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<div>Saeed,</div>
<div><br>
</div>
are you using 0 or 1 indexing for your triangles? You probably want to use 1 indexing.
<div><br>
</div>
<div>Best,</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
<div>
<div>On Jan 20, 2016, at 6:37 PM, saeed zahran <<a href="mailto:saeedzahran@hotmail.com">saeedzahran@hotmail.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div class="hmmessage" style="font-size: 12pt; font-family: Calibri; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<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!<span class="Apple-converted-space"> </span><br>
<br>
Best regards<br>
Saeed Zahran<br>
<br>
<div>> From:<span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a><br>
> Subject: fieldtrip Digest, Vol 62, Issue 18<br>
> To:<span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
> Date: Wed, 20 Jan 2016 12:00:02 +0100<br>
><span class="Apple-converted-space"> </span><br>
> Send fieldtrip mailing list submissions to<br>
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><span class="Apple-converted-space"> </span><br>
> To subscribe or unsubscribe via the World Wide Web, visit<br>
><span class="Apple-converted-space"> </span><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> or, via email, send a message with subject or body 'help' to<br>
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><span class="Apple-converted-space"> </span><br>
> You can reach the person managing the list at<br>
><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-owner@science.ru.nl">fieldtrip-owner@science.ru.nl</a><br>
><span class="Apple-converted-space"> </span><br>
> When replying, please edit your Subject line so it is more specific<br>
> than "Re: Contents of fieldtrip digest..."<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Today's Topics:<br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> ----------------------------------------------------------------------<br>
><span class="Apple-converted-space"> </span><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">lah@pedneuro.uni-kiel.de</a>><br>
> To:<span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@science.ru.nl">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">0c2e8c0fa08db25ba3bb87c130fe0d7f@mail.uni-kiel.de</a>><br>
> Content-Type: text/plain; charset="us-ascii"<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Dear community,<span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><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.<span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Thank you very much in advance for your help!<span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Best,<span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Laith<span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> -------------- next part --------------<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><br>
> Message: 2<br>
> Date: Tue, 19 Jan 2016 16:16:54 +0100<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] 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">CADW7XCCywrPeWqGTqfP6jWoeLuvBo52poPfRyAPy9__VvkbDLg@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><span class="Apple-converted-space"> </span><br>
> Dear Laith,<br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><a href="http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract">http://journal.frontiersin.org/article/10.3389/fnhum.2011.00159/abstract</a><br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><br>
> cfg = [];<br>
> cfg.image = 'figure4_layout_256_Frontiers.png';<br>
> lay = ft_prepare_layout(cfg);<br>
><span class="Apple-converted-space"> </span><br>
> The following tutorial describes the procedure in more details:<br>
><span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/tutorial/layout">http://www.fieldtriptoolbox.org/tutorial/layout</a><br>
><span class="Apple-converted-space"> </span><br>
> Please do not hesitate to get in touch with me for this and other matters.<br>
><span class="Apple-converted-space"> </span><br>
> All the best<br>
> Cris Micheli<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> On Tue, Jan 19, 2016 at 3:35 PM, Laith Hamid <<a href="mailto:lah@pedneuro.uni-kiel.de">lah@pedneuro.uni-kiel.de</a>><br>
> wrote:<br>
><span class="Apple-converted-space"> </span><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>
> ><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> ><span class="Apple-converted-space"> </span><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> ><br>
> -------------- next part --------------<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><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">lah@pedneuro.uni-kiel.de</a>><br>
> To: Fieldtrip <<a href="mailto:fieldtrip@science.ru.nl">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">61e8cefadba890a26ecd0b9adf0bca9b@mail.uni-kiel.de</a>><br>
> Content-Type: text/plain; charset="us-ascii"<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Dear Cris,<br>
><span class="Apple-converted-space"> </span><br>
> thank you very much for your answer. I am refering to an issue that was<br>
> discussed in this thread from April 2013:<span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> [FieldTrip] source analysis EEG data without MRI<span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><br>
> Best,<br>
> Laith<span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> -------------- next part --------------<br>
> An HTML attachment was scrubbed...<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><br>
> Message: 4<br>
> Date: Tue, 19 Jan 2016 16:52:55 +0000<br>
> From: aishwarya selvaraj <<a href="mailto:aishwaryaselvaraj1708@gmail.com">aishwaryaselvaraj1708@gmail.com</a>><br>
> To: "fieldtrip, donders" <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
> Subject: [FieldTrip] Source Localisation<br>
> Message-ID: <<a href="mailto:3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl">3ff5de7a69704e8d9e873e3f94120ad7@EXPRD01.hosting.ru.nl</a>><br>
> Content-Type: text/plain; charset="us-ascii"<br>
><span class="Apple-converted-space"> </span><br>
> Hi guys,<br>
> I'm currently working on source localization of EEG signals .<br>
> Im very new to it .<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Can Anyone provide any inputs ??<br>
> It would be of great help .<br>
><span class="Apple-converted-space"> </span><br>
> --<br>
> Regards,<br>
> Aishwarya<br>
> -------------- next part --------------<br>
> An HTML attachment was scrubbed...<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><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">S.Homolle@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] Source Localisation<br>
> Message-ID:<br>
> <<a href="mailto:2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl">2247A6E8AF3DB04AAB11BDDD86B72F830335254E@exprd01.hosting.ru.nl</a>><br>
> Content-Type: text/plain; charset="iso-8859-1"<br>
><span class="Apple-converted-space"> </span><br>
> Dear Aishwarya,<br>
><span class="Apple-converted-space"> </span><br>
> Under<span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/tutorial">http://www.fieldtriptoolbox.org/tutorial</a><span class="Apple-converted-space"> </span>there are several tutorials about source reconstruction.<br>
><span class="Apple-converted-space"> </span><br>
> My recommended start would be:<br>
><span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem">http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem</a><br>
><span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate">http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate</a><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Hopefully this provides you good start working with EEG source reconstruction<br>
><span class="Apple-converted-space"> </span><br>
> Best regards,<br>
><span class="Apple-converted-space"> </span><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:<span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a><span class="Apple-converted-space"> </span>[<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>]
on behalf of aishwarya selvaraj [<a href="mailto:aishwaryaselvaraj1708@gmail.com">aishwaryaselvaraj1708@gmail.com</a>]<br>
> Sent: Tuesday, January 19, 2016 5:52 PM<br>
> To: fieldtrip, donders<br>
> Subject: [FieldTrip] Source Localisation<br>
><span class="Apple-converted-space"> </span><br>
> Hi guys,<br>
> I'm currently working on source localization of EEG signals .<br>
> Im very new to it .<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Can Anyone provide any inputs ??<br>
> It would be of great help .<br>
><span class="Apple-converted-space"> </span><br>
> --<br>
> Regards,<br>
> Aishwarya<br>
> -------------- next part --------------<br>
> An HTML attachment was scrubbed...<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><br>
> Message: 6<br>
> Date: Tue, 19 Jan 2016 17:49:21 +0000<br>
> From: victoria schroeder <<a href="mailto:vic.schroeder2@gmail.com">vic.schroeder2@gmail.com</a>><br>
> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
> Subject: Re: [FieldTrip] plotting neighbours<br>
> Message-ID:<br>
> <<a href="mailto:CAOWWpozcLgcLNqgF4rMrTRZ_=e8cYCvXgeY5ZJYXx_9YmWnJ_w@mail.gmail.com">CAOWWpozcLgcLNqgF4rMrTRZ_=e8cYCvXgeY5ZJYXx_9YmWnJ_w@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><span class="Apple-converted-space"> </span><br>
> Thank you very much Philipp and Tzvetan!<br>
><span class="Apple-converted-space"> </span><br>
> Things have become much clearer now.<br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><br>
> Error in ft_freqstatistics (line 187)<br>
> cfg.frequency = [max(cfg.frequency(1), fmin), min(cfg.frequency(2), fmax)];<br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> The relevant section of the toturial is provided below.<br>
> Thank you!<br>
><span class="Apple-converted-space"> </span><br>
> Victoria<br>
><span class="Apple-converted-space"> </span><br>
> Permutation test<br>
><span class="Apple-converted-space"> </span><br>
> Now, run *ft_freqstatistics<br>
> <<a href="http://www.fieldtriptoolbox.org/reference/ft_freqstatistics">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">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">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">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">http://www.fieldtriptoolbox.org/faq/how_does_ft_prepare_neighbours_work</a>>.<br>
><span class="Apple-converted-space"> </span><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">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">ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/cluster_permutation_freq/freqFC_planar_cmb.mat</a>>),<br>
> use:<br>
><span class="Apple-converted-space"> </span><br>
> load freqFIC_planar_cmb<br>
> load freqFC_planar_cmb<br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><br>
> cfg.design = design;<br>
> cfg.ivar = 1;<br>
><span class="Apple-converted-space"> </span><br>
> [stat] = ft_freqstatistics(cfg, freqFIC_planar_cmb, freqFC_planar_cmb);<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> 2016-01-18 17:57 GMT+00:00 Tzvetan Popov <<a href="mailto:tzvetan.popov@uni-konstanz.de">tzvetan.popov@uni-konstanz.de</a>>:<br>
><span class="Apple-converted-space"> </span><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>
> ><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> ><span class="Apple-converted-space"> </span><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> ><br>
> -------------- next part --------------<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><br>
> Message: 7<br>
> Date: Tue, 19 Jan 2016 20:50:24 +0100<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] Standard BEM or FEM models for use with<br>
> 256-electrode EEG data recorded with EGI caps<br>
> Message-ID:<br>
> <<a href="mailto:CADW7XCC8BvdVKRAEMw4Jt8v3T6zXjF2zHF_T_4h8ZkuvTbc=1Q@mail.gmail.com">CADW7XCC8BvdVKRAEMw4Jt8v3T6zXjF2zHF_T_4h8ZkuvTbc=1Q@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><span class="Apple-converted-space"> </span><br>
> Dear Laith,<br>
><span class="Apple-converted-space"> </span><br>
> this might be possible if you have the subject-specific MRI by following<br>
> the tutorial here:<br>
><span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem">http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem</a><br>
><span class="Apple-converted-space"> </span><br>
> and using the function ft_prepare_mesh and the tutorial command:<br>
><span class="Apple-converted-space"> </span><br>
> cfg=[];<br>
> cfg.tissue={'brain','skull','scalp'};<br>
> cfg.numvertices = [3000 2000 1000];<br>
> bnd=ft_prepare_mesh(cfg,segmentedmri);<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><a href="ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri">ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/subjectK.mri</a><br>
> and the corresponding segmented version<br>
><span class="Apple-converted-space"> </span><a href="ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat">ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/beamformer_extended/segmentedmri.mat</a><br>
><span class="Apple-converted-space"> </span><br>
> This goes down to the chin. Then you take care of rearranging the position<br>
> of the EEG electrodes according to this:<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel">http://www.fieldtriptoolbox.org/example/align_eeg_electrode_positions_to_bem_headmodel</a><br>
><span class="Apple-converted-space"> </span><br>
> I hope this helped<br>
> Cris<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> On Tue, Jan 19, 2016 at 5:41 PM, Laith Hamid <<a href="mailto:lah@pedneuro.uni-kiel.de">lah@pedneuro.uni-kiel.de</a>><br>
> wrote:<br>
><span class="Apple-converted-space"> </span><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>
> ><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> ><span class="Apple-converted-space"> </span><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> ><br>
> -------------- next part --------------<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><br>
> Message: 8<br>
> Date: Wed, 20 Jan 2016 12:17:12 +0800<br>
> From: Munsif Jatoi <<a href="mailto:munsif.jatoi@gmail.com">munsif.jatoi@gmail.com</a>><br>
> To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
> Subject: Re: [FieldTrip] Source Localisation<br>
> Message-ID:<br>
> <<a href="mailto:CAHnJ=SUHe84yNDVnTLKhGdJBri0mvOdbU0rPqM-Z3-0Gv71Ycg@mail.gmail.com">CAHnJ=SUHe84yNDVnTLKhGdJBri0mvOdbU0rPqM-Z3-0Gv71Ycg@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><span class="Apple-converted-space"> </span><br>
> Dear Aishwarya,<br>
><span class="Apple-converted-space"> </span><br>
> Please refer to main help tutorials.<br>
><span class="Apple-converted-space"> </span><br>
> Also, you can find out the survey papers written in this area. For more,<br>
> SPM website can provide good help.<br>
><span class="Apple-converted-space"> </span><br>
> Best,<br>
> Munsif.<br>
><span class="Apple-converted-space"> </span><br>
> On Wed, Jan 20, 2016 at 1:06 AM, Hom?lle, S. (Simon) <<br>
><span class="Apple-converted-space"> </span><a href="mailto:S.Homolle@donders.ru.nl">S.Homolle@donders.ru.nl</a>> wrote:<br>
><span class="Apple-converted-space"> </span><br>
> > Dear Aishwarya,<br>
> ><br>
> > Under<span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/tutorial">http://www.fieldtriptoolbox.org/tutorial</a><span class="Apple-converted-space"> </span>there are several<br>
> > tutorials about source reconstruction.<br>
> ><br>
> > My recommended start would be:<br>
> ><span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem">http://www.fieldtriptoolbox.org/tutorial/headmodel_eeg_bem</a><br>
> ><span class="Apple-converted-space"> </span><a href="http://www.fieldtriptoolbox.org/tutorial/minimumnormestimate">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:*<span class="Apple-converted-space"> </span><a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a><span class="Apple-converted-space"> </span>[<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>]<br>
> > on behalf of aishwarya selvaraj [<a href="mailto:aishwaryaselvaraj1708@gmail.com">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>
> ><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> ><span class="Apple-converted-space"> </span><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
> ><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> --<span class="Apple-converted-space"> </span><br>
> Munsif Ali H.Jatoi,<br>
><span class="Apple-converted-space"> </span><br>
> Ph D Scholar,<br>
> Centre for Intelligent Signals and Imaging Research,<br>
> Universiti Teknologi PETRONAS,<br>
> Malaysia.<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><a href="http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en">http://scholar.google.com.my/citations?user=Y6g6jOAAAAAJ&hl=en</a><br>
> -------------- next part --------------<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><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">olga.v.sysoeva@gmail.com</a>><br>
> To:<span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@science.ru.nl">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">CADtsnVcJLhrPPfq-P1Htj-RmfgzDDgqNhr8vsAoJ2mxxCV7seQ@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
><span class="Apple-converted-space"> </span><br>
> Dear Fieldtrippers,<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> I'm encounter the problem with MRI interpolation and reslicing using<br>
><span class="Apple-converted-space"> </span><br>
> FT_VOLUMERESLICE.<br>
><span class="Apple-converted-space"> </span><br>
> I have read my MRI from fif.file and this mri variable contains<br>
><span class="Apple-converted-space"> </span><br>
> mri_K0012.unit, 'm'<br>
><span class="Apple-converted-space"> </span><br>
> mri_K0012.dim, [432, 512, 180]<br>
><span class="Apple-converted-space"> </span><br>
> mri_K0012.anatomy, <432, 512, 180 int16><br>
><span class="Apple-converted-space"> </span><br>
> mri_K0012.hdr, (1*1 structure)<br>
><span class="Apple-converted-space"> </span><br>
> mri_K0012.transform, (4*4 double)<br>
><span class="Apple-converted-space"> </span><br>
> mri_K0012.coordsys 'neuromag'.<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Than I used<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> mri = ft_volumereslice([], mri);<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> the output is<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> ?the input is volume data with dimensions [432<br>
> 512 180]<br>
><span class="Apple-converted-space"> </span><br>
> reslicing from [432 512 180] to [256 256 256]<br>
><span class="Apple-converted-space"> </span><br>
> the input is volume data with dimensions [256<br>
> 256 256]<br>
><span class="Apple-converted-space"> </span><br>
> the input is volume data with dimensions [432<br>
> 512 180]<br>
><span class="Apple-converted-space"> </span><br>
> selecting subvolume of 0.0%<br>
><span class="Apple-converted-space"> </span><br>
> reslicing and interpolating anatomy<br>
><span class="Apple-converted-space"> </span><br>
> interpolating<br>
><span class="Apple-converted-space"> </span><br>
> ??? Attempted to access sel(1); index out of<br>
> bounds because numel(sel)=0.<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Error in ==> ft_sourceinterpolate>my_interpn<br>
> at 663<br>
><span class="Apple-converted-space"> </span><br>
> ft_progress(sel(1)/num, 'interpolating<br>
> %.1f%%\n', 100*sel(1)/num);<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Error in ==> ft_sourceinterpolate at 583<br>
><span class="Apple-converted-space"> </span><br>
> av( sel) = my_interpn(fv, ax(sel),<br>
> ay(sel), az(sel), cfg.interpmethod,<br>
><span class="Apple-converted-space"> </span><br>
> cfg.feedback);<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Error in ==> ft_volumereslice at 176<br>
><span class="Apple-converted-space"> </span><br>
> resliced = ft_sourceinterpolate(tmpcfg, mri,<br>
> resliced);?<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><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>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> I'd be thankful for the comments.<br>
><span class="Apple-converted-space"> </span><br>
><span class="Apple-converted-space"> </span><br>
> Best Regards,<br>
><span class="Apple-converted-space"> </span><br>
> Olga.<br>
><span class="Apple-converted-space"> </span><br>
> P.S.Actually, I can project my sources<br>
> meaningfully into not interpolated MRI, altoough the images are<br>
> plotted upside down.<br>
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><span class="Apple-converted-space"> </span><br>
> ------------------------------<br>
><span class="Apple-converted-space"> </span><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
><span class="Apple-converted-space"> </span><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
><span class="Apple-converted-space"> </span><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><span class="Apple-converted-space"> </span><br>
> End of fieldtrip Digest, Vol 62, Issue 18<br>
> *****************************************<br>
</div>
</div>
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