From sharonriwkes at GMAIL.COM Mon Aug 2 14:06:12 2010 From: sharonriwkes at GMAIL.COM (sharon riwkes) Date: Mon, 2 Aug 2010 15:06:12 +0300 Subject: Beamforming with reference channels Message-ID: Hi all, I tried to do source localization, after beamforming with the LCMV method. I did it once for all the MEG channels, and once for MEG channels *AND the reference channels*. I was hoping that using the reference channels will improve the localization by ignoring noise coming from outside of the brain. However, I got the *exact same results for MEG+reference channels* as *for MEG alone!* Does anyone know how to include the reference channels effectively in the LCMV beamforming? Thanks for your help, Sharon Riwkes. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at DONDERS.RU.NL Mon Aug 2 15:23:38 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 2 Aug 2010 15:23:38 +0200 Subject: Beamforming with reference channels In-Reply-To: Message-ID: Hi Sharon, If the results are exactly the same, I guess the references have not been taken into account at all. Although it remains to be seen whether you gain a lot with this approach (my preferred alternative would be to clean the data from external noise using the references and taking into account the correction in the forward computation), it should be possible to do it in fieldtrip. To get it to work, you have to check whether the necessary information is present throughout your analysis pipeline. Importantly, when computing the covariance matrix in ft_timelockanalysis, you have to include the references. The same goes for the computation of the leadfields (if you use ft_prepare_leadfield for that). If this information is still present prior to your call to ft_sourceanalysis, you may want to check whether you have to specify cfg.channel (to include the references, rather than 'MEG' (which may be the default, and causes selection of close-to-the-head sensors only). Just for the record: is it 4D-neuroimaging data you are working on? Best wishes, Jan-Mathijs On Aug 2, 2010, at 2:06 PM, sharon riwkes wrote: > Hi all, > I tried to do source localization, after beamforming with the LCMV > method. I did it once for all the MEG channels, and once for MEG > channels AND the reference channels. I was hoping that using the > reference channels will improve the localization by ignoring noise > coming from outside of the brain. > However, I got the exact same results for MEG+reference channels as > for MEG alone! > Does anyone know how to include the reference channels effectively > in the LCMV beamforming? > Thanks for your help, > Sharon Riwkes. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sharonriwkes at GMAIL.COM Wed Aug 4 13:39:16 2010 From: sharonriwkes at GMAIL.COM (sharon riwkes) Date: Wed, 4 Aug 2010 14:39:16 +0300 Subject: Beamforming with reference channels In-Reply-To: Message-ID: Dear Jan-Mathijs, Thanks for your quick answer! I will check the different possibilities. I think that the problem was in the stage the lead field computation. And yes, this is 4D data. Sharon. On Mon, Aug 2, 2010 at 4:23 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Sharon, > > If the results are exactly the same, I guess the references have not been > taken into account at all. Although it remains to be seen whether you gain a > lot with this approach (my preferred alternative would be to clean the data > from external noise using the references and taking into account the > correction in the forward computation), it should be possible to do it in > fieldtrip. To get it to work, you have to check whether the necessary > information is present throughout your analysis pipeline. Importantly, when > computing the covariance matrix in ft_timelockanalysis, you have to include > the references. The same goes for the computation of the leadfields (if you > use ft_prepare_leadfield for that). If this information is still present > prior to your call to ft_sourceanalysis, you may want to check whether you > have to specify cfg.channel (to include the references, rather than 'MEG' > (which may be the default, and causes selection of close-to-the-head sensors > only). > Just for the record: is it 4D-neuroimaging data you are working on? > > Best wishes, > > Jan-Mathijs > > > On Aug 2, 2010, at 2:06 PM, sharon riwkes wrote: > > Hi all, > I tried to do source localization, after beamforming with the LCMV method. > I did it once for all the MEG channels, and once for MEG channels *AND the > reference channels*. I was hoping that using the reference channels will > improve the localization by ignoring noise coming from outside of the brain. > > However, I got the *exact same results for MEG+reference channels* as *for > MEG alone!* > Does anyone know how to include the reference channels effectively in the > LCMV beamforming? > Thanks for your help, > Sharon Riwkes. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Thu Aug 5 15:49:39 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Thu, 5 Aug 2010 15:49:39 +0200 Subject: significance of coherence differences Message-ID: Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,...] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,...]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Panagiotis.Tsiatsis at TUEBINGEN.MPG.DE Fri Aug 6 10:44:56 2010 From: Panagiotis.Tsiatsis at TUEBINGEN.MPG.DE (Panagiotis Tsiatsis) Date: Fri, 6 Aug 2010 10:44:56 +0200 Subject: Removing ECG artifacts via ICA in a Steady State experiment without EMG Channel (MEG) Message-ID: Dear all, I am a newbie in fieldtrip. First of all I would like to say thanks for your beautiful work and support. I am facing the following problem : I am running a Visual Steady State MEG experiment (CTF scanner) and I want to remove the ECG artifacts but I do not have an EMG channel available. I haven't managed to go fully through the analysis (by the way, I was getting errors when trying to run your ICA ECG example, but let me take another look) but I am worried that by using the 'left' MEG channels (MLT) alone to detect the artifacts I will not manage to go far, as the ECG activity will be obscured by the steady state activity (10 Hz flickering light) and I will not be able to from a proper averaged / typical ECG. Does anybody have any experience with this? I know that it is quite silly to ask you before trying completely and therefore I apologize beforehand. Once I have fully gone through the analysis I can inform you on whether I managed to do it reliably. Thanks and best, Panagiotis ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Mon Aug 9 18:58:57 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Mon, 9 Aug 2010 18:58:57 +0200 Subject: significance of coherence differences In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0176EB70@Mail2-UKD.VMED.UKD> Message-ID: Hi Jan, If you get confused about the literature then I am partly to blame. Things are different for single subject studies (units-of-observation are trials) and multiple subject studies (units-of-observation are subjects). You describe a multiple subject study of the within-subjects type (every subjects participates in both experimental conditions). For a single channel pair and a single frequency bin, the appropriate statistic is the dependent (paired) samples t-statistic or, in a nonparametric framework, the Wilcoxon signed rank sum test. (You mention the Wilcoxon rank sum test, but this is for a study of the between-subjects type.) You apply this test statistic to the condition-specific coherences, obtained by summing and normalizing the trial(taper)-specific cross-spectra. This statistical test works fine (asymptotically, for the dependent samples t-statistic) if the number of trials in the two conditions are equal. The requirement of an equal number of trials follows from the fact that coherence is a biased measure, with the bias being dependent on the number of trials. The situation is different for a single subject study. You may want to have a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals with the multiple comparisons problem. Best, Eric dr. Eric Maris Donders Institute for Brain, Cognition and Behavior Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging Radboud University P.O. Box 9104 6500 HE Nijmegen The Netherlands T:+31 24 3612651 Mobile: 06 39584581 F:+31 24 3616066 E: e. maris at donders.ru.nl From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: donderdag 5 augustus 2010 15:50 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] significance of coherence differences Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Tue Aug 10 09:57:28 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 10 Aug 2010 09:57:28 +0200 Subject: OpenMEEG: libraries not found Message-ID: Dear all, I'm trying to run OpenMEEG from fieldtrip, but the executables complain about libstdc++.so.6 missing. I'm quite sure that libstdc++ v6 is installed, but om_assemble seems to expect it to be in /usr/local/matlab/sys/os/glnx86/, not in /lib/. Unfortunately none of the Tutorials and Read-mes seems to deal with this. I've got no clue, how to handle this and it would be nice, if any of you could help me. Cheers and thanks in advance, Paul PS: When running om_assemble from command line, it runs without any problem -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Tue Aug 10 10:47:52 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Tue, 10 Aug 2010 10:47:52 +0200 Subject: AW: [FIELDTRIP] significance of coherence differences Message-ID: Dear Eric, thank you for your answer. I read the paper and see that your method is a great tool to deal with the MCP and with situations in which one does not know at which frequencies and channels an effect is expected. It is good to know that for the group level (multiple subjects, all measured in the same set of conditions) conventional paired-sample statistics are appropriate, beacause I dont see how the random-partition procedure relates to such a situation. All the best, Jan -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von Eric Maris Gesendet: Mo 09.08.2010 18:58 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] significance of coherence differences Hi Jan, If you get confused about the literature then I am partly to blame. Things are different for single subject studies (units-of-observation are trials) and multiple subject studies (units-of-observation are subjects). You describe a multiple subject study of the within-subjects type (every subjects participates in both experimental conditions). For a single channel pair and a single frequency bin, the appropriate statistic is the dependent (paired) samples t-statistic or, in a nonparametric framework, the Wilcoxon signed rank sum test. (You mention the Wilcoxon rank sum test, but this is for a study of the between-subjects type.) You apply this test statistic to the condition-specific coherences, obtained by summing and normalizing the trial(taper)-specific cross-spectra. This statistical test works fine (asymptotically, for the dependent samples t-statistic) if the number of trials in the two conditions are equal. The requirement of an equal number of trials follows from the fact that coherence is a biased measure, with the bias being dependent on the number of trials. The situation is different for a single subject study. You may want to have a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals with the multiple comparisons problem. Best, Eric dr. Eric Maris Donders Institute for Brain, Cognition and Behavior Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging Radboud University P.O. Box 9104 6500 HE Nijmegen The Netherlands T:+31 24 3612651 Mobile: 06 39584581 F:+31 24 3616066 E: e. maris at donders.ru.nl From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: donderdag 5 augustus 2010 15:50 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] significance of coherence differences Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Tue Aug 10 11:55:26 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 10 Aug 2010 11:55:26 +0200 Subject: OpenMEEG: libraries not found In-Reply-To: <4C610668.30405@gmx.de> Message-ID: Dear all, with a little help of a colleague I was able to run the OpenMEEG executables but we had to move all of the files from the matlab/sys/os/glnx86 folder to another place and link everything from my /usr/lib/ dir to the glnx folder. It works, but really aint the best way in my opinion. Is there another - slightly more sensible - way to go? Cheers, Paul Am 10.08.2010 09:57, schrieb Paul Czienskowski: > Dear all, > > I'm trying to run OpenMEEG from fieldtrip, but the executables > complain about libstdc++.so.6 missing. I'm quite sure that libstdc++ > v6 is installed, but om_assemble seems to expect it to be in > /usr/local/matlab/sys/os/glnx86/, not in /lib/. Unfortunately none of > the Tutorials and Read-mes seems to deal with this. I've got no clue, > how to handle this and it would be nice, if any of you could help me. > > Cheers and thanks in advance, > Paul > > PS: When running om_assemble from command line, it runs without any > problem > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Tue Aug 10 12:47:47 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Tue, 10 Aug 2010 12:47:47 +0200 Subject: AW: [FIELDTRIP] significance of coherence differences In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8BA2E57B@Mail2-UKD.VMED.UKD> Message-ID: Hi Jan, > thank you for your answer. I read the paper and see that your method is > a great tool to deal with the MCP and with situations in which one does > not know at which frequencies and channels an effect is expected. It is > good to know that for the group level (multiple subjects, all measured > in the same set of conditions) conventional paired-sample statistics > are appropriate, beacause I dont see how the random-partition procedure > relates to such a situation. I does not, because the random partitioning procedure only applies to single subject studies (UOs are trials). In a within-subjects multiple subject study the random aspect is in the random permutation of the elements in the paired observations. Best, Eric > > All the best, > Jan > > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von Eric Maris > Gesendet: Mo 09.08.2010 18:58 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] significance of coherence differences > > Hi Jan, > > > > > > If you get confused about the literature then I am partly to blame. > > > > Things are different for single subject studies (units-of-observation > are > trials) and multiple subject studies (units-of-observation are > subjects). > You describe a multiple subject study of the within-subjects type > (every > subjects participates in both experimental conditions). For a single > channel > pair and a single frequency bin, the appropriate statistic is the > dependent > (paired) samples t-statistic or, in a nonparametric framework, the > Wilcoxon > signed rank sum test. (You mention the Wilcoxon rank sum test, but this > is > for a study of the between-subjects type.) You apply this test > statistic to > the condition-specific coherences, obtained by summing and normalizing > the > trial(taper)-specific cross-spectra. This statistical test works fine > (asymptotically, for the dependent samples t-statistic) if the number > of > trials in the two conditions are equal. The requirement of an equal > number > of trials follows from the fact that coherence is a biased measure, > with the > bias being dependent on the number of trials. > > > > The situation is different for a single subject study. You may want to > have > a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals > with > the multiple comparisons problem. > > > > > > Best, > > > > Eric > > > > > > dr. Eric Maris > Donders Institute for Brain, Cognition and Behavior > > Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging > > Radboud University > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > T:+31 24 3612651 > Mobile: 06 39584581 > > F:+31 24 3616066 > E: e. maris at donders.ru.nl > > > > > > > > > > > > > > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On > Behalf > Of Jan Hirschmann > Sent: donderdag 5 augustus 2010 15:50 > To: FIELDTRIP at NIC.SURFNET.NL > Subject: [FIELDTRIP] significance of coherence differences > > > > Dear fieldtrip experts, > > > > I am getting more and more confused about the literature of > significance > tests of coherence differences. The one essential point I did not quite > understand is why conventional tests do not seem to apply. Lets say I > have > two vectors of mean alpha band coherences, relating to two experimental > conditions (continuous data, no trials). The vector entries stem from > different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and > C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from > comparing the two vectors, say, with a Wilcoxon ranksum test? > > > > Thanks for any comments, > > > > Jan Hirschmann > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of > the > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Tue Aug 10 17:46:57 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Tue, 10 Aug 2010 11:46:57 -0400 Subject: inter trial coherence Message-ID: Hello Fieldtrippers, I am now trying to do the frequencyanalysis with my eeg data in Fieldtrip. With the function of 'freqanalysis', i got my TFR data. Now i have a question: does fieldtrip have a function that gives "phase locking factor" or inter-trial coherence (ITC)? I apologize in advance if my questions are too obvious. Thanks for your help, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.vandermeij at DONDERS.RU.NL Wed Aug 11 09:33:41 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Wed, 11 Aug 2010 09:33:41 +0200 Subject: inter trial coherence In-Reply-To: <4C617471.4040809@rotman-baycrest.on.ca> Message-ID: Hi Yu, Have a look at the function ft_connectivityanalysis, that should be able get you what you want. Regards, Roemer On 8/10/2010 5:46 PM, Yu He wrote: > Hello Fieldtrippers, > > I am now trying to do the frequencyanalysis with my eeg data in > Fieldtrip. > > With the function of 'freqanalysis', i got my TFR data. > Now i have a question: does fieldtrip have a function that gives > "phase locking factor" or inter-trial coherence (ITC)? > I apologize in advance if my questions are too obvious. > > Thanks for your help, > > Yu > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Wed Aug 11 09:59:30 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 11 Aug 2010 09:59:30 +0200 Subject: Volume conductor space alignment Message-ID: Dear all, I'm trying to simulate and fit EEG data with different models for my diploma thesis and I have another little question. I wondered if there is any alignment done before or when simulating the data or if the simulation's done in the space the BEM model was created from. I'd like to know this to know if I'd have to align my spaces on my own or if everything is in the space spanned by the fidcial points anyway. Thanks in advance, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From khoechstetter at BESA.DE Wed Aug 11 13:29:35 2010 From: khoechstetter at BESA.DE (Karsten Hoechstetter) Date: Wed, 11 Aug 2010 13:29:35 +0200 Subject: Upcoming BESA Workshop in London (September 9-10) Message-ID: Dear colleagues, I would like to inform you that a 2-day BESA Research workshop will be held in London/UK on September 9-10. This workshop provides a thorough introduction to BESA Research, the software package for comprehensive EEG/MEG data analysis. Target group of the workshop are both novices and existing BESA users. The workshop includes hands-on tutorials on the new features of BESA Research 5.3, e.g. the direct MATLAB interface and CLARA, the new 3D source imaging technique. Covered topics will include: - A theoretical introduction to source analysis - Hands-on source analysis with simulated and real data sets - Data preprocessing in BESA Research: Artifact rejection and correction, channel interpolation, digital filtering, 3D mapping, remontaging, averaging - Coregistration with (f)MRI - Time-frequency analysis and source coherence - Beamforming - 3D volume imaging: CLARA, LORETA, sLORETA, minimum norm etc. - Batch scripting For more information, schedule, and registration, please visit the BESA website at www.besa.de/events/workshops. If you have any further questions, please contact workshop at besa.de. I would be glad to see you on one of these occasions! Best wishes, Karsten Hoechstetter -------------------------------------- Dr. Karsten Hoechstetter MEGIS Software GmbH Gräfelfing, Germany HRB München 109956 CEO Dr. Michael Scherg -------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Wed Aug 11 15:52:31 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Wed, 11 Aug 2010 15:52:31 +0200 Subject: unclosed surfaces with BEM models Message-ID: Dear fieldtrippers, I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with cfg = []; cfg.tissue = [1 2 3]; cfg.numvertices = [1000 2000 3000] cfg.conductivity = [1 1/80 1] cfg.sourceunits = 'cm' cfg.mriunits = 'mm' cfg.method = 'dipoli'; cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg does the triangulation and computes the BEM model up to the following error message: (begin) .... Bmat countdown: 5010 (pass 2) Bmat countdown: 5000 (pass 2) Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) Warning: an error ocurred while running dipoli > In dipoli at 90 In ft_prepare_bemmodel at 112 Error using ==> fread Invalid file identifier. Use fopen to generate a valid file identifier. Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. > In dipoli at 98 In ft_prepare_bemmodel at 112 (end) I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. Best regards, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Wed Aug 11 16:25:37 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Wed, 11 Aug 2010 16:25:37 +0200 Subject: inter trial coherence Message-ID: Thanks Roemer! I am not very clear about function of ft_connectivityanalysis. It is said "FT_CONNECTIVITYANALYIS computes various measures of connectivity between MEG/EEG channels or between source-level signals." when you read the documentation reference. Is that only for between MEG/EEG channels? Regards, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Aug 11 16:35:21 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 11 Aug 2010 16:35:21 +0200 Subject: inter trial coherence In-Reply-To: Message-ID: Dear Yu, Ft_connectivityanalysis works also with different kinds of electrophysiological data. It's on our list to make the documentation to this function clearer. This will hopefully happen soon. For now, I don't think this is the function you need for inter-trial coherence. Ft_connectivityanalysis computes bivariate metrics, i.e. measures of connectivity defined between channel pairs. In your case, you want to estimate the consistency of oscillatory phase across trials (and not the consistency of the phase difference between a pair of channels across trials). So what you need to do is probably something like this: cfg = []; cfg.output = 'fourier'; cfg..... cfg..... cfg..... freq = ft_freqanalysis(cfg, data); Next, to obtain the itc, do the following tmpdat = freq.fourierspctrm; tmpdat = tmpdat(abs(tmpdat)); % this will normalise each trial for its amplitude; itc = abs(mean(tmpdat)); % this will give the itc Best wishes, Jan-Mathijs On Aug 11, 2010, at 4:25 PM, Yu He wrote: > Thanks Roemer! > > I am not very clear about function of ft_connectivityanalysis. It is > said "FT_CONNECTIVITYANALYIS computes various measures of connectivity > between MEG/EEG channels or between source-level signals." when you > read > the documentation reference. > > Is that only for between MEG/EEG channels? > > Regards, > > Yu > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Aug 11 16:50:48 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 11 Aug 2010 16:50:48 +0200 Subject: inter trial coherence In-Reply-To: <2C2E534F-B24F-4D03-A32B-70A15D6ABAFC@donders.ru.nl> Message-ID: Dear Yu, I made a slight typo in my previous mail. Obviously tmpdat = tmpdat(abs(tmpdat)); % this will normalise each trial for its amplitude; should read tmpdat = tmpdat./abs(tmpdat); for the normalization to work. Best wishes, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Wed Aug 11 18:50:23 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Wed, 11 Aug 2010 18:50:23 +0200 Subject: inter trial coherence Message-ID: Dear Jan-Mathijs, That's great! Thank you so much for the step by step explanation. Best regs, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Thu Aug 12 17:52:19 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 12 Aug 2010 17:52:19 +0200 Subject: Units powspctrm Message-ID: Hello together, What units does the powspctrm have? Starting with an EEG signal in microvolts and computing the powerspectrum using freqanalysis what are the units of powspctrm? I tried to figure it out on my own but I am stuck somehow. Here some example code cfg=[]; cfg.method='mtmfft'; cfg.output='pow'; cfg.pad ='maxperlen' cfg.foilim=[1 130] cfg.taper='hanning' cfg.channel=1 cfg.keeptrials='no' R=ft_freqanalysis(cfg,data); I am interested in the units of R.powspctrm Thanks Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Thu Aug 12 21:38:57 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Thu, 12 Aug 2010 21:38:57 +0200 Subject: Units powspctrm In-Reply-To: <942108.4682501281641712211.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hello Martin, A powerspectrum typically has the frequencies on one axis and the power of the corresponding frequencies on the other. The power represents how strong a certain frequency occurs in a signal, given by the square of the voltage per frequency. In your case: square of the microvolts per frequency: uV^2/ Hz Best regards, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] Units powspctrm Hello together, What units does the powspctrm have? Starting with an EEG signal in microvolts and computing the powerspectrum using freqanalysis what are the units of powspctrm? I tried to figure it out on my own but I am stuck somehow. Here some example code cfg=[]; cfg.method='mtmfft'; cfg.output='pow'; cfg.pad ='maxperlen' cfg.foilim=[1 130] cfg.taper='hanning' cfg.channel=1 cfg.keeptrials='no' R=ft_freqanalysis(cfg,data); I am interested in the units of R.powspctrm Thanks Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Thu Aug 12 22:48:14 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 12 Aug 2010 22:48:14 +0200 Subject: Units powspctrm In-Reply-To: <7050041.4682621281641937538.JavaMail.root@watertor.uci.ru.nl> Message-ID: Yes, typically, but is it the case for the powspctrm you get from the mtmfft freqanalysis? I am asking for the following reason: Lets say, I have two experimental conditions A and B and I compute the powerspectra for both of them. When the units actually are uV^2/Hz i could tell for each frequency by how much uV A and B differ. What confuses me is that in ft_freqanalysis_mtmfftthe signal is multiplied with a taper (tap) and thereby scaled. The resulting powspctrm hence does not reflect the the true changes in microvolt. Do I see that correctly, or am I missing something here? Is the powerspectrum corrected for that somewhere else? Regards, Martin 2010/8/12 a.stolk at fcdonders.ru.nl > Hello Martin, > > A powerspectrum typically has the frequencies on one axis and the power of > the corresponding frequencies on the other. The power represents how strong > a certain frequency occurs in a signal, given by the square of the voltage > per frequency. > > In your case: square of the microvolts per frequency: uV^2/ Hz > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Units powspctrm > > Hello together, > > What units does the powspctrm have? > Starting with an EEG signal in microvolts and computing the powerspectrum > using freqanalysis what are the units of powspctrm? > I tried to figure it out on my own but I am stuck somehow. > > Here some example code > > cfg=[]; > cfg.method='mtmfft'; > cfg.output='pow'; > cfg.pad ='maxperlen' > cfg.foilim=[1 130] > cfg.taper='hanning' > cfg.channel=1 > cfg.keeptrials='no' > > R=ft_freqanalysis(cfg,data); > > I am interested in the units of R.powspctrm > > Thanks > Martin > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Fri Aug 13 08:24:50 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Fri, 13 Aug 2010 08:24:50 +0200 Subject: Units powspctrm In-Reply-To: <5621986.4689631281680620957.JavaMail.root@watertor.uci.ru.nl> Message-ID: If you use the same mtmfft settings for both conditions, in theory it should be fine. Make sure that you compute the fourier transformation on equal window lenghts. If you happen to have variable triallengths per condition, my suggestion would be to cut the trials in (e.g.) 1 second pieces. This way your 'frequency resolution' is the same for condition A and B. If your experimental setup allows you, you could choose to normalize your data (e.g. a baselinecorrection) first before making the A and B comparison. This way you correct for (non-)cognitive powerchanges over time (case it's not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste over time, subject habituation effects and whatelse you have. Best, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [FIELDTRIP] Units powspctrm Yes, typically, but is it the case for the powspctrm you get from the mtmfft freqanalysis? I am asking for the following reason: Lets say, I have two experimental conditions A and B and I compute the powerspectra for both of them. When the units actually are uV^2/Hz i could tell for each frequency by how much uV A and B differ. What confuses me is that in ft_freqanalysis_mtmfftthe signal is multiplied with a taper (tap) and thereby scaled. The resulting powspctrm hence does not reflect the the true changes in microvolt. Do I see that correctly, or am I missing something here? Is the powerspectrum corrected for that somewhere else? Regards, Martin 2010/8/12 a.stolk at fcdonders.ru.nl > Hello Martin, > > A powerspectrum typically has the frequencies on one axis and the power of > the corresponding frequencies on the other. The power represents how strong > a certain frequency occurs in a signal, given by the square of the voltage > per frequency. > > In your case: square of the microvolts per frequency: uV^2/ Hz > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Units powspctrm > > Hello together, > > What units does the powspctrm have? > Starting with an EEG signal in microvolts and computing the powerspectrum > using freqanalysis what are the units of powspctrm? > I tried to figure it out on my own but I am stuck somehow. > > Here some example code > > cfg=[]; > cfg.method='mtmfft'; > cfg.output='pow'; > cfg.pad ='maxperlen' > cfg.foilim=[1 130] > cfg.taper='hanning' > cfg.channel=1 > cfg.keeptrials='no' > > R=ft_freqanalysis(cfg,data); > > I am interested in the units of R.powspctrm > > Thanks > Martin > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Aug 13 19:11:12 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 13 Aug 2010 19:11:12 +0200 Subject: coherence again In-Reply-To: A<18555530.4689671281680690002.JavaMail.root@watertor.uci.ru.nl> Message-ID: Dear fieldtrip experts, I have yet another question about the statistical testing of coherence. Again, it relates to the group level, this time to the testing procedure used in "Imaging the motor system's beta-band synchronisation during isometric contraction", Schoffeleln et al., NeuroImage, 2008. There it says: " The null hypothesis that was tested at the voxel level states that the Z-transformed coherence between the EMG and that voxel, accumulated across subjects, is not different from 0. Under this null hypothesis, flipping the sign of the Z-transformed coherence values of a random subset of the subjects before accumulating leads to an alternative observation that belongs to the null distribution." Now, as I understand it, the Z-transformation described here is z=sqrt(-(df-2)*log(1-abs(C)^2)), i.e. z takes only positive values (there is no comparing of conditions here) And accumulation, it later says, means summing up the z-values of all subjects and dividing by sqrt(n) at each voxel. I suppose n is the number of subjects. So "flipping the sign" means multiplying the z-value of some subjects by -1 before summing up? As all z-values were originally positive, this will inevitably decrease the sum. So the original state will inevitably be the extreme end of the distribution. Sorry, I must have some serious error in my thinking here (hope it's not too obvious). Can you help me? Many thanks, Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 13 20:15:08 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 13 Aug 2010 20:15:08 +0200 Subject: unclosed surfaces with BEM models In-Reply-To: <4C62C73F020000570000710A@gwsmtp1.uni-regensburg.de> Message-ID: Hi Gregor, I was trying to to run dipoli to generate the BEM-Models too but often it failed with the very error. With some brains it worked checking everything 'by hand' since the matlab routines to create the surfaces seem to fail sometimes and produce an output that differs from the volume very much (e.g. spikes on the surface). I was facing an error lately when I obviously had some 'Inf' voxels in my volume for some crude reason. You may consider to switch to OpenMEEG because it's much better documented than dipoli (which takes - indeed - no effort at all as dipoli actually is not documented at all) and I think there are prebuilt binaries for Debian on AMD64 infrastructure. If you're trying to run OpenMEEG with more than 3 surfaces, which is supported by OpenMEEG but not by fieldtrip, I may send you my modified scripts. Hope this helps at least a bit. Cheers, Paul Am 11.08.2010 15:52, schrieb Gregor Volberg: > Dear fieldtrippers, > > I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with > > cfg = []; > cfg.tissue = [1 2 3]; > cfg.numvertices = [1000 2000 3000] > cfg.conductivity = [1 1/80 1] > cfg.sourceunits = 'cm' > cfg.mriunits = 'mm' > cfg.method = 'dipoli'; > cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; > vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg > > does the triangulation and computes the BEM model up to the following error message: > > (begin) > .... > Bmat countdown: 5010 (pass 2) > Bmat countdown: 5000 (pass 2) > > > Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface > (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) > > > Warning: an error ocurred while running dipoli >> In dipoli at 90 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. >> In dipoli at 98 > In ft_prepare_bemmodel at 112 > (end) > > I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. > > So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. > > Best regards, Gregor > > > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Mon Aug 16 08:18:13 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Mon, 16 Aug 2010 08:18:13 +0200 Subject: Antw: Re: [FIELDTRIP] unclosed surfaces with BEM models In-Reply-To: <4C658BAC.8060709@gmx.de> Message-ID: Hi Paul, thanks a lot for your reply! I will try OpenMEEG and I hope I can fix the error soon. Meanwhile, I would be very glad if you could send me your modified script for > 3 surfaces. This will surely help... Thanks again, best regards, Gegor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Paul Czienskowski 8/13/2010 8:15 PM >>> Hi Gregor, I was trying to to run dipoli to generate the BEM-Models too but often it failed with the very error. With some brains it worked checking everything 'by hand' since the matlab routines to create the surfaces seem to fail sometimes and produce an output that differs from the volume very much (e.g. spikes on the surface). I was facing an error lately when I obviously had some 'Inf' voxels in my volume for some crude reason. You may consider to switch to OpenMEEG because it's much better documented than dipoli (which takes - indeed - no effort at all as dipoli actually is not documented at all) and I think there are prebuilt binaries for Debian on AMD64 infrastructure. If you're trying to run OpenMEEG with more than 3 surfaces, which is supported by OpenMEEG but not by fieldtrip, I may send you my modified scripts. Hope this helps at least a bit. Cheers, Paul Am 11.08.2010 15:52, schrieb Gregor Volberg: > Dear fieldtrippers, > > I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with > > cfg = []; > cfg.tissue = [1 2 3]; > cfg.numvertices = [1000 2000 3000] > cfg.conductivity = [1 1/80 1] > cfg.sourceunits = 'cm' > cfg.mriunits = 'mm' > cfg.method = 'dipoli'; > cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; > vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg > > does the triangulation and computes the BEM model up to the following error message: > > (begin) > .... > Bmat countdown: 5010 (pass 2) > Bmat countdown: 5000 (pass 2) > > > Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface > (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) > > > Warning: an error ocurred while running dipoli >> In dipoli at 90 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. >> In dipoli at 98 > In ft_prepare_bemmodel at 112 > (end) > > I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. > > So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. > > Best regards, Gregor > > > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Mon Aug 16 09:02:23 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Mon, 16 Aug 2010 09:02:23 +0200 Subject: Space alignment - once again Message-ID: Dear Fieldtrippers, I asked this some days ago and didn't get any answer. I don't want to spam, but I need to know strongly. I wasn't able to find out yet, if the space the dipoles are simulated if I'm running ft_dipolesimulation is in some manner aligned to the fiducial space, or if it's all based on the voxel coordinates. It would be a great help, if someone knew the answer. Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Aug 16 09:34:25 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 16 Aug 2010 09:34:25 +0200 Subject: Space alignment - once again In-Reply-To: <4C68E27D.40902@gmx.de> Message-ID: Hi Paul, The simulation routine doesn't care about the co-registration between the volume conductor model and the sensor array. It is your responsibility to ensure that they are correctly aligned. The sources need to be in the same coordinate frame as the sensors, so that's I guess what you refer to as fiducial space. Obviously, if your sensor positions are expressed in voxel space, you need to specify your sources in voxel space as well. Goood luck, Jan-Mathijs On Aug 16, 2010, at 9:02 AM, Paul Czienskowski wrote: > Dear Fieldtrippers, > > I asked this some days ago and didn't get any answer. I don't want > to spam, but I need to know strongly. > I wasn't able to find out yet, if the space the dipoles are > simulated if I'm running ft_dipolesimulation is in some manner > aligned to the fiducial space, or if it's all based on the voxel > coordinates. It would be a great help, if someone knew the answer. > > Cheers, > Paul > > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Aug 16 10:07:04 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Aug 2010 10:07:04 +0200 Subject: post-doc position available in Paris Message-ID: Dear Fieldtrip list members, Appologies for multiple postings. Please find attached a job opportunity in the group of Florian Waszak. best regards, ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: PostDoc_Paris.pdf Type: application/pdf Size: 79622 bytes Desc: not available URL: -------------- next part -------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Aug 16 10:46:15 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 16 Aug 2010 10:46:15 +0200 Subject: Units powspctrm In-Reply-To: <18555530.4689671281680690002.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Arjen, my point is that I am interested not in the relative difference between signals but in the actual difference in microvolt. I know that this is not the standard thing to do but that is what I need . After playing aroud a bit i come to the following conlcusion Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with an amplitude of 100uV and one with an aplitude of 200uV. Computing a power spectrum using matlab fft function I can eventually read out that the difference between my two signals is 100uV. In ft_freqanalysis_mtmfft the signal is multiplied by a taper line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) pad],[],2); The output can hence not be transformed back right away to the real microvolt values, but happens to be scaled (in my case ) by a factor of ~0.036 (which is the mean value of the taper) At least that is what I think happens. Regards Martin 2010/8/13 a.stolk at fcdonders.ru.nl > If you use the same mtmfft settings for both conditions, in theory it > should be fine. Make sure that you compute the fourier transformation on > equal window lenghts. > > If you happen to have variable triallengths per condition, my suggestion > would be to cut the trials in (e.g.) 1 second pieces. This way your > 'frequency resolution' is the same for condition A and B. > > If your experimental setup allows you, you could choose to normalize your > data (e.g. a baselinecorrection) first before making the A and B comparison. > This way you correct for (non-)cognitive powerchanges over time (case it's > not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste > over time, subject habituation effects and whatelse you have. > > Best, > Arjen > > > > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Yes, typically, but is it the case for the powspctrm you get from the > mtmfft > freqanalysis? > I am asking for the following reason: > > Lets say, I have two experimental conditions A and B and I compute the > powerspectra for both of them. > When the units actually are uV^2/Hz i could tell for each frequency by how > much uV A and B differ. > > What confuses me is that in > ft_freqanalysis_mtmfft< > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > signal is multiplied with a taper (tap) and thereby scaled. > The resulting powspctrm hence does not reflect the the true changes in > microvolt. > Do I see that correctly, or am I missing something here? Is the > powerspectrum corrected for that somewhere else? > > Regards, > Martin > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > Hello Martin, > > > > A powerspectrum typically has the frequencies on one axis and the power > of > > the corresponding frequencies on the other. The power represents how > strong > > a certain frequency occurs in a signal, given by the square of the > voltage > > per frequency. > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > Best regards, > > Arjen > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: [FIELDTRIP] Units powspctrm > > > > Hello together, > > > > What units does the powspctrm have? > > Starting with an EEG signal in microvolts and computing the powerspectrum > > using freqanalysis what are the units of powspctrm? > > I tried to figure it out on my own but I am stuck somehow. > > > > Here some example code > > > > cfg=[]; > > cfg.method='mtmfft'; > > cfg.output='pow'; > > cfg.pad ='maxperlen' > > cfg.foilim=[1 130] > > cfg.taper='hanning' > > cfg.channel=1 > > cfg.keeptrials='no' > > > > R=ft_freqanalysis(cfg,data); > > > > I am interested in the units of R.powspctrm > > > > Thanks > > Martin > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Mon Aug 16 10:48:26 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Mon, 16 Aug 2010 10:48:26 +0200 Subject: Space alignment - once again In-Reply-To: Message-ID: Hi Jan-Mathijs, thank you very much. Since I'm trying to compare different models I'll have to do the alignment with the nasion-pre auricular space but I'm already on it. Just needed the info if I was carrying owls to athens. Cheers, Paul Am 16.08.2010 09:34, schrieb jan-mathijs schoffelen: > Hi Paul, > > The simulation routine doesn't care about the co-registration between > the volume conductor model and the sensor array. It is your > responsibility to ensure that they are correctly aligned. The sources > need to be in the same coordinate frame as the sensors, so that's I > guess what you refer to as fiducial space. Obviously, if your sensor > positions are expressed in voxel space, you need to specify your > sources in voxel space as well. > > Goood luck, > > Jan-Mathijs > > > On Aug 16, 2010, at 9:02 AM, Paul Czienskowski wrote: > >> Dear Fieldtrippers, >> >> I asked this some days ago and didn't get any answer. I don't want to >> spam, but I need to know strongly. >> I wasn't able to find out yet, if the space the dipoles are simulated >> if I'm running ft_dipolesimulation is in some manner aligned to the >> fiducial space, or if it's all based on the voxel coordinates. It >> would be a great help, if someone knew the answer. >> >> Cheers, >> Paul >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of >> the FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From a.stolk at FCDONDERS.RU.NL Mon Aug 16 11:43:07 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Mon, 16 Aug 2010 11:43:07 +0200 Subject: Units powspctrm In-Reply-To: <31473261.4755181281951700131.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Martin, I'm not exactly sure what your question is but I just simulated your example with the following: % simulate one second of data, samplefreq = 512 hz fs = 512; t = (1:fs)/fs; a = sin(2*pi*20*t); b = 2*sin(2*pi*20*t); % twice the amplitude figure; plot(t,a); hold on; plot(t,b,'r'); hold off; % simulate preprocessed data cfg = []; cfg.layout = 'CTF275.lay'; cfg.layout = prepare_layout(cfg); data.label = cfg.layout.label(1:273,1); data2.label = data.label; data.fsample = fs; data2.fsample = data.fsample; for j = 1:273 data.trial{1,1}(j,:) = a; data.time{1,1}(j,:) = t; data2.trial{1,1}(j,:) = b; data2.time{1,1}(j,:) = t; end % ft_freqnalysis_mtmfft cfg = []; cfg.output = 'pow'; cfg.channel = 'MEG'; cfg.method = 'mtmfft'; cfg.taper = 'rectwin'; cfg.foilim = [1 40]; cfg.keeptrials = 'no'; cfg.keeptapers = 'no'; mtmfft = ft_freqanalysis(cfg, data); mtmfft2 = ft_freqanalysis(cfg, data2); % four (2^2) times the power figure; plot(mtmfft.powspctrm(1,:)); hold on; plot(mtmfft2.powspctrm(1,:),'r'); Notice that I used a rectangular window in stead of the hanning taper. One of the features of the Hanning taper is that it cuts off the ends of a window. It, therefore, is much more difficult to make a prediction about the scaling. I'm not sure if this has satisfied you but it's the most I can do. For more information of fft, have a read on http://fieldtrip.fcdonders.nl/tutorial/fourier Best regards, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Monday, August 16, 2010 10:46:15 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [FIELDTRIP] Units powspctrm Hi Arjen, my point is that I am interested not in the relative difference between signals but in the actual difference in microvolt. I know that this is not the standard thing to do but that is what I need . After playing aroud a bit i come to the following conlcusion Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with an amplitude of 100uV and one with an aplitude of 200uV. Computing a power spectrum using matlab fft function I can eventually read out that the difference between my two signals is 100uV. In ft_freqanalysis_mtmfft the signal is multiplied by a taper line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) pad],[],2); The output can hence not be transformed back right away to the real microvolt values, but happens to be scaled (in my case ) by a factor of ~0.036 (which is the mean value of the taper) At least that is what I think happens. Regards Martin 2010/8/13 a.stolk at fcdonders.ru.nl > If you use the same mtmfft settings for both conditions, in theory it > should be fine. Make sure that you compute the fourier transformation on > equal window lenghts. > > If you happen to have variable triallengths per condition, my suggestion > would be to cut the trials in (e.g.) 1 second pieces. This way your > 'frequency resolution' is the same for condition A and B. > > If your experimental setup allows you, you could choose to normalize your > data (e.g. a baselinecorrection) first before making the A and B comparison. > This way you correct for (non-)cognitive powerchanges over time (case it's > not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste > over time, subject habituation effects and whatelse you have. > > Best, > Arjen > > > > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Yes, typically, but is it the case for the powspctrm you get from the > mtmfft > freqanalysis? > I am asking for the following reason: > > Lets say, I have two experimental conditions A and B and I compute the > powerspectra for both of them. > When the units actually are uV^2/Hz i could tell for each frequency by how > much uV A and B differ. > > What confuses me is that in > ft_freqanalysis_mtmfft< > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > signal is multiplied with a taper (tap) and thereby scaled. > The resulting powspctrm hence does not reflect the the true changes in > microvolt. > Do I see that correctly, or am I missing something here? Is the > powerspectrum corrected for that somewhere else? > > Regards, > Martin > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > Hello Martin, > > > > A powerspectrum typically has the frequencies on one axis and the power > of > > the corresponding frequencies on the other. The power represents how > strong > > a certain frequency occurs in a signal, given by the square of the > voltage > > per frequency. > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > Best regards, > > Arjen > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: [FIELDTRIP] Units powspctrm > > > > Hello together, > > > > What units does the powspctrm have? > > Starting with an EEG signal in microvolts and computing the powerspectrum > > using freqanalysis what are the units of powspctrm? > > I tried to figure it out on my own but I am stuck somehow. > > > > Here some example code > > > > cfg=[]; > > cfg.method='mtmfft'; > > cfg.output='pow'; > > cfg.pad ='maxperlen' > > cfg.foilim=[1 130] > > cfg.taper='hanning' > > cfg.channel=1 > > cfg.keeptrials='no' > > > > R=ft_freqanalysis(cfg,data); > > > > I am interested in the units of R.powspctrm > > > > Thanks > > Martin > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Aug 16 12:46:14 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 16 Aug 2010 12:46:14 +0200 Subject: Units powspctrm In-Reply-To: <33048706.4755221281951787469.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Arijen, my question simply was how I can get the actual difference in microvolt between two signals when using fieldtrip. I now have a prtty good idee how to do that. Thanks Martin 2010/8/16 a.stolk at fcdonders.ru.nl > Hi Martin, > > I'm not exactly sure what your question is but I just simulated your > example with the following: > > % simulate one second of data, samplefreq = 512 hz > fs = 512; > t = (1:fs)/fs; > a = sin(2*pi*20*t); > b = 2*sin(2*pi*20*t); % twice the amplitude > figure; plot(t,a); > hold on; plot(t,b,'r'); > hold off; > > % simulate preprocessed data > cfg = []; > cfg.layout = 'CTF275.lay'; > cfg.layout = prepare_layout(cfg); > data.label = cfg.layout.label(1:273,1); > data2.label = data.label; > data.fsample = fs; > data2.fsample = data.fsample; > for j = 1:273 > data.trial{1,1}(j,:) = a; > data.time{1,1}(j,:) = t; > data2.trial{1,1}(j,:) = b; > data2.time{1,1}(j,:) = t; > end > > % ft_freqnalysis_mtmfft > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEG'; > cfg.method = 'mtmfft'; > cfg.taper = 'rectwin'; > cfg.foilim = [1 40]; > cfg.keeptrials = 'no'; > cfg.keeptapers = 'no'; > mtmfft = ft_freqanalysis(cfg, data); > mtmfft2 = ft_freqanalysis(cfg, data2); % four (2^2) times the > power > > figure; plot(mtmfft.powspctrm(1,:)); > hold on; plot(mtmfft2.powspctrm(1,:),'r'); > > Notice that I used a rectangular window in stead of the hanning taper. One > of the features of the Hanning taper is that it cuts off the ends of a > window. It, therefore, is much more difficult to make a prediction about the > scaling. > > I'm not sure if this has satisfied you but it's the most I can do. For more > information of fft, have a read on > http://fieldtrip.fcdonders.nl/tutorial/fourier > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Monday, August 16, 2010 10:46:15 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Hi Arjen, > > my point is that I am interested not in the relative difference between > signals but in the actual difference in microvolt. I know that this is not > the standard thing to do but that is what I need . > > After playing aroud a bit i come to the following conlcusion > > Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with > an > amplitude of 100uV and one with an aplitude of 200uV. > Computing a power spectrum using matlab fft function I can eventually read > out that the difference between my two signals is 100uV. > > In ft_freqanalysis_mtmfft the signal is multiplied by a taper > line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) > pad],[],2); > > The output can hence not be transformed back right away to the real > microvolt values, but happens to be scaled (in my case ) by a factor of > ~0.036 (which is the mean value of the taper) > > At least that is what I think happens. > > Regards > Martin > > > > > > 2010/8/13 a.stolk at fcdonders.ru.nl > > > If you use the same mtmfft settings for both conditions, in theory it > > should be fine. Make sure that you compute the fourier transformation on > > equal window lenghts. > > > > If you happen to have variable triallengths per condition, my suggestion > > would be to cut the trials in (e.g.) 1 second pieces. This way your > > 'frequency resolution' is the same for condition A and B. > > > > If your experimental setup allows you, you could choose to normalize your > > data (e.g. a baselinecorrection) first before making the A and B > comparison. > > This way you correct for (non-)cognitive powerchanges over time (case > it's > > not an ABABABAB etc. design). Such as conductivity reducal of the EEG > paste > > over time, subject habituation effects and whatelse you have. > > > > Best, > > Arjen > > > > > > > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: Re: [FIELDTRIP] Units powspctrm > > > > Yes, typically, but is it the case for the powspctrm you get from the > > mtmfft > > freqanalysis? > > I am asking for the following reason: > > > > Lets say, I have two experimental conditions A and B and I compute the > > powerspectra for both of them. > > When the units actually are uV^2/Hz i could tell for each frequency by > how > > much uV A and B differ. > > > > What confuses me is that in > > ft_freqanalysis_mtmfft< > > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > > signal is multiplied with a taper (tap) and thereby scaled. > > The resulting powspctrm hence does not reflect the the true changes in > > microvolt. > > Do I see that correctly, or am I missing something here? Is the > > powerspectrum corrected for that somewhere else? > > > > Regards, > > Martin > > > > > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > > > Hello Martin, > > > > > > A powerspectrum typically has the frequencies on one axis and the power > > of > > > the corresponding frequencies on the other. The power represents how > > strong > > > a certain frequency occurs in a signal, given by the square of the > > voltage > > > per frequency. > > > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > > > Best regards, > > > Arjen > > > > > > ----- Original Message ----- > > > From: "Martin Bleichner" > > > To: FIELDTRIP at NIC.SURFNET.NL > > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / > Berlin > > / > > > Bern / Rome / Stockholm / Vienna > > > Subject: [FIELDTRIP] Units powspctrm > > > > > > Hello together, > > > > > > What units does the powspctrm have? > > > Starting with an EEG signal in microvolts and computing the > powerspectrum > > > using freqanalysis what are the units of powspctrm? > > > I tried to figure it out on my own but I am stuck somehow. > > > > > > Here some example code > > > > > > cfg=[]; > > > cfg.method='mtmfft'; > > > cfg.output='pow'; > > > cfg.pad ='maxperlen' > > > cfg.foilim=[1 130] > > > cfg.taper='hanning' > > > cfg.channel=1 > > > cfg.keeptrials='no' > > > > > > R=ft_freqanalysis(cfg,data); > > > > > > I am interested in the units of R.powspctrm > > > > > > Thanks > > > Martin > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of > the > > > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG > > > and EEG analysis. See also > > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of > the > > > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG > > > and EEG analysis. See also > > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sara.GonzalezAndino at HCUGE.CH Mon Aug 16 12:48:53 2010 From: Sara.GonzalezAndino at HCUGE.CH (GONZALEZ ANDINO Sara) Date: Mon, 16 Aug 2010 12:48:53 +0200 Subject: post-doc position available in Geneva Message-ID: Dear Fieldtrip list members, Please find attached a job offer in the Electrical Neuroimaging Group of the University of Geneva. Best regards, Sara L. Gonzalez ------------------------- Sara L. Gonzalez Andino, PhD, MER Head of the Electrical Neuroimaging Group Department of Clinical Neurosciences Faculty of Medicine, University of Geneva Phone: +41 22 3728323 Fax: + 41 22 3728333 www.electrical-neuroimaging.ch ________________________________________ De : FieldTrip discussion list [FIELDTRIP at nic.surfnet.nl] de la part de Robert Oostenveld [r.oostenveld at FCDONDERS.RU.NL] Date d'envoi : lundi 16 août 2010 10:07 À : FIELDTRIP at nic.surfnet.nl Objet : [FIELDTRIP] post-doc position available in Paris Dear Fieldtrip list members, Appologies for multiple postings. Please find attached a job opportunity in the group of Florian Waszak. best regards, ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Announce_postdoc.doc Type: application/octet-stream Size: 39936 bytes Desc: Announce_postdoc.doc URL: From alexandre.gramfort at INRIA.FR Tue Aug 17 09:45:05 2010 From: alexandre.gramfort at INRIA.FR (Alexandre Gramfort) Date: Tue, 17 Aug 2010 09:45:05 +0200 Subject: OpenMEEG with 4 layers Message-ID: Hi Gregor, you should now be able to run an EEG forward model with 4 layers with OpenMEEG & Fieldtrip. I've added Paul's scripts to the main FT code. You just need to download today's version of FT. Best, Alexandre ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From thomas.hartmann at UNI-KONSTANZ.DE Tue Aug 17 16:51:38 2010 From: thomas.hartmann at UNI-KONSTANZ.DE (Thomas Hartmann) Date: Tue, 17 Aug 2010 16:51:38 +0200 Subject: difference between mtmconvol and mtmfft Message-ID: hi, from the descriptions of the two functions ft_freqanalysis_mtmconvol and ft_freqanalysis_mtmfft i thought that those two functions should work more or less equivalent - the first just doing it multiple times to get a time-frequency representation. to localize a significant cluster from my tf-representation, i recalculated the fft (including the csd, of course) using the exact same arguments for latency, window-size, frequency, padding, taper etc.... but the results do differ. not dramatically but considerably. does anyone have an explanation for this? thanks a lot in advance, thomas -- Dipl. Psych. Thomas Hartmann OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel.: +49 (0)7531 88 4612 Fax: +49 (0)7531-88 4601 Email: thomas.hartmann at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From khoechstetter at BESA.DE Tue Aug 17 18:05:09 2010 From: khoechstetter at BESA.DE (Karsten Hoechstetter) Date: Tue, 17 Aug 2010 18:05:09 +0200 Subject: Job opening for EEG/MEG scientist at MEGIS Software Message-ID: Open job position MEGIS Software GmbH (Munich, Germany) is searching to hire an EEG/MEG scientist to join our support and development team in Germany. Job profile: The successful applicant will - contribute to the development of new analysis techniques and program features - participate in joint research projects with our customers - represent our products and software at neuroimaging conferences - teach the use of our software at customer workshops worldwide - provide scientific and technical support to our customers (predominantly via email) MEGIS is one of the leading developers of EEG/MEG analysis software. Our BESA programs are widely used software for analysis of EEG and MEG data for both research and clinical applications (see www.besa.de). As a free enterprise in the field of science and research we can offer job positions combining the advantages of both fields: Stay in touch with current front-end research work while enjoying the advantages of a permanent position with adequate salary. Applicant’s profile: - The applicant should have a background in nature science (e.g. physics) or psychology, preferential including a PhD degree. - Experience in EEG/MEG data analysis (practical and/or theoretical) is desired. - Knowledge of the BESA software is helpful, but not a must. - Fluency in written and spoken English are a prerequisite for the announced position. - Since the place of work will be mainly our office in Germany, the applicant should be able to communicate in German. - Experience in MATLAB scripting or other programming skills are helpful. - The applicant should be willing to travel to neuroscientific conferences and workshops worldwide 6-8 times per year. Applications should include a current CV, a letter indicating motivation and skills, and a list of publications. Electronic applications preferred. Please send your application to Theodor Scherg ( tscherg at besa.de) or to: MEGIS Software GmbH Freihamer Str. 18 82166 Graefelfing Germany We are looking forward to hearing from you! -------------------------------------- Dr. Karsten Hoechstetter MEGIS Software GmbH Gräfelfing, Germany HRB München 109956 CEO Dr. Michael Scherg -------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Wed Aug 18 10:10:54 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 18 Aug 2010 10:10:54 +0200 Subject: Mesh space vs. voxel space problem Message-ID: Dear fieldtrippers, when looking at the points of the mesh generated for the BEM generation there was something I stumbled over: There are points with negative coordinates, so the mesh seems to be generated in some other space than the voxel system (maybe just translated in some way?). This wouldn't be a great problem if the ft_dipolefitting wasn't working in voxel but in mesh space, because when searching the valid dipole positions in prepare_dipole_grid on lines 432-434 the bounding_mesh function returns a volume full of zeros since the grid positions don't lie within the volume. I'm using the 20100612 version of fieldtrip and running ft_dipolefitting with automatic grid generation. Is there anything I can do about this besides creating the grid on my own? Thanks in advance, Paul -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Wed Aug 18 10:15:23 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 18 Aug 2010 10:15:23 +0200 Subject: Mesh space vs. voxel space problem In-Reply-To: <4C6B958E.1020601@gmx.de> Message-ID: Okay, seems to be solved - at least a little. I now saw that the grid is created from the electrodes positions and not by the mesh points. I'll have to align these to get it right. Cheers, Paul Am 18.08.2010 10:10, schrieb Paul Czienskowski: > Dear fieldtrippers, > > when looking at the points of the mesh generated for the BEM > generation there was something I stumbled over: There are points with > negative coordinates, so the mesh seems to be generated in some other > space than the voxel system (maybe just translated in some way?). This > wouldn't be a great problem if the ft_dipolefitting wasn't working in > voxel but in mesh space, because when searching the valid dipole > positions in prepare_dipole_grid on lines 432-434 the bounding_mesh > function returns a volume full of zeros since the grid positions don't > lie within the volume. I'm using the 20100612 version of fieldtrip and > running ft_dipolefitting with automatic grid generation. Is there > anything I can do about this besides creating the grid on my own? > > Thanks in advance, > Paul > -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Fri Aug 20 14:13:42 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Fri, 20 Aug 2010 14:13:42 +0200 Subject: mne and ft_sourceinterpolate Message-ID: Dear fieldtrippers, I am trying to extract source activity from timelock-data, and I would like to have this for a whole epoch of 1 sec / 501 sample points. I did an ft_sourceanalysis with method = 'mne', which worked fine and gave the desired source activity (see structure "source" below; field "avg" contains "mom" and "pow"). Next I did an ft_sourceinterpolate with "source" and a standard mri as input. Unfortunately, the resulting structure did not contain an "avg" field any more (see "ivol" below) - my functional data got lost during interpolation. Did someone have a similar problem or does someone know a solution? Many thanks in advance for any help! Gregor P.S.: Source interpolation works without problems with method = 'lcmv', but this gives the mean source activity within the desired time range rather than sample-wise activity. It is not a good idea to apply the lcmv beamformer to consecutive time bins and then concatenate the source activity, am I right? source = xgrid: [-66 -56 -46 -36 -26 -16 -6 4 14 24 34 44 54 64] ygrid: [-105 -95 -85 -75 -65 -55 -45 -35 -25 -15 -5 5 15 25 35 45 55 65] zgrid: [-46 -36 -26 -16 -6 4 14 24 34 44 54 64 74 84] dim: [14 18 14] vol: [1x1 struct] time: [1x501 double] pos: [3528x3 double] inside: [1x1808 double] outside: [1x1720 double] method: 'average' avg: [1x1 struct] cfg: [1x1 struct] ivol = inside: [181x217x181 logical] dim: [181 217 181] transform: [4x4 double] anatomy: [181x217x181 uint8] cfg: [1x1 struct] -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Fri Aug 20 15:01:53 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Fri, 20 Aug 2010 15:01:53 +0200 Subject: mne and ft_sourceinterpolate In-Reply-To: <4C6E8D9602000057000071EB@gwsmtp1.uni-regensburg.de> Message-ID: Dear Gregor, What you want to achieve is as of yet not possible. Ft_sourceinterpolate at the moment only interpolates functional parameters which are scalars, e.g. power, or variance averaged over time (in lcmv). We are working at the moment to make the data representation of different types of source reconstructed results more consistent (beamformer versus mne etc), and first will work towards the possibility of visualizing the functional data (including their time courses) without the interpolation. The thing you can do now is to define a meaningful summary statistic of the reconstructed time course, interpolate this one on the anatomy, and click around the anatomical coordinate of your source of interest. Subsequently you need to reverse engineer (undo the interpolation) to find the corresponding source position in your source structure. Then you can use the plot command to look at the time courses. Best, Jan-Mathijs On Aug 20, 2010, at 2:13 PM, Gregor Volberg wrote: > Dear fieldtrippers, > > I am trying to extract source activity from timelock-data, and I > would like to have this for a whole epoch of 1 sec / 501 sample > points. I did an ft_sourceanalysis with method = 'mne', which worked > fine and gave the desired source activity (see structure "source" > below; field "avg" contains "mom" and "pow"). Next I did an > ft_sourceinterpolate with "source" and a standard mri as input. > Unfortunately, the resulting structure did not contain an "avg" > field any more (see "ivol" below) - my functional data got lost > during interpolation. Did someone have a similar problem or does > someone know a solution? > > Many thanks in advance for any help! > Gregor > > P.S.: Source interpolation works without problems with method = > 'lcmv', but this gives the mean source activity within the desired > time range rather than sample-wise activity. It is not a good idea > to apply the lcmv beamformer to consecutive time bins and then > concatenate the source activity, am I right? > > > > source = > > xgrid: [-66 -56 -46 -36 -26 -16 -6 4 14 24 34 44 54 64] > ygrid: [-105 -95 -85 -75 -65 -55 -45 -35 -25 -15 -5 5 15 25 35 > 45 55 65] > zgrid: [-46 -36 -26 -16 -6 4 14 24 34 44 54 64 74 84] > dim: [14 18 14] > vol: [1x1 struct] > time: [1x501 double] > pos: [3528x3 double] > inside: [1x1808 double] > outside: [1x1720 double] > method: 'average' > avg: [1x1 struct] > cfg: [1x1 struct] > > ivol = > > inside: [181x217x181 logical] > dim: [181 217 181] > transform: [4x4 double] > anatomy: [181x217x181 uint8] > cfg: [1x1 struct] > > > > -- > Dr. rer. nat. Gregor Volberg > ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) > University of Regensburg > Institute for Experimental Psychology > 93040 Regensburg, Germany > Tel: +49 941 943 3862 > Fax: +49 941 943 3233 > http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Erin.Oakman at NYUMC.ORG Tue Aug 24 20:19:40 2010 From: Erin.Oakman at NYUMC.ORG (Oakman, Erin) Date: Tue, 24 Aug 2010 14:19:40 -0400 Subject: using ft_freqstatistics with 4 arguments Message-ID: Hi Fieldtrip list, Apparently the nonparametric freqstatistics funtion can be used with a mixed design, to compare power between 2 groups and 2 conditions, using cfg.method = 'montecarlo'. I am giving 4 arguments to ft_freqstatistics. stats = ft_freqstatistics(cfg, group1-condition1, group1-condition2, group2-condition1, group2-condition2) >>From Robert's suggestion here https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind0803&L=FIELDTRIP&P=R13471, the design matrix has been set up with 1 row for the condition (condition numbers "1", "2"), a second row with the subject number and a third row for the two groups ("1", "2"). I set: cfg.ivar = 1; cfg.uvar = 2; cfg.wvar = 3; The trouble is with resampledesign.m, using it in combination with ft_freqstatistics. When resampledesign.m splits the design matrix into a smaller design matrix, using cfg.war, I get the error ??? the design matrix variables should be constant within a block The design matrix is 3 X 100, like this: condition: 1 1 1 1 1 2 2 2 2 2 1 1 1 1 1 2 2 2 2 2 subj number: 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 group: 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 Should a different design matrix be used in this case? Should cfg.wvar = 2 ? Erin ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From tsauvigny at GOOGLEMAIL.COM Wed Aug 25 11:26:03 2010 From: tsauvigny at GOOGLEMAIL.COM (Thomas Sauvigny) Date: Wed, 25 Aug 2010 11:26:03 +0200 Subject: FieldTrip support Message-ID: Dear fieldtrip users! May I ask for your support because of a problem concerning my within-subject permutation test (EEG-Data)? The goal is to compare two grandaverages with two different conditions, each grandaverage consisting of 4 datasets from 4 subjects, each dataset about 40-50 single trials. I did the preprocessing, timelock and grandaverage: 4 datasets (called x1, x4) for the first condition with the following command: cfg = []; cfg.keeptrials = 'yes'; timelock1 = timelockanalysis(cfg, x1); timelock2 = timelockanalysis(cfg, x2); timelock3 = timelockanalysis(cfg, x3); timelock4 = timelockanalysis(cfg, x4); cfg.channel = 'all' cfg.latency = 'all' cfg.keepindividual = 'yes' cfg.normalizevar = 'N-1' da_test1= timelockgrandaverage (cfg, timelock1, timelock2, timelock3, timelock4) save da_test1 Same way for the second condition: da_test2 Now I start the permutation test (file attached). As result there are no significant clusters highlighted (although there are quite large differences in the ERP-plot). I think because there is a mistake concerning the number of single-trials which fieldtrip takes as the basis for the statistic test. Because the output in the command window shows: selected 30 channels selected 2501 time bins selected 1 frequency bins total number of measurements = 8 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 4 levels number of repeated measurements in each level is 2 2 2 2 computing a parmetric threshold for clustering computing statistic estimated time per randomization is 0 seconds computing statistic 1 from 100 found 7 positive clusters in observed data found 11 negative clusters in observed data stat = prob: [30x2501 double] posclusters: [1x7 struct] posclusterslabelmat: [30x2501 double] posdistribution: [1x100 double] negclusters: [1x11 struct] negclusterslabelmat: [30x2501 double] negdistribution: [1x100 double] mask: [30x2501 logical] stat: [30x2501 double] ref: [30x2501 double] dimord: 'chan_time' label: {30x1 cell} time: [1x2501 double] cfg: [1x1 struct] cfg = xlim: [0 0.1000] zlim: 'maxmin' the input is timelock data with 30 channels and 4000 timebins applying preprocessing options averaging trials averaging trial 1 of 4 averaging trial 2 of 4 averaging trial 3 of 4 averaging trial 4 of 4 reading layout from file easycap32ch-avg.lay So, could this be the mistake that fieldtrip guesses “4” to be the number of all trials (perhaps because 4 datasets in each grandaverage??) And how can I solve this problem? Is there a way to account for the single-trial number when using the permutation test? Thank you very much for your help!! Kind regards Thomas Sauvigny Tübingen University ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: da_test_statistic.m URL: From datashare at SCIENCEDB.NET Wed Aug 25 15:42:37 2010 From: datashare at SCIENCEDB.NET (Science DB datashare) Date: Wed, 25 Aug 2010 15:42:37 +0200 Subject: Announcement : EEG/MEG database Message-ID: Dear Fieldtrip users, Data sharing is a great way to find new collaborators. We would like to announce a our new database for EEG/MEG data on ScienceDB.net The concept is simple: If you have data to share you create a new topic in the EEG/MEG data share group’s forum, where you describe your data, and how you want to share it. Please go to : http://sciencedb.net/groups/eegmeg-data-share/ ScienceDB.net is a non-profit portal for the scientific community. Our service is sponsored by ads and donations. If you have any suggestions or comments, please mail us at datashare at sciencedb.net. Kind regards, Science DB http://sciencedb.net/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Wed Aug 25 18:33:18 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Wed, 25 Aug 2010 18:33:18 +0200 Subject: errors in ft_componentsanalysis Message-ID: Dear Fieldtrippers, I have a little problems with cft_componentanalysis and the 'runica' option When running Fieldtrip20100822 on matlab2008b (on Linux and running filedtripdefs before starting the calculations) I get a complaint about the notorious missing randperm.m ??? Undefined function or method 'randperm' for input arguments of type 'double'. Error in ==> runica at 1063 timeperm=randperm(datalength); % shuffle data order at each step Error in ==> ft_componentanalysis at 252 [weights, sphere] = runica(dat, optarg{:}); I thought that running filedtripdefs would take care of this, but seemingly it doesn't. On the other hand if I run it on matlab 2007a, then ft-componentanalysis/runica stops with a warning that the "try catch" syntax will not be supported in future matlab versions ? I do not get an actual error because whatever happens happens in a try-catch statement so errors are suppressed Any suggestions welcome, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From stan.vanpelt at DONDERS.RU.NL Thu Aug 26 10:22:04 2010 From: stan.vanpelt at DONDERS.RU.NL (Stan van Pelt) Date: Thu, 26 Aug 2010 10:22:04 +0200 Subject: difference between mtmconvol and mtmfft In-Reply-To: <4C6AA1FA.8030508@uni-konstanz.de> Message-ID: Dear Thomas, If I understand you correctly you applied ft_freqanalysis_mtmfft on a piece of data that looked interesting based on ft_freqanalysis_mtmconvol, but this gives slightly different results. Please let someone correct me if I'm wrong, but what I think is going on is that for the calculation of power in a time-freq bin, ft_freqanalysis_mtmconvol uses data from adjacent time windows (because of the temporal smoothing). ft_freqanalysis_mtmconvol on the other hand only uses the data that is within your time-freq bin, because the temporal analysis window is equal to the size (along the temporal dimension) of the input data. Best, Stan Stan van Pelt, PhD Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 68495 Fax: (+31) (0)24 36 10989 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Thomas Hartmann Sent: Tuesday, August 17, 2010 4:52 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] difference between mtmconvol and mtmfft hi, from the descriptions of the two functions ft_freqanalysis_mtmconvol and ft_freqanalysis_mtmfft i thought that those two functions should work more or less equivalent - the first just doing it multiple times to get a time-frequency representation. to localize a significant cluster from my tf-representation, i recalculated the fft (including the csd, of course) using the exact same arguments for latency, window-size, frequency, padding, taper etc.... but the results do differ. not dramatically but considerably. does anyone have an explanation for this? thanks a lot in advance, thomas -- Dipl. Psych. Thomas Hartmann OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel.: +49 (0)7531 88 4612 Fax: +49 (0)7531-88 4601 Email: thomas.hartmann at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 27 07:44:45 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 07:44:45 +0200 Subject: Dipole fitting with openMEEG BEM model Message-ID: Dear all, after creating the BEM model for an individual MRI with OpenMEEG i now tried to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab script crashed saying: ??? Output argument "dsm" (and maybe others) not assigned during call to "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m (openmeeg_dsm)". Error in ==> openmeeg_dsm at 16 The actual error may have been some lines above: /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy I'm not really used to use linux and for this reason not familiar with the error messages. I found out that this has to do with any program accessing the shell script file, but since it just has been created and also been closed by the openmeeg_dsm script I don't get it why some other process should access it. I would be very grateful, if anyone could give me a hint how to solve this problem. Thanks in advance, Paul Czienskowski -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Fri Aug 27 07:58:17 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 07:58:17 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: <4C7750CD.6010004@gmx.de> Message-ID: Addendum: The error occurred when scanning grid location 34104 of 800000. So it seems not to be a general error but more something like a exception occurring every once a while. Ain't very good either. It may be very good if someone could explain me what's going on and how to solve it. Paul Am 27.08.2010 07:44, schrieb Paul Czienskowski: > Dear all, > > after creating the BEM model for an individual MRI with OpenMEEG i now > tried to simulate and fit some dipoles, but when calling > openmeeg_dsm.m the matlab script crashed saying: > > ??? Output argument "dsm" (and maybe others) not assigned during call > to > "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m (openmeeg_dsm)". > > Error in ==> openmeeg_dsm at 16 > > The actual error may have been some lines above: > > /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy > > I'm not really used to use linux and for this reason not familiar with > the error messages. I found out that this has to do with any program > accessing the shell script file, but since it just has been created > and also been closed by the openmeeg_dsm script I don't get it why > some other process should access it. I would be very grateful, if > anyone could give me a hint how to solve this problem. > > Thanks in advance, > > Paul Czienskowski > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at INRIA.FR Fri Aug 27 08:15:31 2010 From: alexandre.gramfort at INRIA.FR (Alexandre Gramfort) Date: Fri, 27 Aug 2010 08:15:31 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: <4C7750CD.6010004@gmx.de> Message-ID: Hello Paul, could you share a script to reproduce the problem? -- Alexandre On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: > Dear all, > > after creating the BEM model for an individual MRI with OpenMEEG i now tried > to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab > script crashed saying: > > ??? Output argument "dsm" (and maybe others) not assigned during call to > "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m > (openmeeg_dsm)". > > Error in ==> openmeeg_dsm at 16 > > The actual error may have been some lines above: > > /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy > > I'm not really used to use linux and for this reason not familiar with the > error messages. I found out that this has to do with any program accessing > the shell script file, but since it just has been created and also been > closed by the openmeeg_dsm script I don't get it why some other process > should access it. I would be very grateful, if anyone could give me a hint > how to solve this problem. > > Thanks in advance, > > Paul Czienskowski > > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 27 08:35:25 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 08:35:25 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: Message-ID: If it helps, of course. I attached the script that's calling ft_dipolefitting and another one called by the first one, that's calling ft_prepare_bemmodel. Also I'm using another meshing routine which I wrote by myself which is a bit slower, bur also a bit more dependable than the fieldtrip method, since the ft method to create the meshes from the segmentation produced some ugly spikes for me. But the output of my routine should be near to the output of the fieldtrip routine when it works, so this should be no difference (actually my locations are transformed a bit to match my electrode space, electrode positions for the segmentation are retrieved by the Get1020 method). Cheers, Paul Am 27.08.2010 08:15, schrieb Alexandre Gramfort: > Hello Paul, > > could you share a script to reproduce the problem? > > -- Alexandre > > On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: >> Dear all, >> >> after creating the BEM model for an individual MRI with OpenMEEG i now tried >> to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab >> script crashed saying: >> >> ??? Output argument "dsm" (and maybe others) not assigned during call to >> "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m >> (openmeeg_dsm)". >> >> Error in ==> openmeeg_dsm at 16 >> >> The actual error may have been some lines above: >> >> /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy >> >> I'm not really used to use linux and for this reason not familiar with the >> error messages. I found out that this has to do with any program accessing >> the shell script file, but since it just has been created and also been >> closed by the openmeeg_dsm script I don't get it why some other process >> should access it. I would be very grateful, if anyone could give me a hint >> how to solve this problem. >> >> Thanks in advance, >> >> Paul Czienskowski >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CzSimulation.m URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CreateBEMModel.m URL: From carsten.wolters at UNI-MUENSTER.DE Fri Aug 27 15:58:05 2010 From: carsten.wolters at UNI-MUENSTER.DE (Dr. Carsten Wolters) Date: Fri, 27 Aug 2010 15:58:05 +0200 Subject: Postdoc/PhD position available Message-ID: Dear colleague, please note the attached job posting for a PostDoc/PhD student. I would be greatful, if you could distribute this posting in your department and forward it to colleagues who might be aware of potential candidates. Thank you and best regards, Carsten Wolters ------------------------------------------ For the german research foundation (DFG) project entitled „"Reconstruction of epilepsy-characteristic sources by means of a simultaneous evaluation of EEG- and MEG-data using calibrated realistic headmodels", the Institute for Biomagnetism and Biosignalanalysis (IBB) of the University of Münster offers a position for a *Research scientist (PostDoc or PhD student).* The position is available for 3 years. Payment is according to Bat2a/TVL13. The research project is a cooperation of the IBB with the epilepsy center Erlangen. It aims at reconstructing epilepsy-characteristic electric potentials and magnetic fields for the identification of the epileptogenic zone to improve the therapy of pharmaco-resistant epilepsies. The main project goal is the development and application of methods for a combined source analysis of Electroencephalography (EEG) and Magnetoencephalography (MEG) data in individually optimized finite element head models. The successful applicant holds a degree in informatics, mathematics, physics, biomedical engineering, electrical engineering or similar, and possesses good programming experience (C++ under Linux). Experience with the measurement and analysis of brain signals is advantageous, but not essential. In order to increase the proportion of female staff members, applications from female scientists are particularly encouraged. Disabled applicants are preferred if qualification is equal. The selection procedure starts as the applications come in. Please send your application to Priv.-Doz. Dr.rer.nat. Carsten H. Wolters Institut für Biomagnetismus und Biosignalanalyse Westfälische Wilhelms-Universität Münster Malmedyweg 15 48149 Münster, Germany Tel.: +49 251 83 56904 Fax: +49 251 83 56874 E-Mail: carsten.wolters at uni-muenster.de Web: biomag.uni-muenster.de ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Anz-DFGEpileps-2010_engl.DOC Type: application/msword Size: 29184 bytes Desc: not available URL: From brian.roach at YALE.EDU Fri Aug 27 20:10:21 2010 From: brian.roach at YALE.EDU (Brian Roach) Date: Fri, 27 Aug 2010 11:10:21 -0700 Subject: Fwd: Post-doctoral training in the Neuroscience of Schizophrenia Message-ID: Please e-mail me if you are interested in applying to the position outlined below: ------------------------------------------------------------------------ University of California San Francisco Three post-doctoral fellowships in translational neuroscience of schizophrenia. Sponsor(s): NIMH Application Date(s): Beginning April 1, 2010 The NIMH-funded T32 Training Grant (Neurobiological mechanisms underlying the symptoms and course of schizophrenia) at the University of California in San Francisco is now accepting applications for post-doctoral fellowships from recent PhDs, MDs, and MD/PhDs. Trainees will work in labs studying the neurobiological mechanisms of the symptoms of schizophrenia and its neuro-developmental and neuro-degenerative course. The core T32 faculty are basic neuroscientists and psychiatrists, working in genetics, brain imaging, electrophysiology, and neuroplasticity. They are: Steve Batki, William Byerley, Benjamin Cheyette, Allison Doupe, Judith Ford, Steven Hamilton, Daniel Mathalon, John Rubenstein, Susan Voglmaier, Sophia Vinogradov, and Mark von Zastrow. T32 Trainees will have extended experience in a laboratory, leading to the submission of research papers and grant proposals. Trainees will be dual-mentored with Research and Career Mentors to guide them both formally and informally, through learning neurobiological methods, producing a body of data, presenting data at national meetings, writing and publishing papers, preparing grant proposals, and attending local and national workshops on launching and maintaining successful careers in biological psychiatry. We seek applications from ethnically diverse scientists who have strong academic credentials and US citizenship or permanent residence. NIH rules for T32 trainees state, "The individual to be trained must be a citizen or a noncitizen national of the United States or have been lawfully admitted for permanent residence by the time of award. Individuals who have been lawfully admitted for permanent residence must have a currently valid Alien Registration Receipt Card (I-551) or other legal verification of such status." Potential applicants are welcome to contact any of the core faculty members. An application form is attached. Additional information can be found by visiting our website (http://psych.ucsf.edu/t32/neuro_scz). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ford_T32_Application 7.doc Type: application/msword Size: 95232 bytes Desc: not available URL: From p.vandenhurk at CS.RU.NL Tue Aug 31 10:44:59 2010 From: p.vandenhurk at CS.RU.NL (Paul van den Hurk) Date: Tue, 31 Aug 2010 10:44:59 +0200 Subject: question about freqgrandaverage In-Reply-To: <4C775CAD.7050507@gmx.de> Message-ID: Dear fieldtrippers, I have a question about the function freqgrandaverage. Since I have been quite strict in deleting noisy channels, quite some channels have been removed from individual datasets. Due to the removal of these channels relatively few channels are left when computing the grand average. Could anyone tell me how to adjust the settings of the function in order to calculate the mean in a specific channel over the remaining subjects that do have nicely looking data instead of completely removing the channel from the grand average calculation if only 1 or 2 subjects would show noisy data in this channel? Or would it be better to use the channelrepair function in order to get interpolated values for each subject in such noisy channels? Thanks for your help, Kind regards, Vriendelijke groet, Paul van den Hurk PhD student in Mind-Brain-Mindfulness Group, Faculty of Science, Radboud University, Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, Tel:+31 24 3652240 Email: p.vandenhurk at cs.ru.nl Visiting address: Room HG02.532 Faculty of Science Toernooiveld 1 Nijmegen -----Oorspronkelijk bericht----- Van: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Namens Paul Czienskowski Verzonden: Friday, August 27, 2010 8:35 AM Aan: FIELDTRIP at NIC.SURFNET.NL Onderwerp: Re: [FIELDTRIP] Dipole fitting with openMEEG BEM model If it helps, of course. I attached the script that's calling ft_dipolefitting and another one called by the first one, that's calling ft_prepare_bemmodel. Also I'm using another meshing routine which I wrote by myself which is a bit slower, bur also a bit more dependable than the fieldtrip method, since the ft method to create the meshes from the segmentation produced some ugly spikes for me. But the output of my routine should be near to the output of the fieldtrip routine when it works, so this should be no difference (actually my locations are transformed a bit to match my electrode space, electrode positions for the segmentation are retrieved by the Get1020 method). Cheers, Paul Am 27.08.2010 08:15, schrieb Alexandre Gramfort: > Hello Paul, > > could you share a script to reproduce the problem? > > -- Alexandre > > On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: >> Dear all, >> >> after creating the BEM model for an individual MRI with OpenMEEG i now tried >> to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab >> script crashed saying: >> >> ??? Output argument "dsm" (and maybe others) not assigned during call to >> "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m >> (openmeeg_dsm)". >> >> Error in ==> openmeeg_dsm at 16 >> >> The actual error may have been some lines above: >> >> /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy >> >> I'm not really used to use linux and for this reason not familiar with the >> error messages. I found out that this has to do with any program accessing >> the shell script file, but since it just has been created and also been >> closed by the openmeeg_dsm script I don't get it why some other process >> should access it. I would be very grateful, if anyone could give me a hint >> how to solve this problem. >> >> Thanks in advance, >> >> Paul Czienskowski >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Tue Aug 31 11:07:48 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 31 Aug 2010 11:07:48 +0200 Subject: topograhies wrong when using componetbrowser on the output of fastica Message-ID: Dear Listusers, I compared fastica and runica in ft_componentanalysis and found their output (with respect to component-topographies) to be absolutely different, although component timecourses agree largely. Remembering an earlier post to this list on how the component topography output was fixed (for runica) I think it's possible that this fix broke the topography display for fastica. The reason I suspect this is because the definitions of what an ica weight is differ in EEGLAB (runica.m) and fastica.m, i.e. they are the inverse of each other. Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From michael.wibral at WEB.DE Tue Aug 31 16:42:43 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 31 Aug 2010 16:42:43 +0200 Subject: ft_preprocessinf; ft_preproc_dftfilter Message-ID: Dear listusers, I found something strange in FT20100826: ft_preprocessing takes cfg.dftfilter = 'yes' as a configuration option and I think it should then issue a call to ft_preproc_dftfilter. However this is never done, if I am not mistaken. I guess it slipped from ft_preprocessing sometiem in the past. Or was it dropped on purpose because other bandstop filters are preferred? Any help on this is appreciated. Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From sharonriwkes at GMAIL.COM Mon Aug 2 14:06:12 2010 From: sharonriwkes at GMAIL.COM (sharon riwkes) Date: Mon, 2 Aug 2010 15:06:12 +0300 Subject: Beamforming with reference channels Message-ID: Hi all, I tried to do source localization, after beamforming with the LCMV method. I did it once for all the MEG channels, and once for MEG channels *AND the reference channels*. I was hoping that using the reference channels will improve the localization by ignoring noise coming from outside of the brain. However, I got the *exact same results for MEG+reference channels* as *for MEG alone!* Does anyone know how to include the reference channels effectively in the LCMV beamforming? Thanks for your help, Sharon Riwkes. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at DONDERS.RU.NL Mon Aug 2 15:23:38 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 2 Aug 2010 15:23:38 +0200 Subject: Beamforming with reference channels In-Reply-To: Message-ID: Hi Sharon, If the results are exactly the same, I guess the references have not been taken into account at all. Although it remains to be seen whether you gain a lot with this approach (my preferred alternative would be to clean the data from external noise using the references and taking into account the correction in the forward computation), it should be possible to do it in fieldtrip. To get it to work, you have to check whether the necessary information is present throughout your analysis pipeline. Importantly, when computing the covariance matrix in ft_timelockanalysis, you have to include the references. The same goes for the computation of the leadfields (if you use ft_prepare_leadfield for that). If this information is still present prior to your call to ft_sourceanalysis, you may want to check whether you have to specify cfg.channel (to include the references, rather than 'MEG' (which may be the default, and causes selection of close-to-the-head sensors only). Just for the record: is it 4D-neuroimaging data you are working on? Best wishes, Jan-Mathijs On Aug 2, 2010, at 2:06 PM, sharon riwkes wrote: > Hi all, > I tried to do source localization, after beamforming with the LCMV > method. I did it once for all the MEG channels, and once for MEG > channels AND the reference channels. I was hoping that using the > reference channels will improve the localization by ignoring noise > coming from outside of the brain. > However, I got the exact same results for MEG+reference channels as > for MEG alone! > Does anyone know how to include the reference channels effectively > in the LCMV beamforming? > Thanks for your help, > Sharon Riwkes. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sharonriwkes at GMAIL.COM Wed Aug 4 13:39:16 2010 From: sharonriwkes at GMAIL.COM (sharon riwkes) Date: Wed, 4 Aug 2010 14:39:16 +0300 Subject: Beamforming with reference channels In-Reply-To: Message-ID: Dear Jan-Mathijs, Thanks for your quick answer! I will check the different possibilities. I think that the problem was in the stage the lead field computation. And yes, this is 4D data. Sharon. On Mon, Aug 2, 2010 at 4:23 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Sharon, > > If the results are exactly the same, I guess the references have not been > taken into account at all. Although it remains to be seen whether you gain a > lot with this approach (my preferred alternative would be to clean the data > from external noise using the references and taking into account the > correction in the forward computation), it should be possible to do it in > fieldtrip. To get it to work, you have to check whether the necessary > information is present throughout your analysis pipeline. Importantly, when > computing the covariance matrix in ft_timelockanalysis, you have to include > the references. The same goes for the computation of the leadfields (if you > use ft_prepare_leadfield for that). If this information is still present > prior to your call to ft_sourceanalysis, you may want to check whether you > have to specify cfg.channel (to include the references, rather than 'MEG' > (which may be the default, and causes selection of close-to-the-head sensors > only). > Just for the record: is it 4D-neuroimaging data you are working on? > > Best wishes, > > Jan-Mathijs > > > On Aug 2, 2010, at 2:06 PM, sharon riwkes wrote: > > Hi all, > I tried to do source localization, after beamforming with the LCMV method. > I did it once for all the MEG channels, and once for MEG channels *AND the > reference channels*. I was hoping that using the reference channels will > improve the localization by ignoring noise coming from outside of the brain. > > However, I got the *exact same results for MEG+reference channels* as *for > MEG alone!* > Does anyone know how to include the reference channels effectively in the > LCMV beamforming? > Thanks for your help, > Sharon Riwkes. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Thu Aug 5 15:49:39 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Thu, 5 Aug 2010 15:49:39 +0200 Subject: significance of coherence differences Message-ID: Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,...] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,...]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Panagiotis.Tsiatsis at TUEBINGEN.MPG.DE Fri Aug 6 10:44:56 2010 From: Panagiotis.Tsiatsis at TUEBINGEN.MPG.DE (Panagiotis Tsiatsis) Date: Fri, 6 Aug 2010 10:44:56 +0200 Subject: Removing ECG artifacts via ICA in a Steady State experiment without EMG Channel (MEG) Message-ID: Dear all, I am a newbie in fieldtrip. First of all I would like to say thanks for your beautiful work and support. I am facing the following problem : I am running a Visual Steady State MEG experiment (CTF scanner) and I want to remove the ECG artifacts but I do not have an EMG channel available. I haven't managed to go fully through the analysis (by the way, I was getting errors when trying to run your ICA ECG example, but let me take another look) but I am worried that by using the 'left' MEG channels (MLT) alone to detect the artifacts I will not manage to go far, as the ECG activity will be obscured by the steady state activity (10 Hz flickering light) and I will not be able to from a proper averaged / typical ECG. Does anybody have any experience with this? I know that it is quite silly to ask you before trying completely and therefore I apologize beforehand. Once I have fully gone through the analysis I can inform you on whether I managed to do it reliably. Thanks and best, Panagiotis ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Mon Aug 9 18:58:57 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Mon, 9 Aug 2010 18:58:57 +0200 Subject: significance of coherence differences In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0176EB70@Mail2-UKD.VMED.UKD> Message-ID: Hi Jan, If you get confused about the literature then I am partly to blame. Things are different for single subject studies (units-of-observation are trials) and multiple subject studies (units-of-observation are subjects). You describe a multiple subject study of the within-subjects type (every subjects participates in both experimental conditions). For a single channel pair and a single frequency bin, the appropriate statistic is the dependent (paired) samples t-statistic or, in a nonparametric framework, the Wilcoxon signed rank sum test. (You mention the Wilcoxon rank sum test, but this is for a study of the between-subjects type.) You apply this test statistic to the condition-specific coherences, obtained by summing and normalizing the trial(taper)-specific cross-spectra. This statistical test works fine (asymptotically, for the dependent samples t-statistic) if the number of trials in the two conditions are equal. The requirement of an equal number of trials follows from the fact that coherence is a biased measure, with the bias being dependent on the number of trials. The situation is different for a single subject study. You may want to have a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals with the multiple comparisons problem. Best, Eric dr. Eric Maris Donders Institute for Brain, Cognition and Behavior Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging Radboud University P.O. Box 9104 6500 HE Nijmegen The Netherlands T:+31 24 3612651 Mobile: 06 39584581 F:+31 24 3616066 E: e. maris at donders.ru.nl From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: donderdag 5 augustus 2010 15:50 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] significance of coherence differences Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Tue Aug 10 09:57:28 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 10 Aug 2010 09:57:28 +0200 Subject: OpenMEEG: libraries not found Message-ID: Dear all, I'm trying to run OpenMEEG from fieldtrip, but the executables complain about libstdc++.so.6 missing. I'm quite sure that libstdc++ v6 is installed, but om_assemble seems to expect it to be in /usr/local/matlab/sys/os/glnx86/, not in /lib/. Unfortunately none of the Tutorials and Read-mes seems to deal with this. I've got no clue, how to handle this and it would be nice, if any of you could help me. Cheers and thanks in advance, Paul PS: When running om_assemble from command line, it runs without any problem -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Tue Aug 10 10:47:52 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Tue, 10 Aug 2010 10:47:52 +0200 Subject: AW: [FIELDTRIP] significance of coherence differences Message-ID: Dear Eric, thank you for your answer. I read the paper and see that your method is a great tool to deal with the MCP and with situations in which one does not know at which frequencies and channels an effect is expected. It is good to know that for the group level (multiple subjects, all measured in the same set of conditions) conventional paired-sample statistics are appropriate, beacause I dont see how the random-partition procedure relates to such a situation. All the best, Jan -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von Eric Maris Gesendet: Mo 09.08.2010 18:58 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] significance of coherence differences Hi Jan, If you get confused about the literature then I am partly to blame. Things are different for single subject studies (units-of-observation are trials) and multiple subject studies (units-of-observation are subjects). You describe a multiple subject study of the within-subjects type (every subjects participates in both experimental conditions). For a single channel pair and a single frequency bin, the appropriate statistic is the dependent (paired) samples t-statistic or, in a nonparametric framework, the Wilcoxon signed rank sum test. (You mention the Wilcoxon rank sum test, but this is for a study of the between-subjects type.) You apply this test statistic to the condition-specific coherences, obtained by summing and normalizing the trial(taper)-specific cross-spectra. This statistical test works fine (asymptotically, for the dependent samples t-statistic) if the number of trials in the two conditions are equal. The requirement of an equal number of trials follows from the fact that coherence is a biased measure, with the bias being dependent on the number of trials. The situation is different for a single subject study. You may want to have a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals with the multiple comparisons problem. Best, Eric dr. Eric Maris Donders Institute for Brain, Cognition and Behavior Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging Radboud University P.O. Box 9104 6500 HE Nijmegen The Netherlands T:+31 24 3612651 Mobile: 06 39584581 F:+31 24 3616066 E: e. maris at donders.ru.nl From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: donderdag 5 augustus 2010 15:50 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] significance of coherence differences Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Tue Aug 10 11:55:26 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 10 Aug 2010 11:55:26 +0200 Subject: OpenMEEG: libraries not found In-Reply-To: <4C610668.30405@gmx.de> Message-ID: Dear all, with a little help of a colleague I was able to run the OpenMEEG executables but we had to move all of the files from the matlab/sys/os/glnx86 folder to another place and link everything from my /usr/lib/ dir to the glnx folder. It works, but really aint the best way in my opinion. Is there another - slightly more sensible - way to go? Cheers, Paul Am 10.08.2010 09:57, schrieb Paul Czienskowski: > Dear all, > > I'm trying to run OpenMEEG from fieldtrip, but the executables > complain about libstdc++.so.6 missing. I'm quite sure that libstdc++ > v6 is installed, but om_assemble seems to expect it to be in > /usr/local/matlab/sys/os/glnx86/, not in /lib/. Unfortunately none of > the Tutorials and Read-mes seems to deal with this. I've got no clue, > how to handle this and it would be nice, if any of you could help me. > > Cheers and thanks in advance, > Paul > > PS: When running om_assemble from command line, it runs without any > problem > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Tue Aug 10 12:47:47 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Tue, 10 Aug 2010 12:47:47 +0200 Subject: AW: [FIELDTRIP] significance of coherence differences In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8BA2E57B@Mail2-UKD.VMED.UKD> Message-ID: Hi Jan, > thank you for your answer. I read the paper and see that your method is > a great tool to deal with the MCP and with situations in which one does > not know at which frequencies and channels an effect is expected. It is > good to know that for the group level (multiple subjects, all measured > in the same set of conditions) conventional paired-sample statistics > are appropriate, beacause I dont see how the random-partition procedure > relates to such a situation. I does not, because the random partitioning procedure only applies to single subject studies (UOs are trials). In a within-subjects multiple subject study the random aspect is in the random permutation of the elements in the paired observations. Best, Eric > > All the best, > Jan > > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von Eric Maris > Gesendet: Mo 09.08.2010 18:58 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] significance of coherence differences > > Hi Jan, > > > > > > If you get confused about the literature then I am partly to blame. > > > > Things are different for single subject studies (units-of-observation > are > trials) and multiple subject studies (units-of-observation are > subjects). > You describe a multiple subject study of the within-subjects type > (every > subjects participates in both experimental conditions). For a single > channel > pair and a single frequency bin, the appropriate statistic is the > dependent > (paired) samples t-statistic or, in a nonparametric framework, the > Wilcoxon > signed rank sum test. (You mention the Wilcoxon rank sum test, but this > is > for a study of the between-subjects type.) You apply this test > statistic to > the condition-specific coherences, obtained by summing and normalizing > the > trial(taper)-specific cross-spectra. This statistical test works fine > (asymptotically, for the dependent samples t-statistic) if the number > of > trials in the two conditions are equal. The requirement of an equal > number > of trials follows from the fact that coherence is a biased measure, > with the > bias being dependent on the number of trials. > > > > The situation is different for a single subject study. You may want to > have > a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals > with > the multiple comparisons problem. > > > > > > Best, > > > > Eric > > > > > > dr. Eric Maris > Donders Institute for Brain, Cognition and Behavior > > Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging > > Radboud University > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > T:+31 24 3612651 > Mobile: 06 39584581 > > F:+31 24 3616066 > E: e. maris at donders.ru.nl > > > > > > > > > > > > > > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On > Behalf > Of Jan Hirschmann > Sent: donderdag 5 augustus 2010 15:50 > To: FIELDTRIP at NIC.SURFNET.NL > Subject: [FIELDTRIP] significance of coherence differences > > > > Dear fieldtrip experts, > > > > I am getting more and more confused about the literature of > significance > tests of coherence differences. The one essential point I did not quite > understand is why conventional tests do not seem to apply. Lets say I > have > two vectors of mean alpha band coherences, relating to two experimental > conditions (continuous data, no trials). The vector entries stem from > different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and > C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from > comparing the two vectors, say, with a Wilcoxon ranksum test? > > > > Thanks for any comments, > > > > Jan Hirschmann > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of > the > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Tue Aug 10 17:46:57 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Tue, 10 Aug 2010 11:46:57 -0400 Subject: inter trial coherence Message-ID: Hello Fieldtrippers, I am now trying to do the frequencyanalysis with my eeg data in Fieldtrip. With the function of 'freqanalysis', i got my TFR data. Now i have a question: does fieldtrip have a function that gives "phase locking factor" or inter-trial coherence (ITC)? I apologize in advance if my questions are too obvious. Thanks for your help, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.vandermeij at DONDERS.RU.NL Wed Aug 11 09:33:41 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Wed, 11 Aug 2010 09:33:41 +0200 Subject: inter trial coherence In-Reply-To: <4C617471.4040809@rotman-baycrest.on.ca> Message-ID: Hi Yu, Have a look at the function ft_connectivityanalysis, that should be able get you what you want. Regards, Roemer On 8/10/2010 5:46 PM, Yu He wrote: > Hello Fieldtrippers, > > I am now trying to do the frequencyanalysis with my eeg data in > Fieldtrip. > > With the function of 'freqanalysis', i got my TFR data. > Now i have a question: does fieldtrip have a function that gives > "phase locking factor" or inter-trial coherence (ITC)? > I apologize in advance if my questions are too obvious. > > Thanks for your help, > > Yu > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Wed Aug 11 09:59:30 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 11 Aug 2010 09:59:30 +0200 Subject: Volume conductor space alignment Message-ID: Dear all, I'm trying to simulate and fit EEG data with different models for my diploma thesis and I have another little question. I wondered if there is any alignment done before or when simulating the data or if the simulation's done in the space the BEM model was created from. I'd like to know this to know if I'd have to align my spaces on my own or if everything is in the space spanned by the fidcial points anyway. Thanks in advance, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From khoechstetter at BESA.DE Wed Aug 11 13:29:35 2010 From: khoechstetter at BESA.DE (Karsten Hoechstetter) Date: Wed, 11 Aug 2010 13:29:35 +0200 Subject: Upcoming BESA Workshop in London (September 9-10) Message-ID: Dear colleagues, I would like to inform you that a 2-day BESA Research workshop will be held in London/UK on September 9-10. This workshop provides a thorough introduction to BESA Research, the software package for comprehensive EEG/MEG data analysis. Target group of the workshop are both novices and existing BESA users. The workshop includes hands-on tutorials on the new features of BESA Research 5.3, e.g. the direct MATLAB interface and CLARA, the new 3D source imaging technique. Covered topics will include: - A theoretical introduction to source analysis - Hands-on source analysis with simulated and real data sets - Data preprocessing in BESA Research: Artifact rejection and correction, channel interpolation, digital filtering, 3D mapping, remontaging, averaging - Coregistration with (f)MRI - Time-frequency analysis and source coherence - Beamforming - 3D volume imaging: CLARA, LORETA, sLORETA, minimum norm etc. - Batch scripting For more information, schedule, and registration, please visit the BESA website at www.besa.de/events/workshops. If you have any further questions, please contact workshop at besa.de. I would be glad to see you on one of these occasions! Best wishes, Karsten Hoechstetter -------------------------------------- Dr. Karsten Hoechstetter MEGIS Software GmbH Gräfelfing, Germany HRB München 109956 CEO Dr. Michael Scherg -------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Wed Aug 11 15:52:31 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Wed, 11 Aug 2010 15:52:31 +0200 Subject: unclosed surfaces with BEM models Message-ID: Dear fieldtrippers, I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with cfg = []; cfg.tissue = [1 2 3]; cfg.numvertices = [1000 2000 3000] cfg.conductivity = [1 1/80 1] cfg.sourceunits = 'cm' cfg.mriunits = 'mm' cfg.method = 'dipoli'; cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg does the triangulation and computes the BEM model up to the following error message: (begin) .... Bmat countdown: 5010 (pass 2) Bmat countdown: 5000 (pass 2) Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) Warning: an error ocurred while running dipoli > In dipoli at 90 In ft_prepare_bemmodel at 112 Error using ==> fread Invalid file identifier. Use fopen to generate a valid file identifier. Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. > In dipoli at 98 In ft_prepare_bemmodel at 112 (end) I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. Best regards, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Wed Aug 11 16:25:37 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Wed, 11 Aug 2010 16:25:37 +0200 Subject: inter trial coherence Message-ID: Thanks Roemer! I am not very clear about function of ft_connectivityanalysis. It is said "FT_CONNECTIVITYANALYIS computes various measures of connectivity between MEG/EEG channels or between source-level signals." when you read the documentation reference. Is that only for between MEG/EEG channels? Regards, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Aug 11 16:35:21 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 11 Aug 2010 16:35:21 +0200 Subject: inter trial coherence In-Reply-To: Message-ID: Dear Yu, Ft_connectivityanalysis works also with different kinds of electrophysiological data. It's on our list to make the documentation to this function clearer. This will hopefully happen soon. For now, I don't think this is the function you need for inter-trial coherence. Ft_connectivityanalysis computes bivariate metrics, i.e. measures of connectivity defined between channel pairs. In your case, you want to estimate the consistency of oscillatory phase across trials (and not the consistency of the phase difference between a pair of channels across trials). So what you need to do is probably something like this: cfg = []; cfg.output = 'fourier'; cfg..... cfg..... cfg..... freq = ft_freqanalysis(cfg, data); Next, to obtain the itc, do the following tmpdat = freq.fourierspctrm; tmpdat = tmpdat(abs(tmpdat)); % this will normalise each trial for its amplitude; itc = abs(mean(tmpdat)); % this will give the itc Best wishes, Jan-Mathijs On Aug 11, 2010, at 4:25 PM, Yu He wrote: > Thanks Roemer! > > I am not very clear about function of ft_connectivityanalysis. It is > said "FT_CONNECTIVITYANALYIS computes various measures of connectivity > between MEG/EEG channels or between source-level signals." when you > read > the documentation reference. > > Is that only for between MEG/EEG channels? > > Regards, > > Yu > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Aug 11 16:50:48 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 11 Aug 2010 16:50:48 +0200 Subject: inter trial coherence In-Reply-To: <2C2E534F-B24F-4D03-A32B-70A15D6ABAFC@donders.ru.nl> Message-ID: Dear Yu, I made a slight typo in my previous mail. Obviously tmpdat = tmpdat(abs(tmpdat)); % this will normalise each trial for its amplitude; should read tmpdat = tmpdat./abs(tmpdat); for the normalization to work. Best wishes, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Wed Aug 11 18:50:23 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Wed, 11 Aug 2010 18:50:23 +0200 Subject: inter trial coherence Message-ID: Dear Jan-Mathijs, That's great! Thank you so much for the step by step explanation. Best regs, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Thu Aug 12 17:52:19 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 12 Aug 2010 17:52:19 +0200 Subject: Units powspctrm Message-ID: Hello together, What units does the powspctrm have? Starting with an EEG signal in microvolts and computing the powerspectrum using freqanalysis what are the units of powspctrm? I tried to figure it out on my own but I am stuck somehow. Here some example code cfg=[]; cfg.method='mtmfft'; cfg.output='pow'; cfg.pad ='maxperlen' cfg.foilim=[1 130] cfg.taper='hanning' cfg.channel=1 cfg.keeptrials='no' R=ft_freqanalysis(cfg,data); I am interested in the units of R.powspctrm Thanks Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Thu Aug 12 21:38:57 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Thu, 12 Aug 2010 21:38:57 +0200 Subject: Units powspctrm In-Reply-To: <942108.4682501281641712211.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hello Martin, A powerspectrum typically has the frequencies on one axis and the power of the corresponding frequencies on the other. The power represents how strong a certain frequency occurs in a signal, given by the square of the voltage per frequency. In your case: square of the microvolts per frequency: uV^2/ Hz Best regards, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] Units powspctrm Hello together, What units does the powspctrm have? Starting with an EEG signal in microvolts and computing the powerspectrum using freqanalysis what are the units of powspctrm? I tried to figure it out on my own but I am stuck somehow. Here some example code cfg=[]; cfg.method='mtmfft'; cfg.output='pow'; cfg.pad ='maxperlen' cfg.foilim=[1 130] cfg.taper='hanning' cfg.channel=1 cfg.keeptrials='no' R=ft_freqanalysis(cfg,data); I am interested in the units of R.powspctrm Thanks Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Thu Aug 12 22:48:14 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 12 Aug 2010 22:48:14 +0200 Subject: Units powspctrm In-Reply-To: <7050041.4682621281641937538.JavaMail.root@watertor.uci.ru.nl> Message-ID: Yes, typically, but is it the case for the powspctrm you get from the mtmfft freqanalysis? I am asking for the following reason: Lets say, I have two experimental conditions A and B and I compute the powerspectra for both of them. When the units actually are uV^2/Hz i could tell for each frequency by how much uV A and B differ. What confuses me is that in ft_freqanalysis_mtmfftthe signal is multiplied with a taper (tap) and thereby scaled. The resulting powspctrm hence does not reflect the the true changes in microvolt. Do I see that correctly, or am I missing something here? Is the powerspectrum corrected for that somewhere else? Regards, Martin 2010/8/12 a.stolk at fcdonders.ru.nl > Hello Martin, > > A powerspectrum typically has the frequencies on one axis and the power of > the corresponding frequencies on the other. The power represents how strong > a certain frequency occurs in a signal, given by the square of the voltage > per frequency. > > In your case: square of the microvolts per frequency: uV^2/ Hz > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Units powspctrm > > Hello together, > > What units does the powspctrm have? > Starting with an EEG signal in microvolts and computing the powerspectrum > using freqanalysis what are the units of powspctrm? > I tried to figure it out on my own but I am stuck somehow. > > Here some example code > > cfg=[]; > cfg.method='mtmfft'; > cfg.output='pow'; > cfg.pad ='maxperlen' > cfg.foilim=[1 130] > cfg.taper='hanning' > cfg.channel=1 > cfg.keeptrials='no' > > R=ft_freqanalysis(cfg,data); > > I am interested in the units of R.powspctrm > > Thanks > Martin > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Fri Aug 13 08:24:50 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Fri, 13 Aug 2010 08:24:50 +0200 Subject: Units powspctrm In-Reply-To: <5621986.4689631281680620957.JavaMail.root@watertor.uci.ru.nl> Message-ID: If you use the same mtmfft settings for both conditions, in theory it should be fine. Make sure that you compute the fourier transformation on equal window lenghts. If you happen to have variable triallengths per condition, my suggestion would be to cut the trials in (e.g.) 1 second pieces. This way your 'frequency resolution' is the same for condition A and B. If your experimental setup allows you, you could choose to normalize your data (e.g. a baselinecorrection) first before making the A and B comparison. This way you correct for (non-)cognitive powerchanges over time (case it's not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste over time, subject habituation effects and whatelse you have. Best, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [FIELDTRIP] Units powspctrm Yes, typically, but is it the case for the powspctrm you get from the mtmfft freqanalysis? I am asking for the following reason: Lets say, I have two experimental conditions A and B and I compute the powerspectra for both of them. When the units actually are uV^2/Hz i could tell for each frequency by how much uV A and B differ. What confuses me is that in ft_freqanalysis_mtmfftthe signal is multiplied with a taper (tap) and thereby scaled. The resulting powspctrm hence does not reflect the the true changes in microvolt. Do I see that correctly, or am I missing something here? Is the powerspectrum corrected for that somewhere else? Regards, Martin 2010/8/12 a.stolk at fcdonders.ru.nl > Hello Martin, > > A powerspectrum typically has the frequencies on one axis and the power of > the corresponding frequencies on the other. The power represents how strong > a certain frequency occurs in a signal, given by the square of the voltage > per frequency. > > In your case: square of the microvolts per frequency: uV^2/ Hz > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Units powspctrm > > Hello together, > > What units does the powspctrm have? > Starting with an EEG signal in microvolts and computing the powerspectrum > using freqanalysis what are the units of powspctrm? > I tried to figure it out on my own but I am stuck somehow. > > Here some example code > > cfg=[]; > cfg.method='mtmfft'; > cfg.output='pow'; > cfg.pad ='maxperlen' > cfg.foilim=[1 130] > cfg.taper='hanning' > cfg.channel=1 > cfg.keeptrials='no' > > R=ft_freqanalysis(cfg,data); > > I am interested in the units of R.powspctrm > > Thanks > Martin > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Aug 13 19:11:12 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 13 Aug 2010 19:11:12 +0200 Subject: coherence again In-Reply-To: A<18555530.4689671281680690002.JavaMail.root@watertor.uci.ru.nl> Message-ID: Dear fieldtrip experts, I have yet another question about the statistical testing of coherence. Again, it relates to the group level, this time to the testing procedure used in "Imaging the motor system's beta-band synchronisation during isometric contraction", Schoffeleln et al., NeuroImage, 2008. There it says: " The null hypothesis that was tested at the voxel level states that the Z-transformed coherence between the EMG and that voxel, accumulated across subjects, is not different from 0. Under this null hypothesis, flipping the sign of the Z-transformed coherence values of a random subset of the subjects before accumulating leads to an alternative observation that belongs to the null distribution." Now, as I understand it, the Z-transformation described here is z=sqrt(-(df-2)*log(1-abs(C)^2)), i.e. z takes only positive values (there is no comparing of conditions here) And accumulation, it later says, means summing up the z-values of all subjects and dividing by sqrt(n) at each voxel. I suppose n is the number of subjects. So "flipping the sign" means multiplying the z-value of some subjects by -1 before summing up? As all z-values were originally positive, this will inevitably decrease the sum. So the original state will inevitably be the extreme end of the distribution. Sorry, I must have some serious error in my thinking here (hope it's not too obvious). Can you help me? Many thanks, Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 13 20:15:08 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 13 Aug 2010 20:15:08 +0200 Subject: unclosed surfaces with BEM models In-Reply-To: <4C62C73F020000570000710A@gwsmtp1.uni-regensburg.de> Message-ID: Hi Gregor, I was trying to to run dipoli to generate the BEM-Models too but often it failed with the very error. With some brains it worked checking everything 'by hand' since the matlab routines to create the surfaces seem to fail sometimes and produce an output that differs from the volume very much (e.g. spikes on the surface). I was facing an error lately when I obviously had some 'Inf' voxels in my volume for some crude reason. You may consider to switch to OpenMEEG because it's much better documented than dipoli (which takes - indeed - no effort at all as dipoli actually is not documented at all) and I think there are prebuilt binaries for Debian on AMD64 infrastructure. If you're trying to run OpenMEEG with more than 3 surfaces, which is supported by OpenMEEG but not by fieldtrip, I may send you my modified scripts. Hope this helps at least a bit. Cheers, Paul Am 11.08.2010 15:52, schrieb Gregor Volberg: > Dear fieldtrippers, > > I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with > > cfg = []; > cfg.tissue = [1 2 3]; > cfg.numvertices = [1000 2000 3000] > cfg.conductivity = [1 1/80 1] > cfg.sourceunits = 'cm' > cfg.mriunits = 'mm' > cfg.method = 'dipoli'; > cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; > vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg > > does the triangulation and computes the BEM model up to the following error message: > > (begin) > .... > Bmat countdown: 5010 (pass 2) > Bmat countdown: 5000 (pass 2) > > > Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface > (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) > > > Warning: an error ocurred while running dipoli >> In dipoli at 90 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. >> In dipoli at 98 > In ft_prepare_bemmodel at 112 > (end) > > I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. > > So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. > > Best regards, Gregor > > > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Mon Aug 16 08:18:13 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Mon, 16 Aug 2010 08:18:13 +0200 Subject: Antw: Re: [FIELDTRIP] unclosed surfaces with BEM models In-Reply-To: <4C658BAC.8060709@gmx.de> Message-ID: Hi Paul, thanks a lot for your reply! I will try OpenMEEG and I hope I can fix the error soon. Meanwhile, I would be very glad if you could send me your modified script for > 3 surfaces. This will surely help... Thanks again, best regards, Gegor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Paul Czienskowski 8/13/2010 8:15 PM >>> Hi Gregor, I was trying to to run dipoli to generate the BEM-Models too but often it failed with the very error. With some brains it worked checking everything 'by hand' since the matlab routines to create the surfaces seem to fail sometimes and produce an output that differs from the volume very much (e.g. spikes on the surface). I was facing an error lately when I obviously had some 'Inf' voxels in my volume for some crude reason. You may consider to switch to OpenMEEG because it's much better documented than dipoli (which takes - indeed - no effort at all as dipoli actually is not documented at all) and I think there are prebuilt binaries for Debian on AMD64 infrastructure. If you're trying to run OpenMEEG with more than 3 surfaces, which is supported by OpenMEEG but not by fieldtrip, I may send you my modified scripts. Hope this helps at least a bit. Cheers, Paul Am 11.08.2010 15:52, schrieb Gregor Volberg: > Dear fieldtrippers, > > I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with > > cfg = []; > cfg.tissue = [1 2 3]; > cfg.numvertices = [1000 2000 3000] > cfg.conductivity = [1 1/80 1] > cfg.sourceunits = 'cm' > cfg.mriunits = 'mm' > cfg.method = 'dipoli'; > cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; > vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg > > does the triangulation and computes the BEM model up to the following error message: > > (begin) > .... > Bmat countdown: 5010 (pass 2) > Bmat countdown: 5000 (pass 2) > > > Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface > (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) > > > Warning: an error ocurred while running dipoli >> In dipoli at 90 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. >> In dipoli at 98 > In ft_prepare_bemmodel at 112 > (end) > > I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. > > So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. > > Best regards, Gregor > > > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Mon Aug 16 09:02:23 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Mon, 16 Aug 2010 09:02:23 +0200 Subject: Space alignment - once again Message-ID: Dear Fieldtrippers, I asked this some days ago and didn't get any answer. I don't want to spam, but I need to know strongly. I wasn't able to find out yet, if the space the dipoles are simulated if I'm running ft_dipolesimulation is in some manner aligned to the fiducial space, or if it's all based on the voxel coordinates. It would be a great help, if someone knew the answer. Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Aug 16 09:34:25 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 16 Aug 2010 09:34:25 +0200 Subject: Space alignment - once again In-Reply-To: <4C68E27D.40902@gmx.de> Message-ID: Hi Paul, The simulation routine doesn't care about the co-registration between the volume conductor model and the sensor array. It is your responsibility to ensure that they are correctly aligned. The sources need to be in the same coordinate frame as the sensors, so that's I guess what you refer to as fiducial space. Obviously, if your sensor positions are expressed in voxel space, you need to specify your sources in voxel space as well. Goood luck, Jan-Mathijs On Aug 16, 2010, at 9:02 AM, Paul Czienskowski wrote: > Dear Fieldtrippers, > > I asked this some days ago and didn't get any answer. I don't want > to spam, but I need to know strongly. > I wasn't able to find out yet, if the space the dipoles are > simulated if I'm running ft_dipolesimulation is in some manner > aligned to the fiducial space, or if it's all based on the voxel > coordinates. It would be a great help, if someone knew the answer. > > Cheers, > Paul > > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Aug 16 10:07:04 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Aug 2010 10:07:04 +0200 Subject: post-doc position available in Paris Message-ID: Dear Fieldtrip list members, Appologies for multiple postings. Please find attached a job opportunity in the group of Florian Waszak. best regards, ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: PostDoc_Paris.pdf Type: application/pdf Size: 79622 bytes Desc: not available URL: -------------- next part -------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Aug 16 10:46:15 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 16 Aug 2010 10:46:15 +0200 Subject: Units powspctrm In-Reply-To: <18555530.4689671281680690002.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Arjen, my point is that I am interested not in the relative difference between signals but in the actual difference in microvolt. I know that this is not the standard thing to do but that is what I need . After playing aroud a bit i come to the following conlcusion Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with an amplitude of 100uV and one with an aplitude of 200uV. Computing a power spectrum using matlab fft function I can eventually read out that the difference between my two signals is 100uV. In ft_freqanalysis_mtmfft the signal is multiplied by a taper line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) pad],[],2); The output can hence not be transformed back right away to the real microvolt values, but happens to be scaled (in my case ) by a factor of ~0.036 (which is the mean value of the taper) At least that is what I think happens. Regards Martin 2010/8/13 a.stolk at fcdonders.ru.nl > If you use the same mtmfft settings for both conditions, in theory it > should be fine. Make sure that you compute the fourier transformation on > equal window lenghts. > > If you happen to have variable triallengths per condition, my suggestion > would be to cut the trials in (e.g.) 1 second pieces. This way your > 'frequency resolution' is the same for condition A and B. > > If your experimental setup allows you, you could choose to normalize your > data (e.g. a baselinecorrection) first before making the A and B comparison. > This way you correct for (non-)cognitive powerchanges over time (case it's > not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste > over time, subject habituation effects and whatelse you have. > > Best, > Arjen > > > > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Yes, typically, but is it the case for the powspctrm you get from the > mtmfft > freqanalysis? > I am asking for the following reason: > > Lets say, I have two experimental conditions A and B and I compute the > powerspectra for both of them. > When the units actually are uV^2/Hz i could tell for each frequency by how > much uV A and B differ. > > What confuses me is that in > ft_freqanalysis_mtmfft< > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > signal is multiplied with a taper (tap) and thereby scaled. > The resulting powspctrm hence does not reflect the the true changes in > microvolt. > Do I see that correctly, or am I missing something here? Is the > powerspectrum corrected for that somewhere else? > > Regards, > Martin > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > Hello Martin, > > > > A powerspectrum typically has the frequencies on one axis and the power > of > > the corresponding frequencies on the other. The power represents how > strong > > a certain frequency occurs in a signal, given by the square of the > voltage > > per frequency. > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > Best regards, > > Arjen > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: [FIELDTRIP] Units powspctrm > > > > Hello together, > > > > What units does the powspctrm have? > > Starting with an EEG signal in microvolts and computing the powerspectrum > > using freqanalysis what are the units of powspctrm? > > I tried to figure it out on my own but I am stuck somehow. > > > > Here some example code > > > > cfg=[]; > > cfg.method='mtmfft'; > > cfg.output='pow'; > > cfg.pad ='maxperlen' > > cfg.foilim=[1 130] > > cfg.taper='hanning' > > cfg.channel=1 > > cfg.keeptrials='no' > > > > R=ft_freqanalysis(cfg,data); > > > > I am interested in the units of R.powspctrm > > > > Thanks > > Martin > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Mon Aug 16 10:48:26 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Mon, 16 Aug 2010 10:48:26 +0200 Subject: Space alignment - once again In-Reply-To: Message-ID: Hi Jan-Mathijs, thank you very much. Since I'm trying to compare different models I'll have to do the alignment with the nasion-pre auricular space but I'm already on it. Just needed the info if I was carrying owls to athens. Cheers, Paul Am 16.08.2010 09:34, schrieb jan-mathijs schoffelen: > Hi Paul, > > The simulation routine doesn't care about the co-registration between > the volume conductor model and the sensor array. It is your > responsibility to ensure that they are correctly aligned. The sources > need to be in the same coordinate frame as the sensors, so that's I > guess what you refer to as fiducial space. Obviously, if your sensor > positions are expressed in voxel space, you need to specify your > sources in voxel space as well. > > Goood luck, > > Jan-Mathijs > > > On Aug 16, 2010, at 9:02 AM, Paul Czienskowski wrote: > >> Dear Fieldtrippers, >> >> I asked this some days ago and didn't get any answer. I don't want to >> spam, but I need to know strongly. >> I wasn't able to find out yet, if the space the dipoles are simulated >> if I'm running ft_dipolesimulation is in some manner aligned to the >> fiducial space, or if it's all based on the voxel coordinates. It >> would be a great help, if someone knew the answer. >> >> Cheers, >> Paul >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of >> the FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From a.stolk at FCDONDERS.RU.NL Mon Aug 16 11:43:07 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Mon, 16 Aug 2010 11:43:07 +0200 Subject: Units powspctrm In-Reply-To: <31473261.4755181281951700131.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Martin, I'm not exactly sure what your question is but I just simulated your example with the following: % simulate one second of data, samplefreq = 512 hz fs = 512; t = (1:fs)/fs; a = sin(2*pi*20*t); b = 2*sin(2*pi*20*t); % twice the amplitude figure; plot(t,a); hold on; plot(t,b,'r'); hold off; % simulate preprocessed data cfg = []; cfg.layout = 'CTF275.lay'; cfg.layout = prepare_layout(cfg); data.label = cfg.layout.label(1:273,1); data2.label = data.label; data.fsample = fs; data2.fsample = data.fsample; for j = 1:273 data.trial{1,1}(j,:) = a; data.time{1,1}(j,:) = t; data2.trial{1,1}(j,:) = b; data2.time{1,1}(j,:) = t; end % ft_freqnalysis_mtmfft cfg = []; cfg.output = 'pow'; cfg.channel = 'MEG'; cfg.method = 'mtmfft'; cfg.taper = 'rectwin'; cfg.foilim = [1 40]; cfg.keeptrials = 'no'; cfg.keeptapers = 'no'; mtmfft = ft_freqanalysis(cfg, data); mtmfft2 = ft_freqanalysis(cfg, data2); % four (2^2) times the power figure; plot(mtmfft.powspctrm(1,:)); hold on; plot(mtmfft2.powspctrm(1,:),'r'); Notice that I used a rectangular window in stead of the hanning taper. One of the features of the Hanning taper is that it cuts off the ends of a window. It, therefore, is much more difficult to make a prediction about the scaling. I'm not sure if this has satisfied you but it's the most I can do. For more information of fft, have a read on http://fieldtrip.fcdonders.nl/tutorial/fourier Best regards, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Monday, August 16, 2010 10:46:15 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [FIELDTRIP] Units powspctrm Hi Arjen, my point is that I am interested not in the relative difference between signals but in the actual difference in microvolt. I know that this is not the standard thing to do but that is what I need . After playing aroud a bit i come to the following conlcusion Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with an amplitude of 100uV and one with an aplitude of 200uV. Computing a power spectrum using matlab fft function I can eventually read out that the difference between my two signals is 100uV. In ft_freqanalysis_mtmfft the signal is multiplied by a taper line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) pad],[],2); The output can hence not be transformed back right away to the real microvolt values, but happens to be scaled (in my case ) by a factor of ~0.036 (which is the mean value of the taper) At least that is what I think happens. Regards Martin 2010/8/13 a.stolk at fcdonders.ru.nl > If you use the same mtmfft settings for both conditions, in theory it > should be fine. Make sure that you compute the fourier transformation on > equal window lenghts. > > If you happen to have variable triallengths per condition, my suggestion > would be to cut the trials in (e.g.) 1 second pieces. This way your > 'frequency resolution' is the same for condition A and B. > > If your experimental setup allows you, you could choose to normalize your > data (e.g. a baselinecorrection) first before making the A and B comparison. > This way you correct for (non-)cognitive powerchanges over time (case it's > not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste > over time, subject habituation effects and whatelse you have. > > Best, > Arjen > > > > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Yes, typically, but is it the case for the powspctrm you get from the > mtmfft > freqanalysis? > I am asking for the following reason: > > Lets say, I have two experimental conditions A and B and I compute the > powerspectra for both of them. > When the units actually are uV^2/Hz i could tell for each frequency by how > much uV A and B differ. > > What confuses me is that in > ft_freqanalysis_mtmfft< > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > signal is multiplied with a taper (tap) and thereby scaled. > The resulting powspctrm hence does not reflect the the true changes in > microvolt. > Do I see that correctly, or am I missing something here? Is the > powerspectrum corrected for that somewhere else? > > Regards, > Martin > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > Hello Martin, > > > > A powerspectrum typically has the frequencies on one axis and the power > of > > the corresponding frequencies on the other. The power represents how > strong > > a certain frequency occurs in a signal, given by the square of the > voltage > > per frequency. > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > Best regards, > > Arjen > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: [FIELDTRIP] Units powspctrm > > > > Hello together, > > > > What units does the powspctrm have? > > Starting with an EEG signal in microvolts and computing the powerspectrum > > using freqanalysis what are the units of powspctrm? > > I tried to figure it out on my own but I am stuck somehow. > > > > Here some example code > > > > cfg=[]; > > cfg.method='mtmfft'; > > cfg.output='pow'; > > cfg.pad ='maxperlen' > > cfg.foilim=[1 130] > > cfg.taper='hanning' > > cfg.channel=1 > > cfg.keeptrials='no' > > > > R=ft_freqanalysis(cfg,data); > > > > I am interested in the units of R.powspctrm > > > > Thanks > > Martin > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Aug 16 12:46:14 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 16 Aug 2010 12:46:14 +0200 Subject: Units powspctrm In-Reply-To: <33048706.4755221281951787469.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Arijen, my question simply was how I can get the actual difference in microvolt between two signals when using fieldtrip. I now have a prtty good idee how to do that. Thanks Martin 2010/8/16 a.stolk at fcdonders.ru.nl > Hi Martin, > > I'm not exactly sure what your question is but I just simulated your > example with the following: > > % simulate one second of data, samplefreq = 512 hz > fs = 512; > t = (1:fs)/fs; > a = sin(2*pi*20*t); > b = 2*sin(2*pi*20*t); % twice the amplitude > figure; plot(t,a); > hold on; plot(t,b,'r'); > hold off; > > % simulate preprocessed data > cfg = []; > cfg.layout = 'CTF275.lay'; > cfg.layout = prepare_layout(cfg); > data.label = cfg.layout.label(1:273,1); > data2.label = data.label; > data.fsample = fs; > data2.fsample = data.fsample; > for j = 1:273 > data.trial{1,1}(j,:) = a; > data.time{1,1}(j,:) = t; > data2.trial{1,1}(j,:) = b; > data2.time{1,1}(j,:) = t; > end > > % ft_freqnalysis_mtmfft > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEG'; > cfg.method = 'mtmfft'; > cfg.taper = 'rectwin'; > cfg.foilim = [1 40]; > cfg.keeptrials = 'no'; > cfg.keeptapers = 'no'; > mtmfft = ft_freqanalysis(cfg, data); > mtmfft2 = ft_freqanalysis(cfg, data2); % four (2^2) times the > power > > figure; plot(mtmfft.powspctrm(1,:)); > hold on; plot(mtmfft2.powspctrm(1,:),'r'); > > Notice that I used a rectangular window in stead of the hanning taper. One > of the features of the Hanning taper is that it cuts off the ends of a > window. It, therefore, is much more difficult to make a prediction about the > scaling. > > I'm not sure if this has satisfied you but it's the most I can do. For more > information of fft, have a read on > http://fieldtrip.fcdonders.nl/tutorial/fourier > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Monday, August 16, 2010 10:46:15 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Hi Arjen, > > my point is that I am interested not in the relative difference between > signals but in the actual difference in microvolt. I know that this is not > the standard thing to do but that is what I need . > > After playing aroud a bit i come to the following conlcusion > > Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with > an > amplitude of 100uV and one with an aplitude of 200uV. > Computing a power spectrum using matlab fft function I can eventually read > out that the difference between my two signals is 100uV. > > In ft_freqanalysis_mtmfft the signal is multiplied by a taper > line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) > pad],[],2); > > The output can hence not be transformed back right away to the real > microvolt values, but happens to be scaled (in my case ) by a factor of > ~0.036 (which is the mean value of the taper) > > At least that is what I think happens. > > Regards > Martin > > > > > > 2010/8/13 a.stolk at fcdonders.ru.nl > > > If you use the same mtmfft settings for both conditions, in theory it > > should be fine. Make sure that you compute the fourier transformation on > > equal window lenghts. > > > > If you happen to have variable triallengths per condition, my suggestion > > would be to cut the trials in (e.g.) 1 second pieces. This way your > > 'frequency resolution' is the same for condition A and B. > > > > If your experimental setup allows you, you could choose to normalize your > > data (e.g. a baselinecorrection) first before making the A and B > comparison. > > This way you correct for (non-)cognitive powerchanges over time (case > it's > > not an ABABABAB etc. design). Such as conductivity reducal of the EEG > paste > > over time, subject habituation effects and whatelse you have. > > > > Best, > > Arjen > > > > > > > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: Re: [FIELDTRIP] Units powspctrm > > > > Yes, typically, but is it the case for the powspctrm you get from the > > mtmfft > > freqanalysis? > > I am asking for the following reason: > > > > Lets say, I have two experimental conditions A and B and I compute the > > powerspectra for both of them. > > When the units actually are uV^2/Hz i could tell for each frequency by > how > > much uV A and B differ. > > > > What confuses me is that in > > ft_freqanalysis_mtmfft< > > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > > signal is multiplied with a taper (tap) and thereby scaled. > > The resulting powspctrm hence does not reflect the the true changes in > > microvolt. > > Do I see that correctly, or am I missing something here? Is the > > powerspectrum corrected for that somewhere else? > > > > Regards, > > Martin > > > > > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > > > Hello Martin, > > > > > > A powerspectrum typically has the frequencies on one axis and the power > > of > > > the corresponding frequencies on the other. The power represents how > > strong > > > a certain frequency occurs in a signal, given by the square of the > > voltage > > > per frequency. > > > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > > > Best regards, > > > Arjen > > > > > > ----- Original Message ----- > > > From: "Martin Bleichner" > > > To: FIELDTRIP at NIC.SURFNET.NL > > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / > Berlin > > / > > > Bern / Rome / Stockholm / Vienna > > > Subject: [FIELDTRIP] Units powspctrm > > > > > > Hello together, > > > > > > What units does the powspctrm have? > > > Starting with an EEG signal in microvolts and computing the > powerspectrum > > > using freqanalysis what are the units of powspctrm? > > > I tried to figure it out on my own but I am stuck somehow. > > > > > > Here some example code > > > > > > cfg=[]; > > > cfg.method='mtmfft'; > > > cfg.output='pow'; > > > cfg.pad ='maxperlen' > > > cfg.foilim=[1 130] > > > cfg.taper='hanning' > > > cfg.channel=1 > > > cfg.keeptrials='no' > > > > > > R=ft_freqanalysis(cfg,data); > > > > > > I am interested in the units of R.powspctrm > > > > > > Thanks > > > Martin > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of > the > > > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG > > > and EEG analysis. See also > > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of > the > > > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG > > > and EEG analysis. See also > > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sara.GonzalezAndino at HCUGE.CH Mon Aug 16 12:48:53 2010 From: Sara.GonzalezAndino at HCUGE.CH (GONZALEZ ANDINO Sara) Date: Mon, 16 Aug 2010 12:48:53 +0200 Subject: post-doc position available in Geneva Message-ID: Dear Fieldtrip list members, Please find attached a job offer in the Electrical Neuroimaging Group of the University of Geneva. Best regards, Sara L. Gonzalez ------------------------- Sara L. Gonzalez Andino, PhD, MER Head of the Electrical Neuroimaging Group Department of Clinical Neurosciences Faculty of Medicine, University of Geneva Phone: +41 22 3728323 Fax: + 41 22 3728333 www.electrical-neuroimaging.ch ________________________________________ De : FieldTrip discussion list [FIELDTRIP at nic.surfnet.nl] de la part de Robert Oostenveld [r.oostenveld at FCDONDERS.RU.NL] Date d'envoi : lundi 16 août 2010 10:07 À : FIELDTRIP at nic.surfnet.nl Objet : [FIELDTRIP] post-doc position available in Paris Dear Fieldtrip list members, Appologies for multiple postings. Please find attached a job opportunity in the group of Florian Waszak. best regards, ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Announce_postdoc.doc Type: application/octet-stream Size: 39936 bytes Desc: Announce_postdoc.doc URL: From alexandre.gramfort at INRIA.FR Tue Aug 17 09:45:05 2010 From: alexandre.gramfort at INRIA.FR (Alexandre Gramfort) Date: Tue, 17 Aug 2010 09:45:05 +0200 Subject: OpenMEEG with 4 layers Message-ID: Hi Gregor, you should now be able to run an EEG forward model with 4 layers with OpenMEEG & Fieldtrip. I've added Paul's scripts to the main FT code. You just need to download today's version of FT. Best, Alexandre ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From thomas.hartmann at UNI-KONSTANZ.DE Tue Aug 17 16:51:38 2010 From: thomas.hartmann at UNI-KONSTANZ.DE (Thomas Hartmann) Date: Tue, 17 Aug 2010 16:51:38 +0200 Subject: difference between mtmconvol and mtmfft Message-ID: hi, from the descriptions of the two functions ft_freqanalysis_mtmconvol and ft_freqanalysis_mtmfft i thought that those two functions should work more or less equivalent - the first just doing it multiple times to get a time-frequency representation. to localize a significant cluster from my tf-representation, i recalculated the fft (including the csd, of course) using the exact same arguments for latency, window-size, frequency, padding, taper etc.... but the results do differ. not dramatically but considerably. does anyone have an explanation for this? thanks a lot in advance, thomas -- Dipl. Psych. Thomas Hartmann OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel.: +49 (0)7531 88 4612 Fax: +49 (0)7531-88 4601 Email: thomas.hartmann at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From khoechstetter at BESA.DE Tue Aug 17 18:05:09 2010 From: khoechstetter at BESA.DE (Karsten Hoechstetter) Date: Tue, 17 Aug 2010 18:05:09 +0200 Subject: Job opening for EEG/MEG scientist at MEGIS Software Message-ID: Open job position MEGIS Software GmbH (Munich, Germany) is searching to hire an EEG/MEG scientist to join our support and development team in Germany. Job profile: The successful applicant will - contribute to the development of new analysis techniques and program features - participate in joint research projects with our customers - represent our products and software at neuroimaging conferences - teach the use of our software at customer workshops worldwide - provide scientific and technical support to our customers (predominantly via email) MEGIS is one of the leading developers of EEG/MEG analysis software. Our BESA programs are widely used software for analysis of EEG and MEG data for both research and clinical applications (see www.besa.de). As a free enterprise in the field of science and research we can offer job positions combining the advantages of both fields: Stay in touch with current front-end research work while enjoying the advantages of a permanent position with adequate salary. Applicant’s profile: - The applicant should have a background in nature science (e.g. physics) or psychology, preferential including a PhD degree. - Experience in EEG/MEG data analysis (practical and/or theoretical) is desired. - Knowledge of the BESA software is helpful, but not a must. - Fluency in written and spoken English are a prerequisite for the announced position. - Since the place of work will be mainly our office in Germany, the applicant should be able to communicate in German. - Experience in MATLAB scripting or other programming skills are helpful. - The applicant should be willing to travel to neuroscientific conferences and workshops worldwide 6-8 times per year. Applications should include a current CV, a letter indicating motivation and skills, and a list of publications. Electronic applications preferred. Please send your application to Theodor Scherg ( tscherg at besa.de) or to: MEGIS Software GmbH Freihamer Str. 18 82166 Graefelfing Germany We are looking forward to hearing from you! -------------------------------------- Dr. Karsten Hoechstetter MEGIS Software GmbH Gräfelfing, Germany HRB München 109956 CEO Dr. Michael Scherg -------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Wed Aug 18 10:10:54 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 18 Aug 2010 10:10:54 +0200 Subject: Mesh space vs. voxel space problem Message-ID: Dear fieldtrippers, when looking at the points of the mesh generated for the BEM generation there was something I stumbled over: There are points with negative coordinates, so the mesh seems to be generated in some other space than the voxel system (maybe just translated in some way?). This wouldn't be a great problem if the ft_dipolefitting wasn't working in voxel but in mesh space, because when searching the valid dipole positions in prepare_dipole_grid on lines 432-434 the bounding_mesh function returns a volume full of zeros since the grid positions don't lie within the volume. I'm using the 20100612 version of fieldtrip and running ft_dipolefitting with automatic grid generation. Is there anything I can do about this besides creating the grid on my own? Thanks in advance, Paul -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Wed Aug 18 10:15:23 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 18 Aug 2010 10:15:23 +0200 Subject: Mesh space vs. voxel space problem In-Reply-To: <4C6B958E.1020601@gmx.de> Message-ID: Okay, seems to be solved - at least a little. I now saw that the grid is created from the electrodes positions and not by the mesh points. I'll have to align these to get it right. Cheers, Paul Am 18.08.2010 10:10, schrieb Paul Czienskowski: > Dear fieldtrippers, > > when looking at the points of the mesh generated for the BEM > generation there was something I stumbled over: There are points with > negative coordinates, so the mesh seems to be generated in some other > space than the voxel system (maybe just translated in some way?). This > wouldn't be a great problem if the ft_dipolefitting wasn't working in > voxel but in mesh space, because when searching the valid dipole > positions in prepare_dipole_grid on lines 432-434 the bounding_mesh > function returns a volume full of zeros since the grid positions don't > lie within the volume. I'm using the 20100612 version of fieldtrip and > running ft_dipolefitting with automatic grid generation. Is there > anything I can do about this besides creating the grid on my own? > > Thanks in advance, > Paul > -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Fri Aug 20 14:13:42 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Fri, 20 Aug 2010 14:13:42 +0200 Subject: mne and ft_sourceinterpolate Message-ID: Dear fieldtrippers, I am trying to extract source activity from timelock-data, and I would like to have this for a whole epoch of 1 sec / 501 sample points. I did an ft_sourceanalysis with method = 'mne', which worked fine and gave the desired source activity (see structure "source" below; field "avg" contains "mom" and "pow"). Next I did an ft_sourceinterpolate with "source" and a standard mri as input. Unfortunately, the resulting structure did not contain an "avg" field any more (see "ivol" below) - my functional data got lost during interpolation. Did someone have a similar problem or does someone know a solution? Many thanks in advance for any help! Gregor P.S.: Source interpolation works without problems with method = 'lcmv', but this gives the mean source activity within the desired time range rather than sample-wise activity. It is not a good idea to apply the lcmv beamformer to consecutive time bins and then concatenate the source activity, am I right? source = xgrid: [-66 -56 -46 -36 -26 -16 -6 4 14 24 34 44 54 64] ygrid: [-105 -95 -85 -75 -65 -55 -45 -35 -25 -15 -5 5 15 25 35 45 55 65] zgrid: [-46 -36 -26 -16 -6 4 14 24 34 44 54 64 74 84] dim: [14 18 14] vol: [1x1 struct] time: [1x501 double] pos: [3528x3 double] inside: [1x1808 double] outside: [1x1720 double] method: 'average' avg: [1x1 struct] cfg: [1x1 struct] ivol = inside: [181x217x181 logical] dim: [181 217 181] transform: [4x4 double] anatomy: [181x217x181 uint8] cfg: [1x1 struct] -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Fri Aug 20 15:01:53 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Fri, 20 Aug 2010 15:01:53 +0200 Subject: mne and ft_sourceinterpolate In-Reply-To: <4C6E8D9602000057000071EB@gwsmtp1.uni-regensburg.de> Message-ID: Dear Gregor, What you want to achieve is as of yet not possible. Ft_sourceinterpolate at the moment only interpolates functional parameters which are scalars, e.g. power, or variance averaged over time (in lcmv). We are working at the moment to make the data representation of different types of source reconstructed results more consistent (beamformer versus mne etc), and first will work towards the possibility of visualizing the functional data (including their time courses) without the interpolation. The thing you can do now is to define a meaningful summary statistic of the reconstructed time course, interpolate this one on the anatomy, and click around the anatomical coordinate of your source of interest. Subsequently you need to reverse engineer (undo the interpolation) to find the corresponding source position in your source structure. Then you can use the plot command to look at the time courses. Best, Jan-Mathijs On Aug 20, 2010, at 2:13 PM, Gregor Volberg wrote: > Dear fieldtrippers, > > I am trying to extract source activity from timelock-data, and I > would like to have this for a whole epoch of 1 sec / 501 sample > points. I did an ft_sourceanalysis with method = 'mne', which worked > fine and gave the desired source activity (see structure "source" > below; field "avg" contains "mom" and "pow"). Next I did an > ft_sourceinterpolate with "source" and a standard mri as input. > Unfortunately, the resulting structure did not contain an "avg" > field any more (see "ivol" below) - my functional data got lost > during interpolation. Did someone have a similar problem or does > someone know a solution? > > Many thanks in advance for any help! > Gregor > > P.S.: Source interpolation works without problems with method = > 'lcmv', but this gives the mean source activity within the desired > time range rather than sample-wise activity. It is not a good idea > to apply the lcmv beamformer to consecutive time bins and then > concatenate the source activity, am I right? > > > > source = > > xgrid: [-66 -56 -46 -36 -26 -16 -6 4 14 24 34 44 54 64] > ygrid: [-105 -95 -85 -75 -65 -55 -45 -35 -25 -15 -5 5 15 25 35 > 45 55 65] > zgrid: [-46 -36 -26 -16 -6 4 14 24 34 44 54 64 74 84] > dim: [14 18 14] > vol: [1x1 struct] > time: [1x501 double] > pos: [3528x3 double] > inside: [1x1808 double] > outside: [1x1720 double] > method: 'average' > avg: [1x1 struct] > cfg: [1x1 struct] > > ivol = > > inside: [181x217x181 logical] > dim: [181 217 181] > transform: [4x4 double] > anatomy: [181x217x181 uint8] > cfg: [1x1 struct] > > > > -- > Dr. rer. nat. Gregor Volberg > ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) > University of Regensburg > Institute for Experimental Psychology > 93040 Regensburg, Germany > Tel: +49 941 943 3862 > Fax: +49 941 943 3233 > http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Erin.Oakman at NYUMC.ORG Tue Aug 24 20:19:40 2010 From: Erin.Oakman at NYUMC.ORG (Oakman, Erin) Date: Tue, 24 Aug 2010 14:19:40 -0400 Subject: using ft_freqstatistics with 4 arguments Message-ID: Hi Fieldtrip list, Apparently the nonparametric freqstatistics funtion can be used with a mixed design, to compare power between 2 groups and 2 conditions, using cfg.method = 'montecarlo'. I am giving 4 arguments to ft_freqstatistics. stats = ft_freqstatistics(cfg, group1-condition1, group1-condition2, group2-condition1, group2-condition2) >>From Robert's suggestion here https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind0803&L=FIELDTRIP&P=R13471, the design matrix has been set up with 1 row for the condition (condition numbers "1", "2"), a second row with the subject number and a third row for the two groups ("1", "2"). I set: cfg.ivar = 1; cfg.uvar = 2; cfg.wvar = 3; The trouble is with resampledesign.m, using it in combination with ft_freqstatistics. When resampledesign.m splits the design matrix into a smaller design matrix, using cfg.war, I get the error ??? the design matrix variables should be constant within a block The design matrix is 3 X 100, like this: condition: 1 1 1 1 1 2 2 2 2 2 1 1 1 1 1 2 2 2 2 2 subj number: 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 group: 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 Should a different design matrix be used in this case? Should cfg.wvar = 2 ? Erin ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From tsauvigny at GOOGLEMAIL.COM Wed Aug 25 11:26:03 2010 From: tsauvigny at GOOGLEMAIL.COM (Thomas Sauvigny) Date: Wed, 25 Aug 2010 11:26:03 +0200 Subject: FieldTrip support Message-ID: Dear fieldtrip users! May I ask for your support because of a problem concerning my within-subject permutation test (EEG-Data)? The goal is to compare two grandaverages with two different conditions, each grandaverage consisting of 4 datasets from 4 subjects, each dataset about 40-50 single trials. I did the preprocessing, timelock and grandaverage: 4 datasets (called x1, x4) for the first condition with the following command: cfg = []; cfg.keeptrials = 'yes'; timelock1 = timelockanalysis(cfg, x1); timelock2 = timelockanalysis(cfg, x2); timelock3 = timelockanalysis(cfg, x3); timelock4 = timelockanalysis(cfg, x4); cfg.channel = 'all' cfg.latency = 'all' cfg.keepindividual = 'yes' cfg.normalizevar = 'N-1' da_test1= timelockgrandaverage (cfg, timelock1, timelock2, timelock3, timelock4) save da_test1 Same way for the second condition: da_test2 Now I start the permutation test (file attached). As result there are no significant clusters highlighted (although there are quite large differences in the ERP-plot). I think because there is a mistake concerning the number of single-trials which fieldtrip takes as the basis for the statistic test. Because the output in the command window shows: selected 30 channels selected 2501 time bins selected 1 frequency bins total number of measurements = 8 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 4 levels number of repeated measurements in each level is 2 2 2 2 computing a parmetric threshold for clustering computing statistic estimated time per randomization is 0 seconds computing statistic 1 from 100 found 7 positive clusters in observed data found 11 negative clusters in observed data stat = prob: [30x2501 double] posclusters: [1x7 struct] posclusterslabelmat: [30x2501 double] posdistribution: [1x100 double] negclusters: [1x11 struct] negclusterslabelmat: [30x2501 double] negdistribution: [1x100 double] mask: [30x2501 logical] stat: [30x2501 double] ref: [30x2501 double] dimord: 'chan_time' label: {30x1 cell} time: [1x2501 double] cfg: [1x1 struct] cfg = xlim: [0 0.1000] zlim: 'maxmin' the input is timelock data with 30 channels and 4000 timebins applying preprocessing options averaging trials averaging trial 1 of 4 averaging trial 2 of 4 averaging trial 3 of 4 averaging trial 4 of 4 reading layout from file easycap32ch-avg.lay So, could this be the mistake that fieldtrip guesses “4” to be the number of all trials (perhaps because 4 datasets in each grandaverage??) And how can I solve this problem? Is there a way to account for the single-trial number when using the permutation test? Thank you very much for your help!! Kind regards Thomas Sauvigny Tübingen University ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: da_test_statistic.m URL: From datashare at SCIENCEDB.NET Wed Aug 25 15:42:37 2010 From: datashare at SCIENCEDB.NET (Science DB datashare) Date: Wed, 25 Aug 2010 15:42:37 +0200 Subject: Announcement : EEG/MEG database Message-ID: Dear Fieldtrip users, Data sharing is a great way to find new collaborators. We would like to announce a our new database for EEG/MEG data on ScienceDB.net The concept is simple: If you have data to share you create a new topic in the EEG/MEG data share group’s forum, where you describe your data, and how you want to share it. Please go to : http://sciencedb.net/groups/eegmeg-data-share/ ScienceDB.net is a non-profit portal for the scientific community. Our service is sponsored by ads and donations. If you have any suggestions or comments, please mail us at datashare at sciencedb.net. Kind regards, Science DB http://sciencedb.net/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Wed Aug 25 18:33:18 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Wed, 25 Aug 2010 18:33:18 +0200 Subject: errors in ft_componentsanalysis Message-ID: Dear Fieldtrippers, I have a little problems with cft_componentanalysis and the 'runica' option When running Fieldtrip20100822 on matlab2008b (on Linux and running filedtripdefs before starting the calculations) I get a complaint about the notorious missing randperm.m ??? Undefined function or method 'randperm' for input arguments of type 'double'. Error in ==> runica at 1063 timeperm=randperm(datalength); % shuffle data order at each step Error in ==> ft_componentanalysis at 252 [weights, sphere] = runica(dat, optarg{:}); I thought that running filedtripdefs would take care of this, but seemingly it doesn't. On the other hand if I run it on matlab 2007a, then ft-componentanalysis/runica stops with a warning that the "try catch" syntax will not be supported in future matlab versions ? I do not get an actual error because whatever happens happens in a try-catch statement so errors are suppressed Any suggestions welcome, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From stan.vanpelt at DONDERS.RU.NL Thu Aug 26 10:22:04 2010 From: stan.vanpelt at DONDERS.RU.NL (Stan van Pelt) Date: Thu, 26 Aug 2010 10:22:04 +0200 Subject: difference between mtmconvol and mtmfft In-Reply-To: <4C6AA1FA.8030508@uni-konstanz.de> Message-ID: Dear Thomas, If I understand you correctly you applied ft_freqanalysis_mtmfft on a piece of data that looked interesting based on ft_freqanalysis_mtmconvol, but this gives slightly different results. Please let someone correct me if I'm wrong, but what I think is going on is that for the calculation of power in a time-freq bin, ft_freqanalysis_mtmconvol uses data from adjacent time windows (because of the temporal smoothing). ft_freqanalysis_mtmconvol on the other hand only uses the data that is within your time-freq bin, because the temporal analysis window is equal to the size (along the temporal dimension) of the input data. Best, Stan Stan van Pelt, PhD Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 68495 Fax: (+31) (0)24 36 10989 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Thomas Hartmann Sent: Tuesday, August 17, 2010 4:52 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] difference between mtmconvol and mtmfft hi, from the descriptions of the two functions ft_freqanalysis_mtmconvol and ft_freqanalysis_mtmfft i thought that those two functions should work more or less equivalent - the first just doing it multiple times to get a time-frequency representation. to localize a significant cluster from my tf-representation, i recalculated the fft (including the csd, of course) using the exact same arguments for latency, window-size, frequency, padding, taper etc.... but the results do differ. not dramatically but considerably. does anyone have an explanation for this? thanks a lot in advance, thomas -- Dipl. Psych. Thomas Hartmann OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel.: +49 (0)7531 88 4612 Fax: +49 (0)7531-88 4601 Email: thomas.hartmann at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 27 07:44:45 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 07:44:45 +0200 Subject: Dipole fitting with openMEEG BEM model Message-ID: Dear all, after creating the BEM model for an individual MRI with OpenMEEG i now tried to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab script crashed saying: ??? Output argument "dsm" (and maybe others) not assigned during call to "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m (openmeeg_dsm)". Error in ==> openmeeg_dsm at 16 The actual error may have been some lines above: /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy I'm not really used to use linux and for this reason not familiar with the error messages. I found out that this has to do with any program accessing the shell script file, but since it just has been created and also been closed by the openmeeg_dsm script I don't get it why some other process should access it. I would be very grateful, if anyone could give me a hint how to solve this problem. Thanks in advance, Paul Czienskowski -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Fri Aug 27 07:58:17 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 07:58:17 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: <4C7750CD.6010004@gmx.de> Message-ID: Addendum: The error occurred when scanning grid location 34104 of 800000. So it seems not to be a general error but more something like a exception occurring every once a while. Ain't very good either. It may be very good if someone could explain me what's going on and how to solve it. Paul Am 27.08.2010 07:44, schrieb Paul Czienskowski: > Dear all, > > after creating the BEM model for an individual MRI with OpenMEEG i now > tried to simulate and fit some dipoles, but when calling > openmeeg_dsm.m the matlab script crashed saying: > > ??? Output argument "dsm" (and maybe others) not assigned during call > to > "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m (openmeeg_dsm)". > > Error in ==> openmeeg_dsm at 16 > > The actual error may have been some lines above: > > /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy > > I'm not really used to use linux and for this reason not familiar with > the error messages. I found out that this has to do with any program > accessing the shell script file, but since it just has been created > and also been closed by the openmeeg_dsm script I don't get it why > some other process should access it. I would be very grateful, if > anyone could give me a hint how to solve this problem. > > Thanks in advance, > > Paul Czienskowski > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at INRIA.FR Fri Aug 27 08:15:31 2010 From: alexandre.gramfort at INRIA.FR (Alexandre Gramfort) Date: Fri, 27 Aug 2010 08:15:31 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: <4C7750CD.6010004@gmx.de> Message-ID: Hello Paul, could you share a script to reproduce the problem? -- Alexandre On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: > Dear all, > > after creating the BEM model for an individual MRI with OpenMEEG i now tried > to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab > script crashed saying: > > ??? Output argument "dsm" (and maybe others) not assigned during call to > "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m > (openmeeg_dsm)". > > Error in ==> openmeeg_dsm at 16 > > The actual error may have been some lines above: > > /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy > > I'm not really used to use linux and for this reason not familiar with the > error messages. I found out that this has to do with any program accessing > the shell script file, but since it just has been created and also been > closed by the openmeeg_dsm script I don't get it why some other process > should access it. I would be very grateful, if anyone could give me a hint > how to solve this problem. > > Thanks in advance, > > Paul Czienskowski > > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 27 08:35:25 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 08:35:25 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: Message-ID: If it helps, of course. I attached the script that's calling ft_dipolefitting and another one called by the first one, that's calling ft_prepare_bemmodel. Also I'm using another meshing routine which I wrote by myself which is a bit slower, bur also a bit more dependable than the fieldtrip method, since the ft method to create the meshes from the segmentation produced some ugly spikes for me. But the output of my routine should be near to the output of the fieldtrip routine when it works, so this should be no difference (actually my locations are transformed a bit to match my electrode space, electrode positions for the segmentation are retrieved by the Get1020 method). Cheers, Paul Am 27.08.2010 08:15, schrieb Alexandre Gramfort: > Hello Paul, > > could you share a script to reproduce the problem? > > -- Alexandre > > On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: >> Dear all, >> >> after creating the BEM model for an individual MRI with OpenMEEG i now tried >> to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab >> script crashed saying: >> >> ??? Output argument "dsm" (and maybe others) not assigned during call to >> "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m >> (openmeeg_dsm)". >> >> Error in ==> openmeeg_dsm at 16 >> >> The actual error may have been some lines above: >> >> /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy >> >> I'm not really used to use linux and for this reason not familiar with the >> error messages. I found out that this has to do with any program accessing >> the shell script file, but since it just has been created and also been >> closed by the openmeeg_dsm script I don't get it why some other process >> should access it. I would be very grateful, if anyone could give me a hint >> how to solve this problem. >> >> Thanks in advance, >> >> Paul Czienskowski >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CzSimulation.m URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CreateBEMModel.m URL: From carsten.wolters at UNI-MUENSTER.DE Fri Aug 27 15:58:05 2010 From: carsten.wolters at UNI-MUENSTER.DE (Dr. Carsten Wolters) Date: Fri, 27 Aug 2010 15:58:05 +0200 Subject: Postdoc/PhD position available Message-ID: Dear colleague, please note the attached job posting for a PostDoc/PhD student. I would be greatful, if you could distribute this posting in your department and forward it to colleagues who might be aware of potential candidates. Thank you and best regards, Carsten Wolters ------------------------------------------ For the german research foundation (DFG) project entitled „"Reconstruction of epilepsy-characteristic sources by means of a simultaneous evaluation of EEG- and MEG-data using calibrated realistic headmodels", the Institute for Biomagnetism and Biosignalanalysis (IBB) of the University of Münster offers a position for a *Research scientist (PostDoc or PhD student).* The position is available for 3 years. Payment is according to Bat2a/TVL13. The research project is a cooperation of the IBB with the epilepsy center Erlangen. It aims at reconstructing epilepsy-characteristic electric potentials and magnetic fields for the identification of the epileptogenic zone to improve the therapy of pharmaco-resistant epilepsies. The main project goal is the development and application of methods for a combined source analysis of Electroencephalography (EEG) and Magnetoencephalography (MEG) data in individually optimized finite element head models. The successful applicant holds a degree in informatics, mathematics, physics, biomedical engineering, electrical engineering or similar, and possesses good programming experience (C++ under Linux). Experience with the measurement and analysis of brain signals is advantageous, but not essential. In order to increase the proportion of female staff members, applications from female scientists are particularly encouraged. Disabled applicants are preferred if qualification is equal. The selection procedure starts as the applications come in. Please send your application to Priv.-Doz. Dr.rer.nat. Carsten H. Wolters Institut für Biomagnetismus und Biosignalanalyse Westfälische Wilhelms-Universität Münster Malmedyweg 15 48149 Münster, Germany Tel.: +49 251 83 56904 Fax: +49 251 83 56874 E-Mail: carsten.wolters at uni-muenster.de Web: biomag.uni-muenster.de ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Anz-DFGEpileps-2010_engl.DOC Type: application/msword Size: 29184 bytes Desc: not available URL: From brian.roach at YALE.EDU Fri Aug 27 20:10:21 2010 From: brian.roach at YALE.EDU (Brian Roach) Date: Fri, 27 Aug 2010 11:10:21 -0700 Subject: Fwd: Post-doctoral training in the Neuroscience of Schizophrenia Message-ID: Please e-mail me if you are interested in applying to the position outlined below: ------------------------------------------------------------------------ University of California San Francisco Three post-doctoral fellowships in translational neuroscience of schizophrenia. Sponsor(s): NIMH Application Date(s): Beginning April 1, 2010 The NIMH-funded T32 Training Grant (Neurobiological mechanisms underlying the symptoms and course of schizophrenia) at the University of California in San Francisco is now accepting applications for post-doctoral fellowships from recent PhDs, MDs, and MD/PhDs. Trainees will work in labs studying the neurobiological mechanisms of the symptoms of schizophrenia and its neuro-developmental and neuro-degenerative course. The core T32 faculty are basic neuroscientists and psychiatrists, working in genetics, brain imaging, electrophysiology, and neuroplasticity. They are: Steve Batki, William Byerley, Benjamin Cheyette, Allison Doupe, Judith Ford, Steven Hamilton, Daniel Mathalon, John Rubenstein, Susan Voglmaier, Sophia Vinogradov, and Mark von Zastrow. T32 Trainees will have extended experience in a laboratory, leading to the submission of research papers and grant proposals. Trainees will be dual-mentored with Research and Career Mentors to guide them both formally and informally, through learning neurobiological methods, producing a body of data, presenting data at national meetings, writing and publishing papers, preparing grant proposals, and attending local and national workshops on launching and maintaining successful careers in biological psychiatry. We seek applications from ethnically diverse scientists who have strong academic credentials and US citizenship or permanent residence. NIH rules for T32 trainees state, "The individual to be trained must be a citizen or a noncitizen national of the United States or have been lawfully admitted for permanent residence by the time of award. Individuals who have been lawfully admitted for permanent residence must have a currently valid Alien Registration Receipt Card (I-551) or other legal verification of such status." Potential applicants are welcome to contact any of the core faculty members. An application form is attached. Additional information can be found by visiting our website (http://psych.ucsf.edu/t32/neuro_scz). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ford_T32_Application 7.doc Type: application/msword Size: 95232 bytes Desc: not available URL: From p.vandenhurk at CS.RU.NL Tue Aug 31 10:44:59 2010 From: p.vandenhurk at CS.RU.NL (Paul van den Hurk) Date: Tue, 31 Aug 2010 10:44:59 +0200 Subject: question about freqgrandaverage In-Reply-To: <4C775CAD.7050507@gmx.de> Message-ID: Dear fieldtrippers, I have a question about the function freqgrandaverage. Since I have been quite strict in deleting noisy channels, quite some channels have been removed from individual datasets. Due to the removal of these channels relatively few channels are left when computing the grand average. Could anyone tell me how to adjust the settings of the function in order to calculate the mean in a specific channel over the remaining subjects that do have nicely looking data instead of completely removing the channel from the grand average calculation if only 1 or 2 subjects would show noisy data in this channel? Or would it be better to use the channelrepair function in order to get interpolated values for each subject in such noisy channels? Thanks for your help, Kind regards, Vriendelijke groet, Paul van den Hurk PhD student in Mind-Brain-Mindfulness Group, Faculty of Science, Radboud University, Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, Tel:+31 24 3652240 Email: p.vandenhurk at cs.ru.nl Visiting address: Room HG02.532 Faculty of Science Toernooiveld 1 Nijmegen -----Oorspronkelijk bericht----- Van: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Namens Paul Czienskowski Verzonden: Friday, August 27, 2010 8:35 AM Aan: FIELDTRIP at NIC.SURFNET.NL Onderwerp: Re: [FIELDTRIP] Dipole fitting with openMEEG BEM model If it helps, of course. I attached the script that's calling ft_dipolefitting and another one called by the first one, that's calling ft_prepare_bemmodel. Also I'm using another meshing routine which I wrote by myself which is a bit slower, bur also a bit more dependable than the fieldtrip method, since the ft method to create the meshes from the segmentation produced some ugly spikes for me. But the output of my routine should be near to the output of the fieldtrip routine when it works, so this should be no difference (actually my locations are transformed a bit to match my electrode space, electrode positions for the segmentation are retrieved by the Get1020 method). Cheers, Paul Am 27.08.2010 08:15, schrieb Alexandre Gramfort: > Hello Paul, > > could you share a script to reproduce the problem? > > -- Alexandre > > On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: >> Dear all, >> >> after creating the BEM model for an individual MRI with OpenMEEG i now tried >> to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab >> script crashed saying: >> >> ??? Output argument "dsm" (and maybe others) not assigned during call to >> "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m >> (openmeeg_dsm)". >> >> Error in ==> openmeeg_dsm at 16 >> >> The actual error may have been some lines above: >> >> /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy >> >> I'm not really used to use linux and for this reason not familiar with the >> error messages. I found out that this has to do with any program accessing >> the shell script file, but since it just has been created and also been >> closed by the openmeeg_dsm script I don't get it why some other process >> should access it. I would be very grateful, if anyone could give me a hint >> how to solve this problem. >> >> Thanks in advance, >> >> Paul Czienskowski >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Tue Aug 31 11:07:48 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 31 Aug 2010 11:07:48 +0200 Subject: topograhies wrong when using componetbrowser on the output of fastica Message-ID: Dear Listusers, I compared fastica and runica in ft_componentanalysis and found their output (with respect to component-topographies) to be absolutely different, although component timecourses agree largely. Remembering an earlier post to this list on how the component topography output was fixed (for runica) I think it's possible that this fix broke the topography display for fastica. The reason I suspect this is because the definitions of what an ica weight is differ in EEGLAB (runica.m) and fastica.m, i.e. they are the inverse of each other. Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From michael.wibral at WEB.DE Tue Aug 31 16:42:43 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 31 Aug 2010 16:42:43 +0200 Subject: ft_preprocessinf; ft_preproc_dftfilter Message-ID: Dear listusers, I found something strange in FT20100826: ft_preprocessing takes cfg.dftfilter = 'yes' as a configuration option and I think it should then issue a call to ft_preproc_dftfilter. However this is never done, if I am not mistaken. I guess it slipped from ft_preprocessing sometiem in the past. Or was it dropped on purpose because other bandstop filters are preferred? Any help on this is appreciated. Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From sharonriwkes at GMAIL.COM Mon Aug 2 14:06:12 2010 From: sharonriwkes at GMAIL.COM (sharon riwkes) Date: Mon, 2 Aug 2010 15:06:12 +0300 Subject: Beamforming with reference channels Message-ID: Hi all, I tried to do source localization, after beamforming with the LCMV method. I did it once for all the MEG channels, and once for MEG channels *AND the reference channels*. I was hoping that using the reference channels will improve the localization by ignoring noise coming from outside of the brain. However, I got the *exact same results for MEG+reference channels* as *for MEG alone!* Does anyone know how to include the reference channels effectively in the LCMV beamforming? Thanks for your help, Sharon Riwkes. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at DONDERS.RU.NL Mon Aug 2 15:23:38 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 2 Aug 2010 15:23:38 +0200 Subject: Beamforming with reference channels In-Reply-To: Message-ID: Hi Sharon, If the results are exactly the same, I guess the references have not been taken into account at all. Although it remains to be seen whether you gain a lot with this approach (my preferred alternative would be to clean the data from external noise using the references and taking into account the correction in the forward computation), it should be possible to do it in fieldtrip. To get it to work, you have to check whether the necessary information is present throughout your analysis pipeline. Importantly, when computing the covariance matrix in ft_timelockanalysis, you have to include the references. The same goes for the computation of the leadfields (if you use ft_prepare_leadfield for that). If this information is still present prior to your call to ft_sourceanalysis, you may want to check whether you have to specify cfg.channel (to include the references, rather than 'MEG' (which may be the default, and causes selection of close-to-the-head sensors only). Just for the record: is it 4D-neuroimaging data you are working on? Best wishes, Jan-Mathijs On Aug 2, 2010, at 2:06 PM, sharon riwkes wrote: > Hi all, > I tried to do source localization, after beamforming with the LCMV > method. I did it once for all the MEG channels, and once for MEG > channels AND the reference channels. I was hoping that using the > reference channels will improve the localization by ignoring noise > coming from outside of the brain. > However, I got the exact same results for MEG+reference channels as > for MEG alone! > Does anyone know how to include the reference channels effectively > in the LCMV beamforming? > Thanks for your help, > Sharon Riwkes. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sharonriwkes at GMAIL.COM Wed Aug 4 13:39:16 2010 From: sharonriwkes at GMAIL.COM (sharon riwkes) Date: Wed, 4 Aug 2010 14:39:16 +0300 Subject: Beamforming with reference channels In-Reply-To: Message-ID: Dear Jan-Mathijs, Thanks for your quick answer! I will check the different possibilities. I think that the problem was in the stage the lead field computation. And yes, this is 4D data. Sharon. On Mon, Aug 2, 2010 at 4:23 PM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Hi Sharon, > > If the results are exactly the same, I guess the references have not been > taken into account at all. Although it remains to be seen whether you gain a > lot with this approach (my preferred alternative would be to clean the data > from external noise using the references and taking into account the > correction in the forward computation), it should be possible to do it in > fieldtrip. To get it to work, you have to check whether the necessary > information is present throughout your analysis pipeline. Importantly, when > computing the covariance matrix in ft_timelockanalysis, you have to include > the references. The same goes for the computation of the leadfields (if you > use ft_prepare_leadfield for that). If this information is still present > prior to your call to ft_sourceanalysis, you may want to check whether you > have to specify cfg.channel (to include the references, rather than 'MEG' > (which may be the default, and causes selection of close-to-the-head sensors > only). > Just for the record: is it 4D-neuroimaging data you are working on? > > Best wishes, > > Jan-Mathijs > > > On Aug 2, 2010, at 2:06 PM, sharon riwkes wrote: > > Hi all, > I tried to do source localization, after beamforming with the LCMV method. > I did it once for all the MEG channels, and once for MEG channels *AND the > reference channels*. I was hoping that using the reference channels will > improve the localization by ignoring noise coming from outside of the brain. > > However, I got the *exact same results for MEG+reference channels* as *for > MEG alone!* > Does anyone know how to include the reference channels effectively in the > LCMV beamforming? > Thanks for your help, > Sharon Riwkes. > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Thu Aug 5 15:49:39 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Thu, 5 Aug 2010 15:49:39 +0200 Subject: significance of coherence differences Message-ID: Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,...] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,...]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Panagiotis.Tsiatsis at TUEBINGEN.MPG.DE Fri Aug 6 10:44:56 2010 From: Panagiotis.Tsiatsis at TUEBINGEN.MPG.DE (Panagiotis Tsiatsis) Date: Fri, 6 Aug 2010 10:44:56 +0200 Subject: Removing ECG artifacts via ICA in a Steady State experiment without EMG Channel (MEG) Message-ID: Dear all, I am a newbie in fieldtrip. First of all I would like to say thanks for your beautiful work and support. I am facing the following problem : I am running a Visual Steady State MEG experiment (CTF scanner) and I want to remove the ECG artifacts but I do not have an EMG channel available. I haven't managed to go fully through the analysis (by the way, I was getting errors when trying to run your ICA ECG example, but let me take another look) but I am worried that by using the 'left' MEG channels (MLT) alone to detect the artifacts I will not manage to go far, as the ECG activity will be obscured by the steady state activity (10 Hz flickering light) and I will not be able to from a proper averaged / typical ECG. Does anybody have any experience with this? I know that it is quite silly to ask you before trying completely and therefore I apologize beforehand. Once I have fully gone through the analysis I can inform you on whether I managed to do it reliably. Thanks and best, Panagiotis ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Mon Aug 9 18:58:57 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Mon, 9 Aug 2010 18:58:57 +0200 Subject: significance of coherence differences In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8B0176EB70@Mail2-UKD.VMED.UKD> Message-ID: Hi Jan, If you get confused about the literature then I am partly to blame. Things are different for single subject studies (units-of-observation are trials) and multiple subject studies (units-of-observation are subjects). You describe a multiple subject study of the within-subjects type (every subjects participates in both experimental conditions). For a single channel pair and a single frequency bin, the appropriate statistic is the dependent (paired) samples t-statistic or, in a nonparametric framework, the Wilcoxon signed rank sum test. (You mention the Wilcoxon rank sum test, but this is for a study of the between-subjects type.) You apply this test statistic to the condition-specific coherences, obtained by summing and normalizing the trial(taper)-specific cross-spectra. This statistical test works fine (asymptotically, for the dependent samples t-statistic) if the number of trials in the two conditions are equal. The requirement of an equal number of trials follows from the fact that coherence is a biased measure, with the bias being dependent on the number of trials. The situation is different for a single subject study. You may want to have a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals with the multiple comparisons problem. Best, Eric dr. Eric Maris Donders Institute for Brain, Cognition and Behavior Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging Radboud University P.O. Box 9104 6500 HE Nijmegen The Netherlands T:+31 24 3612651 Mobile: 06 39584581 F:+31 24 3616066 E: e. maris at donders.ru.nl From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: donderdag 5 augustus 2010 15:50 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] significance of coherence differences Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Tue Aug 10 09:57:28 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 10 Aug 2010 09:57:28 +0200 Subject: OpenMEEG: libraries not found Message-ID: Dear all, I'm trying to run OpenMEEG from fieldtrip, but the executables complain about libstdc++.so.6 missing. I'm quite sure that libstdc++ v6 is installed, but om_assemble seems to expect it to be in /usr/local/matlab/sys/os/glnx86/, not in /lib/. Unfortunately none of the Tutorials and Read-mes seems to deal with this. I've got no clue, how to handle this and it would be nice, if any of you could help me. Cheers and thanks in advance, Paul PS: When running om_assemble from command line, it runs without any problem -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Tue Aug 10 10:47:52 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Tue, 10 Aug 2010 10:47:52 +0200 Subject: AW: [FIELDTRIP] significance of coherence differences Message-ID: Dear Eric, thank you for your answer. I read the paper and see that your method is a great tool to deal with the MCP and with situations in which one does not know at which frequencies and channels an effect is expected. It is good to know that for the group level (multiple subjects, all measured in the same set of conditions) conventional paired-sample statistics are appropriate, beacause I dont see how the random-partition procedure relates to such a situation. All the best, Jan -----Ursprüngliche Nachricht----- Von: FieldTrip discussion list im Auftrag von Eric Maris Gesendet: Mo 09.08.2010 18:58 An: FIELDTRIP at NIC.SURFNET.NL Betreff: Re: [FIELDTRIP] significance of coherence differences Hi Jan, If you get confused about the literature then I am partly to blame. Things are different for single subject studies (units-of-observation are trials) and multiple subject studies (units-of-observation are subjects). You describe a multiple subject study of the within-subjects type (every subjects participates in both experimental conditions). For a single channel pair and a single frequency bin, the appropriate statistic is the dependent (paired) samples t-statistic or, in a nonparametric framework, the Wilcoxon signed rank sum test. (You mention the Wilcoxon rank sum test, but this is for a study of the between-subjects type.) You apply this test statistic to the condition-specific coherences, obtained by summing and normalizing the trial(taper)-specific cross-spectra. This statistical test works fine (asymptotically, for the dependent samples t-statistic) if the number of trials in the two conditions are equal. The requirement of an equal number of trials follows from the fact that coherence is a biased measure, with the bias being dependent on the number of trials. The situation is different for a single subject study. You may want to have a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals with the multiple comparisons problem. Best, Eric dr. Eric Maris Donders Institute for Brain, Cognition and Behavior Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging Radboud University P.O. Box 9104 6500 HE Nijmegen The Netherlands T:+31 24 3612651 Mobile: 06 39584581 F:+31 24 3616066 E: e. maris at donders.ru.nl From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Jan Hirschmann Sent: donderdag 5 augustus 2010 15:50 To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] significance of coherence differences Dear fieldtrip experts, I am getting more and more confused about the literature of significance tests of coherence differences. The one essential point I did not quite understand is why conventional tests do not seem to apply. Lets say I have two vectors of mean alpha band coherences, relating to two experimental conditions (continuous data, no trials). The vector entries stem from different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from comparing the two vectors, say, with a Wilcoxon ranksum test? Thanks for any comments, Jan Hirschmann ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Tue Aug 10 11:55:26 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Tue, 10 Aug 2010 11:55:26 +0200 Subject: OpenMEEG: libraries not found In-Reply-To: <4C610668.30405@gmx.de> Message-ID: Dear all, with a little help of a colleague I was able to run the OpenMEEG executables but we had to move all of the files from the matlab/sys/os/glnx86 folder to another place and link everything from my /usr/lib/ dir to the glnx folder. It works, but really aint the best way in my opinion. Is there another - slightly more sensible - way to go? Cheers, Paul Am 10.08.2010 09:57, schrieb Paul Czienskowski: > Dear all, > > I'm trying to run OpenMEEG from fieldtrip, but the executables > complain about libstdc++.so.6 missing. I'm quite sure that libstdc++ > v6 is installed, but om_assemble seems to expect it to be in > /usr/local/matlab/sys/os/glnx86/, not in /lib/. Unfortunately none of > the Tutorials and Read-mes seems to deal with this. I've got no clue, > how to handle this and it would be nice, if any of you could help me. > > Cheers and thanks in advance, > Paul > > PS: When running om_assemble from command line, it runs without any > problem > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From e.maris at DONDERS.RU.NL Tue Aug 10 12:47:47 2010 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Tue, 10 Aug 2010 12:47:47 +0200 Subject: AW: [FIELDTRIP] significance of coherence differences In-Reply-To: <72E993C35FB11743B79FF9286E5B6D8BA2E57B@Mail2-UKD.VMED.UKD> Message-ID: Hi Jan, > thank you for your answer. I read the paper and see that your method is > a great tool to deal with the MCP and with situations in which one does > not know at which frequencies and channels an effect is expected. It is > good to know that for the group level (multiple subjects, all measured > in the same set of conditions) conventional paired-sample statistics > are appropriate, beacause I dont see how the random-partition procedure > relates to such a situation. I does not, because the random partitioning procedure only applies to single subject studies (UOs are trials). In a within-subjects multiple subject study the random aspect is in the random permutation of the elements in the paired observations. Best, Eric > > All the best, > Jan > > > > > -----Ursprüngliche Nachricht----- > Von: FieldTrip discussion list im Auftrag von Eric Maris > Gesendet: Mo 09.08.2010 18:58 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: Re: [FIELDTRIP] significance of coherence differences > > Hi Jan, > > > > > > If you get confused about the literature then I am partly to blame. > > > > Things are different for single subject studies (units-of-observation > are > trials) and multiple subject studies (units-of-observation are > subjects). > You describe a multiple subject study of the within-subjects type > (every > subjects participates in both experimental conditions). For a single > channel > pair and a single frequency bin, the appropriate statistic is the > dependent > (paired) samples t-statistic or, in a nonparametric framework, the > Wilcoxon > signed rank sum test. (You mention the Wilcoxon rank sum test, but this > is > for a study of the between-subjects type.) You apply this test > statistic to > the condition-specific coherences, obtained by summing and normalizing > the > trial(taper)-specific cross-spectra. This statistical test works fine > (asymptotically, for the dependent samples t-statistic) if the number > of > trials in the two conditions are equal. The requirement of an equal > number > of trials follows from the fact that coherence is a biased measure, > with the > bias being dependent on the number of trials. > > > > The situation is different for a single subject study. You may want to > have > a look at our paper (Maris, Schoffelen, Fries, 2007), which also deals > with > the multiple comparisons problem. > > > > > > Best, > > > > Eric > > > > > > dr. Eric Maris > Donders Institute for Brain, Cognition and Behavior > > Center for Cognition and F.C. Donders Center for Cognitive Neuroimaging > > Radboud University > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > T:+31 24 3612651 > Mobile: 06 39584581 > > F:+31 24 3616066 > E: e. maris at donders.ru.nl > > > > > > > > > > > > > > From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On > Behalf > Of Jan Hirschmann > Sent: donderdag 5 augustus 2010 15:50 > To: FIELDTRIP at NIC.SURFNET.NL > Subject: [FIELDTRIP] significance of coherence differences > > > > Dear fieldtrip experts, > > > > I am getting more and more confused about the literature of > significance > tests of coherence differences. The one essential point I did not quite > understand is why conventional tests do not seem to apply. Lets say I > have > two vectors of mean alpha band coherences, relating to two experimental > conditions (continuous data, no trials). The vector entries stem from > different subjects: C1=[meancoh_cond1_subj1, meancoh_cond1_subj2,.] and > C2=[meancoh_cond2_subj1, meancoh_cond2_subj2,.]. What keeps me from > comparing the two vectors, say, with a Wilcoxon ranksum test? > > > > Thanks for any comments, > > > > Jan Hirschmann > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of > the > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Tue Aug 10 17:46:57 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Tue, 10 Aug 2010 11:46:57 -0400 Subject: inter trial coherence Message-ID: Hello Fieldtrippers, I am now trying to do the frequencyanalysis with my eeg data in Fieldtrip. With the function of 'freqanalysis', i got my TFR data. Now i have a question: does fieldtrip have a function that gives "phase locking factor" or inter-trial coherence (ITC)? I apologize in advance if my questions are too obvious. Thanks for your help, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.vandermeij at DONDERS.RU.NL Wed Aug 11 09:33:41 2010 From: r.vandermeij at DONDERS.RU.NL (Roemer van der Meij) Date: Wed, 11 Aug 2010 09:33:41 +0200 Subject: inter trial coherence In-Reply-To: <4C617471.4040809@rotman-baycrest.on.ca> Message-ID: Hi Yu, Have a look at the function ft_connectivityanalysis, that should be able get you what you want. Regards, Roemer On 8/10/2010 5:46 PM, Yu He wrote: > Hello Fieldtrippers, > > I am now trying to do the frequencyanalysis with my eeg data in > Fieldtrip. > > With the function of 'freqanalysis', i got my TFR data. > Now i have a question: does fieldtrip have a function that gives > "phase locking factor" or inter-trial coherence (ITC)? > I apologize in advance if my questions are too obvious. > > Thanks for your help, > > Yu > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Wed Aug 11 09:59:30 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 11 Aug 2010 09:59:30 +0200 Subject: Volume conductor space alignment Message-ID: Dear all, I'm trying to simulate and fit EEG data with different models for my diploma thesis and I have another little question. I wondered if there is any alignment done before or when simulating the data or if the simulation's done in the space the BEM model was created from. I'd like to know this to know if I'd have to align my spaces on my own or if everything is in the space spanned by the fidcial points anyway. Thanks in advance, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From khoechstetter at BESA.DE Wed Aug 11 13:29:35 2010 From: khoechstetter at BESA.DE (Karsten Hoechstetter) Date: Wed, 11 Aug 2010 13:29:35 +0200 Subject: Upcoming BESA Workshop in London (September 9-10) Message-ID: Dear colleagues, I would like to inform you that a 2-day BESA Research workshop will be held in London/UK on September 9-10. This workshop provides a thorough introduction to BESA Research, the software package for comprehensive EEG/MEG data analysis. Target group of the workshop are both novices and existing BESA users. The workshop includes hands-on tutorials on the new features of BESA Research 5.3, e.g. the direct MATLAB interface and CLARA, the new 3D source imaging technique. Covered topics will include: - A theoretical introduction to source analysis - Hands-on source analysis with simulated and real data sets - Data preprocessing in BESA Research: Artifact rejection and correction, channel interpolation, digital filtering, 3D mapping, remontaging, averaging - Coregistration with (f)MRI - Time-frequency analysis and source coherence - Beamforming - 3D volume imaging: CLARA, LORETA, sLORETA, minimum norm etc. - Batch scripting For more information, schedule, and registration, please visit the BESA website at www.besa.de/events/workshops. If you have any further questions, please contact workshop at besa.de. I would be glad to see you on one of these occasions! Best wishes, Karsten Hoechstetter -------------------------------------- Dr. Karsten Hoechstetter MEGIS Software GmbH Gräfelfing, Germany HRB München 109956 CEO Dr. Michael Scherg -------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Wed Aug 11 15:52:31 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Wed, 11 Aug 2010 15:52:31 +0200 Subject: unclosed surfaces with BEM models Message-ID: Dear fieldtrippers, I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with cfg = []; cfg.tissue = [1 2 3]; cfg.numvertices = [1000 2000 3000] cfg.conductivity = [1 1/80 1] cfg.sourceunits = 'cm' cfg.mriunits = 'mm' cfg.method = 'dipoli'; cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg does the triangulation and computes the BEM model up to the following error message: (begin) .... Bmat countdown: 5010 (pass 2) Bmat countdown: 5000 (pass 2) Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) Warning: an error ocurred while running dipoli > In dipoli at 90 In ft_prepare_bemmodel at 112 Error using ==> fread Invalid file identifier. Use fopen to generate a valid file identifier. Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. > In dipoli at 98 In ft_prepare_bemmodel at 112 (end) I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. Best regards, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Wed Aug 11 16:25:37 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Wed, 11 Aug 2010 16:25:37 +0200 Subject: inter trial coherence Message-ID: Thanks Roemer! I am not very clear about function of ft_connectivityanalysis. It is said "FT_CONNECTIVITYANALYIS computes various measures of connectivity between MEG/EEG channels or between source-level signals." when you read the documentation reference. Is that only for between MEG/EEG channels? Regards, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Aug 11 16:35:21 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 11 Aug 2010 16:35:21 +0200 Subject: inter trial coherence In-Reply-To: Message-ID: Dear Yu, Ft_connectivityanalysis works also with different kinds of electrophysiological data. It's on our list to make the documentation to this function clearer. This will hopefully happen soon. For now, I don't think this is the function you need for inter-trial coherence. Ft_connectivityanalysis computes bivariate metrics, i.e. measures of connectivity defined between channel pairs. In your case, you want to estimate the consistency of oscillatory phase across trials (and not the consistency of the phase difference between a pair of channels across trials). So what you need to do is probably something like this: cfg = []; cfg.output = 'fourier'; cfg..... cfg..... cfg..... freq = ft_freqanalysis(cfg, data); Next, to obtain the itc, do the following tmpdat = freq.fourierspctrm; tmpdat = tmpdat(abs(tmpdat)); % this will normalise each trial for its amplitude; itc = abs(mean(tmpdat)); % this will give the itc Best wishes, Jan-Mathijs On Aug 11, 2010, at 4:25 PM, Yu He wrote: > Thanks Roemer! > > I am not very clear about function of ft_connectivityanalysis. It is > said "FT_CONNECTIVITYANALYIS computes various measures of connectivity > between MEG/EEG channels or between source-level signals." when you > read > the documentation reference. > > Is that only for between MEG/EEG channels? > > Regards, > > Yu > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Wed Aug 11 16:50:48 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Wed, 11 Aug 2010 16:50:48 +0200 Subject: inter trial coherence In-Reply-To: <2C2E534F-B24F-4D03-A32B-70A15D6ABAFC@donders.ru.nl> Message-ID: Dear Yu, I made a slight typo in my previous mail. Obviously tmpdat = tmpdat(abs(tmpdat)); % this will normalise each trial for its amplitude; should read tmpdat = tmpdat./abs(tmpdat); for the normalization to work. Best wishes, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From yhe at ROTMAN-BAYCREST.ON.CA Wed Aug 11 18:50:23 2010 From: yhe at ROTMAN-BAYCREST.ON.CA (Yu He) Date: Wed, 11 Aug 2010 18:50:23 +0200 Subject: inter trial coherence Message-ID: Dear Jan-Mathijs, That's great! Thank you so much for the step by step explanation. Best regs, Yu ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Thu Aug 12 17:52:19 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 12 Aug 2010 17:52:19 +0200 Subject: Units powspctrm Message-ID: Hello together, What units does the powspctrm have? Starting with an EEG signal in microvolts and computing the powerspectrum using freqanalysis what are the units of powspctrm? I tried to figure it out on my own but I am stuck somehow. Here some example code cfg=[]; cfg.method='mtmfft'; cfg.output='pow'; cfg.pad ='maxperlen' cfg.foilim=[1 130] cfg.taper='hanning' cfg.channel=1 cfg.keeptrials='no' R=ft_freqanalysis(cfg,data); I am interested in the units of R.powspctrm Thanks Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Thu Aug 12 21:38:57 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Thu, 12 Aug 2010 21:38:57 +0200 Subject: Units powspctrm In-Reply-To: <942108.4682501281641712211.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hello Martin, A powerspectrum typically has the frequencies on one axis and the power of the corresponding frequencies on the other. The power represents how strong a certain frequency occurs in a signal, given by the square of the voltage per frequency. In your case: square of the microvolts per frequency: uV^2/ Hz Best regards, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: [FIELDTRIP] Units powspctrm Hello together, What units does the powspctrm have? Starting with an EEG signal in microvolts and computing the powerspectrum using freqanalysis what are the units of powspctrm? I tried to figure it out on my own but I am stuck somehow. Here some example code cfg=[]; cfg.method='mtmfft'; cfg.output='pow'; cfg.pad ='maxperlen' cfg.foilim=[1 130] cfg.taper='hanning' cfg.channel=1 cfg.keeptrials='no' R=ft_freqanalysis(cfg,data); I am interested in the units of R.powspctrm Thanks Martin ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Thu Aug 12 22:48:14 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Thu, 12 Aug 2010 22:48:14 +0200 Subject: Units powspctrm In-Reply-To: <7050041.4682621281641937538.JavaMail.root@watertor.uci.ru.nl> Message-ID: Yes, typically, but is it the case for the powspctrm you get from the mtmfft freqanalysis? I am asking for the following reason: Lets say, I have two experimental conditions A and B and I compute the powerspectra for both of them. When the units actually are uV^2/Hz i could tell for each frequency by how much uV A and B differ. What confuses me is that in ft_freqanalysis_mtmfftthe signal is multiplied with a taper (tap) and thereby scaled. The resulting powspctrm hence does not reflect the the true changes in microvolt. Do I see that correctly, or am I missing something here? Is the powerspectrum corrected for that somewhere else? Regards, Martin 2010/8/12 a.stolk at fcdonders.ru.nl > Hello Martin, > > A powerspectrum typically has the frequencies on one axis and the power of > the corresponding frequencies on the other. The power represents how strong > a certain frequency occurs in a signal, given by the square of the voltage > per frequency. > > In your case: square of the microvolts per frequency: uV^2/ Hz > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Units powspctrm > > Hello together, > > What units does the powspctrm have? > Starting with an EEG signal in microvolts and computing the powerspectrum > using freqanalysis what are the units of powspctrm? > I tried to figure it out on my own but I am stuck somehow. > > Here some example code > > cfg=[]; > cfg.method='mtmfft'; > cfg.output='pow'; > cfg.pad ='maxperlen' > cfg.foilim=[1 130] > cfg.taper='hanning' > cfg.channel=1 > cfg.keeptrials='no' > > R=ft_freqanalysis(cfg,data); > > I am interested in the units of R.powspctrm > > Thanks > Martin > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at FCDONDERS.RU.NL Fri Aug 13 08:24:50 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Fri, 13 Aug 2010 08:24:50 +0200 Subject: Units powspctrm In-Reply-To: <5621986.4689631281680620957.JavaMail.root@watertor.uci.ru.nl> Message-ID: If you use the same mtmfft settings for both conditions, in theory it should be fine. Make sure that you compute the fourier transformation on equal window lenghts. If you happen to have variable triallengths per condition, my suggestion would be to cut the trials in (e.g.) 1 second pieces. This way your 'frequency resolution' is the same for condition A and B. If your experimental setup allows you, you could choose to normalize your data (e.g. a baselinecorrection) first before making the A and B comparison. This way you correct for (non-)cognitive powerchanges over time (case it's not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste over time, subject habituation effects and whatelse you have. Best, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [FIELDTRIP] Units powspctrm Yes, typically, but is it the case for the powspctrm you get from the mtmfft freqanalysis? I am asking for the following reason: Lets say, I have two experimental conditions A and B and I compute the powerspectra for both of them. When the units actually are uV^2/Hz i could tell for each frequency by how much uV A and B differ. What confuses me is that in ft_freqanalysis_mtmfftthe signal is multiplied with a taper (tap) and thereby scaled. The resulting powspctrm hence does not reflect the the true changes in microvolt. Do I see that correctly, or am I missing something here? Is the powerspectrum corrected for that somewhere else? Regards, Martin 2010/8/12 a.stolk at fcdonders.ru.nl > Hello Martin, > > A powerspectrum typically has the frequencies on one axis and the power of > the corresponding frequencies on the other. The power represents how strong > a certain frequency occurs in a signal, given by the square of the voltage > per frequency. > > In your case: square of the microvolts per frequency: uV^2/ Hz > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: [FIELDTRIP] Units powspctrm > > Hello together, > > What units does the powspctrm have? > Starting with an EEG signal in microvolts and computing the powerspectrum > using freqanalysis what are the units of powspctrm? > I tried to figure it out on my own but I am stuck somehow. > > Here some example code > > cfg=[]; > cfg.method='mtmfft'; > cfg.output='pow'; > cfg.pad ='maxperlen' > cfg.foilim=[1 130] > cfg.taper='hanning' > cfg.channel=1 > cfg.keeptrials='no' > > R=ft_freqanalysis(cfg,data); > > I am interested in the units of R.powspctrm > > Thanks > Martin > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Jan.Hirschmann at MED.UNI-DUESSELDORF.DE Fri Aug 13 19:11:12 2010 From: Jan.Hirschmann at MED.UNI-DUESSELDORF.DE (Jan Hirschmann) Date: Fri, 13 Aug 2010 19:11:12 +0200 Subject: coherence again In-Reply-To: A<18555530.4689671281680690002.JavaMail.root@watertor.uci.ru.nl> Message-ID: Dear fieldtrip experts, I have yet another question about the statistical testing of coherence. Again, it relates to the group level, this time to the testing procedure used in "Imaging the motor system's beta-band synchronisation during isometric contraction", Schoffeleln et al., NeuroImage, 2008. There it says: " The null hypothesis that was tested at the voxel level states that the Z-transformed coherence between the EMG and that voxel, accumulated across subjects, is not different from 0. Under this null hypothesis, flipping the sign of the Z-transformed coherence values of a random subset of the subjects before accumulating leads to an alternative observation that belongs to the null distribution." Now, as I understand it, the Z-transformation described here is z=sqrt(-(df-2)*log(1-abs(C)^2)), i.e. z takes only positive values (there is no comparing of conditions here) And accumulation, it later says, means summing up the z-values of all subjects and dividing by sqrt(n) at each voxel. I suppose n is the number of subjects. So "flipping the sign" means multiplying the z-value of some subjects by -1 before summing up? As all z-values were originally positive, this will inevitably decrease the sum. So the original state will inevitably be the extreme end of the distribution. Sorry, I must have some serious error in my thinking here (hope it's not too obvious). Can you help me? Many thanks, Jan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 13 20:15:08 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 13 Aug 2010 20:15:08 +0200 Subject: unclosed surfaces with BEM models In-Reply-To: <4C62C73F020000570000710A@gwsmtp1.uni-regensburg.de> Message-ID: Hi Gregor, I was trying to to run dipoli to generate the BEM-Models too but often it failed with the very error. With some brains it worked checking everything 'by hand' since the matlab routines to create the surfaces seem to fail sometimes and produce an output that differs from the volume very much (e.g. spikes on the surface). I was facing an error lately when I obviously had some 'Inf' voxels in my volume for some crude reason. You may consider to switch to OpenMEEG because it's much better documented than dipoli (which takes - indeed - no effort at all as dipoli actually is not documented at all) and I think there are prebuilt binaries for Debian on AMD64 infrastructure. If you're trying to run OpenMEEG with more than 3 surfaces, which is supported by OpenMEEG but not by fieldtrip, I may send you my modified scripts. Hope this helps at least a bit. Cheers, Paul Am 11.08.2010 15:52, schrieb Gregor Volberg: > Dear fieldtrippers, > > I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with > > cfg = []; > cfg.tissue = [1 2 3]; > cfg.numvertices = [1000 2000 3000] > cfg.conductivity = [1 1/80 1] > cfg.sourceunits = 'cm' > cfg.mriunits = 'mm' > cfg.method = 'dipoli'; > cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; > vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg > > does the triangulation and computes the BEM model up to the following error message: > > (begin) > .... > Bmat countdown: 5010 (pass 2) > Bmat countdown: 5000 (pass 2) > > > Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface > (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) > > > Warning: an error ocurred while running dipoli >> In dipoli at 90 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. >> In dipoli at 98 > In ft_prepare_bemmodel at 112 > (end) > > I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. > > So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. > > Best regards, Gregor > > > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Mon Aug 16 08:18:13 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Mon, 16 Aug 2010 08:18:13 +0200 Subject: Antw: Re: [FIELDTRIP] unclosed surfaces with BEM models In-Reply-To: <4C658BAC.8060709@gmx.de> Message-ID: Hi Paul, thanks a lot for your reply! I will try OpenMEEG and I hope I can fix the error soon. Meanwhile, I would be very glad if you could send me your modified script for > 3 surfaces. This will surely help... Thanks again, best regards, Gegor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Paul Czienskowski 8/13/2010 8:15 PM >>> Hi Gregor, I was trying to to run dipoli to generate the BEM-Models too but often it failed with the very error. With some brains it worked checking everything 'by hand' since the matlab routines to create the surfaces seem to fail sometimes and produce an output that differs from the volume very much (e.g. spikes on the surface). I was facing an error lately when I obviously had some 'Inf' voxels in my volume for some crude reason. You may consider to switch to OpenMEEG because it's much better documented than dipoli (which takes - indeed - no effort at all as dipoli actually is not documented at all) and I think there are prebuilt binaries for Debian on AMD64 infrastructure. If you're trying to run OpenMEEG with more than 3 surfaces, which is supported by OpenMEEG but not by fieldtrip, I may send you my modified scripts. Hope this helps at least a bit. Cheers, Paul Am 11.08.2010 15:52, schrieb Gregor Volberg: > Dear fieldtrippers, > > I encounter a notorious error message about unclosed surfaces when computing forward BEM models from individual MR anatomies. In oder to rule out that the error arose during segmentation, I then used the example data from the tutorial "Create BEM headmodel for EEG". Running the code with > > cfg = []; > cfg.tissue = [1 2 3]; > cfg.numvertices = [1000 2000 3000] > cfg.conductivity = [1 1/80 1] > cfg.sourceunits = 'cm' > cfg.mriunits = 'mm' > cfg.method = 'dipoli'; > cfg.dipoli = '/home/vog20246/loctmp/m-lib/fieldtrip-20100810/external/dipoli'; > vol = ft_prepare_bemmodel(cfg, mri); %where mri contains field .seg > > does the triangulation and computes the BEM model up to the following error message: > > (begin) > .... > Bmat countdown: 5010 (pass 2) > Bmat countdown: 5000 (pass 2) > > > Fatal error in dipoli: interface /tmp/tp610e7212_00c2_4baa_a23e_3c28760eda25.tri is not a single closed surface > (totsolangle= -2.0000 from vertex 1 of /tmp/tp7926a65d_2628_4e7d_9d88_44651dfa8674.tri ) > > > Warning: an error ocurred while running dipoli >> In dipoli at 90 > In ft_prepare_bemmodel at 112 > Error using ==> fread > Invalid file identifier. Use fopen to generate a valid file identifier. > Warning: File '/tmp/tpac730b26_4dd7_4599_814f_69b80a106b51.ama' not found. >> In dipoli at 98 > In ft_prepare_bemmodel at 112 > (end) > > I then tried the same code with the standard_vol distributed with fieldtrip, and received the same error message, again after 1/6 of the second pass (2500 of 3000) was computed. Next I tried cfg.method = 'bemcp' instead of 'dipoli' and got a warning message "Matrix is singular, close to singular or badly scaled" and NaNs as output. According to recent postings in this group, this error occurs if the three compartements intersect at one or more points. > > So, something in my code seems to tell fieldtrip that the surfaces are intersecting or incomplete. Is there anything I am missing? Any hint would be greatly appreciated. I use Matlab 7.8.0 (R2009a) on Debian Linux 64 bit and just updated my fieldtrip version to 20100810. > > Best regards, Gregor > > > -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Mon Aug 16 09:02:23 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Mon, 16 Aug 2010 09:02:23 +0200 Subject: Space alignment - once again Message-ID: Dear Fieldtrippers, I asked this some days ago and didn't get any answer. I don't want to spam, but I need to know strongly. I wasn't able to find out yet, if the space the dipoles are simulated if I'm running ft_dipolesimulation is in some manner aligned to the fiducial space, or if it's all based on the voxel coordinates. It would be a great help, if someone knew the answer. Cheers, Paul -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Mon Aug 16 09:34:25 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Mon, 16 Aug 2010 09:34:25 +0200 Subject: Space alignment - once again In-Reply-To: <4C68E27D.40902@gmx.de> Message-ID: Hi Paul, The simulation routine doesn't care about the co-registration between the volume conductor model and the sensor array. It is your responsibility to ensure that they are correctly aligned. The sources need to be in the same coordinate frame as the sensors, so that's I guess what you refer to as fiducial space. Obviously, if your sensor positions are expressed in voxel space, you need to specify your sources in voxel space as well. Goood luck, Jan-Mathijs On Aug 16, 2010, at 9:02 AM, Paul Czienskowski wrote: > Dear Fieldtrippers, > > I asked this some days ago and didn't get any answer. I don't want > to spam, but I need to know strongly. > I wasn't able to find out yet, if the space the dipoles are > simulated if I'm running ft_dipolesimulation is in some manner > aligned to the fiducial space, or if it's all based on the voxel > coordinates. It would be a great help, if someone knew the answer. > > Cheers, > Paul > > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Aug 16 10:07:04 2010 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Aug 2010 10:07:04 +0200 Subject: post-doc position available in Paris Message-ID: Dear Fieldtrip list members, Appologies for multiple postings. Please find attached a job opportunity in the group of Florian Waszak. best regards, ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: PostDoc_Paris.pdf Type: application/pdf Size: 79622 bytes Desc: not available URL: -------------- next part -------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Aug 16 10:46:15 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 16 Aug 2010 10:46:15 +0200 Subject: Units powspctrm In-Reply-To: <18555530.4689671281680690002.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Arjen, my point is that I am interested not in the relative difference between signals but in the actual difference in microvolt. I know that this is not the standard thing to do but that is what I need . After playing aroud a bit i come to the following conlcusion Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with an amplitude of 100uV and one with an aplitude of 200uV. Computing a power spectrum using matlab fft function I can eventually read out that the difference between my two signals is 100uV. In ft_freqanalysis_mtmfft the signal is multiplied by a taper line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) pad],[],2); The output can hence not be transformed back right away to the real microvolt values, but happens to be scaled (in my case ) by a factor of ~0.036 (which is the mean value of the taper) At least that is what I think happens. Regards Martin 2010/8/13 a.stolk at fcdonders.ru.nl > If you use the same mtmfft settings for both conditions, in theory it > should be fine. Make sure that you compute the fourier transformation on > equal window lenghts. > > If you happen to have variable triallengths per condition, my suggestion > would be to cut the trials in (e.g.) 1 second pieces. This way your > 'frequency resolution' is the same for condition A and B. > > If your experimental setup allows you, you could choose to normalize your > data (e.g. a baselinecorrection) first before making the A and B comparison. > This way you correct for (non-)cognitive powerchanges over time (case it's > not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste > over time, subject habituation effects and whatelse you have. > > Best, > Arjen > > > > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Yes, typically, but is it the case for the powspctrm you get from the > mtmfft > freqanalysis? > I am asking for the following reason: > > Lets say, I have two experimental conditions A and B and I compute the > powerspectra for both of them. > When the units actually are uV^2/Hz i could tell for each frequency by how > much uV A and B differ. > > What confuses me is that in > ft_freqanalysis_mtmfft< > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > signal is multiplied with a taper (tap) and thereby scaled. > The resulting powspctrm hence does not reflect the the true changes in > microvolt. > Do I see that correctly, or am I missing something here? Is the > powerspectrum corrected for that somewhere else? > > Regards, > Martin > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > Hello Martin, > > > > A powerspectrum typically has the frequencies on one axis and the power > of > > the corresponding frequencies on the other. The power represents how > strong > > a certain frequency occurs in a signal, given by the square of the > voltage > > per frequency. > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > Best regards, > > Arjen > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: [FIELDTRIP] Units powspctrm > > > > Hello together, > > > > What units does the powspctrm have? > > Starting with an EEG signal in microvolts and computing the powerspectrum > > using freqanalysis what are the units of powspctrm? > > I tried to figure it out on my own but I am stuck somehow. > > > > Here some example code > > > > cfg=[]; > > cfg.method='mtmfft'; > > cfg.output='pow'; > > cfg.pad ='maxperlen' > > cfg.foilim=[1 130] > > cfg.taper='hanning' > > cfg.channel=1 > > cfg.keeptrials='no' > > > > R=ft_freqanalysis(cfg,data); > > > > I am interested in the units of R.powspctrm > > > > Thanks > > Martin > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Mon Aug 16 10:48:26 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Mon, 16 Aug 2010 10:48:26 +0200 Subject: Space alignment - once again In-Reply-To: Message-ID: Hi Jan-Mathijs, thank you very much. Since I'm trying to compare different models I'll have to do the alignment with the nasion-pre auricular space but I'm already on it. Just needed the info if I was carrying owls to athens. Cheers, Paul Am 16.08.2010 09:34, schrieb jan-mathijs schoffelen: > Hi Paul, > > The simulation routine doesn't care about the co-registration between > the volume conductor model and the sensor array. It is your > responsibility to ensure that they are correctly aligned. The sources > need to be in the same coordinate frame as the sensors, so that's I > guess what you refer to as fiducial space. Obviously, if your sensor > positions are expressed in voxel space, you need to specify your > sources in voxel space as well. > > Goood luck, > > Jan-Mathijs > > > On Aug 16, 2010, at 9:02 AM, Paul Czienskowski wrote: > >> Dear Fieldtrippers, >> >> I asked this some days ago and didn't get any answer. I don't want to >> spam, but I need to know strongly. >> I wasn't able to find out yet, if the space the dipoles are simulated >> if I'm running ft_dipolesimulation is in some manner aligned to the >> fiducial space, or if it's all based on the voxel coordinates. It >> would be a great help, if someone knew the answer. >> >> Cheers, >> Paul >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> The aim of this list is to facilitate the discussion between users of >> the FieldTrip toolbox, to share experiences and to discuss new ideas >> for MEG and EEG analysis. See also >> http://listserv.surfnet.nl/archives/fieldtrip.html and >> http://www.ru.nl/neuroimaging/fieldtrip. >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3668063 > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From a.stolk at FCDONDERS.RU.NL Mon Aug 16 11:43:07 2010 From: a.stolk at FCDONDERS.RU.NL (a.stolk@fcdonders.ru.nl) Date: Mon, 16 Aug 2010 11:43:07 +0200 Subject: Units powspctrm In-Reply-To: <31473261.4755181281951700131.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Martin, I'm not exactly sure what your question is but I just simulated your example with the following: % simulate one second of data, samplefreq = 512 hz fs = 512; t = (1:fs)/fs; a = sin(2*pi*20*t); b = 2*sin(2*pi*20*t); % twice the amplitude figure; plot(t,a); hold on; plot(t,b,'r'); hold off; % simulate preprocessed data cfg = []; cfg.layout = 'CTF275.lay'; cfg.layout = prepare_layout(cfg); data.label = cfg.layout.label(1:273,1); data2.label = data.label; data.fsample = fs; data2.fsample = data.fsample; for j = 1:273 data.trial{1,1}(j,:) = a; data.time{1,1}(j,:) = t; data2.trial{1,1}(j,:) = b; data2.time{1,1}(j,:) = t; end % ft_freqnalysis_mtmfft cfg = []; cfg.output = 'pow'; cfg.channel = 'MEG'; cfg.method = 'mtmfft'; cfg.taper = 'rectwin'; cfg.foilim = [1 40]; cfg.keeptrials = 'no'; cfg.keeptapers = 'no'; mtmfft = ft_freqanalysis(cfg, data); mtmfft2 = ft_freqanalysis(cfg, data2); % four (2^2) times the power figure; plot(mtmfft.powspctrm(1,:)); hold on; plot(mtmfft2.powspctrm(1,:),'r'); Notice that I used a rectangular window in stead of the hanning taper. One of the features of the Hanning taper is that it cuts off the ends of a window. It, therefore, is much more difficult to make a prediction about the scaling. I'm not sure if this has satisfied you but it's the most I can do. For more information of fft, have a read on http://fieldtrip.fcdonders.nl/tutorial/fourier Best regards, Arjen ----- Original Message ----- From: "Martin Bleichner" To: FIELDTRIP at NIC.SURFNET.NL Sent: Monday, August 16, 2010 10:46:15 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [FIELDTRIP] Units powspctrm Hi Arjen, my point is that I am interested not in the relative difference between signals but in the actual difference in microvolt. I know that this is not the standard thing to do but that is what I need . After playing aroud a bit i come to the following conlcusion Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with an amplitude of 100uV and one with an aplitude of 200uV. Computing a power spectrum using matlab fft function I can eventually read out that the difference between my two signals is 100uV. In ft_freqanalysis_mtmfft the signal is multiplied by a taper line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) pad],[],2); The output can hence not be transformed back right away to the real microvolt values, but happens to be scaled (in my case ) by a factor of ~0.036 (which is the mean value of the taper) At least that is what I think happens. Regards Martin 2010/8/13 a.stolk at fcdonders.ru.nl > If you use the same mtmfft settings for both conditions, in theory it > should be fine. Make sure that you compute the fourier transformation on > equal window lenghts. > > If you happen to have variable triallengths per condition, my suggestion > would be to cut the trials in (e.g.) 1 second pieces. This way your > 'frequency resolution' is the same for condition A and B. > > If your experimental setup allows you, you could choose to normalize your > data (e.g. a baselinecorrection) first before making the A and B comparison. > This way you correct for (non-)cognitive powerchanges over time (case it's > not an ABABABAB etc. design). Such as conductivity reducal of the EEG paste > over time, subject habituation effects and whatelse you have. > > Best, > Arjen > > > > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Yes, typically, but is it the case for the powspctrm you get from the > mtmfft > freqanalysis? > I am asking for the following reason: > > Lets say, I have two experimental conditions A and B and I compute the > powerspectra for both of them. > When the units actually are uV^2/Hz i could tell for each frequency by how > much uV A and B differ. > > What confuses me is that in > ft_freqanalysis_mtmfft< > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > signal is multiplied with a taper (tap) and thereby scaled. > The resulting powspctrm hence does not reflect the the true changes in > microvolt. > Do I see that correctly, or am I missing something here? Is the > powerspectrum corrected for that somewhere else? > > Regards, > Martin > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > Hello Martin, > > > > A powerspectrum typically has the frequencies on one axis and the power > of > > the corresponding frequencies on the other. The power represents how > strong > > a certain frequency occurs in a signal, given by the square of the > voltage > > per frequency. > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > Best regards, > > Arjen > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: [FIELDTRIP] Units powspctrm > > > > Hello together, > > > > What units does the powspctrm have? > > Starting with an EEG signal in microvolts and computing the powerspectrum > > using freqanalysis what are the units of powspctrm? > > I tried to figure it out on my own but I am stuck somehow. > > > > Here some example code > > > > cfg=[]; > > cfg.method='mtmfft'; > > cfg.output='pow'; > > cfg.pad ='maxperlen' > > cfg.foilim=[1 130] > > cfg.taper='hanning' > > cfg.channel=1 > > cfg.keeptrials='no' > > > > R=ft_freqanalysis(cfg,data); > > > > I am interested in the units of R.powspctrm > > > > Thanks > > Martin > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From bleichner.martin at GMAIL.COM Mon Aug 16 12:46:14 2010 From: bleichner.martin at GMAIL.COM (Martin Bleichner) Date: Mon, 16 Aug 2010 12:46:14 +0200 Subject: Units powspctrm In-Reply-To: <33048706.4755221281951787469.JavaMail.root@watertor.uci.ru.nl> Message-ID: Hi Arijen, my question simply was how I can get the actual difference in microvolt between two signals when using fieldtrip. I now have a prtty good idee how to do that. Thanks Martin 2010/8/16 a.stolk at fcdonders.ru.nl > Hi Martin, > > I'm not exactly sure what your question is but I just simulated your > example with the following: > > % simulate one second of data, samplefreq = 512 hz > fs = 512; > t = (1:fs)/fs; > a = sin(2*pi*20*t); > b = 2*sin(2*pi*20*t); % twice the amplitude > figure; plot(t,a); > hold on; plot(t,b,'r'); > hold off; > > % simulate preprocessed data > cfg = []; > cfg.layout = 'CTF275.lay'; > cfg.layout = prepare_layout(cfg); > data.label = cfg.layout.label(1:273,1); > data2.label = data.label; > data.fsample = fs; > data2.fsample = data.fsample; > for j = 1:273 > data.trial{1,1}(j,:) = a; > data.time{1,1}(j,:) = t; > data2.trial{1,1}(j,:) = b; > data2.time{1,1}(j,:) = t; > end > > % ft_freqnalysis_mtmfft > cfg = []; > cfg.output = 'pow'; > cfg.channel = 'MEG'; > cfg.method = 'mtmfft'; > cfg.taper = 'rectwin'; > cfg.foilim = [1 40]; > cfg.keeptrials = 'no'; > cfg.keeptapers = 'no'; > mtmfft = ft_freqanalysis(cfg, data); > mtmfft2 = ft_freqanalysis(cfg, data2); % four (2^2) times the > power > > figure; plot(mtmfft.powspctrm(1,:)); > hold on; plot(mtmfft2.powspctrm(1,:),'r'); > > Notice that I used a rectangular window in stead of the hanning taper. One > of the features of the Hanning taper is that it cuts off the ends of a > window. It, therefore, is much more difficult to make a prediction about the > scaling. > > I'm not sure if this has satisfied you but it's the most I can do. For more > information of fft, have a read on > http://fieldtrip.fcdonders.nl/tutorial/fourier > > Best regards, > Arjen > > ----- Original Message ----- > From: "Martin Bleichner" > To: FIELDTRIP at NIC.SURFNET.NL > Sent: Monday, August 16, 2010 10:46:15 AM GMT +01:00 Amsterdam / Berlin / > Bern / Rome / Stockholm / Vienna > Subject: Re: [FIELDTRIP] Units powspctrm > > Hi Arjen, > > my point is that I am interested not in the relative difference between > signals but in the actual difference in microvolt. I know that this is not > the standard thing to do but that is what I need . > > After playing aroud a bit i come to the following conlcusion > > Lets say I have two signals (pure sine 20 Hz; sampling freq 512) one with > an > amplitude of 100uV and one with an aplitude of 200uV. > Computing a power spectrum using matlab fft function I can eventually read > out that the difference between my two signals is 100uV. > > In ft_freqanalysis_mtmfft the signal is multiplied by a taper > line 340 dum=fft([data.trial{perlop}(sgnindx(sgnlop),:).*tap(taplop,:) > pad],[],2); > > The output can hence not be transformed back right away to the real > microvolt values, but happens to be scaled (in my case ) by a factor of > ~0.036 (which is the mean value of the taper) > > At least that is what I think happens. > > Regards > Martin > > > > > > 2010/8/13 a.stolk at fcdonders.ru.nl > > > If you use the same mtmfft settings for both conditions, in theory it > > should be fine. Make sure that you compute the fourier transformation on > > equal window lenghts. > > > > If you happen to have variable triallengths per condition, my suggestion > > would be to cut the trials in (e.g.) 1 second pieces. This way your > > 'frequency resolution' is the same for condition A and B. > > > > If your experimental setup allows you, you could choose to normalize your > > data (e.g. a baselinecorrection) first before making the A and B > comparison. > > This way you correct for (non-)cognitive powerchanges over time (case > it's > > not an ABABABAB etc. design). Such as conductivity reducal of the EEG > paste > > over time, subject habituation effects and whatelse you have. > > > > Best, > > Arjen > > > > > > > > > > ----- Original Message ----- > > From: "Martin Bleichner" > > To: FIELDTRIP at NIC.SURFNET.NL > > Sent: Thursday, August 12, 2010 10:48:14 PM GMT +01:00 Amsterdam / Berlin > / > > Bern / Rome / Stockholm / Vienna > > Subject: Re: [FIELDTRIP] Units powspctrm > > > > Yes, typically, but is it the case for the powspctrm you get from the > > mtmfft > > freqanalysis? > > I am asking for the following reason: > > > > Lets say, I have two experimental conditions A and B and I compute the > > powerspectra for both of them. > > When the units actually are uV^2/Hz i could tell for each frequency by > how > > much uV A and B differ. > > > > What confuses me is that in > > ft_freqanalysis_mtmfft< > > http://fieldtrip.fcdonders.nl/reference/ft_freqanalysis_mtmfft>the > > signal is multiplied with a taper (tap) and thereby scaled. > > The resulting powspctrm hence does not reflect the the true changes in > > microvolt. > > Do I see that correctly, or am I missing something here? Is the > > powerspectrum corrected for that somewhere else? > > > > Regards, > > Martin > > > > > > > > 2010/8/12 a.stolk at fcdonders.ru.nl > > > > > Hello Martin, > > > > > > A powerspectrum typically has the frequencies on one axis and the power > > of > > > the corresponding frequencies on the other. The power represents how > > strong > > > a certain frequency occurs in a signal, given by the square of the > > voltage > > > per frequency. > > > > > > In your case: square of the microvolts per frequency: uV^2/ Hz > > > > > > Best regards, > > > Arjen > > > > > > ----- Original Message ----- > > > From: "Martin Bleichner" > > > To: FIELDTRIP at NIC.SURFNET.NL > > > Sent: Thursday, August 12, 2010 5:52:19 PM GMT +01:00 Amsterdam / > Berlin > > / > > > Bern / Rome / Stockholm / Vienna > > > Subject: [FIELDTRIP] Units powspctrm > > > > > > Hello together, > > > > > > What units does the powspctrm have? > > > Starting with an EEG signal in microvolts and computing the > powerspectrum > > > using freqanalysis what are the units of powspctrm? > > > I tried to figure it out on my own but I am stuck somehow. > > > > > > Here some example code > > > > > > cfg=[]; > > > cfg.method='mtmfft'; > > > cfg.output='pow'; > > > cfg.pad ='maxperlen' > > > cfg.foilim=[1 130] > > > cfg.taper='hanning' > > > cfg.channel=1 > > > cfg.keeptrials='no' > > > > > > R=ft_freqanalysis(cfg,data); > > > > > > I am interested in the units of R.powspctrm > > > > > > Thanks > > > Martin > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of > the > > > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG > > > and EEG analysis. See also > > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > > ---------------------------------- > > > The aim of this list is to facilitate the discussion between users of > the > > > FieldTrip toolbox, to share experiences and to discuss new ideas for > MEG > > > and EEG analysis. See also > > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > > and EEG analysis. See also > > http://listserv.surfnet.nl/archives/fieldtrip.html and > > http://www.ru.nl/neuroimaging/fieldtrip. > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG > and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Sara.GonzalezAndino at HCUGE.CH Mon Aug 16 12:48:53 2010 From: Sara.GonzalezAndino at HCUGE.CH (GONZALEZ ANDINO Sara) Date: Mon, 16 Aug 2010 12:48:53 +0200 Subject: post-doc position available in Geneva Message-ID: Dear Fieldtrip list members, Please find attached a job offer in the Electrical Neuroimaging Group of the University of Geneva. Best regards, Sara L. Gonzalez ------------------------- Sara L. Gonzalez Andino, PhD, MER Head of the Electrical Neuroimaging Group Department of Clinical Neurosciences Faculty of Medicine, University of Geneva Phone: +41 22 3728323 Fax: + 41 22 3728333 www.electrical-neuroimaging.ch ________________________________________ De : FieldTrip discussion list [FIELDTRIP at nic.surfnet.nl] de la part de Robert Oostenveld [r.oostenveld at FCDONDERS.RU.NL] Date d'envoi : lundi 16 août 2010 10:07 À : FIELDTRIP at nic.surfnet.nl Objet : [FIELDTRIP] post-doc position available in Paris Dear Fieldtrip list members, Appologies for multiple postings. Please find attached a job opportunity in the group of Florian Waszak. best regards, ----------------------------------------------------------- Robert Oostenveld, PhD Senior Researcher & MEG Physicist Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Announce_postdoc.doc Type: application/octet-stream Size: 39936 bytes Desc: Announce_postdoc.doc URL: From alexandre.gramfort at INRIA.FR Tue Aug 17 09:45:05 2010 From: alexandre.gramfort at INRIA.FR (Alexandre Gramfort) Date: Tue, 17 Aug 2010 09:45:05 +0200 Subject: OpenMEEG with 4 layers Message-ID: Hi Gregor, you should now be able to run an EEG forward model with 4 layers with OpenMEEG & Fieldtrip. I've added Paul's scripts to the main FT code. You just need to download today's version of FT. Best, Alexandre ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From thomas.hartmann at UNI-KONSTANZ.DE Tue Aug 17 16:51:38 2010 From: thomas.hartmann at UNI-KONSTANZ.DE (Thomas Hartmann) Date: Tue, 17 Aug 2010 16:51:38 +0200 Subject: difference between mtmconvol and mtmfft Message-ID: hi, from the descriptions of the two functions ft_freqanalysis_mtmconvol and ft_freqanalysis_mtmfft i thought that those two functions should work more or less equivalent - the first just doing it multiple times to get a time-frequency representation. to localize a significant cluster from my tf-representation, i recalculated the fft (including the csd, of course) using the exact same arguments for latency, window-size, frequency, padding, taper etc.... but the results do differ. not dramatically but considerably. does anyone have an explanation for this? thanks a lot in advance, thomas -- Dipl. Psych. Thomas Hartmann OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel.: +49 (0)7531 88 4612 Fax: +49 (0)7531-88 4601 Email: thomas.hartmann at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From khoechstetter at BESA.DE Tue Aug 17 18:05:09 2010 From: khoechstetter at BESA.DE (Karsten Hoechstetter) Date: Tue, 17 Aug 2010 18:05:09 +0200 Subject: Job opening for EEG/MEG scientist at MEGIS Software Message-ID: Open job position MEGIS Software GmbH (Munich, Germany) is searching to hire an EEG/MEG scientist to join our support and development team in Germany. Job profile: The successful applicant will - contribute to the development of new analysis techniques and program features - participate in joint research projects with our customers - represent our products and software at neuroimaging conferences - teach the use of our software at customer workshops worldwide - provide scientific and technical support to our customers (predominantly via email) MEGIS is one of the leading developers of EEG/MEG analysis software. Our BESA programs are widely used software for analysis of EEG and MEG data for both research and clinical applications (see www.besa.de). As a free enterprise in the field of science and research we can offer job positions combining the advantages of both fields: Stay in touch with current front-end research work while enjoying the advantages of a permanent position with adequate salary. Applicant’s profile: - The applicant should have a background in nature science (e.g. physics) or psychology, preferential including a PhD degree. - Experience in EEG/MEG data analysis (practical and/or theoretical) is desired. - Knowledge of the BESA software is helpful, but not a must. - Fluency in written and spoken English are a prerequisite for the announced position. - Since the place of work will be mainly our office in Germany, the applicant should be able to communicate in German. - Experience in MATLAB scripting or other programming skills are helpful. - The applicant should be willing to travel to neuroscientific conferences and workshops worldwide 6-8 times per year. Applications should include a current CV, a letter indicating motivation and skills, and a list of publications. Electronic applications preferred. Please send your application to Theodor Scherg ( tscherg at besa.de) or to: MEGIS Software GmbH Freihamer Str. 18 82166 Graefelfing Germany We are looking forward to hearing from you! -------------------------------------- Dr. Karsten Hoechstetter MEGIS Software GmbH Gräfelfing, Germany HRB München 109956 CEO Dr. Michael Scherg -------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Wed Aug 18 10:10:54 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 18 Aug 2010 10:10:54 +0200 Subject: Mesh space vs. voxel space problem Message-ID: Dear fieldtrippers, when looking at the points of the mesh generated for the BEM generation there was something I stumbled over: There are points with negative coordinates, so the mesh seems to be generated in some other space than the voxel system (maybe just translated in some way?). This wouldn't be a great problem if the ft_dipolefitting wasn't working in voxel but in mesh space, because when searching the valid dipole positions in prepare_dipole_grid on lines 432-434 the bounding_mesh function returns a volume full of zeros since the grid positions don't lie within the volume. I'm using the 20100612 version of fieldtrip and running ft_dipolefitting with automatic grid generation. Is there anything I can do about this besides creating the grid on my own? Thanks in advance, Paul -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Wed Aug 18 10:15:23 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Wed, 18 Aug 2010 10:15:23 +0200 Subject: Mesh space vs. voxel space problem In-Reply-To: <4C6B958E.1020601@gmx.de> Message-ID: Okay, seems to be solved - at least a little. I now saw that the grid is created from the electrodes positions and not by the mesh points. I'll have to align these to get it right. Cheers, Paul Am 18.08.2010 10:10, schrieb Paul Czienskowski: > Dear fieldtrippers, > > when looking at the points of the mesh generated for the BEM > generation there was something I stumbled over: There are points with > negative coordinates, so the mesh seems to be generated in some other > space than the voxel system (maybe just translated in some way?). This > wouldn't be a great problem if the ft_dipolefitting wasn't working in > voxel but in mesh space, because when searching the valid dipole > positions in prepare_dipole_grid on lines 432-434 the bounding_mesh > function returns a volume full of zeros since the grid positions don't > lie within the volume. I'm using the 20100612 version of fieldtrip and > running ft_dipolefitting with automatic grid generation. Is there > anything I can do about this besides creating the grid on my own? > > Thanks in advance, > Paul > -- Paul Czienskowski Max Planck institute for human development Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE Fri Aug 20 14:13:42 2010 From: Gregor.Volberg at PSYCHOLOGIE.UNI-REGENSBURG.DE (Gregor Volberg) Date: Fri, 20 Aug 2010 14:13:42 +0200 Subject: mne and ft_sourceinterpolate Message-ID: Dear fieldtrippers, I am trying to extract source activity from timelock-data, and I would like to have this for a whole epoch of 1 sec / 501 sample points. I did an ft_sourceanalysis with method = 'mne', which worked fine and gave the desired source activity (see structure "source" below; field "avg" contains "mom" and "pow"). Next I did an ft_sourceinterpolate with "source" and a standard mri as input. Unfortunately, the resulting structure did not contain an "avg" field any more (see "ivol" below) - my functional data got lost during interpolation. Did someone have a similar problem or does someone know a solution? Many thanks in advance for any help! Gregor P.S.: Source interpolation works without problems with method = 'lcmv', but this gives the mean source activity within the desired time range rather than sample-wise activity. It is not a good idea to apply the lcmv beamformer to consecutive time bins and then concatenate the source activity, am I right? source = xgrid: [-66 -56 -46 -36 -26 -16 -6 4 14 24 34 44 54 64] ygrid: [-105 -95 -85 -75 -65 -55 -45 -35 -25 -15 -5 5 15 25 35 45 55 65] zgrid: [-46 -36 -26 -16 -6 4 14 24 34 44 54 64 74 84] dim: [14 18 14] vol: [1x1 struct] time: [1x501 double] pos: [3528x3 double] inside: [1x1808 double] outside: [1x1720 double] method: 'average' avg: [1x1 struct] cfg: [1x1 struct] ivol = inside: [181x217x181 logical] dim: [181 217 181] transform: [4x4 double] anatomy: [181x217x181 uint8] cfg: [1x1 struct] -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From jan.schoffelen at DONDERS.RU.NL Fri Aug 20 15:01:53 2010 From: jan.schoffelen at DONDERS.RU.NL (jan-mathijs schoffelen) Date: Fri, 20 Aug 2010 15:01:53 +0200 Subject: mne and ft_sourceinterpolate In-Reply-To: <4C6E8D9602000057000071EB@gwsmtp1.uni-regensburg.de> Message-ID: Dear Gregor, What you want to achieve is as of yet not possible. Ft_sourceinterpolate at the moment only interpolates functional parameters which are scalars, e.g. power, or variance averaged over time (in lcmv). We are working at the moment to make the data representation of different types of source reconstructed results more consistent (beamformer versus mne etc), and first will work towards the possibility of visualizing the functional data (including their time courses) without the interpolation. The thing you can do now is to define a meaningful summary statistic of the reconstructed time course, interpolate this one on the anatomy, and click around the anatomical coordinate of your source of interest. Subsequently you need to reverse engineer (undo the interpolation) to find the corresponding source position in your source structure. Then you can use the plot command to look at the time courses. Best, Jan-Mathijs On Aug 20, 2010, at 2:13 PM, Gregor Volberg wrote: > Dear fieldtrippers, > > I am trying to extract source activity from timelock-data, and I > would like to have this for a whole epoch of 1 sec / 501 sample > points. I did an ft_sourceanalysis with method = 'mne', which worked > fine and gave the desired source activity (see structure "source" > below; field "avg" contains "mom" and "pow"). Next I did an > ft_sourceinterpolate with "source" and a standard mri as input. > Unfortunately, the resulting structure did not contain an "avg" > field any more (see "ivol" below) - my functional data got lost > during interpolation. Did someone have a similar problem or does > someone know a solution? > > Many thanks in advance for any help! > Gregor > > P.S.: Source interpolation works without problems with method = > 'lcmv', but this gives the mean source activity within the desired > time range rather than sample-wise activity. It is not a good idea > to apply the lcmv beamformer to consecutive time bins and then > concatenate the source activity, am I right? > > > > source = > > xgrid: [-66 -56 -46 -36 -26 -16 -6 4 14 24 34 44 54 64] > ygrid: [-105 -95 -85 -75 -65 -55 -45 -35 -25 -15 -5 5 15 25 35 > 45 55 65] > zgrid: [-46 -36 -26 -16 -6 4 14 24 34 44 54 64 74 84] > dim: [14 18 14] > vol: [1x1 struct] > time: [1x501 double] > pos: [3528x3 double] > inside: [1x1808 double] > outside: [1x1720 double] > method: 'average' > avg: [1x1 struct] > cfg: [1x1 struct] > > ivol = > > inside: [181x217x181 logical] > dim: [181 217 181] > transform: [4x4 double] > anatomy: [181x217x181 uint8] > cfg: [1x1 struct] > > > > -- > Dr. rer. nat. Gregor Volberg > ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) > University of Regensburg > Institute for Experimental Psychology > 93040 Regensburg, Germany > Tel: +49 941 943 3862 > Fax: +49 941 943 3233 > http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3668063 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Erin.Oakman at NYUMC.ORG Tue Aug 24 20:19:40 2010 From: Erin.Oakman at NYUMC.ORG (Oakman, Erin) Date: Tue, 24 Aug 2010 14:19:40 -0400 Subject: using ft_freqstatistics with 4 arguments Message-ID: Hi Fieldtrip list, Apparently the nonparametric freqstatistics funtion can be used with a mixed design, to compare power between 2 groups and 2 conditions, using cfg.method = 'montecarlo'. I am giving 4 arguments to ft_freqstatistics. stats = ft_freqstatistics(cfg, group1-condition1, group1-condition2, group2-condition1, group2-condition2) >>From Robert's suggestion here https://listserv.surfnet.nl/scripts/wa.cgi?A2=ind0803&L=FIELDTRIP&P=R13471, the design matrix has been set up with 1 row for the condition (condition numbers "1", "2"), a second row with the subject number and a third row for the two groups ("1", "2"). I set: cfg.ivar = 1; cfg.uvar = 2; cfg.wvar = 3; The trouble is with resampledesign.m, using it in combination with ft_freqstatistics. When resampledesign.m splits the design matrix into a smaller design matrix, using cfg.war, I get the error ??? the design matrix variables should be constant within a block The design matrix is 3 X 100, like this: condition: 1 1 1 1 1 2 2 2 2 2 1 1 1 1 1 2 2 2 2 2 subj number: 1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10 group: 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 Should a different design matrix be used in this case? Should cfg.wvar = 2 ? Erin ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From tsauvigny at GOOGLEMAIL.COM Wed Aug 25 11:26:03 2010 From: tsauvigny at GOOGLEMAIL.COM (Thomas Sauvigny) Date: Wed, 25 Aug 2010 11:26:03 +0200 Subject: FieldTrip support Message-ID: Dear fieldtrip users! May I ask for your support because of a problem concerning my within-subject permutation test (EEG-Data)? The goal is to compare two grandaverages with two different conditions, each grandaverage consisting of 4 datasets from 4 subjects, each dataset about 40-50 single trials. I did the preprocessing, timelock and grandaverage: 4 datasets (called x1, x4) for the first condition with the following command: cfg = []; cfg.keeptrials = 'yes'; timelock1 = timelockanalysis(cfg, x1); timelock2 = timelockanalysis(cfg, x2); timelock3 = timelockanalysis(cfg, x3); timelock4 = timelockanalysis(cfg, x4); cfg.channel = 'all' cfg.latency = 'all' cfg.keepindividual = 'yes' cfg.normalizevar = 'N-1' da_test1= timelockgrandaverage (cfg, timelock1, timelock2, timelock3, timelock4) save da_test1 Same way for the second condition: da_test2 Now I start the permutation test (file attached). As result there are no significant clusters highlighted (although there are quite large differences in the ERP-plot). I think because there is a mistake concerning the number of single-trials which fieldtrip takes as the basis for the statistic test. Because the output in the command window shows: selected 30 channels selected 2501 time bins selected 1 frequency bins total number of measurements = 8 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 4 levels number of repeated measurements in each level is 2 2 2 2 computing a parmetric threshold for clustering computing statistic estimated time per randomization is 0 seconds computing statistic 1 from 100 found 7 positive clusters in observed data found 11 negative clusters in observed data stat = prob: [30x2501 double] posclusters: [1x7 struct] posclusterslabelmat: [30x2501 double] posdistribution: [1x100 double] negclusters: [1x11 struct] negclusterslabelmat: [30x2501 double] negdistribution: [1x100 double] mask: [30x2501 logical] stat: [30x2501 double] ref: [30x2501 double] dimord: 'chan_time' label: {30x1 cell} time: [1x2501 double] cfg: [1x1 struct] cfg = xlim: [0 0.1000] zlim: 'maxmin' the input is timelock data with 30 channels and 4000 timebins applying preprocessing options averaging trials averaging trial 1 of 4 averaging trial 2 of 4 averaging trial 3 of 4 averaging trial 4 of 4 reading layout from file easycap32ch-avg.lay So, could this be the mistake that fieldtrip guesses “4” to be the number of all trials (perhaps because 4 datasets in each grandaverage??) And how can I solve this problem? Is there a way to account for the single-trial number when using the permutation test? Thank you very much for your help!! Kind regards Thomas Sauvigny Tübingen University ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: da_test_statistic.m URL: From datashare at SCIENCEDB.NET Wed Aug 25 15:42:37 2010 From: datashare at SCIENCEDB.NET (Science DB datashare) Date: Wed, 25 Aug 2010 15:42:37 +0200 Subject: Announcement : EEG/MEG database Message-ID: Dear Fieldtrip users, Data sharing is a great way to find new collaborators. We would like to announce a our new database for EEG/MEG data on ScienceDB.net The concept is simple: If you have data to share you create a new topic in the EEG/MEG data share group’s forum, where you describe your data, and how you want to share it. Please go to : http://sciencedb.net/groups/eegmeg-data-share/ ScienceDB.net is a non-profit portal for the scientific community. Our service is sponsored by ads and donations. If you have any suggestions or comments, please mail us at datashare at sciencedb.net. Kind regards, Science DB http://sciencedb.net/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Wed Aug 25 18:33:18 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Wed, 25 Aug 2010 18:33:18 +0200 Subject: errors in ft_componentsanalysis Message-ID: Dear Fieldtrippers, I have a little problems with cft_componentanalysis and the 'runica' option When running Fieldtrip20100822 on matlab2008b (on Linux and running filedtripdefs before starting the calculations) I get a complaint about the notorious missing randperm.m ??? Undefined function or method 'randperm' for input arguments of type 'double'. Error in ==> runica at 1063 timeperm=randperm(datalength); % shuffle data order at each step Error in ==> ft_componentanalysis at 252 [weights, sphere] = runica(dat, optarg{:}); I thought that running filedtripdefs would take care of this, but seemingly it doesn't. On the other hand if I run it on matlab 2007a, then ft-componentanalysis/runica stops with a warning that the "try catch" syntax will not be supported in future matlab versions ? I do not get an actual error because whatever happens happens in a try-catch statement so errors are suppressed Any suggestions welcome, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From stan.vanpelt at DONDERS.RU.NL Thu Aug 26 10:22:04 2010 From: stan.vanpelt at DONDERS.RU.NL (Stan van Pelt) Date: Thu, 26 Aug 2010 10:22:04 +0200 Subject: difference between mtmconvol and mtmfft In-Reply-To: <4C6AA1FA.8030508@uni-konstanz.de> Message-ID: Dear Thomas, If I understand you correctly you applied ft_freqanalysis_mtmfft on a piece of data that looked interesting based on ft_freqanalysis_mtmconvol, but this gives slightly different results. Please let someone correct me if I'm wrong, but what I think is going on is that for the calculation of power in a time-freq bin, ft_freqanalysis_mtmconvol uses data from adjacent time windows (because of the temporal smoothing). ft_freqanalysis_mtmconvol on the other hand only uses the data that is within your time-freq bin, because the temporal analysis window is equal to the size (along the temporal dimension) of the input data. Best, Stan Stan van Pelt, PhD Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 68495 Fax: (+31) (0)24 36 10989 -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of Thomas Hartmann Sent: Tuesday, August 17, 2010 4:52 PM To: FIELDTRIP at NIC.SURFNET.NL Subject: [FIELDTRIP] difference between mtmconvol and mtmfft hi, from the descriptions of the two functions ft_freqanalysis_mtmconvol and ft_freqanalysis_mtmfft i thought that those two functions should work more or less equivalent - the first just doing it multiple times to get a time-frequency representation. to localize a significant cluster from my tf-representation, i recalculated the fft (including the csd, of course) using the exact same arguments for latency, window-size, frequency, padding, taper etc.... but the results do differ. not dramatically but considerably. does anyone have an explanation for this? thanks a lot in advance, thomas -- Dipl. Psych. Thomas Hartmann OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel.: +49 (0)7531 88 4612 Fax: +49 (0)7531-88 4601 Email: thomas.hartmann at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 27 07:44:45 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 07:44:45 +0200 Subject: Dipole fitting with openMEEG BEM model Message-ID: Dear all, after creating the BEM model for an individual MRI with OpenMEEG i now tried to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab script crashed saying: ??? Output argument "dsm" (and maybe others) not assigned during call to "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m (openmeeg_dsm)". Error in ==> openmeeg_dsm at 16 The actual error may have been some lines above: /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy I'm not really used to use linux and for this reason not familiar with the error messages. I found out that this has to do with any program accessing the shell script file, but since it just has been created and also been closed by the openmeeg_dsm script I don't get it why some other process should access it. I would be very grateful, if anyone could give me a hint how to solve this problem. Thanks in advance, Paul Czienskowski -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From paul_c at GMX.DE Fri Aug 27 07:58:17 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 07:58:17 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: <4C7750CD.6010004@gmx.de> Message-ID: Addendum: The error occurred when scanning grid location 34104 of 800000. So it seems not to be a general error but more something like a exception occurring every once a while. Ain't very good either. It may be very good if someone could explain me what's going on and how to solve it. Paul Am 27.08.2010 07:44, schrieb Paul Czienskowski: > Dear all, > > after creating the BEM model for an individual MRI with OpenMEEG i now > tried to simulate and fit some dipoles, but when calling > openmeeg_dsm.m the matlab script crashed saying: > > ??? Output argument "dsm" (and maybe others) not assigned during call > to > "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m (openmeeg_dsm)". > > Error in ==> openmeeg_dsm at 16 > > The actual error may have been some lines above: > > /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy > > I'm not really used to use linux and for this reason not familiar with > the error messages. I found out that this has to do with any program > accessing the shell script file, but since it just has been created > and also been closed by the openmeeg_dsm script I don't get it why > some other process should access it. I would be very grateful, if > anyone could give me a hint how to solve this problem. > > Thanks in advance, > > Paul Czienskowski > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexandre.gramfort at INRIA.FR Fri Aug 27 08:15:31 2010 From: alexandre.gramfort at INRIA.FR (Alexandre Gramfort) Date: Fri, 27 Aug 2010 08:15:31 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: <4C7750CD.6010004@gmx.de> Message-ID: Hello Paul, could you share a script to reproduce the problem? -- Alexandre On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: > Dear all, > > after creating the BEM model for an individual MRI with OpenMEEG i now tried > to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab > script crashed saying: > > ??? Output argument "dsm" (and maybe others) not assigned during call to > "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m > (openmeeg_dsm)". > > Error in ==> openmeeg_dsm at 16 > > The actual error may have been some lines above: > > /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy > > I'm not really used to use linux and for this reason not familiar with the > error messages. I found out that this has to do with any program accessing > the shell script file, but since it just has been created and also been > closed by the openmeeg_dsm script I don't get it why some other process > should access it. I would be very grateful, if anyone could give me a hint > how to solve this problem. > > Thanks in advance, > > Paul Czienskowski > > -- > Paul Czienskowski > Björnsonstr. 25 > 12163 Berlin > > Tel.: (+49)(0)30/221609359 > Handy: (+49)(0)1788378772 > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From paul_c at GMX.DE Fri Aug 27 08:35:25 2010 From: paul_c at GMX.DE (Paul Czienskowski) Date: Fri, 27 Aug 2010 08:35:25 +0200 Subject: Dipole fitting with openMEEG BEM model In-Reply-To: Message-ID: If it helps, of course. I attached the script that's calling ft_dipolefitting and another one called by the first one, that's calling ft_prepare_bemmodel. Also I'm using another meshing routine which I wrote by myself which is a bit slower, bur also a bit more dependable than the fieldtrip method, since the ft method to create the meshes from the segmentation produced some ugly spikes for me. But the output of my routine should be near to the output of the fieldtrip routine when it works, so this should be no difference (actually my locations are transformed a bit to match my electrode space, electrode positions for the segmentation are retrieved by the Get1020 method). Cheers, Paul Am 27.08.2010 08:15, schrieb Alexandre Gramfort: > Hello Paul, > > could you share a script to reproduce the problem? > > -- Alexandre > > On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: >> Dear all, >> >> after creating the BEM model for an individual MRI with OpenMEEG i now tried >> to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab >> script crashed saying: >> >> ??? Output argument "dsm" (and maybe others) not assigned during call to >> "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m >> (openmeeg_dsm)". >> >> Error in ==> openmeeg_dsm at 16 >> >> The actual error may have been some lines above: >> >> /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy >> >> I'm not really used to use linux and for this reason not familiar with the >> error messages. I found out that this has to do with any program accessing >> the shell script file, but since it just has been created and also been >> closed by the openmeeg_dsm script I don't get it why some other process >> should access it. I would be very grateful, if anyone could give me a hint >> how to solve this problem. >> >> Thanks in advance, >> >> Paul Czienskowski >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CzSimulation.m URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: CreateBEMModel.m URL: From carsten.wolters at UNI-MUENSTER.DE Fri Aug 27 15:58:05 2010 From: carsten.wolters at UNI-MUENSTER.DE (Dr. Carsten Wolters) Date: Fri, 27 Aug 2010 15:58:05 +0200 Subject: Postdoc/PhD position available Message-ID: Dear colleague, please note the attached job posting for a PostDoc/PhD student. I would be greatful, if you could distribute this posting in your department and forward it to colleagues who might be aware of potential candidates. Thank you and best regards, Carsten Wolters ------------------------------------------ For the german research foundation (DFG) project entitled „"Reconstruction of epilepsy-characteristic sources by means of a simultaneous evaluation of EEG- and MEG-data using calibrated realistic headmodels", the Institute for Biomagnetism and Biosignalanalysis (IBB) of the University of Münster offers a position for a *Research scientist (PostDoc or PhD student).* The position is available for 3 years. Payment is according to Bat2a/TVL13. The research project is a cooperation of the IBB with the epilepsy center Erlangen. It aims at reconstructing epilepsy-characteristic electric potentials and magnetic fields for the identification of the epileptogenic zone to improve the therapy of pharmaco-resistant epilepsies. The main project goal is the development and application of methods for a combined source analysis of Electroencephalography (EEG) and Magnetoencephalography (MEG) data in individually optimized finite element head models. The successful applicant holds a degree in informatics, mathematics, physics, biomedical engineering, electrical engineering or similar, and possesses good programming experience (C++ under Linux). Experience with the measurement and analysis of brain signals is advantageous, but not essential. In order to increase the proportion of female staff members, applications from female scientists are particularly encouraged. Disabled applicants are preferred if qualification is equal. The selection procedure starts as the applications come in. Please send your application to Priv.-Doz. Dr.rer.nat. Carsten H. Wolters Institut für Biomagnetismus und Biosignalanalyse Westfälische Wilhelms-Universität Münster Malmedyweg 15 48149 Münster, Germany Tel.: +49 251 83 56904 Fax: +49 251 83 56874 E-Mail: carsten.wolters at uni-muenster.de Web: biomag.uni-muenster.de ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Anz-DFGEpileps-2010_engl.DOC Type: application/msword Size: 29184 bytes Desc: not available URL: From brian.roach at YALE.EDU Fri Aug 27 20:10:21 2010 From: brian.roach at YALE.EDU (Brian Roach) Date: Fri, 27 Aug 2010 11:10:21 -0700 Subject: Fwd: Post-doctoral training in the Neuroscience of Schizophrenia Message-ID: Please e-mail me if you are interested in applying to the position outlined below: ------------------------------------------------------------------------ University of California San Francisco Three post-doctoral fellowships in translational neuroscience of schizophrenia. Sponsor(s): NIMH Application Date(s): Beginning April 1, 2010 The NIMH-funded T32 Training Grant (Neurobiological mechanisms underlying the symptoms and course of schizophrenia) at the University of California in San Francisco is now accepting applications for post-doctoral fellowships from recent PhDs, MDs, and MD/PhDs. Trainees will work in labs studying the neurobiological mechanisms of the symptoms of schizophrenia and its neuro-developmental and neuro-degenerative course. The core T32 faculty are basic neuroscientists and psychiatrists, working in genetics, brain imaging, electrophysiology, and neuroplasticity. They are: Steve Batki, William Byerley, Benjamin Cheyette, Allison Doupe, Judith Ford, Steven Hamilton, Daniel Mathalon, John Rubenstein, Susan Voglmaier, Sophia Vinogradov, and Mark von Zastrow. T32 Trainees will have extended experience in a laboratory, leading to the submission of research papers and grant proposals. Trainees will be dual-mentored with Research and Career Mentors to guide them both formally and informally, through learning neurobiological methods, producing a body of data, presenting data at national meetings, writing and publishing papers, preparing grant proposals, and attending local and national workshops on launching and maintaining successful careers in biological psychiatry. We seek applications from ethnically diverse scientists who have strong academic credentials and US citizenship or permanent residence. NIH rules for T32 trainees state, "The individual to be trained must be a citizen or a noncitizen national of the United States or have been lawfully admitted for permanent residence by the time of award. Individuals who have been lawfully admitted for permanent residence must have a currently valid Alien Registration Receipt Card (I-551) or other legal verification of such status." Potential applicants are welcome to contact any of the core faculty members. An application form is attached. Additional information can be found by visiting our website (http://psych.ucsf.edu/t32/neuro_scz). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ford_T32_Application 7.doc Type: application/msword Size: 95232 bytes Desc: not available URL: From p.vandenhurk at CS.RU.NL Tue Aug 31 10:44:59 2010 From: p.vandenhurk at CS.RU.NL (Paul van den Hurk) Date: Tue, 31 Aug 2010 10:44:59 +0200 Subject: question about freqgrandaverage In-Reply-To: <4C775CAD.7050507@gmx.de> Message-ID: Dear fieldtrippers, I have a question about the function freqgrandaverage. Since I have been quite strict in deleting noisy channels, quite some channels have been removed from individual datasets. Due to the removal of these channels relatively few channels are left when computing the grand average. Could anyone tell me how to adjust the settings of the function in order to calculate the mean in a specific channel over the remaining subjects that do have nicely looking data instead of completely removing the channel from the grand average calculation if only 1 or 2 subjects would show noisy data in this channel? Or would it be better to use the channelrepair function in order to get interpolated values for each subject in such noisy channels? Thanks for your help, Kind regards, Vriendelijke groet, Paul van den Hurk PhD student in Mind-Brain-Mindfulness Group, Faculty of Science, Radboud University, Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, Tel:+31 24 3652240 Email: p.vandenhurk at cs.ru.nl Visiting address: Room HG02.532 Faculty of Science Toernooiveld 1 Nijmegen -----Oorspronkelijk bericht----- Van: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] Namens Paul Czienskowski Verzonden: Friday, August 27, 2010 8:35 AM Aan: FIELDTRIP at NIC.SURFNET.NL Onderwerp: Re: [FIELDTRIP] Dipole fitting with openMEEG BEM model If it helps, of course. I attached the script that's calling ft_dipolefitting and another one called by the first one, that's calling ft_prepare_bemmodel. Also I'm using another meshing routine which I wrote by myself which is a bit slower, bur also a bit more dependable than the fieldtrip method, since the ft method to create the meshes from the segmentation produced some ugly spikes for me. But the output of my routine should be near to the output of the fieldtrip routine when it works, so this should be no difference (actually my locations are transformed a bit to match my electrode space, electrode positions for the segmentation are retrieved by the Get1020 method). Cheers, Paul Am 27.08.2010 08:15, schrieb Alexandre Gramfort: > Hello Paul, > > could you share a script to reproduce the problem? > > -- Alexandre > > On Fri, Aug 27, 2010 at 7:44 AM, Paul Czienskowski wrote: >> Dear all, >> >> after creating the BEM model for an individual MRI with OpenMEEG i now tried >> to simulate and fit some dipoles, but when calling openmeeg_dsm.m the matlab >> script crashed saying: >> >> ??? Output argument "dsm" (and maybe others) not assigned during call to >> "/home/paulc/Matlab/fieldtrip-20100612/external/openmeeg/openmeeg_dsm.m >> (openmeeg_dsm)". >> >> Error in ==> openmeeg_dsm at 16 >> >> The actual error may have been some lines above: >> >> /bin/bash: ./tp230651.sh: /usr/bin/env: bad interpreter: Text file busy >> >> I'm not really used to use linux and for this reason not familiar with the >> error messages. I found out that this has to do with any program accessing >> the shell script file, but since it just has been created and also been >> closed by the openmeeg_dsm script I don't get it why some other process >> should access it. I would be very grateful, if anyone could give me a hint >> how to solve this problem. >> >> Thanks in advance, >> >> Paul Czienskowski >> >> -- >> Paul Czienskowski >> Björnsonstr. 25 >> 12163 Berlin >> >> Tel.: (+49)(0)30/221609359 >> Handy: (+49)(0)1788378772 >> >> ---------------------------------- >> >> The aim of this list is to facilitate the discussion between users of the >> FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and >> EEG analysis. >> >> http://listserv.surfnet.nl/archives/fieldtrip.html >> >> http://www.ru.nl/fcdonders/fieldtrip/ -- Paul Czienskowski Max Planck institute for human development Lentzeallee 94 14195 Berlin Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Tue Aug 31 11:07:48 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 31 Aug 2010 11:07:48 +0200 Subject: topograhies wrong when using componetbrowser on the output of fastica Message-ID: Dear Listusers, I compared fastica and runica in ft_componentanalysis and found their output (with respect to component-topographies) to be absolutely different, although component timecourses agree largely. Remembering an earlier post to this list on how the component topography output was fixed (for runica) I think it's possible that this fix broke the topography display for fastica. The reason I suspect this is because the definitions of what an ica weight is differ in EEGLAB (runica.m) and fastica.m, i.e. they are the inverse of each other. Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: From michael.wibral at WEB.DE Tue Aug 31 16:42:43 2010 From: michael.wibral at WEB.DE (Michael Wibral) Date: Tue, 31 Aug 2010 16:42:43 +0200 Subject: ft_preprocessinf; ft_preproc_dftfilter Message-ID: Dear listusers, I found something strange in FT20100826: ft_preprocessing takes cfg.dftfilter = 'yes' as a configuration option and I think it should then issue a call to ft_preproc_dftfilter. However this is never done, if I am not mistaken. I guess it slipped from ft_preprocessing sometiem in the past. Or was it dropped on purpose because other bandstop filters are preferred? Any help on this is appreciated. Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 628 bytes Desc: not available URL: