<div dir="ltr">Hi <span style="font-size:12.8px">Saeed,</span><div><span style="font-size:12.8px">if the content of your triangulation connectivity matrices </span><span style="font-size:12.8px"><i>skinf, uterusf, </i></span><span style="font-size:12.8px"><i>uterinecontentf</i> is not made of integers you probably get the error you mentioned. Could this be the case?</span></div><div><span style="font-size:12.8px">Out of curiosity, are you doing fetal recordings?</span></div><div><span style="font-size:12.8px"><br></span></div><div><span style="font-size:12.8px">Cris</span></div><div><span style="font-size:12.8px"><br></span></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Jan 20, 2016 at 6:37 PM, saeed zahran <span dir="ltr"><<a href="mailto:saeedzahran@hotmail.com" target="_blank">saeedzahran@hotmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div dir="ltr">Dear Fieldtrip community,<br><br>I define the volume conductor as:<br><br>vol = [];<br>vol.bnd(1).pnt=skinpnt<br>vol.bnd(1).tri=skinf<br> <br> vol.bnd(2).pnt=uteruspnt<br> vol.bnd(2).tri=uterusf<br> <br> vol.bnd(3).pnt=uterinecontentpnt<br> vol.bnd(3).tri=uterinecontentf<br> <br> vol.cond = c;<br><br><br>But it result with the below error:<br><br>Subscript indices must either be real positive integers or logicals.<br><br>Error in triangle4pt (line 57)<br> sph_pnt = pnt([tri(jj,:) lv],:);<br><br>Error in ft_headmodel_bemcp (line 101)<br>vol = triangle4pt(vol);<br><br>Error in ft_prepare_headmodel (line 253)<br> vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);<br><br>Error in openmeeg_eeg_leadfield_example_me (line 91)<br>vol = ft_prepare_headmodel(cfg, vol);<br> <br><br>Thank you very much in advance for your help! <br><br>Best regards<br>Saeed Zahran<br><br><div>> From: <a href="mailto:fieldtrip-request@science.ru.nl" target="_blank">fieldtrip-request@science.ru.nl</a><br>> Subject: fieldtrip Digest, Vol 62, Issue 18<br>> To: <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>> Date: Wed, 20 Jan 2016 12:00:02 +0100<br>> <br>> Send fieldtrip mailing list submissions to<br>> <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>> <br>> To subscribe or unsubscribe via the World Wide Web, visit<br>> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>> or, via email, send a message with subject or body 'help' to<br>> <a href="mailto:fieldtrip-request@science.ru.nl" target="_blank">fieldtrip-request@science.ru.nl</a><br>> <br>> You can reach the person managing the list at<br>> <a href="mailto:fieldtrip-owner@science.ru.nl" target="_blank">fieldtrip-owner@science.ru.nl</a><br>> <br>> When replying, please edit your Subject line so it is more specific<br>> than "Re: Contents of fieldtrip digest..."<br>> <br>> <br>> Today's Topics:<br>> <br>> 1. Standard BEM or FEM models for use with 256-electrode EEG<br>> data recorded with EGI caps (Laith Hamid)<br>> 2. Re: Standard BEM or FEM models for use with 256-electrode EEG<br>> data recorded with EGI caps (Cristiano Micheli)<br>> 3. Standard BEM or FEM models for use with 256-electrode EEG<br>> data recorded with EGI caps (Laith Hamid)<br>> 4. Source Localisation (aishwarya selvaraj)<br>> 5. Re: Source Localisation (Hom?lle)<br>> 6. Re: plotting neighbours (victoria schroeder)<br>> 7. Re: Standard BEM or FEM models for use with 256-electrode EEG<br>> data recorded with EGI caps (Cristiano Micheli)<br>> 8. Re: Source Localisation (Munsif Jatoi)<br>> 9. problems with mri interpolation (Olga Sysoeva)<br>> <br>> <br>> ----------------------------------------------------------------------<br>> <br>> Message: 1<br>> Date: Tue, 19 Jan 2016 15:35:00 +0100<br>> From: Laith Hamid <<a href="mailto:lah@pedneuro.uni-kiel.de" target="_blank">lah@pedneuro.uni-kiel.de</a>><br>> To: <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>> Subject: [FieldTrip] Standard BEM or FEM models for use with<br>> 256-electrode EEG data recorded with EGI caps<br>> Message-ID: <<a href="mailto:0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de" target="_blank">0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de</a>><br>> Content-Type: text/plain; charset="us-ascii"<br>> <br>> <br>> <br>> Dear community, <br>> <br>> My name is Laith Hamid and I am working in the University Medical<br>> Complex of Schleswig-Holstein in Kiel on source analysis of epileptic<br>> spikes and seizures. Currently I am analysing an EEG data set that was<br>> recorded using a 256-channel EGI system and I wanted to ask whether you<br>> have a standard BEM or FEM head Subscript indices must either be real positive integers or logicals.<br><br>Error in triangle4pt (line 57)<br> sph_pnt = pnt([tri(jj,:) lv],:);<br><br>Error in ft_headmodel_bemcp (line 101)<br>vol = triangle4pt(vol);<br><br>Error in ft_prepare_headmodel (line 253)<br> vol = ft_headmodel_bemcp(geometry, 'conductivity', cfg.conductivity);<br><br>Error in openmeeg_eeg_leadfield_example_me (line 91)<br>vol = ft_prepare_headmodel(cfg, vol);<br> model that extends enough downwards to<br>> accomodate all 256 electrodes. The current standard BEM model in the<br>> template folder of Fieldtrip isn't appropriate for source analysis of<br>> 256-channel EGI data. <br>> <br>> Thank you very much in advance for your help! <br>> <br>> Best, <br>> <br>> Laith <br>> <br>> <br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/f8805c11/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> Message: 2<br>> Date: Tue, 19 Jan 2016 16:16:54 +0100<br>> From: Cristiano Micheli <<a href="mailto:michelic72@gmail.com" target="_blank">michelic72@gmail.com</a>><br>> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>> Subject: Re: [FieldTrip] Standard BEM or FEM models for use with<br>> 256-electrode EEG data recorded with EGI caps<br>> Message-ID:<br>> <<a href="mailto:CADW7XCCywrPeWqGTqfP6jWoeLuvBo52poPfRyAPy9__VvkbDLg@mail.gmail.com" target="_blank">CADW7XCCywrPeWqGTqfP6jWoeLuvBo52poPfRyAPy9__VvkbDLg@mail.gmail.com</a>><br>> Content-Type: text/plain; charset="utf-8"<br>> <br>> Dear Laith,<br>> <br>> thanks for your question. You could refer to a factory schematic layout<br>> such as the one in figure 4 of this publication:<br>> <a href="http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract" target="_blank">http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract</a><br>> <br>> and subsequently use the function ft_prepare_layout to manually track the<br>> points of the custom design on your own (if you dont want to wait for<br>> somebody from the FT to do the same for you).<br>> <br>> cfg = [];<br>> cfg.image = 'figure4_layout_256_Frontiers.png';<br>> lay = ft_prepare_layout(cfg);<br>> <br>> The following tutorial describes the procedure in more details:<br>> <a href="http://www.fieldtriptoolbox.org/tutorial/layout" target="_blank">http://www.fieldtriptoolbox.org/tutorial/layout</a><br>> <br>> Please do not hesitate to get in touch with me for this and other matters.<br>> <br>> All the best<br>> Cris Micheli<br>> <br>> <br>> <br>> <br>> On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid <<a href="mailto:lah@pedneuro.uni-kiel.de" target="_blank">lah@pedneuro.uni-kiel.de</a>><br>> wrote:<br>> <br>> > Dear community,<br>> ><br>> > My name is Laith Hamid and I am working in the University Medical Complex<br>> > of Schleswig-Holstein in Kiel on source analysis of epileptic spikes and<br>> > seizures. Currently I am analysing an EEG data set that was recorded using<br>> > a 256-channel EGI system and I wanted to ask whether you have a standard<br>> > BEM or FEM head model that extends enough downwards to accomodate all 256<br>> > electrodes. The current standard BEM model in the template folder of<br>> > Fieldtrip isn't appropriate for source analysis of 256-channel EGI data.<br>> ><br>> > Thank you very much in advance for your help!<br>> ><br>> > Best,<br>> ><br>> > Laith<br>> ><br>> ><br>> ><br>> ><br>> > _______________________________________________<br>> > fieldtrip mailing list<br>> > <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">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>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/659988fa/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> Message: 3<br>> Date: Tue, 19 Jan 2016 17:41:48 +0100<br>> From: Laith Hamid <<a href="mailto:lah@pedneuro.uni-kiel.de" target="_blank">lah@pedneuro.uni-kiel.de</a>><br>> To: Fieldtrip <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>> Subject: [FieldTrip] Standard BEM or FEM models for use with<br>> 256-electrode EEG data recorded with EGI caps<br>> Message-ID: <<a href="mailto:61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de" target="_blank">61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de</a>><br>> Content-Type: text/plain; charset="us-ascii"<br>> <br>> <br>> <br>> Dear Cris,<br>> <br>> thank you very much for your answer. I am refering to an issue that was<br>> discussed in this thread from April 2013: <br>> <br>> [FieldTrip] source analysis EEG data without MRI <br>> <br>> The thread however does not offer a segmentation or head model for<br>> download. Some electrodes in the EGI 256-electrodes cap are placed on<br>> the cheeks or on the back of the neck and these areas are not modeled by<br>> the standard BEM skin compartment in the standard BEM model. My question<br>> was about a standard segmentation that extends the skin (and skull)<br>> compartment downwards to allow these electrodes to sit on the nodes of<br>> the skin mesh.<br>> <br>> Best,<br>> Laith <br>> <br>> <br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/49665b0c/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> Message: 4<br>> Date: Tue, 19 Jan 2016 16:52:55 +0000<br>> From: aishwarya selvaraj <<a href="mailto:aishwaryaselvaraj1708@gmail.com" target="_blank">aishwaryaselvaraj1708@gmail.com</a>><br>> To: "fieldtrip, donders" <<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a>><br>> Subject: [FieldTrip] Source Localisation<br>> Message-ID: <<a href="mailto:3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl" target="_blank">3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl</a>><br>> Content-Type: text/plain; charset="us-ascii"<br>> <br>> Hi guys,<br>> I'm currently working on source localization of EEG signals .<br>> Im very new to it .<br>> <br>> <br>> Can Anyone provide any inputs ??<br>> It would be of great help .<br>> <br>> --<br>> Regards,<br>> Aishwarya<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/3459ed12/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> Message: 5<br>> Date: Tue, 19 Jan 2016 17:06:13 +0000<br>> From: Hom?lle, S. (Simon) <<a href="mailto:S.Homolle@donders.ru.nl" target="_blank">S.Homolle@donders.ru.nl</a>><br>> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>> Subject: Re: [FieldTrip] Source Localisation<br>> Message-ID:<br>> <<a href="mailto:2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl" target="_blank">2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl</a>><br>> Content-Type: text/plain; charset="iso-8859-1"<br>> <br>> Dear Aishwarya,<br>> <br>> Under <a href="http://www.fieldtriptoolbox.org/tutorial" target="_blank">http://www.fieldtriptoolbox.org/tutorial</a> there are several tutorials about source reconstruction.<br>> <br>> My recommended start would be:<br>> <a href="http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem" target="_blank">http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem</a><br>> <a href="http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate" target="_blank">http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate</a><br>> <br>> <br>> Hopefully this provides you good start working with EEG source reconstruction<br>> <br>> Best regards,<br>> <br>> Simon Hom?lle<br>> PhD Candidate<br>> Donders Institute for Brain, Cognition and Behaviour<br>> Centre for Cognitive Neuroimaging<br>> Radboud University Nijmegen<br>> Phone: +31-(0)24-36-65059<br>> ________________________________<br>> From: <a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a> [<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>] on behalf of aishwarya selvaraj [<a href="mailto:aishwaryaselvaraj1708@gmail.com" target="_blank">aishwaryaselvaraj1708@gmail.com</a>]<br>> Sent: Tuesday, January 19, 2016 5:52 PM<br>> To: fieldtrip, donders<br>> Subject: [FieldTrip] Source Localisation<br>> <br>> Hi guys,<br>> I'm currently working on source localization of EEG signals .<br>> Im very new to it .<br>> <br>> <br>> Can Anyone provide any inputs ??<br>> It would be of great help .<br>> <br>> --<br>> Regards,<br>> Aishwarya<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/d2425227/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> Message: 6<br>> Date: Tue, 19 Jan 2016 17:49:21 +0000<br>> From: victoria schroeder <<a href="mailto:vic.schroeder2@gmail.com" target="_blank">vic.schroeder2@gmail.com</a>><br>> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>> Subject: Re: [FieldTrip] plotting neighbours<br>> Message-ID:<br>> <CAOWWpozcLgcLNqgF4rMrTRZ_=<a href="mailto:e8cYCvXgeY5ZJYXx_9YmWnJ_w@mail.gmail.com" target="_blank">e8cYCvXgeY5ZJYXx_9YmWnJ_w@mail.gmail.com</a>><br>> Content-Type: text/plain; charset="utf-8"<br>> <br>> Thank you very much Philipp and Tzvetan!<br>> <br>> Things have become much clearer now.<br>> <br>> I would like to follow up with a very related question. I am trying to<br>> replicate the analysis for the cluster based permutation test using the<br>> code and the data provided. However, i run into two problems here<br>> <br>> First, i get the following error if i use the original code:<br>> Attempted to access cfg.frequency(2); index out of bounds because<br>> numel(cfg.frequency)=1.<br>> <br>> Error in ft_freqstatistics (line 187)<br>> cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)];<br>> <br>> Therefore , i change the input cfg.frequency=20 to cfg.frequency=[20 20].<br>> However, then no significant clusters are found. Which becomes clear when<br>> trying to plot the cluster or by looking at the output of<br>> ft_freqstatistics.<br>> <br>> Does the change in the code , change the output? How can i avoid the error<br>> mentioned above and still get the same output from ft_freqstatistics as the<br>> one provided on the webpage?<br>> <br>> <br>> The relevant section of the toturial is provided below.<br>> Thank you!<br>> <br>> Victoria<br>> <br>> Permutation test<br>> <br>> Now, run *ft_freqstatistics<br>> <<a href="http://www.fieldtriptoolbox.org/reference/ft_freqstatistics" target="_blank">http://www.fieldtriptoolbox.org/reference/ft_freqstatistics</a>>* to compare<br>> freqFIC_planar_cmb and freqFC_planar_cmb. Except for the field cfg.latency,<br>> the following configuration is identical to the configuration that was used<br>> for comparing event-related averages in the cluster-based permutation tests<br>> on event related fields tutorial<br>> <<a href="http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock" target="_blank">http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock</a>>.<br>> Also see this tutorial<br>> <<a href="http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock" target="_blank">http://www.fieldtriptoolbox.org/tutorial/cluster_permutation_timelock</a>> for<br>> a detailed explanation of all the configuration settings. You can read more<br>> about the *ft_prepare_neighbours<br>> <<a href="http://www.fieldtriptoolbox.org/reference/ft_prepare_neighbours" target="_blank">http://www.fieldtriptoolbox.org/reference/ft_prepare_neighbours</a>>* function<br>> in the FAQ's<br>> <<a href="http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work" target="_blank">http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work</a>>.<br>> <br>> To load the planar gradient TFRs (also available on the FieldTrip FTP<br>> servers,freqFIC_planar_cmb.mat<br>> <<a href="ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat" target="_blank">ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFIC_planar_cmb.mat</a>><br>> and freqFC_planar_cmb.mat<br>> <<a href="ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat" target="_blank">ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat</a>>),<br>> use:<br>> <br>> load freqFIC_planar_cmb<br>> load freqFC_planar_cmb<br>> <br>> cfg = [];<br>> cfg.channel = {'MEG', '-MLP31', '-MLO12'};<br>> cfg.latency = 'all';<br>> cfg.frequency = 20;<br>> cfg.method = 'montecarlo';<br>> cfg.statistic = 'ft_statfun_indepsamplesT';<br>> cfg.correctm = 'cluster';<br>> cfg.clusteralpha = 0.05;<br>> cfg.clusterstatistic = 'maxsum';<br>> cfg.minnbchan = 2;<br>> cfg.tail = 0;<br>> cfg.clustertail = 0;<br>> cfg.alpha = 0.025;<br>> cfg.numrandomization = 500;<br>> % prepare_neighbours determines what sensors may form clusters<br>> cfg_neighb.method = 'distance';<br>> cfg.neighbours = ft_prepare_neighbours(cfg_neighb, dataFC);<br>> <br>> design = zeros(1,size(freqFIC_planar_cmb.powspctrm,1) +<br>> size(freqFC_planar_cmb.powspctrm,1));<br>> design(1,1:size(freqFIC_planar_cmb.powspctrm,1)) = 1;<br>> design(1,(size(freqFIC_planar_cmb.powspctrm,1)+1):(size(freqFIC_planar_cmb.powspctrm,1)+...<br>> size(freqFC_planar_cmb.powspctrm,1))) = 2;<br>> <br>> cfg.design = design;<br>> cfg.ivar = 1;<br>> <br>> [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb);<br>> <br>> <br>> <br>> 2016-01-18 17:57 GMT+00:00 Tzvetan Popov <<a href="mailto:tzvetan.popov@uni-konstanz.de" target="_blank">tzvetan.popov@uni-konstanz.de</a>>:<br>> <br>> ><br>> > Hi Victoria,<br>> ><br>> > oopsy, I think I confused you dramatically. I?m sorry for this. You are<br>> > right I was only scrolling up to the part where the mags were analyzed. As<br>> > for combining the MEG*2 and MEG*3 I was wrong there too. Of course you can<br>> > threat them separately, as I was naively thinking as non-neuormag user, but<br>> > indeed combination of both is recommended as I have now learned :-)(thanks<br>> > Phillip). I ran the following steps and I guess this should work for you.<br>> > best<br>> > tzvetan<br>> ><br>> > %%<br>> > cfg = [];<br>> > ComCon = ft_combineplanar(cfg,FreqCon);<br>> > %%<br>> > cfg = []<br>> > cfg.method = 'triangulation';<br>> > cfg.layout = 'neuromag306cmb.lay';<br>> > cfg.senstype = 'MEG';<br>> > neighbours = ft_prepare_neighbours(cfg, ComCon)<br>> > %%<br>> > % plot neighbours<br>> > cfg=[];<br>> > cfg.neighbours = neighbours;<br>> > cfg.layout = 'neuromag306cmb.lay';<br>> > ft_neighbourplot(cfg);<br>> ><br>> ><br>> ><br>> > _______________________________________________<br>> > fieldtrip mailing list<br>> > <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">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>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/de08d8f1/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> Message: 7<br>> Date: Tue, 19 Jan 2016 20:50:24 +0100<br>> From: Cristiano Micheli <<a href="mailto:michelic72@gmail.com" target="_blank">michelic72@gmail.com</a>><br>> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>> Subject: Re: [FieldTrip] Standard BEM or FEM models for use with<br>> 256-electrode EEG data recorded with EGI caps<br>> Message-ID:<br>> <CADW7XCC8BvdVKRAEMw4Jt8v3T6zXjF2zHF_T_4h8ZkuvTbc=<a href="mailto:1Q@mail.gmail.com" target="_blank">1Q@mail.gmail.com</a>><br>> Content-Type: text/plain; charset="utf-8"<br>> <br>> Dear Laith,<br>> <br>> this might be possible if you have the subject-specific MRI by following<br>> the tutorial here:<br>> <a href="http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem" target="_blank">http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem</a><br>> <br>> and using the function ft_prepare_mesh and the tutorial command:<br>> <br>> cfg=[];<br>> cfg.tissue={'brain','skull','scalp'};<br>> cfg.numvertices = [3000 2000 1000];<br>> bnd=ft_prepare_mesh(cfg,segmentedmri);<br>> <br>> <br>> which uses the segmented MRI (see tutorial). The bnd(3) variable should<br>> contain your triangulated surface with 1000 vertices. Let me know if that<br>> works. Of course you should see the skin and the neck in the original MRI.<br>> <br>> If you do not have an anatomical MRI that extends down to the chin you<br>> could try with a template, such as this:<br>> <a href="ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri" target="_blank">ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri</a><br>> and the corresponding segmented version<br>> <a href="ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat" target="_blank">ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat</a><br>> <br>> This goes down to the chin. Then you take care of rearranging the position<br>> of the EEG electrodes according to this:<br>> <br>> <a href="http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel" target="_blank">http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel</a><br>> <br>> I hope this helped<br>> Cris<br>> <br>> <br>> <br>> <br>> On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid <<a href="mailto:lah@pedneuro.uni-kiel.de" target="_blank">lah@pedneuro.uni-kiel.de</a>><br>> wrote:<br>> <br>> > Dear Cris,<br>> ><br>> > thank you very much for your answer. I am refering to an issue that was<br>> > discussed in this thread from April 2013:<br>> ><br>> ><br>> > [FieldTrip] source analysis EEG data without MRI<br>> ><br>> ><br>> > The thread however does not offer a segmentation or head model for<br>> > download. Some electrodes in the EGI 256-electrodes cap are placed on the<br>> > cheeks or on the back of the neck and these areas are not modeled by the<br>> > standard BEM skin compartment in the standard BEM model. My question was<br>> > about a standard segmentation that extends the skin (and skull) compartment<br>> > downwards to allow these electrodes to sit on the nodes of the skin mesh.<br>> ><br>> > Best,<br>> > Laith<br>> ><br>> ><br>> ><br>> ><br>> > _______________________________________________<br>> > fieldtrip mailing list<br>> > <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">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>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160119/0e42f0b5/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> Message: 8<br>> Date: Wed, 20 Jan 2016 12:17:12 +0800<br>> From: Munsif Jatoi <<a href="mailto:munsif.jatoi@gmail.com" target="_blank">munsif.jatoi@gmail.com</a>><br>> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a>><br>> Subject: Re: [FieldTrip] Source Localisation<br>> Message-ID:<br>> <CAHnJ=<a href="mailto:SUHe84yNDVnTLKhGdJBri0mvOdbU0rPqM-Z3-0Gv71Ycg@mail.gmail.com" target="_blank">SUHe84yNDVnTLKhGdJBri0mvOdbU0rPqM-Z3-0Gv71Ycg@mail.gmail.com</a>><br>> Content-Type: text/plain; charset="utf-8"<br>> <br>> Dear Aishwarya,<br>> <br>> Please refer to main help tutorials.<br>> <br>> Also, you can find out the survey papers written in this area. For more,<br>> SPM website can provide good help.<br>> <br>> Best,<br>> Munsif.<br>> <br>> On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) <<br>> <a href="mailto:S.Homolle@donders.ru.nl" target="_blank">S.Homolle@donders.ru.nl</a>> wrote:<br>> <br>> > Dear Aishwarya,<br>> ><br>> > Under <a href="http://www.fieldtriptoolbox.org/tutorial" target="_blank">http://www.fieldtriptoolbox.org/tutorial</a> there are several<br>> > tutorials about source reconstruction.<br>> ><br>> > My recommended start would be:<br>> > <a href="http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem" target="_blank">http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem</a><br>> > <a href="http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate" target="_blank">http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate</a><br>> ><br>> ><br>> > Hopefully this provides you good start working with EEG source<br>> > reconstruction<br>> ><br>> > Best regards,<br>> ><br>> > Simon Hom?lle<br>> > PhD Candidate<br>> > Donders Institute for Brain, Cognition and Behaviour<br>> > Centre for Cognitive Neuroimaging<br>> > Radboud University Nijmegen<br>> > Phone: +31-(0)24-36-65059<br>> > ------------------------------<br>> > *From:* <a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a> [<a href="mailto:fieldtrip-bounces@science.ru.nl" target="_blank">fieldtrip-bounces@science.ru.nl</a>]<br>> > on behalf of aishwarya selvaraj [<a href="mailto:aishwaryaselvaraj1708@gmail.com" target="_blank">aishwaryaselvaraj1708@gmail.com</a>]<br>> > *Sent:* Tuesday, January 19, 2016 5:52 PM<br>> > *To:* fieldtrip, donders<br>> > *Subject:* [FieldTrip] Source Localisation<br>> ><br>> > Hi guys,<br>> > I'm currently working on source localization of EEG signals .<br>> > Im very new to it .<br>> ><br>> ><br>> > Can Anyone provide any inputs ??<br>> > It would be of great help .<br>> ><br>> > --<br>> > Regards,<br>> > Aishwarya<br>> ><br>> > _______________________________________________<br>> > fieldtrip mailing list<br>> > <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">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>> -- <br>> Munsif Ali H.Jatoi,<br>> <br>> Ph D Scholar,<br>> Centre for Intelligent Signals and Imaging Research,<br>> Universiti Teknologi PETRONAS,<br>> Malaysia.<br>> <br>> <a href="http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en" target="_blank">http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en</a><br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/4f6391e8/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> Message: 9<br>> Date: Wed, 20 Jan 2016 13:36:16 +0300<br>> From: Olga Sysoeva <<a href="mailto:olga.v.sysoeva@gmail.com" target="_blank">olga.v.sysoeva@gmail.com</a>><br>> To: <a href="mailto:fieldtrip@science.ru.nl" target="_blank">fieldtrip@science.ru.nl</a><br>> Subject: [FieldTrip] problems with mri interpolation<br>> Message-ID:<br>> <<a href="mailto:CADtsnVcJLhrPPfq-P1Htj-RmfgzDDgqNhr8vsAoJ2mxxCV7seQ@mail.gmail.com" target="_blank">CADtsnVcJLhrPPfq-P1Htj-RmfgzDDgqNhr8vsAoJ2mxxCV7seQ@mail.gmail.com</a>><br>> Content-Type: text/plain; charset="utf-8"<br>> <br>> Dear Fieldtrippers,<br>> <br>> <br>> I'm encounter the problem with MRI interpolation and reslicing using<br>> <br>> FT_VOLUMERESLICE.<br>> <br>> I have read my MRI from fif.file and this mri variable contains<br>> <br>> mri_K0012.unit, 'm'<br>> <br>> mri_K0012.dim, [432, 512, 180]<br>> <br>> mri_K0012.anatomy, <432, 512, 180 int16><br>> <br>> mri_K0012.hdr, (1*1 structure)<br>> <br>> mri_K0012.transform, (4*4 double)<br>> <br>> mri_K0012.coordsys 'neuromag'.<br>> <br>> <br>> Than I used<br>> <br>> <br>> mri = ft_volumereslice([], mri);<br>> <br>> <br>> the output is<br>> <br>> <br>> ?the input is volume data with dimensions [432<br>> 512 180]<br>> <br>> reslicing from [432 512 180] to [256 256 256]<br>> <br>> the input is volume data with dimensions [256<br>> 256 256]<br>> <br>> the input is volume data with dimensions [432<br>> 512 180]<br>> <br>> selecting subvolume of 0.0%<br>> <br>> reslicing and interpolating anatomy<br>> <br>> interpolating<br>> <br>> ??? Attempted to access sel(1); index out of<br>> bounds because numel(sel)=0.<br>> <br>> <br>> Error in ==> ft_sourceinterpolate>my_interpn<br>> at 663<br>> <br>> ft_progress(sel(1)/num, 'interpolating<br>> %.1f%%\n', 100*sel(1)/num);<br>> <br>> <br>> Error in ==> ft_sourceinterpolate at 583<br>> <br>> av( sel) = my_interpn(fv, ax(sel),<br>> ay(sel), az(sel), cfg.interpmethod,<br>> <br>> cfg.feedback);<br>> <br>> <br>> Error in ==> ft_volumereslice at 176<br>> <br>> resliced = ft_sourceinterpolate(tmpcfg, mri,<br>> resliced);?<br>> <br>> <br>> I'm using matlab 7.6.0 (R2008a) and recently<br>> downloaded fieltrip (also in my previous version of 2013 the error<br>> was the same).<br>> <br>> <br>> I'd be thankful for the comments.<br>> <br>> <br>> Best Regards,<br>> <br>> Olga.<br>> <br>> P.S.Actually, I can project my sources<br>> meaningfully into not interpolated MRI, altoough the images are<br>> plotted upside down.<br>> -------------- next part --------------<br>> An HTML attachment was scrubbed...<br>> URL: <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20160120/653068d3/attachment-0001.html</a>><br>> <br>> ------------------------------<br>> <br>> _______________________________________________<br>> fieldtrip mailing list<br>> <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">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>> End of fieldtrip Digest, Vol 62, Issue 18<br>> *****************************************<br></div> </div></div>
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