<div dir="ltr">Hi Mathias, <div><br></div><div>You can adjust the regularization parameter, "lamda", I think the default is zero. </div><div><br></div><div>Best, </div><div><br></div><div>Azeez</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Jun 24, 2016 at 8:58 AM, Dr.-Ing. Matthias Dümpelmann <span dir="ltr"><<a href="mailto:matthias.duempelmann@uniklinik-freiburg.de" target="_blank">matthias.duempelmann@uniklinik-freiburg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="DE" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif"">Dear Az,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">I defined now two intervals, one showing rhythmic seizure activity and one baseline interval prior to the seizure as you can see on the screenshot.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">Now it localizes as expected in the right temporal lobe.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">I only wonder about the very small “activation” volume.<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">Thank you,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">Matthias<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""><u></u> <u></u></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a> [mailto:<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>]
<b>Im Auftrag von </b>Azeez Adebimpe<br>
<b>Gesendet:</b> Thursday, June 23, 2016 3:57 PM<br>
<b>An:</b> FieldTrip discussion list<br>
<b>Betreff:</b> Re: [FieldTrip] Seizure localization problems<u></u><u></u></span></p>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Hi Mathias, <u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">DICS and LCMV can also give reasonable result but require some normalization. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Try to estimate to neural activity index as explained in this tutorial.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="http://www.fieldtriptoolbox.org/tutorial/beamformer" target="_blank">http://www.fieldtriptoolbox.org/tutorial/beamformer</a> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Best,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Az<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Thu, Jun 23, 2016 at 2:51 PM, Dr.-Ing. Matthias Dümpelmann <<a href="mailto:matthias.duempelmann@uniklinik-freiburg.de" target="_blank">matthias.duempelmann@uniklinik-freiburg.de</a>> wrote:<u></u><u></u></p>
<div>
<div>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">Dear Azeez,</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">thank you for your suggestion.</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">Just exchanging
</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal" style="text-autospace:none">
<span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:forestgreen">cfg.method = 'dics';</span><u></u><u></u></p>
<p class="MsoNormal" style="text-autospace:none">
<span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><u></u><u></u></p>
<p class="MsoNormal" style="text-autospace:none">
<span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">to</span><u></u><u></u></p>
<p class="MsoNormal" style="text-autospace:none">
<span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black"> </span><u></u><u></u></p>
<p class="MsoNormal" style="text-autospace:none">
<span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">cfg.method =
</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:#a020f0">'eloreta'</span><span lang="EN-US" style="font-size:10.0pt;font-family:"Courier New";color:black">;</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">resulted in a reasonable solution (see attachment).</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">I also get useful results using MUIC or sLORETA in the frequency domain as the methods are implemented
in ASA.</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">This makes me even more suspicious, what is going wrong with the DICS algorithm.</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">Best regards,</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif"">Matthias</span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Arial","sans-serif""> </span><u></u><u></u></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a> [mailto:<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>]
<b>Im Auftrag von </b>Azeez Adebimpe<br>
<b>Gesendet:</b> Thursday, June 23, 2016 11:08 AM<br>
<b>An:</b> FieldTrip discussion list<br>
<b>Cc:</b> Nino Epitashvili<br>
<b>Betreff:</b> Re: [FieldTrip] Seizure localization problems</span><u></u><u></u></p>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<p class="MsoNormal">Hi Mathias,<u></u><u></u></p>
<div>
<p class="MsoNormal">I will suggest you try other method like eLORETA or MNE first and compare the result.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Best,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">AZ<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
<div>
<p class="MsoNormal">On Thu, Jun 23, 2016 at 9:34 AM, Dr.-Ing. Matthias Dümpelmann <<a href="mailto:matthias.duempelmann@uniklinik-freiburg.de" target="_blank">matthias.duempelmann@uniklinik-freiburg.de</a>>
wrote:<u></u><u></u></p>
<p class="MsoNormal">Dear colleagues,<br>
<br>
we are trying to evaluate systematically the localization of rhythmic activity at the onset of epileptic seizures in patients, who are subsequently evaluated with intracranial recordings.<br>
<br>
We are trying to use DICS but quite often receive results, which are obviously wrong. In the attached screenshots you can see the peace of EEG, which is evaluated and the localization result with a maximum in the cerebellum.<br>
<br>
This a typical localization for the cases with obvious miss localizations. A further seizure with a similar EEG pattern was localized in the right temporal lobe, which matches the EEG pattern and also the intracranial findings.<br>
<br>
Head model is generated with ASA, also the electrodes file is in the ASA format. The geometrical match of source points, head model and electrodes is checked using ft_plot_.... methods.<br>
<br>
Here is the code sniplet relevant for the localization algorithm:<br>
<br>
% Analysis frequency<br>
SourceFrequency = 4.0<br>
<br>
% read eeg, electrodes and volume conductor model<br>
%[dat] = ft_read_data(filename);<br>
hdr = ft_read_header(filename);<br>
elec = ft_read_sens(elecfile, 'fileformat','asa_elc');<br>
headmodel = ft_read_vol(volumefilename,'fileformat','asa_vol');<br>
mri = ft_read_mri(mrifilename, 'fileformat','asa_mri');<br>
<br>
% eeg data preprocessing<br>
cfgeeg.dataset = filename;<br>
cfgeeg.continuous = 'yes'<br>
cfg.covariance = 'yes';<br>
cfg.covariancewindow = 'all';<br>
cfg.demean = 'yes'<br>
<br>
[data] = ft_preprocessing(cfgeeg);<br>
<br>
% Freqanalysis for beamformer<br>
cfg = [];<br>
cfg.channel = {'*'};<br>
cfg.method = 'mtmfft';<br>
cfg.foilim = [1 100];<br>
cfg.tapsmofrq = 4;<br>
cfg.taper = 'hanning';<br>
cfg.output = 'powandcsd';<br>
<br>
<br>
% for common filter over conditions<br>
powcsd_all = ft_freqanalysis(cfg, data);<br>
<br>
% Create leadfield grid<br>
cfg = [];<br>
cfg.channel = elec.label;<br>
cfg.elec = elec;<br>
cfg.headmodel = headmodel;<br>
cfg.dics.reducerank = 3; % default for MEG is 2, for EEG is 3<br>
cfg.grid.resolution = 0.5; % use a 3-D grid with a 0.5 cm resolution<br>
cfg.grid.unit = 'cm';<br>
cfg.grid.tight = 'yes';<br>
[grid] = ft_prepare_leadfield(cfg);<br>
<br>
% source analysis<br>
cfg = [];<br>
cfg.channel = elec.label;<br>
cfg.method = 'dics';<br>
cfg.frequency = SourceFrequency;<br>
cfg.grid = grid;<br>
cfg.headmodel = headmodel;<br>
cfg.elec = elec;<br>
cfg.senstype = 'EEG';<br>
cfg.dics.keepfilter = 'yes'; % We wish to use the calculated filter later on<br>
cfg.dics.projectnoise = 'yes';<br>
cfg.dics.lambda = '0.3%';<br>
source_raw = ft_sourceanalysis(cfg, powcsd_all);<br>
<br>
<br>
I played with a couple of parameters like cfg.dics.lambda, but without success.<br>
<br>
Do you have ideas how to improve our localization results ?<br>
<br>
Thank you,<br>
<br>
Matthias<br>
<br>
<br>
<br>
UNIVERSITÄTSKLINIKUM FREIBURG<br>
Epileptologie<br>
Breisacher Str. 64 · 79106 Freiburg<br>
Telefon: <a href="tel:%2B49%20761%20270-52410" target="_blank">+49 761 270-52410</a><br>
<a href="mailto:matthias.duempelmann@uniklinik-freiburg.de" target="_blank">matthias.duempelmann@uniklinik-freiburg.de</a><br>
<br>
<a href="http://www.uniklinik-freiburg.de" target="_blank">www.uniklinik-freiburg.de</a><br>
<br>
<br>
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<p class="MsoNormal"> <u></u><u></u></p>
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