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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Dear Elena,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">A late follow-up to Jens’ reply regarding the greenish colors outside the brain. I think it simply has to do with you
colormap settings. Zero-values will be green according to the colormap of your first plot, but black according to the colormap of your second plot. See also
<a href="http://www.fieldtriptoolbox.org/development/tutorial/plotting">http://www.fieldtriptoolbox.org/development/tutorial/plotting</a> (search for ‘colormap’).<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Stan<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext"> fieldtrip-bounces@science.ru.nl
[mailto:fieldtrip-bounces@science.ru.nl] <b>On Behalf Of </b>"Jens Klinzing, Uni Tübingen"<br>
<b>Sent:</b> woensdag 25 januari 2017 10:29<br>
<b>To:</b> FieldTrip discussion list <fieldtrip@science.ru.nl><br>
<b>Subject:</b> Re: [FieldTrip] EEG source reconstruction using DICS method<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear Elena,<br>
I'm glad the first problem is solved. <br>
<br>
About the second one: Are you referring to the yellowish background outside of the brain? My first guess would be that this is a mere plotting issue. Can you check whether there actually are non-NAN or even non-zero values for grid points marked as 'outside'
(before interpolation and before and after contrasting)? If not, you know it is a problem with the plotting.<br>
<br>
Best,<br>
Jens<br>
<br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal" style="vertical-align:middle"><a href="mailto:krugliakova.es@gmail.com">Elena Krugliakova</a><o:p></o:p></p>
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<span style="color:#909AA4">Donnerstag, 19. Januar 2017 13:55</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4">Dear Jens,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">Thank you for your answer!<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">1. Indeed, I found where ft_sourceanalysis starts to recompute transfer matrix and just loaded precomputed headmodel and sensors. Now everything is fine, and it takes several seconds to run ft_sourceanalysis.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4">2. About homogeneous "noise outside the mri scan".
<br>
Noise appears after I calculate difference between two sources, following tutorial
<a href="http://www.fieldtriptoolbox.org/tutorial/beamformer">http://www.fieldtriptoolbox.org/tutorial/beamformer</a>. However, sourceplot for not-contrasted conditions looks good. Maybe you could give me an advice, how to get rid of this background noise.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">Kind Regards,<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4">Elena<br>
<br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4"><br>
With difference calculation:<br>
<br>
cfg = [];<br>
cfg.elec = elec;<br>
cfg.headmodel = vol;<br>
cfg.grid = leadfield;<br>
cfg.keepleadfield = 'yes' <br>
cfg.projectnoise = 'yes';<br>
cfg.frequency = [10 15];<br>
cfg.method = 'dics';<br>
cfg.dics.projectnoise = 'yes';<br>
cfg.dics.lambda = '5%'; <br>
cfg.dics.keepfilter = 'yes';<br>
cfg.dics.realfilter = 'yes';<br>
sourcePNandBS = ft_sourceanalysis(cfg, freq_PNandBS);<br>
cfg.grid.filter = sourcePNandBS.avg.filter;<br>
sourcePN = ft_sourceanalysis(cfg, freq_PN_Post);<br>
sourceBS = ft_sourceanalysis(cfg, freq_BS_Post);<br>
<b>sourceDiff.avg.pow = (sourcePN.avg.pow - sourceBS.avg.pow) ./ sourceBS.avg.pow;</b><br>
<br>
cfg = [];<br>
cfg.parameter = 'avg.pow';<br>
sourceDiffInt = ft_sourceinterpolate(cfg, sourceDiff, mri);<br>
<br>
cfg = [];<br>
sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);<br>
<br>
cfg = [];<br>
cfg.method = 'ortho';<br>
cfg.funparameter = 'avg.pow';<br>
cfg.maskparameter = cfg.funparameter;<br>
cfg.opacitymap = 'rampup'; <br>
ft_sourceplot(cfg, sourceDiffIntNorm);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4"> figure<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4"><img border="0" width="332" height="249" style="width:3.4583in;height:2.5937in" id="_x0000_i1025" src="cid:image002.png@01D27D31.DFF635D0" alt="Inline images 1" name="image.png"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4"><br>
<br>
<br>
<br>
Without difference calculation:<br>
<br>
cfg = [];<br>
cfg.elec = elec;<br>
.......... <br>
sourcePNandBS = ft_sourceanalysis(cfg, freq_PNandBS);<br>
<br>
cfg.grid.filter = sourcePNandBS.avg.filter;<br>
<br>
sourcePN = ft_sourceanalysis(cfg, freq_PN_Post);<br>
sourcePN.avg.pow = sourcePN.avg.pow ./ sourcePN.avg.noise;<br>
<br>
cfg = [];<br>
cfg.parameter = 'avg.pow';<br>
sourcePN = ft_sourceinterpolate(cfg, sourcePN, mri);<br>
<br>
cfg = [];<br>
sourcePNIntNorm = ft_volumenormalise(cfg, sourcePNInt);<br>
<br>
cfg = [];<br>
cfg.method = 'ortho';<br>
cfg.funparameter = 'avg.pow';<br>
cfg.maskparameter = cfg.funparameter;<br>
cfg.opacitymap = 'rampup'; <br>
ft_sourceplot(cfg, sourcePNIntNorm);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">figure<br>
<img border="0" width="381" height="286" style="width:3.9687in;height:2.9791in" id="_x0000_i1026" src="cid:image004.png@01D27D31.DFF635D0" alt="Inline images 2" name="image.png"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></span></p>
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<p class="MsoNormal" style="vertical-align:middle"><a href="mailto:jens.klinzing@uni-tuebingen.de">Jens Klinzing, Uni Tübingen</a><o:p></o:p></p>
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<span style="color:#909AA4">Donnerstag, 19. Januar 2017 10:09</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4">Dear Elena,<br>
<br>
Question 1:<br>
I assume the reason it takes so long is that you are using a FEM-based headmodel. For FEM, ft_sourceanalysis computes a huge transfer matrix on-the-fly (by calling prepare_headmodel - ft_prepare_vol_sens - sb_transfer) every time you do a source reconstruction.
For more information see <a href="http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=1967">
http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=1967</a> .<br>
<br>
You can circumvent the issue by computing the transfer matrix beforehand and changing the code in a way that it doesnt compute a new transfer matrix if you have already provided one.
<br>
<br>
Alternatively you could use a BEM headmodel (dipoli if possible since bemcp seems to have issues
<a href="http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2817">http://bugzilla.fieldtriptoolbox.org/show_bug.cgi?id=2817</a>).<br>
<br>
Question 2:<br>
Did you check your segmentation, the headmodel and the coregistration of electrodes/head every step of the way? If you fill all inside voxels with 1s and plot that, do you see an obvious shift/rotation of the "activity" in relation to the MRI?<br>
<br>
Best,<br>
Jens<o:p></o:p></span></p>
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<p class="MsoNormal" style="vertical-align:middle"><a href="mailto:krugliakova.es@gmail.com">Elena Krugliakova</a><o:p></o:p></p>
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<p class="MsoNormal" align="right" style="text-align:right;vertical-align:middle">
<span style="color:#909AA4">Montag, 9. Januar 2017 12:48</span><o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4">Dear Fieldtrip community,
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4">I have a question regarding source reconstruction using the 'dics' method applied to EEG data.
<br>
I have two problems: first, even with 32GB of RAM it takes 9 hours to call one ft_sourceanalysis. Maybe, there is a way to optimise the procedure somehow?
<br>
<br>
Second, at the end of analysis I obtain a very strange figure, on which I see activity localised outside the mri scan. Mistake on which step of analysis might cause this problem?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">As a template I used <a href="http://www.fieldtriptoolbox.org/tutorial/beamformer">
http://www.fieldtriptoolbox.org/tutorial/beamformer</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">Please, find my script below.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4"> <br>
Thank you in advance!<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">Kind Regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">Elena <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4">Script:<br>
<br>
% freqanalysis<br>
cfg = [];<br>
cfg.toilim = [-0.5 -0.1]; % prestimulus<br>
Pre = ft_redefinetrial(cfg, MyData);<br>
cfg = [];<br>
cfg.toilim = [0.9 1.3]; % poststimulus<br>
Post = ft_redefinetrial(cfg, MyData);<br>
cfg = [];<br>
dataAll = ft_appenddata([], Pre, Post);<br>
<br>
cfg = [];<br>
cfg.method = 'mtmfft';<br>
cfg.output = 'powandcsd'<br>
cfg.keeptrials = 'no';<br>
cfg.taper = 'dpss';<br>
cfg.foi = 35;<br>
cfg.tapsmofrq = 4;<br>
<br>
freq_Pre = ft_freqanalysis(cfg, Pre);<br>
freq_Post = ft_freqanalysis(cfg, Post);<br>
freq_PrePost = ft_freqanalysis(cfg, dataAll);<br>
<br>
%% headmodel preparation --- with standard brain<br>
mri = ft_read_mri('Subject01.mri');<br>
cfg = [];<br>
cfg.dim = mri.dim;<br>
mri = ft_volumereslice(cfg,mri);<br>
<br>
cfg = [];<br>
cfg.output = {'gray','white','csf','skull','scalp'}<br>
segmentedmri = ft_volumesegment(cfg, mri);<br>
<br>
cfg = [];<br>
cfg.shift = 0.3;<br>
cfg.method = 'hexahedral';<br>
cfg.tissue = {'gray','white','csf','skull','scalp'}<br>
cfg.numvertices = [800, 800, 800, 400, 200];<br>
cfg.unit = segmentedmri.unit<br>
bndFEM = ft_prepare_mesh(cfg,segmentedmri);<br>
<br>
cfg = [];<br>
cfg.method ='simbio';<br>
cfg.conductivity = [0.33 0.14 1.79 0.01 0.43];<br>
vol_simbio_lowresol = ft_prepare_headmodel(cfg, bndFEM);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">%% loading aligned electrodes<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="color:#909AA4">load elec_aligned % 109 EEG electrodes<br>
<br>
%% leadfield preparation<br>
cfg = [];<br>
cfg.elec = elec_aligned;<br>
cfg.vol = vol_simbio_lowresol;<br>
cfg.channel = 'all';<br>
cfg.reducerank = 3; % 3 for eeg<br>
cfg.grid.unit = 'mm';<br>
cfg.grid.resolution = 10;<br>
leadfield_FEM_lowresol = ft_prepare_leadfield(cfg);<br>
<br>
%% sourceanalysis<br>
cfg = [];<br>
cfg.frequency = 35;<br>
cfg.vol = vol_simbio_lowresol;<br>
cfg.grid = leadfield_FEM_lowresol<br>
cfg.projectnoise = 'yes';<br>
cfg.method = 'dics';<br>
cfg.dics.projectnoise = 'yes';<br>
cfg.dics.lambda = '5%';<br>
cfg.dics.keepfilter = 'yes';<br>
cfg.dics.realfilter = 'yes';<br>
sourceAll = ft_sourceanalysis(cfg, freq_PrePost);<br>
cfg.grid.filter = sourceAll.avg.filter;<br>
<br>
sourcePre_con = ft_sourceanalysis(cfg, freq_Pre);<br>
<br>
sourcePost_con = ft_sourceanalysis(cfg, freq_Post);<br>
<br>
sourceDiff = sourcePost_con;<br>
sourceDiff.avg.pow = (sourcePost_con.avg.pow - sourcePre_con.avg.pow) ./ sourcePre_con.avg.pow;<br>
<br>
%% sourceplot<br>
cfg = [];<br>
cfg.downsample = 2;<br>
cfg.parameter = 'pow';<br>
sourceDiffInt = ft_sourceinterpolate(cfg, sourceDiff, mri);<br>
<br>
cfg = [];<br>
sourceDiffIntNorm = ft_volumenormalise(cfg, sourceDiffInt);<br>
<br>
cfg = [];<br>
cfg.method = 'glassbrain';<br>
cfg.funparameter = 'pow';<br>
cfg.maskparameter = cfg.funparameter;<br>
ft_sourceplot(cfg, sourceDiffIntNorm);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:#909AA4">_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></span></p>
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