Netherlands<br>
><br>
> Email : <a href="mailto:V.piai@donders.ru.nl">V.piai@donders.ru.nl</a><br>
> Phone : <a href="tel:%2B31%2024%203612635" value="+31243612635">+31 24 3612635</a><br>
> <a href="http://www.vitoriapiai.com" target="_blank">www.vitoriapiai.com</a><br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><br>
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Message: 2<br>
Date: Thu, 21 Nov 2013 13:39:30 -0500<br>
From: Cristiano Micheli <<a href="mailto:michelic72@gmail.com">michelic72@gmail.com</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] Motor beta activity - DICS solution more<br>
noisy than sensor data?<br>
Message-ID:<br>
<<a href="mailto:CADW7XCCf9aAPYFTF9iCuMnRgYHA6hhoPBbex0ihkJNB_b3ah5Q@mail.gmail.com">CADW7XCCf9aAPYFTF9iCuMnRgYHA6hhoPBbex0ihkJNB_b3ah5Q@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Dear Eelke, very interesting topic. Please find my two cents below:<br>
<br>
<br>
On Thu, Nov 21, 2013 at 11:36 AM, Eelke Spaak <<a href="mailto:eelke.spaak@donders.ru.nl">eelke.spaak@donders.ru.nl</a>>wrote:<br>
<br>
> Fellow FieldTrippers,<br>
><br>
> Currently I am looking at a contrast for left- versus right-hand index<br>
> finger button presses. As expected, on sensor level (combined planar<br>
> gradient, grand average) I see a clear lateralisation in beta band<br>
> power starting at least 0.5s before the button press (see<br>
> <a href="https://db.tt/Rtch3Qjy" target="_blank">https://db.tt/Rtch3Qjy</a>). Both 'blobs' are significant; there is<br>
> clearly more beta power ipsilateral to the response hand. I would<br>
> prefer to do further analyses on source level, so I attempt to<br>
> reconstruct the sources for this effect using DICS beamformer (common<br>
> filter, applied to both conditions separately; fixedori and realfilter<br>
> = 'yes'). The grand average results for this (again contrast left vs<br>
> right response hand) are shown at <a href="https://db.tt/IBQZG0d8" target="_blank">https://db.tt/IBQZG0d8</a> . (Ignore the<br>
> R/L-flip, this is radiological convention.)<br>
><br>
<br>
<br>
There might be issues with:<br>
- head positions/distance of single subjects in the dewar<br>
- something happening in the transition axial -> planar gradiometers<br>
conversion<br>
- orientation of the brain motor sources<br>
- inverse problem reconstruction<br>
- magnitude of the power effects for the different subjects<br>
- forward model issues<br>
<br>
Let me comment briefly on point 4. If the sources in the motor cortex are<br>
bilateral (as expected to different extents from ipsi to contra) and are<br>
temporally correlated, this constitutes an issue for the beamformer<br>
algorithm (van Veen et al.1993) especially if the sources are near (and<br>
lead fields highly correlated).<br>
There are workarounds to localize the single contributions of<br>
primary/secondary motor sources, but this implies the use of regional<br>
suppression (a nulling beamformer) and it is a tedious procedure to apply.<br>
Might be worth to look into that though. Let me know if you have interest<br>
in this.<br>
<br>
<br>
<br>
> As you can see, the source level solution is much more blurry than on<br>
> sensor level. This picture is without using any regularisation (lambda<br>
> parameter), the results are even worse when I use lambda = '5%'. The<br>
> negative blob (right hand higher power than left) becomes 'marginally<br>
> significant' on source level (p ~ 0.06) where it was p < 0.001 on<br>
> sensor level. The positive blob is nowhere near significant. Also, the<br>
> individual results are much less topographically consistent on source<br>
> than on sensor level (explaining the worse statistics).<br>
><br>
<br>
On this point: using regularization is useful to invert the real(csd)<br>
matrix if it is ill-conditioned, but might blur the source reconstruction.<br>
On the other hand not using it might also be detrimental on the source<br>
reconstruction. Therefore applying it depends on the condition number of<br>
your csd. Is the matrix full rank? If not you might consider regularizing.<br>
Did you previously use ICA/PCA to get rid of artifacts? If yes that will<br>
have a negative effect on the condition number. and you might consider<br>
cranking down the ICA components rejection to the big spiky components -if<br>
any- and let the beamformer filter reject the smaller ones (in magnitude).<br>
Are you using cluster statistics based on the maxval? Maybe another<br>
statistics might give different results, given that the maxval might be due<br>
to artifacts (muscular, heart, ...)<br>
<br>
<br>
> I have checked the segmentation of my MRIs, the 'gray' seems to be<br>
> nicely within the head all the time. Also, I have manually verified<br>
> the alignment of headmodel, sourcemodel, and gradiometer information<br>
> for all subjects.<br>
><br>
<br>
Do all subjects sit with the top of the head at the same distance from the<br>
dewar? This is easily visualized by plotting the headmodel together with<br>
the head coordinates' sensors.<br>
By experience with CTF systems not all subjects' heads are at the same<br>
distance from the top (because they slip down, or they reposition 'cause<br>
they can't see out of the dewar, they also move!). This might hinder the<br>
SNR of the raw data to start with.<br>
It seems the grand average is still significant, but might be due to the<br>
contribution of a few good subjects.<br>
You may also want to consider the movement correction GLM method at the<br>
source level. Maybe it gives you back some SNR.<br>
<br>
<br>
> As a final note, the above sensor-level plot was taken from a 'slice'<br>
> out of a planar-gradient time-frequency analysis (mtmconvol). The<br>
> ingredient for the beamformer was an mtmfft fourier spectrum on the<br>
> axial gradiometer data, obtained for just the time-frequency range of<br>
> interest (subselect toilim [-0.5 0], mtmfft foi = 23, tapsmofrq = 7).<br>
> When I compute condition-averaged power based on these fourier spectra<br>
> and look at the contrast, the results are again as expected:<br>
> <a href="https://db.tt/n2P3UKcQ" target="_blank">https://db.tt/n2P3UKcQ</a> (of course less localised because of axial<br>
> gradient vs planar). The freq structures underlying this contrast are<br>
> exactly the same as those going into ft_sourceanalysis, so the problem<br>
> must be in the source analysis step (and/or in the preparation of the<br>
> geometric information, although these seem fine by visual inspection).<br>
><br>
> Does anyone have any idea that might explain these seemingly<br>
> contradictory results? I would have expected demixing to improve<br>
> signal-to-noise ratio, rather than worsen it.<br>
><br>
<br>
Yes, but it can also depend on different extents from FFT-level analysis.<br>
Have you played around with spectral smoothing, by for example lowering the<br>
number of tapers, or changing to a single condition contrast like<br>
activation vs baseline in the beamformer?<br>
What is the grand average vs single subject lateralization effect/single<br>
condition effect/ planar or axial effect? Is it there for all single<br>
subjects?<br>
<br>
I hope the comments helped a bit.<br>
<br>
All the best!<br>
Cristiano<br>
<br>
<br>
><br>
> Thanks!<br>
> Best,<br>
> Eelke<br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
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Message: 3<br>
Date: Thu, 21 Nov 2013 21:45:49 +0100 (CET)<br>
From: Stan van Pelt <<a href="mailto:stan.vanpelt@fcdonders.ru.nl">stan.vanpelt@fcdonders.ru.nl</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] Motor beta activity - DICS solution more<br>
noisy than sensor data?<br>
Message-ID:<br>
<<a href="mailto:513733919.261511.1385066749005.JavaMail.root@indus.zimbra.ru.nl">513733919.261511.1385066749005.JavaMail.root@indus.zimbra.ru.nl</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Eelke, Have you tried comparing the results with a time-domain beamformer? You could e.g. try LCMV on 15-25Hz-bandpassed data. This should give you in theory similar results. Best, Stan ----- Oorspronkelijk bericht -----<br>
> Van: "Eelke Spaak" <<a href="mailto:eelke.spaak@donders.ru.nl">eelke.spaak@donders.ru.nl</a>><br>
> Aan: "FieldTrip discussion list" <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
> Verzonden: Donderdag 21 november 2013 18:27:43<br>
> Onderwerp: Re: [FieldTrip] Motor beta activity - DICS solution more<br>
> noisy than sensor data?<br>
> Thanks for the input Vit?ria. Are you using Fourier input to<br>
> sourceanalysis, or 'powandcsd'? I'm wondering whether the csd<br>
> computation inside sourceanalysis might be to blame. Will investigate<br>
> this tomorrow :)<br>
> Eelke<br>
> On Nov 21, 2013 6:01 PM, "Vitoria Piai" < <a href="mailto:v.piai.research@gmail.com">v.piai.research@gmail.com</a> ><br>
> wrote:<br>
> > Hi all, Eelke,<br>
> > Maybe adding to Eelke's remark, although I'm not working with motor<br>
> > beta activity and lateralised index.<br>
> > I'm also using DICS and my very clear, focal sensor-level effects<br>
> > all<br>
> > of a sudden become localised to the whole brain or a whole<br>
> > hemisphere!<br>
> > I happen to have heard from Jan-Mathijs that there may something<br>
> > going<br>
> > on at the moment, but at least for now, Eelke, I don't think this<br>
> > error is unique to our data (and I was actually going to post my<br>
> > incompatible sensor-source results here soon, so now it's less work<br>
> > for me :)<br>
> > Looking forward to hearing your updates,<br>
> > (I'm interrupting my source-level analyses for the time to get a<br>
> > better feeling for the sensor-level data first)<br>
> > Vit?ria<br>
> > On 21-11-2013 17:36, Eelke Spaak wrote:<br>
> > > Fellow FieldTrippers,<br>
> > > Currently I am looking at a contrast for left- versus right-hand<br>
> > > index<br>
> > > finger button presses. As expected, on sensor level (combined<br>
> > > planar<br>
> > > gradient, grand average) I see a clear lateralisation in beta band<br>
> > > power starting at least 0.5s before the button press (see<br>
> > > <a href="https://db.tt/Rtch3Qjy" target="_blank">https://db.tt/Rtch3Qjy</a> ). Both 'blobs' are significant; there is<br>
> > > clearly more beta power ipsilateral to the response hand. I would<br>
> > > prefer to do further analyses on source level, so I attempt to<br>
> > > reconstruct the sources for this effect using DICS beamformer<br>
> > > (common<br>
> > > filter, applied to both conditions separately; fixedori and<br>
> > > realfilter<br>
> > > = 'yes'). The grand average results for this (again contrast left<br>
> > > vs<br>
> > > right response hand) are shown at <a href="https://db.tt/IBQZG0d8" target="_blank">https://db.tt/IBQZG0d8</a> . (Ignore<br>
> > > the<br>
> > > R/L-flip, this is radiological convention.)<br>
> > > As you can see, the source level solution is much more blurry than<br>
> > > on<br>
> > > sensor level. This picture is without using any regularisation<br>
> > > (lambda<br>
> > > parameter), the results are even worse when I use lambda = '5%'.<br>
> > > The<br>
> > > negative blob (right hand higher power than left) becomes<br>
> > > 'marginally<br>
> > > significant' on source level (p ~ 0.06) where it was p < 0.001 on<br>
> > > sensor level. The positive blob is nowhere near significant. Also,<br>
> > > the<br>
> > > individual results are much less topographically consistent on<br>
> > > source<br>
> > > than on sensor level (explaining the worse statistics).<br>
> > > I have checked the segmentation of my MRIs, the 'gray' seems to be<br>
> > > nicely within the head all the time. Also, I have manually<br>
> > > verified<br>
> > > the alignment of headmodel, sourcemodel, and gradiometer<br>
> > > information<br>
> > > for all subjects.<br>
> > > As a final note, the above sensor-level plot was taken from a<br>
> > > 'slice'<br>
> > > out of a planar-gradient time-frequency analysis (mtmconvol). The<br>
> > > ingredient for the beamformer was an mtmfft fourier spectrum on<br>
> > > the<br>
> > > axial gradiometer data, obtained for just the time-frequency range<br>
> > > of<br>
> > > interest (subselect toilim [-0.5 0], mtmfft foi = 23, tapsmofrq =<br>
> > > 7).<br>
> > > When I compute condition-averaged power based on these fourier<br>
> > > spectra<br>
> > > and look at the contrast, the results are again as expected:<br>
> > > <a href="https://db.tt/n2P3UKcQ" target="_blank">https://db.tt/n2P3UKcQ</a> (of course less localised because of axial<br>
> > > gradient vs planar). The freq structures underlying this contrast<br>
> > > are<br>
> > > exactly the same as those going into ft_sourceanalysis, so the<br>
> > > problem<br>
> > > must be in the source analysis step (and/or in the preparation of<br>
> > > the<br>
> > > geometric information, although these seem fine by visual<br>
> > > inspection).<br>
> > > Does anyone have any idea that might explain these seemingly<br>
> > > contradictory results? I would have expected demixing to improve<br>
> > > signal-to-noise ratio, rather than worsen it.<br>
> > > Thanks!<br>
> > > Best,<br>
> > > Eelke<br>
> > > ______________________________ _________________<br>
> > > fieldtrip mailing list<br>
> > > <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> > > <a href="http://mailman.science.ru.nl/" target="_blank">http://mailman.science.ru.nl/</a> mailman/listinfo/fieldtrip<br>
> > --<br>
> > Vit?ria Piai<br>
> > PhD Candidate<br>
> > Donders Institute for Brain, Cognition and Behaviour<br>
> > Centre for Cognition, Radboud University Nijmegen<br>
> > Montessorilaan 3, B.01.05<br>
> > 6525 HR Nijmegen<br>
> > The Netherlands<br>
> > Email : <a href="mailto:V.piai@donders.ru.nl">V.piai@donders.ru.nl</a><br>
> > Phone : <a href="tel:%2B31%2024%203612635" value="+31243612635">+31 24 3612635</a><br>
> > <a href="http://www.vitoriapiai.com" target="_blank">www.vitoriapiai.com</a><br>
> > ______________________________ _________________<br>
> > fieldtrip mailing list<br>
> > <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> > <a href="http://mailman.science.ru.nl/" target="_blank">http://mailman.science.ru.nl/</a> mailman/listinfo/fieldtrip<br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
-- Stan van Pelt, PhD Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Montessorilaan 3, B.01.19 6525 HR Nijmegen tel: <a href="tel:024-3616288" value="+31243616288">024-3616288</a><br>
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End of fieldtrip Digest, Vol 36, Issue 34<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div><div><font face="arial, helvetica, sans-serif">Haiteng Jiang</font></div><div><font face="arial, helvetica, sans-serif">PhD candidate</font></div><div><font face="arial, helvetica, sans-serif">Neuronal Oscillations Group</font></div>
<div><font face="arial, helvetica, sans-serif">Donders Institute for Brain, Cognition and Behaviour</font></div><div><font face="arial, helvetica, sans-serif">Centre for Cognitive Neuroimaging</font></div><div><font face="arial, helvetica, sans-serif">Radboud University Nijmegen</font></div>
<div><span style="line-height:18px;background-color:rgb(255,255,255)"><font face="arial, helvetica, sans-serif"><br></font></span></div><div><span style="line-height:18px;background-color:rgb(255,255,255)"><font face="arial, helvetica, sans-serif">Visiting address</font></span></div>
<div><div style="text-align:left;background-color:rgb(255,255,255)"><div><span style="line-height:18px"><font face="arial, helvetica, sans-serif">Room 2.32</font></span></div><div><span style="line-height:18px"><font face="arial, helvetica, sans-serif">Donders Centre for Cognitive Neuroimaging</font></span></div>
<div><span style="line-height:18px"><font face="arial, helvetica, sans-serif">Kapittelweg 29</font></span></div><div><span style="line-height:18px"><font face="arial, helvetica, sans-serif">6525 EN Nijmegen</font></span></div>
<div><span style="line-height:18px"><font face="arial, helvetica, sans-serif">the Netherlands</font></span></div><div><span style="line-height:18px"><font face="arial, helvetica, sans-serif"><br></font></span></div></div>
</div><div><font face="arial, helvetica, sans-serif"> Tel.: +31 (0)243668291</font></div></div><div><font face="arial, helvetica, sans-serif"> Web: <a href="https://sites.google.com/site/haitengjiang/" target="_blank">https://sites.google.com/site/haitengjiang/</a></font></div>
</div></div>