From raminazodiaval at gmail.com Mon Jul 1 13:47:47 2013 From: raminazodiaval at gmail.com (Ramin Azodi) Date: Mon, 1 Jul 2013 13:47:47 +0200 Subject: [FieldTrip] More details about cfg.statistic = 'diff_itc' , Message-ID: Hello, I performed cfg.statistic = 'diff_itc' on two experiment conditions: resting state and during stimulus (each contains 50 trials). As an output, I got values from 0 to 0.6. I tried to find some documents/papers about the meaning of 'diff_itc', and the possibility to interpolate my results but all my attempts failed to success. Could someone tell me more about this function and the possibly give me some reference papers? Best, Ramin -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Mon Jul 1 14:10:39 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 1 Jul 2013 14:10:39 +0200 Subject: [FieldTrip] ROI selection of beamformer grid points In-Reply-To: <1483937264.1423478.1372252022737.JavaMail.root@draco.zimbra.ru.nl> References: <1483937264.1423478.1372252022737.JavaMail.root@draco.zimbra.ru.nl> Message-ID: Hi Marieke, In case you hadn't already, it's easier to do things in MNI coordinates (like select grid points from atlases) if the source reconstruction was already done using warped grid points from MNI to subject-specific space. See here for help on that. If you have done that, then replace the .pos field in each subject with the grid.pos from the MNI, and no need to ft_sourceinterpolate. If the question is more regarding the templates, see here for more tips, including info on the useful ft_read_atlas function. Cheers, Johanna 2013/6/26 Marieke van de Nieuwenhuijzen < m.vandenieuwenhuijzen at fcdonders.ru.nl> > Dear Fieldtrippers, > > I am running my analyses on time courses reconstructed in source space. > Basically, that means that my working dataset is a matrix of grid point x > time. What I want to do now is do some analyses on a subset of that > dataset, a bit analogous to selecting some sensors to restrict analyses to. > Therefore, what I would ideally want to do, is select a subset of grid > points corresponding to a specific location (for example only the occipital > grid points, or only the grid points corresponding to a specific atlas > label). > > Does anyone have any suggestions about how I should go about selecting > specific grid points? Is there perhaps some grid based atlas, or is it > possible to select grid points based on their corresponding mni coordinates > which you get after running ft_sourceinterpolate and ft_volumenormalise (in > other words, is it possible to reverse ft_volumenormalise and > ft_sourceinterpolate to map the mni coordinates to the grid points instead > of the grid points to mni representation). > > Any pointers would be much appreciated. > > Best, > Marieke > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 1 14:12:41 2013 From: cornabel at googlemail.com (cornelius abel) Date: Mon, 01 Jul 2013 14:12:41 +0200 Subject: [FieldTrip] freq / time range for source analysis? Message-ID: <51D17239.2070009@googlemail.com> Dear FT-List, in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. We found a nice significant cluster in the lower gamma range and in the first half of the time range. Please have a look at the two figures. http://dropcanvas.com/0fnvn Fig a is the multiplotTFR of stat, showing only significant areas. Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. Now, we are not sure how to pick the time and freq range for a subsequent source analysis. Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? Any ideas? Greetings, Cornelius -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 1 14:21:10 2013 From: cornabel at googlemail.com (Cornelius Abel) Date: Mon, 1 Jul 2013 14:21:10 +0200 Subject: [FieldTrip] freq / time range for source analysis? Message-ID: Dear FT-List, in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. We found a nice significant cluster in the lower gamma range and in the first half of the time range. Please have a look at the two figures. http://dropcanvas.com/0fnvn Fig a is the multiplotTFR of stat, showing only significant areas. Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. Now, we are not sure how to pick the time and freq range for a subsequent source analysis. Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? Any ideas? Greetings, Cornelius -------------- next part -------------- An HTML attachment was scrubbed... URL: From mengtongxiao at gmail.com Mon Jul 1 14:41:18 2013 From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=) Date: Mon, 1 Jul 2013 20:41:18 +0800 Subject: [FieldTrip] about ft_connectivity_powcorr_ortho Message-ID: dear all I use hilbert get the complex signal.and use the ft_connectivity_powcorr_ortho compute power envelope correlation . But I find the result contrast to the PLV. 1that why? the power envelope correlation of 1 not mean strong function relation? best. xiao -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Jul 1 15:39:49 2013 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 1 Jul 2013 15:39:49 +0200 Subject: [FieldTrip] freq / time range for source analysis? In-Reply-To: <51D17239.2070009@googlemail.com> References: <51D17239.2070009@googlemail.com> Message-ID: <3126EA9B-FD00-4CFA-95A7-62809C6BD222@psi.ucm.es> Hi Cornelius, I had the same kind of data and I picked the whole time frequency range of the cluster. It depends a bit on how big your clusters are and if there is a theoretical reason to split time and frequency windows (for example high and low gamma, etc.). Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 01/07/2013, a las 14:12, cornelius abel escribió: > Dear FT-List, > > in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. > We found a nice significant cluster in the lower gamma range and in the first half of the time range. > Please have a look at the two figures. > > http://dropcanvas.com/0fnvn > > Fig a is the multiplotTFR of stat, showing only significant areas. > Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. > > Now, we are not sure how to pick the time and freq range for a subsequent source analysis. > Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? > > Any ideas? > > Greetings, Cornelius > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jakob.wischniowski at uni-ulm.de Mon Jul 1 18:57:11 2013 From: jakob.wischniowski at uni-ulm.de (Jakob) Date: Mon, 1 Jul 2013 18:57:11 +0200 Subject: [FieldTrip] Matlab 2012/2013 In-Reply-To: <51C85906.2090204@uni-konstanz.de> References: <51C85906.2090204@uni-konstanz.de> Message-ID: Dear David, I'm facing following bug: While performing the artifact rejection summary function, dragging the mouse over the channels won't work: The "selecting box" for dragging simply won't appear while holding down the left mouse button/trackpad button. I'm running Matlab 2013a on an Apple OSX 10.8.4 (Mountain Lion) machine. Is this a known issue? Best regards! Jakob Wischniowski Am 24.06.2013 um 16:34 schrieb David Schubring : > Dear FieldTrip Users, > > I was wondering if the incompatibility issues with fieldtrip and the latest MATLAB 2013a version still exist (and if so, which bugs exactly occur)? > > (Some of our Matlab 2012a/b installations stopped working, maybe due to the latest java-update, and only the 2013 version still works.) > > Thanks in advance and best regards, > David Schubring > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From drivolta81 at gmail.com Tue Jul 2 12:15:57 2013 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 2 Jul 2013 12:15:57 +0200 Subject: [FieldTrip] Special issue - Research topic Message-ID: Dear FieldTrippers, I would like to advertise a Special Issue hosted by Frontiers in Human Neuroscience entitled: "Facing the other: Novel theories and methods in face perception research". Here is the link: http://www.frontiersin.org/Human_Neuroscience/researchtopics/Facing_the_other_Novel_theorie/1903 Topic Editors: Davide Rivolta, Max Planck Society, Germany Aina Puce, Indiana University, USA Mark A. Williams, Macquarie University, Australia Deadline for abstract submission: 30 Nov 2013 Deadline for full article submission: 28 Feb 2014 Abstract: We rely heavily on faces during social interactions. Humans possess the ability to recognise thousands of people very quickly and accurately without effort. The serious social difficulties that follow abnormalities of the face recognition system (i.e., prosopagnosia) strongly underline the importance of typical face skills in our everyday life. Over the last fifty years, research on prosopagnosia, along with research in the healthy population, has provided insights into the cognitive and neural features behind typical face recognition. This has also been achieved thanks to non-invasive neuroimaging techniques such as functional Magnetic Resonance Imaging (fMRI), Electroencephalography (EEG), Magnetoencephalography (MEG), Diffusion Tensor Imaging (DTI) and Transcranial Magnetic Stimulation (TMS). However, there is still much debate about the cognitive and neural mechanisms of face perception. In the current “Research Topic” we plan to gather experimental works, opinions, commentaries, mini-reviews and reviews that focus on new or novel theories and methods in face perception research. Where is the field at the moment? Do we need to re-think the experimental procedures we have adopted so far? Again, what kind of techniques (or combination of them) and analysis methods will be important in the future? From the experimental point of view we invite both behavioural and neuroimaging contributions (e.g., fMRI, EEG, MEG, DTI and TMS). Despite the main emphasis on face perception, memory and identification, we will also consider original works that focus on other aspects of face processing, such as expression recognition, attractiveness judgments and face imagery. In addition, animal investigations and experimental manipulations that alter face recognition abilities in typical human subjects (e.g., hypnosis) are also welcome. Overall, we are proposing a Research Topic that looks at face processing using different perspectives and welcome contributions from different domains such as psychology, neurology, neuroscience, cognitive science and philosophy. Last year we lost two giants in the field: Shlomo Bentin and Truett Allison. We dedicate this Research Topic to them and their pioneering studies. Bests, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From zriouil.imane at gmail.com Tue Jul 2 14:42:00 2013 From: zriouil.imane at gmail.com (z.imane) Date: Tue, 2 Jul 2013 14:42:00 +0200 Subject: [FieldTrip] (no subject) Message-ID: I have a signal of a certain frequency. if I resampled to a smaller frequency. is that I have a loss of information? -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Tue Jul 2 15:21:10 2013 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Tue, 2 Jul 2013 15:21:10 +0200 (CEST) Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: <001d01ce7727$03efcc40$0bcf64c0$@herring@fcdonders.ru.nl> Dear z.imane, If you resample to a smaller frequency you will reduce the number of data points. You will therefore most certainly lose data. Whether you lose 'information' depends on whether there is data relevant to you in frequency bands that cannot be analyzed after resampling. Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of z.imane Sent: dinsdag 2 juli 2013 14:42 To: FieldTrip discussion list Subject: [FieldTrip] (no subject) I have a signal of a certain frequency. if I resampled to a smaller frequency. is that I have a loss of information? -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Tue Jul 2 15:25:26 2013 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Tue, 2 Jul 2013 14:25:26 +0100 Subject: [FieldTrip] (no subject) In-Reply-To: <51d2d3e9.480a0f0a.7ffd.fffffd6aSMTPIN_ADDED_BROKEN@mx.google.com> References: <51d2d3e9.480a0f0a.7ffd.fffffd6aSMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: This might explain it http://en.wikipedia.org/wiki/Nyquist%E2%80%93Shannon_sampling_theorem Vladimir On Tue, Jul 2, 2013 at 2:21 PM, Herring, J.D. (Jim) < j.herring at fcdonders.ru.nl> wrote: > Dear z.imane,**** > > ** ** > > If you resample to a smaller frequency you will reduce the number of data > points. You will therefore most certainly lose data. Whether you lose > ‘information’ depends on whether there is data relevant to you in frequency > bands that cannot be analyzed after resampling. **** > > ** ** > > Best,**** > > ** ** > > Jim**** > > ** ** > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *z.imane > *Sent:* dinsdag 2 juli 2013 14:42 > *To:* FieldTrip discussion list > *Subject:* [FieldTrip] (no subject)**** > > ** ** > > I have a signal of a certain frequency. if I resampled to a smaller > frequency. is that I have a loss of information? > **** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From marianapbranco1 at gmail.com Tue Jul 2 16:20:54 2013 From: marianapbranco1 at gmail.com (Mariana Branco) Date: Tue, 2 Jul 2013 16:20:54 +0200 Subject: [FieldTrip] Online preprocessing In-Reply-To: <519DEAA1.5030402@donders.ru.nl> References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com> <519DE377.1020805@donders.ru.nl> <519DEAA1.5030402@donders.ru.nl> Message-ID: <2BAA5F99-7514-421D-ABB9-E3C0FD8A807B@gmail.com> Dear fieldtrippers, In the follow up of my previous questions: I know am able to stream realtime data form the Biosemi to matlab. In my matlab script I am sending triggers through the parallel port to the biosemi (i.e 2 or 4 for two different events). When The EEG was being recorded using the ActiView interface the trigger once sent was permanently associated with all incoming samples until a new trigger is sent (so event.type=TRIGGER for all samples). However, when streaming from the cmd using biosemi2ft, the trigger only appears once (when is sent) and the follow up samples are only headed with event.type=CM_IN_RANGE and event.value=0 or 1. Is it possible to configure it as in ActiView, which means all samples after sending a trigger are headed with event.type=TRIGGER and event.value=2 or 4? Regards, Mariana Branco On 23 May 2013, at 12:08, Jörn M. Horschig wrote: > Hi Mariana, > > ft_preprocessing demeans by the whole time window, in your 0s to 5s. The baseline window you specify depends on the time axis itself, if it goes from 0s to 5s, then defining [0 3] is fine. If it goes from -3 to 2s, then you need to define [-3 0]. Time is relative :) > Also, please check ft_timelockbaseline. But such a simple thing as subtracting a number from a matrix can also easily be done without relying on a fieldtrip function :) > > Best, > Jörn > > On 5/23/2013 11:57 AM, Mariana Branco wrote: >> Hi Jörn, >> >> Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do. >> >> Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial. >> In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong? >> >> Thank you again for all the advices, I will definitely pose more question in the future. >> >> Mariana Branco >> >> On 23 May 2013, at 11:37, "Jörn M. Horschig" wrote: >> >>> Hi Mariana, >>> >>> On 5/23/2013 10:25 AM, Mariana Branco wrote: >>>> Hello, >>>> >>>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. >>>> My questions are: >>>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time? >>> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does). Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure. >>>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure? >>> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start. >>> >>>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this? >>> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this. >>>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing? >>> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this). >>> >>> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions. >>> >>> Good luck! >>> Best, >>> Jörn >>> >>>> I am sorry for all the questions. >>> No problem, no way to know everything :) >>> >>>> Regards, >>>> >>>> Mariana Branco >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> -- >>> Jörn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> FieldTrip Development Team >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel: +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From giulia.rizza at tiscali.it Wed Jul 3 10:49:29 2013 From: giulia.rizza at tiscali.it (Giulia Rizza) Date: Wed, 3 Jul 2013 10:49:29 +0200 (CEST) Subject: [FieldTrip] unit ft_freqanalysis Message-ID: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> Dear Fieldtrip users I have a quick question. I've performed a Time Frequency Analysis with ft_freqanalysis using 'wavelet' as a method and 'relchange' as a baseline normalization for the plot. What is the unit for the ERD/ERS in the plot? Thank you so much for you help Giulia Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più di uno spot in TV. Per ogni nuovo abbonato 30 € di premio per te e per lui! Un amico al mese e parli e navighi sempre gratis: http://freelosophy.tiscali.it/ From a.stolk8 at gmail.com Wed Jul 3 10:55:39 2013 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 3 Jul 2013 10:55:39 +0200 Subject: [FieldTrip] unit ft_freqanalysis In-Reply-To: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> References: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> Message-ID: Hi Giulia, Baseline correction method 'relchange' computes the relative change according [ (task-baseline)/baseline ], i.e. a ratio centered around zero. If you multiply with 100, you get the relative change (from baseline) expressed in percentages. best regards, Arjen 2013/7/3 Giulia Rizza > Dear Fieldtrip users > I have a quick question. > I've performed a Time Frequency > Analysis with ft_freqanalysis using 'wavelet' as a method and 'relchange' > as a > baseline normalization for the plot. > What is the unit for the ERD/ERS in the > plot? > Thank you so much for you help > Giulia > > > Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più > di uno spot in TV. Per ogni nuovo abbonato 30 € di premio per te e per lui! > Un amico al mese e parli e navighi sempre gratis: > http://freelosophy.tiscali.it/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Wed Jul 3 16:21:14 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Wed, 3 Jul 2013 10:21:14 -0400 Subject: [FieldTrip] e-mail spoofing by ResearchGate Message-ID: This is unrelated to FieldTrip, but I think it still falls within the general interest of the community. Beware of e-mail spoofing by a company called ResearchGate. They send an e-mail that seems to come from a colleague of yours asking you to join, when in fact that colleague knows nothing about it. It is a spoofing scam. Just something to be aware of. Aaron Schurger ---------- Forwarded message ---------- From: Aaron Schurger Date: Wed, Jul 3, 2013 at 10:11 AM Subject: Re: ResearchGate: Response to your inquiry To: User Care You said "one of your co-authors claimed a publication on ResearchGate and invited you as a co-author". But which one of my co-authors? It was not the one who's e-mail address was listed as the "sender", because I asked that individual and they had not initiated any invitation. Why would you send me an e-mail showing the name "Anne Treisman" as the sender (see attached), with Anne's photo in the message saying explicitly "Anne Treisman invited you to join ResearchGate," when in fact Anne Treisman had not invited me to join ResearchGate. This is called "e-mail spoofing". In fact Treisman only joined ResearchGate in order to stop being harassed by e-mails purportedly from her colleague Bob Desimone, who in fact never invited her to join ResearchGate either! My first e-mail was polite. This one won't be - stop the bullshit. Sincerely, Aaron Schurger On Wed, Jul 3, 2013 at 9:13 AM, User Care wrote: > Hello, > > 2 Jul 2013: >> I've received e-mail "invitations" to join ResearchGate from people that I >> know, and when I asked if they had sent the invitation they said 'no'. I >> have colleagues who have all had the same experience (including the one who >> supposedly "invited" me). This does not inspire trust in your service. I >> certainly will not join. > > Thank you for your message. > > You received this notice because one of your co-authors claimed a publication on ResearchGate and invited you as a co-author. If you'd like to be put on our black list (meaning that we'll never email you again) - please follow the link in the footer of the email you received. > > Please do let us know if you have any further questions, > > Regards, > User Care -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Gmail - Anne Treisman invited you to join ResearchGate.pdf Type: application/pdf Size: 126588 bytes Desc: not available URL: From politzerahless at gmail.com Wed Jul 3 16:41:30 2013 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 3 Jul 2013 09:41:30 -0500 Subject: [FieldTrip] e-mail spoofing by ResearchGate Message-ID: Hi Aaron, I just wanted to clarify, Researchgate is not just a scam, it's a real site that some (although certainly not all) researchers use, similar to Academia.edu and things like that; see http://www.forbes.com/sites/alexknapp/2012/03/15/researchgate-wants-to-be-facebook-for-scientists/. I'm not sure why you were getting unsolicited e-mails; it's possible that when your colleagues signed up they accidentally forgot to uncheck an option to automatically invite co-authors (I've certainly made mistakes like that before on other places), or it might not be any fault of theirs and it might be some legitimate bug or something, or I guess it's possible you were getting e-mails from some other site masquerading as the actual ResearchGate. (I do admit even the real site does send a lot of e-mail notifications, but like Facebook and other things I've been able to change my preferences to stop getting most of them.) But anyway I just wanted to clarify what Researchgate actually is. Hope you get your problem resolved. Best, Steve Message: 1 > Date: Wed, 3 Jul 2013 10:21:14 -0400 > From: Aaron Schurger > To: FieldTrip discussion list > Subject: [FieldTrip] e-mail spoofing by ResearchGate > Message-ID: > < > CALeeyATYwZ7u1BuiWBx72Dn7tU5jZjuuf3pho9bgt33A-1Xy6A at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > This is unrelated to FieldTrip, but I think it still falls within the > general interest of the community. > > Beware of e-mail spoofing by a company called ResearchGate. They send > an e-mail that seems to come from a colleague of yours asking you to > join, when in fact that colleague knows nothing about it. It is a > spoofing scam. Just something to be aware of. > > Aaron Schurger > -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Wed Jul 3 21:03:35 2013 From: frank.ye.mei at gmail.com (Frank Mei) Date: Wed, 3 Jul 2013 15:03:35 -0400 Subject: [FieldTrip] beamformer Message-ID: Hello FieldtripList, In the beamformer tutorial ( http://fieldtrip.fcdonders.nl/tutorial/beamformer), the contrast of (post-pre)/pre was calculated. I am wondering why can't one just calculate (post-pre), instead. Could someone explain that? thanks, Ye Mei -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Wed Jul 3 21:16:12 2013 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 3 Jul 2013 21:16:12 +0200 Subject: [FieldTrip] beamformer In-Reply-To: References: Message-ID: Hi Ye Mei, Source-reconstructed activity (using the beamformer method) typically has a depth-bias (see van Veen et al., IEEE '97). Taking the relative increase/decrease of activity from baseline (effectively implementing a normalization per grid point location) is less prone to this bias as compared to taking the absolute difference. Hope this answers your question, Arjen 2013/7/3 Frank Mei > Hello FieldtripList, > > In the beamformer tutorial ( > http://fieldtrip.fcdonders.nl/tutorial/beamformer), the contrast of > (post-pre)/pre was calculated. I am wondering why can't one just > calculate (post-pre), instead. > > Could someone explain that? > > thanks, > Ye Mei > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Wed Jul 3 21:35:59 2013 From: frank.ye.mei at gmail.com (Frank Mei) Date: Wed, 3 Jul 2013 15:35:59 -0400 Subject: [FieldTrip] the right normalsation? Message-ID: Hello FieldtripList, I am trying to differentiate brain areas responsible for two different conditions using the method show in the tutorial( http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so far I have tried to subtract condition# 1 minus the #2, and divided by the average of the baseline period (pre-stimuli presentation), i.e., (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this division is for normalisation purposes. Is this the right normalsation? What normalization do you suggest to use? Is it necessary to normalise? thanks Ye -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Jul 4 10:39:00 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 04 Jul 2013 10:39:00 +0200 Subject: [FieldTrip] the right normalsation? In-Reply-To: References: Message-ID: <51D534A4.6080207@donders.ru.nl> Dear Ye, normalizing has different purposes. On the one hand, as Arjen pointed out, it is necessary to normalize in source space to get rid of the depth bias (well, alternatively you could normalize the leadfields). On the other hand, it makes averaging over subjects reasonable - otherwise differences in e.g. scalp conducitivity (for EEG) or headshape and size (for MEG) might lead to biasing an average in favour of some subjects. It is just the same reason as using a baseline when analysing ERPs/ERFs. Furthermore, there is no correct way of normalizing. As I said, you could also normalize the leadfield rather than normalizing by conditions. I think the most important thing to remember is that a) you need some contrast or b) you need to normalize the leadfield For a) it would be sufficient to use Post#1/Post#2, but I would rather not contrast two conditions normalized by two baselines. This gets really hard in interpretation (e.g. is the observed effect caused by a difference in baseline or a different in stimulus processing?). My favourite is log(Post#1/Post#2) or taking the z-score. Taking the logarithm has the advantage that extreme values get squashed nearer together, thereby reducing the influence of outliers. Z-scoring achieves a similar thing by explicitly normalizing by the variance. I would suggest for you to create some synthetic signals or values and play around with different ways of normalizing to get a feeling for what you are doing and what influence this has. I test different cases (e.g. 3: difference in prestim but no difference in poststim, no difference in prestim but difference in poststim and difference in prestim and poststim) and apply different normalizations/contrasts. Good luck :) Best, Jörn On 7/3/2013 9:35 PM, Frank Mei wrote: > Hello FieldtripList, > > I am trying to differentiate brain areas responsible for two different > conditions using the method show in the > tutorial(http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so > far I have tried to subtract condition# 1 minus the #2, and divided by > the average of the baseline period (pre-stimuli presentation), i.e., > (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this division > is for normalisation purposes. Is this the right normalsation? What > normalization do you suggest to use? Is it necessary to normalise? > > thanks > Ye > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From pgoodin at swin.edu.au Thu Jul 4 13:24:42 2013 From: pgoodin at swin.edu.au (Peter Goodin) Date: Thu, 4 Jul 2013 11:24:42 +0000 Subject: [FieldTrip] Running ICA on neuromag tsss data Message-ID: Hi Fieldtrip list, I've been using ICA (fastICA specifically) to clean blinks and cardiac artefact from my MEG data (neuromag 306 system) but find that I get some components that are "off" for a period and "on" for a period, or in other words some trials have the components "on" and others "off". I'm assuming these "off" periods are due to the differing dimensionality within the data due to the block by block rw nature of tsss, but when they're "on", they seem to contain a higher amplitude signal to the other components. My questions are: Are these on / off components due the differing dimensionality between blocks due to the tsss process? Is it more likely they contain data relating to the brain, something else such as movement, a mix of the two or it's simply impossible to tell? Thanks to anyone who can shed some light on this, Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate. Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.marshall at fcdonders.ru.nl Thu Jul 4 17:00:44 2013 From: t.marshall at fcdonders.ru.nl (Tom Marshall) Date: Thu, 04 Jul 2013 17:00:44 +0200 Subject: [FieldTrip] the right normalsation? In-Reply-To: <51D534A4.6080207@donders.ru.nl> References: <51D534A4.6080207@donders.ru.nl> Message-ID: <51D58E1C.6080002@fcdonders.ru.nl> Hi Jörn > My favourite is log(Post#1/Post#2) or taking the z-score. Could you expand on 'taking the z-score'? This could be interpreted in different ways, which might control for different sources of variance. To throw a bit more fuel on this fire... the problem with log ratios - ie log(post#1/post#2) - is that they ignore the prestimulus period altogether. That always seemed a bit funny to me. Presumably the brain response to your event of interest is somehow dependent on the brain state at the time the event happens ;) Of course one can independently test the hypothesis that the prestimulus periods differ, but how to be confident that they do not? On Thursday, July 04, 2013 10:39:00 AM, "Jörn M. Horschig" wrote: > Dear Ye, > > normalizing has different purposes. On the one hand, as Arjen pointed > out, it is necessary to normalize in source space to get rid of the > depth bias (well, alternatively you could normalize the leadfields). > On the other hand, it makes averaging over subjects reasonable - > otherwise differences in e.g. scalp conducitivity (for EEG) or > headshape and size (for MEG) might lead to biasing an average in > favour of some subjects. It is just the same reason as using a > baseline when analysing ERPs/ERFs. > Furthermore, there is no correct way of normalizing. As I said, you > could also normalize the leadfield rather than normalizing by > conditions. I think the most important thing to remember is that > a) you need some contrast or > b) you need to normalize the leadfield > > For a) it would be sufficient to use Post#1/Post#2, but I would rather > not contrast two conditions normalized by two baselines. This gets > really hard in interpretation (e.g. is the observed effect caused by a > difference in baseline or a different in stimulus processing?). My > favourite is log(Post#1/Post#2) or taking the z-score. Taking the > logarithm has the advantage that extreme values get squashed nearer > together, thereby reducing the influence of outliers. Z-scoring > achieves a similar thing by explicitly normalizing by the variance. > I would suggest for you to create some synthetic signals or values and > play around with different ways of normalizing to get a feeling for > what you are doing and what influence this has. I test different cases > (e.g. 3: difference in prestim but no difference in poststim, no > difference in prestim but difference in poststim and difference in > prestim and poststim) and apply different normalizations/contrasts. > > Good luck :) > Best, > Jörn > > > On 7/3/2013 9:35 PM, Frank Mei wrote: >> Hello FieldtripList, >> >> I am trying to differentiate brain areas responsible for two >> different conditions using the method show in the >> tutorial(http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so >> far I have tried to subtract condition# 1 minus the #2, and divided >> by the average of the baseline period (pre-stimuli presentation), >> i.e., (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this >> division is for normalisation purposes. Is this the right >> normalsation? What normalization do you suggest to use? Is it >> necessary to normalise? >> >> thanks >> Ye >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Tom Marshall, MSc. Neuronal Oscillations Group, Donders Centre for Cognitive Neuroimaging tel: +31(0)243668487 email: t.marshall at fcdonders.ru.nl postal: PO Box 9101, 6500HB, Nijmegen, The Netherlands visiting: Kapittelweg 29, 6525EN, Nijmegen, The Netherlands From aaron.schurger at gmail.com Thu Jul 4 21:33:29 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Thu, 4 Jul 2013 15:33:29 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question Message-ID: Hi, When you read in a data file using ft_preprocessing, with high-pass filtering, is the high-pass filter applied before the data are epoched (i.e. on the entire time series for the whole data file), or is the high-pass filter applied separately to each epoch? For very low frequencies (with period longer than one data epoch) this will make a difference. Thanks! Aaron -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From thomas.hartmann at th-ht.de Thu Jul 4 22:31:31 2013 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Thu, 04 Jul 2013 22:31:31 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: References: Message-ID: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> hi aaron, filtering is generally applied after the data have been epoched. to avoid the filter artifacts you are speaking about, we normally define epochs that are sufficiently larger so that these artifacts would be in data we are not interested in. about 1s at both ends of the epoch should be enough in most cases. but you better check... later you can use ft_redefinetrial to discard that extra data. hope this helps. best, thomas Aaron Schurger schrieb: >Hi, >When you read in a data file using ft_preprocessing, with high-pass >filtering, is the high-pass filter applied before the data are epoched >(i.e. on the entire time series for the whole data file), or is the >high-pass filter applied separately to each epoch? For very low >frequencies (with period longer than one data epoch) this will make a >difference. >Thanks! >Aaron > >-- >Aaron Schurger, PhD >Post-doctoral researcher >INSERM U992 / NeuroSpin >CEA - Saclay, France >+33-1-69-08-66-47 >aaron.schurger at gmail.com >http://www.unicog.org >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 5 03:51:45 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Thu, 4 Jul 2013 21:51:45 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> Message-ID: Thanks, Thomas. What if I wanted to apply the filtering to the entire time series first, and then extract the trial epochs after filtering? Is there a way to do that? Thanks, Aaron On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann wrote: > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: >> >> Hi, >> When you read in a data file using ft_preprocessing, with high-pass >> filtering, is the high-pass filter applied before the data are epoched >> (i.e. on the entire time series for the whole data file), or is the >> high-pass filter applied separately to each epoch? For very low >> frequencies (with period longer than one data epoch) this will make a >> difference. >> Thanks! >> Aaron >> >> -- >> Aaron Schurger, PhD >> Post-doctoral researcher >> INSERM U992 / NeuroSpin >> CEA - Saclay, France >> +33-1-69-08-66-47 >> aaron.schurger at gmail.com >> http://www.unicog.org >> ________________________________ >> >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From jm.horschig at donders.ru.nl Fri Jul 5 08:41:50 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 05 Jul 2013 08:41:50 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> Message-ID: <51D66AAE.70307@donders.ru.nl> Hi Aaron, in that case you need to define only one trial, going from 0 to the end of the recording and call ft_preprocessing. Not sure if this will work, but something like / cfg = [];// // ...// // hdr = ft_read_header(cfg.dataset);// // cfg.trl = [0 hdr.nSamples 0];// // data = ft_preprocessing(cfg);/ Subsequently you might want to try using ft_redefinetrial to get the epochs you are interested in. Note however that you need to have sufficient memory for reading all your data in. I am not sure how much memory you have, how long your recording is, how high your sampling rate and how many channels you have. If Matlab crashes when reading in everything, you would need to use trialpadding, or need to think of something clever yourself :) Would be great if you could let us know how you solve this in the end so that we can refer to that if someone else in future has a similar question. Best, Jörn On 7/5/2013 3:51 AM, Aaron Schurger wrote: > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: >> hi aaron, >> filtering is generally applied after the data have been epoched. to avoid >> the filter artifacts you are speaking about, we normally define epochs that >> are sufficiently larger so that these artifacts would be in data we are not >> interested in. about 1s at both ends of the epoch should be enough in most >> cases. but you better check... later you can use ft_redefinetrial to discard >> that extra data. >> hope this helps. >> best, >> thomas >> >> >> >> Aaron Schurger schrieb: >>> Hi, >>> When you read in a data file using ft_preprocessing, with high-pass >>> filtering, is the high-pass filter applied before the data are epoched >>> (i.e. on the entire time series for the whole data file), or is the >>> high-pass filter applied separately to each epoch? For very low >>> frequencies (with period longer than one data epoch) this will make a >>> difference. >>> Thanks! >>> Aaron >>> >>> -- >>> Aaron Schurger, PhD >>> Post-doctoral researcher >>> INSERM U992 / NeuroSpin >>> CEA - Saclay, France >>> +33-1-69-08-66-47 >>> aaron.schurger at gmail.com >>> http://www.unicog.org >>> ________________________________ >>> >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. Thomas Hartmann >> >> CIMeC - Center for Mind/Brain Sciences >> Università degli Studi di Trento >> via delle Regole, 101 >> 38060 Mattarello (TN) >> ITALY >> >> Tel: +39 0461 28 2779 >> Fax: +39 0461 28 3066 >> Email: thomas.hartmann at th-ht.de >> Homepage: http://sites.google.com/site/obobcimec/ >> >> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >> Doyle) >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri Jul 5 08:51:41 2013 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 5 Jul 2013 08:51:41 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: <46B38EE6-90F1-4B4F-8753-6F465EE39EC5@gmail.com> Hi Aaron (et al.) another way to filter the whole recording is the workaround using EEGlab. By default, you always read in the whole recording in EEGlab and apply all filters to the whole recording. After filtering, you can use eeglab2fieldtrip.m to move your filtered data from EEGlab to field trip. Note however, that Jörn's concern regarding your memory still applies. Also, filtering the whole recording takes quite some time. Best, Julian Am 05.07.2013 um 08:41 schrieb Jörn M. Horschig: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of the recording and call ft_preprocessing. Not sure if this will work, but something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs you are interested in. > > Note however that you need to have sufficient memory for reading all your data in. I am not sure how much memory you have, how long your recording is, how high your sampling rate and how many channels you have. If Matlab crashes when reading in everything, you would need to use trialpadding, or need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: >> Thanks, Thomas. What if I wanted to apply the filtering to the entire >> time series first, and then extract the trial epochs after filtering? >> Is there a way to do that? >> Thanks, >> Aaron >> >> On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann >> wrote: >>> hi aaron, >>> filtering is generally applied after the data have been epoched. to avoid >>> the filter artifacts you are speaking about, we normally define epochs that >>> are sufficiently larger so that these artifacts would be in data we are not >>> interested in. about 1s at both ends of the epoch should be enough in most >>> cases. but you better check... later you can use ft_redefinetrial to discard >>> that extra data. >>> hope this helps. >>> best, >>> thomas >>> >>> >>> >>> Aaron Schurger schrieb: >>>> Hi, >>>> When you read in a data file using ft_preprocessing, with high-pass >>>> filtering, is the high-pass filter applied before the data are epoched >>>> (i.e. on the entire time series for the whole data file), or is the >>>> high-pass filter applied separately to each epoch? For very low >>>> frequencies (with period longer than one data epoch) this will make a >>>> difference. >>>> Thanks! >>>> Aaron >>>> >>>> -- >>>> Aaron Schurger, PhD >>>> Post-doctoral researcher >>>> INSERM U992 / NeuroSpin >>>> CEA - Saclay, France >>>> +33-1-69-08-66-47 >>>> aaron.schurger at gmail.com >>>> http://www.unicog.org >>>> ________________________________ >>>> >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> Dr. Thomas Hartmann >>> >>> CIMeC - Center for Mind/Brain Sciences >>> Università degli Studi di Trento >>> via delle Regole, 101 >>> 38060 Mattarello (TN) >>> ITALY >>> >>> Tel: +39 0461 28 2779 >>> Fax: +39 0461 28 3066 >>> Email: thomas.hartmann at th-ht.de >>> Homepage: http://sites.google.com/site/obobcimec/ >>> >>> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >>> Doyle) >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.backus at donders.ru.nl Fri Jul 5 09:38:55 2013 From: a.backus at donders.ru.nl (Alexander Backus) Date: Fri, 5 Jul 2013 09:38:55 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields Message-ID: Hi, When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to covert to 3rd order gradient, it replaces the values in data.grad.chanpos and data.grad.chanori with NaNs. I assume this is done because they are no longer valid. When digging into the low-level code I found something about mismatching number of channels. Anyway, when I want to subsequently covert to planar gradient (does this actually makes sense?) or create a source model, I need these grad values. I have two questions: 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why are NaNs inserted in the grad subfields? 2) Can I still use the data for planar gradient conversion or source modeling by using the earlier stored old gradient info (pre ft_denoise_synthetic) or is this ill-advised and is there a more wise course of action? Thanks in advance, Best, Alexander Backus -- Alexander R. Backus, MSc PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Memory and Space Research Group www.doellerlab.com P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands Telephone: +31(0)24 36 10754 -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Fri Jul 5 10:16:11 2013 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Fri, 05 Jul 2013 10:16:11 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: <51D680CB.7040906@th-ht.de> hi, i would do this: /% do definetrial for all data...// //cfg = [];// //cfg.dataset = 'younameit.data';// //cfg.trialdef.triallength = Inf;// //cfg.trialdef.ntrials = 1;// // //cfg = ft_definetrial(cfg);// // //% preprocess all the data// //cfg.hpfilter = 'yes';// //cfg.hpfreq = 0.5;// // //alldata = ft_preprocessing(cfg);// // //% now we do definetrials for our trials...// //cfg = [];// //cfg.//trialdef.prestim = 2;// //cfg.trialdef.poststim = 2;// //cfg.trialdef.eventype = 'YourEventType';// //cfg.trialdef.eventvalue = [1 2 3 4 5];// // //cfg = ft_definetrial(cfg);// // //% now we use the trl field we just created for ft_redefinetrial...// //data_epochs = ft_redefinetrial(cfg, alldata);/ i havent tested the code but it should be more or less fine.. and the good thing is that you stay within the high level fieldtrip functions.... best, thomas On 05.07.2013 08:41, "Jörn M. Horschig" wrote: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the > end of the recording and call ft_preprocessing. Not sure if this will > work, but something like > > / cfg = [];// > // ...// > // hdr = ft_read_header(cfg.dataset);// > // cfg.trl = [0 hdr.nSamples 0];// > // data = ft_preprocessing(cfg);/ > > Subsequently you might want to try using ft_redefinetrial to get the > epochs you are interested in. > > Note however that you need to have sufficient memory for reading all > your data in. I am not sure how much memory you have, how long your > recording is, how high your sampling rate and how many channels you > have. If Matlab crashes when reading in everything, you would need to > use trialpadding, or need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end > so that we can refer to that if someone else in future has a similar > question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: >> Thanks, Thomas. What if I wanted to apply the filtering to the entire >> time series first, and then extract the trial epochs after filtering? >> Is there a way to do that? >> Thanks, >> Aaron >> >> On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann >> wrote: >>> hi aaron, >>> filtering is generally applied after the data have been epoched. to avoid >>> the filter artifacts you are speaking about, we normally define epochs that >>> are sufficiently larger so that these artifacts would be in data we are not >>> interested in. about 1s at both ends of the epoch should be enough in most >>> cases. but you better check... later you can use ft_redefinetrial to discard >>> that extra data. >>> hope this helps. >>> best, >>> thomas >>> >>> >>> >>> Aaron Schurger schrieb: >>>> Hi, >>>> When you read in a data file using ft_preprocessing, with high-pass >>>> filtering, is the high-pass filter applied before the data are epoched >>>> (i.e. on the entire time series for the whole data file), or is the >>>> high-pass filter applied separately to each epoch? For very low >>>> frequencies (with period longer than one data epoch) this will make a >>>> difference. >>>> Thanks! >>>> Aaron >>>> >>>> -- >>>> Aaron Schurger, PhD >>>> Post-doctoral researcher >>>> INSERM U992 / NeuroSpin >>>> CEA - Saclay, France >>>> +33-1-69-08-66-47 >>>> aaron.schurger at gmail.com >>>> http://www.unicog.org >>>> ________________________________ >>>> >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> Dr. Thomas Hartmann >>> >>> CIMeC - Center for Mind/Brain Sciences >>> Università degli Studi di Trento >>> via delle Regole, 101 >>> 38060 Mattarello (TN) >>> ITALY >>> >>> Tel: +39 0461 28 2779 >>> Fax: +39 0461 28 3066 >>> Email:thomas.hartmann at th-ht.de >>> Homepage:http://sites.google.com/site/obobcimec/ >>> >>> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >>> Doyle) >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 5 16:03:29 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 5 Jul 2013 10:03:29 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: Thanks, Jörn. If memory is an issue, I suppose I could try doing the filtering one channel at a time, applying redefinetrial to each channel (one at a time), and then put the resulting epochs back together in a field-trip structure. I'll let you know what I come up with (if I find a good solution). Memory may not end up being an issue because my recording sessions were only about 5 min long each, and with 8 Gb of RAM, should be OK. Cheers, Aaron On Fri, Jul 5, 2013 at 2:41 AM, "Jörn M. Horschig" wrote: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of > the recording and call ft_preprocessing. Not sure if this will work, but > something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs > you are interested in. > > Note however that you need to have sufficient memory for reading all your > data in. I am not sure how much memory you have, how long your recording is, > how high your sampling rate and how many channels you have. If Matlab > crashes when reading in everything, you would need to use trialpadding, or > need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so > that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: > > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: > > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: > > Hi, > When you read in a data file using ft_preprocessing, with high-pass > filtering, is the high-pass filter applied before the data are epoched > (i.e. on the entire time series for the whole data file), or is the > high-pass filter applied separately to each epoch? For very low > frequencies (with period longer than one data epoch) this will make a > difference. > Thanks! > Aaron > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > ________________________________ > > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From aaron.schurger at gmail.com Fri Jul 5 16:25:32 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 5 Jul 2013 10:25:32 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D680CB.7040906@th-ht.de> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> <51D680CB.7040906@th-ht.de> Message-ID: Hi, Thomas, Yes, this is roughly what I tried to do, but I couldn't get it to work at first. But I used ft_preprocessing instead of ft_redefinetrial, and I think that was the mistake. With ft_redefinetrial, now it works just fine. Simple - thanks! By the way, when the trials are redefined, fieldtrip always reports "found 31 events" and then "created 30 trials" (there are 30 trials in each block). Why does fieldtrip always report one extra event per run? Thanks! Aaron On Fri, Jul 5, 2013 at 4:16 AM, Thomas Hartmann wrote: > hi, > i would do this: > > % do definetrial for all data... > cfg = []; > cfg.dataset = 'younameit.data'; > cfg.trialdef.triallength = Inf; > cfg.trialdef.ntrials = 1; > > cfg = ft_definetrial(cfg); > > % preprocess all the data > cfg.hpfilter = 'yes'; > cfg.hpfreq = 0.5; > > alldata = ft_preprocessing(cfg); > > % now we do definetrials for our trials... > cfg = []; > cfg.trialdef.prestim = 2; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventype = 'YourEventType'; > cfg.trialdef.eventvalue = [1 2 3 4 5]; > > cfg = ft_definetrial(cfg); > > % now we use the trl field we just created for ft_redefinetrial... > data_epochs = ft_redefinetrial(cfg, alldata); > > i havent tested the code but it should be more or less fine.. and the good > thing is that you stay within the high level fieldtrip functions.... > > best, > thomas > > > > > On 05.07.2013 08:41, "Jörn M. Horschig" wrote: > > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of > the recording and call ft_preprocessing. Not sure if this will work, but > something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs > you are interested in. > > Note however that you need to have sufficient memory for reading all your > data in. I am not sure how much memory you have, how long your recording is, > how high your sampling rate and how many channels you have. If Matlab > crashes when reading in everything, you would need to use trialpadding, or > need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so > that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: > > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: > > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: > > Hi, > When you read in a data file using ft_preprocessing, with high-pass > filtering, is the high-pass filter applied before the data are epoched > (i.e. on the entire time series for the whole data file), or is the > high-pass filter applied separately to each epoch? For very low > frequencies (with period longer than one data epoch) this will make a > difference. > Thanks! > Aaron > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > ________________________________ > > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From szabbanto at gmail.com Fri Jul 5 16:51:36 2013 From: szabbanto at gmail.com (=?ISO-8859-1?Q?Szabolcs_Szeb=E9nyi?=) Date: Fri, 5 Jul 2013 16:51:36 +0200 Subject: [FieldTrip] Question about ft_freqanalysis using wavelet method Message-ID: Dear Fieldtrip developers and users, I have a question about ft_freqanalysis when I use the 'wavelet' method. When I call this fieldtrip function with the specifications below, I get an error message right at the first trial: Error using zeros Out of memory. Type HELP MEMORY for your options. Error in ft_freqanalysis (line 601) if powflg, powspctrm = nan+zeros(ntrials,nchan,nfoi,ntoi,cfg.precision); end Here are my specifications: cfg = []; cfg.trials = find(data.trialinfo(:,3) == iPhase); cfg.channel = 'MEG'; cfg.method = 'wavelet'; cfg.toi = -1.5:0.005:4; cfg.foi = 30:1:90; cfg.width = 5; cfg.keeptrials = 'yes'; cfg.output = 'pow'; cfg.pad = 'maxperlen'; cfg.padtype = 'zero'; cfg.polyremoval = 0; I tried out the wavelet approach already for lower frequencies (foi = 1:0.5:30; toi = -1.5:0.1:4; width = 7) and it worked fine for that. For the higher frequencies above, it cannot proceed further to the 2nd trial with 60GB memory either, so I think, the problem is somewhere else. The data itself consists of 275 trials, with a sampling rate of 600Hz; 273 channels CTF MEG. I would highly appreciate if you could tell me where the problem is and what I should change in order to proceed. Thank you in advance for your help, Szabolcs Szebényi -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcpiastra at libero.it Fri Jul 5 17:47:32 2013 From: mcpiastra at libero.it (mcpiastra at libero.it) Date: Fri, 5 Jul 2013 17:47:32 +0200 (CEST) Subject: [FieldTrip] source_recontruction with intracranial sensors Message-ID: <20502312.13722601373039252586.JavaMail.defaultUser@defaultHost> Dear Fieldtrip developers and users, I have some problems with source reconstruction starting with intracranial sensors. Schematic details are below. Aim: do source reconstruction using BEM for the forward problem and mne for the inverse problem. Dataset: stereoEEG recording (50 sec) Notation: I'll use the same nomenclature of the one in the tutorial Since we have intracranial sensors, our aim is to build the forward model (leadfield structure) starting from a mesh whose cortical sheet has a higher spatial resolution. To do that we approached the problem in two ways: 1) we substituted the innermost sheet, built by ft_prepare_mesh, with the Freesurfer cortical mesh (4180 vertices). We put dipoles on the mesh nodes and then we built the head model and calculate the leadfield matrices (one for each dipole). Solving the inverse problem, in source.avg.pow there were values with order of magnitude of 10^{-30}- 10^{-20}. This is due to the fact that the matrix vol.mat (one of the output of ft_prepare_headmodel) had values very different if we compared the entries in correspondence to the Fieldtrip meshes and the ones in correspondence to the Freesurfer mesh. This difference had the order of magnitude equal to 10^{9}. Due to this pathology, we tried a different way to compute the forward model (following more the tutorial). 2) we built the head model using the default Fieldtrip meshes (all of the three sheets) without substituting any sheet. (We just fixed the number of nodes for the innermost sheet equal to the Freesurfer one.) This avoided high differences in vol.mat. Freesurfer mesh vertices were used to determine dipole positions, as we did before. In this case we obtained values of source.avg.pow of the order of 10^ {-6} In both cases we preprocessed the dataset with ft_timelockanalysis and we used the regularization parameter lambda (for the mne method) equal to 0.2. Our questions are: 1) what is vol.mat? Which order of magnitude should have its values? We didn't manage to explore the building process of it. (We suppose this matrix has electrical information interpolated through the mesh vertices.) As consequences: 2) which is the order of magnitude expected for the values of source.avg.pow ? And which is its unit of measure? 3) Is it correct the interpretation of: source.avg.mom and source.avg.pow as the evolution through time of the electric dipole moment and the radiated power of the dipole, respectively? 4) In order to apply a regularization approach to solve the inverse problem we though that the best way was to introduce the noise covariation matrix built by the function ft_timelockanalysis which is subsequently controlled by the lambda parameter. Is there any criterion to choose the best lambda? Can we avoid to pass through ft_timelockanalysis to regularize the solution? Many thanks, Maria Carla Piastra PhD student in Bioengeneering c/o BioLab @ DIBRIS University of Genova, ITALY From zriouil.imane at gmail.com Fri Jul 5 21:44:41 2013 From: zriouil.imane at gmail.com (z.imane) Date: Fri, 5 Jul 2013 20:44:41 +0100 Subject: [FieldTrip] Computing the spike triggered average LFP Message-ID: Hi i would applying the paragraph "Computing the spike triggered average LFP" in tutorial "Preprocessing and analysis of spike and local field potential data" in matlab. if you explain this pocess more, because i don't understand it. -------------- next part -------------- An HTML attachment was scrubbed... URL: From baharbahar395 at yahoo.com Sat Jul 6 08:05:37 2013 From: baharbahar395 at yahoo.com (Bahar Bahar) Date: Sat, 6 Jul 2013 14:05:37 +0800 (SGT) Subject: [FieldTrip] sLORETA Message-ID: <1373090737.76319.YahooMailNeo@web192303.mail.sg3.yahoo.com> Hi dear all, I have computed sloreta from ERP data via the software, but I do not know what is the unit of the values resulted in transformation. Can any one help me about that? -------------- next part -------------- An HTML attachment was scrubbed... URL: From baharbahar395 at yahoo.com Sat Jul 6 08:15:53 2013 From: baharbahar395 at yahoo.com (Bahar Bahar) Date: Sat, 6 Jul 2013 14:15:53 +0800 (SGT) Subject: [FieldTrip] Sloreta Message-ID: <1373091353.41529.YahooMailNeo@web192306.mail.sg3.yahoo.com> Hi dear all, I have computed sloreta from ERP data via the Sloreta software, but I did not figure out the unit of the values resulted in transformation. Can any one help me about that? Thanks, Bahar -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Sat Jul 6 09:53:09 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Sat, 6 Jul 2013 09:53:09 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data Message-ID: Dear All, after running source statistics I tried to plot the result. However, I always get the error that cfg.parameter 'all' can't be used since there is "no such field". I know that I can also specify single parameters, i.e. only the ones I want to interpolate. However, I would like to know why it doesn't work for me with all the parameters... Maybe it's only a minor thing, i.e. the FT version. But I want to make sure that there is no major error in my pipeline. Any help is as always very appreciated! Thanks! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Sat Jul 6 14:19:58 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sat, 06 Jul 2013 14:19:58 +0200 Subject: [FieldTrip] Question about ft_freqanalysis using wavelet method In-Reply-To: References: Message-ID: <51D80B6E.5040704@donders.ru.nl> Hi Szabi, That error has nothing to do with the wavelet approach but with the fact that you want to have steps of 5ms (as specified in cfg.toi) for your TFR. FieldTrip will create one big data matrin nTrials x nChannels x nSamples x nFrequencies. With the settings you specified this will be quite huge, and it does not fit into memory when Matlab tries to initiate that variable. I would suggest you use 50ms steps, that is sufficient especially given that you need some tens of milliseconds for estimating the frequency content anyway. An alternative would be to use the torque/maui cluster at the Donders and request a session with loads of memory :) Best, Jörn On 7/5/2013 4:51 PM, Szabolcs Szebényi wrote: > Dear Fieldtrip developers and users, > > I have a question about ft_freqanalysis when I use the 'wavelet' > method. When I call this fieldtrip function with the specifications > below, I get an error message right at the first trial: > > Error using zeros > Out of memory. Type HELP MEMORY for your options. > > Error in ft_freqanalysis (line 601) > if powflg, powspctrm = > nan+zeros(ntrials,nchan,nfoi,ntoi,cfg.precision); > end > > Here are my specifications: > > cfg = []; > cfg.trials = find(data.trialinfo(:,3) == iPhase); > cfg.channel = 'MEG'; > cfg.method = 'wavelet'; > cfg.toi = -1.5:0.005:4; > cfg.foi = 30:1:90; > cfg.width = 5; > cfg.keeptrials = 'yes'; > cfg.output = 'pow'; > cfg.pad = 'maxperlen'; > cfg.padtype = 'zero'; > cfg.polyremoval = 0; > > I tried out the wavelet approach already for lower frequencies (foi = > 1:0.5:30; toi = -1.5:0.1:4; width = 7) and it worked fine for that. > For the higher frequencies above, it cannot proceed further to the 2nd > trial with 60GB memory either, so I think, the problem is somewhere else. > > The data itself consists of 275 trials, with a sampling rate of 600Hz; > 273 channels CTF MEG. > > I would highly appreciate if you could tell me where the problem is > and what I should change in order to proceed. > > > Thank you in advance for your help, > > Szabolcs Szebényi > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Jul 7 19:41:51 2013 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 7 Jul 2013 19:41:51 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data Message-ID: Hi Andreas , It is annoying that it doesn't work if you specify cfg.parameter 'all' and I don't know why either. However , I have a very simple solution for this by interpolating 'stat' and 'mask' then combining afterwards when you want to plot your statistic result. The FT code is something like this: cfg = []; cfg.voxelcoord = 'no'; cfg.parameter = 'stat'; cfg.interpmethod = 'nearest'; cfg.coordsys = 'mni'; statplot = ft_sourceinterpolate(cfg, stat,mri); cfg = []; cfg.voxelcoord = 'no'; cfg.parameter = 'mask'; cfg.interpmethod = 'nearest'; cfg.coordsys = 'mni'; mask = ft_sourceinterpolate(cfg, stat,mri); statplot.mask = mask.mask; Hope this helps. Best, Haiteng > Message: 3 > Date: Sat, 6 Jul 2013 09:53:09 +0200 > From: Andreas Sauer > To: FieldTrip discussion list > Subject: [FieldTrip] ft_sourceinterpolate with stats data > Message-ID: > < > CAHLSopWD2Q-RuAMJrvwZJGAajB6aUbDyrDN6_SFMdqu7HOgZ0g at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > after running source statistics I tried to plot the result. However, I > always get the error that cfg.parameter 'all' can't be used since there is > "no such field". > > I know that I can also specify single parameters, i.e. only the ones I want > to interpolate. However, I would like to know why it doesn't work for me > with all the parameters... Maybe it's only a minor thing, i.e. the FT > version. But I want to make sure that there is no major error in my > pipeline. > > Any help is as always very appreciated! Thanks! > > Best, > > Andreas > > -- > Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstra?e 46 > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130706/b595b2e2/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 32, Issue 11 > ***************************************** > -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Jul 7 20:17:58 2013 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 7 Jul 2013 20:17:58 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields Message-ID: Hi Alexander, I am not clear about what's ft_denoise_synthetic doing. However , I don't have such problem when I use . The reason you get 'mismatching number of channels' probably because you specify cfg.channel ='MEG' instead of including all channels. My FT code is something like this: % reading cfg = []; cfg.dataset = dataset; cfg.trialdef.eventtype = ''; cfg.trialdef.eventvalue = ; cfg.continuous = 'yes'; cfg.channel= 'all'; cfg.trialdef.prestim = ; cfg.trialdef.poststim = ; cfg = ft_definetrial(cfg); trl = cfg.trl; cfg.detrend ='yes'; cfg.demean = 'yes'; data= ft_preprocessing(cfg); cfg.gradient = 'G3BR'; data= ft_denoise_synthetic(cfg,data); In my pipeline , the grad changes into NAN only after I run I ICA to remove artifacts . I replace this grad with previous good gradient information and assume it is fine for the latter source reconstruction. Hope this helps. Best, Haiteng > > > Message: 2 > Date: Fri, 5 Jul 2013 09:38:55 +0200 > From: Alexander Backus > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in > grad fields > Message-ID: > < > CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to > covert to 3rd order gradient, it replaces the values in data.grad.chanpos > and data.grad.chanori with NaNs. > > I assume this is done because they are no longer valid. > When digging into the low-level code I found something about mismatching > number of channels. > > Anyway, when I want to subsequently covert to planar gradient (does this > actually makes sense?) or create a source model, I need these grad values. > > I have two questions: > > 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why > are NaNs inserted in the grad subfields? > > 2) Can I still use the data for planar gradient conversion or source > modeling by using the earlier stored old gradient info (pre > ft_denoise_synthetic) or is this ill-advised and is there a more wise > course of action? > > Thanks in advance, > Best, > Alexander Backus > -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Mon Jul 8 10:34:06 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Mon, 8 Jul 2013 10:34:06 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data In-Reply-To: References: Message-ID: Thanks for your answer, Haiteng! It also works for me when I interpolate i.e. 'stat'. However, it would be good to know why 'all' does not work, since it is described in the tutorial... Best, Andreas 2013/7/7 Haiteng Jiang > Hi Andreas , > It is annoying that it doesn't work if you specify cfg.parameter > 'all' and I don't know why either. However , I have a very simple > solution for this by interpolating 'stat' and 'mask' then combining > afterwards when you want to plot your statistic result. The FT code is > something like this: > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'stat'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > statplot = ft_sourceinterpolate(cfg, stat,mri); > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'mask'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > mask = ft_sourceinterpolate(cfg, > stat,mri); > statplot.mask = mask.mask; > Hope this helps. > > Best, > Haiteng > > > > >> Message: 3 >> Date: Sat, 6 Jul 2013 09:53:09 +0200 >> From: Andreas Sauer >> To: FieldTrip discussion list >> Subject: [FieldTrip] ft_sourceinterpolate with stats data >> Message-ID: >> < >> CAHLSopWD2Q-RuAMJrvwZJGAajB6aUbDyrDN6_SFMdqu7HOgZ0g at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear All, >> >> after running source statistics I tried to plot the result. However, I >> always get the error that cfg.parameter 'all' can't be used since there is >> "no such field". >> > > >> >> I know that I can also specify single parameters, i.e. only the ones I >> want >> to interpolate. However, I would like to know why it doesn't work for me >> with all the parameters... Maybe it's only a minor thing, i.e. the FT >> version. But I want to make sure that there is no major error in my >> pipeline. >> >> Any help is as always very appreciated! Thanks! >> >> Best, >> >> Andreas >> >> -- >> Andreas Sauer >> Max Planck Institute for Brain Research >> Deutschordenstra?e 46 >> >> 60528 Frankfurt am Main >> Germany >> >> T: +49 69 96769 278 >> F: +49 69 96769 327 >> Email: sauer.mpih at gmail.com >> www.brain.mpg.de >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130706/b595b2e2/attachment-0001.html >> > >> >> ------------------------------ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 32, Issue 11 >> ***************************************** >> > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Dipl.-Psych. Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 8 11:30:39 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 08 Jul 2013 11:30:39 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data In-Reply-To: References: Message-ID: <51DA86BF.3000801@donders.ru.nl> Hi Andreas, all the chiefs are on vacation right now, and I do not know if it should work or why it does not. Therefore, I created a bug on bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2218 You can also sign up there and add yourself to the CC list to stay informed about the progress on this. In the meanwhile I would suggest to do as Haiteng proposed, as this is the only way to go right now. Thanks for reporting :) Best, Jörn On 7/8/2013 10:34 AM, Andreas Sauer wrote: > Thanks for your answer, Haiteng! It also works for me when I > interpolate i.e. 'stat'. However, it would be good to know why 'all' > does not work, since it is described in the tutorial... > > Best, > > Andreas > > > 2013/7/7 Haiteng Jiang > > > Hi Andreas , > It is annoying that it doesn't work if you > specify cfg.parameter 'all' and I don't know why either. However > , I have a very simple solution for this by interpolating 'stat' > and 'mask' then combining afterwards when you want to plot your > statistic result. The FT code is something like this: > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'stat'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > statplot = ft_sourceinterpolate(cfg, stat,mri); > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'mask'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > mask = ft_sourceinterpolate(cfg, > stat,mri); > statplot.mask = mask.mask; > Hope this helps. > Best, > Haiteng > > Message: 3 > Date: Sat, 6 Jul 2013 09:53:09 +0200 > From: Andreas Sauer > > To: FieldTrip discussion list > > Subject: [FieldTrip] ft_sourceinterpolate with stats data > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > Dear All, > > after running source statistics I tried to plot the result. > However, I > always get the error that cfg.parameter 'all' can't be used > since there is > "no such field". > > > I know that I can also specify single parameters, i.e. only > the ones I want > to interpolate. However, I would like to know why it doesn't > work for me > with all the parameters... Maybe it's only a minor thing, i.e. > the FT > version. But I want to make sure that there is no major error > in my > pipeline. > > Any help is as always very appreciated! Thanks! > > Best, > > Andreas > > -- > Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstra?e 46 > > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 32, Issue 11 > ***************************************** > > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Dipl.-Psych. Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstraße 46 > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 8 11:33:29 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 08 Jul 2013 11:33:29 +0200 Subject: [FieldTrip] Computing the spike triggered average LFP In-Reply-To: References: Message-ID: <51DA8769.6000006@donders.ru.nl> Dear Zriouil, the problem you described is rather incomplete. If you adress certain sections in particular and state in more detail what exactly you do not understand, there might be more people abel to help you. Usually, the tutorial aim at being sufficient to get started, but if they are unclear on particular location, we would be glad to hear your thought on where they are unclear and what information needs to be added to improve them. Best, Jörn On 7/5/2013 9:44 PM, z.imane wrote: > Hi > > i would applying the paragraph "Computing the spike triggered average > LFP" in tutorial "Preprocessing and analysis of spike and local field > potential data" in matlab. if you explain this pocess more, because i > don't understand it. > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hubert.preissl at uni-tuebingen.de Mon Jul 8 11:33:59 2013 From: hubert.preissl at uni-tuebingen.de (Hubert Preissl) Date: Mon, 08 Jul 2013 11:33:59 +0200 Subject: [FieldTrip] =?windows-1252?q?6th_Autumn_School_=93Move_the_Brain?= =?windows-1252?q?=94=2C_T=FCbingen=2C_30thSeptember_-2th_October_2013?= In-Reply-To: References: Message-ID: <51DA8787.3010904@uni-tuebingen.de> Hello, we are pleased to announce the upcoming 6^th Autumn School "Move the Brain" in Tübingen. Confirmed speakers: *Douglas Cheyne, *Hospital for Sick Children, Toronto, Canada *Sarang S. Dalal, *University of Konstanz, Germany *Joachim Gross, *University of Glasgow, UK *Todd Hare, *University of Zürich, Switzerland *Floris de Lang, *Donders Institute, Nijmegen, Netherlands *Jyrki Mäkelä, *Helsinki University Central Hospital, Finland *Hilke Plassmann, *INSEAD, France *Alfons Schnitzler, *University of Düsseldorf, Germany For application and further information on the scientific program please visit our website: http://www.mp.uni-tuebingen.de/mp/index.php?id=412 We look forward meeting you in Tübingen! Best regards, Hubert Preissl -- Dr. Hubert Preissl fMEG Center phone: ++49-(0)7071-2987704 Otfried Müller Str 47 fax: ++49-(0)7071-295706 72076 Tübingen, Germany email: hubert.preissl at uni-tuebingen.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From zriouil.imane at gmail.com Mon Jul 8 12:47:03 2013 From: zriouil.imane at gmail.com (z.imane) Date: Mon, 8 Jul 2013 12:47:03 +0200 Subject: [FieldTrip] Computing the spike triggered average LFP In-Reply-To: <51DA8769.6000006@donders.ru.nl> References: <51DA8769.6000006@donders.ru.nl> Message-ID: Thank you for your response. I wish to plotting LFP based on spike using a program that I want to create. and for the obtained the same graph as in the tutorial. the problem is that I do not understand how the function ft_spiketriggeredaverage computes the avererage of the LFP around the spikes, while the spikes and LFP are recorded in the same period, and how he detect the spike? -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.mercier at einstein.yu.edu Mon Jul 8 15:32:02 2013 From: manuel.mercier at einstein.yu.edu (Manuel Mercier) Date: Mon, 8 Jul 2013 13:32:02 +0000 Subject: [FieldTrip] ft_connectivityanalysis and PLV formula Message-ID: Dear Fieldtrip Community I am still stuck with the implementation of PLV. To be sure that I understand properly the principle of Phase Locking Value, I wrote a code to compute it. That code (see below) gave me the same results as ft_connectivityanalysis. plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)) -angle(data.fourierspctrm(:,electrode_2,:,:)))),1))); (data.fourierspctrm being produced by ft_freqanalysis). However, I then realized that the subtraction between the two angles should be done in the complex plane as in: plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)))) - exp(1i*(angle(data.fourierspctrm(:,electrode_2,:,:))))))),1))); I doubt that PLV computed through FT is wrong, but then I am circumspect since the first formula is somewhat no correct and give the same results a as ft_connectivityanalysis. I went to FT code and got confused by the way ft_connectivity_corr use the cross spectrum to compute PLV. I would greatly appreciate if someone could tell me where I am missing/misunderstanding something. Thanks you for your help, Manuel ________________________________ Manuel Mercier, PhD Research Fellow Cognitive Neurophysiology Laboratory, Children’s Evaluation and Rehabilitation Center (CERC), Departments of Pediatrics and Neuroscience Albert Einstein College of Medicine, 1225 Morris Park Avenue Bronx , NY 10461 phone: +1 (718) 862 1859 fax: +1 (718) 862 1807 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manuel Mercier [manuel.mercier at einstein.yu.edu] Sent: Friday, June 28, 2013 4:43 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] PLV formula Dear Fieldtripers Sometime ago I wrote for myself a function that was computing PLV and some related non parametric statistics. (Phase Locking Value as define as the mean across trials of the phase angle difference recorded at two loci ; based on Lachaux et al., 1999, HBM). I implemented PLV in matlab using the following formula: plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)) ... -angle(data.fourierspctrm(:,cmb(2),:,:)))),1))); with cmb(1) and cmb(2) being the indices of the electrodes of interest (between which PLV is computed). I compared my results with the ft_connectivityanalysis function from Fieldtrip and the results were exactly the same. So far so good. But I recently went back to my code, and I was a little bit confused. Since I was dealing with angles, I though that the best way to do the subtraction should be done in the complex plane Like: plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)))) ... - exp(1i*(angle(data.fourierspctrm(:,cmb(2),:,:))))))),1))); (for instance if the two angles: pi/2 and -pi/2 the direct subtraction will give pi, whereas in the complex plan it will be pi/2 - with the norm x2). The result I got with this code is obviously different from the previous one, and what I got from Fieldtrip. I went back to the archive of the mailing list but didn't find a clear answer to my point. Does anyone can enlighten me ? Thanks ! Manuel -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Tue Jul 9 00:45:37 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Tue, 9 Jul 2013 00:45:37 +0200 Subject: [FieldTrip] sEEG Source Imaging - mne solution Message-ID: Dear FieldTrip comunity, i'm dealing with MNE source reconstruction of sEEG signals. I would like to know if it is possible to use the mesh of the source-model, obtained by MNE_Suite, as the 'brain' mesh (the inner ) of the head model prepared with ft_prepare_headmodel with the 'dipoli' method, solving the forward problem. I've tried to make this step to get a more accurate inverse solution but my results seemed completely wrong and totally different by the ones obtained using a 'traditional' head model built with ft_prepare:headmodel in the 'dipoli' case. Thanks for your attention, Alberto Ghione -------------- next part -------------- An HTML attachment was scrubbed... URL: From robince at gmail.com Tue Jul 9 18:14:40 2013 From: robince at gmail.com (Robin) Date: Tue, 9 Jul 2013 17:14:40 +0100 Subject: [FieldTrip] obtaining voxel locations Message-ID: I was wondering how to get the voxel positions (or origin and voxel size) for a fieltrip mri structure. I have an anatomical scan which I have normalised to the T1 brain: >> mrin mrin = anatomy: [181x217x181 double] transform: [4x4 double] dim: [181 217 181] params: [1x1 struct] initial: [4x4 double] coordsys: 'spm' cfg: [1x1 struct] I can I obtain the location of any voxel in MNI coordinates (mm or cm)? When loading a Nifti file (with load_nii) I can find origin and voxel_size with: voxel_size = abs(nii.hdr.dime.pixdim(2:4)); % vol in mm origin = round(abs(nii.hdr.hist.originator(1:3))); and then posmm = (vox-origin) .* voxel_size. Is there any way to do the same from the fieldtrip structure? I can't find the corresponding header information. Thanks Robin -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.backus at donders.ru.nl Tue Jul 9 18:46:40 2013 From: a.backus at donders.ru.nl (Alexander Backus) Date: Tue, 9 Jul 2013 18:46:40 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields In-Reply-To: References: Message-ID: Thanks for your answer Haiteng. To share our findings on this topic: After some more debugging, we realized that it could indeed be the ICA function that inserts NaNs into the grad info. It seems ft_denoise_synthetic only changes the grad info for some reference channels... We now use Haiteng's trick of replacing the post-ICA grad info, with the post-denoise grad info, however, it feels somewhat dangerous to perform such "dirty" fixes, since that grad info is probably removed for a certain reason. We are oblivious to its impact subsequent steps like planar transform and source reconstruction. In addition, we dug up the following page on the FieldTrip wiki which explains the denoising. http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work Thanks! Cheers, Alexander On Sun, Jul 7, 2013 at 8:17 PM, Haiteng Jiang wrote: > Hi Alexander, > I am not clear about what's ft_denoise_synthetic doing. However , I > don't have such problem when I use . The reason you get > 'mismatching number of channels' probably because you specify cfg.channel > ='MEG' instead of including all channels. My FT code is something like > this: > > % reading > cfg = []; > cfg.dataset = dataset; > cfg.trialdef.eventtype = ''; > cfg.trialdef.eventvalue = ; > cfg.continuous = 'yes'; > cfg.channel= 'all'; > cfg.trialdef.prestim = ; > cfg.trialdef.poststim = ; > cfg = ft_definetrial(cfg); > trl = cfg.trl; > cfg.detrend ='yes'; > cfg.demean = 'yes'; > data= ft_preprocessing(cfg); > cfg.gradient = 'G3BR'; > data= ft_denoise_synthetic(cfg,data); > > In my pipeline , the grad changes into NAN only after I run I ICA to > remove artifacts . I replace this grad with previous good gradient > information and assume it is fine for the latter source reconstruction. > Hope this helps. > Best, > Haiteng > > >> >> >> Message: 2 >> Date: Fri, 5 Jul 2013 09:38:55 +0200 >> From: Alexander Backus >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in >> grad fields >> Message-ID: >> < >> CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi, >> >> When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to >> covert to 3rd order gradient, it replaces the values in data.grad.chanpos >> and data.grad.chanori with NaNs. >> >> I assume this is done because they are no longer valid. >> When digging into the low-level code I found something about mismatching >> number of channels. >> >> Anyway, when I want to subsequently covert to planar gradient (does this >> actually makes sense?) or create a source model, I need these grad values. >> >> I have two questions: >> >> 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why >> are NaNs inserted in the grad subfields? >> >> 2) Can I still use the data for planar gradient conversion or source >> modeling by using the earlier stored old gradient info (pre >> ft_denoise_synthetic) or is this ill-advised and is there a more wise >> course of action? >> >> Thanks in advance, >> Best, >> Alexander Backus >> > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Alexander R. Backus, MSc PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Memory and Space Research Group www.doellerlab.com P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands Telephone: +31(0)24 36 10754 -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:12:01 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:42:01 +0430 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields In-Reply-To: References: Message-ID: *Hello,** * I am mohsen alimoradi, MSc student of artificial intelligence in Qazvin Azad University. * **I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot* On Tue, Jul 9, 2013 at 9:16 PM, Alexander Backus wrote: > Thanks for your answer Haiteng. > > To share our findings on this topic: > > After some more debugging, we realized that it could indeed be the ICA > function that inserts NaNs into the grad info. > > It seems ft_denoise_synthetic only changes the grad info for some > reference channels... > > We now use Haiteng's trick of replacing the post-ICA grad info, with the > post-denoise grad info, however, it feels somewhat dangerous to perform > such "dirty" fixes, since that grad info is probably removed for a certain > reason. We are oblivious to its impact subsequent steps like planar > transform and source reconstruction. > > In addition, we dug up the following page on the FieldTrip wiki which > explains the denoising. > > http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work > > Thanks! > > Cheers, > Alexander > > > On Sun, Jul 7, 2013 at 8:17 PM, Haiteng Jiang wrote: > >> Hi Alexander, >> I am not clear about what's ft_denoise_synthetic doing. However , >> I don't have such problem when I use . The reason you get >> 'mismatching number of channels' probably because you specify cfg.channel >> ='MEG' instead of including all channels. My FT code is something like >> this: >> >> % reading >> cfg = []; >> cfg.dataset = dataset; >> cfg.trialdef.eventtype = ''; >> cfg.trialdef.eventvalue = ; >> cfg.continuous = 'yes'; >> cfg.channel= 'all'; >> cfg.trialdef.prestim = ; >> cfg.trialdef.poststim = ; >> cfg = ft_definetrial(cfg); >> trl = cfg.trl; >> cfg.detrend ='yes'; >> cfg.demean = 'yes'; >> data= ft_preprocessing(cfg); >> cfg.gradient = 'G3BR'; >> data= ft_denoise_synthetic(cfg,data); >> >> In my pipeline , the grad changes into NAN only after I run I ICA to >> remove artifacts . I replace this grad with previous good gradient >> information and assume it is fine for the latter source reconstruction. >> Hope this helps. >> Best, >> Haiteng >> >> >>> >>> >>> Message: 2 >>> Date: Fri, 5 Jul 2013 09:38:55 +0200 >>> From: Alexander Backus >>> To: fieldtrip at science.ru.nl >>> Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in >>> grad fields >>> Message-ID: >>> < >>> CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> >>> Hi, >>> >>> When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to >>> covert to 3rd order gradient, it replaces the values in data.grad.chanpos >>> and data.grad.chanori with NaNs. >>> >>> I assume this is done because they are no longer valid. >>> When digging into the low-level code I found something about mismatching >>> number of channels. >>> >>> Anyway, when I want to subsequently covert to planar gradient (does this >>> actually makes sense?) or create a source model, I need these grad >>> values. >>> >>> I have two questions: >>> >>> 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why >>> are NaNs inserted in the grad subfields? >>> >>> 2) Can I still use the data for planar gradient conversion or source >>> modeling by using the earlier stored old gradient info (pre >>> ft_denoise_synthetic) or is this ill-advised and is there a more wise >>> course of action? >>> >>> Thanks in advance, >>> Best, >>> Alexander Backus >>> >> >> >> >> -- >> Haiteng Jiang >> PhD candidate >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> >> Visiting address >> Room 2.32 >> Donders Centre for Cognitive Neuroimaging >> Kapittelweg 29 >> 6525 EN Nijmegen >> the Netherlands >> >> Tel.: +31 (0)243668291 >> Web: https://sites.google.com/site/haitengjiang/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Alexander R. Backus, MSc > PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Memory and Space Research Group > www.doellerlab.com > > P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands > Telephone: +31(0)24 36 10754 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:12:17 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:42:17 +0430 Subject: [FieldTrip] obtaining voxel locations In-Reply-To: References: Message-ID: *Hello,** * I am mohsen alimoradi, MSc student of artificial intelligence in Qazvin Azad University. * **I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot * On Tue, Jul 9, 2013 at 8:44 PM, Robin wrote: > I was wondering how to get the voxel positions (or origin and voxel size) > for a fieltrip mri structure. > > I have an anatomical scan which I have normalised to the T1 brain: > > >> mrin > > mrin = > > anatomy: [181x217x181 double] > transform: [4x4 double] > dim: [181 217 181] > params: [1x1 struct] > initial: [4x4 double] > coordsys: 'spm' > cfg: [1x1 struct] > > I can I obtain the location of any voxel in MNI coordinates (mm or cm)? > When loading a Nifti file (with load_nii) I can find origin and voxel_size > with: > > voxel_size = abs(nii.hdr.dime.pixdim(2:4)); % vol in mm > origin = round(abs(nii.hdr.hist.originator(1:3))); > > and then posmm = (vox-origin) .* voxel_size. Is there any way to do the > same from the fieldtrip structure? I can't find the corresponding header > information. > > Thanks > > Robin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:14:01 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:44:01 +0430 Subject: [FieldTrip] (no subject) Message-ID: *Hello,** * ***I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot* -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Thu Jul 11 17:09:40 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Thu, 11 Jul 2013 17:09:40 +0200 Subject: [FieldTrip] ft_megrealign how to avoid? Message-ID: Dear all, I have CTF MEG data and I am interested in a gamma band topographies. We recorded two sessions for every subject. Now I would like to compare grand averages of these two sessions over all subjects(n=13). Without realignment these grand average topographies look ok and according to our expectation. However, I know that it would be reasonable to do realignment of all datasets (n=13x2) to common template. I have tried that with ft_megrealign which uses method suggested by Knösche, 2002 and this doesn't work. It gives me very weird results, meaning that topographies are totally changed and some new occipital activity emerges. I have plotted single subject head models(singleshell) together with sensors and they are accurately aligned. Then I tried different inwardshift options for ft_megrealign and this didn't bring so much success. So my question is, could I go without the realignment and what I need to do in order to overcome problem with realignment? -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Thu Jul 11 17:58:54 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 11 Jul 2013 17:58:54 +0200 (CEST) Subject: [FieldTrip] ft_megrealign how to avoid? In-Reply-To: Message-ID: <1783486843.2033915.1373558334245.JavaMail.root@sculptor.zimbra.ru.nl> Hi Nenad, You may want to check whether there are systematic differences (over the whole group of subjects) in head position in the first place. Here's an example page showing how to check head position/movement in MEG: http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis The same page also indicates how to 'regress out' variance accounted for by (different) head position. Applying this method on the datasets combined (trials of the two conditions for each subject) allows you to eliminate head position as a potential confound (by using ft_regressconfound prior to computing subject-level statistics). I have no first hand experience on to what extent megrealign can reduce the effects of different head position between two conditions, but from our experiences here we know that systematic differences in head position between conditions may even be noticeable at the source level. Optimally, one thus tries to minimize the influence of head movement wherever possible, i.e. already at recording. This may come in too late for your current dataset, but this online 'realignment' method may improve between- but also within-session consistency in future studies of yours involving the CTF MEG system (a Neuromag version is being developed): http://fieldtrip.fcdonders.nl/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session Hope these documentation pages may be of any help, Arjen ----- Oorspronkelijk bericht ----- > Van: "Nenad Polomac" > Aan: fieldtrip at science.ru.nl > Verzonden: Donderdag 11 juli 2013 17:09:40 > Onderwerp: [FieldTrip] ft_megrealign how to avoid? > Dear all, > I have CTF MEG data and I am interested in a gamma band topographies. > We recorded two sessions for every subject. Now I would like to > compare grand averages of these two sessions over all subjects(n=13). > Without realignment these grand average topographies look ok and > according to our expectation. However, I know that it would be > reasonable to do realignment of all datasets (n=13x2) to common > template. I have tried that with ft_megrealign which uses method > suggested by Knösche, 2002 and this doesn't work. It gives me very > weird results, meaning that topographies are totally changed and some > new occipital activity emerges. I have plotted single subject head > models(singleshell) together with sensors and they are accurately > aligned. Then I tried different inwardshift options for ft_megrealign > and this didn't bring so much success. So my question is, could I go > without the realignment and what I need to do in order to overcome > problem with realignment? > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Jul 11 18:18:33 2013 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 11 Jul 2013 18:18:33 +0200 Subject: [FieldTrip] Fwd: 17-18 October, 2013: NatMEG inauguration conference at Karolinska Institutet, Stockholm. In-Reply-To: References: Message-ID: Dear FieldTrippers, We are very happy to announce the inauguration conference for NatMEG, the brand-new National Swedish MEG facility. Please find the invitation attached. Have a great summer, Stephen -------------- next part -------------- A non-text attachment was scrubbed... Name: Invitation to NatMEG inauguration conference.pdf Type: application/pdf Size: 228355 bytes Desc: not available URL: From ali.b.sharif at gmail.com Thu Jul 11 19:30:19 2013 From: ali.b.sharif at gmail.com (Ali Bahramisharif) Date: Thu, 11 Jul 2013 19:30:19 +0200 Subject: [FieldTrip] Fwd: 17-18 October, 2013: NatMEG inauguration conference at Karolinska Institutet, Stockholm. In-Reply-To: References: Message-ID: In the list of speakers, I see Stephen's name among the heads. Great! Ali On Thu, Jul 11, 2013 at 6:18 PM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear FieldTrippers, > > We are very happy to announce the inauguration conference for NatMEG, > the brand-new National Swedish MEG facility. Please find the > invitation attached. > > Have a great summer, > > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamid.mohseni at eng.ox.ac.uk Fri Jul 12 15:25:29 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Fri, 12 Jul 2013 14:25:29 +0100 Subject: [FieldTrip] baseline correction Message-ID: Dear All, I am trying to do baseline correction using a specified window, e.g,: cfg.demean = 'yes'; cfg.baselinewindow = [-0.5 0]; but it seems to me fieldtrip always performs demaen in respect to the whole time window and ignores cfg.baselinewindow. I am wondering if it is a bug or I am missing something? -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Fri Jul 12 15:43:35 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Fri, 12 Jul 2013 15:43:35 +0200 Subject: [FieldTrip] ft_megrealign how to avoid? Message-ID: Dear Arjen, Thank you very much for you answer! I forgot to mention that I applied ft_megrealign on averaged single subject data since we are interested in evoked auditory early gamma response. I am familiar with the online and offline methods for removing variance which comes from head movement. These are very useful tolls. I've tested ft_regresconfound before and it worked fine. However, it will not be very helpful in this case. Because if I apply ft_regresconfound as you suggested than I will loose gradiometers information and than ft_megrealign will not work. Furthermore my evoked gamma grand average topographies (TFR of planar and axial gradiometers) look now as expected without any transformation(ft_regresconfound or ft_megrealign). So what I need is some objective evidence that condition difference is due to experiment rather than different head positions. :) Thank you and all the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 12 20:48:53 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 12 Jul 2013 11:48:53 -0700 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: I think you want the cfg.blc option. Demean will indeed remove the mean, as advertised! cfg.blc = ... cfg.blcwindow = [...] In general, however, I would advise against any baseline correction, unless you have a blocked design and have no choice. Best, Aaron On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni wrote: > Dear All, > > I am trying to do baseline correction using a specified window, e.g,: > > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > > but it seems to me fieldtrip always performs demaen in respect to the whole > time window and ignores cfg.baselinewindow. > > I am wondering if it is a bug or I am missing something? > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From hamid.mohseni at eng.ox.ac.uk Fri Jul 12 22:12:43 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Fri, 12 Jul 2013 21:12:43 +0100 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: Thanks for your answer, but I think they are the same. On Friday, 12 July 2013, Aaron Schurger wrote: > I think you want the cfg.blc option. Demean will indeed remove the > mean, as advertised! > cfg.blc = ... > cfg.blcwindow = [...] > > In general, however, I would advise against any baseline correction, > unless you have a blocked design and have no choice. > > Best, > Aaron > > On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni > > wrote: > > Dear All, > > > > I am trying to do baseline correction using a specified window, e.g,: > > > > cfg.demean = 'yes'; > > cfg.baselinewindow = [-0.5 0]; > > > > but it seems to me fieldtrip always performs demaen in respect to the > whole > > time window and ignores cfg.baselinewindow. > > > > I am wondering if it is a bug or I am missing something? > > > > -- > > Hamid R. Mohseni, PhD > > Post-Doctoral Research Assistant > > Institute of Biomedical Engineering > > University of Oxford, OX3 7DQ, UK > > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Fri Jul 12 23:05:01 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Fri, 12 Jul 2013 23:05:01 +0200 (CEST) Subject: [FieldTrip] ft_megrealign how to avoid? In-Reply-To: Message-ID: <1979422110.2049419.1373663101977.JavaMail.root@sculptor.zimbra.ru.nl> Dear Nenad, You're welcome of course. You're right that after head movement compensation using ft_regressconfound, the sensor level data ideally is not used anymore for source modeling (see http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis -> bottom page, for why this is problematic), i.e. as is required for ft_megrealign. Optimally, ft_regressconfound is therefore used as a last step just prior to ft_XXXstatistics, whether at the sensor level (after ft_megrealign) or at the source level. To address your objective, i.e. showing that a difference is due to the experimental manipulation and not due to different head positions; using ft_regressconfound on trials of, say, condition A and B combined will remove any trial-by-trial signal variance that is due to different head positions from the mean head position of condition A and B. In other words, if a systematic difference observed between condition A and B is caused by systematically different head position between condition A and B, this difference will be removed by ft_regressconfound. If not, the difference may not be caused by different head position, and you have good indication to exclude head position as a potential confound. Yours, Arjen ----- Oorspronkelijk bericht ----- > Van: "Nenad Polomac" > Aan: fieldtrip at science.ru.nl > Verzonden: Vrijdag 12 juli 2013 15:43:35 > Onderwerp: Re: [FieldTrip] ft_megrealign how to avoid? > Dear Arjen, > Thank you very much for you answer! I forgot to mention that I applied > ft_megrealign on averaged single subject data since we are interested > in evoked auditory early gamma response. I am familiar with the online > and offline methods for removing variance which comes from head > movement. These are very useful tolls. I've tested ft_regresconfound > before and it worked fine. However, it will not be very helpful in > this case. Because if I apply ft_regresconfound as you suggested than > I will loose gradiometers information and than ft_megrealign will not > work. Furthermore my evoked gamma grand average topographies (TFR of > planar and axial gradiometers) look now as expected without any > transformation(ft_regresconfound or ft_megrealign). So what I need is > some objective evidence that condition difference is due to experiment > rather than different head positions. :) > Thank you and all the best! > Nenad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stidimitriadis at gmail.com Sat Jul 13 11:08:39 2013 From: stidimitriadis at gmail.com (Stavros Dimitriadis) Date: Sat, 13 Jul 2013 12:08:39 +0300 Subject: [FieldTrip] 3D spline interpolation Message-ID: Dear all I am trying to do 3D spline interpolation of a MEG dataset based on axial gradiometer according to the following methodological paper ! Bastiaansena & Thomas R. KnoÈsche."Tangential derivative mapping of axial MEG applied to event-related desynchronization research' Clinical Neurophysiology 111 (2000) 1300±1305. Is there any function in fieldtrip that do this kind of transformation ? Best Dimitriadis Stavros , PhD http://users.auth.gr/~stdimitr/index.html http://neuroinformatics.gr/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Sat Jul 13 11:48:04 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Sat, 13 Jul 2013 11:48:04 +0200 Subject: [FieldTrip] 3D spline interpolation Message-ID: Dear Stavros, You should have look on this http://fieldtrip.fcdonders.nl/tutorial/eventrelatedaveraging#calculate_the_planar_gradient. That is an explanation how to perform it on ERF data. And here you can find pipeline for time freq analysis. http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#procedure The ft_megplanar and ft_combineplanar together transform axial to planar gradients. Have look in the functions help as well. The paper you mentioned is cited here in the Fildtrip documentation. All the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Sun Jul 14 22:19:16 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Mon, 15 Jul 2013 00:49:16 +0430 Subject: [FieldTrip] Fwd: (no subject) In-Reply-To: References: Message-ID: Dear fieldtripers I'm going to use Fieldstrip toolbox for removing noise. but I confronted with a small problem. I was wondering if you could tell me how I could use “.mat” format in Fieldtrip's toolbox. In this regard, I want to ask you FieldTrip, if it is possible for you guide me as soon as possible. I am looking forward to hearing from you. Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Sun Jul 14 22:21:09 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Mon, 15 Jul 2013 00:51:09 +0430 Subject: [FieldTrip] How .mat format used in FieldTrip toolbox Message-ID: Dear fieldtripers I'm going to use Fieldstrip toolbox for removing noise. but I confronted with a small problem. I was wondering if you could tell me how I could use “.mat” format in Fieldtrip's toolbox. In this regard, I want to ask you FieldTrip, if it is possible for you guide me as soon as possible. I am looking forward to hearing from you. Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 15 10:15:14 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 15 Jul 2013 10:15:14 +0200 Subject: [FieldTrip] Fwd: Announcement of Donders Discussions 2013 In-Reply-To: <449335090.2248168.1373799535995.JavaMail.root@indus.zimbra.ru.nl> References: <449335090.2248168.1373799535995.JavaMail.root@indus.zimbra.ru.nl> Message-ID: See below; apologies for multiple postings. ---------- Forwarded message ---------- From: Vogel, S. (Susanne) Date: 14 July 2013 12:58 Subject: Announcement of Donders Discussions 2013 To: fieldtrip-owner at science.ru.nl Dear fieltrip list owner, We are happy to announce the Donders Discussions 2013 and we would be happy if you could distribute this announcement to the fieldrip list or other interested PhD students. With best regards, Susanne ---- Dear PhD student, We are pleased to announce the Donders Discussions 2013: a two-day conference for PhD students in all fields of (cognitive) neuroscience which will take place on October 31st and November 1st in Nijmegen, The Netherlands. The aim of the Donders Discussions is to bring PhD students together in an informal, interdisciplinary atmosphere. Last year we welcomed over 150 participants from all over Europe. We invite you to join us and make this year’s edition an even bigger success! Our exciting program features brains of many kinds, including baby brains, sleeping, stressed and disordered brains, linguistic, attentive and aging brains, and of course investigated brains (where we review methodological innovations). We also offer interactive workshops on science communication and career management. For more information and registration please visit www.ru.nl/dondersdiscussions. We warmly invite all participants to submit a poster abstract. Registration will open on July 15, the deadline is September 16, but registration may close earlier if the maximum number of participants has been reached. The registration fee is €45. If you have any questions, don’t hesitate to e-mail us on discussions2013 at donders.ru.nl. For the latest updates and special offers, join us on facebook (facebook.com/dondersdiscussions2013) or twitter (discussions2013). We look forward to seeing you in Nijmegen! The Donders Discussions committee 2013 From jan.schoffelen at donders.ru.nl Mon Jul 15 10:43:07 2013 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 15 Jul 2013 10:43:07 +0200 Subject: [FieldTrip] ft_connectivityanalysis and PLV formula In-Reply-To: References: Message-ID: Hi Manuel, The first formula is correct, the second isn't. Hint: when working with the complex representation in the second formula you should use a multiplication, rather than a subtraction, and take the negative angle for the second signal. In other words exp(1i.*angle(x)) .* exp(-1i.*angle(y)). This is the same as: exp(1i.*(angle(x)-angle(y))). Hope this helps, Jan-Mathijs On Jul 8, 2013, at 3:32 PM, Manuel Mercier wrote: > Dear Fieldtrip Community > I am still stuck with the implementation of PLV. To be sure that I understand properly the principle of Phase Locking Value, I wrote a code to compute it. That code (see below) gave me the same results as ft_connectivityanalysis. > plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)) -angle(data.fourierspctrm(:,electrode_2,:,:)))),1))); > (data.fourierspctrm being produced by ft_freqanalysis). > > However, I then realized that the subtraction between the two angles should be done in the complex plane as in: > plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)))) - exp(1i*(angle(data.fourierspctrm(:,electrode_2,:,:))))))),1))); > > I doubt that PLV computed through FT is wrong, but then I am circumspect since the first formula is somewhat no correct and give the same results a as ft_connectivityanalysis. > I went to FT code and got confused by the way ft_connectivity_corr use the cross spectrum to compute PLV. > I would greatly appreciate if someone could tell me where I am missing/misunderstanding something. > Thanks you for your help, > > Manuel > > > > Manuel Mercier, PhD > Research Fellow > > Cognitive Neurophysiology Laboratory, > Children’s Evaluation and Rehabilitation Center (CERC), > Departments of Pediatrics and Neuroscience > Albert Einstein College of Medicine, > 1225 Morris Park Avenue > Bronx , NY 10461 > > phone: +1 (718) 862 1859 > fax: +1 (718) 862 1807 > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manuel Mercier [manuel.mercier at einstein.yu.edu] > Sent: Friday, June 28, 2013 4:43 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] PLV formula > > Dear Fieldtripers > Sometime ago I wrote for myself a function that was computing PLV and some related non parametric statistics. > (Phase Locking Value as define as the mean across trials of the phase angle difference recorded at two loci ; based on Lachaux et al., 1999, HBM). > I implemented PLV in matlab using the following formula: > plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)) ... > -angle(data.fourierspctrm(:,cmb(2),:,:)))),1))); > with cmb(1) and cmb(2) being the indices of the electrodes of interest (between which PLV is computed). > I compared my results with the ft_connectivityanalysis function from Fieldtrip and the results were exactly the same. > So far so good. > > But I recently went back to my code, and I was a little bit confused. > Since I was dealing with angles, I though that the best way to do the subtraction should be done in the complex plane > Like: > plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)))) ... > - exp(1i*(angle(data.fourierspctrm(:,cmb(2),:,:))))))),1))); > (for instance if the two angles: pi/2 and -pi/2 the direct subtraction will give pi, > whereas in the complex plan it will be pi/2 - with the norm x2). > > The result I got with this code is obviously different from the previous one, and what I got from Fieldtrip. > I went back to the archive of the mailing list but didn't find a clear answer to my point. Does anyone can enlighten me ? > Thanks ! > > Manuel > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 15 10:51:32 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 15 Jul 2013 10:51:32 +0200 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: <51E3B814.5060000@donders.ru.nl> Dear Hamid, I guess your problem is precisely this one: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2220 Will be fixed asap :) Best, Jörn On 7/12/2013 10:12 PM, Hamid Mohseni wrote: > Thanks for your answer, but I think they are the same. > > On Friday, 12 July 2013, Aaron Schurger wrote: > > I think you want the cfg.blc option. Demean will indeed remove the > mean, as advertised! > cfg.blc = ... > cfg.blcwindow = [...] > > In general, however, I would advise against any baseline correction, > unless you have a blocked design and have no choice. > > Best, > Aaron > > On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni > > wrote: > > Dear All, > > > > I am trying to do baseline correction using a specified window, > e.g,: > > > > cfg.demean = 'yes'; > > cfg.baselinewindow = [-0.5 0]; > > > > but it seems to me fieldtrip always performs demaen in respect > to the whole > > time window and ignores cfg.baselinewindow. > > > > I am wondering if it is a bug or I am missing something? > > > > -- > > Hamid R. Mohseni, PhD > > Post-Doctoral Research Assistant > > Institute of Biomedical Engineering > > University of Oxford, OX3 7DQ, UK > > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamid.mohseni at eng.ox.ac.uk Mon Jul 15 11:16:14 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Mon, 15 Jul 2013 10:16:14 +0100 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: great, thanks. On 15 July 2013 09:51, "Jörn M. Horschig" wrote: > Dear Hamid, > > I guess your problem is precisely this one: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2220 > Will be fixed asap :) > > Best, > Jörn > > > On 7/12/2013 10:12 PM, Hamid Mohseni wrote: > > Thanks for your answer, but I think they are the same. > > On Friday, 12 July 2013, Aaron Schurger wrote: > >> I think you want the cfg.blc option. Demean will indeed remove the >> mean, as advertised! >> cfg.blc = ... >> cfg.blcwindow = [...] >> >> In general, however, I would advise against any baseline correction, >> unless you have a blocked design and have no choice. >> >> Best, >> Aaron >> >> On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni >> wrote: >> > Dear All, >> > >> > I am trying to do baseline correction using a specified window, e.g,: >> > >> > cfg.demean = 'yes'; >> > cfg.baselinewindow = [-0.5 0]; >> > >> > but it seems to me fieldtrip always performs demaen in respect to the >> whole >> > time window and ignores cfg.baselinewindow. >> > >> > I am wondering if it is a bug or I am missing something? >> > >> > -- >> > Hamid R. Mohseni, PhD >> > Post-Doctoral Research Assistant >> > Institute of Biomedical Engineering >> > University of Oxford, OX3 7DQ, UK >> > Tel: +44 (0) 1865 2 83826 >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Aaron Schurger, PhD >> Post-doctoral researcher >> INSERM U992 / NeuroSpin >> CEA - Saclay, France >> +33-1-69-08-66-47 >> aaron.schurger at gmail.com >> http://www.unicog.org >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmontefusco at med.uchile.cl Mon Jul 15 16:04:32 2013 From: rmontefusco at med.uchile.cl (Rodrigo Montefusco) Date: Mon, 15 Jul 2013 10:04:32 -0400 Subject: [FieldTrip] Fwd: (no subject) In-Reply-To: References: Message-ID: Hi Mohsen Can you provide more details? Which is your particular question? Your help sounds a little bit general. Best Y On Sun, Jul 14, 2013 at 4:19 PM, Mohsen moradi wrote: > Dear fieldtripers > > I'm going to use Fieldstrip toolbox for removing noise. but I confronted > with a small problem. > I was wondering if you could tell me how I could use “.mat” format in > Fieldtrip's toolbox. > In this regard, I want to ask you FieldTrip, if it is possible for you > guide me as soon as possible. > I am looking forward to hearing from you. > > Best Regards > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Tue Jul 16 14:11:06 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Tue, 16 Jul 2013 13:11:06 +0100 Subject: [FieldTrip] 2D surface spline interpolation Message-ID: Dear all, I am working on spatiotemporal mapping of 2D and 3D EEG data. I want to develop the method of surface interpolation, what is the function in FieldTrip that develops this interpolation method. I hope you will send me positive and helpful response. Thanks a lot in advance! Best, ahmed -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Jul 16 14:54:19 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 16 Jul 2013 14:54:19 +0200 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: Message-ID: <51E5427B.2020103@donders.ru.nl> Dear Ahmed, there are several functions making use of (spline) interpolation, e.g. ft_channelrepair for reconstructing time-courses of missing or bad channels, or ft_scalpcurrentdensity for spatial filtering of data. Also ft_megrealign is doing some interpolation magic, but I don't know what method that function is using. In case you are interested in low-level functions, they are in FieldTrip/private, called splint.m and sphericalSplineInterpolate.m (afaik both doing essentially the same, just different implementations of the same method). Best, Jörn On 7/16/2013 2:11 PM, ingenieur eniso wrote: > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the > function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > > Thanks a lot in advance! > > Best, > > ahmed > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jul 16 14:55:05 2013 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 16 Jul 2013 14:55:05 +0200 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: Message-ID: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Hi Ahmed, For the visualization of sensor topographies, fieldtrip relies on the 'griddata' function from matlab. You can type 'doc griddata' on the matlab command line for more information. Note that this is not a function that is specific to fieldtrip. For actual interpolation of data, FieldTrip has a ft_channelrepair function, which implements (among others) a spherical spline interpolation. Best wishes, Jan-Mathijs On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > Thanks a lot in advance! > Best, > ahmed > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jakob.wischniowski at uni-ulm.de Wed Jul 17 02:27:18 2013 From: jakob.wischniowski at uni-ulm.de (Jakob) Date: Wed, 17 Jul 2013 02:27:18 +0200 Subject: [FieldTrip] rejectvisual/summary on Mac OS X In-Reply-To: References: <51C85906.2090204@uni-konstanz.de> Message-ID: <79A73D01-FB88-41A6-A12C-70D742C68F74@uni-ulm.de> Dear all, I'm running Matlab 2013a on an Apple OSX 10.8.4 (Mountain Lion) machine. While performing the rejectvisual/summary function, dragging the mouse over the channels won't work: The "selecting box" for dragging simply won't appear while holding down the left mouse button/trackpad button. I was wondering if anyone is experiencing the same problem? Best regards! Jakob From Sara.Bogels at mpi.nl Wed Jul 17 12:30:01 2013 From: Sara.Bogels at mpi.nl (=?ISO-8859-1?Q?Sara_B=F6gels?=) Date: Wed, 17 Jul 2013 12:30:01 +0200 Subject: [FieldTrip] problem with ft_multiplotER In-Reply-To: References: Message-ID: <51E67229.8040001@mpi.nl> Hi all, I have a very specific problem with the ft_multiplotER function. For 2 of my 24 participants, the function gives an error-message when I try to plot the averages of two conditions at the same time. Plotting them one by one is not a problem. There appears to be a specific point in time (different for the two participants) when this goes wrong. If I avoid that time (by using cfg.xlim) it works fine. My trials have different lengths and I used "cfg.vartrllength = 2;" when calling ft_timelockanalysis (not sure whether this is relevant). The error message I get is "Error in ft_multiplotER (line 616) yval(i,:) = datamatrix{i}(m,:);" I cannot find out what happens in this line. Can anyone tell me what this might be referring to? Thank you, Sara From jm.horschig at donders.ru.nl Wed Jul 17 13:44:15 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 17 Jul 2013 13:44:15 +0200 Subject: [FieldTrip] problem with ft_multiplotER In-Reply-To: <51E67229.8040001@mpi.nl> References: <51E67229.8040001@mpi.nl> Message-ID: <51E6838F.3050302@donders.ru.nl> Dear Sara, What you describe sounds like a bug to me. It looks like that in these lines the averages of the two conditions should be concatenated into one matrix, and apparently something goes wrong. However, you truncated the error message a bit (you pasted the line where the error occurs, but not the error message itself). If one of us developers should look into this further, it would be great if you register and create a bugreport on bugzilla.fconders.nl. Preferably would be to upload a snippet of your data, e.g. timelockstructures of one participant, and some lines of code which reproduce the error. We can then look into this further and fix this as soon as possible :) Best, Jörn On 7/17/2013 12:30 PM, Sara Bögels wrote: > Hi all, > > I have a very specific problem with the ft_multiplotER function. For 2 > of my 24 participants, the function gives an error-message when I try > to plot the averages of two conditions at the same time. Plotting them > one by one is not a problem. There appears to be a specific point in > time (different for the two participants) when this goes wrong. If I > avoid that time (by using cfg.xlim) it works fine. My trials have > different lengths and I used "cfg.vartrllength = 2;" when calling > ft_timelockanalysis (not sure whether this is relevant). > > The error message I get is > "Error in ft_multiplotER (line 616) > yval(i,:) = datamatrix{i}(m,:);" > > I cannot find out what happens in this line. Can anyone tell me what > this might be referring to? > > Thank you, > Sara > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From christophe.grova at mcgill.ca Wed Jul 17 16:11:58 2013 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Wed, 17 Jul 2013 10:11:58 -0400 Subject: [FieldTrip] Postdoctoral Position Available et the Montreal Neurological Institute In-Reply-To: Message-ID: Postdoctoral Position Available et the Montreal Neurological Institute Multimodal Functional Imaging Laboratory, Biomedical Engineering Dpt, Montreal Neurological Institute, McGill University, Montreal, Canada The candidate will join a multidisciplinary team composed of neurologists and methodologists within the Multimodal Functional Imaging Laboratory and in close collaboration with the epilepsy group of the Montreal Neurological Institute. A brief description of the project can be found below. The main role of the candidate will be to recruit patients, to assist data acquisition and to identify epileptic events on recorded signals. (S)he will be trained to contribute to data acquisition and to use dedicated source localization and data fusion techniques developed locally. Initial appointment is for 1 year, with possibility of renewal up to 3 years. Project: Multimodal investigation of epileptic activity using simultaneous EEG/MEG and EEG/NIRS acquisitions. The proposed project aims at localizing and characterizing the generators of epileptic activity using simultaneous acquisitions of ElectroEncephaloGraphy (EEG) with Magneto-EncephaloGraphy (MEG), as well as simultaneous acquisitions of EEG with Near Infra-Red Spectroscopy (NIRS). ElectroEncephaloGraphy (EEG) and Magneto-EncephaloGraphy (MEG) are respectively measuring on the scalp electric and magnetic fields generated by neuronal activity at a millisecond scale, providing a detailed description of brain activity using 275 MEG sensors and 56 EEG electrodes. Combined with EEG measuring brain electric activity on the scalp, NIRS allows studying hemodynamic processes at the time of spontaneous epileptic activity. The specificity of NIRS data is its ability to measure local changes oxy-hemoglobin (HbO) and deoxy-hemoglobin (HbR), exploiting absorption properties of infrared light within brain tissue using optic fibers placed on the surface of the head (temporal resolution: 10 ms, 16 sources x 32 detectors, penetration: 2-3 cm from the surface of the head). The candidate will be trained to use the first Brainsight NIRS device developped by Rogue-Research Inc, with which we were able to record promising preliminary data. While methodological developpments in the lab will consist in 3D reconstruction of the generators of EEG, MEG and NIRS signals and assessing multimodal concordances between bioelectrical neuronal signals and hemodynamic processes, the purpose of this Postdoctoral project will be to assess the integrity of neurovascular coupling processes at the time of epileptic discharges, using a unique multimodal environment involving EEG/MEG, EEG/NIRS and also EEG/fMRI recordings. Close collaborations with the epilepsy group of the Montreal Neurological Institute, involving notably Dr E. Kobayashi MD-PhD, Dr F. Dubeau MD-PhD and Dr. J. Gotman PhD, will provide access to patient populations and additional clinical expertise for this project. Requirements: The candidate should be an MD (neurologist) with previous training in epileptology and neurophysiology (EEG). Expertise in analyzing MEG or NIRS signals and/or computational skills including neuroimaging softwares are appreciated additional qualification. The candidate should be fluent in English (and if possible French) due to the patient population studied. Supervisor: Christophe Grova Ph.D. Assistant Professor, Biomedical Engineering Assistant Professor, Neurology & Neurosurgery Director of the Multimodal Functional Imaging Laboratory Email: christophe.grova at mcgill.ca Multi FunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage Please send your CV, a motivation letter and reference letters to christophe.grova at mcgill.ca *************************** Christophe Grova, PhD Assistant Professor Biomedical Engineering Dpt Neurology and Neurosurgery Dpt Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute Centre de Recherches en Mathématiques Biomedical Engineering Department - Room 304 McGill University 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 email : christophe.grova at mcgill.ca tel : (514) 398 2516 fax : (514) 398 7461 web: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe http://www.bmed.mcgill.ca/ MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Wed Jul 17 17:16:14 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Wed, 17 Jul 2013 17:16:14 +0200 Subject: [FieldTrip] Error in Beamforming analysis due to units? Message-ID: Dear all, I'm having a hard time understanding my beamforming analysis/results. I set up the analysis pipeline as described in the tutorial(s). First, I create my template grid as shown below: ---------------------- % Step 1: CREATE A TEMPLATE template = ft_read_mri([TemplateDir 'T1.nii']); template.coordsys = 'spm'; % Step 2: Segment the template brain and construct a volume conduction % model (i.e. head model): this is needed for the inside/outside detection of voxels cfg = []; template_seg = ft_volumesegment(cfg,template); cfg = []; cfg.method = 'singleshell'; template_vol = ft_prepare_headmodel(cfg,template_seg); template_vol = ft_convert_units(template_vol,'cm'); % Step 3: Construct the dipole grid in the template brain coordinates. % The source units are in cm cfg = []; cfg.grid.xgrid = -20:1:20; cfg.grid.ygrid = -20:1:20; cfg.grid.zgrid = -10:1:20; cfg.unit = 'cm'; cfg.grid.tight = 'yes'; cfg.inwardshift = -1.5; % negative inwardshift leads to an outwardshift of the brain's surface cfg.reducerank = 'no'; cfg.vol = template_vol; template_grid = ft_prepare_sourcemodel(cfg); % Step 4: Make a figure with the template head model and dipole grid figure hold on; ft_plot_vol(template_vol,'facecolor','cortex','edgecolor','none'); alpha 0.5; camlight; ft_plot_mesh(template_grid.pos(template_grid.inside,:)); ---------------------- Some of my colleagues also add another step where they convert the template grid units from 'cm' to 'mm' since MNI space is in 'mm'. Since this is not mentioned in the tutorial, I skipped that step. In the next steps for creating the single subject's grid and headmodel I follow exactly the steps described in the tutorial to create single subject grids in MNI space. When I check the segmentation everything looks fine. I then of course use this grid to calculate the sources, also as described in the tutorial. At the end I put the template grid position fields onto the subject's baseline normalized source (sourceDiff_tem). ----------------------------------------------------- for k = 1:length(cond) cfg = []; eval(['cfg.frequency = freqAll.Cond_',num2str(cond(k)),'.freq;']); cfg.method = 'dics'; cfg.grid = grid; % Here it gives .pos, .inside, .outside to the structure cfg.vol = vol; cfg.dim = grid.dim; eval(['cfg.grad = Cond_',num2str(cond(k)),'.hdr.grad;']); cfg.lambda = '5%'; cfg.reducerank = 'no'; cfg.projectnoise = 'yes'; cfg.realfilter = 'yes'; cfg.keepfilter = 'yes'; % the output saves the computed inverse filter eval(['sourceAll.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqAll.Cond_',num2str(cond(k)),');']) % use the pre-calculated common filter here eval(['cfg.grid.filter = sourceAll.Cond_',num2str(cond(k)),'.avg.filter;']); eval(['sourcePre.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqPre.Cond_',num2str(cond(k)),');']) eval(['sourcePost.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqPost.Cond_',num2str(cond(k)),');']) % compute the contrast of (post-pre)/pre (normalization of the power with the baseline activity) eval(['sourceDiff.Cond_',num2str(cond(k)),' = sourcePost.Cond_',num2str(cond(k)),';']) eval(['sourceDiff.Cond_',num2str(cond(k)),'.avg.pow = (sourcePost.Cond_',num2str(cond(k)),'.avg.pow-sourcePre.Cond_',num2str(cond(k)),'.avg.pow) ./ sourcePre.Cond_',num2str(cond(k)),'.avg.pow;']); % put the template grid positions (x,y,z & pos) into the source structure eval(['sourceDiff_tem.Cond_',num2str(cond(k)),' = sourceDiff.Cond_',num2str(cond(k)),';']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.pos = template_grid.pos;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.xgrid = template_grid.xgrid;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.ygrid = template_grid.ygrid;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.zgrid = template_grid.zgrid;']); end ----------------------------------------------------- If I then look at the data of this sourceDiff_tem, i.e. of condition 1, plotted on a surface file, it looks a bit strange to me (see Fig1). Also, I am not able to plot this data with cfg.method 'slice'. I get the error that the dimensions do not match. pos: [5780x3 double] dim: [17 20 17] avg: [1x1 struct] var: [1x1 struct] dimord: 'voxel' inside: [2985x1 double] outside: [2795x1 double] df: [5780x1 double] cfg: [1x1 struct] I then tried it the 'old' way and took the Diff_Source of each subject, interpolated this to the subject's anatomy and normalized it. With that I get a result that makes more sense to me (Fig2). However, also with this I am not able to plot it with cfg.method 'slice'. Actually, the slices I can only use for plotting the stats. So I guess that something is wrong here and that I have an error somewhere in my script. However, I really can't find it. Our guess is that it has something to do with the units and the conversion(s) from one space to the other. I went through all the tutorials again and again but I can't see the mistake. I am stuck and therefore would really appreciate any help on that matter! Thanks a lot! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig1.png Type: image/png Size: 295434 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig2.png Type: image/png Size: 291696 bytes Desc: not available URL: From mushfa.yousuf at googlemail.com Wed Jul 17 17:50:27 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Wed, 17 Jul 2013 17:50:27 +0200 Subject: [FieldTrip] Load Error Message-ID: Hello; I have a preprocessed data structure in the fieldtrip which I want to load in SPM for the 3D source reconstruction. this data Structute includes * fsample * label * trial * time * grad * elec I have converted this data structure to spm format using function spm_eeg_ft2spm. But when I try to load the converted file to SPM, it gives me the following error The requested file is not ready for source reconstruction. See matlab window for details on matlab following message appears checkmeeg: no sensor positions are defined. Please help me out to troubleshoot this problem. Any help will be appreciated. Regards; Mushfa Yousuf -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Jul 17 17:55:54 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 17 Jul 2013 17:55:54 +0200 Subject: [FieldTrip] Load Error In-Reply-To: References: Message-ID: <51E6BE8A.2000804@donders.ru.nl> Hi Mushfa, hm, you provided elec and grad information, do you indeed have combined EEG/MEG data? Maybe SPM does not like that - I know that FieldTrip would not like that ;) - so you could try with either of them and see whether that works. Best, Jörn On 7/17/2013 5:50 PM, Mushfa Yousuf wrote: > Hello; > > I have a preprocessed data structure in the fieldtrip which I want to > load in SPM for the 3D source reconstruction. > > this data Structute includes > > * fsample > * label > * trial > * time > * grad > * elec > > I have converted this data structure to spm format using function > spm_eeg_ft2spm. > > But when I try to load the converted file to SPM, it gives me the > following error > > The requested file is not ready for source reconstruction. See matlab > window for details > > on matlab following message appears > > checkmeeg: no sensor positions are defined. > > > Please help me out to troubleshoot this problem. Any help will be > appreciated. > > Regards; > > Mushfa Yousuf > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Wed Jul 17 18:00:46 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Wed, 17 Jul 2013 18:00:46 +0200 Subject: [FieldTrip] Load Error In-Reply-To: <51E6BE8A.2000804@donders.ru.nl> References: <51E6BE8A.2000804@donders.ru.nl> Message-ID: Hello Jörn; I also tried without elec and grad in the structure but it doesn't help me out. Regards, Mushfa Yousuf On Wed, Jul 17, 2013 at 5:55 PM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Hi Mushfa, > > hm, you provided elec and grad information, do you indeed have combined > EEG/MEG data? Maybe SPM does not like that - I know that FieldTrip would > not like that ;) - so you could try with either of them and see whether > that works. > > Best, > Jörn > > > On 7/17/2013 5:50 PM, Mushfa Yousuf wrote: > > Hello; > > I have a preprocessed data structure in the fieldtrip which I want to > load in SPM for the 3D source reconstruction. > > this data Structute includes > > * fsample > * label > * trial > * time > * grad > * elec > > I have converted this data structure to spm format using function > spm_eeg_ft2spm. > > But when I try to load the converted file to SPM, it gives me the > following error > > The requested file is not ready for source reconstruction. See matlab > window for details > > on matlab following message appears > > checkmeeg: no sensor positions are defined. > > > Please help me out to troubleshoot this problem. Any help will be > appreciated. > > Regards; > > Mushfa Yousuf > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From antony.passaro at gmail.com Wed Jul 17 19:08:41 2013 From: antony.passaro at gmail.com (Antony Passaro) Date: Wed, 17 Jul 2013 13:08:41 -0400 Subject: [FieldTrip] Error using indepsamplesZcoh with cluster statistics Message-ID: Hi all, I'm having an issue running freqstatistics using the indepsamplesZcoh and a cluster correction. The indepsamplesZcoh portion seems to run just fine but I get an error when I try to perform the cluster statistics. The first issue is error1: The error describes a dimension mismatch at line 297 of ft_statistics_montecarlo: statrand(:,:,i) = getfield(dum, 'stat'); Apparently the output (dum) from indepsamplesZcoh collapses my 100 frequencies and 100 timepoints into 10000 points (nchancmb/2 x 10000) but the dimensions of statrand are nchancmb/2 x 100 x Nrand which obviously creates a dimension mismatch. I can get past that part if I set avgovertime = 'yes' which takes me to error 2: "To RESHAPE the number of elements must not change" refers to line 202 in clusterstat.m, posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); Here, cfg.dim is nchan x 100 freq x 1 (avgtime) which obviously doesn't match postailobs dimensions of nchancmb/2 x 100. I thought perhaps the ndepsamplesZcoh function is not supposed to be used in conjunction with the cluster statistics but the Maris 2007 paper appears to use the two together. Any help with this would be much appreciated. Below is the code that that I'm using: cfg = []; %cfg.avgovertime = 'yes'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'parametric'; cfg.minnbchan = 2; cfg.correcttail = 'alpha'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesZcoh'; cfg.parameter = 'fourierspctrm'; cfg.computecritval = 'yes'; cfg.neighbours = neighbours; cfg.numrandomization = 99; cfg.alpha = 0.05; cfg.tail = 0; design = ones(1, 90); design(91:180)=2; cfg.design = design; cfg.label = freqL.label; stat = ft_freqstatistics(cfg, freqL,freqR); Thanks, -Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From Natalia.Egorova at mrc-cbu.cam.ac.uk Wed Jul 17 19:11:24 2013 From: Natalia.Egorova at mrc-cbu.cam.ac.uk (Natalia Egorova) Date: Wed, 17 Jul 2013 17:11:24 +0000 Subject: [FieldTrip] neuromag - sources Message-ID: Hi, I have a question. When doing source reconstruction in the frequency domain with DICS I got a bit confused using neuromag data. Since there are both gradiometer and magnetometer sensors, which sensors are used for source reconstruction by default (if the .grad contains all 360)? Is it possible to use all MEG data, or should MEGGRAD and MEGMAG-based sources be calculated separately? Thanks in advance, Nataila -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Wed Jul 17 20:03:49 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Wed, 17 Jul 2013 19:03:49 +0100 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> References: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Message-ID: Hi Jörn and jan-mathijs, thank you very much for help. All the best Ahmed 2013/7/16 jan-mathijs schoffelen > Hi Ahmed, > > For the visualization of sensor topographies, fieldtrip relies on the > 'griddata' function from matlab. You can type 'doc griddata' on the matlab > command line for more information. Note that this is not a function that is > specific to fieldtrip. > > For actual interpolation of data, FieldTrip has a ft_channelrepair > function, which implements (among others) a spherical spline interpolation. > > > Best wishes, > Jan-Mathijs > > On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: > > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the > function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > > Thanks a lot in advance! > > Best, > > ahmed > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Thu Jul 18 12:10:00 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Thu, 18 Jul 2013 12:10:00 +0200 Subject: [FieldTrip] Error in Beamforming analysis due to units? Problem solved! Message-ID: Dear all, I just solved the problem with the beamforming analysis. So please ignore my previous mail on that! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Thu Jul 18 17:02:34 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Thu, 18 Jul 2013 16:02:34 +0100 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Message-ID: Hi , I use the splint.m function to implement the spherical spline interpolation. But an error is occured: ??? Error using ==> rdivide Matrix dimensions must agree. Error in ==> splint at 58 elc1 = elc1 ./ repmat(sqrt(sum(elc1.^2,2)), 1, 3); Error in ==> eeg_interp_sph_spline_test at 50 [V2, L2, L1] = splint(elc1, V, elc2) I have written following program in Matlab elc1=[x y z]'; elc2=[0.430 0.050 -0.010]'; [V2, L2, L1] = splint(elc1, V, elc2) with [x y z]=[-0.0176 0.0907 0.0071 0.0024 0.0924 0.0076 0.0284 0.0879 0.0075 -0.0085 0.0903 0.0190 0.0153 0.0895 0.0189 -0.0391 0.0836 0.0089 -0.0156 0.0868 0.0286 0.0299 0.0823 0.0305 0.0559 0.0735 0.0080 -0.0329 0.0805 0.0321 -0.0043 0.0789 0.0485 0.0155 0.0785 0.0468 0.0462 0.0726 0.0344 -0.0618 0.0683 0.0105 -0.0509 0.0719 0.0289 -0.0418 0.0694 0.0451 -0.0200 0.0725 0.0542 0.0040 0.0690 0.0618 0.0332 0.0657 0.0563 0.0507 0.0593 0.0501 0.0674 0.0552 0.0315 0.0770 0.0510 0.0080 -0.0651 0.0617 0.0234 -0.0560 0.0608 0.0420 -0.0406 0.0598 0.0580 -0.0080 0.0579 0.0720 0.0196 0.0538 0.0729 0.0444 0.0515 0.0631 0.0678 0.0422 0.0471 0.0803 0.0412 0.0213 -0.0738 0.0546 -0.0128 -0.0782 0.0496 0.0047 -0.0692 0.0506 0.0353 -0.0518 0.0466 0.0611 -0.0288 0.0444 0.0761 0.0018 0.0412 0.0830 0.0296 0.0370 0.0797 0.0582 0.0294 0.0659 0.0799 0.0258 0.0392 0.0902 0.0207 0.0049 0.0842 0.0364 -0.0135 -0.0831 0.0366 0.0188 -0.0709 0.0332 0.0497 -0.0493 0.0303 0.0724 -0.0187 0.0239 0.0876 0.0157 0.0212 0.0889 0.0488 0.0165 0.0771 0.0758 0.0093 0.0526 0.0905 0.0016 0.0200 -0.0846 0.0327 -0.0191 -0.0914 0.0153 -0.0017 -0.0851 0.0124 0.0345 -0.0648 0.0150 0.0646 -0.0401 0.0047 0.0834 0.0295 -0.0054 0.0877 0.0596 -0.0112 0.0701 0.0821 -0.0158 0.0400 0.0916 -0.0140 0.0023 0.0909 0.0050 -0.0172 -0.0913 -0.0021 0.0158 -0.0805 -0.0014 0.0459 -0.0562 -0.0090 0.0732 -0.0215 -0.0170 0.0885 0.0119 -0.0205 0.0896 0.0468 -0.0289 0.0746 0.0717 -0.0317 0.0494 0.0852 -0.0321 0.0173 -0.0856 -0.0313 -0.0167 -0.0906 -0.0195 -0.0002 -0.0861 -0.0199 0.0279 -0.0681 -0.0230 0.0585 -0.0375 -0.0303 0.0791 -0.0029 -0.0388 0.0841 0.0277 -0.0432 0.0772 0.0560 -0.0450 0.0586 0.0738 -0.0459 0.0322 0.0801 -0.0466 0.0005 0.0692 -0.0591 -0.0177 -0.0828 -0.0397 0.0127 -0.0751 -0.0381 0.0389 -0.0556 -0.0426 0.0607 -0.0218 -0.0555 0.0709 0.0119 -0.0587 0.0707 0.0402 -0.0598 0.0583 0.0588 -0.0606 0.0383 0.0698 -0.0602 0.0099 -0.0681 -0.0592 -0.0211 -0.0770 -0.0512 -0.0056 -0.0725 -0.0542 0.0200 -0.0626 -0.0544 0.0415 -0.0372 -0.0663 0.0531 -0.0075 -0.0692 0.0613 0.0157 -0.0732 0.0547 0.0438 -0.0705 0.0413 0.0567 -0.0703 0.0209 0.0630 -0.0678 -0.0043 0.0545 -0.0723 -0.0201 -0.0558 -0.0683 0.0284 -0.0226 -0.0794 0.0421 0.0036 -0.0823 0.0425 0.0386 -0.0810 0.0235 -0.0654 -0.0655 0.0051 -0.0452 -0.0802 0.0113 -0.0322 -0.0824 0.0276 -0.0078 -0.0884 0.0267 0.0175 -0.0876 0.0247 0.0282 -0.0877 0.0104 0.0510 -0.0772 0.0057 -0.0193 -0.0900 0.0110 0.0060 -0.0919 0.0105 -0.0556 -0.0736 -0.0089 -0.0287 -0.0879 -0.0060 -0.0054 -0.0924 -0.0056 0.0148 -0.0913 -0.0057 0.0422 -0.0820 -0.0095 -0.0168 -0.0899 -0.0149 0.0059 -0.0913 -0.0151 -0.0258 -0.0854 -0.0253 -0.0063 -0.0889 -0.0255 0.0142 -0.0880 -0.0254 -0.0398 0.0828 -0.0126 -0.0116 0.0913 -0.0111 0.0115 0.0914 -0.0103 0.0378 0.0841 -0.0101] V = [3.3540 1.9345 0.5927 2.6217 1.3858 5.1010 3.2264 0.3127 -1.2031 4.8916 2.2626 0.7324 -0.8725 8.8664 7.1630 5.9588 3.6880 1.7445 -0.4065 -1.4554 -2.5648 -2.8607 9.7859 8.1602 5.9181 2.3645 0.3716 -1.0117 -2.4332 -3.0173 9.7933 11.8346 10.4268 7.4601 4.5098 1.8013 -0.3755 -1.7671 -2.9153 -3.5252 -3.2862 13.3333 10.0548 6.8787 3.4798 0.8774 -0.9168 -2.3297 -3.1422 11.8833 13.2409 11.6124 8.3419 4.8045 0.6147 -0.8466 -2.0623 -2.8388 -3.2469 12.1843 9.6097 6.2738 3.3943 1.4797 0.0743 -1.2483 -2.0240 8.5136 10.3840 9.7096 7.3371 4.4194 2.6834 1.0785 -0.2747 -1.3383 -1.4970 -0.4476 8.3757 7.6361 5.7288 3.4908 1.8043 0.7450 -0.1646 -0.7976 6.1441 7.2345 7.0914 6.2035 4.1770 2.5408 1.8116 0.3820 -0.1287 -0.4707 0.2793 5.3026 3.5360 2.1660 0.7409 6.1342 4.4963 3.6572 2.5199 1.7607 1.3430 0.4600 3.2784 2.1011 5.2801 3.5401 2.6195 2.0038 0.7776 3.1047 2.2821 3.3528 2.6710 1.9100 5.1250 2.9475 1.6662 0.1915] I haven't found a solution though. So, what is wrong? Thanks a lot in advance! Best, ahmed 2013/7/17 ingenieur eniso > Hi Jörn and jan-mathijs, > > > thank you very much for help. > > All the best > Ahmed > > > 2013/7/16 jan-mathijs schoffelen > >> Hi Ahmed, >> >> For the visualization of sensor topographies, fieldtrip relies on the >> 'griddata' function from matlab. You can type 'doc griddata' on the matlab >> command line for more information. Note that this is not a function that is >> specific to fieldtrip. >> >> For actual interpolation of data, FieldTrip has a ft_channelrepair >> function, which implements (among others) a spherical spline interpolation. >> >> >> Best wishes, >> Jan-Mathijs >> >> On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: >> >> Dear all, >> I am working on spatiotemporal mapping of 2D and 3D EEG data. >> I want to develop the method of surface interpolation, what is the >> function in FieldTrip that develops this interpolation method. >> >> I hope you will send me positive and helpful response. >> >> Thanks a lot in advance! >> >> Best, >> >> ahmed >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> http://www.hettaligebrein.nl >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Thu Jul 18 17:23:43 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Thu, 18 Jul 2013 17:23:43 +0200 Subject: [FieldTrip] MNE source imaging - EEG Message-ID: Dear Fieldtrippers, I would like to know if it is possible to use a detailed downsampled mesh from FreeSurfer tassellation ( representing also the gyrus and the sulcus) as the 'brain' mesh in the method 'dipoli' in BEM computation (having supposed the three layers: 'scalp', 'skull' and 'brain'). I've tried to do this but vol.mat gained really high values (10^8) which led to really high values of the leadfield matrix. Thanks, Alberto Ghione University of Genoa -------------- next part -------------- An HTML attachment was scrubbed... URL: From virginie.van.wassenhove at gmail.com Thu Jul 18 20:21:49 2013 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Thu, 18 Jul 2013 20:21:49 +0200 Subject: [FieldTrip] Postdoctoral position available at Neurospin, France Message-ID: Dear all, please see below or here ( https://sites.google.com/site/virginievanwassenhove/opportunities) for a fellowship openings at NeuroSpin MEG, France! *-------**-------**-------**-------**-------**-------**-------**-------* *Postdoctoral Fellowship - *please, put *POSTDOC* in the email subject. *-------**-------**-------**-------**-------**-------**-------**-------* Due to a postdoctoral fellow having found a permanent position, we have a new opening in the group! Applications are invited from a talented, dynamic, committed, and enthusiastic researcher. The ideal applicant will have a sound experience in the analysis of MEG and/or EEG data and a strong record and research interest in cognitive neurosciences. The selected postdoctoral fellow will lead MEG studies as part of the ERC funded project “Mind Time”. A set of studies will specifically aim at using classifiers and decoding techniques with MEG data. The researcher will be expected to work closely with and supervise (master, phd) students involved in the project. Some involvement in organizational and managerial aspects specific to these projects can be expected. *Requirements:* - should hold a PhD in cognitive neurosciences, neurosciences, psychology, and/or related fields - a strong record of published work - prior experience with MEG/EEG techniques - sound signal processing skills - sound programming skills (matlab, python) Applicants from outside the European Union are welcome but must qualify for a valid visa. French speaking is not a requirement as long as the English language is mastered. * * *Starting date*: asap *Salary*: commensurate with experience. The position will be initially funded for one year (renewable for an additional 2 years).** * * *Application package* *CV* (incl. a list of publications) *Two letters of recommendation* (or contacts from which those could be obtained) *A letter of intent with a statement of research interests* *Applications will be considered until the position is filled.* * * *-------**-------**-------**-------**-------**-------**-------**-------* *Master students - p*lease, put *GRAD *in the email subject *-------**-------**-------**-------**-------**-------**-------**-------* Applications are invited from ambitious and talented students at the level of Master. The ideal applicants will have some lab experience in working with Human participants, and will be familiarized with one or several non-invasive neuroimaging techniques and/or electrophysiology. The applicant will be versed in cognitive neurosciences and demonstrate excellent scholarship. The selected candidate will show a strong academic record and interests in pursuing a PhD in cognitive neurosciences. *Requirements for the candidates:* - master level in cognitive neurosciences, neurosciences, psychology, and/or related fields - a strong academic record - some experience/familiarization with neuroimaging techniques or electrophysiology - fair understanding of signal processing - good programming skills and willingness to improve (matlab, python) Applicants from outside the European Union are welcome but they must qualify for a valid visa. French speaking is not a requirement as long as the English language is mastered. * * *Starting date*: asap and negotiable. *Application package* - *CV* - *A letter of motivation with a statement of research interests* - *Two letters of recommendation* (or contacts from which those could be obtained)*-* . Best wishes, Virginie -- Virginie van Wassenhove Exec Dir NeuroSpin MEG Group leader, Brain Dynamics CEA.DSV.I2BM.NeuroSpin - INSERM Cognitive Neuroimaging Unit Bât 145 Point Courrier 156 Gif s/ Yvette F-91191 FRANCE +33(0)1.69.08.1667 Virginie.van.Wassenhove at gmail.com https://sites.google.com/site/virginievanwassenhove/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From lei.niu at einstein.yu.edu Thu Jul 18 21:52:13 2013 From: lei.niu at einstein.yu.edu (Lei Niu) Date: Thu, 18 Jul 2013 19:52:13 +0000 Subject: [FieldTrip] question about to get the numbers of rejected trials Message-ID: Dear Fieldtrippers, I am new one to use the fieldtrip, and have a question about the rejected trials. To be simply, let we say: 1) the original data is data_org, one singal trial in 32 channel, with 2 different trigger codes and 100 trials per trigger. 2) I process the data to the data_stimulus, incuding 200 trials. Each trial has prestim = 0.1, poststim = 1; 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I get data_reject, including 190 trials. Here is the problem. I found the prestim is too short, I want to increase the prestim time to 0.5. How can I get the numbers of rejected 10 trials to do ft_redefinetrial? Thanks, Lei Niu Albert Einstein College of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From kyle.hird at gmail.com Fri Jul 19 00:24:48 2013 From: kyle.hird at gmail.com (Kyle Hird) Date: Thu, 18 Jul 2013 18:24:48 -0400 Subject: [FieldTrip] Peer module thinks it has too little memory Message-ID: Hi I am attempting to set up the distributed peer system on a 32-bit Linux machine, using version 20130419 from the ftp server (I'm using the shipped binaries because peerslave segfaults on receiving a job if compiled on my system). My tests involve one local slave and one local master on this four-core machine with 4GB of memory. After starting the slave peer, I attempt to run the example command peercellfun(@rand, {10, 20, 30}, 'UniformOutput', false). This fails with the message: 'there are no slave peers available that meet the memory requirements' Examining the output of the slave peer, it contains the following lines (edited for personal info): executing job 1 from myusername at HOSTNAME (jobid=672774519, memreq=2147483648, timreq=3600) executing job took 0.042167 seconds and 22957802788233216 bytes executing job 2 from myusername at HOSTNAME (jobid=1862053136, memreq=2147483648, timreq=3600) executing job took 0.001907 seconds and 22957802787971072 bytes While the times seem reasonable for such a simple problem, the memory usage does not (nearly 23,000 terabytes). The memory usage is reported by fexec, which in turn calculates it from the output of memprofile. Memprofile itself appears to discover resident and virtual size from getmem. I looked at the source for getmem and it appears that it should return -1 in my case (because the elif block for PLATFORM_LINUX is empty), causing memprofile_sample to report zeros for both. However, if I invoke memprofile_sample by using memprofile('info') at the command line, I get: ans = time: 1.3742e+09 mem: 3.6693e+18 I wonder exactly what is happening when getmem gets called. I'm not too experienced with C, but from my understanding the #if statement is evaluated at compile time, so getmem will behave according to the platform on which it was compiled, which may be different from that on which it is executed. As written, the function won't compile on my system due to the absence of . I can't actually find the binary mex getmem in the module, so although the source has mexFunction framework in it, I can't call it from MATLAB. What behaviour should I be getting from memprofile? Should I be doing something differently to get peercellfun to behave correctly? Thanks for your consideration Kyle Hird From samarakm at mail.uc.edu Fri Jul 19 02:24:32 2013 From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm)) Date: Fri, 19 Jul 2013 00:24:32 +0000 Subject: [FieldTrip] Using ft_sourceplot to visualize simulated dipoles Message-ID: <158540F0F1AD27479479077742EA83C5215B90A5@BY2PRD0111MB511.prod.exchangelabs.com> Hello, I am a rookie to fieldtrip, and I have a pretty basic question. I am trying to visually see what a dipole/s would look like after using the function ft_dipolesimulation(cfg). Can I use ft_sourceplot to do this. (I know the BESA_Dipole Simulator gives a nice visual description of the dipoles). My primary objective is to visually compare a simulated dipole/s with its reconstructed counterpart. The reconstruction can be done using any of the source analysis methods. I would really appreciate if anyone could assist me with this problem. Thank you, Kasun Samarasinghe -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Fri Jul 19 11:40:01 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Fri, 19 Jul 2013 11:40:01 +0200 Subject: [FieldTrip] 'ft_prepare_layout' Error Message-ID: Hello ; I am receiving the following error while using ft_prepare_layout ??? Index exceeds matrix dimensions. Error in ==> ft_prepare_layout>sens2lay at 788 mindist = mindist(1:round(numel(label)/4)); Error in ==> ft_prepare_layout at 285 lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, cfg.style); Error in ==> spm_eeg_project3D at 27 lay = ft_prepare_layout(cfg); Notice that I am using MEG channels and the above function perfectly works when I used the EEG channel. For me itt seems like there is any problem with my '.grad' structure ? Kindly please help me to toubleshoot this problem. Regards; Mushfa Yousuf -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Fri Jul 19 12:34:37 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Fri, 19 Jul 2013 12:34:37 +0200 Subject: [FieldTrip] 'ft_prepare_layout' Error In-Reply-To: References: Message-ID: hello ; or it has something to do with layout ? because this msg appears after this line *creating layout for neuromag306 system* * * ??? Index exceeds matrix dimensions. Error in ==> ft_prepare_layout>sens2lay at 788 mindist = mindist(1:round(numel(label)/4)); Error in ==> ft_prepare_layout at 285 lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, cfg.style); Error in ==> spm_eeg_project3D at 27 lay = ft_prepare_layout(cfg); Regards; Mushfa Yousuf On Fri, Jul 19, 2013 at 11:40 AM, Mushfa Yousuf < mushfa.yousuf at googlemail.com> wrote: > Hello ; > > I am receiving the following error while using ft_prepare_layout > > > ??? Index exceeds matrix dimensions. > > Error in ==> ft_prepare_layout>sens2lay at 788 > mindist = mindist(1:round(numel(label)/4)); > > Error in ==> ft_prepare_layout at 285 > lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, > cfg.style); > > Error in ==> spm_eeg_project3D at 27 > lay = ft_prepare_layout(cfg); > > Notice that I am using MEG channels and the above function perfectly works > when I used the EEG channel. > > For me itt seems like there is any problem with my '.grad' structure ? > > > > Kindly please help me to toubleshoot this problem. > > > Regards; > > Mushfa Yousuf > -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Sat Jul 20 21:45:44 2013 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Sat, 20 Jul 2013 21:45:44 +0200 Subject: [FieldTrip] question about to get the numbers of rejected trials In-Reply-To: References: Message-ID: Dear Lei, I think that you are asking that you want to run the steps again, with prestim =0.5 but with rejecting the same 10 trials that you already have decided to reject? If so, the numbers of rejected trials should be inside data_reject.cfg (or possibly data_reject.cfg.previous). But note that by including more prestim time, you might also find a need to reject more trials if there is an artifact in the new included prestim time-points. If you use ft_redefinetrial, I think you only would shift where the time 0.0 is, but not add more data to each trial, so it depends which you want to do. Best regards, Johanna 2013/7/18 Lei Niu > Dear Fieldtrippers, > > I am new one to use the fieldtrip, and have a question about the rejected > trials. > To be simply, let we say: > 1) the original data is data_org, one singal trial in 32 channel, with 2 > different trigger codes and 100 trials per trigger. > 2) I process the data to the data_stimulus, incuding 200 trials. Each > trial has prestim = 0.1, > poststim = 1; > 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I > get data_reject, including 190 trials. > > Here is the problem. I found the prestim is too short, I want to increase > the prestim time to 0.5. How can I get the numbers of rejected 10 trials to > do ft_redefinetrial? > > Thanks, > Lei Niu > Albert Einstein College of Medicine > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Mon Jul 22 10:35:50 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Mon, 22 Jul 2013 10:35:50 +0200 Subject: [FieldTrip] Source time series signals Message-ID: Dear Fieldtrippers, I performed the source reconstruction using the MNE method; i would like to ask what type of signal is 'source.avg.pow', is it correct to assume that it is the time series related to a specific source? Thanks for your attention, Alberto Ghione University of Genoa -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Mon Jul 22 10:56:30 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Mon, 22 Jul 2013 10:56:30 +0200 Subject: [FieldTrip] Fieldtrip to SPM Message-ID: Dear all, I would like to convert my MEG CTF data analysed with Fieldtrip into the SPM format in order to do dynamic causal modeling. I am familiar with explanations from the spm manual and spm_eeg_ft2spm function. Is there any more detailed source of information about this? To make more concrete I have successfully converted my data but it seems something is missing from the structure which explains MEG header information. Thank you in advance! Nenad Polomac -------------- next part -------------- An HTML attachment was scrubbed... URL: From Johanna.Fiess at uni-konstanz.de Mon Jul 22 14:40:47 2013 From: Johanna.Fiess at uni-konstanz.de (=?iso-8859-1?Q?Johanna_Fie=DF?=) Date: Mon, 22 Jul 2013 14:40:47 +0200 Subject: [FieldTrip] different frequency bins Message-ID: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Dear all, whenever I try to compute the statistics for (MEG) time-frequency data, this error message comes up: computing statistic over the frequency range [8.000 11.000] computing statistic over the time range [0.300 1.100] Error using ft_appendfreq (line 250) the input data structures have non-unique frequency bins, concatenation across frequency is not possible Error in ft_appendfreq (line 139) freq = ft_appendfreq(tmpcfg, varargin{:}); Error in ft_freqstatistics (line 231) data = ft_appendfreq(cfg, varargin{:}); Out of 35 participants in total, (only) three show slightly different frequency bins (starting point 2.0001 instead of 1.9998) – if I remove them from the average, the error message disappears. If renaming the freq-structure of those three participants, the error message disappears, too. Could anyone tell me what causes this problem or how I should handle it? Thanks a lot in advance! Johanna PS: I'm running Matlab R2012b & fieldtrip-20130515 %% stats design=[1:10,1:10; ones(1,10),ones(1,10)*2]; cfg = []; cfg.frequency = [8 11]; cfg.latency = [.3 1.1]; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clustertail = 0; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.numrandomization = 500; cfg.alpha = 0.05; cfg.avgoverfreq = 'yes'; % cfg.avgovertime = 'yes'; cfg.design = design; cfg.neighbours = neighbours; cfg.ivar = 2; stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); cfg = []; cfg.alpha = 0.3; cfg.parameter = 'stat'; cfg.zlim = [-3 2]; cfg.layout = '4D148.lay'; ft_clusterplot(cfg, stat); -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 22 14:50:16 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 22 Jul 2013 14:50:16 +0200 Subject: [FieldTrip] different frequency bins In-Reply-To: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> References: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Message-ID: <51ED2A88.60304@donders.ru.nl> Dear Johanna, the problem is that the trial length you put into freqanalysis differed across subjects, leading to a different frequency resolution across participants. FieldTrip realizes that and errors because 1.9998 is not 2.0001 ;) I would propose you re-do the frequencyanalysis with the same time window/trial length for all participants. Maybe you should first check why your trials have different lengths and if that is desired or you did another mistake somewhere in your analysis. If you want to different trial lengths, you can use a padding cfg option in ft_freqanalysis to pad trials to a fixed length. Good luck ;) Best, Jörn On 7/22/2013 2:40 PM, Johanna Fieß wrote: > Dear all, > > whenever I try to compute the statistics for (MEG) time-frequency > data, this error message comes up: > > computing statistic over the frequency range [8.000 11.000] > computing statistic over the time range [0.300 1.100] > Error using ft_appendfreq (line 250) > the input data structures have non-unique frequency bins, > concatenation across frequency is not possible > > Error in ft_appendfreq (line 139) > freq = ft_appendfreq(tmpcfg, varargin{:}); > > Error in ft_freqstatistics (line 231) > data = ft_appendfreq(cfg, varargin{:}); > > Out of 35 participants in total, (only) three show slightly different > frequency bins (starting point 2.0001 instead of 1.9998) -- if I > remove them from the average, the error message disappears. > If renaming the freq-structure of those three participants, the error > message disappears, too. > > Could anyone tell me what causes this problem or how I should handle it? > > Thanks a lot in advance! > > Johanna > > > PS: I'm running Matlab R2012b & fieldtrip-20130515 > %% stats > design=[1:10,1:10; ones(1,10),ones(1,10)*2]; > > cfg = []; > cfg.frequency = [8 11]; > cfg.latency = [.3 1.1]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clustertail =0; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.numrandomization = 500; > cfg.alpha = 0.05; > > cfg.avgoverfreq = 'yes'; > % cfg.avgovertime = 'yes'; > cfg.design = design; > cfg.neighbours = neighbours; > cfg.ivar = 2; > > > stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); > cfg = []; > cfg.alpha = 0.3; > cfg.parameter = 'stat'; > cfg.zlim = [-3 2]; > cfg.layout = '4D148.lay'; > ft_clusterplot(cfg, stat); > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 22 14:53:27 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 22 Jul 2013 14:53:27 +0200 Subject: [FieldTrip] Source time series signals In-Reply-To: References: Message-ID: <51ED2B47.5000408@donders.ru.nl> Dear Alberto, the abbreviation stands for *pow*er of the *av*era*g*e across your observation(s) of the *source*-reconstructed data :) If I am not mistaken, there should be a .mom field (if you set cfg.keepmom = 'yes') which contains the time-resolved data rather than the power. Best, Jörn On 7/22/2013 10:35 AM, Alberto Ghione wrote: > Dear Fieldtrippers, > I performed the source reconstruction using the MNE method; i would > like to ask what type of signal is 'source.avg.pow', > is it correct to assume that it is the time series related to a > specific source? > > Thanks for your attention, > Alberto Ghione > University of Genoa > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 22 15:00:39 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 22 Jul 2013 15:00:39 +0200 Subject: [FieldTrip] different frequency bins In-Reply-To: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> References: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Message-ID: Dear Johanna, The slight differences in frequency bins was probably caused by a slightly different trial length for some of your participants. When doing frequency analysis, the frequency resolution is determined by the length of your data. (You can have a look at e.g. this FAQ entry: http://fieldtrip.fcdonders.nl/faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean for more information.) You mention that the differences in frequency bins are very small. In your case, therefore, I would solve (or 'patch' ;) ) the problem by simply doing something like: participantB.freq = participantA.freq; for all participants B with the aberrant frequency axis. Of course, this only makes sense if the frequency axes between participants A and B are actually almost identical! Hope this helps, Best regards, Eelke On 22 July 2013 14:40, Johanna Fieß wrote: > Dear all, > > whenever I try to compute the statistics for (MEG) time-frequency data, this > error message comes up: > > computing statistic over the frequency range [8.000 11.000] > computing statistic over the time range [0.300 1.100] > Error using ft_appendfreq (line 250) > the input data structures have non-unique frequency bins, concatenation > across frequency is not possible > > Error in ft_appendfreq (line 139) > freq = ft_appendfreq(tmpcfg, varargin{:}); > > Error in ft_freqstatistics (line 231) > data = ft_appendfreq(cfg, varargin{:}); > > Out of 35 participants in total, (only) three show slightly different > frequency bins (starting point 2.0001 instead of 1.9998) – if I remove them > from the average, the error message disappears. > If renaming the freq-structure of those three participants, the error > message disappears, too. > > Could anyone tell me what causes this problem or how I should handle it? > > Thanks a lot in advance! > > Johanna > > > PS: I'm running Matlab R2012b & fieldtrip-20130515 > %% stats > design=[1:10,1:10; ones(1,10),ones(1,10)*2]; > > cfg = []; > cfg.frequency = [8 11]; > cfg.latency = [.3 1.1]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clustertail = 0; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.numrandomization = 500; > cfg.alpha = 0.05; > > cfg.avgoverfreq = 'yes'; > % cfg.avgovertime = 'yes'; > cfg.design = design; > cfg.neighbours = neighbours; > cfg.ivar = 2; > > > stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); > cfg = []; > cfg.alpha = 0.3; > cfg.parameter = 'stat'; > cfg.zlim = [-3 2]; > cfg.layout = '4D148.lay'; > ft_clusterplot(cfg, stat); > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lei.niu at einstein.yu.edu Mon Jul 22 15:11:42 2013 From: lei.niu at einstein.yu.edu (Lei Niu) Date: Mon, 22 Jul 2013 13:11:42 +0000 Subject: [FieldTrip] question about to get the numbers of rejected trials In-Reply-To: References: , Message-ID: Dear Johanna, Thank you very much for your reply. I have resolved the problem following your suggestions. Thanks, Lei ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Johanna Zumer [johanna.zumer at gmail.com] Sent: Saturday, July 20, 2013 3:45 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] question about to get the numbers of rejected trials Dear Lei, I think that you are asking that you want to run the steps again, with prestim =0.5 but with rejecting the same 10 trials that you already have decided to reject? If so, the numbers of rejected trials should be inside data_reject.cfg (or possibly data_reject.cfg.previous). But note that by including more prestim time, you might also find a need to reject more trials if there is an artifact in the new included prestim time-points. If you use ft_redefinetrial, I think you only would shift where the time 0.0 is, but not add more data to each trial, so it depends which you want to do. Best regards, Johanna 2013/7/18 Lei Niu > Dear Fieldtrippers, I am new one to use the fieldtrip, and have a question about the rejected trials. To be simply, let we say: 1) the original data is data_org, one singal trial in 32 channel, with 2 different trigger codes and 100 trials per trigger. 2) I process the data to the data_stimulus, incuding 200 trials. Each trial has prestim = 0.1, poststim = 1; 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I get data_reject, including 190 trials. Here is the problem. I found the prestim is too short, I want to increase the prestim time to 0.5. How can I get the numbers of rejected 10 trials to do ft_redefinetrial? Thanks, Lei Niu Albert Einstein College of Medicine _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From kyle.hird+fieldtrip at gmail.com Mon Jul 22 18:54:38 2013 From: kyle.hird+fieldtrip at gmail.com (Kyle Hird) Date: Mon, 22 Jul 2013 12:54:38 -0400 Subject: [FieldTrip] Peer module thinks it has too little memory In-Reply-To: References: Message-ID: I've investigated my issue a bit further and found a couple of things that may be of use for anyone attempting to diagnose the problem. I mentioned previously that the instance of MATLAB which is running peerslave segfaults when it receives a job if I compile the toolbox on my system. On inspection of the stack trace, I find memprofile twice- the only file from FieldTrip to show up at all. So I run memprofile directly from the private directory with a couple of different options. With 'info', it appears to correctly measure memory usage- approximately 110MB (the distributed binary reported an unrealistically high number). However, when set up to repeatedly sample using 'on' and 'off', memprofile segfaults when 'off' is given, and returns an almost-identical stack trace as when peerslave was run. If 'off' is given to memprofile without first having given 'on', the error does not occur. Other ways to trigger the segfault are, once setting memprofile('on'), to give MATLAB the commands 'exit' or 'clear mex'. I added some mexPrintf statements to try and pinpoint what instruction is causing the segfault. Based on this, the block of code beginning with else if (strcasecmp(command, "off")==0) completes execution correctly. However, nothing in exitFun appears to be executed, not even a print statement I put on the first line. I'm not sure what could cause this problem, but hopefully someone on the list can make sense of this. Thanks for your consideration Kyle Hird From jm.horschig at donders.ru.nl Tue Jul 23 09:41:56 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 23 Jul 2013 09:41:56 +0200 Subject: [FieldTrip] Getting started with realtime EEG data In-Reply-To: References: <9EDC29E4-D79B-4777-A3C6-0C5E5E2C9E0F@donders.ru.nl> Message-ID: <51EE33C3.7020204@donders.ru.nl> Hi Eric, I was just reading up on this conversation and since you mentioned that you do not have any signal processing experience, I thought it'd be nice to point to http://www.dspguide.com/ (free online book) Good luck with oscillating in your sleep :) Best, Jörn On 3/6/2013 9:08 AM, Eelke Spaak wrote: > Hi Eric, > > Yes, FieldTrip's raw data format is the same regardless of acquisition > device, so I expect no problems switching from one device to another. > Note, though, that I have not worked with the realtime buffer, but I > think it ought to work the same as with offline data processing. > > Certain analysis pipelines (e.g. source reconstruction) require > accurate information about the electrode positions. The ease at which > you could obtain these might differ between different devices. > However, based on the info you've given so far I guess this will not > be a problem for you. > > Best, > Eelke > > On 6 March 2013 05:24, Eric Mill wrote: >> Sorry, that was a very long response on my part - but the one actual >> question I have in there is, how easy is it to switch from one EEG device to >> another? Should I expect to have to rework my code entirely, or will the >> core data format and signal processing work be the same? Is standardizing >> the data stream one of the things using an intermediary like Field Trip >> does? >> >> -- Eric >> >> >> On Sun, Mar 3, 2013 at 5:26 PM, Eric Mill wrote: >>> This is extremely helpful, and just what I was looking for, thank you >>> (both Robert and Stefan). I have a few followup questions you've inspired. >>> >>> How "swappable" is the hardware? Do all EEG's fundamentally produce the >>> same data from the same brain activity? And/or, does FieldTrip always expose >>> data in its buffer in the same format? >>> >>> For example, I would be fine investing the $750 for an Emotiv 14-channel >>> EEG, or even the $1200 for a KT88-1016, but not until after I've done some >>> development with a cheaper device first. However, I would not want to have >>> to rewrite all my code, or much of it, if I switch devices. >>> >>> I do have a requirement that I can have the same code work with either >>> live or replayed data. From how you describe its buffer approach, it sounds >>> like that's a core value of FieldTrip, and will make that requirement much >>> easier to satisfy. >>> >>> Also, I do have one peculiar requirement, which is that the hardware be >>> suitable for wearing during ordinary sleeping at home. This is more a >>> requirement for the final (potentially more expensive) device, than the >>> development device. The promotional photo for the Emotiv EEG, for example, >>> looks like it might not be so great for that. >>> >>> I think I will be using WebSockets, but there will be an intermediate >>> server. So, I will have a computer (perhaps a Raspberry Pi) receive data >>> from the EEG, and then immediately stream it up an open TCP connection to a >>> web server. This server will then stream it down to the individual browsers >>> of visiting users, and JavaScript will do the visualization, in something >>> like Three.js or Processing.js. >>> >>> So I don't think I'd be making a JavaScript implementation of FieldTrip, >>> but I believe the server software could be made to be general purpose, and >>> reusable in the work of others like yourselves. That would be a satisfying >>> byproduct. >>> >>> The idea here is that the resulting website will show fully live and real >>> time EEG data, specifically while I am sleeping. Since I only sleep for ~1/3 >>> of any given day, the ability to replay things will be helpful in giving the >>> site utility during the other 2/3. >>> >>> I've never done any signal processing before, not even so much as a fast >>> Fourier transform. But I'm willing to learn! I'll be consulting the tutorial >>> you've kindly written, but if you have any suggestions of learning material >>> I should look at when figuring out how to (for example) detect when a >>> subject has entered levels of sleep given streams of EEG data, it would be a >>> lot of help to me. >>> >>> Unfortunately, the paper you linked to >>> (http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8986.2012.01471.x/full) >>> is behind a paywall and is $35, but if you recommend it highly enough, I'll >>> check it out. >>> >>> Again, thank you for being so welcome to a newbie, and for the >>> recommendations and links. >>> >>> -- Eric >>> >>> >>> On Sun, Mar 3, 2013 at 4:58 AM, Robert Oostenveld >>> wrote: >>>> Hi Eric, >>>> >>>> I think that NeuroSky renamed and discontinued some of their products >>>> since we made the initial implementation of the ThinkCap. I am still able >>>> to find documentation here >>>> http://developer.neurosky.com/docs/lib/exe/fetch.php?media=thinkcap:thinkcap_headset_user_manual.pdf >>>> and http://developer.neurosky.com/docs/doku.php?id=thinkcap. I cannot tell >>>> whether the complete sets now sold by NeuroSky still use the same software >>>> interface, but NeuroSky is rather open with their development tools. >>>> >>>> Alternatives you may consider are the Emotiv Epoc or the DIY OpenEEG. The >>>> Epoc has more channels and a head mount for the electrodes. For the Epoc you >>>> have to look into teh different SDK options, the cheapest version only gives >>>> access to processed data, not to the raw data. For both the Epoc and openeeg >>>> a implementation of a stand-allone executable is available in >>>> http://fieldtrip.fcdonders.nl/development/realtime/implementation. LIke for >>>> the ThinkCap, this copies the data to a "fieldtrip buffer", where another >>>> (c/c++/java/python/matlab) application can easily read it from and do the >>>> signal processing, not having to worry about the buffering and data >>>> representation any more. >>>> >>>> I know it falls outside your budget, but have a look at >>>> http://engineuring.wordpress.com/2009/06/15/writing-your-own-soft-for-a-really-cheap-eeg-hardware-for-brain-computer-interfacing. >>>> These KT88-1016 systems are available from ebay. >>>> >>>> Let me add a bit from the developers perspective and software design. The >>>> rationale for the fieldtrip buffer is that it allows us to develop analysis >>>> pipelines using EEG data files on disk (using ft_read_data). Once the >>>> offline analysis pipeline performs as desired, we just switch from reading >>>> to disk to reading from the buffer (also ft_read_data). We happen to do this >>>> using MATLAB for the rapid application development, but the same strategy >>>> (develop for file, run in real-time) can be used with another programming >>>> environment. >>>> >>>> I think that for signal processing you'll better off if you develop the >>>> code using some good quality data from a file on disk. You can always enact >>>> a real-time data stream by replaying data from that EEG file, or using the >>>> sine2ft GUIs (see realtime/bin). Otherwise you'll be doing all development, >>>> constantly having to wear the headset. That is fine for artefact detection >>>> (you can blink while you code), but not if the tasks get more complicated, >>>> e.g. relaxing to increase your occipital alpha/10Hz won't work well if you >>>> also have in realtime have to monitor whether your applications picks up the >>>> alpha. >>>> >>>> Some time ago we (i.e. Boris Reuderink and me) looked into the >>>> possibilities of a web-standards implementation. Web Sockets would be >>>> needed in Javascript if we want to have the browser connect to a "fieldtrip >>>> buffer" TCP server. The Web Sockets still seemed a bit risky w.r.t. it >>>> working on all platforms. A server-side implementation offers more choice, >>>> python/java/php reading the data from a FT buffer or from the device, and >>>> then pass it on in html format to the connected web ) but would not scale as >>>> easily with multiple client connections if data processing needs to be done >>>> on the server. We then considered the best option to be to implement a >>>> RESTless server implementation. The server would one the one hand contains >>>> the FT buffer (where it receives the data over low-level TCP) and on the >>>> other hand have a web server with the RESTless interface. I.e. the requests >>>> that are represented here >>>> http://fieldtrip.fcdonders.nl/development/realtime/buffer_protocol would >>>> each translate to a http call like "http://ftbuffer.donders.nl/get/hdr" and >>>> "http://ftbuffer.donders.nl/get/dat?begsample=xx&endsample=xx". You can ask >>>> Boris (CC) offline whether he has given it further thought. >>>> >>>> best regards, >>>> Robert >>>> >>>> >>>> >>>> On 2 Mar 2013, at 3:12, Eric Mill wrote: >>>> >>>>> Hi all, >>>>> >>>>> My apologies if this is off-topic here, since you all seem like very >>>>> busy experts! >>>>> >>>>> I'm trying to figure out what I need to get started with capturing >>>>> real-time EEG data using consumer-priced headsets (<$200). I don't actually >>>>> have any interest in using MATLAB, though - I just want to capture the raw >>>>> data, in real time. >>>>> >>>>> I see that FieldTrip has a realtime acquisition module for NeuroSky's >>>>> "ThinkCap", though I can't find a current product by NeuroSky called that. >>>>> Is there something else of theirs I could buy that would work with >>>>> FieldTrip? >>>>> >>>>> Or, should I be looking elsewhere entirely? What should someone who >>>>> wants real-time EEG data do? >>>>> >>>>> My plan is to stream this data and visualize it on the web in real >>>>> time. My background is in web development, not cognitive science, but I'm >>>>> willing to learn what I have to make something interesting. I'd also love to >>>>> have the project result in libraries useful for other people in the field. >>>>> >>>>> Thanks for any advice you can give on what EEG to buy, and/or where to >>>>> learn the core concepts I'll need to use the data. >>>>> >>>>> -- Eric >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From K.Kalogianni at tudelft.nl Tue Jul 23 19:05:52 2013 From: K.Kalogianni at tudelft.nl (Konstantina Kalogianni) Date: Tue, 23 Jul 2013 17:05:52 +0000 Subject: [FieldTrip] music_SL In-Reply-To: <4DF682D3A10EAC46B462A46E16F0B049128DF845@SRV366.tudelft.net> References: <4DF682D3A10EAC46B462A46E16F0B049128DF845@SRV366.tudelft.net> Message-ID: <96D063C2-1544-4FB2-BAA6-D4DD736FD6CE@tudelft.nl> Sent from my iPhone Begin forwarded message: Dear fieldtripers, I want to use the music algorithm for source localization on SEP data(somatosensory evoked potentials) and I would like some help.: Those are my questions 1.The music algorithm needs a number of components (i.e dipoles) and I am wondering where to specify that. For the moment I ‘ve just edited the music.m file for that, but I was wondering if there is a more efficient way. 2.Does the algorithm needs a prestimulus part of the data for comparison that will be used in the covariance matrix? 3. How do I plot the results for music algorithm if I am only interested in one dipole activated? Should I set a roi before? Thanks in advance Nadia Kalogianni -------------- next part -------------- An HTML attachment was scrubbed... URL: From robince at gmail.com Wed Jul 24 10:16:02 2013 From: robince at gmail.com (Robin) Date: Wed, 24 Jul 2013 09:16:02 +0100 Subject: [FieldTrip] matlab stops showing functional images! Message-ID: Hi all, Sorry for a question which might be slightly off topic. I am plotting functional images over anatomy with the 'slice' method of ft_sourceplot. On one machine this has stopped working. The anatomy displays and the functional colorbar is displayed correctly (I can update the CData attribute and see the colorbar update) - but I do not see any part of the functional map. I think it is something related to OpenGL (the renderer for the figure is definitely set to opengl) on this particular computer (the exact same code works on other machines). The setup is CentOS 6 with Matlab R2012a. I have restarted Matlab and the machine but it still doesn't show up - I haven't changed any Matlab settings as far as I know. I am a bit stuck with this so wondered if anyone here might have seen anything like it before? Cheers Robin -------------- next part -------------- An HTML attachment was scrubbed... URL: From Yingying.Wang at cchmc.org Thu Jul 25 08:10:57 2013 From: Yingying.Wang at cchmc.org (Wang, Yingying) Date: Thu, 25 Jul 2013 06:10:57 +0000 Subject: [FieldTrip] website is down In-Reply-To: <018501ce88fd$932b3970$b981ac50$@hotmail.com> References: <018501ce88fd$932b3970$b981ac50$@hotmail.com> Message-ID: <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> http://fieldtrip.fcdonders.nl/ is down. When will it come back? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Jul 25 08:50:25 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 25 Jul 2013 08:50:25 +0200 Subject: [FieldTrip] website is down In-Reply-To: <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> References: <018501ce88fd$932b3970$b981ac50$@hotmail.com> <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> Message-ID: Dear list, We apologize for the present website issues, and working as best we can to get the website up again. Most likely, it will be back up later today. Best, Eelke On 25 July 2013 08:10, Wang, Yingying wrote: > http://fieldtrip.fcdonders.nl/ is down. > > When will it come back? > > Thanks. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From constantino.mendezbertolo at ctb.upm.es Fri Jul 26 18:46:23 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Fri, 26 Jul 2013 18:46:23 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics Message-ID: Greetings, We have Timelock data (LFPs). In order to run cluster based permutation tests we generated a Template similar to a Freqdata structure, with size(Template.powspctrm) = 9 1 1 320 Template.dimord = subj_chan_freq_time We set cfg.neighbouts = [] and run ft_freqstatistics (method ='montecarlo'; correctm = 'cluster', etc) * * This way we can run permutation tests and explore the output, hence, clusters are made on time. What we would like to do is: - *Selecting a minimum amount of consecutive time-bins for a cluster to be considered.* * * For example: Only if (say) 10 consecutive time points are above threshold (whether 'maxsum' or 'wcm' criteria are being used) fieldtrip should consider it a cluster. If just one solely sample point is above clusteralpha threshold, it should not be considered. Is it possible? It would similar to cfg.minnbchan, but in time. Only a cfg.minnbtbin does not exist! As we are already tricking freqstats to believe is working with freqdata (with just one frequency) I am not sure if this is possible. If someone has got some input it would be much appreciated -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Fri Jul 26 19:54:38 2013 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Fri, 26 Jul 2013 19:54:38 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: Message-ID: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> I think cfg.minnbchan, applies also to time bins. s ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > cfg.minnbchan, -------------- next part -------------- An HTML attachment was scrubbed... URL: From constantino.mendezbertolo at ctb.upm.es Fri Jul 26 20:55:36 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Fri, 26 Jul 2013 20:55:36 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> Message-ID: Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations This is the error (with neighbours) V V V Error in clusterstat>makechanneighbstructmat (line 519) [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); Error in clusterstat (line 59) channeighbstructmat = makechanneighbstructmat(cfg); Error in statistics_montecarlo (line 320) [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ft_freqstatistics (line 267) [stat, cfg] = statmethod(cfg, dat, cfg.design); While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: > > I think cfg.minnbchan, applies also to time bins. > > s > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > > cfg.minnbchan, > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN -------------- next part -------------- An HTML attachment was scrubbed... URL: From mengtongxiao at gmail.com Mon Jul 29 04:44:49 2013 From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=) Date: Mon, 29 Jul 2013 10:44:49 +0800 Subject: [FieldTrip] EEG source reconstruction Message-ID: Dear all I do EEG source analyse,But I use the method as the follow got strong function connectivity from different brain areas.（eg.correlation）and strength is similar; I want konw the code with source reconstruction is right? Or some stimulate can prove the code that is right. (the VOL and sourcemode form template) cfg = []; cfg.covariance = 'yes'; cfg.vartrllength = 2; cfg.covariancewindow = 'all'; timelock = ft_timelockanalysis(cfg, data); cfg = []; cfg.channel = {'EEG'}; cfg.vol = vol; cfg.reducerank = 3; cfg.normalize ='yes'; cfg.elec = data_org.hdr.elec; cfg.grid =sourcemodel; [grid]= ft_prepare_leadfield(cfg); cfg = []; cfg.method = 'lcmv'; cfg.vol = vol; cfg.grid = grid; cfg.lcmv.fixedori = 'yes'; cfg.elec = data.hdr.elec; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; source1 = ft_sourceanalysis(cfg, timelock); thanks in advance xiao -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 29 07:48:59 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 29 Jul 2013 07:48:59 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> Message-ID: <51F6024B.8070000@donders.ru.nl> Dear Constantino, I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. Best, Jörn On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: > Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no > cluster (not even with minnbchan = 1) were there was a cluster before > (without cfg.minnbchan) > > Using cfg.neighbours = 'triangulation', or 'distance', with or without > cfg.minnbchan computes the statistics but fails prior to compute the > clusters in the randomizations > > This is the error (with neighbours) V V V > > Error in clusterstat>makechanneighbstructmat (line 519) > [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); > > Error in clusterstat (line 59) > channeighbstructmat = makechanneighbstructmat(cfg); > > Error in statistics_montecarlo (line 320) > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ft_freqstatistics (line 267) > [stat, cfg] = statmethod(cfg, dat, cfg.design); > > > While it seems it is minnbchan what will be helpful, we do not come up > with an idea. Maybe, besides tricking fieldtrip to think we have > frequency data we should also trick him to believe that points in time > are channels? :) > > > El 26 de julio de 2013 19:54, smoratti at psi.ucm.es > > escribió: > > > I think cfg.minnbchan, applies also to time bins. > > s > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de > Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > >> cfg.minnbchan, > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Constantino Méndez-Bértolo > Laboratorio de Neurociencia Clínica,Centro de Tecnología Biomédica (CTB) > > Parque Científico y Tecnológico de la UPM, Campus de Montegancedo > > 28223 Pozuelo deAlarcón, Madrid, SPAIN > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From constantino.mendezbertolo at ctb.upm.es Mon Jul 29 13:06:43 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Mon, 29 Jul 2013 13:06:43 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: <51F6024B.8070000@donders.ru.nl> References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> <51F6024B.8070000@donders.ru.nl> Message-ID: Dear Jörn, Thanks for your response. You are sensibly confused. It is because we wanted to do the statistics (montecarlo; correctm = cluster) with just one channel per data/individual. [As was pointed out above: size(Template.powspctrm) = 9 1 1 320; Template.dimord = subj_chan_freq_time], and ft_timelockstatistics would ask me for a neighbourstructure relenteless, while ft_freqstatistics is ok with cfg.neighbour = [] and so clusters in time. Hence the unorthodoxy. I did a function that parses the mask of the already computed stat finding '1s', determining the span and setting zeros on an arbitrary width-criteria; which serves the purpose but it is not as ellegant as it would be my own statfun. Cheers, Tino 2013/7/29 "Jörn M. Horschig" > > Dear Constantino, > > I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). > > The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. > > Best, > Jörn > > > On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: >> >> Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) >> >> Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations >> >> This is the error (with neighbours) V V V >> >> Error in clusterstat>makechanneighbstructmat (line 519) >> [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); >> >> Error in clusterstat (line 59) >> channeighbstructmat = makechanneighbstructmat(cfg); >> >> Error in statistics_montecarlo (line 320) >> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >> >> Error in ft_freqstatistics (line 267) >> [stat, cfg] = statmethod(cfg, dat, cfg.design); >> >> >> While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) >> >> >> El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: >>> >>> >>> I think cfg.minnbchan, applies also to time bins. >>> >>> s >>> >>> ________________________________________________________ >>> Stephan Moratti, PhD >>> >>> see also: http://web.me.com/smoratti/ >>> >>> Universidad Complutense de Madrid >>> Facultad de Psicología >>> Departamento de Psicología Básica I >>> Campus de Somosaguas >>> 28223 Pozuelo de Alarcón (Madrid) >>> Spain >>> >>> and >>> >>> Center for Biomedical Technology >>> Laboratory for Cognitive and Computational Neuroscience >>> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >>> Campus Montegancedo >>> 28223 Pozuelo de Alarcón (Madrid) >>> Spain >>> >>> >>> email: smoratti at psi.ucm.es >>> Tel.:    +34 679219982 >>> >>> El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: >>> >>>> cfg.minnbchan, >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> Constantino Méndez-Bértolo >> Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) >> >> Parque Científico y Tecnológico de la UPM, Campus de Montegancedo >> >> 28223 Pozuelo de Alarcón, Madrid, SPAIN >> >> >> [image] >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN [image] From jm.horschig at donders.ru.nl Mon Jul 29 13:54:12 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 29 Jul 2013 13:54:12 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> <51F6024B.8070000@donders.ru.nl> Message-ID: <51F657E4.60001@donders.ru.nl> Dear Tino, As I said, try cfg.avgoverchan='yes' with ft_timelockstatistics, then cfg.neighbours can be anything. K>> cfg.neighbours = []; K>> cfg.avgoverchan = 'yes'; K>> [stat] = ft_timelockstatistics(cfg, timelockFIC, timelockFC); [...] using a cluster-based method for multiple comparison correction the returned probabilities and the thresholded mask are corrected for multiple comparisons the call to "ft_timelockstatistics" took 2 seconds K>> You'd still require an own statfun for what you want though ;) Best, Jörn On 7/29/2013 1:06 PM, Constantino Méndez Bértolo wrote: > Dear Jörn, > > Thanks for your response. You are sensibly confused. It is because we > wanted to do the statistics (montecarlo; correctm = cluster) with just > one channel per data/individual. [As was pointed out above: > size(Template.powspctrm) = 9 1 1 320; Template.dimord = > subj_chan_freq_time], and ft_timelockstatistics would ask me for a > neighbourstructure relenteless, while ft_freqstatistics is ok with > cfg.neighbour = [] and so clusters in time. Hence the unorthodoxy. > > I did a function that parses the mask of the already computed stat > finding '1s', determining the span and setting zeros on an arbitrary > width-criteria; which serves the purpose but it is not as ellegant as > it would be my own statfun. > > Cheers, > Tino > > > 2013/7/29 "Jörn M. Horschig" >> Dear Constantino, >> >> I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). >> >> The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. >> >> Best, >> Jörn >> >> >> On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: >>> Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) >>> >>> Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations >>> >>> This is the error (with neighbours) V V V >>> >>> Error in clusterstat>makechanneighbstructmat (line 519) >>> [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); >>> >>> Error in clusterstat (line 59) >>> channeighbstructmat = makechanneighbstructmat(cfg); >>> >>> Error in statistics_montecarlo (line 320) >>> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >>> >>> Error in ft_freqstatistics (line 267) >>> [stat, cfg] = statmethod(cfg, dat, cfg.design); >>> >>> >>> While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) >>> >>> >>> El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: >>>> >>>> I think cfg.minnbchan, applies also to time bins. >>>> >>>> s >>>> >>>> ________________________________________________________ >>>> Stephan Moratti, PhD >>>> >>>> see also: http://web.me.com/smoratti/ >>>> >>>> Universidad Complutense de Madrid >>>> Facultad de Psicología >>>> Departamento de Psicología Básica I >>>> Campus de Somosaguas >>>> 28223 Pozuelo de Alarcón (Madrid) >>>> Spain >>>> >>>> and >>>> >>>> Center for Biomedical Technology >>>> Laboratory for Cognitive and Computational Neuroscience >>>> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >>>> Campus Montegancedo >>>> 28223 Pozuelo de Alarcón (Madrid) >>>> Spain >>>> >>>> >>>> email: smoratti at psi.ucm.es >>>> Tel.: +34 679219982 >>>> >>>> El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: >>>> >>>>> cfg.minnbchan, >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Constantino Méndez-Bértolo >>> Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) >>> >>> Parque Científico y Tecnológico de la UPM, Campus de Montegancedo >>> >>> 28223 Pozuelo de Alarcón, Madrid, SPAIN >>> >>> >>> [image] >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From alexis.makin at liverpool.ac.uk Mon Jul 29 17:33:13 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 16:33:13 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing Message-ID: Hi I already have data which has been cleaned, filtered and artefact rejected etc. It is now .mat format (trials X electrodes X time). I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields data.label % cell-array containing strings, Nchan X 1 data.fsample % sampling frequency in Hz, single number data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M but when I try to run ft_freqanalysis(cfg, data) on this I get the following error messages: ??? Error using ==> ft_checkdata at 366 This function requires raw, comp or mvar data as input. Error in ==> ft_freqanalysis at 219 data = ft_checkdata(data, 'datatype', {'raw', 'comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? cheers, Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 29 17:51:38 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 29 Jul 2013 17:51:38 +0200 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: Hi Alexis, How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. Best, Eelke Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected > etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which > should be compatible with ft_freqanalysis: > > Alternatively, if you already are able to read the data into Matlab, you > can reformat that data within Matlab into a datastructure that is > compatible with FieldTrip. Raw data that is comparable with the output of > preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a > simple problem? > > Is it common to use fieldtrip functions on data which has already been > preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexis.makin at liverpool.ac.uk Mon Jul 29 17:59:33 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 16:59:33 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: <3E0B8C1F-B490-48FD-A1F6-1F9209F43E14@liv.ac.uk> data = label: {64x1 cell} fsample: 128 trials: {1x60 cell} times: {1x60 cell} On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > > Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: > Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? > > Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexis.makin at liverpool.ac.uk Mon Jul 29 18:03:29 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 17:03:29 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: Hi, thanks for your reply, so that's what my data structure looks like. Is it common to use fieldtrip functions on data which has already been cleaned and epoched elsewhere? Alexis On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > > Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: > Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? > > Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Jul 29 18:19:48 2013 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 29 Jul 2013 16:19:48 +0000 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: <16338_1375114551_51F69537_16338_213_1_D9DA6D7F-1D2F-49F7-95B1-47F3A4453A85@liv.ac.uk> References: , <16338_1375114551_51F69537_16338_213_1_D9DA6D7F-1D2F-49F7-95B1-47F3A4453A85@liv.ac.uk> Message-ID: Hi Alexis, it may just be that ft_checkdata is unhappy with the subfields '.trials' and '.times' instead of '.trial' and '.time'. Good luck, best Max ________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "Alexis [alexis.makin at liverpool.ac.uk] Gesendet: Montag, 29. Juli 2013 18:03 Bis: FieldTrip discussion list Betreff: Re: [FieldTrip] ft_freqanalysis without ft_preprocessing Hi, thanks for your reply, so that's what my data structure looks like. Is it common to use fieldtrip functions on data which has already been cleaned and epoched elsewhere? Alexis On 29 Jul 2013, at 16:51, Eelke Spaak wrote: Hi Alexis, How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. Best, Eelke Op 29 jul. 2013 17:36 schreef "Alexis" > het volgende: Hi I already have data which has been cleaned, filtered and artefact rejected etc. It is now .mat format (trials X electrodes X time). I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields data.label % cell-array containing strings, Nchan X 1 data.fsample % sampling frequency in Hz, single number data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M but when I try to run ft_freqanalysis(cfg, data) on this I get the following error messages: ??? Error using ==> ft_checkdata at 366 This function requires raw, comp or mvar data as input. Error in ==> ft_freqanalysis at 219 data = ft_checkdata(data, 'datatype', {'raw', 'comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? cheers, Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ From eelke.spaak at donders.ru.nl Mon Jul 29 18:22:45 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 29 Jul 2013 18:22:45 +0200 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: 'trial' and 'time' should be singular :) Eelke Op 29 jul. 2013 18:13 schreef "Alexis" het volgende: > Hi, thanks for your reply, > > so that's what my data structure looks like. > > Is it common to use fieldtrip functions on data which has already been > cleaned and epoched elsewhere? > > Alexis > > On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display > when you type 'data' at the prompt? The error message suggests that it is > not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > Op 29 jul. 2013 17:36 schreef "Alexis" het > volgende: > >> Hi >> >> I already have data which has been cleaned, filtered and artefact >> rejected etc. >> >> It is now .mat format (trials X electrodes X time). >> >> I can follow the advice from the wiki below to make a structure which >> should be compatible with ft_freqanalysis: >> >> Alternatively, if you already are able to read the data into Matlab, you >> can reformat that data within Matlab into a datastructure that is >> compatible with FieldTrip. Raw data that is comparable with the output of >> preprocessing should consist of a structure with the fields >> >> data.label % cell-array containing strings, Nchan X 1 >> data.fsample % sampling frequency in Hz, single number >> data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples >> data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector >> data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M >> >> >> but when I try to run ft_freqanalysis(cfg, data) on this >> >> I get the following error messages: >> >> ??? Error using ==> ft_checkdata at 366 >> This function requires raw, comp or mvar data as input. >> >> Error in ==> ft_freqanalysis at 219 >> data = ft_checkdata(data, 'datatype', {'raw', 'comp', >> 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); >> >> How to I tell the ft_checkdata function what datatype I have? Is this a >> simple problem? >> >> Is it common to use fieldtrip functions on data which has already been >> preprocessed in another way? Or is this not advisable? >> >> cheers, >> >> >> Alexis >> alexis.makin at liv.ac.uk >> >> Network: www.liv.ac.uk/perception-action/ >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Tue Jul 30 10:27:05 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 30 Jul 2013 10:27:05 +0200 Subject: [FieldTrip] EEG source reconstruction In-Reply-To: References: Message-ID: Dear Xiao, The code doesn't look wrong at first glance. However, with beamforming, the pre-processing of the 'data' is just as important of a step, so be sure you are using the optimal time windows for your research question, and optimal frequency filtering, if desired, etc. Also, check that the units of data.hdr.elec is the same as the vol and sourcemodel. Also, is there a reason you use data_org.hdr.elec in one instance, and the data.hdr.elec in another instance? Best, Johanna 2013/7/29 陈雪 > Dear all > > I do EEG source analyse,But I use the method as the follow got strong > function connectivity from different brain areas.（eg.correlation）and > strength is similar; > I want konw the code with source reconstruction is right? > Or some stimulate can prove the code that is right. > (the VOL and sourcemode form template) > > > cfg = []; > cfg.covariance = 'yes'; > cfg.vartrllength = 2; > cfg.covariancewindow = 'all'; > timelock = ft_timelockanalysis(cfg, data); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.vol = vol; > cfg.reducerank = 3; > cfg.normalize ='yes'; > cfg.elec = data_org.hdr.elec; > cfg.grid =sourcemodel; > [grid]= ft_prepare_leadfield(cfg); > > > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = vol; > cfg.grid = grid; > cfg.lcmv.fixedori = 'yes'; > cfg.elec = data.hdr.elec; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > source1 = ft_sourceanalysis(cfg, timelock); > > thanks in advance > xiao > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erica.boschin at queens.ox.ac.uk Tue Jul 30 16:29:27 2013 From: erica.boschin at queens.ox.ac.uk (Erica Boschin) Date: Tue, 30 Jul 2013 15:29:27 +0100 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script Message-ID: Dear Fieldtrip users, In trying to run ft_timelockanalysis I keep getting the following error: ??? Error using ==> CalcMD5 at 70 Cannot find MEX script This error should allegedly occur when the path is the same as the parent folder for the script, which is not my case. I have tried recompiling the mex files in private and src, with no luck. Has anyone ever experienced this error and if so, could point me towards a solution? I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS 10.6.8. I do not get the error if I try to run the exact same script in Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not sure whether it might be a specs issue or something else. Many thanks, Erica From johanna.zumer at donders.ru.nl Tue Jul 30 16:40:43 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 30 Jul 2013 16:40:43 +0200 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script In-Reply-To: References: Message-ID: Dear Erica, Is the computer on which it fails a 32-bit? If so, this is a known problem: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2010 Feel free to 'cc' yourself onto this bug report. Best, Johanna 2013/7/30 Erica Boschin > Dear Fieldtrip users, > > In trying to run ft_timelockanalysis I keep getting the following error: > > ??? Error using ==> CalcMD5 at 70 > Cannot find MEX script > > This error should allegedly occur when the path is the same as the parent > folder for the script, which is not my case. I have tried recompiling the > mex files in private and src, with no luck. > > Has anyone ever experienced this error and if so, could point me towards a > solution? > > I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS > 10.6.8. I do not get the error if I try to run the exact same script in > Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not > sure whether it might be a specs issue or something else. > > Many thanks, > Erica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erica.boschin at queens.ox.ac.uk Tue Jul 30 17:09:29 2013 From: erica.boschin at queens.ox.ac.uk (Erica Boschin) Date: Tue, 30 Jul 2013 16:09:29 +0100 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script In-Reply-To: References: Message-ID: <1800336A-B1AB-4093-9168-84DFA73BD82C@queens.ox.ac.uk> Dear Johanna, it is indeed a 32-bit, thanks for letting me know it's a bug. Best wishes, Erica On Jul 30, 2013, at 3:40 PM, Johanna Zumer wrote: > Dear Erica, > > Is the computer on which it fails a 32-bit? If so, this is a known problem: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2010 Feel free to 'cc' yourself onto this bug report. > > Best, > Johanna > > > 2013/7/30 Erica Boschin > Dear Fieldtrip users, > > In trying to run ft_timelockanalysis I keep getting the following error: > > ??? Error using ==> CalcMD5 at 70 > Cannot find MEX script > > This error should allegedly occur when the path is the same as the parent folder for the script, which is not my case. I have tried recompiling the mex files in private and src, with no luck. > > Has anyone ever experienced this error and if so, could point me towards a solution? > > I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS 10.6.8. I do not get the error if I try to run the exact same script in Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not sure whether it might be a specs issue or something else. > > Many thanks, > Erica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ggonesc at upo.es Wed Jul 31 09:05:34 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 09:05:34 +0200 Subject: [FieldTrip] ancova for sources analysis Message-ID: <167095db43e3fd69.51f8d35e@upo.es> Dear fieldtrip experts, I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? Many thanks in advanced, Gabriel -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Jul 31 09:55:58 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 31 Jul 2013 09:55:58 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> References: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: <51F8C30E.8010004@donders.ru.nl> Hi Gabriel, hmm, you could try to use ft_regressconfound, see http://www.ncbi.nlm.nih.gov/pubmed/23246857 I am not aware of other functionality in FT, but that should do pretty much what you want . Best, Jörn On 7/31/2013 9:05 AM, Gabriel Gonzalez Escamilla wrote: > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the > effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Wed Jul 31 09:56:02 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Wed, 31 Jul 2013 09:56:02 +0200 (CEST) Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Dear Gabriel, This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? Yours, Arjen ----- Oorspronkelijk bericht ----- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > Dear fieldtrip experts, > I'm wondering if it is possible to perform an ancova or to remove the > effect of a covariate in a source analysis? > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Jul 31 09:58:39 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 31 Jul 2013 09:58:39 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> References: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: Dear Gabriel, To do a full ANCOVA, you would have to write your own 'statfun' to use in the statistics routines. This is not super-hard to do, but is also far from trivial. However, there might be a much easier solution. There is a function called ft_regressconfound which linearly regresses out a 'confound' or covariate from raw, freq, or source data. Would it be an option to use this function first, and then do ft_sourcestatistics on the cleaned data? Note that ft_regressconfound only supports one value per trial, per confound; so the covariates cannot be fully time-resolved. Best, Eelke On 31 July 2013 09:05, Gabriel Gonzalez Escamilla wrote: > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect > of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ggonesc at upo.es Wed Jul 31 10:55:44 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 10:55:44 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> References: <167095db43e3fd69.51f8d35e@upo.es> <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <23400797220a159c.51f8ed30@upo.es> Thanks for your quick ans Arjen, It seems to do what I want, I'm trying to correct grandaveraged source data in which my data is a 1xNsubjs structure, each subject containing 29232 positions. I'm wondering how would be the correct way to input the age of each subject as a counfound. I have tried to set a structure, were each field was the age of each subject, but the ft_regressconfound seems not to work with structures, so I change it. I've also tried to set as a double array (1xNsubjects), but says that "the number of my confound matrix does not match with the number of trials/subjects"; to which I have input the cfg.counfound as a double array (Nsubjsx1), but now I'm getting an error saying that there is not an existing field in the data.trial structure called "pow". Is there something missing on my data? How can I get that pow field into my data comming from ft_grandaverage? Best Regards, Gabriel ----- Mensaje original ----- De: "Stolk, A." Fecha: Miércoles, 31 de Julio de 2013, 10:04 am Asunto: Re: [FieldTrip] ancova for sources analysis A: FieldTrip discussion list p { margin: 0; } > Dear Gabriel, > > This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). > > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? > > Yours, > Arjen > ----------------------------------------------------------- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip --------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggonesc at upo.es
http://www.upo.es/neuroaging/es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ggonesc at upo.es Wed Jul 31 11:56:33 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 11:56:33 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> References: <167095db43e3fd69.51f8d35e@upo.es> <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <2264a36963356fbe.51f8fb71@upo.es> Thank you all for your responses. The last problem I did wrote is now solved, see below. I had a field called 'stat' instead of the 'pow', I'm guessing this field was set before, so, now i'm using this field as if it was the 'pow' I needed and it's working, Is that OK?  Now it takes me to the next question, my data has the avg field, and it says that will update the descriptives but that the 'method' is missing, is this update necessary? or can I just skeep it? Many thanks in advanced, Gabriel ----- Mensaje original ----- De: "Stolk, A." Fecha: Miércoles, 31 de Julio de 2013, 10:04 am Asunto: Re: [FieldTrip] ancova for sources analysis A: FieldTrip discussion list p { margin: 0; } > Dear Gabriel, > > This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). > > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? > > Yours, > Arjen > ----------------------------------------------------------- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip --------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggonesc at upo.es
http://www.upo.es/neuroaging/es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From raminazodiaval at gmail.com Mon Jul 1 13:47:47 2013 From: raminazodiaval at gmail.com (Ramin Azodi) Date: Mon, 1 Jul 2013 13:47:47 +0200 Subject: [FieldTrip] More details about cfg.statistic = 'diff_itc' , Message-ID: Hello, I performed cfg.statistic = 'diff_itc' on two experiment conditions: resting state and during stimulus (each contains 50 trials). As an output, I got values from 0 to 0.6. I tried to find some documents/papers about the meaning of 'diff_itc', and the possibility to interpolate my results but all my attempts failed to success. Could someone tell me more about this function and the possibly give me some reference papers? Best, Ramin -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Mon Jul 1 14:10:39 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 1 Jul 2013 14:10:39 +0200 Subject: [FieldTrip] ROI selection of beamformer grid points In-Reply-To: <1483937264.1423478.1372252022737.JavaMail.root@draco.zimbra.ru.nl> References: <1483937264.1423478.1372252022737.JavaMail.root@draco.zimbra.ru.nl> Message-ID: Hi Marieke, In case you hadn't already, it's easier to do things in MNI coordinates (like select grid points from atlases) if the source reconstruction was already done using warped grid points from MNI to subject-specific space. See here for help on that. If you have done that, then replace the .pos field in each subject with the grid.pos from the MNI, and no need to ft_sourceinterpolate. If the question is more regarding the templates, see here for more tips, including info on the useful ft_read_atlas function. Cheers, Johanna 2013/6/26 Marieke van de Nieuwenhuijzen < m.vandenieuwenhuijzen at fcdonders.ru.nl> > Dear Fieldtrippers, > > I am running my analyses on time courses reconstructed in source space. > Basically, that means that my working dataset is a matrix of grid point x > time. What I want to do now is do some analyses on a subset of that > dataset, a bit analogous to selecting some sensors to restrict analyses to. > Therefore, what I would ideally want to do, is select a subset of grid > points corresponding to a specific location (for example only the occipital > grid points, or only the grid points corresponding to a specific atlas > label). > > Does anyone have any suggestions about how I should go about selecting > specific grid points? Is there perhaps some grid based atlas, or is it > possible to select grid points based on their corresponding mni coordinates > which you get after running ft_sourceinterpolate and ft_volumenormalise (in > other words, is it possible to reverse ft_volumenormalise and > ft_sourceinterpolate to map the mni coordinates to the grid points instead > of the grid points to mni representation). > > Any pointers would be much appreciated. > > Best, > Marieke > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 1 14:12:41 2013 From: cornabel at googlemail.com (cornelius abel) Date: Mon, 01 Jul 2013 14:12:41 +0200 Subject: [FieldTrip] freq / time range for source analysis? Message-ID: <51D17239.2070009@googlemail.com> Dear FT-List, in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. We found a nice significant cluster in the lower gamma range and in the first half of the time range. Please have a look at the two figures. http://dropcanvas.com/0fnvn Fig a is the multiplotTFR of stat, showing only significant areas. Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. Now, we are not sure how to pick the time and freq range for a subsequent source analysis. Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? Any ideas? Greetings, Cornelius -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 1 14:21:10 2013 From: cornabel at googlemail.com (Cornelius Abel) Date: Mon, 1 Jul 2013 14:21:10 +0200 Subject: [FieldTrip] freq / time range for source analysis? Message-ID: Dear FT-List, in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. We found a nice significant cluster in the lower gamma range and in the first half of the time range. Please have a look at the two figures. http://dropcanvas.com/0fnvn Fig a is the multiplotTFR of stat, showing only significant areas. Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. Now, we are not sure how to pick the time and freq range for a subsequent source analysis. Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? Any ideas? Greetings, Cornelius -------------- next part -------------- An HTML attachment was scrubbed... URL: From mengtongxiao at gmail.com Mon Jul 1 14:41:18 2013 From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=) Date: Mon, 1 Jul 2013 20:41:18 +0800 Subject: [FieldTrip] about ft_connectivity_powcorr_ortho Message-ID: dear all I use hilbert get the complex signal.and use the ft_connectivity_powcorr_ortho compute power envelope correlation . But I find the result contrast to the PLV. 1that why? the power envelope correlation of 1 not mean strong function relation? best. xiao -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Jul 1 15:39:49 2013 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 1 Jul 2013 15:39:49 +0200 Subject: [FieldTrip] freq / time range for source analysis? In-Reply-To: <51D17239.2070009@googlemail.com> References: <51D17239.2070009@googlemail.com> Message-ID: <3126EA9B-FD00-4CFA-95A7-62809C6BD222@psi.ucm.es> Hi Cornelius, I had the same kind of data and I picked the whole time frequency range of the cluster. It depends a bit on how big your clusters are and if there is a theoretical reason to split time and frequency windows (for example high and low gamma, etc.). Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 01/07/2013, a las 14:12, cornelius abel escribió: > Dear FT-List, > > in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. > We found a nice significant cluster in the lower gamma range and in the first half of the time range. > Please have a look at the two figures. > > http://dropcanvas.com/0fnvn > > Fig a is the multiplotTFR of stat, showing only significant areas. > Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. > > Now, we are not sure how to pick the time and freq range for a subsequent source analysis. > Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? > > Any ideas? > > Greetings, Cornelius > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jakob.wischniowski at uni-ulm.de Mon Jul 1 18:57:11 2013 From: jakob.wischniowski at uni-ulm.de (Jakob) Date: Mon, 1 Jul 2013 18:57:11 +0200 Subject: [FieldTrip] Matlab 2012/2013 In-Reply-To: <51C85906.2090204@uni-konstanz.de> References: <51C85906.2090204@uni-konstanz.de> Message-ID: Dear David, I'm facing following bug: While performing the artifact rejection summary function, dragging the mouse over the channels won't work: The "selecting box" for dragging simply won't appear while holding down the left mouse button/trackpad button. I'm running Matlab 2013a on an Apple OSX 10.8.4 (Mountain Lion) machine. Is this a known issue? Best regards! Jakob Wischniowski Am 24.06.2013 um 16:34 schrieb David Schubring : > Dear FieldTrip Users, > > I was wondering if the incompatibility issues with fieldtrip and the latest MATLAB 2013a version still exist (and if so, which bugs exactly occur)? > > (Some of our Matlab 2012a/b installations stopped working, maybe due to the latest java-update, and only the 2013 version still works.) > > Thanks in advance and best regards, > David Schubring > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From drivolta81 at gmail.com Tue Jul 2 12:15:57 2013 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 2 Jul 2013 12:15:57 +0200 Subject: [FieldTrip] Special issue - Research topic Message-ID: Dear FieldTrippers, I would like to advertise a Special Issue hosted by Frontiers in Human Neuroscience entitled: "Facing the other: Novel theories and methods in face perception research". Here is the link: http://www.frontiersin.org/Human_Neuroscience/researchtopics/Facing_the_other_Novel_theorie/1903 Topic Editors: Davide Rivolta, Max Planck Society, Germany Aina Puce, Indiana University, USA Mark A. Williams, Macquarie University, Australia Deadline for abstract submission: 30 Nov 2013 Deadline for full article submission: 28 Feb 2014 Abstract: We rely heavily on faces during social interactions. Humans possess the ability to recognise thousands of people very quickly and accurately without effort. The serious social difficulties that follow abnormalities of the face recognition system (i.e., prosopagnosia) strongly underline the importance of typical face skills in our everyday life. Over the last fifty years, research on prosopagnosia, along with research in the healthy population, has provided insights into the cognitive and neural features behind typical face recognition. This has also been achieved thanks to non-invasive neuroimaging techniques such as functional Magnetic Resonance Imaging (fMRI), Electroencephalography (EEG), Magnetoencephalography (MEG), Diffusion Tensor Imaging (DTI) and Transcranial Magnetic Stimulation (TMS). However, there is still much debate about the cognitive and neural mechanisms of face perception. In the current “Research Topic” we plan to gather experimental works, opinions, commentaries, mini-reviews and reviews that focus on new or novel theories and methods in face perception research. Where is the field at the moment? Do we need to re-think the experimental procedures we have adopted so far? Again, what kind of techniques (or combination of them) and analysis methods will be important in the future? From the experimental point of view we invite both behavioural and neuroimaging contributions (e.g., fMRI, EEG, MEG, DTI and TMS). Despite the main emphasis on face perception, memory and identification, we will also consider original works that focus on other aspects of face processing, such as expression recognition, attractiveness judgments and face imagery. In addition, animal investigations and experimental manipulations that alter face recognition abilities in typical human subjects (e.g., hypnosis) are also welcome. Overall, we are proposing a Research Topic that looks at face processing using different perspectives and welcome contributions from different domains such as psychology, neurology, neuroscience, cognitive science and philosophy. Last year we lost two giants in the field: Shlomo Bentin and Truett Allison. We dedicate this Research Topic to them and their pioneering studies. Bests, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From zriouil.imane at gmail.com Tue Jul 2 14:42:00 2013 From: zriouil.imane at gmail.com (z.imane) Date: Tue, 2 Jul 2013 14:42:00 +0200 Subject: [FieldTrip] (no subject) Message-ID: I have a signal of a certain frequency. if I resampled to a smaller frequency. is that I have a loss of information? -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Tue Jul 2 15:21:10 2013 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Tue, 2 Jul 2013 15:21:10 +0200 (CEST) Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: <001d01ce7727$03efcc40$0bcf64c0$@herring@fcdonders.ru.nl> Dear z.imane, If you resample to a smaller frequency you will reduce the number of data points. You will therefore most certainly lose data. Whether you lose 'information' depends on whether there is data relevant to you in frequency bands that cannot be analyzed after resampling. Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of z.imane Sent: dinsdag 2 juli 2013 14:42 To: FieldTrip discussion list Subject: [FieldTrip] (no subject) I have a signal of a certain frequency. if I resampled to a smaller frequency. is that I have a loss of information? -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Tue Jul 2 15:25:26 2013 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Tue, 2 Jul 2013 14:25:26 +0100 Subject: [FieldTrip] (no subject) In-Reply-To: <51d2d3e9.480a0f0a.7ffd.fffffd6aSMTPIN_ADDED_BROKEN@mx.google.com> References: <51d2d3e9.480a0f0a.7ffd.fffffd6aSMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: This might explain it http://en.wikipedia.org/wiki/Nyquist%E2%80%93Shannon_sampling_theorem Vladimir On Tue, Jul 2, 2013 at 2:21 PM, Herring, J.D. (Jim) < j.herring at fcdonders.ru.nl> wrote: > Dear z.imane,**** > > ** ** > > If you resample to a smaller frequency you will reduce the number of data > points. You will therefore most certainly lose data. Whether you lose > ‘information’ depends on whether there is data relevant to you in frequency > bands that cannot be analyzed after resampling. **** > > ** ** > > Best,**** > > ** ** > > Jim**** > > ** ** > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *z.imane > *Sent:* dinsdag 2 juli 2013 14:42 > *To:* FieldTrip discussion list > *Subject:* [FieldTrip] (no subject)**** > > ** ** > > I have a signal of a certain frequency. if I resampled to a smaller > frequency. is that I have a loss of information? > **** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From marianapbranco1 at gmail.com Tue Jul 2 16:20:54 2013 From: marianapbranco1 at gmail.com (Mariana Branco) Date: Tue, 2 Jul 2013 16:20:54 +0200 Subject: [FieldTrip] Online preprocessing In-Reply-To: <519DEAA1.5030402@donders.ru.nl> References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com> <519DE377.1020805@donders.ru.nl> <519DEAA1.5030402@donders.ru.nl> Message-ID: <2BAA5F99-7514-421D-ABB9-E3C0FD8A807B@gmail.com> Dear fieldtrippers, In the follow up of my previous questions: I know am able to stream realtime data form the Biosemi to matlab. In my matlab script I am sending triggers through the parallel port to the biosemi (i.e 2 or 4 for two different events). When The EEG was being recorded using the ActiView interface the trigger once sent was permanently associated with all incoming samples until a new trigger is sent (so event.type=TRIGGER for all samples). However, when streaming from the cmd using biosemi2ft, the trigger only appears once (when is sent) and the follow up samples are only headed with event.type=CM_IN_RANGE and event.value=0 or 1. Is it possible to configure it as in ActiView, which means all samples after sending a trigger are headed with event.type=TRIGGER and event.value=2 or 4? Regards, Mariana Branco On 23 May 2013, at 12:08, Jörn M. Horschig wrote: > Hi Mariana, > > ft_preprocessing demeans by the whole time window, in your 0s to 5s. The baseline window you specify depends on the time axis itself, if it goes from 0s to 5s, then defining [0 3] is fine. If it goes from -3 to 2s, then you need to define [-3 0]. Time is relative :) > Also, please check ft_timelockbaseline. But such a simple thing as subtracting a number from a matrix can also easily be done without relying on a fieldtrip function :) > > Best, > Jörn > > On 5/23/2013 11:57 AM, Mariana Branco wrote: >> Hi Jörn, >> >> Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do. >> >> Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial. >> In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong? >> >> Thank you again for all the advices, I will definitely pose more question in the future. >> >> Mariana Branco >> >> On 23 May 2013, at 11:37, "Jörn M. Horschig" wrote: >> >>> Hi Mariana, >>> >>> On 5/23/2013 10:25 AM, Mariana Branco wrote: >>>> Hello, >>>> >>>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. >>>> My questions are: >>>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time? >>> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does). Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure. >>>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure? >>> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start. >>> >>>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this? >>> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this. >>>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing? >>> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this). >>> >>> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions. >>> >>> Good luck! >>> Best, >>> Jörn >>> >>>> I am sorry for all the questions. >>> No problem, no way to know everything :) >>> >>>> Regards, >>>> >>>> Mariana Branco >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> -- >>> Jörn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> FieldTrip Development Team >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel: +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From giulia.rizza at tiscali.it Wed Jul 3 10:49:29 2013 From: giulia.rizza at tiscali.it (Giulia Rizza) Date: Wed, 3 Jul 2013 10:49:29 +0200 (CEST) Subject: [FieldTrip] unit ft_freqanalysis Message-ID: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> Dear Fieldtrip users I have a quick question. I've performed a Time Frequency Analysis with ft_freqanalysis using 'wavelet' as a method and 'relchange' as a baseline normalization for the plot. What is the unit for the ERD/ERS in the plot? Thank you so much for you help Giulia Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più di uno spot in TV. Per ogni nuovo abbonato 30 € di premio per te e per lui! Un amico al mese e parli e navighi sempre gratis: http://freelosophy.tiscali.it/ From a.stolk8 at gmail.com Wed Jul 3 10:55:39 2013 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 3 Jul 2013 10:55:39 +0200 Subject: [FieldTrip] unit ft_freqanalysis In-Reply-To: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> References: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> Message-ID: Hi Giulia, Baseline correction method 'relchange' computes the relative change according [ (task-baseline)/baseline ], i.e. a ratio centered around zero. If you multiply with 100, you get the relative change (from baseline) expressed in percentages. best regards, Arjen 2013/7/3 Giulia Rizza > Dear Fieldtrip users > I have a quick question. > I've performed a Time Frequency > Analysis with ft_freqanalysis using 'wavelet' as a method and 'relchange' > as a > baseline normalization for the plot. > What is the unit for the ERD/ERS in the > plot? > Thank you so much for you help > Giulia > > > Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più > di uno spot in TV. Per ogni nuovo abbonato 30 € di premio per te e per lui! > Un amico al mese e parli e navighi sempre gratis: > http://freelosophy.tiscali.it/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Wed Jul 3 16:21:14 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Wed, 3 Jul 2013 10:21:14 -0400 Subject: [FieldTrip] e-mail spoofing by ResearchGate Message-ID: This is unrelated to FieldTrip, but I think it still falls within the general interest of the community. Beware of e-mail spoofing by a company called ResearchGate. They send an e-mail that seems to come from a colleague of yours asking you to join, when in fact that colleague knows nothing about it. It is a spoofing scam. Just something to be aware of. Aaron Schurger ---------- Forwarded message ---------- From: Aaron Schurger Date: Wed, Jul 3, 2013 at 10:11 AM Subject: Re: ResearchGate: Response to your inquiry To: User Care You said "one of your co-authors claimed a publication on ResearchGate and invited you as a co-author". But which one of my co-authors? It was not the one who's e-mail address was listed as the "sender", because I asked that individual and they had not initiated any invitation. Why would you send me an e-mail showing the name "Anne Treisman" as the sender (see attached), with Anne's photo in the message saying explicitly "Anne Treisman invited you to join ResearchGate," when in fact Anne Treisman had not invited me to join ResearchGate. This is called "e-mail spoofing". In fact Treisman only joined ResearchGate in order to stop being harassed by e-mails purportedly from her colleague Bob Desimone, who in fact never invited her to join ResearchGate either! My first e-mail was polite. This one won't be - stop the bullshit. Sincerely, Aaron Schurger On Wed, Jul 3, 2013 at 9:13 AM, User Care wrote: > Hello, > > 2 Jul 2013: >> I've received e-mail "invitations" to join ResearchGate from people that I >> know, and when I asked if they had sent the invitation they said 'no'. I >> have colleagues who have all had the same experience (including the one who >> supposedly "invited" me). This does not inspire trust in your service. I >> certainly will not join. > > Thank you for your message. > > You received this notice because one of your co-authors claimed a publication on ResearchGate and invited you as a co-author. If you'd like to be put on our black list (meaning that we'll never email you again) - please follow the link in the footer of the email you received. > > Please do let us know if you have any further questions, > > Regards, > User Care -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Gmail - Anne Treisman invited you to join ResearchGate.pdf Type: application/pdf Size: 126588 bytes Desc: not available URL: From politzerahless at gmail.com Wed Jul 3 16:41:30 2013 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 3 Jul 2013 09:41:30 -0500 Subject: [FieldTrip] e-mail spoofing by ResearchGate Message-ID: Hi Aaron, I just wanted to clarify, Researchgate is not just a scam, it's a real site that some (although certainly not all) researchers use, similar to Academia.edu and things like that; see http://www.forbes.com/sites/alexknapp/2012/03/15/researchgate-wants-to-be-facebook-for-scientists/. I'm not sure why you were getting unsolicited e-mails; it's possible that when your colleagues signed up they accidentally forgot to uncheck an option to automatically invite co-authors (I've certainly made mistakes like that before on other places), or it might not be any fault of theirs and it might be some legitimate bug or something, or I guess it's possible you were getting e-mails from some other site masquerading as the actual ResearchGate. (I do admit even the real site does send a lot of e-mail notifications, but like Facebook and other things I've been able to change my preferences to stop getting most of them.) But anyway I just wanted to clarify what Researchgate actually is. Hope you get your problem resolved. Best, Steve Message: 1 > Date: Wed, 3 Jul 2013 10:21:14 -0400 > From: Aaron Schurger > To: FieldTrip discussion list > Subject: [FieldTrip] e-mail spoofing by ResearchGate > Message-ID: > < > CALeeyATYwZ7u1BuiWBx72Dn7tU5jZjuuf3pho9bgt33A-1Xy6A at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > This is unrelated to FieldTrip, but I think it still falls within the > general interest of the community. > > Beware of e-mail spoofing by a company called ResearchGate. They send > an e-mail that seems to come from a colleague of yours asking you to > join, when in fact that colleague knows nothing about it. It is a > spoofing scam. Just something to be aware of. > > Aaron Schurger > -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Wed Jul 3 21:03:35 2013 From: frank.ye.mei at gmail.com (Frank Mei) Date: Wed, 3 Jul 2013 15:03:35 -0400 Subject: [FieldTrip] beamformer Message-ID: Hello FieldtripList, In the beamformer tutorial ( http://fieldtrip.fcdonders.nl/tutorial/beamformer), the contrast of (post-pre)/pre was calculated. I am wondering why can't one just calculate (post-pre), instead. Could someone explain that? thanks, Ye Mei -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Wed Jul 3 21:16:12 2013 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 3 Jul 2013 21:16:12 +0200 Subject: [FieldTrip] beamformer In-Reply-To: References: Message-ID: Hi Ye Mei, Source-reconstructed activity (using the beamformer method) typically has a depth-bias (see van Veen et al., IEEE '97). Taking the relative increase/decrease of activity from baseline (effectively implementing a normalization per grid point location) is less prone to this bias as compared to taking the absolute difference. Hope this answers your question, Arjen 2013/7/3 Frank Mei > Hello FieldtripList, > > In the beamformer tutorial ( > http://fieldtrip.fcdonders.nl/tutorial/beamformer), the contrast of > (post-pre)/pre was calculated. I am wondering why can't one just > calculate (post-pre), instead. > > Could someone explain that? > > thanks, > Ye Mei > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Wed Jul 3 21:35:59 2013 From: frank.ye.mei at gmail.com (Frank Mei) Date: Wed, 3 Jul 2013 15:35:59 -0400 Subject: [FieldTrip] the right normalsation? Message-ID: Hello FieldtripList, I am trying to differentiate brain areas responsible for two different conditions using the method show in the tutorial( http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so far I have tried to subtract condition# 1 minus the #2, and divided by the average of the baseline period (pre-stimuli presentation), i.e., (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this division is for normalisation purposes. Is this the right normalsation? What normalization do you suggest to use? Is it necessary to normalise? thanks Ye -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Jul 4 10:39:00 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 04 Jul 2013 10:39:00 +0200 Subject: [FieldTrip] the right normalsation? In-Reply-To: References: Message-ID: <51D534A4.6080207@donders.ru.nl> Dear Ye, normalizing has different purposes. On the one hand, as Arjen pointed out, it is necessary to normalize in source space to get rid of the depth bias (well, alternatively you could normalize the leadfields). On the other hand, it makes averaging over subjects reasonable - otherwise differences in e.g. scalp conducitivity (for EEG) or headshape and size (for MEG) might lead to biasing an average in favour of some subjects. It is just the same reason as using a baseline when analysing ERPs/ERFs. Furthermore, there is no correct way of normalizing. As I said, you could also normalize the leadfield rather than normalizing by conditions. I think the most important thing to remember is that a) you need some contrast or b) you need to normalize the leadfield For a) it would be sufficient to use Post#1/Post#2, but I would rather not contrast two conditions normalized by two baselines. This gets really hard in interpretation (e.g. is the observed effect caused by a difference in baseline or a different in stimulus processing?). My favourite is log(Post#1/Post#2) or taking the z-score. Taking the logarithm has the advantage that extreme values get squashed nearer together, thereby reducing the influence of outliers. Z-scoring achieves a similar thing by explicitly normalizing by the variance. I would suggest for you to create some synthetic signals or values and play around with different ways of normalizing to get a feeling for what you are doing and what influence this has. I test different cases (e.g. 3: difference in prestim but no difference in poststim, no difference in prestim but difference in poststim and difference in prestim and poststim) and apply different normalizations/contrasts. Good luck :) Best, Jörn On 7/3/2013 9:35 PM, Frank Mei wrote: > Hello FieldtripList, > > I am trying to differentiate brain areas responsible for two different > conditions using the method show in the > tutorial(http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so > far I have tried to subtract condition# 1 minus the #2, and divided by > the average of the baseline period (pre-stimuli presentation), i.e., > (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this division > is for normalisation purposes. Is this the right normalsation? What > normalization do you suggest to use? Is it necessary to normalise? > > thanks > Ye > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From pgoodin at swin.edu.au Thu Jul 4 13:24:42 2013 From: pgoodin at swin.edu.au (Peter Goodin) Date: Thu, 4 Jul 2013 11:24:42 +0000 Subject: [FieldTrip] Running ICA on neuromag tsss data Message-ID: Hi Fieldtrip list, I've been using ICA (fastICA specifically) to clean blinks and cardiac artefact from my MEG data (neuromag 306 system) but find that I get some components that are "off" for a period and "on" for a period, or in other words some trials have the components "on" and others "off". I'm assuming these "off" periods are due to the differing dimensionality within the data due to the block by block rw nature of tsss, but when they're "on", they seem to contain a higher amplitude signal to the other components. My questions are: Are these on / off components due the differing dimensionality between blocks due to the tsss process? Is it more likely they contain data relating to the brain, something else such as movement, a mix of the two or it's simply impossible to tell? Thanks to anyone who can shed some light on this, Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate. Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.marshall at fcdonders.ru.nl Thu Jul 4 17:00:44 2013 From: t.marshall at fcdonders.ru.nl (Tom Marshall) Date: Thu, 04 Jul 2013 17:00:44 +0200 Subject: [FieldTrip] the right normalsation? In-Reply-To: <51D534A4.6080207@donders.ru.nl> References: <51D534A4.6080207@donders.ru.nl> Message-ID: <51D58E1C.6080002@fcdonders.ru.nl> Hi Jörn > My favourite is log(Post#1/Post#2) or taking the z-score. Could you expand on 'taking the z-score'? This could be interpreted in different ways, which might control for different sources of variance. To throw a bit more fuel on this fire... the problem with log ratios - ie log(post#1/post#2) - is that they ignore the prestimulus period altogether. That always seemed a bit funny to me. Presumably the brain response to your event of interest is somehow dependent on the brain state at the time the event happens ;) Of course one can independently test the hypothesis that the prestimulus periods differ, but how to be confident that they do not? On Thursday, July 04, 2013 10:39:00 AM, "Jörn M. Horschig" wrote: > Dear Ye, > > normalizing has different purposes. On the one hand, as Arjen pointed > out, it is necessary to normalize in source space to get rid of the > depth bias (well, alternatively you could normalize the leadfields). > On the other hand, it makes averaging over subjects reasonable - > otherwise differences in e.g. scalp conducitivity (for EEG) or > headshape and size (for MEG) might lead to biasing an average in > favour of some subjects. It is just the same reason as using a > baseline when analysing ERPs/ERFs. > Furthermore, there is no correct way of normalizing. As I said, you > could also normalize the leadfield rather than normalizing by > conditions. I think the most important thing to remember is that > a) you need some contrast or > b) you need to normalize the leadfield > > For a) it would be sufficient to use Post#1/Post#2, but I would rather > not contrast two conditions normalized by two baselines. This gets > really hard in interpretation (e.g. is the observed effect caused by a > difference in baseline or a different in stimulus processing?). My > favourite is log(Post#1/Post#2) or taking the z-score. Taking the > logarithm has the advantage that extreme values get squashed nearer > together, thereby reducing the influence of outliers. Z-scoring > achieves a similar thing by explicitly normalizing by the variance. > I would suggest for you to create some synthetic signals or values and > play around with different ways of normalizing to get a feeling for > what you are doing and what influence this has. I test different cases > (e.g. 3: difference in prestim but no difference in poststim, no > difference in prestim but difference in poststim and difference in > prestim and poststim) and apply different normalizations/contrasts. > > Good luck :) > Best, > Jörn > > > On 7/3/2013 9:35 PM, Frank Mei wrote: >> Hello FieldtripList, >> >> I am trying to differentiate brain areas responsible for two >> different conditions using the method show in the >> tutorial(http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so >> far I have tried to subtract condition# 1 minus the #2, and divided >> by the average of the baseline period (pre-stimuli presentation), >> i.e., (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this >> division is for normalisation purposes. Is this the right >> normalsation? What normalization do you suggest to use? Is it >> necessary to normalise? >> >> thanks >> Ye >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Tom Marshall, MSc. Neuronal Oscillations Group, Donders Centre for Cognitive Neuroimaging tel: +31(0)243668487 email: t.marshall at fcdonders.ru.nl postal: PO Box 9101, 6500HB, Nijmegen, The Netherlands visiting: Kapittelweg 29, 6525EN, Nijmegen, The Netherlands From aaron.schurger at gmail.com Thu Jul 4 21:33:29 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Thu, 4 Jul 2013 15:33:29 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question Message-ID: Hi, When you read in a data file using ft_preprocessing, with high-pass filtering, is the high-pass filter applied before the data are epoched (i.e. on the entire time series for the whole data file), or is the high-pass filter applied separately to each epoch? For very low frequencies (with period longer than one data epoch) this will make a difference. Thanks! Aaron -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From thomas.hartmann at th-ht.de Thu Jul 4 22:31:31 2013 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Thu, 04 Jul 2013 22:31:31 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: References: Message-ID: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> hi aaron, filtering is generally applied after the data have been epoched. to avoid the filter artifacts you are speaking about, we normally define epochs that are sufficiently larger so that these artifacts would be in data we are not interested in. about 1s at both ends of the epoch should be enough in most cases. but you better check... later you can use ft_redefinetrial to discard that extra data. hope this helps. best, thomas Aaron Schurger schrieb: >Hi, >When you read in a data file using ft_preprocessing, with high-pass >filtering, is the high-pass filter applied before the data are epoched >(i.e. on the entire time series for the whole data file), or is the >high-pass filter applied separately to each epoch? For very low >frequencies (with period longer than one data epoch) this will make a >difference. >Thanks! >Aaron > >-- >Aaron Schurger, PhD >Post-doctoral researcher >INSERM U992 / NeuroSpin >CEA - Saclay, France >+33-1-69-08-66-47 >aaron.schurger at gmail.com >http://www.unicog.org >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 5 03:51:45 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Thu, 4 Jul 2013 21:51:45 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> Message-ID: Thanks, Thomas. What if I wanted to apply the filtering to the entire time series first, and then extract the trial epochs after filtering? Is there a way to do that? Thanks, Aaron On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann wrote: > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: >> >> Hi, >> When you read in a data file using ft_preprocessing, with high-pass >> filtering, is the high-pass filter applied before the data are epoched >> (i.e. on the entire time series for the whole data file), or is the >> high-pass filter applied separately to each epoch? For very low >> frequencies (with period longer than one data epoch) this will make a >> difference. >> Thanks! >> Aaron >> >> -- >> Aaron Schurger, PhD >> Post-doctoral researcher >> INSERM U992 / NeuroSpin >> CEA - Saclay, France >> +33-1-69-08-66-47 >> aaron.schurger at gmail.com >> http://www.unicog.org >> ________________________________ >> >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From jm.horschig at donders.ru.nl Fri Jul 5 08:41:50 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 05 Jul 2013 08:41:50 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> Message-ID: <51D66AAE.70307@donders.ru.nl> Hi Aaron, in that case you need to define only one trial, going from 0 to the end of the recording and call ft_preprocessing. Not sure if this will work, but something like / cfg = [];// // ...// // hdr = ft_read_header(cfg.dataset);// // cfg.trl = [0 hdr.nSamples 0];// // data = ft_preprocessing(cfg);/ Subsequently you might want to try using ft_redefinetrial to get the epochs you are interested in. Note however that you need to have sufficient memory for reading all your data in. I am not sure how much memory you have, how long your recording is, how high your sampling rate and how many channels you have. If Matlab crashes when reading in everything, you would need to use trialpadding, or need to think of something clever yourself :) Would be great if you could let us know how you solve this in the end so that we can refer to that if someone else in future has a similar question. Best, Jörn On 7/5/2013 3:51 AM, Aaron Schurger wrote: > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: >> hi aaron, >> filtering is generally applied after the data have been epoched. to avoid >> the filter artifacts you are speaking about, we normally define epochs that >> are sufficiently larger so that these artifacts would be in data we are not >> interested in. about 1s at both ends of the epoch should be enough in most >> cases. but you better check... later you can use ft_redefinetrial to discard >> that extra data. >> hope this helps. >> best, >> thomas >> >> >> >> Aaron Schurger schrieb: >>> Hi, >>> When you read in a data file using ft_preprocessing, with high-pass >>> filtering, is the high-pass filter applied before the data are epoched >>> (i.e. on the entire time series for the whole data file), or is the >>> high-pass filter applied separately to each epoch? For very low >>> frequencies (with period longer than one data epoch) this will make a >>> difference. >>> Thanks! >>> Aaron >>> >>> -- >>> Aaron Schurger, PhD >>> Post-doctoral researcher >>> INSERM U992 / NeuroSpin >>> CEA - Saclay, France >>> +33-1-69-08-66-47 >>> aaron.schurger at gmail.com >>> http://www.unicog.org >>> ________________________________ >>> >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. Thomas Hartmann >> >> CIMeC - Center for Mind/Brain Sciences >> Università degli Studi di Trento >> via delle Regole, 101 >> 38060 Mattarello (TN) >> ITALY >> >> Tel: +39 0461 28 2779 >> Fax: +39 0461 28 3066 >> Email: thomas.hartmann at th-ht.de >> Homepage: http://sites.google.com/site/obobcimec/ >> >> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >> Doyle) >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri Jul 5 08:51:41 2013 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 5 Jul 2013 08:51:41 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: <46B38EE6-90F1-4B4F-8753-6F465EE39EC5@gmail.com> Hi Aaron (et al.) another way to filter the whole recording is the workaround using EEGlab. By default, you always read in the whole recording in EEGlab and apply all filters to the whole recording. After filtering, you can use eeglab2fieldtrip.m to move your filtered data from EEGlab to field trip. Note however, that Jörn's concern regarding your memory still applies. Also, filtering the whole recording takes quite some time. Best, Julian Am 05.07.2013 um 08:41 schrieb Jörn M. Horschig: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of the recording and call ft_preprocessing. Not sure if this will work, but something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs you are interested in. > > Note however that you need to have sufficient memory for reading all your data in. I am not sure how much memory you have, how long your recording is, how high your sampling rate and how many channels you have. If Matlab crashes when reading in everything, you would need to use trialpadding, or need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: >> Thanks, Thomas. What if I wanted to apply the filtering to the entire >> time series first, and then extract the trial epochs after filtering? >> Is there a way to do that? >> Thanks, >> Aaron >> >> On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann >> wrote: >>> hi aaron, >>> filtering is generally applied after the data have been epoched. to avoid >>> the filter artifacts you are speaking about, we normally define epochs that >>> are sufficiently larger so that these artifacts would be in data we are not >>> interested in. about 1s at both ends of the epoch should be enough in most >>> cases. but you better check... later you can use ft_redefinetrial to discard >>> that extra data. >>> hope this helps. >>> best, >>> thomas >>> >>> >>> >>> Aaron Schurger schrieb: >>>> Hi, >>>> When you read in a data file using ft_preprocessing, with high-pass >>>> filtering, is the high-pass filter applied before the data are epoched >>>> (i.e. on the entire time series for the whole data file), or is the >>>> high-pass filter applied separately to each epoch? For very low >>>> frequencies (with period longer than one data epoch) this will make a >>>> difference. >>>> Thanks! >>>> Aaron >>>> >>>> -- >>>> Aaron Schurger, PhD >>>> Post-doctoral researcher >>>> INSERM U992 / NeuroSpin >>>> CEA - Saclay, France >>>> +33-1-69-08-66-47 >>>> aaron.schurger at gmail.com >>>> http://www.unicog.org >>>> ________________________________ >>>> >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> Dr. Thomas Hartmann >>> >>> CIMeC - Center for Mind/Brain Sciences >>> Università degli Studi di Trento >>> via delle Regole, 101 >>> 38060 Mattarello (TN) >>> ITALY >>> >>> Tel: +39 0461 28 2779 >>> Fax: +39 0461 28 3066 >>> Email: thomas.hartmann at th-ht.de >>> Homepage: http://sites.google.com/site/obobcimec/ >>> >>> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >>> Doyle) >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.backus at donders.ru.nl Fri Jul 5 09:38:55 2013 From: a.backus at donders.ru.nl (Alexander Backus) Date: Fri, 5 Jul 2013 09:38:55 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields Message-ID: Hi, When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to covert to 3rd order gradient, it replaces the values in data.grad.chanpos and data.grad.chanori with NaNs. I assume this is done because they are no longer valid. When digging into the low-level code I found something about mismatching number of channels. Anyway, when I want to subsequently covert to planar gradient (does this actually makes sense?) or create a source model, I need these grad values. I have two questions: 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why are NaNs inserted in the grad subfields? 2) Can I still use the data for planar gradient conversion or source modeling by using the earlier stored old gradient info (pre ft_denoise_synthetic) or is this ill-advised and is there a more wise course of action? Thanks in advance, Best, Alexander Backus -- Alexander R. Backus, MSc PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Memory and Space Research Group www.doellerlab.com P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands Telephone: +31(0)24 36 10754 -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Fri Jul 5 10:16:11 2013 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Fri, 05 Jul 2013 10:16:11 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: <51D680CB.7040906@th-ht.de> hi, i would do this: /% do definetrial for all data...// //cfg = [];// //cfg.dataset = 'younameit.data';// //cfg.trialdef.triallength = Inf;// //cfg.trialdef.ntrials = 1;// // //cfg = ft_definetrial(cfg);// // //% preprocess all the data// //cfg.hpfilter = 'yes';// //cfg.hpfreq = 0.5;// // //alldata = ft_preprocessing(cfg);// // //% now we do definetrials for our trials...// //cfg = [];// //cfg.//trialdef.prestim = 2;// //cfg.trialdef.poststim = 2;// //cfg.trialdef.eventype = 'YourEventType';// //cfg.trialdef.eventvalue = [1 2 3 4 5];// // //cfg = ft_definetrial(cfg);// // //% now we use the trl field we just created for ft_redefinetrial...// //data_epochs = ft_redefinetrial(cfg, alldata);/ i havent tested the code but it should be more or less fine.. and the good thing is that you stay within the high level fieldtrip functions.... best, thomas On 05.07.2013 08:41, "Jörn M. Horschig" wrote: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the > end of the recording and call ft_preprocessing. Not sure if this will > work, but something like > > / cfg = [];// > // ...// > // hdr = ft_read_header(cfg.dataset);// > // cfg.trl = [0 hdr.nSamples 0];// > // data = ft_preprocessing(cfg);/ > > Subsequently you might want to try using ft_redefinetrial to get the > epochs you are interested in. > > Note however that you need to have sufficient memory for reading all > your data in. I am not sure how much memory you have, how long your > recording is, how high your sampling rate and how many channels you > have. If Matlab crashes when reading in everything, you would need to > use trialpadding, or need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end > so that we can refer to that if someone else in future has a similar > question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: >> Thanks, Thomas. What if I wanted to apply the filtering to the entire >> time series first, and then extract the trial epochs after filtering? >> Is there a way to do that? >> Thanks, >> Aaron >> >> On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann >> wrote: >>> hi aaron, >>> filtering is generally applied after the data have been epoched. to avoid >>> the filter artifacts you are speaking about, we normally define epochs that >>> are sufficiently larger so that these artifacts would be in data we are not >>> interested in. about 1s at both ends of the epoch should be enough in most >>> cases. but you better check... later you can use ft_redefinetrial to discard >>> that extra data. >>> hope this helps. >>> best, >>> thomas >>> >>> >>> >>> Aaron Schurger schrieb: >>>> Hi, >>>> When you read in a data file using ft_preprocessing, with high-pass >>>> filtering, is the high-pass filter applied before the data are epoched >>>> (i.e. on the entire time series for the whole data file), or is the >>>> high-pass filter applied separately to each epoch? For very low >>>> frequencies (with period longer than one data epoch) this will make a >>>> difference. >>>> Thanks! >>>> Aaron >>>> >>>> -- >>>> Aaron Schurger, PhD >>>> Post-doctoral researcher >>>> INSERM U992 / NeuroSpin >>>> CEA - Saclay, France >>>> +33-1-69-08-66-47 >>>> aaron.schurger at gmail.com >>>> http://www.unicog.org >>>> ________________________________ >>>> >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> Dr. Thomas Hartmann >>> >>> CIMeC - Center for Mind/Brain Sciences >>> Università degli Studi di Trento >>> via delle Regole, 101 >>> 38060 Mattarello (TN) >>> ITALY >>> >>> Tel: +39 0461 28 2779 >>> Fax: +39 0461 28 3066 >>> Email:thomas.hartmann at th-ht.de >>> Homepage:http://sites.google.com/site/obobcimec/ >>> >>> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >>> Doyle) >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 5 16:03:29 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 5 Jul 2013 10:03:29 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: Thanks, Jörn. If memory is an issue, I suppose I could try doing the filtering one channel at a time, applying redefinetrial to each channel (one at a time), and then put the resulting epochs back together in a field-trip structure. I'll let you know what I come up with (if I find a good solution). Memory may not end up being an issue because my recording sessions were only about 5 min long each, and with 8 Gb of RAM, should be OK. Cheers, Aaron On Fri, Jul 5, 2013 at 2:41 AM, "Jörn M. Horschig" wrote: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of > the recording and call ft_preprocessing. Not sure if this will work, but > something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs > you are interested in. > > Note however that you need to have sufficient memory for reading all your > data in. I am not sure how much memory you have, how long your recording is, > how high your sampling rate and how many channels you have. If Matlab > crashes when reading in everything, you would need to use trialpadding, or > need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so > that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: > > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: > > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: > > Hi, > When you read in a data file using ft_preprocessing, with high-pass > filtering, is the high-pass filter applied before the data are epoched > (i.e. on the entire time series for the whole data file), or is the > high-pass filter applied separately to each epoch? For very low > frequencies (with period longer than one data epoch) this will make a > difference. > Thanks! > Aaron > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > ________________________________ > > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From aaron.schurger at gmail.com Fri Jul 5 16:25:32 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 5 Jul 2013 10:25:32 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D680CB.7040906@th-ht.de> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> <51D680CB.7040906@th-ht.de> Message-ID: Hi, Thomas, Yes, this is roughly what I tried to do, but I couldn't get it to work at first. But I used ft_preprocessing instead of ft_redefinetrial, and I think that was the mistake. With ft_redefinetrial, now it works just fine. Simple - thanks! By the way, when the trials are redefined, fieldtrip always reports "found 31 events" and then "created 30 trials" (there are 30 trials in each block). Why does fieldtrip always report one extra event per run? Thanks! Aaron On Fri, Jul 5, 2013 at 4:16 AM, Thomas Hartmann wrote: > hi, > i would do this: > > % do definetrial for all data... > cfg = []; > cfg.dataset = 'younameit.data'; > cfg.trialdef.triallength = Inf; > cfg.trialdef.ntrials = 1; > > cfg = ft_definetrial(cfg); > > % preprocess all the data > cfg.hpfilter = 'yes'; > cfg.hpfreq = 0.5; > > alldata = ft_preprocessing(cfg); > > % now we do definetrials for our trials... > cfg = []; > cfg.trialdef.prestim = 2; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventype = 'YourEventType'; > cfg.trialdef.eventvalue = [1 2 3 4 5]; > > cfg = ft_definetrial(cfg); > > % now we use the trl field we just created for ft_redefinetrial... > data_epochs = ft_redefinetrial(cfg, alldata); > > i havent tested the code but it should be more or less fine.. and the good > thing is that you stay within the high level fieldtrip functions.... > > best, > thomas > > > > > On 05.07.2013 08:41, "Jörn M. Horschig" wrote: > > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of > the recording and call ft_preprocessing. Not sure if this will work, but > something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs > you are interested in. > > Note however that you need to have sufficient memory for reading all your > data in. I am not sure how much memory you have, how long your recording is, > how high your sampling rate and how many channels you have. If Matlab > crashes when reading in everything, you would need to use trialpadding, or > need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so > that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: > > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: > > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: > > Hi, > When you read in a data file using ft_preprocessing, with high-pass > filtering, is the high-pass filter applied before the data are epoched > (i.e. on the entire time series for the whole data file), or is the > high-pass filter applied separately to each epoch? For very low > frequencies (with period longer than one data epoch) this will make a > difference. > Thanks! > Aaron > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > ________________________________ > > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From szabbanto at gmail.com Fri Jul 5 16:51:36 2013 From: szabbanto at gmail.com (=?ISO-8859-1?Q?Szabolcs_Szeb=E9nyi?=) Date: Fri, 5 Jul 2013 16:51:36 +0200 Subject: [FieldTrip] Question about ft_freqanalysis using wavelet method Message-ID: Dear Fieldtrip developers and users, I have a question about ft_freqanalysis when I use the 'wavelet' method. When I call this fieldtrip function with the specifications below, I get an error message right at the first trial: Error using zeros Out of memory. Type HELP MEMORY for your options. Error in ft_freqanalysis (line 601) if powflg, powspctrm = nan+zeros(ntrials,nchan,nfoi,ntoi,cfg.precision); end Here are my specifications: cfg = []; cfg.trials = find(data.trialinfo(:,3) == iPhase); cfg.channel = 'MEG'; cfg.method = 'wavelet'; cfg.toi = -1.5:0.005:4; cfg.foi = 30:1:90; cfg.width = 5; cfg.keeptrials = 'yes'; cfg.output = 'pow'; cfg.pad = 'maxperlen'; cfg.padtype = 'zero'; cfg.polyremoval = 0; I tried out the wavelet approach already for lower frequencies (foi = 1:0.5:30; toi = -1.5:0.1:4; width = 7) and it worked fine for that. For the higher frequencies above, it cannot proceed further to the 2nd trial with 60GB memory either, so I think, the problem is somewhere else. The data itself consists of 275 trials, with a sampling rate of 600Hz; 273 channels CTF MEG. I would highly appreciate if you could tell me where the problem is and what I should change in order to proceed. Thank you in advance for your help, Szabolcs Szebényi -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcpiastra at libero.it Fri Jul 5 17:47:32 2013 From: mcpiastra at libero.it (mcpiastra at libero.it) Date: Fri, 5 Jul 2013 17:47:32 +0200 (CEST) Subject: [FieldTrip] source_recontruction with intracranial sensors Message-ID: <20502312.13722601373039252586.JavaMail.defaultUser@defaultHost> Dear Fieldtrip developers and users, I have some problems with source reconstruction starting with intracranial sensors. Schematic details are below. Aim: do source reconstruction using BEM for the forward problem and mne for the inverse problem. Dataset: stereoEEG recording (50 sec) Notation: I'll use the same nomenclature of the one in the tutorial Since we have intracranial sensors, our aim is to build the forward model (leadfield structure) starting from a mesh whose cortical sheet has a higher spatial resolution. To do that we approached the problem in two ways: 1) we substituted the innermost sheet, built by ft_prepare_mesh, with the Freesurfer cortical mesh (4180 vertices). We put dipoles on the mesh nodes and then we built the head model and calculate the leadfield matrices (one for each dipole). Solving the inverse problem, in source.avg.pow there were values with order of magnitude of 10^{-30}- 10^{-20}. This is due to the fact that the matrix vol.mat (one of the output of ft_prepare_headmodel) had values very different if we compared the entries in correspondence to the Fieldtrip meshes and the ones in correspondence to the Freesurfer mesh. This difference had the order of magnitude equal to 10^{9}. Due to this pathology, we tried a different way to compute the forward model (following more the tutorial). 2) we built the head model using the default Fieldtrip meshes (all of the three sheets) without substituting any sheet. (We just fixed the number of nodes for the innermost sheet equal to the Freesurfer one.) This avoided high differences in vol.mat. Freesurfer mesh vertices were used to determine dipole positions, as we did before. In this case we obtained values of source.avg.pow of the order of 10^ {-6} In both cases we preprocessed the dataset with ft_timelockanalysis and we used the regularization parameter lambda (for the mne method) equal to 0.2. Our questions are: 1) what is vol.mat? Which order of magnitude should have its values? We didn't manage to explore the building process of it. (We suppose this matrix has electrical information interpolated through the mesh vertices.) As consequences: 2) which is the order of magnitude expected for the values of source.avg.pow ? And which is its unit of measure? 3) Is it correct the interpretation of: source.avg.mom and source.avg.pow as the evolution through time of the electric dipole moment and the radiated power of the dipole, respectively? 4) In order to apply a regularization approach to solve the inverse problem we though that the best way was to introduce the noise covariation matrix built by the function ft_timelockanalysis which is subsequently controlled by the lambda parameter. Is there any criterion to choose the best lambda? Can we avoid to pass through ft_timelockanalysis to regularize the solution? Many thanks, Maria Carla Piastra PhD student in Bioengeneering c/o BioLab @ DIBRIS University of Genova, ITALY From zriouil.imane at gmail.com Fri Jul 5 21:44:41 2013 From: zriouil.imane at gmail.com (z.imane) Date: Fri, 5 Jul 2013 20:44:41 +0100 Subject: [FieldTrip] Computing the spike triggered average LFP Message-ID: Hi i would applying the paragraph "Computing the spike triggered average LFP" in tutorial "Preprocessing and analysis of spike and local field potential data" in matlab. if you explain this pocess more, because i don't understand it. -------------- next part -------------- An HTML attachment was scrubbed... URL: From baharbahar395 at yahoo.com Sat Jul 6 08:05:37 2013 From: baharbahar395 at yahoo.com (Bahar Bahar) Date: Sat, 6 Jul 2013 14:05:37 +0800 (SGT) Subject: [FieldTrip] sLORETA Message-ID: <1373090737.76319.YahooMailNeo@web192303.mail.sg3.yahoo.com> Hi dear all, I have computed sloreta from ERP data via the software, but I do not know what is the unit of the values resulted in transformation. Can any one help me about that? -------------- next part -------------- An HTML attachment was scrubbed... URL: From baharbahar395 at yahoo.com Sat Jul 6 08:15:53 2013 From: baharbahar395 at yahoo.com (Bahar Bahar) Date: Sat, 6 Jul 2013 14:15:53 +0800 (SGT) Subject: [FieldTrip] Sloreta Message-ID: <1373091353.41529.YahooMailNeo@web192306.mail.sg3.yahoo.com> Hi dear all, I have computed sloreta from ERP data via the Sloreta software, but I did not figure out the unit of the values resulted in transformation. Can any one help me about that? Thanks, Bahar -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Sat Jul 6 09:53:09 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Sat, 6 Jul 2013 09:53:09 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data Message-ID: Dear All, after running source statistics I tried to plot the result. However, I always get the error that cfg.parameter 'all' can't be used since there is "no such field". I know that I can also specify single parameters, i.e. only the ones I want to interpolate. However, I would like to know why it doesn't work for me with all the parameters... Maybe it's only a minor thing, i.e. the FT version. But I want to make sure that there is no major error in my pipeline. Any help is as always very appreciated! Thanks! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Sat Jul 6 14:19:58 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sat, 06 Jul 2013 14:19:58 +0200 Subject: [FieldTrip] Question about ft_freqanalysis using wavelet method In-Reply-To: References: Message-ID: <51D80B6E.5040704@donders.ru.nl> Hi Szabi, That error has nothing to do with the wavelet approach but with the fact that you want to have steps of 5ms (as specified in cfg.toi) for your TFR. FieldTrip will create one big data matrin nTrials x nChannels x nSamples x nFrequencies. With the settings you specified this will be quite huge, and it does not fit into memory when Matlab tries to initiate that variable. I would suggest you use 50ms steps, that is sufficient especially given that you need some tens of milliseconds for estimating the frequency content anyway. An alternative would be to use the torque/maui cluster at the Donders and request a session with loads of memory :) Best, Jörn On 7/5/2013 4:51 PM, Szabolcs Szebényi wrote: > Dear Fieldtrip developers and users, > > I have a question about ft_freqanalysis when I use the 'wavelet' > method. When I call this fieldtrip function with the specifications > below, I get an error message right at the first trial: > > Error using zeros > Out of memory. Type HELP MEMORY for your options. > > Error in ft_freqanalysis (line 601) > if powflg, powspctrm = > nan+zeros(ntrials,nchan,nfoi,ntoi,cfg.precision); > end > > Here are my specifications: > > cfg = []; > cfg.trials = find(data.trialinfo(:,3) == iPhase); > cfg.channel = 'MEG'; > cfg.method = 'wavelet'; > cfg.toi = -1.5:0.005:4; > cfg.foi = 30:1:90; > cfg.width = 5; > cfg.keeptrials = 'yes'; > cfg.output = 'pow'; > cfg.pad = 'maxperlen'; > cfg.padtype = 'zero'; > cfg.polyremoval = 0; > > I tried out the wavelet approach already for lower frequencies (foi = > 1:0.5:30; toi = -1.5:0.1:4; width = 7) and it worked fine for that. > For the higher frequencies above, it cannot proceed further to the 2nd > trial with 60GB memory either, so I think, the problem is somewhere else. > > The data itself consists of 275 trials, with a sampling rate of 600Hz; > 273 channels CTF MEG. > > I would highly appreciate if you could tell me where the problem is > and what I should change in order to proceed. > > > Thank you in advance for your help, > > Szabolcs Szebényi > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Jul 7 19:41:51 2013 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 7 Jul 2013 19:41:51 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data Message-ID: Hi Andreas , It is annoying that it doesn't work if you specify cfg.parameter 'all' and I don't know why either. However , I have a very simple solution for this by interpolating 'stat' and 'mask' then combining afterwards when you want to plot your statistic result. The FT code is something like this: cfg = []; cfg.voxelcoord = 'no'; cfg.parameter = 'stat'; cfg.interpmethod = 'nearest'; cfg.coordsys = 'mni'; statplot = ft_sourceinterpolate(cfg, stat,mri); cfg = []; cfg.voxelcoord = 'no'; cfg.parameter = 'mask'; cfg.interpmethod = 'nearest'; cfg.coordsys = 'mni'; mask = ft_sourceinterpolate(cfg, stat,mri); statplot.mask = mask.mask; Hope this helps. Best, Haiteng > Message: 3 > Date: Sat, 6 Jul 2013 09:53:09 +0200 > From: Andreas Sauer > To: FieldTrip discussion list > Subject: [FieldTrip] ft_sourceinterpolate with stats data > Message-ID: > < > CAHLSopWD2Q-RuAMJrvwZJGAajB6aUbDyrDN6_SFMdqu7HOgZ0g at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > after running source statistics I tried to plot the result. However, I > always get the error that cfg.parameter 'all' can't be used since there is > "no such field". > > I know that I can also specify single parameters, i.e. only the ones I want > to interpolate. However, I would like to know why it doesn't work for me > with all the parameters... Maybe it's only a minor thing, i.e. the FT > version. But I want to make sure that there is no major error in my > pipeline. > > Any help is as always very appreciated! Thanks! > > Best, > > Andreas > > -- > Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstra?e 46 > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130706/b595b2e2/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 32, Issue 11 > ***************************************** > -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Jul 7 20:17:58 2013 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 7 Jul 2013 20:17:58 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields Message-ID: Hi Alexander, I am not clear about what's ft_denoise_synthetic doing. However , I don't have such problem when I use . The reason you get 'mismatching number of channels' probably because you specify cfg.channel ='MEG' instead of including all channels. My FT code is something like this: % reading cfg = []; cfg.dataset = dataset; cfg.trialdef.eventtype = ''; cfg.trialdef.eventvalue = ; cfg.continuous = 'yes'; cfg.channel= 'all'; cfg.trialdef.prestim = ; cfg.trialdef.poststim = ; cfg = ft_definetrial(cfg); trl = cfg.trl; cfg.detrend ='yes'; cfg.demean = 'yes'; data= ft_preprocessing(cfg); cfg.gradient = 'G3BR'; data= ft_denoise_synthetic(cfg,data); In my pipeline , the grad changes into NAN only after I run I ICA to remove artifacts . I replace this grad with previous good gradient information and assume it is fine for the latter source reconstruction. Hope this helps. Best, Haiteng > > > Message: 2 > Date: Fri, 5 Jul 2013 09:38:55 +0200 > From: Alexander Backus > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in > grad fields > Message-ID: > < > CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to > covert to 3rd order gradient, it replaces the values in data.grad.chanpos > and data.grad.chanori with NaNs. > > I assume this is done because they are no longer valid. > When digging into the low-level code I found something about mismatching > number of channels. > > Anyway, when I want to subsequently covert to planar gradient (does this > actually makes sense?) or create a source model, I need these grad values. > > I have two questions: > > 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why > are NaNs inserted in the grad subfields? > > 2) Can I still use the data for planar gradient conversion or source > modeling by using the earlier stored old gradient info (pre > ft_denoise_synthetic) or is this ill-advised and is there a more wise > course of action? > > Thanks in advance, > Best, > Alexander Backus > -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Mon Jul 8 10:34:06 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Mon, 8 Jul 2013 10:34:06 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data In-Reply-To: References: Message-ID: Thanks for your answer, Haiteng! It also works for me when I interpolate i.e. 'stat'. However, it would be good to know why 'all' does not work, since it is described in the tutorial... Best, Andreas 2013/7/7 Haiteng Jiang > Hi Andreas , > It is annoying that it doesn't work if you specify cfg.parameter > 'all' and I don't know why either. However , I have a very simple > solution for this by interpolating 'stat' and 'mask' then combining > afterwards when you want to plot your statistic result. The FT code is > something like this: > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'stat'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > statplot = ft_sourceinterpolate(cfg, stat,mri); > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'mask'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > mask = ft_sourceinterpolate(cfg, > stat,mri); > statplot.mask = mask.mask; > Hope this helps. > > Best, > Haiteng > > > > >> Message: 3 >> Date: Sat, 6 Jul 2013 09:53:09 +0200 >> From: Andreas Sauer >> To: FieldTrip discussion list >> Subject: [FieldTrip] ft_sourceinterpolate with stats data >> Message-ID: >> < >> CAHLSopWD2Q-RuAMJrvwZJGAajB6aUbDyrDN6_SFMdqu7HOgZ0g at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear All, >> >> after running source statistics I tried to plot the result. However, I >> always get the error that cfg.parameter 'all' can't be used since there is >> "no such field". >> > > >> >> I know that I can also specify single parameters, i.e. only the ones I >> want >> to interpolate. However, I would like to know why it doesn't work for me >> with all the parameters... Maybe it's only a minor thing, i.e. the FT >> version. But I want to make sure that there is no major error in my >> pipeline. >> >> Any help is as always very appreciated! Thanks! >> >> Best, >> >> Andreas >> >> -- >> Andreas Sauer >> Max Planck Institute for Brain Research >> Deutschordenstra?e 46 >> >> 60528 Frankfurt am Main >> Germany >> >> T: +49 69 96769 278 >> F: +49 69 96769 327 >> Email: sauer.mpih at gmail.com >> www.brain.mpg.de >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130706/b595b2e2/attachment-0001.html >> > >> >> ------------------------------ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 32, Issue 11 >> ***************************************** >> > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Dipl.-Psych. Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 8 11:30:39 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 08 Jul 2013 11:30:39 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data In-Reply-To: References: Message-ID: <51DA86BF.3000801@donders.ru.nl> Hi Andreas, all the chiefs are on vacation right now, and I do not know if it should work or why it does not. Therefore, I created a bug on bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2218 You can also sign up there and add yourself to the CC list to stay informed about the progress on this. In the meanwhile I would suggest to do as Haiteng proposed, as this is the only way to go right now. Thanks for reporting :) Best, Jörn On 7/8/2013 10:34 AM, Andreas Sauer wrote: > Thanks for your answer, Haiteng! It also works for me when I > interpolate i.e. 'stat'. However, it would be good to know why 'all' > does not work, since it is described in the tutorial... > > Best, > > Andreas > > > 2013/7/7 Haiteng Jiang > > > Hi Andreas , > It is annoying that it doesn't work if you > specify cfg.parameter 'all' and I don't know why either. However > , I have a very simple solution for this by interpolating 'stat' > and 'mask' then combining afterwards when you want to plot your > statistic result. The FT code is something like this: > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'stat'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > statplot = ft_sourceinterpolate(cfg, stat,mri); > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'mask'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > mask = ft_sourceinterpolate(cfg, > stat,mri); > statplot.mask = mask.mask; > Hope this helps. > Best, > Haiteng > > Message: 3 > Date: Sat, 6 Jul 2013 09:53:09 +0200 > From: Andreas Sauer > > To: FieldTrip discussion list > > Subject: [FieldTrip] ft_sourceinterpolate with stats data > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > Dear All, > > after running source statistics I tried to plot the result. > However, I > always get the error that cfg.parameter 'all' can't be used > since there is > "no such field". > > > I know that I can also specify single parameters, i.e. only > the ones I want > to interpolate. However, I would like to know why it doesn't > work for me > with all the parameters... Maybe it's only a minor thing, i.e. > the FT > version. But I want to make sure that there is no major error > in my > pipeline. > > Any help is as always very appreciated! Thanks! > > Best, > > Andreas > > -- > Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstra?e 46 > > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 32, Issue 11 > ***************************************** > > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Dipl.-Psych. Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstraße 46 > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 8 11:33:29 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 08 Jul 2013 11:33:29 +0200 Subject: [FieldTrip] Computing the spike triggered average LFP In-Reply-To: References: Message-ID: <51DA8769.6000006@donders.ru.nl> Dear Zriouil, the problem you described is rather incomplete. If you adress certain sections in particular and state in more detail what exactly you do not understand, there might be more people abel to help you. Usually, the tutorial aim at being sufficient to get started, but if they are unclear on particular location, we would be glad to hear your thought on where they are unclear and what information needs to be added to improve them. Best, Jörn On 7/5/2013 9:44 PM, z.imane wrote: > Hi > > i would applying the paragraph "Computing the spike triggered average > LFP" in tutorial "Preprocessing and analysis of spike and local field > potential data" in matlab. if you explain this pocess more, because i > don't understand it. > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hubert.preissl at uni-tuebingen.de Mon Jul 8 11:33:59 2013 From: hubert.preissl at uni-tuebingen.de (Hubert Preissl) Date: Mon, 08 Jul 2013 11:33:59 +0200 Subject: [FieldTrip] =?windows-1252?q?6th_Autumn_School_=93Move_the_Brain?= =?windows-1252?q?=94=2C_T=FCbingen=2C_30thSeptember_-2th_October_2013?= In-Reply-To: References: Message-ID: <51DA8787.3010904@uni-tuebingen.de> Hello, we are pleased to announce the upcoming 6^th Autumn School "Move the Brain" in Tübingen. Confirmed speakers: *Douglas Cheyne, *Hospital for Sick Children, Toronto, Canada *Sarang S. Dalal, *University of Konstanz, Germany *Joachim Gross, *University of Glasgow, UK *Todd Hare, *University of Zürich, Switzerland *Floris de Lang, *Donders Institute, Nijmegen, Netherlands *Jyrki Mäkelä, *Helsinki University Central Hospital, Finland *Hilke Plassmann, *INSEAD, France *Alfons Schnitzler, *University of Düsseldorf, Germany For application and further information on the scientific program please visit our website: http://www.mp.uni-tuebingen.de/mp/index.php?id=412 We look forward meeting you in Tübingen! Best regards, Hubert Preissl -- Dr. Hubert Preissl fMEG Center phone: ++49-(0)7071-2987704 Otfried Müller Str 47 fax: ++49-(0)7071-295706 72076 Tübingen, Germany email: hubert.preissl at uni-tuebingen.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From zriouil.imane at gmail.com Mon Jul 8 12:47:03 2013 From: zriouil.imane at gmail.com (z.imane) Date: Mon, 8 Jul 2013 12:47:03 +0200 Subject: [FieldTrip] Computing the spike triggered average LFP In-Reply-To: <51DA8769.6000006@donders.ru.nl> References: <51DA8769.6000006@donders.ru.nl> Message-ID: Thank you for your response. I wish to plotting LFP based on spike using a program that I want to create. and for the obtained the same graph as in the tutorial. the problem is that I do not understand how the function ft_spiketriggeredaverage computes the avererage of the LFP around the spikes, while the spikes and LFP are recorded in the same period, and how he detect the spike? -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.mercier at einstein.yu.edu Mon Jul 8 15:32:02 2013 From: manuel.mercier at einstein.yu.edu (Manuel Mercier) Date: Mon, 8 Jul 2013 13:32:02 +0000 Subject: [FieldTrip] ft_connectivityanalysis and PLV formula Message-ID: Dear Fieldtrip Community I am still stuck with the implementation of PLV. To be sure that I understand properly the principle of Phase Locking Value, I wrote a code to compute it. That code (see below) gave me the same results as ft_connectivityanalysis. plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)) -angle(data.fourierspctrm(:,electrode_2,:,:)))),1))); (data.fourierspctrm being produced by ft_freqanalysis). However, I then realized that the subtraction between the two angles should be done in the complex plane as in: plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)))) - exp(1i*(angle(data.fourierspctrm(:,electrode_2,:,:))))))),1))); I doubt that PLV computed through FT is wrong, but then I am circumspect since the first formula is somewhat no correct and give the same results a as ft_connectivityanalysis. I went to FT code and got confused by the way ft_connectivity_corr use the cross spectrum to compute PLV. I would greatly appreciate if someone could tell me where I am missing/misunderstanding something. Thanks you for your help, Manuel ________________________________ Manuel Mercier, PhD Research Fellow Cognitive Neurophysiology Laboratory, Children’s Evaluation and Rehabilitation Center (CERC), Departments of Pediatrics and Neuroscience Albert Einstein College of Medicine, 1225 Morris Park Avenue Bronx , NY 10461 phone: +1 (718) 862 1859 fax: +1 (718) 862 1807 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manuel Mercier [manuel.mercier at einstein.yu.edu] Sent: Friday, June 28, 2013 4:43 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] PLV formula Dear Fieldtripers Sometime ago I wrote for myself a function that was computing PLV and some related non parametric statistics. (Phase Locking Value as define as the mean across trials of the phase angle difference recorded at two loci ; based on Lachaux et al., 1999, HBM). I implemented PLV in matlab using the following formula: plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)) ... -angle(data.fourierspctrm(:,cmb(2),:,:)))),1))); with cmb(1) and cmb(2) being the indices of the electrodes of interest (between which PLV is computed). I compared my results with the ft_connectivityanalysis function from Fieldtrip and the results were exactly the same. So far so good. But I recently went back to my code, and I was a little bit confused. Since I was dealing with angles, I though that the best way to do the subtraction should be done in the complex plane Like: plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)))) ... - exp(1i*(angle(data.fourierspctrm(:,cmb(2),:,:))))))),1))); (for instance if the two angles: pi/2 and -pi/2 the direct subtraction will give pi, whereas in the complex plan it will be pi/2 - with the norm x2). The result I got with this code is obviously different from the previous one, and what I got from Fieldtrip. I went back to the archive of the mailing list but didn't find a clear answer to my point. Does anyone can enlighten me ? Thanks ! Manuel -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Tue Jul 9 00:45:37 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Tue, 9 Jul 2013 00:45:37 +0200 Subject: [FieldTrip] sEEG Source Imaging - mne solution Message-ID: Dear FieldTrip comunity, i'm dealing with MNE source reconstruction of sEEG signals. I would like to know if it is possible to use the mesh of the source-model, obtained by MNE_Suite, as the 'brain' mesh (the inner ) of the head model prepared with ft_prepare_headmodel with the 'dipoli' method, solving the forward problem. I've tried to make this step to get a more accurate inverse solution but my results seemed completely wrong and totally different by the ones obtained using a 'traditional' head model built with ft_prepare:headmodel in the 'dipoli' case. Thanks for your attention, Alberto Ghione -------------- next part -------------- An HTML attachment was scrubbed... URL: From robince at gmail.com Tue Jul 9 18:14:40 2013 From: robince at gmail.com (Robin) Date: Tue, 9 Jul 2013 17:14:40 +0100 Subject: [FieldTrip] obtaining voxel locations Message-ID: I was wondering how to get the voxel positions (or origin and voxel size) for a fieltrip mri structure. I have an anatomical scan which I have normalised to the T1 brain: >> mrin mrin = anatomy: [181x217x181 double] transform: [4x4 double] dim: [181 217 181] params: [1x1 struct] initial: [4x4 double] coordsys: 'spm' cfg: [1x1 struct] I can I obtain the location of any voxel in MNI coordinates (mm or cm)? When loading a Nifti file (with load_nii) I can find origin and voxel_size with: voxel_size = abs(nii.hdr.dime.pixdim(2:4)); % vol in mm origin = round(abs(nii.hdr.hist.originator(1:3))); and then posmm = (vox-origin) .* voxel_size. Is there any way to do the same from the fieldtrip structure? I can't find the corresponding header information. Thanks Robin -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.backus at donders.ru.nl Tue Jul 9 18:46:40 2013 From: a.backus at donders.ru.nl (Alexander Backus) Date: Tue, 9 Jul 2013 18:46:40 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields In-Reply-To: References: Message-ID: Thanks for your answer Haiteng. To share our findings on this topic: After some more debugging, we realized that it could indeed be the ICA function that inserts NaNs into the grad info. It seems ft_denoise_synthetic only changes the grad info for some reference channels... We now use Haiteng's trick of replacing the post-ICA grad info, with the post-denoise grad info, however, it feels somewhat dangerous to perform such "dirty" fixes, since that grad info is probably removed for a certain reason. We are oblivious to its impact subsequent steps like planar transform and source reconstruction. In addition, we dug up the following page on the FieldTrip wiki which explains the denoising. http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work Thanks! Cheers, Alexander On Sun, Jul 7, 2013 at 8:17 PM, Haiteng Jiang wrote: > Hi Alexander, > I am not clear about what's ft_denoise_synthetic doing. However , I > don't have such problem when I use . The reason you get > 'mismatching number of channels' probably because you specify cfg.channel > ='MEG' instead of including all channels. My FT code is something like > this: > > % reading > cfg = []; > cfg.dataset = dataset; > cfg.trialdef.eventtype = ''; > cfg.trialdef.eventvalue = ; > cfg.continuous = 'yes'; > cfg.channel= 'all'; > cfg.trialdef.prestim = ; > cfg.trialdef.poststim = ; > cfg = ft_definetrial(cfg); > trl = cfg.trl; > cfg.detrend ='yes'; > cfg.demean = 'yes'; > data= ft_preprocessing(cfg); > cfg.gradient = 'G3BR'; > data= ft_denoise_synthetic(cfg,data); > > In my pipeline , the grad changes into NAN only after I run I ICA to > remove artifacts . I replace this grad with previous good gradient > information and assume it is fine for the latter source reconstruction. > Hope this helps. > Best, > Haiteng > > >> >> >> Message: 2 >> Date: Fri, 5 Jul 2013 09:38:55 +0200 >> From: Alexander Backus >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in >> grad fields >> Message-ID: >> < >> CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi, >> >> When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to >> covert to 3rd order gradient, it replaces the values in data.grad.chanpos >> and data.grad.chanori with NaNs. >> >> I assume this is done because they are no longer valid. >> When digging into the low-level code I found something about mismatching >> number of channels. >> >> Anyway, when I want to subsequently covert to planar gradient (does this >> actually makes sense?) or create a source model, I need these grad values. >> >> I have two questions: >> >> 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why >> are NaNs inserted in the grad subfields? >> >> 2) Can I still use the data for planar gradient conversion or source >> modeling by using the earlier stored old gradient info (pre >> ft_denoise_synthetic) or is this ill-advised and is there a more wise >> course of action? >> >> Thanks in advance, >> Best, >> Alexander Backus >> > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Alexander R. Backus, MSc PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Memory and Space Research Group www.doellerlab.com P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands Telephone: +31(0)24 36 10754 -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:12:01 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:42:01 +0430 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields In-Reply-To: References: Message-ID: *Hello,** * I am mohsen alimoradi, MSc student of artificial intelligence in Qazvin Azad University. * **I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot* On Tue, Jul 9, 2013 at 9:16 PM, Alexander Backus wrote: > Thanks for your answer Haiteng. > > To share our findings on this topic: > > After some more debugging, we realized that it could indeed be the ICA > function that inserts NaNs into the grad info. > > It seems ft_denoise_synthetic only changes the grad info for some > reference channels... > > We now use Haiteng's trick of replacing the post-ICA grad info, with the > post-denoise grad info, however, it feels somewhat dangerous to perform > such "dirty" fixes, since that grad info is probably removed for a certain > reason. We are oblivious to its impact subsequent steps like planar > transform and source reconstruction. > > In addition, we dug up the following page on the FieldTrip wiki which > explains the denoising. > > http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work > > Thanks! > > Cheers, > Alexander > > > On Sun, Jul 7, 2013 at 8:17 PM, Haiteng Jiang wrote: > >> Hi Alexander, >> I am not clear about what's ft_denoise_synthetic doing. However , >> I don't have such problem when I use . The reason you get >> 'mismatching number of channels' probably because you specify cfg.channel >> ='MEG' instead of including all channels. My FT code is something like >> this: >> >> % reading >> cfg = []; >> cfg.dataset = dataset; >> cfg.trialdef.eventtype = ''; >> cfg.trialdef.eventvalue = ; >> cfg.continuous = 'yes'; >> cfg.channel= 'all'; >> cfg.trialdef.prestim = ; >> cfg.trialdef.poststim = ; >> cfg = ft_definetrial(cfg); >> trl = cfg.trl; >> cfg.detrend ='yes'; >> cfg.demean = 'yes'; >> data= ft_preprocessing(cfg); >> cfg.gradient = 'G3BR'; >> data= ft_denoise_synthetic(cfg,data); >> >> In my pipeline , the grad changes into NAN only after I run I ICA to >> remove artifacts . I replace this grad with previous good gradient >> information and assume it is fine for the latter source reconstruction. >> Hope this helps. >> Best, >> Haiteng >> >> >>> >>> >>> Message: 2 >>> Date: Fri, 5 Jul 2013 09:38:55 +0200 >>> From: Alexander Backus >>> To: fieldtrip at science.ru.nl >>> Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in >>> grad fields >>> Message-ID: >>> < >>> CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> >>> Hi, >>> >>> When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to >>> covert to 3rd order gradient, it replaces the values in data.grad.chanpos >>> and data.grad.chanori with NaNs. >>> >>> I assume this is done because they are no longer valid. >>> When digging into the low-level code I found something about mismatching >>> number of channels. >>> >>> Anyway, when I want to subsequently covert to planar gradient (does this >>> actually makes sense?) or create a source model, I need these grad >>> values. >>> >>> I have two questions: >>> >>> 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why >>> are NaNs inserted in the grad subfields? >>> >>> 2) Can I still use the data for planar gradient conversion or source >>> modeling by using the earlier stored old gradient info (pre >>> ft_denoise_synthetic) or is this ill-advised and is there a more wise >>> course of action? >>> >>> Thanks in advance, >>> Best, >>> Alexander Backus >>> >> >> >> >> -- >> Haiteng Jiang >> PhD candidate >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> >> Visiting address >> Room 2.32 >> Donders Centre for Cognitive Neuroimaging >> Kapittelweg 29 >> 6525 EN Nijmegen >> the Netherlands >> >> Tel.: +31 (0)243668291 >> Web: https://sites.google.com/site/haitengjiang/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Alexander R. Backus, MSc > PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Memory and Space Research Group > www.doellerlab.com > > P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands > Telephone: +31(0)24 36 10754 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:12:17 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:42:17 +0430 Subject: [FieldTrip] obtaining voxel locations In-Reply-To: References: Message-ID: *Hello,** * I am mohsen alimoradi, MSc student of artificial intelligence in Qazvin Azad University. * **I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot * On Tue, Jul 9, 2013 at 8:44 PM, Robin wrote: > I was wondering how to get the voxel positions (or origin and voxel size) > for a fieltrip mri structure. > > I have an anatomical scan which I have normalised to the T1 brain: > > >> mrin > > mrin = > > anatomy: [181x217x181 double] > transform: [4x4 double] > dim: [181 217 181] > params: [1x1 struct] > initial: [4x4 double] > coordsys: 'spm' > cfg: [1x1 struct] > > I can I obtain the location of any voxel in MNI coordinates (mm or cm)? > When loading a Nifti file (with load_nii) I can find origin and voxel_size > with: > > voxel_size = abs(nii.hdr.dime.pixdim(2:4)); % vol in mm > origin = round(abs(nii.hdr.hist.originator(1:3))); > > and then posmm = (vox-origin) .* voxel_size. Is there any way to do the > same from the fieldtrip structure? I can't find the corresponding header > information. > > Thanks > > Robin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:14:01 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:44:01 +0430 Subject: [FieldTrip] (no subject) Message-ID: *Hello,** * ***I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot* -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Thu Jul 11 17:09:40 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Thu, 11 Jul 2013 17:09:40 +0200 Subject: [FieldTrip] ft_megrealign how to avoid? Message-ID: Dear all, I have CTF MEG data and I am interested in a gamma band topographies. We recorded two sessions for every subject. Now I would like to compare grand averages of these two sessions over all subjects(n=13). Without realignment these grand average topographies look ok and according to our expectation. However, I know that it would be reasonable to do realignment of all datasets (n=13x2) to common template. I have tried that with ft_megrealign which uses method suggested by Knösche, 2002 and this doesn't work. It gives me very weird results, meaning that topographies are totally changed and some new occipital activity emerges. I have plotted single subject head models(singleshell) together with sensors and they are accurately aligned. Then I tried different inwardshift options for ft_megrealign and this didn't bring so much success. So my question is, could I go without the realignment and what I need to do in order to overcome problem with realignment? -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Thu Jul 11 17:58:54 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 11 Jul 2013 17:58:54 +0200 (CEST) Subject: [FieldTrip] ft_megrealign how to avoid? In-Reply-To: Message-ID: <1783486843.2033915.1373558334245.JavaMail.root@sculptor.zimbra.ru.nl> Hi Nenad, You may want to check whether there are systematic differences (over the whole group of subjects) in head position in the first place. Here's an example page showing how to check head position/movement in MEG: http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis The same page also indicates how to 'regress out' variance accounted for by (different) head position. Applying this method on the datasets combined (trials of the two conditions for each subject) allows you to eliminate head position as a potential confound (by using ft_regressconfound prior to computing subject-level statistics). I have no first hand experience on to what extent megrealign can reduce the effects of different head position between two conditions, but from our experiences here we know that systematic differences in head position between conditions may even be noticeable at the source level. Optimally, one thus tries to minimize the influence of head movement wherever possible, i.e. already at recording. This may come in too late for your current dataset, but this online 'realignment' method may improve between- but also within-session consistency in future studies of yours involving the CTF MEG system (a Neuromag version is being developed): http://fieldtrip.fcdonders.nl/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session Hope these documentation pages may be of any help, Arjen ----- Oorspronkelijk bericht ----- > Van: "Nenad Polomac" > Aan: fieldtrip at science.ru.nl > Verzonden: Donderdag 11 juli 2013 17:09:40 > Onderwerp: [FieldTrip] ft_megrealign how to avoid? > Dear all, > I have CTF MEG data and I am interested in a gamma band topographies. > We recorded two sessions for every subject. Now I would like to > compare grand averages of these two sessions over all subjects(n=13). > Without realignment these grand average topographies look ok and > according to our expectation. However, I know that it would be > reasonable to do realignment of all datasets (n=13x2) to common > template. I have tried that with ft_megrealign which uses method > suggested by Knösche, 2002 and this doesn't work. It gives me very > weird results, meaning that topographies are totally changed and some > new occipital activity emerges. I have plotted single subject head > models(singleshell) together with sensors and they are accurately > aligned. Then I tried different inwardshift options for ft_megrealign > and this didn't bring so much success. So my question is, could I go > without the realignment and what I need to do in order to overcome > problem with realignment? > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Jul 11 18:18:33 2013 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 11 Jul 2013 18:18:33 +0200 Subject: [FieldTrip] Fwd: 17-18 October, 2013: NatMEG inauguration conference at Karolinska Institutet, Stockholm. In-Reply-To: References: Message-ID: Dear FieldTrippers, We are very happy to announce the inauguration conference for NatMEG, the brand-new National Swedish MEG facility. Please find the invitation attached. Have a great summer, Stephen -------------- next part -------------- A non-text attachment was scrubbed... Name: Invitation to NatMEG inauguration conference.pdf Type: application/pdf Size: 228355 bytes Desc: not available URL: From ali.b.sharif at gmail.com Thu Jul 11 19:30:19 2013 From: ali.b.sharif at gmail.com (Ali Bahramisharif) Date: Thu, 11 Jul 2013 19:30:19 +0200 Subject: [FieldTrip] Fwd: 17-18 October, 2013: NatMEG inauguration conference at Karolinska Institutet, Stockholm. In-Reply-To: References: Message-ID: In the list of speakers, I see Stephen's name among the heads. Great! Ali On Thu, Jul 11, 2013 at 6:18 PM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear FieldTrippers, > > We are very happy to announce the inauguration conference for NatMEG, > the brand-new National Swedish MEG facility. Please find the > invitation attached. > > Have a great summer, > > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamid.mohseni at eng.ox.ac.uk Fri Jul 12 15:25:29 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Fri, 12 Jul 2013 14:25:29 +0100 Subject: [FieldTrip] baseline correction Message-ID: Dear All, I am trying to do baseline correction using a specified window, e.g,: cfg.demean = 'yes'; cfg.baselinewindow = [-0.5 0]; but it seems to me fieldtrip always performs demaen in respect to the whole time window and ignores cfg.baselinewindow. I am wondering if it is a bug or I am missing something? -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Fri Jul 12 15:43:35 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Fri, 12 Jul 2013 15:43:35 +0200 Subject: [FieldTrip] ft_megrealign how to avoid? Message-ID: Dear Arjen, Thank you very much for you answer! I forgot to mention that I applied ft_megrealign on averaged single subject data since we are interested in evoked auditory early gamma response. I am familiar with the online and offline methods for removing variance which comes from head movement. These are very useful tolls. I've tested ft_regresconfound before and it worked fine. However, it will not be very helpful in this case. Because if I apply ft_regresconfound as you suggested than I will loose gradiometers information and than ft_megrealign will not work. Furthermore my evoked gamma grand average topographies (TFR of planar and axial gradiometers) look now as expected without any transformation(ft_regresconfound or ft_megrealign). So what I need is some objective evidence that condition difference is due to experiment rather than different head positions. :) Thank you and all the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 12 20:48:53 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 12 Jul 2013 11:48:53 -0700 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: I think you want the cfg.blc option. Demean will indeed remove the mean, as advertised! cfg.blc = ... cfg.blcwindow = [...] In general, however, I would advise against any baseline correction, unless you have a blocked design and have no choice. Best, Aaron On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni wrote: > Dear All, > > I am trying to do baseline correction using a specified window, e.g,: > > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > > but it seems to me fieldtrip always performs demaen in respect to the whole > time window and ignores cfg.baselinewindow. > > I am wondering if it is a bug or I am missing something? > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From hamid.mohseni at eng.ox.ac.uk Fri Jul 12 22:12:43 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Fri, 12 Jul 2013 21:12:43 +0100 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: Thanks for your answer, but I think they are the same. On Friday, 12 July 2013, Aaron Schurger wrote: > I think you want the cfg.blc option. Demean will indeed remove the > mean, as advertised! > cfg.blc = ... > cfg.blcwindow = [...] > > In general, however, I would advise against any baseline correction, > unless you have a blocked design and have no choice. > > Best, > Aaron > > On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni > > wrote: > > Dear All, > > > > I am trying to do baseline correction using a specified window, e.g,: > > > > cfg.demean = 'yes'; > > cfg.baselinewindow = [-0.5 0]; > > > > but it seems to me fieldtrip always performs demaen in respect to the > whole > > time window and ignores cfg.baselinewindow. > > > > I am wondering if it is a bug or I am missing something? > > > > -- > > Hamid R. Mohseni, PhD > > Post-Doctoral Research Assistant > > Institute of Biomedical Engineering > > University of Oxford, OX3 7DQ, UK > > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Fri Jul 12 23:05:01 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Fri, 12 Jul 2013 23:05:01 +0200 (CEST) Subject: [FieldTrip] ft_megrealign how to avoid? In-Reply-To: Message-ID: <1979422110.2049419.1373663101977.JavaMail.root@sculptor.zimbra.ru.nl> Dear Nenad, You're welcome of course. You're right that after head movement compensation using ft_regressconfound, the sensor level data ideally is not used anymore for source modeling (see http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis -> bottom page, for why this is problematic), i.e. as is required for ft_megrealign. Optimally, ft_regressconfound is therefore used as a last step just prior to ft_XXXstatistics, whether at the sensor level (after ft_megrealign) or at the source level. To address your objective, i.e. showing that a difference is due to the experimental manipulation and not due to different head positions; using ft_regressconfound on trials of, say, condition A and B combined will remove any trial-by-trial signal variance that is due to different head positions from the mean head position of condition A and B. In other words, if a systematic difference observed between condition A and B is caused by systematically different head position between condition A and B, this difference will be removed by ft_regressconfound. If not, the difference may not be caused by different head position, and you have good indication to exclude head position as a potential confound. Yours, Arjen ----- Oorspronkelijk bericht ----- > Van: "Nenad Polomac" > Aan: fieldtrip at science.ru.nl > Verzonden: Vrijdag 12 juli 2013 15:43:35 > Onderwerp: Re: [FieldTrip] ft_megrealign how to avoid? > Dear Arjen, > Thank you very much for you answer! I forgot to mention that I applied > ft_megrealign on averaged single subject data since we are interested > in evoked auditory early gamma response. I am familiar with the online > and offline methods for removing variance which comes from head > movement. These are very useful tolls. I've tested ft_regresconfound > before and it worked fine. However, it will not be very helpful in > this case. Because if I apply ft_regresconfound as you suggested than > I will loose gradiometers information and than ft_megrealign will not > work. Furthermore my evoked gamma grand average topographies (TFR of > planar and axial gradiometers) look now as expected without any > transformation(ft_regresconfound or ft_megrealign). So what I need is > some objective evidence that condition difference is due to experiment > rather than different head positions. :) > Thank you and all the best! > Nenad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stidimitriadis at gmail.com Sat Jul 13 11:08:39 2013 From: stidimitriadis at gmail.com (Stavros Dimitriadis) Date: Sat, 13 Jul 2013 12:08:39 +0300 Subject: [FieldTrip] 3D spline interpolation Message-ID: Dear all I am trying to do 3D spline interpolation of a MEG dataset based on axial gradiometer according to the following methodological paper ! Bastiaansena & Thomas R. KnoÈsche."Tangential derivative mapping of axial MEG applied to event-related desynchronization research' Clinical Neurophysiology 111 (2000) 1300±1305. Is there any function in fieldtrip that do this kind of transformation ? Best Dimitriadis Stavros , PhD http://users.auth.gr/~stdimitr/index.html http://neuroinformatics.gr/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Sat Jul 13 11:48:04 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Sat, 13 Jul 2013 11:48:04 +0200 Subject: [FieldTrip] 3D spline interpolation Message-ID: Dear Stavros, You should have look on this http://fieldtrip.fcdonders.nl/tutorial/eventrelatedaveraging#calculate_the_planar_gradient. That is an explanation how to perform it on ERF data. And here you can find pipeline for time freq analysis. http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#procedure The ft_megplanar and ft_combineplanar together transform axial to planar gradients. Have look in the functions help as well. The paper you mentioned is cited here in the Fildtrip documentation. All the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Sun Jul 14 22:19:16 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Mon, 15 Jul 2013 00:49:16 +0430 Subject: [FieldTrip] Fwd: (no subject) In-Reply-To: References: Message-ID: Dear fieldtripers I'm going to use Fieldstrip toolbox for removing noise. but I confronted with a small problem. I was wondering if you could tell me how I could use “.mat” format in Fieldtrip's toolbox. In this regard, I want to ask you FieldTrip, if it is possible for you guide me as soon as possible. I am looking forward to hearing from you. Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Sun Jul 14 22:21:09 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Mon, 15 Jul 2013 00:51:09 +0430 Subject: [FieldTrip] How .mat format used in FieldTrip toolbox Message-ID: Dear fieldtripers I'm going to use Fieldstrip toolbox for removing noise. but I confronted with a small problem. I was wondering if you could tell me how I could use “.mat” format in Fieldtrip's toolbox. In this regard, I want to ask you FieldTrip, if it is possible for you guide me as soon as possible. I am looking forward to hearing from you. Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 15 10:15:14 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 15 Jul 2013 10:15:14 +0200 Subject: [FieldTrip] Fwd: Announcement of Donders Discussions 2013 In-Reply-To: <449335090.2248168.1373799535995.JavaMail.root@indus.zimbra.ru.nl> References: <449335090.2248168.1373799535995.JavaMail.root@indus.zimbra.ru.nl> Message-ID: See below; apologies for multiple postings. ---------- Forwarded message ---------- From: Vogel, S. (Susanne) Date: 14 July 2013 12:58 Subject: Announcement of Donders Discussions 2013 To: fieldtrip-owner at science.ru.nl Dear fieltrip list owner, We are happy to announce the Donders Discussions 2013 and we would be happy if you could distribute this announcement to the fieldrip list or other interested PhD students. With best regards, Susanne ---- Dear PhD student, We are pleased to announce the Donders Discussions 2013: a two-day conference for PhD students in all fields of (cognitive) neuroscience which will take place on October 31st and November 1st in Nijmegen, The Netherlands. The aim of the Donders Discussions is to bring PhD students together in an informal, interdisciplinary atmosphere. Last year we welcomed over 150 participants from all over Europe. We invite you to join us and make this year’s edition an even bigger success! Our exciting program features brains of many kinds, including baby brains, sleeping, stressed and disordered brains, linguistic, attentive and aging brains, and of course investigated brains (where we review methodological innovations). We also offer interactive workshops on science communication and career management. For more information and registration please visit www.ru.nl/dondersdiscussions. We warmly invite all participants to submit a poster abstract. Registration will open on July 15, the deadline is September 16, but registration may close earlier if the maximum number of participants has been reached. The registration fee is €45. If you have any questions, don’t hesitate to e-mail us on discussions2013 at donders.ru.nl. For the latest updates and special offers, join us on facebook (facebook.com/dondersdiscussions2013) or twitter (discussions2013). We look forward to seeing you in Nijmegen! The Donders Discussions committee 2013 From jan.schoffelen at donders.ru.nl Mon Jul 15 10:43:07 2013 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 15 Jul 2013 10:43:07 +0200 Subject: [FieldTrip] ft_connectivityanalysis and PLV formula In-Reply-To: References: Message-ID: Hi Manuel, The first formula is correct, the second isn't. Hint: when working with the complex representation in the second formula you should use a multiplication, rather than a subtraction, and take the negative angle for the second signal. In other words exp(1i.*angle(x)) .* exp(-1i.*angle(y)). This is the same as: exp(1i.*(angle(x)-angle(y))). Hope this helps, Jan-Mathijs On Jul 8, 2013, at 3:32 PM, Manuel Mercier wrote: > Dear Fieldtrip Community > I am still stuck with the implementation of PLV. To be sure that I understand properly the principle of Phase Locking Value, I wrote a code to compute it. That code (see below) gave me the same results as ft_connectivityanalysis. > plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)) -angle(data.fourierspctrm(:,electrode_2,:,:)))),1))); > (data.fourierspctrm being produced by ft_freqanalysis). > > However, I then realized that the subtraction between the two angles should be done in the complex plane as in: > plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)))) - exp(1i*(angle(data.fourierspctrm(:,electrode_2,:,:))))))),1))); > > I doubt that PLV computed through FT is wrong, but then I am circumspect since the first formula is somewhat no correct and give the same results a as ft_connectivityanalysis. > I went to FT code and got confused by the way ft_connectivity_corr use the cross spectrum to compute PLV. > I would greatly appreciate if someone could tell me where I am missing/misunderstanding something. > Thanks you for your help, > > Manuel > > > > Manuel Mercier, PhD > Research Fellow > > Cognitive Neurophysiology Laboratory, > Children’s Evaluation and Rehabilitation Center (CERC), > Departments of Pediatrics and Neuroscience > Albert Einstein College of Medicine, > 1225 Morris Park Avenue > Bronx , NY 10461 > > phone: +1 (718) 862 1859 > fax: +1 (718) 862 1807 > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manuel Mercier [manuel.mercier at einstein.yu.edu] > Sent: Friday, June 28, 2013 4:43 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] PLV formula > > Dear Fieldtripers > Sometime ago I wrote for myself a function that was computing PLV and some related non parametric statistics. > (Phase Locking Value as define as the mean across trials of the phase angle difference recorded at two loci ; based on Lachaux et al., 1999, HBM). > I implemented PLV in matlab using the following formula: > plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)) ... > -angle(data.fourierspctrm(:,cmb(2),:,:)))),1))); > with cmb(1) and cmb(2) being the indices of the electrodes of interest (between which PLV is computed). > I compared my results with the ft_connectivityanalysis function from Fieldtrip and the results were exactly the same. > So far so good. > > But I recently went back to my code, and I was a little bit confused. > Since I was dealing with angles, I though that the best way to do the subtraction should be done in the complex plane > Like: > plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)))) ... > - exp(1i*(angle(data.fourierspctrm(:,cmb(2),:,:))))))),1))); > (for instance if the two angles: pi/2 and -pi/2 the direct subtraction will give pi, > whereas in the complex plan it will be pi/2 - with the norm x2). > > The result I got with this code is obviously different from the previous one, and what I got from Fieldtrip. > I went back to the archive of the mailing list but didn't find a clear answer to my point. Does anyone can enlighten me ? > Thanks ! > > Manuel > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 15 10:51:32 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 15 Jul 2013 10:51:32 +0200 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: <51E3B814.5060000@donders.ru.nl> Dear Hamid, I guess your problem is precisely this one: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2220 Will be fixed asap :) Best, Jörn On 7/12/2013 10:12 PM, Hamid Mohseni wrote: > Thanks for your answer, but I think they are the same. > > On Friday, 12 July 2013, Aaron Schurger wrote: > > I think you want the cfg.blc option. Demean will indeed remove the > mean, as advertised! > cfg.blc = ... > cfg.blcwindow = [...] > > In general, however, I would advise against any baseline correction, > unless you have a blocked design and have no choice. > > Best, > Aaron > > On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni > > wrote: > > Dear All, > > > > I am trying to do baseline correction using a specified window, > e.g,: > > > > cfg.demean = 'yes'; > > cfg.baselinewindow = [-0.5 0]; > > > > but it seems to me fieldtrip always performs demaen in respect > to the whole > > time window and ignores cfg.baselinewindow. > > > > I am wondering if it is a bug or I am missing something? > > > > -- > > Hamid R. Mohseni, PhD > > Post-Doctoral Research Assistant > > Institute of Biomedical Engineering > > University of Oxford, OX3 7DQ, UK > > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamid.mohseni at eng.ox.ac.uk Mon Jul 15 11:16:14 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Mon, 15 Jul 2013 10:16:14 +0100 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: great, thanks. On 15 July 2013 09:51, "Jörn M. Horschig" wrote: > Dear Hamid, > > I guess your problem is precisely this one: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2220 > Will be fixed asap :) > > Best, > Jörn > > > On 7/12/2013 10:12 PM, Hamid Mohseni wrote: > > Thanks for your answer, but I think they are the same. > > On Friday, 12 July 2013, Aaron Schurger wrote: > >> I think you want the cfg.blc option. Demean will indeed remove the >> mean, as advertised! >> cfg.blc = ... >> cfg.blcwindow = [...] >> >> In general, however, I would advise against any baseline correction, >> unless you have a blocked design and have no choice. >> >> Best, >> Aaron >> >> On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni >> wrote: >> > Dear All, >> > >> > I am trying to do baseline correction using a specified window, e.g,: >> > >> > cfg.demean = 'yes'; >> > cfg.baselinewindow = [-0.5 0]; >> > >> > but it seems to me fieldtrip always performs demaen in respect to the >> whole >> > time window and ignores cfg.baselinewindow. >> > >> > I am wondering if it is a bug or I am missing something? >> > >> > -- >> > Hamid R. Mohseni, PhD >> > Post-Doctoral Research Assistant >> > Institute of Biomedical Engineering >> > University of Oxford, OX3 7DQ, UK >> > Tel: +44 (0) 1865 2 83826 >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Aaron Schurger, PhD >> Post-doctoral researcher >> INSERM U992 / NeuroSpin >> CEA - Saclay, France >> +33-1-69-08-66-47 >> aaron.schurger at gmail.com >> http://www.unicog.org >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmontefusco at med.uchile.cl Mon Jul 15 16:04:32 2013 From: rmontefusco at med.uchile.cl (Rodrigo Montefusco) Date: Mon, 15 Jul 2013 10:04:32 -0400 Subject: [FieldTrip] Fwd: (no subject) In-Reply-To: References: Message-ID: Hi Mohsen Can you provide more details? Which is your particular question? Your help sounds a little bit general. Best Y On Sun, Jul 14, 2013 at 4:19 PM, Mohsen moradi wrote: > Dear fieldtripers > > I'm going to use Fieldstrip toolbox for removing noise. but I confronted > with a small problem. > I was wondering if you could tell me how I could use “.mat” format in > Fieldtrip's toolbox. > In this regard, I want to ask you FieldTrip, if it is possible for you > guide me as soon as possible. > I am looking forward to hearing from you. > > Best Regards > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Tue Jul 16 14:11:06 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Tue, 16 Jul 2013 13:11:06 +0100 Subject: [FieldTrip] 2D surface spline interpolation Message-ID: Dear all, I am working on spatiotemporal mapping of 2D and 3D EEG data. I want to develop the method of surface interpolation, what is the function in FieldTrip that develops this interpolation method. I hope you will send me positive and helpful response. Thanks a lot in advance! Best, ahmed -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Jul 16 14:54:19 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 16 Jul 2013 14:54:19 +0200 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: Message-ID: <51E5427B.2020103@donders.ru.nl> Dear Ahmed, there are several functions making use of (spline) interpolation, e.g. ft_channelrepair for reconstructing time-courses of missing or bad channels, or ft_scalpcurrentdensity for spatial filtering of data. Also ft_megrealign is doing some interpolation magic, but I don't know what method that function is using. In case you are interested in low-level functions, they are in FieldTrip/private, called splint.m and sphericalSplineInterpolate.m (afaik both doing essentially the same, just different implementations of the same method). Best, Jörn On 7/16/2013 2:11 PM, ingenieur eniso wrote: > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the > function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > > Thanks a lot in advance! > > Best, > > ahmed > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jul 16 14:55:05 2013 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 16 Jul 2013 14:55:05 +0200 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: Message-ID: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Hi Ahmed, For the visualization of sensor topographies, fieldtrip relies on the 'griddata' function from matlab. You can type 'doc griddata' on the matlab command line for more information. Note that this is not a function that is specific to fieldtrip. For actual interpolation of data, FieldTrip has a ft_channelrepair function, which implements (among others) a spherical spline interpolation. Best wishes, Jan-Mathijs On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > Thanks a lot in advance! > Best, > ahmed > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jakob.wischniowski at uni-ulm.de Wed Jul 17 02:27:18 2013 From: jakob.wischniowski at uni-ulm.de (Jakob) Date: Wed, 17 Jul 2013 02:27:18 +0200 Subject: [FieldTrip] rejectvisual/summary on Mac OS X In-Reply-To: References: <51C85906.2090204@uni-konstanz.de> Message-ID: <79A73D01-FB88-41A6-A12C-70D742C68F74@uni-ulm.de> Dear all, I'm running Matlab 2013a on an Apple OSX 10.8.4 (Mountain Lion) machine. While performing the rejectvisual/summary function, dragging the mouse over the channels won't work: The "selecting box" for dragging simply won't appear while holding down the left mouse button/trackpad button. I was wondering if anyone is experiencing the same problem? Best regards! Jakob From Sara.Bogels at mpi.nl Wed Jul 17 12:30:01 2013 From: Sara.Bogels at mpi.nl (=?ISO-8859-1?Q?Sara_B=F6gels?=) Date: Wed, 17 Jul 2013 12:30:01 +0200 Subject: [FieldTrip] problem with ft_multiplotER In-Reply-To: References: Message-ID: <51E67229.8040001@mpi.nl> Hi all, I have a very specific problem with the ft_multiplotER function. For 2 of my 24 participants, the function gives an error-message when I try to plot the averages of two conditions at the same time. Plotting them one by one is not a problem. There appears to be a specific point in time (different for the two participants) when this goes wrong. If I avoid that time (by using cfg.xlim) it works fine. My trials have different lengths and I used "cfg.vartrllength = 2;" when calling ft_timelockanalysis (not sure whether this is relevant). The error message I get is "Error in ft_multiplotER (line 616) yval(i,:) = datamatrix{i}(m,:);" I cannot find out what happens in this line. Can anyone tell me what this might be referring to? Thank you, Sara From jm.horschig at donders.ru.nl Wed Jul 17 13:44:15 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 17 Jul 2013 13:44:15 +0200 Subject: [FieldTrip] problem with ft_multiplotER In-Reply-To: <51E67229.8040001@mpi.nl> References: <51E67229.8040001@mpi.nl> Message-ID: <51E6838F.3050302@donders.ru.nl> Dear Sara, What you describe sounds like a bug to me. It looks like that in these lines the averages of the two conditions should be concatenated into one matrix, and apparently something goes wrong. However, you truncated the error message a bit (you pasted the line where the error occurs, but not the error message itself). If one of us developers should look into this further, it would be great if you register and create a bugreport on bugzilla.fconders.nl. Preferably would be to upload a snippet of your data, e.g. timelockstructures of one participant, and some lines of code which reproduce the error. We can then look into this further and fix this as soon as possible :) Best, Jörn On 7/17/2013 12:30 PM, Sara Bögels wrote: > Hi all, > > I have a very specific problem with the ft_multiplotER function. For 2 > of my 24 participants, the function gives an error-message when I try > to plot the averages of two conditions at the same time. Plotting them > one by one is not a problem. There appears to be a specific point in > time (different for the two participants) when this goes wrong. If I > avoid that time (by using cfg.xlim) it works fine. My trials have > different lengths and I used "cfg.vartrllength = 2;" when calling > ft_timelockanalysis (not sure whether this is relevant). > > The error message I get is > "Error in ft_multiplotER (line 616) > yval(i,:) = datamatrix{i}(m,:);" > > I cannot find out what happens in this line. Can anyone tell me what > this might be referring to? > > Thank you, > Sara > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From christophe.grova at mcgill.ca Wed Jul 17 16:11:58 2013 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Wed, 17 Jul 2013 10:11:58 -0400 Subject: [FieldTrip] Postdoctoral Position Available et the Montreal Neurological Institute In-Reply-To: Message-ID: Postdoctoral Position Available et the Montreal Neurological Institute Multimodal Functional Imaging Laboratory, Biomedical Engineering Dpt, Montreal Neurological Institute, McGill University, Montreal, Canada The candidate will join a multidisciplinary team composed of neurologists and methodologists within the Multimodal Functional Imaging Laboratory and in close collaboration with the epilepsy group of the Montreal Neurological Institute. A brief description of the project can be found below. The main role of the candidate will be to recruit patients, to assist data acquisition and to identify epileptic events on recorded signals. (S)he will be trained to contribute to data acquisition and to use dedicated source localization and data fusion techniques developed locally. Initial appointment is for 1 year, with possibility of renewal up to 3 years. Project: Multimodal investigation of epileptic activity using simultaneous EEG/MEG and EEG/NIRS acquisitions. The proposed project aims at localizing and characterizing the generators of epileptic activity using simultaneous acquisitions of ElectroEncephaloGraphy (EEG) with Magneto-EncephaloGraphy (MEG), as well as simultaneous acquisitions of EEG with Near Infra-Red Spectroscopy (NIRS). ElectroEncephaloGraphy (EEG) and Magneto-EncephaloGraphy (MEG) are respectively measuring on the scalp electric and magnetic fields generated by neuronal activity at a millisecond scale, providing a detailed description of brain activity using 275 MEG sensors and 56 EEG electrodes. Combined with EEG measuring brain electric activity on the scalp, NIRS allows studying hemodynamic processes at the time of spontaneous epileptic activity. The specificity of NIRS data is its ability to measure local changes oxy-hemoglobin (HbO) and deoxy-hemoglobin (HbR), exploiting absorption properties of infrared light within brain tissue using optic fibers placed on the surface of the head (temporal resolution: 10 ms, 16 sources x 32 detectors, penetration: 2-3 cm from the surface of the head). The candidate will be trained to use the first Brainsight NIRS device developped by Rogue-Research Inc, with which we were able to record promising preliminary data. While methodological developpments in the lab will consist in 3D reconstruction of the generators of EEG, MEG and NIRS signals and assessing multimodal concordances between bioelectrical neuronal signals and hemodynamic processes, the purpose of this Postdoctoral project will be to assess the integrity of neurovascular coupling processes at the time of epileptic discharges, using a unique multimodal environment involving EEG/MEG, EEG/NIRS and also EEG/fMRI recordings. Close collaborations with the epilepsy group of the Montreal Neurological Institute, involving notably Dr E. Kobayashi MD-PhD, Dr F. Dubeau MD-PhD and Dr. J. Gotman PhD, will provide access to patient populations and additional clinical expertise for this project. Requirements: The candidate should be an MD (neurologist) with previous training in epileptology and neurophysiology (EEG). Expertise in analyzing MEG or NIRS signals and/or computational skills including neuroimaging softwares are appreciated additional qualification. The candidate should be fluent in English (and if possible French) due to the patient population studied. Supervisor: Christophe Grova Ph.D. Assistant Professor, Biomedical Engineering Assistant Professor, Neurology & Neurosurgery Director of the Multimodal Functional Imaging Laboratory Email: christophe.grova at mcgill.ca Multi FunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage Please send your CV, a motivation letter and reference letters to christophe.grova at mcgill.ca *************************** Christophe Grova, PhD Assistant Professor Biomedical Engineering Dpt Neurology and Neurosurgery Dpt Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute Centre de Recherches en Mathématiques Biomedical Engineering Department - Room 304 McGill University 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 email : christophe.grova at mcgill.ca tel : (514) 398 2516 fax : (514) 398 7461 web: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe http://www.bmed.mcgill.ca/ MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Wed Jul 17 17:16:14 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Wed, 17 Jul 2013 17:16:14 +0200 Subject: [FieldTrip] Error in Beamforming analysis due to units? Message-ID: Dear all, I'm having a hard time understanding my beamforming analysis/results. I set up the analysis pipeline as described in the tutorial(s). First, I create my template grid as shown below: ---------------------- % Step 1: CREATE A TEMPLATE template = ft_read_mri([TemplateDir 'T1.nii']); template.coordsys = 'spm'; % Step 2: Segment the template brain and construct a volume conduction % model (i.e. head model): this is needed for the inside/outside detection of voxels cfg = []; template_seg = ft_volumesegment(cfg,template); cfg = []; cfg.method = 'singleshell'; template_vol = ft_prepare_headmodel(cfg,template_seg); template_vol = ft_convert_units(template_vol,'cm'); % Step 3: Construct the dipole grid in the template brain coordinates. % The source units are in cm cfg = []; cfg.grid.xgrid = -20:1:20; cfg.grid.ygrid = -20:1:20; cfg.grid.zgrid = -10:1:20; cfg.unit = 'cm'; cfg.grid.tight = 'yes'; cfg.inwardshift = -1.5; % negative inwardshift leads to an outwardshift of the brain's surface cfg.reducerank = 'no'; cfg.vol = template_vol; template_grid = ft_prepare_sourcemodel(cfg); % Step 4: Make a figure with the template head model and dipole grid figure hold on; ft_plot_vol(template_vol,'facecolor','cortex','edgecolor','none'); alpha 0.5; camlight; ft_plot_mesh(template_grid.pos(template_grid.inside,:)); ---------------------- Some of my colleagues also add another step where they convert the template grid units from 'cm' to 'mm' since MNI space is in 'mm'. Since this is not mentioned in the tutorial, I skipped that step. In the next steps for creating the single subject's grid and headmodel I follow exactly the steps described in the tutorial to create single subject grids in MNI space. When I check the segmentation everything looks fine. I then of course use this grid to calculate the sources, also as described in the tutorial. At the end I put the template grid position fields onto the subject's baseline normalized source (sourceDiff_tem). ----------------------------------------------------- for k = 1:length(cond) cfg = []; eval(['cfg.frequency = freqAll.Cond_',num2str(cond(k)),'.freq;']); cfg.method = 'dics'; cfg.grid = grid; % Here it gives .pos, .inside, .outside to the structure cfg.vol = vol; cfg.dim = grid.dim; eval(['cfg.grad = Cond_',num2str(cond(k)),'.hdr.grad;']); cfg.lambda = '5%'; cfg.reducerank = 'no'; cfg.projectnoise = 'yes'; cfg.realfilter = 'yes'; cfg.keepfilter = 'yes'; % the output saves the computed inverse filter eval(['sourceAll.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqAll.Cond_',num2str(cond(k)),');']) % use the pre-calculated common filter here eval(['cfg.grid.filter = sourceAll.Cond_',num2str(cond(k)),'.avg.filter;']); eval(['sourcePre.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqPre.Cond_',num2str(cond(k)),');']) eval(['sourcePost.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqPost.Cond_',num2str(cond(k)),');']) % compute the contrast of (post-pre)/pre (normalization of the power with the baseline activity) eval(['sourceDiff.Cond_',num2str(cond(k)),' = sourcePost.Cond_',num2str(cond(k)),';']) eval(['sourceDiff.Cond_',num2str(cond(k)),'.avg.pow = (sourcePost.Cond_',num2str(cond(k)),'.avg.pow-sourcePre.Cond_',num2str(cond(k)),'.avg.pow) ./ sourcePre.Cond_',num2str(cond(k)),'.avg.pow;']); % put the template grid positions (x,y,z & pos) into the source structure eval(['sourceDiff_tem.Cond_',num2str(cond(k)),' = sourceDiff.Cond_',num2str(cond(k)),';']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.pos = template_grid.pos;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.xgrid = template_grid.xgrid;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.ygrid = template_grid.ygrid;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.zgrid = template_grid.zgrid;']); end ----------------------------------------------------- If I then look at the data of this sourceDiff_tem, i.e. of condition 1, plotted on a surface file, it looks a bit strange to me (see Fig1). Also, I am not able to plot this data with cfg.method 'slice'. I get the error that the dimensions do not match. pos: [5780x3 double] dim: [17 20 17] avg: [1x1 struct] var: [1x1 struct] dimord: 'voxel' inside: [2985x1 double] outside: [2795x1 double] df: [5780x1 double] cfg: [1x1 struct] I then tried it the 'old' way and took the Diff_Source of each subject, interpolated this to the subject's anatomy and normalized it. With that I get a result that makes more sense to me (Fig2). However, also with this I am not able to plot it with cfg.method 'slice'. Actually, the slices I can only use for plotting the stats. So I guess that something is wrong here and that I have an error somewhere in my script. However, I really can't find it. Our guess is that it has something to do with the units and the conversion(s) from one space to the other. I went through all the tutorials again and again but I can't see the mistake. I am stuck and therefore would really appreciate any help on that matter! Thanks a lot! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig1.png Type: image/png Size: 295434 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig2.png Type: image/png Size: 291696 bytes Desc: not available URL: From mushfa.yousuf at googlemail.com Wed Jul 17 17:50:27 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Wed, 17 Jul 2013 17:50:27 +0200 Subject: [FieldTrip] Load Error Message-ID: Hello; I have a preprocessed data structure in the fieldtrip which I want to load in SPM for the 3D source reconstruction. this data Structute includes * fsample * label * trial * time * grad * elec I have converted this data structure to spm format using function spm_eeg_ft2spm. But when I try to load the converted file to SPM, it gives me the following error The requested file is not ready for source reconstruction. See matlab window for details on matlab following message appears checkmeeg: no sensor positions are defined. Please help me out to troubleshoot this problem. Any help will be appreciated. Regards; Mushfa Yousuf -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Jul 17 17:55:54 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 17 Jul 2013 17:55:54 +0200 Subject: [FieldTrip] Load Error In-Reply-To: References: Message-ID: <51E6BE8A.2000804@donders.ru.nl> Hi Mushfa, hm, you provided elec and grad information, do you indeed have combined EEG/MEG data? Maybe SPM does not like that - I know that FieldTrip would not like that ;) - so you could try with either of them and see whether that works. Best, Jörn On 7/17/2013 5:50 PM, Mushfa Yousuf wrote: > Hello; > > I have a preprocessed data structure in the fieldtrip which I want to > load in SPM for the 3D source reconstruction. > > this data Structute includes > > * fsample > * label > * trial > * time > * grad > * elec > > I have converted this data structure to spm format using function > spm_eeg_ft2spm. > > But when I try to load the converted file to SPM, it gives me the > following error > > The requested file is not ready for source reconstruction. See matlab > window for details > > on matlab following message appears > > checkmeeg: no sensor positions are defined. > > > Please help me out to troubleshoot this problem. Any help will be > appreciated. > > Regards; > > Mushfa Yousuf > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Wed Jul 17 18:00:46 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Wed, 17 Jul 2013 18:00:46 +0200 Subject: [FieldTrip] Load Error In-Reply-To: <51E6BE8A.2000804@donders.ru.nl> References: <51E6BE8A.2000804@donders.ru.nl> Message-ID: Hello Jörn; I also tried without elec and grad in the structure but it doesn't help me out. Regards, Mushfa Yousuf On Wed, Jul 17, 2013 at 5:55 PM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Hi Mushfa, > > hm, you provided elec and grad information, do you indeed have combined > EEG/MEG data? Maybe SPM does not like that - I know that FieldTrip would > not like that ;) - so you could try with either of them and see whether > that works. > > Best, > Jörn > > > On 7/17/2013 5:50 PM, Mushfa Yousuf wrote: > > Hello; > > I have a preprocessed data structure in the fieldtrip which I want to > load in SPM for the 3D source reconstruction. > > this data Structute includes > > * fsample > * label > * trial > * time > * grad > * elec > > I have converted this data structure to spm format using function > spm_eeg_ft2spm. > > But when I try to load the converted file to SPM, it gives me the > following error > > The requested file is not ready for source reconstruction. See matlab > window for details > > on matlab following message appears > > checkmeeg: no sensor positions are defined. > > > Please help me out to troubleshoot this problem. Any help will be > appreciated. > > Regards; > > Mushfa Yousuf > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From antony.passaro at gmail.com Wed Jul 17 19:08:41 2013 From: antony.passaro at gmail.com (Antony Passaro) Date: Wed, 17 Jul 2013 13:08:41 -0400 Subject: [FieldTrip] Error using indepsamplesZcoh with cluster statistics Message-ID: Hi all, I'm having an issue running freqstatistics using the indepsamplesZcoh and a cluster correction. The indepsamplesZcoh portion seems to run just fine but I get an error when I try to perform the cluster statistics. The first issue is error1: The error describes a dimension mismatch at line 297 of ft_statistics_montecarlo: statrand(:,:,i) = getfield(dum, 'stat'); Apparently the output (dum) from indepsamplesZcoh collapses my 100 frequencies and 100 timepoints into 10000 points (nchancmb/2 x 10000) but the dimensions of statrand are nchancmb/2 x 100 x Nrand which obviously creates a dimension mismatch. I can get past that part if I set avgovertime = 'yes' which takes me to error 2: "To RESHAPE the number of elements must not change" refers to line 202 in clusterstat.m, posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); Here, cfg.dim is nchan x 100 freq x 1 (avgtime) which obviously doesn't match postailobs dimensions of nchancmb/2 x 100. I thought perhaps the ndepsamplesZcoh function is not supposed to be used in conjunction with the cluster statistics but the Maris 2007 paper appears to use the two together. Any help with this would be much appreciated. Below is the code that that I'm using: cfg = []; %cfg.avgovertime = 'yes'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'parametric'; cfg.minnbchan = 2; cfg.correcttail = 'alpha'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesZcoh'; cfg.parameter = 'fourierspctrm'; cfg.computecritval = 'yes'; cfg.neighbours = neighbours; cfg.numrandomization = 99; cfg.alpha = 0.05; cfg.tail = 0; design = ones(1, 90); design(91:180)=2; cfg.design = design; cfg.label = freqL.label; stat = ft_freqstatistics(cfg, freqL,freqR); Thanks, -Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From Natalia.Egorova at mrc-cbu.cam.ac.uk Wed Jul 17 19:11:24 2013 From: Natalia.Egorova at mrc-cbu.cam.ac.uk (Natalia Egorova) Date: Wed, 17 Jul 2013 17:11:24 +0000 Subject: [FieldTrip] neuromag - sources Message-ID: Hi, I have a question. When doing source reconstruction in the frequency domain with DICS I got a bit confused using neuromag data. Since there are both gradiometer and magnetometer sensors, which sensors are used for source reconstruction by default (if the .grad contains all 360)? Is it possible to use all MEG data, or should MEGGRAD and MEGMAG-based sources be calculated separately? Thanks in advance, Nataila -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Wed Jul 17 20:03:49 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Wed, 17 Jul 2013 19:03:49 +0100 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> References: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Message-ID: Hi Jörn and jan-mathijs, thank you very much for help. All the best Ahmed 2013/7/16 jan-mathijs schoffelen > Hi Ahmed, > > For the visualization of sensor topographies, fieldtrip relies on the > 'griddata' function from matlab. You can type 'doc griddata' on the matlab > command line for more information. Note that this is not a function that is > specific to fieldtrip. > > For actual interpolation of data, FieldTrip has a ft_channelrepair > function, which implements (among others) a spherical spline interpolation. > > > Best wishes, > Jan-Mathijs > > On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: > > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the > function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > > Thanks a lot in advance! > > Best, > > ahmed > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Thu Jul 18 12:10:00 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Thu, 18 Jul 2013 12:10:00 +0200 Subject: [FieldTrip] Error in Beamforming analysis due to units? Problem solved! Message-ID: Dear all, I just solved the problem with the beamforming analysis. So please ignore my previous mail on that! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Thu Jul 18 17:02:34 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Thu, 18 Jul 2013 16:02:34 +0100 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Message-ID: Hi , I use the splint.m function to implement the spherical spline interpolation. But an error is occured: ??? Error using ==> rdivide Matrix dimensions must agree. Error in ==> splint at 58 elc1 = elc1 ./ repmat(sqrt(sum(elc1.^2,2)), 1, 3); Error in ==> eeg_interp_sph_spline_test at 50 [V2, L2, L1] = splint(elc1, V, elc2) I have written following program in Matlab elc1=[x y z]'; elc2=[0.430 0.050 -0.010]'; [V2, L2, L1] = splint(elc1, V, elc2) with [x y z]=[-0.0176 0.0907 0.0071 0.0024 0.0924 0.0076 0.0284 0.0879 0.0075 -0.0085 0.0903 0.0190 0.0153 0.0895 0.0189 -0.0391 0.0836 0.0089 -0.0156 0.0868 0.0286 0.0299 0.0823 0.0305 0.0559 0.0735 0.0080 -0.0329 0.0805 0.0321 -0.0043 0.0789 0.0485 0.0155 0.0785 0.0468 0.0462 0.0726 0.0344 -0.0618 0.0683 0.0105 -0.0509 0.0719 0.0289 -0.0418 0.0694 0.0451 -0.0200 0.0725 0.0542 0.0040 0.0690 0.0618 0.0332 0.0657 0.0563 0.0507 0.0593 0.0501 0.0674 0.0552 0.0315 0.0770 0.0510 0.0080 -0.0651 0.0617 0.0234 -0.0560 0.0608 0.0420 -0.0406 0.0598 0.0580 -0.0080 0.0579 0.0720 0.0196 0.0538 0.0729 0.0444 0.0515 0.0631 0.0678 0.0422 0.0471 0.0803 0.0412 0.0213 -0.0738 0.0546 -0.0128 -0.0782 0.0496 0.0047 -0.0692 0.0506 0.0353 -0.0518 0.0466 0.0611 -0.0288 0.0444 0.0761 0.0018 0.0412 0.0830 0.0296 0.0370 0.0797 0.0582 0.0294 0.0659 0.0799 0.0258 0.0392 0.0902 0.0207 0.0049 0.0842 0.0364 -0.0135 -0.0831 0.0366 0.0188 -0.0709 0.0332 0.0497 -0.0493 0.0303 0.0724 -0.0187 0.0239 0.0876 0.0157 0.0212 0.0889 0.0488 0.0165 0.0771 0.0758 0.0093 0.0526 0.0905 0.0016 0.0200 -0.0846 0.0327 -0.0191 -0.0914 0.0153 -0.0017 -0.0851 0.0124 0.0345 -0.0648 0.0150 0.0646 -0.0401 0.0047 0.0834 0.0295 -0.0054 0.0877 0.0596 -0.0112 0.0701 0.0821 -0.0158 0.0400 0.0916 -0.0140 0.0023 0.0909 0.0050 -0.0172 -0.0913 -0.0021 0.0158 -0.0805 -0.0014 0.0459 -0.0562 -0.0090 0.0732 -0.0215 -0.0170 0.0885 0.0119 -0.0205 0.0896 0.0468 -0.0289 0.0746 0.0717 -0.0317 0.0494 0.0852 -0.0321 0.0173 -0.0856 -0.0313 -0.0167 -0.0906 -0.0195 -0.0002 -0.0861 -0.0199 0.0279 -0.0681 -0.0230 0.0585 -0.0375 -0.0303 0.0791 -0.0029 -0.0388 0.0841 0.0277 -0.0432 0.0772 0.0560 -0.0450 0.0586 0.0738 -0.0459 0.0322 0.0801 -0.0466 0.0005 0.0692 -0.0591 -0.0177 -0.0828 -0.0397 0.0127 -0.0751 -0.0381 0.0389 -0.0556 -0.0426 0.0607 -0.0218 -0.0555 0.0709 0.0119 -0.0587 0.0707 0.0402 -0.0598 0.0583 0.0588 -0.0606 0.0383 0.0698 -0.0602 0.0099 -0.0681 -0.0592 -0.0211 -0.0770 -0.0512 -0.0056 -0.0725 -0.0542 0.0200 -0.0626 -0.0544 0.0415 -0.0372 -0.0663 0.0531 -0.0075 -0.0692 0.0613 0.0157 -0.0732 0.0547 0.0438 -0.0705 0.0413 0.0567 -0.0703 0.0209 0.0630 -0.0678 -0.0043 0.0545 -0.0723 -0.0201 -0.0558 -0.0683 0.0284 -0.0226 -0.0794 0.0421 0.0036 -0.0823 0.0425 0.0386 -0.0810 0.0235 -0.0654 -0.0655 0.0051 -0.0452 -0.0802 0.0113 -0.0322 -0.0824 0.0276 -0.0078 -0.0884 0.0267 0.0175 -0.0876 0.0247 0.0282 -0.0877 0.0104 0.0510 -0.0772 0.0057 -0.0193 -0.0900 0.0110 0.0060 -0.0919 0.0105 -0.0556 -0.0736 -0.0089 -0.0287 -0.0879 -0.0060 -0.0054 -0.0924 -0.0056 0.0148 -0.0913 -0.0057 0.0422 -0.0820 -0.0095 -0.0168 -0.0899 -0.0149 0.0059 -0.0913 -0.0151 -0.0258 -0.0854 -0.0253 -0.0063 -0.0889 -0.0255 0.0142 -0.0880 -0.0254 -0.0398 0.0828 -0.0126 -0.0116 0.0913 -0.0111 0.0115 0.0914 -0.0103 0.0378 0.0841 -0.0101] V = [3.3540 1.9345 0.5927 2.6217 1.3858 5.1010 3.2264 0.3127 -1.2031 4.8916 2.2626 0.7324 -0.8725 8.8664 7.1630 5.9588 3.6880 1.7445 -0.4065 -1.4554 -2.5648 -2.8607 9.7859 8.1602 5.9181 2.3645 0.3716 -1.0117 -2.4332 -3.0173 9.7933 11.8346 10.4268 7.4601 4.5098 1.8013 -0.3755 -1.7671 -2.9153 -3.5252 -3.2862 13.3333 10.0548 6.8787 3.4798 0.8774 -0.9168 -2.3297 -3.1422 11.8833 13.2409 11.6124 8.3419 4.8045 0.6147 -0.8466 -2.0623 -2.8388 -3.2469 12.1843 9.6097 6.2738 3.3943 1.4797 0.0743 -1.2483 -2.0240 8.5136 10.3840 9.7096 7.3371 4.4194 2.6834 1.0785 -0.2747 -1.3383 -1.4970 -0.4476 8.3757 7.6361 5.7288 3.4908 1.8043 0.7450 -0.1646 -0.7976 6.1441 7.2345 7.0914 6.2035 4.1770 2.5408 1.8116 0.3820 -0.1287 -0.4707 0.2793 5.3026 3.5360 2.1660 0.7409 6.1342 4.4963 3.6572 2.5199 1.7607 1.3430 0.4600 3.2784 2.1011 5.2801 3.5401 2.6195 2.0038 0.7776 3.1047 2.2821 3.3528 2.6710 1.9100 5.1250 2.9475 1.6662 0.1915] I haven't found a solution though. So, what is wrong? Thanks a lot in advance! Best, ahmed 2013/7/17 ingenieur eniso > Hi Jörn and jan-mathijs, > > > thank you very much for help. > > All the best > Ahmed > > > 2013/7/16 jan-mathijs schoffelen > >> Hi Ahmed, >> >> For the visualization of sensor topographies, fieldtrip relies on the >> 'griddata' function from matlab. You can type 'doc griddata' on the matlab >> command line for more information. Note that this is not a function that is >> specific to fieldtrip. >> >> For actual interpolation of data, FieldTrip has a ft_channelrepair >> function, which implements (among others) a spherical spline interpolation. >> >> >> Best wishes, >> Jan-Mathijs >> >> On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: >> >> Dear all, >> I am working on spatiotemporal mapping of 2D and 3D EEG data. >> I want to develop the method of surface interpolation, what is the >> function in FieldTrip that develops this interpolation method. >> >> I hope you will send me positive and helpful response. >> >> Thanks a lot in advance! >> >> Best, >> >> ahmed >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> http://www.hettaligebrein.nl >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Thu Jul 18 17:23:43 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Thu, 18 Jul 2013 17:23:43 +0200 Subject: [FieldTrip] MNE source imaging - EEG Message-ID: Dear Fieldtrippers, I would like to know if it is possible to use a detailed downsampled mesh from FreeSurfer tassellation ( representing also the gyrus and the sulcus) as the 'brain' mesh in the method 'dipoli' in BEM computation (having supposed the three layers: 'scalp', 'skull' and 'brain'). I've tried to do this but vol.mat gained really high values (10^8) which led to really high values of the leadfield matrix. Thanks, Alberto Ghione University of Genoa -------------- next part -------------- An HTML attachment was scrubbed... URL: From virginie.van.wassenhove at gmail.com Thu Jul 18 20:21:49 2013 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Thu, 18 Jul 2013 20:21:49 +0200 Subject: [FieldTrip] Postdoctoral position available at Neurospin, France Message-ID: Dear all, please see below or here ( https://sites.google.com/site/virginievanwassenhove/opportunities) for a fellowship openings at NeuroSpin MEG, France! *-------**-------**-------**-------**-------**-------**-------**-------* *Postdoctoral Fellowship - *please, put *POSTDOC* in the email subject. *-------**-------**-------**-------**-------**-------**-------**-------* Due to a postdoctoral fellow having found a permanent position, we have a new opening in the group! Applications are invited from a talented, dynamic, committed, and enthusiastic researcher. The ideal applicant will have a sound experience in the analysis of MEG and/or EEG data and a strong record and research interest in cognitive neurosciences. The selected postdoctoral fellow will lead MEG studies as part of the ERC funded project “Mind Time”. A set of studies will specifically aim at using classifiers and decoding techniques with MEG data. The researcher will be expected to work closely with and supervise (master, phd) students involved in the project. Some involvement in organizational and managerial aspects specific to these projects can be expected. *Requirements:* - should hold a PhD in cognitive neurosciences, neurosciences, psychology, and/or related fields - a strong record of published work - prior experience with MEG/EEG techniques - sound signal processing skills - sound programming skills (matlab, python) Applicants from outside the European Union are welcome but must qualify for a valid visa. French speaking is not a requirement as long as the English language is mastered. * * *Starting date*: asap *Salary*: commensurate with experience. The position will be initially funded for one year (renewable for an additional 2 years).** * * *Application package* *CV* (incl. a list of publications) *Two letters of recommendation* (or contacts from which those could be obtained) *A letter of intent with a statement of research interests* *Applications will be considered until the position is filled.* * * *-------**-------**-------**-------**-------**-------**-------**-------* *Master students - p*lease, put *GRAD *in the email subject *-------**-------**-------**-------**-------**-------**-------**-------* Applications are invited from ambitious and talented students at the level of Master. The ideal applicants will have some lab experience in working with Human participants, and will be familiarized with one or several non-invasive neuroimaging techniques and/or electrophysiology. The applicant will be versed in cognitive neurosciences and demonstrate excellent scholarship. The selected candidate will show a strong academic record and interests in pursuing a PhD in cognitive neurosciences. *Requirements for the candidates:* - master level in cognitive neurosciences, neurosciences, psychology, and/or related fields - a strong academic record - some experience/familiarization with neuroimaging techniques or electrophysiology - fair understanding of signal processing - good programming skills and willingness to improve (matlab, python) Applicants from outside the European Union are welcome but they must qualify for a valid visa. French speaking is not a requirement as long as the English language is mastered. * * *Starting date*: asap and negotiable. *Application package* - *CV* - *A letter of motivation with a statement of research interests* - *Two letters of recommendation* (or contacts from which those could be obtained)*-* . Best wishes, Virginie -- Virginie van Wassenhove Exec Dir NeuroSpin MEG Group leader, Brain Dynamics CEA.DSV.I2BM.NeuroSpin - INSERM Cognitive Neuroimaging Unit Bât 145 Point Courrier 156 Gif s/ Yvette F-91191 FRANCE +33(0)1.69.08.1667 Virginie.van.Wassenhove at gmail.com https://sites.google.com/site/virginievanwassenhove/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From lei.niu at einstein.yu.edu Thu Jul 18 21:52:13 2013 From: lei.niu at einstein.yu.edu (Lei Niu) Date: Thu, 18 Jul 2013 19:52:13 +0000 Subject: [FieldTrip] question about to get the numbers of rejected trials Message-ID: Dear Fieldtrippers, I am new one to use the fieldtrip, and have a question about the rejected trials. To be simply, let we say: 1) the original data is data_org, one singal trial in 32 channel, with 2 different trigger codes and 100 trials per trigger. 2) I process the data to the data_stimulus, incuding 200 trials. Each trial has prestim = 0.1, poststim = 1; 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I get data_reject, including 190 trials. Here is the problem. I found the prestim is too short, I want to increase the prestim time to 0.5. How can I get the numbers of rejected 10 trials to do ft_redefinetrial? Thanks, Lei Niu Albert Einstein College of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From kyle.hird at gmail.com Fri Jul 19 00:24:48 2013 From: kyle.hird at gmail.com (Kyle Hird) Date: Thu, 18 Jul 2013 18:24:48 -0400 Subject: [FieldTrip] Peer module thinks it has too little memory Message-ID: Hi I am attempting to set up the distributed peer system on a 32-bit Linux machine, using version 20130419 from the ftp server (I'm using the shipped binaries because peerslave segfaults on receiving a job if compiled on my system). My tests involve one local slave and one local master on this four-core machine with 4GB of memory. After starting the slave peer, I attempt to run the example command peercellfun(@rand, {10, 20, 30}, 'UniformOutput', false). This fails with the message: 'there are no slave peers available that meet the memory requirements' Examining the output of the slave peer, it contains the following lines (edited for personal info): executing job 1 from myusername at HOSTNAME (jobid=672774519, memreq=2147483648, timreq=3600) executing job took 0.042167 seconds and 22957802788233216 bytes executing job 2 from myusername at HOSTNAME (jobid=1862053136, memreq=2147483648, timreq=3600) executing job took 0.001907 seconds and 22957802787971072 bytes While the times seem reasonable for such a simple problem, the memory usage does not (nearly 23,000 terabytes). The memory usage is reported by fexec, which in turn calculates it from the output of memprofile. Memprofile itself appears to discover resident and virtual size from getmem. I looked at the source for getmem and it appears that it should return -1 in my case (because the elif block for PLATFORM_LINUX is empty), causing memprofile_sample to report zeros for both. However, if I invoke memprofile_sample by using memprofile('info') at the command line, I get: ans = time: 1.3742e+09 mem: 3.6693e+18 I wonder exactly what is happening when getmem gets called. I'm not too experienced with C, but from my understanding the #if statement is evaluated at compile time, so getmem will behave according to the platform on which it was compiled, which may be different from that on which it is executed. As written, the function won't compile on my system due to the absence of . I can't actually find the binary mex getmem in the module, so although the source has mexFunction framework in it, I can't call it from MATLAB. What behaviour should I be getting from memprofile? Should I be doing something differently to get peercellfun to behave correctly? Thanks for your consideration Kyle Hird From samarakm at mail.uc.edu Fri Jul 19 02:24:32 2013 From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm)) Date: Fri, 19 Jul 2013 00:24:32 +0000 Subject: [FieldTrip] Using ft_sourceplot to visualize simulated dipoles Message-ID: <158540F0F1AD27479479077742EA83C5215B90A5@BY2PRD0111MB511.prod.exchangelabs.com> Hello, I am a rookie to fieldtrip, and I have a pretty basic question. I am trying to visually see what a dipole/s would look like after using the function ft_dipolesimulation(cfg). Can I use ft_sourceplot to do this. (I know the BESA_Dipole Simulator gives a nice visual description of the dipoles). My primary objective is to visually compare a simulated dipole/s with its reconstructed counterpart. The reconstruction can be done using any of the source analysis methods. I would really appreciate if anyone could assist me with this problem. Thank you, Kasun Samarasinghe -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Fri Jul 19 11:40:01 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Fri, 19 Jul 2013 11:40:01 +0200 Subject: [FieldTrip] 'ft_prepare_layout' Error Message-ID: Hello ; I am receiving the following error while using ft_prepare_layout ??? Index exceeds matrix dimensions. Error in ==> ft_prepare_layout>sens2lay at 788 mindist = mindist(1:round(numel(label)/4)); Error in ==> ft_prepare_layout at 285 lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, cfg.style); Error in ==> spm_eeg_project3D at 27 lay = ft_prepare_layout(cfg); Notice that I am using MEG channels and the above function perfectly works when I used the EEG channel. For me itt seems like there is any problem with my '.grad' structure ? Kindly please help me to toubleshoot this problem. Regards; Mushfa Yousuf -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Fri Jul 19 12:34:37 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Fri, 19 Jul 2013 12:34:37 +0200 Subject: [FieldTrip] 'ft_prepare_layout' Error In-Reply-To: References: Message-ID: hello ; or it has something to do with layout ? because this msg appears after this line *creating layout for neuromag306 system* * * ??? Index exceeds matrix dimensions. Error in ==> ft_prepare_layout>sens2lay at 788 mindist = mindist(1:round(numel(label)/4)); Error in ==> ft_prepare_layout at 285 lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, cfg.style); Error in ==> spm_eeg_project3D at 27 lay = ft_prepare_layout(cfg); Regards; Mushfa Yousuf On Fri, Jul 19, 2013 at 11:40 AM, Mushfa Yousuf < mushfa.yousuf at googlemail.com> wrote: > Hello ; > > I am receiving the following error while using ft_prepare_layout > > > ??? Index exceeds matrix dimensions. > > Error in ==> ft_prepare_layout>sens2lay at 788 > mindist = mindist(1:round(numel(label)/4)); > > Error in ==> ft_prepare_layout at 285 > lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, > cfg.style); > > Error in ==> spm_eeg_project3D at 27 > lay = ft_prepare_layout(cfg); > > Notice that I am using MEG channels and the above function perfectly works > when I used the EEG channel. > > For me itt seems like there is any problem with my '.grad' structure ? > > > > Kindly please help me to toubleshoot this problem. > > > Regards; > > Mushfa Yousuf > -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Sat Jul 20 21:45:44 2013 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Sat, 20 Jul 2013 21:45:44 +0200 Subject: [FieldTrip] question about to get the numbers of rejected trials In-Reply-To: References: Message-ID: Dear Lei, I think that you are asking that you want to run the steps again, with prestim =0.5 but with rejecting the same 10 trials that you already have decided to reject? If so, the numbers of rejected trials should be inside data_reject.cfg (or possibly data_reject.cfg.previous). But note that by including more prestim time, you might also find a need to reject more trials if there is an artifact in the new included prestim time-points. If you use ft_redefinetrial, I think you only would shift where the time 0.0 is, but not add more data to each trial, so it depends which you want to do. Best regards, Johanna 2013/7/18 Lei Niu > Dear Fieldtrippers, > > I am new one to use the fieldtrip, and have a question about the rejected > trials. > To be simply, let we say: > 1) the original data is data_org, one singal trial in 32 channel, with 2 > different trigger codes and 100 trials per trigger. > 2) I process the data to the data_stimulus, incuding 200 trials. Each > trial has prestim = 0.1, > poststim = 1; > 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I > get data_reject, including 190 trials. > > Here is the problem. I found the prestim is too short, I want to increase > the prestim time to 0.5. How can I get the numbers of rejected 10 trials to > do ft_redefinetrial? > > Thanks, > Lei Niu > Albert Einstein College of Medicine > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Mon Jul 22 10:35:50 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Mon, 22 Jul 2013 10:35:50 +0200 Subject: [FieldTrip] Source time series signals Message-ID: Dear Fieldtrippers, I performed the source reconstruction using the MNE method; i would like to ask what type of signal is 'source.avg.pow', is it correct to assume that it is the time series related to a specific source? Thanks for your attention, Alberto Ghione University of Genoa -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Mon Jul 22 10:56:30 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Mon, 22 Jul 2013 10:56:30 +0200 Subject: [FieldTrip] Fieldtrip to SPM Message-ID: Dear all, I would like to convert my MEG CTF data analysed with Fieldtrip into the SPM format in order to do dynamic causal modeling. I am familiar with explanations from the spm manual and spm_eeg_ft2spm function. Is there any more detailed source of information about this? To make more concrete I have successfully converted my data but it seems something is missing from the structure which explains MEG header information. Thank you in advance! Nenad Polomac -------------- next part -------------- An HTML attachment was scrubbed... URL: From Johanna.Fiess at uni-konstanz.de Mon Jul 22 14:40:47 2013 From: Johanna.Fiess at uni-konstanz.de (=?iso-8859-1?Q?Johanna_Fie=DF?=) Date: Mon, 22 Jul 2013 14:40:47 +0200 Subject: [FieldTrip] different frequency bins Message-ID: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Dear all, whenever I try to compute the statistics for (MEG) time-frequency data, this error message comes up: computing statistic over the frequency range [8.000 11.000] computing statistic over the time range [0.300 1.100] Error using ft_appendfreq (line 250) the input data structures have non-unique frequency bins, concatenation across frequency is not possible Error in ft_appendfreq (line 139) freq = ft_appendfreq(tmpcfg, varargin{:}); Error in ft_freqstatistics (line 231) data = ft_appendfreq(cfg, varargin{:}); Out of 35 participants in total, (only) three show slightly different frequency bins (starting point 2.0001 instead of 1.9998) – if I remove them from the average, the error message disappears. If renaming the freq-structure of those three participants, the error message disappears, too. Could anyone tell me what causes this problem or how I should handle it? Thanks a lot in advance! Johanna PS: I'm running Matlab R2012b & fieldtrip-20130515 %% stats design=[1:10,1:10; ones(1,10),ones(1,10)*2]; cfg = []; cfg.frequency = [8 11]; cfg.latency = [.3 1.1]; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clustertail = 0; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.numrandomization = 500; cfg.alpha = 0.05; cfg.avgoverfreq = 'yes'; % cfg.avgovertime = 'yes'; cfg.design = design; cfg.neighbours = neighbours; cfg.ivar = 2; stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); cfg = []; cfg.alpha = 0.3; cfg.parameter = 'stat'; cfg.zlim = [-3 2]; cfg.layout = '4D148.lay'; ft_clusterplot(cfg, stat); -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 22 14:50:16 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 22 Jul 2013 14:50:16 +0200 Subject: [FieldTrip] different frequency bins In-Reply-To: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> References: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Message-ID: <51ED2A88.60304@donders.ru.nl> Dear Johanna, the problem is that the trial length you put into freqanalysis differed across subjects, leading to a different frequency resolution across participants. FieldTrip realizes that and errors because 1.9998 is not 2.0001 ;) I would propose you re-do the frequencyanalysis with the same time window/trial length for all participants. Maybe you should first check why your trials have different lengths and if that is desired or you did another mistake somewhere in your analysis. If you want to different trial lengths, you can use a padding cfg option in ft_freqanalysis to pad trials to a fixed length. Good luck ;) Best, Jörn On 7/22/2013 2:40 PM, Johanna Fieß wrote: > Dear all, > > whenever I try to compute the statistics for (MEG) time-frequency > data, this error message comes up: > > computing statistic over the frequency range [8.000 11.000] > computing statistic over the time range [0.300 1.100] > Error using ft_appendfreq (line 250) > the input data structures have non-unique frequency bins, > concatenation across frequency is not possible > > Error in ft_appendfreq (line 139) > freq = ft_appendfreq(tmpcfg, varargin{:}); > > Error in ft_freqstatistics (line 231) > data = ft_appendfreq(cfg, varargin{:}); > > Out of 35 participants in total, (only) three show slightly different > frequency bins (starting point 2.0001 instead of 1.9998) -- if I > remove them from the average, the error message disappears. > If renaming the freq-structure of those three participants, the error > message disappears, too. > > Could anyone tell me what causes this problem or how I should handle it? > > Thanks a lot in advance! > > Johanna > > > PS: I'm running Matlab R2012b & fieldtrip-20130515 > %% stats > design=[1:10,1:10; ones(1,10),ones(1,10)*2]; > > cfg = []; > cfg.frequency = [8 11]; > cfg.latency = [.3 1.1]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clustertail =0; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.numrandomization = 500; > cfg.alpha = 0.05; > > cfg.avgoverfreq = 'yes'; > % cfg.avgovertime = 'yes'; > cfg.design = design; > cfg.neighbours = neighbours; > cfg.ivar = 2; > > > stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); > cfg = []; > cfg.alpha = 0.3; > cfg.parameter = 'stat'; > cfg.zlim = [-3 2]; > cfg.layout = '4D148.lay'; > ft_clusterplot(cfg, stat); > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 22 14:53:27 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 22 Jul 2013 14:53:27 +0200 Subject: [FieldTrip] Source time series signals In-Reply-To: References: Message-ID: <51ED2B47.5000408@donders.ru.nl> Dear Alberto, the abbreviation stands for *pow*er of the *av*era*g*e across your observation(s) of the *source*-reconstructed data :) If I am not mistaken, there should be a .mom field (if you set cfg.keepmom = 'yes') which contains the time-resolved data rather than the power. Best, Jörn On 7/22/2013 10:35 AM, Alberto Ghione wrote: > Dear Fieldtrippers, > I performed the source reconstruction using the MNE method; i would > like to ask what type of signal is 'source.avg.pow', > is it correct to assume that it is the time series related to a > specific source? > > Thanks for your attention, > Alberto Ghione > University of Genoa > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 22 15:00:39 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 22 Jul 2013 15:00:39 +0200 Subject: [FieldTrip] different frequency bins In-Reply-To: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> References: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Message-ID: Dear Johanna, The slight differences in frequency bins was probably caused by a slightly different trial length for some of your participants. When doing frequency analysis, the frequency resolution is determined by the length of your data. (You can have a look at e.g. this FAQ entry: http://fieldtrip.fcdonders.nl/faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean for more information.) You mention that the differences in frequency bins are very small. In your case, therefore, I would solve (or 'patch' ;) ) the problem by simply doing something like: participantB.freq = participantA.freq; for all participants B with the aberrant frequency axis. Of course, this only makes sense if the frequency axes between participants A and B are actually almost identical! Hope this helps, Best regards, Eelke On 22 July 2013 14:40, Johanna Fieß wrote: > Dear all, > > whenever I try to compute the statistics for (MEG) time-frequency data, this > error message comes up: > > computing statistic over the frequency range [8.000 11.000] > computing statistic over the time range [0.300 1.100] > Error using ft_appendfreq (line 250) > the input data structures have non-unique frequency bins, concatenation > across frequency is not possible > > Error in ft_appendfreq (line 139) > freq = ft_appendfreq(tmpcfg, varargin{:}); > > Error in ft_freqstatistics (line 231) > data = ft_appendfreq(cfg, varargin{:}); > > Out of 35 participants in total, (only) three show slightly different > frequency bins (starting point 2.0001 instead of 1.9998) – if I remove them > from the average, the error message disappears. > If renaming the freq-structure of those three participants, the error > message disappears, too. > > Could anyone tell me what causes this problem or how I should handle it? > > Thanks a lot in advance! > > Johanna > > > PS: I'm running Matlab R2012b & fieldtrip-20130515 > %% stats > design=[1:10,1:10; ones(1,10),ones(1,10)*2]; > > cfg = []; > cfg.frequency = [8 11]; > cfg.latency = [.3 1.1]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clustertail = 0; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.numrandomization = 500; > cfg.alpha = 0.05; > > cfg.avgoverfreq = 'yes'; > % cfg.avgovertime = 'yes'; > cfg.design = design; > cfg.neighbours = neighbours; > cfg.ivar = 2; > > > stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); > cfg = []; > cfg.alpha = 0.3; > cfg.parameter = 'stat'; > cfg.zlim = [-3 2]; > cfg.layout = '4D148.lay'; > ft_clusterplot(cfg, stat); > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lei.niu at einstein.yu.edu Mon Jul 22 15:11:42 2013 From: lei.niu at einstein.yu.edu (Lei Niu) Date: Mon, 22 Jul 2013 13:11:42 +0000 Subject: [FieldTrip] question about to get the numbers of rejected trials In-Reply-To: References: , Message-ID: Dear Johanna, Thank you very much for your reply. I have resolved the problem following your suggestions. Thanks, Lei ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Johanna Zumer [johanna.zumer at gmail.com] Sent: Saturday, July 20, 2013 3:45 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] question about to get the numbers of rejected trials Dear Lei, I think that you are asking that you want to run the steps again, with prestim =0.5 but with rejecting the same 10 trials that you already have decided to reject? If so, the numbers of rejected trials should be inside data_reject.cfg (or possibly data_reject.cfg.previous). But note that by including more prestim time, you might also find a need to reject more trials if there is an artifact in the new included prestim time-points. If you use ft_redefinetrial, I think you only would shift where the time 0.0 is, but not add more data to each trial, so it depends which you want to do. Best regards, Johanna 2013/7/18 Lei Niu > Dear Fieldtrippers, I am new one to use the fieldtrip, and have a question about the rejected trials. To be simply, let we say: 1) the original data is data_org, one singal trial in 32 channel, with 2 different trigger codes and 100 trials per trigger. 2) I process the data to the data_stimulus, incuding 200 trials. Each trial has prestim = 0.1, poststim = 1; 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I get data_reject, including 190 trials. Here is the problem. I found the prestim is too short, I want to increase the prestim time to 0.5. How can I get the numbers of rejected 10 trials to do ft_redefinetrial? Thanks, Lei Niu Albert Einstein College of Medicine _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From kyle.hird+fieldtrip at gmail.com Mon Jul 22 18:54:38 2013 From: kyle.hird+fieldtrip at gmail.com (Kyle Hird) Date: Mon, 22 Jul 2013 12:54:38 -0400 Subject: [FieldTrip] Peer module thinks it has too little memory In-Reply-To: References: Message-ID: I've investigated my issue a bit further and found a couple of things that may be of use for anyone attempting to diagnose the problem. I mentioned previously that the instance of MATLAB which is running peerslave segfaults when it receives a job if I compile the toolbox on my system. On inspection of the stack trace, I find memprofile twice- the only file from FieldTrip to show up at all. So I run memprofile directly from the private directory with a couple of different options. With 'info', it appears to correctly measure memory usage- approximately 110MB (the distributed binary reported an unrealistically high number). However, when set up to repeatedly sample using 'on' and 'off', memprofile segfaults when 'off' is given, and returns an almost-identical stack trace as when peerslave was run. If 'off' is given to memprofile without first having given 'on', the error does not occur. Other ways to trigger the segfault are, once setting memprofile('on'), to give MATLAB the commands 'exit' or 'clear mex'. I added some mexPrintf statements to try and pinpoint what instruction is causing the segfault. Based on this, the block of code beginning with else if (strcasecmp(command, "off")==0) completes execution correctly. However, nothing in exitFun appears to be executed, not even a print statement I put on the first line. I'm not sure what could cause this problem, but hopefully someone on the list can make sense of this. Thanks for your consideration Kyle Hird From jm.horschig at donders.ru.nl Tue Jul 23 09:41:56 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 23 Jul 2013 09:41:56 +0200 Subject: [FieldTrip] Getting started with realtime EEG data In-Reply-To: References: <9EDC29E4-D79B-4777-A3C6-0C5E5E2C9E0F@donders.ru.nl> Message-ID: <51EE33C3.7020204@donders.ru.nl> Hi Eric, I was just reading up on this conversation and since you mentioned that you do not have any signal processing experience, I thought it'd be nice to point to http://www.dspguide.com/ (free online book) Good luck with oscillating in your sleep :) Best, Jörn On 3/6/2013 9:08 AM, Eelke Spaak wrote: > Hi Eric, > > Yes, FieldTrip's raw data format is the same regardless of acquisition > device, so I expect no problems switching from one device to another. > Note, though, that I have not worked with the realtime buffer, but I > think it ought to work the same as with offline data processing. > > Certain analysis pipelines (e.g. source reconstruction) require > accurate information about the electrode positions. The ease at which > you could obtain these might differ between different devices. > However, based on the info you've given so far I guess this will not > be a problem for you. > > Best, > Eelke > > On 6 March 2013 05:24, Eric Mill wrote: >> Sorry, that was a very long response on my part - but the one actual >> question I have in there is, how easy is it to switch from one EEG device to >> another? Should I expect to have to rework my code entirely, or will the >> core data format and signal processing work be the same? Is standardizing >> the data stream one of the things using an intermediary like Field Trip >> does? >> >> -- Eric >> >> >> On Sun, Mar 3, 2013 at 5:26 PM, Eric Mill wrote: >>> This is extremely helpful, and just what I was looking for, thank you >>> (both Robert and Stefan). I have a few followup questions you've inspired. >>> >>> How "swappable" is the hardware? Do all EEG's fundamentally produce the >>> same data from the same brain activity? And/or, does FieldTrip always expose >>> data in its buffer in the same format? >>> >>> For example, I would be fine investing the $750 for an Emotiv 14-channel >>> EEG, or even the $1200 for a KT88-1016, but not until after I've done some >>> development with a cheaper device first. However, I would not want to have >>> to rewrite all my code, or much of it, if I switch devices. >>> >>> I do have a requirement that I can have the same code work with either >>> live or replayed data. From how you describe its buffer approach, it sounds >>> like that's a core value of FieldTrip, and will make that requirement much >>> easier to satisfy. >>> >>> Also, I do have one peculiar requirement, which is that the hardware be >>> suitable for wearing during ordinary sleeping at home. This is more a >>> requirement for the final (potentially more expensive) device, than the >>> development device. The promotional photo for the Emotiv EEG, for example, >>> looks like it might not be so great for that. >>> >>> I think I will be using WebSockets, but there will be an intermediate >>> server. So, I will have a computer (perhaps a Raspberry Pi) receive data >>> from the EEG, and then immediately stream it up an open TCP connection to a >>> web server. This server will then stream it down to the individual browsers >>> of visiting users, and JavaScript will do the visualization, in something >>> like Three.js or Processing.js. >>> >>> So I don't think I'd be making a JavaScript implementation of FieldTrip, >>> but I believe the server software could be made to be general purpose, and >>> reusable in the work of others like yourselves. That would be a satisfying >>> byproduct. >>> >>> The idea here is that the resulting website will show fully live and real >>> time EEG data, specifically while I am sleeping. Since I only sleep for ~1/3 >>> of any given day, the ability to replay things will be helpful in giving the >>> site utility during the other 2/3. >>> >>> I've never done any signal processing before, not even so much as a fast >>> Fourier transform. But I'm willing to learn! I'll be consulting the tutorial >>> you've kindly written, but if you have any suggestions of learning material >>> I should look at when figuring out how to (for example) detect when a >>> subject has entered levels of sleep given streams of EEG data, it would be a >>> lot of help to me. >>> >>> Unfortunately, the paper you linked to >>> (http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8986.2012.01471.x/full) >>> is behind a paywall and is $35, but if you recommend it highly enough, I'll >>> check it out. >>> >>> Again, thank you for being so welcome to a newbie, and for the >>> recommendations and links. >>> >>> -- Eric >>> >>> >>> On Sun, Mar 3, 2013 at 4:58 AM, Robert Oostenveld >>> wrote: >>>> Hi Eric, >>>> >>>> I think that NeuroSky renamed and discontinued some of their products >>>> since we made the initial implementation of the ThinkCap. I am still able >>>> to find documentation here >>>> http://developer.neurosky.com/docs/lib/exe/fetch.php?media=thinkcap:thinkcap_headset_user_manual.pdf >>>> and http://developer.neurosky.com/docs/doku.php?id=thinkcap. I cannot tell >>>> whether the complete sets now sold by NeuroSky still use the same software >>>> interface, but NeuroSky is rather open with their development tools. >>>> >>>> Alternatives you may consider are the Emotiv Epoc or the DIY OpenEEG. The >>>> Epoc has more channels and a head mount for the electrodes. For the Epoc you >>>> have to look into teh different SDK options, the cheapest version only gives >>>> access to processed data, not to the raw data. For both the Epoc and openeeg >>>> a implementation of a stand-allone executable is available in >>>> http://fieldtrip.fcdonders.nl/development/realtime/implementation. LIke for >>>> the ThinkCap, this copies the data to a "fieldtrip buffer", where another >>>> (c/c++/java/python/matlab) application can easily read it from and do the >>>> signal processing, not having to worry about the buffering and data >>>> representation any more. >>>> >>>> I know it falls outside your budget, but have a look at >>>> http://engineuring.wordpress.com/2009/06/15/writing-your-own-soft-for-a-really-cheap-eeg-hardware-for-brain-computer-interfacing. >>>> These KT88-1016 systems are available from ebay. >>>> >>>> Let me add a bit from the developers perspective and software design. The >>>> rationale for the fieldtrip buffer is that it allows us to develop analysis >>>> pipelines using EEG data files on disk (using ft_read_data). Once the >>>> offline analysis pipeline performs as desired, we just switch from reading >>>> to disk to reading from the buffer (also ft_read_data). We happen to do this >>>> using MATLAB for the rapid application development, but the same strategy >>>> (develop for file, run in real-time) can be used with another programming >>>> environment. >>>> >>>> I think that for signal processing you'll better off if you develop the >>>> code using some good quality data from a file on disk. You can always enact >>>> a real-time data stream by replaying data from that EEG file, or using the >>>> sine2ft GUIs (see realtime/bin). Otherwise you'll be doing all development, >>>> constantly having to wear the headset. That is fine for artefact detection >>>> (you can blink while you code), but not if the tasks get more complicated, >>>> e.g. relaxing to increase your occipital alpha/10Hz won't work well if you >>>> also have in realtime have to monitor whether your applications picks up the >>>> alpha. >>>> >>>> Some time ago we (i.e. Boris Reuderink and me) looked into the >>>> possibilities of a web-standards implementation. Web Sockets would be >>>> needed in Javascript if we want to have the browser connect to a "fieldtrip >>>> buffer" TCP server. The Web Sockets still seemed a bit risky w.r.t. it >>>> working on all platforms. A server-side implementation offers more choice, >>>> python/java/php reading the data from a FT buffer or from the device, and >>>> then pass it on in html format to the connected web ) but would not scale as >>>> easily with multiple client connections if data processing needs to be done >>>> on the server. We then considered the best option to be to implement a >>>> RESTless server implementation. The server would one the one hand contains >>>> the FT buffer (where it receives the data over low-level TCP) and on the >>>> other hand have a web server with the RESTless interface. I.e. the requests >>>> that are represented here >>>> http://fieldtrip.fcdonders.nl/development/realtime/buffer_protocol would >>>> each translate to a http call like "http://ftbuffer.donders.nl/get/hdr" and >>>> "http://ftbuffer.donders.nl/get/dat?begsample=xx&endsample=xx". You can ask >>>> Boris (CC) offline whether he has given it further thought. >>>> >>>> best regards, >>>> Robert >>>> >>>> >>>> >>>> On 2 Mar 2013, at 3:12, Eric Mill wrote: >>>> >>>>> Hi all, >>>>> >>>>> My apologies if this is off-topic here, since you all seem like very >>>>> busy experts! >>>>> >>>>> I'm trying to figure out what I need to get started with capturing >>>>> real-time EEG data using consumer-priced headsets (<$200). I don't actually >>>>> have any interest in using MATLAB, though - I just want to capture the raw >>>>> data, in real time. >>>>> >>>>> I see that FieldTrip has a realtime acquisition module for NeuroSky's >>>>> "ThinkCap", though I can't find a current product by NeuroSky called that. >>>>> Is there something else of theirs I could buy that would work with >>>>> FieldTrip? >>>>> >>>>> Or, should I be looking elsewhere entirely? What should someone who >>>>> wants real-time EEG data do? >>>>> >>>>> My plan is to stream this data and visualize it on the web in real >>>>> time. My background is in web development, not cognitive science, but I'm >>>>> willing to learn what I have to make something interesting. I'd also love to >>>>> have the project result in libraries useful for other people in the field. >>>>> >>>>> Thanks for any advice you can give on what EEG to buy, and/or where to >>>>> learn the core concepts I'll need to use the data. >>>>> >>>>> -- Eric >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From K.Kalogianni at tudelft.nl Tue Jul 23 19:05:52 2013 From: K.Kalogianni at tudelft.nl (Konstantina Kalogianni) Date: Tue, 23 Jul 2013 17:05:52 +0000 Subject: [FieldTrip] music_SL In-Reply-To: <4DF682D3A10EAC46B462A46E16F0B049128DF845@SRV366.tudelft.net> References: <4DF682D3A10EAC46B462A46E16F0B049128DF845@SRV366.tudelft.net> Message-ID: <96D063C2-1544-4FB2-BAA6-D4DD736FD6CE@tudelft.nl> Sent from my iPhone Begin forwarded message: Dear fieldtripers, I want to use the music algorithm for source localization on SEP data(somatosensory evoked potentials) and I would like some help.: Those are my questions 1.The music algorithm needs a number of components (i.e dipoles) and I am wondering where to specify that. For the moment I ‘ve just edited the music.m file for that, but I was wondering if there is a more efficient way. 2.Does the algorithm needs a prestimulus part of the data for comparison that will be used in the covariance matrix? 3. How do I plot the results for music algorithm if I am only interested in one dipole activated? Should I set a roi before? Thanks in advance Nadia Kalogianni -------------- next part -------------- An HTML attachment was scrubbed... URL: From robince at gmail.com Wed Jul 24 10:16:02 2013 From: robince at gmail.com (Robin) Date: Wed, 24 Jul 2013 09:16:02 +0100 Subject: [FieldTrip] matlab stops showing functional images! Message-ID: Hi all, Sorry for a question which might be slightly off topic. I am plotting functional images over anatomy with the 'slice' method of ft_sourceplot. On one machine this has stopped working. The anatomy displays and the functional colorbar is displayed correctly (I can update the CData attribute and see the colorbar update) - but I do not see any part of the functional map. I think it is something related to OpenGL (the renderer for the figure is definitely set to opengl) on this particular computer (the exact same code works on other machines). The setup is CentOS 6 with Matlab R2012a. I have restarted Matlab and the machine but it still doesn't show up - I haven't changed any Matlab settings as far as I know. I am a bit stuck with this so wondered if anyone here might have seen anything like it before? Cheers Robin -------------- next part -------------- An HTML attachment was scrubbed... URL: From Yingying.Wang at cchmc.org Thu Jul 25 08:10:57 2013 From: Yingying.Wang at cchmc.org (Wang, Yingying) Date: Thu, 25 Jul 2013 06:10:57 +0000 Subject: [FieldTrip] website is down In-Reply-To: <018501ce88fd$932b3970$b981ac50$@hotmail.com> References: <018501ce88fd$932b3970$b981ac50$@hotmail.com> Message-ID: <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> http://fieldtrip.fcdonders.nl/ is down. When will it come back? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Jul 25 08:50:25 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 25 Jul 2013 08:50:25 +0200 Subject: [FieldTrip] website is down In-Reply-To: <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> References: <018501ce88fd$932b3970$b981ac50$@hotmail.com> <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> Message-ID: Dear list, We apologize for the present website issues, and working as best we can to get the website up again. Most likely, it will be back up later today. Best, Eelke On 25 July 2013 08:10, Wang, Yingying wrote: > http://fieldtrip.fcdonders.nl/ is down. > > When will it come back? > > Thanks. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From constantino.mendezbertolo at ctb.upm.es Fri Jul 26 18:46:23 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Fri, 26 Jul 2013 18:46:23 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics Message-ID: Greetings, We have Timelock data (LFPs). In order to run cluster based permutation tests we generated a Template similar to a Freqdata structure, with size(Template.powspctrm) = 9 1 1 320 Template.dimord = subj_chan_freq_time We set cfg.neighbouts = [] and run ft_freqstatistics (method ='montecarlo'; correctm = 'cluster', etc) * * This way we can run permutation tests and explore the output, hence, clusters are made on time. What we would like to do is: - *Selecting a minimum amount of consecutive time-bins for a cluster to be considered.* * * For example: Only if (say) 10 consecutive time points are above threshold (whether 'maxsum' or 'wcm' criteria are being used) fieldtrip should consider it a cluster. If just one solely sample point is above clusteralpha threshold, it should not be considered. Is it possible? It would similar to cfg.minnbchan, but in time. Only a cfg.minnbtbin does not exist! As we are already tricking freqstats to believe is working with freqdata (with just one frequency) I am not sure if this is possible. If someone has got some input it would be much appreciated -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Fri Jul 26 19:54:38 2013 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Fri, 26 Jul 2013 19:54:38 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: Message-ID: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> I think cfg.minnbchan, applies also to time bins. s ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > cfg.minnbchan, -------------- next part -------------- An HTML attachment was scrubbed... URL: From constantino.mendezbertolo at ctb.upm.es Fri Jul 26 20:55:36 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Fri, 26 Jul 2013 20:55:36 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> Message-ID: Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations This is the error (with neighbours) V V V Error in clusterstat>makechanneighbstructmat (line 519) [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); Error in clusterstat (line 59) channeighbstructmat = makechanneighbstructmat(cfg); Error in statistics_montecarlo (line 320) [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ft_freqstatistics (line 267) [stat, cfg] = statmethod(cfg, dat, cfg.design); While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: > > I think cfg.minnbchan, applies also to time bins. > > s > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > > cfg.minnbchan, > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN -------------- next part -------------- An HTML attachment was scrubbed... URL: From mengtongxiao at gmail.com Mon Jul 29 04:44:49 2013 From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=) Date: Mon, 29 Jul 2013 10:44:49 +0800 Subject: [FieldTrip] EEG source reconstruction Message-ID: Dear all I do EEG source analyse,But I use the method as the follow got strong function connectivity from different brain areas.（eg.correlation）and strength is similar; I want konw the code with source reconstruction is right? Or some stimulate can prove the code that is right. (the VOL and sourcemode form template) cfg = []; cfg.covariance = 'yes'; cfg.vartrllength = 2; cfg.covariancewindow = 'all'; timelock = ft_timelockanalysis(cfg, data); cfg = []; cfg.channel = {'EEG'}; cfg.vol = vol; cfg.reducerank = 3; cfg.normalize ='yes'; cfg.elec = data_org.hdr.elec; cfg.grid =sourcemodel; [grid]= ft_prepare_leadfield(cfg); cfg = []; cfg.method = 'lcmv'; cfg.vol = vol; cfg.grid = grid; cfg.lcmv.fixedori = 'yes'; cfg.elec = data.hdr.elec; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; source1 = ft_sourceanalysis(cfg, timelock); thanks in advance xiao -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 29 07:48:59 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 29 Jul 2013 07:48:59 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> Message-ID: <51F6024B.8070000@donders.ru.nl> Dear Constantino, I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. Best, Jörn On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: > Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no > cluster (not even with minnbchan = 1) were there was a cluster before > (without cfg.minnbchan) > > Using cfg.neighbours = 'triangulation', or 'distance', with or without > cfg.minnbchan computes the statistics but fails prior to compute the > clusters in the randomizations > > This is the error (with neighbours) V V V > > Error in clusterstat>makechanneighbstructmat (line 519) > [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); > > Error in clusterstat (line 59) > channeighbstructmat = makechanneighbstructmat(cfg); > > Error in statistics_montecarlo (line 320) > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ft_freqstatistics (line 267) > [stat, cfg] = statmethod(cfg, dat, cfg.design); > > > While it seems it is minnbchan what will be helpful, we do not come up > with an idea. Maybe, besides tricking fieldtrip to think we have > frequency data we should also trick him to believe that points in time > are channels? :) > > > El 26 de julio de 2013 19:54, smoratti at psi.ucm.es > > escribió: > > > I think cfg.minnbchan, applies also to time bins. > > s > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de > Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > >> cfg.minnbchan, > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Constantino Méndez-Bértolo > Laboratorio de Neurociencia Clínica,Centro de Tecnología Biomédica (CTB) > > Parque Científico y Tecnológico de la UPM, Campus de Montegancedo > > 28223 Pozuelo deAlarcón, Madrid, SPAIN > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From constantino.mendezbertolo at ctb.upm.es Mon Jul 29 13:06:43 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Mon, 29 Jul 2013 13:06:43 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: <51F6024B.8070000@donders.ru.nl> References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> <51F6024B.8070000@donders.ru.nl> Message-ID: Dear Jörn, Thanks for your response. You are sensibly confused. It is because we wanted to do the statistics (montecarlo; correctm = cluster) with just one channel per data/individual. [As was pointed out above: size(Template.powspctrm) = 9 1 1 320; Template.dimord = subj_chan_freq_time], and ft_timelockstatistics would ask me for a neighbourstructure relenteless, while ft_freqstatistics is ok with cfg.neighbour = [] and so clusters in time. Hence the unorthodoxy. I did a function that parses the mask of the already computed stat finding '1s', determining the span and setting zeros on an arbitrary width-criteria; which serves the purpose but it is not as ellegant as it would be my own statfun. Cheers, Tino 2013/7/29 "Jörn M. Horschig" > > Dear Constantino, > > I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). > > The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. > > Best, > Jörn > > > On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: >> >> Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) >> >> Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations >> >> This is the error (with neighbours) V V V >> >> Error in clusterstat>makechanneighbstructmat (line 519) >> [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); >> >> Error in clusterstat (line 59) >> channeighbstructmat = makechanneighbstructmat(cfg); >> >> Error in statistics_montecarlo (line 320) >> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >> >> Error in ft_freqstatistics (line 267) >> [stat, cfg] = statmethod(cfg, dat, cfg.design); >> >> >> While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) >> >> >> El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: >>> >>> >>> I think cfg.minnbchan, applies also to time bins. >>> >>> s >>> >>> ________________________________________________________ >>> Stephan Moratti, PhD >>> >>> see also: http://web.me.com/smoratti/ >>> >>> Universidad Complutense de Madrid >>> Facultad de Psicología >>> Departamento de Psicología Básica I >>> Campus de Somosaguas >>> 28223 Pozuelo de Alarcón (Madrid) >>> Spain >>> >>> and >>> >>> Center for Biomedical Technology >>> Laboratory for Cognitive and Computational Neuroscience >>> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >>> Campus Montegancedo >>> 28223 Pozuelo de Alarcón (Madrid) >>> Spain >>> >>> >>> email: smoratti at psi.ucm.es >>> Tel.:    +34 679219982 >>> >>> El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: >>> >>>> cfg.minnbchan, >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> Constantino Méndez-Bértolo >> Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) >> >> Parque Científico y Tecnológico de la UPM, Campus de Montegancedo >> >> 28223 Pozuelo de Alarcón, Madrid, SPAIN >> >> >> [image] >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN [image] From jm.horschig at donders.ru.nl Mon Jul 29 13:54:12 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 29 Jul 2013 13:54:12 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> <51F6024B.8070000@donders.ru.nl> Message-ID: <51F657E4.60001@donders.ru.nl> Dear Tino, As I said, try cfg.avgoverchan='yes' with ft_timelockstatistics, then cfg.neighbours can be anything. K>> cfg.neighbours = []; K>> cfg.avgoverchan = 'yes'; K>> [stat] = ft_timelockstatistics(cfg, timelockFIC, timelockFC); [...] using a cluster-based method for multiple comparison correction the returned probabilities and the thresholded mask are corrected for multiple comparisons the call to "ft_timelockstatistics" took 2 seconds K>> You'd still require an own statfun for what you want though ;) Best, Jörn On 7/29/2013 1:06 PM, Constantino Méndez Bértolo wrote: > Dear Jörn, > > Thanks for your response. You are sensibly confused. It is because we > wanted to do the statistics (montecarlo; correctm = cluster) with just > one channel per data/individual. [As was pointed out above: > size(Template.powspctrm) = 9 1 1 320; Template.dimord = > subj_chan_freq_time], and ft_timelockstatistics would ask me for a > neighbourstructure relenteless, while ft_freqstatistics is ok with > cfg.neighbour = [] and so clusters in time. Hence the unorthodoxy. > > I did a function that parses the mask of the already computed stat > finding '1s', determining the span and setting zeros on an arbitrary > width-criteria; which serves the purpose but it is not as ellegant as > it would be my own statfun. > > Cheers, > Tino > > > 2013/7/29 "Jörn M. Horschig" >> Dear Constantino, >> >> I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). >> >> The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. >> >> Best, >> Jörn >> >> >> On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: >>> Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) >>> >>> Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations >>> >>> This is the error (with neighbours) V V V >>> >>> Error in clusterstat>makechanneighbstructmat (line 519) >>> [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); >>> >>> Error in clusterstat (line 59) >>> channeighbstructmat = makechanneighbstructmat(cfg); >>> >>> Error in statistics_montecarlo (line 320) >>> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >>> >>> Error in ft_freqstatistics (line 267) >>> [stat, cfg] = statmethod(cfg, dat, cfg.design); >>> >>> >>> While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) >>> >>> >>> El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: >>>> >>>> I think cfg.minnbchan, applies also to time bins. >>>> >>>> s >>>> >>>> ________________________________________________________ >>>> Stephan Moratti, PhD >>>> >>>> see also: http://web.me.com/smoratti/ >>>> >>>> Universidad Complutense de Madrid >>>> Facultad de Psicología >>>> Departamento de Psicología Básica I >>>> Campus de Somosaguas >>>> 28223 Pozuelo de Alarcón (Madrid) >>>> Spain >>>> >>>> and >>>> >>>> Center for Biomedical Technology >>>> Laboratory for Cognitive and Computational Neuroscience >>>> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >>>> Campus Montegancedo >>>> 28223 Pozuelo de Alarcón (Madrid) >>>> Spain >>>> >>>> >>>> email: smoratti at psi.ucm.es >>>> Tel.: +34 679219982 >>>> >>>> El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: >>>> >>>>> cfg.minnbchan, >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Constantino Méndez-Bértolo >>> Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) >>> >>> Parque Científico y Tecnológico de la UPM, Campus de Montegancedo >>> >>> 28223 Pozuelo de Alarcón, Madrid, SPAIN >>> >>> >>> [image] >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From alexis.makin at liverpool.ac.uk Mon Jul 29 17:33:13 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 16:33:13 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing Message-ID: Hi I already have data which has been cleaned, filtered and artefact rejected etc. It is now .mat format (trials X electrodes X time). I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields data.label % cell-array containing strings, Nchan X 1 data.fsample % sampling frequency in Hz, single number data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M but when I try to run ft_freqanalysis(cfg, data) on this I get the following error messages: ??? Error using ==> ft_checkdata at 366 This function requires raw, comp or mvar data as input. Error in ==> ft_freqanalysis at 219 data = ft_checkdata(data, 'datatype', {'raw', 'comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? cheers, Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 29 17:51:38 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 29 Jul 2013 17:51:38 +0200 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: Hi Alexis, How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. Best, Eelke Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected > etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which > should be compatible with ft_freqanalysis: > > Alternatively, if you already are able to read the data into Matlab, you > can reformat that data within Matlab into a datastructure that is > compatible with FieldTrip. Raw data that is comparable with the output of > preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a > simple problem? > > Is it common to use fieldtrip functions on data which has already been > preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexis.makin at liverpool.ac.uk Mon Jul 29 17:59:33 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 16:59:33 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: <3E0B8C1F-B490-48FD-A1F6-1F9209F43E14@liv.ac.uk> data = label: {64x1 cell} fsample: 128 trials: {1x60 cell} times: {1x60 cell} On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > > Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: > Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? > > Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexis.makin at liverpool.ac.uk Mon Jul 29 18:03:29 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 17:03:29 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: Hi, thanks for your reply, so that's what my data structure looks like. Is it common to use fieldtrip functions on data which has already been cleaned and epoched elsewhere? Alexis On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > > Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: > Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? > > Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Jul 29 18:19:48 2013 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 29 Jul 2013 16:19:48 +0000 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: <16338_1375114551_51F69537_16338_213_1_D9DA6D7F-1D2F-49F7-95B1-47F3A4453A85@liv.ac.uk> References: , <16338_1375114551_51F69537_16338_213_1_D9DA6D7F-1D2F-49F7-95B1-47F3A4453A85@liv.ac.uk> Message-ID: Hi Alexis, it may just be that ft_checkdata is unhappy with the subfields '.trials' and '.times' instead of '.trial' and '.time'. Good luck, best Max ________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "Alexis [alexis.makin at liverpool.ac.uk] Gesendet: Montag, 29. Juli 2013 18:03 Bis: FieldTrip discussion list Betreff: Re: [FieldTrip] ft_freqanalysis without ft_preprocessing Hi, thanks for your reply, so that's what my data structure looks like. Is it common to use fieldtrip functions on data which has already been cleaned and epoched elsewhere? Alexis On 29 Jul 2013, at 16:51, Eelke Spaak wrote: Hi Alexis, How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. Best, Eelke Op 29 jul. 2013 17:36 schreef "Alexis" > het volgende: Hi I already have data which has been cleaned, filtered and artefact rejected etc. It is now .mat format (trials X electrodes X time). I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields data.label % cell-array containing strings, Nchan X 1 data.fsample % sampling frequency in Hz, single number data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M but when I try to run ft_freqanalysis(cfg, data) on this I get the following error messages: ??? Error using ==> ft_checkdata at 366 This function requires raw, comp or mvar data as input. Error in ==> ft_freqanalysis at 219 data = ft_checkdata(data, 'datatype', {'raw', 'comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? cheers, Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ From eelke.spaak at donders.ru.nl Mon Jul 29 18:22:45 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 29 Jul 2013 18:22:45 +0200 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: 'trial' and 'time' should be singular :) Eelke Op 29 jul. 2013 18:13 schreef "Alexis" het volgende: > Hi, thanks for your reply, > > so that's what my data structure looks like. > > Is it common to use fieldtrip functions on data which has already been > cleaned and epoched elsewhere? > > Alexis > > On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display > when you type 'data' at the prompt? The error message suggests that it is > not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > Op 29 jul. 2013 17:36 schreef "Alexis" het > volgende: > >> Hi >> >> I already have data which has been cleaned, filtered and artefact >> rejected etc. >> >> It is now .mat format (trials X electrodes X time). >> >> I can follow the advice from the wiki below to make a structure which >> should be compatible with ft_freqanalysis: >> >> Alternatively, if you already are able to read the data into Matlab, you >> can reformat that data within Matlab into a datastructure that is >> compatible with FieldTrip. Raw data that is comparable with the output of >> preprocessing should consist of a structure with the fields >> >> data.label % cell-array containing strings, Nchan X 1 >> data.fsample % sampling frequency in Hz, single number >> data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples >> data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector >> data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M >> >> >> but when I try to run ft_freqanalysis(cfg, data) on this >> >> I get the following error messages: >> >> ??? Error using ==> ft_checkdata at 366 >> This function requires raw, comp or mvar data as input. >> >> Error in ==> ft_freqanalysis at 219 >> data = ft_checkdata(data, 'datatype', {'raw', 'comp', >> 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); >> >> How to I tell the ft_checkdata function what datatype I have? Is this a >> simple problem? >> >> Is it common to use fieldtrip functions on data which has already been >> preprocessed in another way? Or is this not advisable? >> >> cheers, >> >> >> Alexis >> alexis.makin at liv.ac.uk >> >> Network: www.liv.ac.uk/perception-action/ >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Tue Jul 30 10:27:05 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 30 Jul 2013 10:27:05 +0200 Subject: [FieldTrip] EEG source reconstruction In-Reply-To: References: Message-ID: Dear Xiao, The code doesn't look wrong at first glance. However, with beamforming, the pre-processing of the 'data' is just as important of a step, so be sure you are using the optimal time windows for your research question, and optimal frequency filtering, if desired, etc. Also, check that the units of data.hdr.elec is the same as the vol and sourcemodel. Also, is there a reason you use data_org.hdr.elec in one instance, and the data.hdr.elec in another instance? Best, Johanna 2013/7/29 陈雪 > Dear all > > I do EEG source analyse,But I use the method as the follow got strong > function connectivity from different brain areas.（eg.correlation）and > strength is similar; > I want konw the code with source reconstruction is right? > Or some stimulate can prove the code that is right. > (the VOL and sourcemode form template) > > > cfg = []; > cfg.covariance = 'yes'; > cfg.vartrllength = 2; > cfg.covariancewindow = 'all'; > timelock = ft_timelockanalysis(cfg, data); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.vol = vol; > cfg.reducerank = 3; > cfg.normalize ='yes'; > cfg.elec = data_org.hdr.elec; > cfg.grid =sourcemodel; > [grid]= ft_prepare_leadfield(cfg); > > > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = vol; > cfg.grid = grid; > cfg.lcmv.fixedori = 'yes'; > cfg.elec = data.hdr.elec; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > source1 = ft_sourceanalysis(cfg, timelock); > > thanks in advance > xiao > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erica.boschin at queens.ox.ac.uk Tue Jul 30 16:29:27 2013 From: erica.boschin at queens.ox.ac.uk (Erica Boschin) Date: Tue, 30 Jul 2013 15:29:27 +0100 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script Message-ID: Dear Fieldtrip users, In trying to run ft_timelockanalysis I keep getting the following error: ??? Error using ==> CalcMD5 at 70 Cannot find MEX script This error should allegedly occur when the path is the same as the parent folder for the script, which is not my case. I have tried recompiling the mex files in private and src, with no luck. Has anyone ever experienced this error and if so, could point me towards a solution? I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS 10.6.8. I do not get the error if I try to run the exact same script in Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not sure whether it might be a specs issue or something else. Many thanks, Erica From johanna.zumer at donders.ru.nl Tue Jul 30 16:40:43 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 30 Jul 2013 16:40:43 +0200 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script In-Reply-To: References: Message-ID: Dear Erica, Is the computer on which it fails a 32-bit? If so, this is a known problem: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2010 Feel free to 'cc' yourself onto this bug report. Best, Johanna 2013/7/30 Erica Boschin > Dear Fieldtrip users, > > In trying to run ft_timelockanalysis I keep getting the following error: > > ??? Error using ==> CalcMD5 at 70 > Cannot find MEX script > > This error should allegedly occur when the path is the same as the parent > folder for the script, which is not my case. I have tried recompiling the > mex files in private and src, with no luck. > > Has anyone ever experienced this error and if so, could point me towards a > solution? > > I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS > 10.6.8. I do not get the error if I try to run the exact same script in > Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not > sure whether it might be a specs issue or something else. > > Many thanks, > Erica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erica.boschin at queens.ox.ac.uk Tue Jul 30 17:09:29 2013 From: erica.boschin at queens.ox.ac.uk (Erica Boschin) Date: Tue, 30 Jul 2013 16:09:29 +0100 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script In-Reply-To: References: Message-ID: <1800336A-B1AB-4093-9168-84DFA73BD82C@queens.ox.ac.uk> Dear Johanna, it is indeed a 32-bit, thanks for letting me know it's a bug. Best wishes, Erica On Jul 30, 2013, at 3:40 PM, Johanna Zumer wrote: > Dear Erica, > > Is the computer on which it fails a 32-bit? If so, this is a known problem: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2010 Feel free to 'cc' yourself onto this bug report. > > Best, > Johanna > > > 2013/7/30 Erica Boschin > Dear Fieldtrip users, > > In trying to run ft_timelockanalysis I keep getting the following error: > > ??? Error using ==> CalcMD5 at 70 > Cannot find MEX script > > This error should allegedly occur when the path is the same as the parent folder for the script, which is not my case. I have tried recompiling the mex files in private and src, with no luck. > > Has anyone ever experienced this error and if so, could point me towards a solution? > > I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS 10.6.8. I do not get the error if I try to run the exact same script in Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not sure whether it might be a specs issue or something else. > > Many thanks, > Erica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ggonesc at upo.es Wed Jul 31 09:05:34 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 09:05:34 +0200 Subject: [FieldTrip] ancova for sources analysis Message-ID: <167095db43e3fd69.51f8d35e@upo.es> Dear fieldtrip experts, I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? Many thanks in advanced, Gabriel -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Jul 31 09:55:58 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 31 Jul 2013 09:55:58 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> References: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: <51F8C30E.8010004@donders.ru.nl> Hi Gabriel, hmm, you could try to use ft_regressconfound, see http://www.ncbi.nlm.nih.gov/pubmed/23246857 I am not aware of other functionality in FT, but that should do pretty much what you want . Best, Jörn On 7/31/2013 9:05 AM, Gabriel Gonzalez Escamilla wrote: > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the > effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Wed Jul 31 09:56:02 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Wed, 31 Jul 2013 09:56:02 +0200 (CEST) Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Dear Gabriel, This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? Yours, Arjen ----- Oorspronkelijk bericht ----- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > Dear fieldtrip experts, > I'm wondering if it is possible to perform an ancova or to remove the > effect of a covariate in a source analysis? > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Jul 31 09:58:39 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 31 Jul 2013 09:58:39 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> References: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: Dear Gabriel, To do a full ANCOVA, you would have to write your own 'statfun' to use in the statistics routines. This is not super-hard to do, but is also far from trivial. However, there might be a much easier solution. There is a function called ft_regressconfound which linearly regresses out a 'confound' or covariate from raw, freq, or source data. Would it be an option to use this function first, and then do ft_sourcestatistics on the cleaned data? Note that ft_regressconfound only supports one value per trial, per confound; so the covariates cannot be fully time-resolved. Best, Eelke On 31 July 2013 09:05, Gabriel Gonzalez Escamilla wrote: > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect > of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ggonesc at upo.es Wed Jul 31 10:55:44 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 10:55:44 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> References: <167095db43e3fd69.51f8d35e@upo.es> <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <23400797220a159c.51f8ed30@upo.es> Thanks for your quick ans Arjen, It seems to do what I want, I'm trying to correct grandaveraged source data in which my data is a 1xNsubjs structure, each subject containing 29232 positions. I'm wondering how would be the correct way to input the age of each subject as a counfound. I have tried to set a structure, were each field was the age of each subject, but the ft_regressconfound seems not to work with structures, so I change it. I've also tried to set as a double array (1xNsubjects), but says that "the number of my confound matrix does not match with the number of trials/subjects"; to which I have input the cfg.counfound as a double array (Nsubjsx1), but now I'm getting an error saying that there is not an existing field in the data.trial structure called "pow". Is there something missing on my data? How can I get that pow field into my data comming from ft_grandaverage? Best Regards, Gabriel ----- Mensaje original ----- De: "Stolk, A." Fecha: Miércoles, 31 de Julio de 2013, 10:04 am Asunto: Re: [FieldTrip] ancova for sources analysis A: FieldTrip discussion list p { margin: 0; } > Dear Gabriel, > > This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). > > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? > > Yours, > Arjen > ----------------------------------------------------------- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip --------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggonesc at upo.es
http://www.upo.es/neuroaging/es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ggonesc at upo.es Wed Jul 31 11:56:33 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 11:56:33 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> References: <167095db43e3fd69.51f8d35e@upo.es> <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <2264a36963356fbe.51f8fb71@upo.es> Thank you all for your responses. The last problem I did wrote is now solved, see below. I had a field called 'stat' instead of the 'pow', I'm guessing this field was set before, so, now i'm using this field as if it was the 'pow' I needed and it's working, Is that OK?  Now it takes me to the next question, my data has the avg field, and it says that will update the descriptives but that the 'method' is missing, is this update necessary? or can I just skeep it? Many thanks in advanced, Gabriel ----- Mensaje original ----- De: "Stolk, A." Fecha: Miércoles, 31 de Julio de 2013, 10:04 am Asunto: Re: [FieldTrip] ancova for sources analysis A: FieldTrip discussion list p { margin: 0; } > Dear Gabriel, > > This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). > > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? > > Yours, > Arjen > ----------------------------------------------------------- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip --------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggonesc at upo.es
http://www.upo.es/neuroaging/es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From raminazodiaval at gmail.com Mon Jul 1 13:47:47 2013 From: raminazodiaval at gmail.com (Ramin Azodi) Date: Mon, 1 Jul 2013 13:47:47 +0200 Subject: [FieldTrip] More details about cfg.statistic = 'diff_itc' , Message-ID: Hello, I performed cfg.statistic = 'diff_itc' on two experiment conditions: resting state and during stimulus (each contains 50 trials). As an output, I got values from 0 to 0.6. I tried to find some documents/papers about the meaning of 'diff_itc', and the possibility to interpolate my results but all my attempts failed to success. Could someone tell me more about this function and the possibly give me some reference papers? Best, Ramin -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Mon Jul 1 14:10:39 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Mon, 1 Jul 2013 14:10:39 +0200 Subject: [FieldTrip] ROI selection of beamformer grid points In-Reply-To: <1483937264.1423478.1372252022737.JavaMail.root@draco.zimbra.ru.nl> References: <1483937264.1423478.1372252022737.JavaMail.root@draco.zimbra.ru.nl> Message-ID: Hi Marieke, In case you hadn't already, it's easier to do things in MNI coordinates (like select grid points from atlases) if the source reconstruction was already done using warped grid points from MNI to subject-specific space. See here for help on that. If you have done that, then replace the .pos field in each subject with the grid.pos from the MNI, and no need to ft_sourceinterpolate. If the question is more regarding the templates, see here for more tips, including info on the useful ft_read_atlas function. Cheers, Johanna 2013/6/26 Marieke van de Nieuwenhuijzen < m.vandenieuwenhuijzen at fcdonders.ru.nl> > Dear Fieldtrippers, > > I am running my analyses on time courses reconstructed in source space. > Basically, that means that my working dataset is a matrix of grid point x > time. What I want to do now is do some analyses on a subset of that > dataset, a bit analogous to selecting some sensors to restrict analyses to. > Therefore, what I would ideally want to do, is select a subset of grid > points corresponding to a specific location (for example only the occipital > grid points, or only the grid points corresponding to a specific atlas > label). > > Does anyone have any suggestions about how I should go about selecting > specific grid points? Is there perhaps some grid based atlas, or is it > possible to select grid points based on their corresponding mni coordinates > which you get after running ft_sourceinterpolate and ft_volumenormalise (in > other words, is it possible to reverse ft_volumenormalise and > ft_sourceinterpolate to map the mni coordinates to the grid points instead > of the grid points to mni representation). > > Any pointers would be much appreciated. > > Best, > Marieke > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 1 14:12:41 2013 From: cornabel at googlemail.com (cornelius abel) Date: Mon, 01 Jul 2013 14:12:41 +0200 Subject: [FieldTrip] freq / time range for source analysis? Message-ID: <51D17239.2070009@googlemail.com> Dear FT-List, in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. We found a nice significant cluster in the lower gamma range and in the first half of the time range. Please have a look at the two figures. http://dropcanvas.com/0fnvn Fig a is the multiplotTFR of stat, showing only significant areas. Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. Now, we are not sure how to pick the time and freq range for a subsequent source analysis. Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? Any ideas? Greetings, Cornelius -------------- next part -------------- An HTML attachment was scrubbed... URL: From cornabel at googlemail.com Mon Jul 1 14:21:10 2013 From: cornabel at googlemail.com (Cornelius Abel) Date: Mon, 1 Jul 2013 14:21:10 +0200 Subject: [FieldTrip] freq / time range for source analysis? Message-ID: Dear FT-List, in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. We found a nice significant cluster in the lower gamma range and in the first half of the time range. Please have a look at the two figures. http://dropcanvas.com/0fnvn Fig a is the multiplotTFR of stat, showing only significant areas. Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. Now, we are not sure how to pick the time and freq range for a subsequent source analysis. Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? Any ideas? Greetings, Cornelius -------------- next part -------------- An HTML attachment was scrubbed... URL: From mengtongxiao at gmail.com Mon Jul 1 14:41:18 2013 From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=) Date: Mon, 1 Jul 2013 20:41:18 +0800 Subject: [FieldTrip] about ft_connectivity_powcorr_ortho Message-ID: dear all I use hilbert get the complex signal.and use the ft_connectivity_powcorr_ortho compute power envelope correlation . But I find the result contrast to the PLV. 1that why? the power envelope correlation of 1 not mean strong function relation? best. xiao -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon Jul 1 15:39:49 2013 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Mon, 1 Jul 2013 15:39:49 +0200 Subject: [FieldTrip] freq / time range for source analysis? In-Reply-To: <51D17239.2070009@googlemail.com> References: <51D17239.2070009@googlemail.com> Message-ID: <3126EA9B-FD00-4CFA-95A7-62809C6BD222@psi.ucm.es> Hi Cornelius, I had the same kind of data and I picked the whole time frequency range of the cluster. It depends a bit on how big your clusters are and if there is a theoretical reason to split time and frequency windows (for example high and low gamma, etc.). Best, Stephan ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 01/07/2013, a las 14:12, cornelius abel escribió: > Dear FT-List, > > in an MEG experiment we tested the power difference (40-100Hz, 10 tapsmofreq) between two experimental conditions not averaging over time and frequency. > We found a nice significant cluster in the lower gamma range and in the first half of the time range. > Please have a look at the two figures. > > http://dropcanvas.com/0fnvn > > Fig a is the multiplotTFR of stat, showing only significant areas. > Fig b is the sum over channels of the significance mask giving the number of significant channels at the corresponding freq/time point. > > Now, we are not sure how to pick the time and freq range for a subsequent source analysis. > Should we take the whole time/freq range in which any channel/time/freq combination became significant? Or is it better to pick some center value, also to increase power in the source analysis? > > Any ideas? > > Greetings, Cornelius > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jakob.wischniowski at uni-ulm.de Mon Jul 1 18:57:11 2013 From: jakob.wischniowski at uni-ulm.de (Jakob) Date: Mon, 1 Jul 2013 18:57:11 +0200 Subject: [FieldTrip] Matlab 2012/2013 In-Reply-To: <51C85906.2090204@uni-konstanz.de> References: <51C85906.2090204@uni-konstanz.de> Message-ID: Dear David, I'm facing following bug: While performing the artifact rejection summary function, dragging the mouse over the channels won't work: The "selecting box" for dragging simply won't appear while holding down the left mouse button/trackpad button. I'm running Matlab 2013a on an Apple OSX 10.8.4 (Mountain Lion) machine. Is this a known issue? Best regards! Jakob Wischniowski Am 24.06.2013 um 16:34 schrieb David Schubring : > Dear FieldTrip Users, > > I was wondering if the incompatibility issues with fieldtrip and the latest MATLAB 2013a version still exist (and if so, which bugs exactly occur)? > > (Some of our Matlab 2012a/b installations stopped working, maybe due to the latest java-update, and only the 2013 version still works.) > > Thanks in advance and best regards, > David Schubring > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From drivolta81 at gmail.com Tue Jul 2 12:15:57 2013 From: drivolta81 at gmail.com (Davide Rivolta) Date: Tue, 2 Jul 2013 12:15:57 +0200 Subject: [FieldTrip] Special issue - Research topic Message-ID: Dear FieldTrippers, I would like to advertise a Special Issue hosted by Frontiers in Human Neuroscience entitled: "Facing the other: Novel theories and methods in face perception research". Here is the link: http://www.frontiersin.org/Human_Neuroscience/researchtopics/Facing_the_other_Novel_theorie/1903 Topic Editors: Davide Rivolta, Max Planck Society, Germany Aina Puce, Indiana University, USA Mark A. Williams, Macquarie University, Australia Deadline for abstract submission: 30 Nov 2013 Deadline for full article submission: 28 Feb 2014 Abstract: We rely heavily on faces during social interactions. Humans possess the ability to recognise thousands of people very quickly and accurately without effort. The serious social difficulties that follow abnormalities of the face recognition system (i.e., prosopagnosia) strongly underline the importance of typical face skills in our everyday life. Over the last fifty years, research on prosopagnosia, along with research in the healthy population, has provided insights into the cognitive and neural features behind typical face recognition. This has also been achieved thanks to non-invasive neuroimaging techniques such as functional Magnetic Resonance Imaging (fMRI), Electroencephalography (EEG), Magnetoencephalography (MEG), Diffusion Tensor Imaging (DTI) and Transcranial Magnetic Stimulation (TMS). However, there is still much debate about the cognitive and neural mechanisms of face perception. In the current “Research Topic” we plan to gather experimental works, opinions, commentaries, mini-reviews and reviews that focus on new or novel theories and methods in face perception research. Where is the field at the moment? Do we need to re-think the experimental procedures we have adopted so far? Again, what kind of techniques (or combination of them) and analysis methods will be important in the future? From the experimental point of view we invite both behavioural and neuroimaging contributions (e.g., fMRI, EEG, MEG, DTI and TMS). Despite the main emphasis on face perception, memory and identification, we will also consider original works that focus on other aspects of face processing, such as expression recognition, attractiveness judgments and face imagery. In addition, animal investigations and experimental manipulations that alter face recognition abilities in typical human subjects (e.g., hypnosis) are also welcome. Overall, we are proposing a Research Topic that looks at face processing using different perspectives and welcome contributions from different domains such as psychology, neurology, neuroscience, cognitive science and philosophy. Last year we lost two giants in the field: Shlomo Bentin and Truett Allison. We dedicate this Research Topic to them and their pioneering studies. Bests, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From zriouil.imane at gmail.com Tue Jul 2 14:42:00 2013 From: zriouil.imane at gmail.com (z.imane) Date: Tue, 2 Jul 2013 14:42:00 +0200 Subject: [FieldTrip] (no subject) Message-ID: I have a signal of a certain frequency. if I resampled to a smaller frequency. is that I have a loss of information? -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.herring at fcdonders.ru.nl Tue Jul 2 15:21:10 2013 From: j.herring at fcdonders.ru.nl (Herring, J.D. (Jim)) Date: Tue, 2 Jul 2013 15:21:10 +0200 (CEST) Subject: [FieldTrip] (no subject) In-Reply-To: References: Message-ID: <001d01ce7727$03efcc40$0bcf64c0$@herring@fcdonders.ru.nl> Dear z.imane, If you resample to a smaller frequency you will reduce the number of data points. You will therefore most certainly lose data. Whether you lose 'information' depends on whether there is data relevant to you in frequency bands that cannot be analyzed after resampling. Best, Jim From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of z.imane Sent: dinsdag 2 juli 2013 14:42 To: FieldTrip discussion list Subject: [FieldTrip] (no subject) I have a signal of a certain frequency. if I resampled to a smaller frequency. is that I have a loss of information? -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Tue Jul 2 15:25:26 2013 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Tue, 2 Jul 2013 14:25:26 +0100 Subject: [FieldTrip] (no subject) In-Reply-To: <51d2d3e9.480a0f0a.7ffd.fffffd6aSMTPIN_ADDED_BROKEN@mx.google.com> References: <51d2d3e9.480a0f0a.7ffd.fffffd6aSMTPIN_ADDED_BROKEN@mx.google.com> Message-ID: This might explain it http://en.wikipedia.org/wiki/Nyquist%E2%80%93Shannon_sampling_theorem Vladimir On Tue, Jul 2, 2013 at 2:21 PM, Herring, J.D. (Jim) < j.herring at fcdonders.ru.nl> wrote: > Dear z.imane,**** > > ** ** > > If you resample to a smaller frequency you will reduce the number of data > points. You will therefore most certainly lose data. Whether you lose > ‘information’ depends on whether there is data relevant to you in frequency > bands that cannot be analyzed after resampling. **** > > ** ** > > Best,**** > > ** ** > > Jim**** > > ** ** > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *z.imane > *Sent:* dinsdag 2 juli 2013 14:42 > *To:* FieldTrip discussion list > *Subject:* [FieldTrip] (no subject)**** > > ** ** > > I have a signal of a certain frequency. if I resampled to a smaller > frequency. is that I have a loss of information? > **** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > ** ** > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From marianapbranco1 at gmail.com Tue Jul 2 16:20:54 2013 From: marianapbranco1 at gmail.com (Mariana Branco) Date: Tue, 2 Jul 2013 16:20:54 +0200 Subject: [FieldTrip] Online preprocessing In-Reply-To: <519DEAA1.5030402@donders.ru.nl> References: <1FDFE75C-E4A5-4F6D-B860-76647C558465@gmail.com> <519DE377.1020805@donders.ru.nl> <519DEAA1.5030402@donders.ru.nl> Message-ID: <2BAA5F99-7514-421D-ABB9-E3C0FD8A807B@gmail.com> Dear fieldtrippers, In the follow up of my previous questions: I know am able to stream realtime data form the Biosemi to matlab. In my matlab script I am sending triggers through the parallel port to the biosemi (i.e 2 or 4 for two different events). When The EEG was being recorded using the ActiView interface the trigger once sent was permanently associated with all incoming samples until a new trigger is sent (so event.type=TRIGGER for all samples). However, when streaming from the cmd using biosemi2ft, the trigger only appears once (when is sent) and the follow up samples are only headed with event.type=CM_IN_RANGE and event.value=0 or 1. Is it possible to configure it as in ActiView, which means all samples after sending a trigger are headed with event.type=TRIGGER and event.value=2 or 4? Regards, Mariana Branco On 23 May 2013, at 12:08, Jörn M. Horschig wrote: > Hi Mariana, > > ft_preprocessing demeans by the whole time window, in your 0s to 5s. The baseline window you specify depends on the time axis itself, if it goes from 0s to 5s, then defining [0 3] is fine. If it goes from -3 to 2s, then you need to define [-3 0]. Time is relative :) > Also, please check ft_timelockbaseline. But such a simple thing as subtracting a number from a matrix can also easily be done without relying on a fieldtrip function :) > > Best, > Jörn > > On 5/23/2013 11:57 AM, Mariana Branco wrote: >> Hi Jörn, >> >> Thank you very much for answering. I definitely still have a lot to understand about online implementation, which I will do. >> >> Another specific doubt came up when I was trying to understand the function ft_preprocessing. My offline data is composed of 40 trials of approx. 9-10s paradigms. I have a cued motor task at 3s (lasting 5s) and I use 0s until 3s as baseline to each trial. >> In the examples used in fieldtrip it is possible to chose the 'demean' option and specify the baseline period in seconds. My question is how exactly does the ft_preprocessing function corrects the baseline? Also, the examples define the baseline window with negative time, but I defined the baselinewindow=[0 3]. Is it wrong? >> >> Thank you again for all the advices, I will definitely pose more question in the future. >> >> Mariana Branco >> >> On 23 May 2013, at 11:37, "Jörn M. Horschig" wrote: >> >>> Hi Mariana, >>> >>> On 5/23/2013 10:25 AM, Mariana Branco wrote: >>>> Hello, >>>> >>>> I am new in the BCI research field, and I am starting to implement an online BCI system using the Fieldtrip toolbox to detect ERD/ERS features. I already did two offline experiments using this toolbox, but now I am having some doubts about how to adapt the offline signal processing functions into real-time; I started by simulating real-time data from a file. >>>> My questions are: >>>> 1) To process the data real-time using ft_preprocessing is it first necessary to define trials (with ft_definetrial)? If so, how can I define the trial if it is real-time? >>> no, you should use ft_read_data directly. The way to go is to check the header of your buffer for new events using ft_read_event. Upon detection of a relevant trigger, you need to use the returned event sample to compute your beginning and endsample manually (this is what ft_definetrial, or more precisely, your trialfun, usually does). Then you can use ft_read_data to read data from the buffer into memory. ft_read_data returns a datamatrix that can be used to create your data.trial field. Also, you need to manually create the rest of the data-structure. >>>> 2) Is it possible to still use the function ft_preprocessing and ft_resampledata in real-time with the same specifications of offline procedure? >>> It is definitely possible, once you converted the matrix to a regular fieldtrip structure. However, since it is about speed in online processing, you can think about using low-level functions of FieldTrip directly. Note that for resampling, you can also set up the shared memory (eg. acq2ftx) such that is downsamples right from the start. >>> >>>> 3) When simulating data stream (with two matlab sessions) the function ft_realtime_powerestimate(cfg) reports an error related to the "arg 3 (overlap)" on the welch's method. How can I correct this? >>> Do not use Welch's method, use another function. I don't know about this particular example function, but I think you would greatly benefit from finding out where the error is yourself. Note that online streaming od data *is* complicated and requires *you* to have knowledge about this. >>>> 4) Also, for synchronous/triggered data analysis it is available the function ft_realtime_average. Is it possible to explain how can this example function be used for implementation of my own feature processing and extraction function. Does it preprocess the data in an alternative way to ft_preprocessing? >>> It should be an example, yes. Usually, there should be, as explained above, some ft_read_event statement to read the trigger value(s). In that particular example, the trialfun is used rather than ft_read_data directly, but trialfun is basically a wrapper around ft_read_data. Also, in that example a bunch of trials is read in, not just one. The thing you need to do to adjust this is to filter out the event structure such that only in case of the trigger of interest some data processing is done (you can use ft_filter_event for this). >>> >>> My best advise for you is to read all (most) example functions and adjust them so that they run in your lab. Then sketch a flow diagram how triggers/data will be sent and read, try to implement this yourself (by copy&pasting relevant parts out of the example functions). If you have specific questions, feel free to always ask, but as this stage (please excuse my bluntnessI think you do not really know what needs to be done. I could write a lot about this, but I think you will benefit more if you first try yourself (especially because I do not know how your lab is set up and how things needs to be adjusted). But, as just said, feel free to write again when you have other questions. >>> >>> Good luck! >>> Best, >>> Jörn >>> >>>> I am sorry for all the questions. >>> No problem, no way to know everything :) >>> >>>> Regards, >>>> >>>> Mariana Branco >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> -- >>> Jörn M. Horschig >>> PhD Student >>> Donders Institute for Brain, Cognition and Behaviour >>> Centre for Cognitive Neuroimaging >>> Radboud University Nijmegen >>> Neuronal Oscillations Group >>> FieldTrip Development Team >>> >>> P.O. Box 9101 >>> NL-6500 HB Nijmegen >>> The Netherlands >>> >>> Contact: >>> E-Mail: jm.horschig at donders.ru.nl >>> Tel: +31-(0)24-36-68493 >>> Web: http://www.ru.nl/donders >>> >>> Visiting address: >>> Trigon, room 2.30 >>> Kapittelweg 29 >>> NL-6525 EN Nijmegen >>> The Netherlands >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From giulia.rizza at tiscali.it Wed Jul 3 10:49:29 2013 From: giulia.rizza at tiscali.it (Giulia Rizza) Date: Wed, 3 Jul 2013 10:49:29 +0200 (CEST) Subject: [FieldTrip] unit ft_freqanalysis Message-ID: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> Dear Fieldtrip users I have a quick question. I've performed a Time Frequency Analysis with ft_freqanalysis using 'wavelet' as a method and 'relchange' as a baseline normalization for the plot. What is the unit for the ERD/ERS in the plot? Thank you so much for you help Giulia Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più di uno spot in TV. Per ogni nuovo abbonato 30 € di premio per te e per lui! Un amico al mese e parli e navighi sempre gratis: http://freelosophy.tiscali.it/ From a.stolk8 at gmail.com Wed Jul 3 10:55:39 2013 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 3 Jul 2013 10:55:39 +0200 Subject: [FieldTrip] unit ft_freqanalysis In-Reply-To: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> References: <14677136.38491372841369146.JavaMail.defaultUser@defaultHost> Message-ID: Hi Giulia, Baseline correction method 'relchange' computes the relative change according [ (task-baseline)/baseline ], i.e. a ratio centered around zero. If you multiply with 100, you get the relative change (from baseline) expressed in percentages. best regards, Arjen 2013/7/3 Giulia Rizza > Dear Fieldtrip users > I have a quick question. > I've performed a Time Frequency > Analysis with ft_freqanalysis using 'wavelet' as a method and 'relchange' > as a > baseline normalization for the plot. > What is the unit for the ERD/ERS in the > plot? > Thank you so much for you help > Giulia > > > Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più > di uno spot in TV. Per ogni nuovo abbonato 30 € di premio per te e per lui! > Un amico al mese e parli e navighi sempre gratis: > http://freelosophy.tiscali.it/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Wed Jul 3 16:21:14 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Wed, 3 Jul 2013 10:21:14 -0400 Subject: [FieldTrip] e-mail spoofing by ResearchGate Message-ID: This is unrelated to FieldTrip, but I think it still falls within the general interest of the community. Beware of e-mail spoofing by a company called ResearchGate. They send an e-mail that seems to come from a colleague of yours asking you to join, when in fact that colleague knows nothing about it. It is a spoofing scam. Just something to be aware of. Aaron Schurger ---------- Forwarded message ---------- From: Aaron Schurger Date: Wed, Jul 3, 2013 at 10:11 AM Subject: Re: ResearchGate: Response to your inquiry To: User Care You said "one of your co-authors claimed a publication on ResearchGate and invited you as a co-author". But which one of my co-authors? It was not the one who's e-mail address was listed as the "sender", because I asked that individual and they had not initiated any invitation. Why would you send me an e-mail showing the name "Anne Treisman" as the sender (see attached), with Anne's photo in the message saying explicitly "Anne Treisman invited you to join ResearchGate," when in fact Anne Treisman had not invited me to join ResearchGate. This is called "e-mail spoofing". In fact Treisman only joined ResearchGate in order to stop being harassed by e-mails purportedly from her colleague Bob Desimone, who in fact never invited her to join ResearchGate either! My first e-mail was polite. This one won't be - stop the bullshit. Sincerely, Aaron Schurger On Wed, Jul 3, 2013 at 9:13 AM, User Care wrote: > Hello, > > 2 Jul 2013: >> I've received e-mail "invitations" to join ResearchGate from people that I >> know, and when I asked if they had sent the invitation they said 'no'. I >> have colleagues who have all had the same experience (including the one who >> supposedly "invited" me). This does not inspire trust in your service. I >> certainly will not join. > > Thank you for your message. > > You received this notice because one of your co-authors claimed a publication on ResearchGate and invited you as a co-author. If you'd like to be put on our black list (meaning that we'll never email you again) - please follow the link in the footer of the email you received. > > Please do let us know if you have any further questions, > > Regards, > User Care -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Gmail - Anne Treisman invited you to join ResearchGate.pdf Type: application/pdf Size: 126588 bytes Desc: not available URL: From politzerahless at gmail.com Wed Jul 3 16:41:30 2013 From: politzerahless at gmail.com (Stephen Politzer-Ahles) Date: Wed, 3 Jul 2013 09:41:30 -0500 Subject: [FieldTrip] e-mail spoofing by ResearchGate Message-ID: Hi Aaron, I just wanted to clarify, Researchgate is not just a scam, it's a real site that some (although certainly not all) researchers use, similar to Academia.edu and things like that; see http://www.forbes.com/sites/alexknapp/2012/03/15/researchgate-wants-to-be-facebook-for-scientists/. I'm not sure why you were getting unsolicited e-mails; it's possible that when your colleagues signed up they accidentally forgot to uncheck an option to automatically invite co-authors (I've certainly made mistakes like that before on other places), or it might not be any fault of theirs and it might be some legitimate bug or something, or I guess it's possible you were getting e-mails from some other site masquerading as the actual ResearchGate. (I do admit even the real site does send a lot of e-mail notifications, but like Facebook and other things I've been able to change my preferences to stop getting most of them.) But anyway I just wanted to clarify what Researchgate actually is. Hope you get your problem resolved. Best, Steve Message: 1 > Date: Wed, 3 Jul 2013 10:21:14 -0400 > From: Aaron Schurger > To: FieldTrip discussion list > Subject: [FieldTrip] e-mail spoofing by ResearchGate > Message-ID: > < > CALeeyATYwZ7u1BuiWBx72Dn7tU5jZjuuf3pho9bgt33A-1Xy6A at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > This is unrelated to FieldTrip, but I think it still falls within the > general interest of the community. > > Beware of e-mail spoofing by a company called ResearchGate. They send > an e-mail that seems to come from a colleague of yours asking you to > join, when in fact that colleague knows nothing about it. It is a > spoofing scam. Just something to be aware of. > > Aaron Schurger > -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Wed Jul 3 21:03:35 2013 From: frank.ye.mei at gmail.com (Frank Mei) Date: Wed, 3 Jul 2013 15:03:35 -0400 Subject: [FieldTrip] beamformer Message-ID: Hello FieldtripList, In the beamformer tutorial ( http://fieldtrip.fcdonders.nl/tutorial/beamformer), the contrast of (post-pre)/pre was calculated. I am wondering why can't one just calculate (post-pre), instead. Could someone explain that? thanks, Ye Mei -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk8 at gmail.com Wed Jul 3 21:16:12 2013 From: a.stolk8 at gmail.com (Arjen Stolk) Date: Wed, 3 Jul 2013 21:16:12 +0200 Subject: [FieldTrip] beamformer In-Reply-To: References: Message-ID: Hi Ye Mei, Source-reconstructed activity (using the beamformer method) typically has a depth-bias (see van Veen et al., IEEE '97). Taking the relative increase/decrease of activity from baseline (effectively implementing a normalization per grid point location) is less prone to this bias as compared to taking the absolute difference. Hope this answers your question, Arjen 2013/7/3 Frank Mei > Hello FieldtripList, > > In the beamformer tutorial ( > http://fieldtrip.fcdonders.nl/tutorial/beamformer), the contrast of > (post-pre)/pre was calculated. I am wondering why can't one just > calculate (post-pre), instead. > > Could someone explain that? > > thanks, > Ye Mei > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Wed Jul 3 21:35:59 2013 From: frank.ye.mei at gmail.com (Frank Mei) Date: Wed, 3 Jul 2013 15:35:59 -0400 Subject: [FieldTrip] the right normalsation? Message-ID: Hello FieldtripList, I am trying to differentiate brain areas responsible for two different conditions using the method show in the tutorial( http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so far I have tried to subtract condition# 1 minus the #2, and divided by the average of the baseline period (pre-stimuli presentation), i.e., (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this division is for normalisation purposes. Is this the right normalsation? What normalization do you suggest to use? Is it necessary to normalise? thanks Ye -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Thu Jul 4 10:39:00 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Thu, 04 Jul 2013 10:39:00 +0200 Subject: [FieldTrip] the right normalsation? In-Reply-To: References: Message-ID: <51D534A4.6080207@donders.ru.nl> Dear Ye, normalizing has different purposes. On the one hand, as Arjen pointed out, it is necessary to normalize in source space to get rid of the depth bias (well, alternatively you could normalize the leadfields). On the other hand, it makes averaging over subjects reasonable - otherwise differences in e.g. scalp conducitivity (for EEG) or headshape and size (for MEG) might lead to biasing an average in favour of some subjects. It is just the same reason as using a baseline when analysing ERPs/ERFs. Furthermore, there is no correct way of normalizing. As I said, you could also normalize the leadfield rather than normalizing by conditions. I think the most important thing to remember is that a) you need some contrast or b) you need to normalize the leadfield For a) it would be sufficient to use Post#1/Post#2, but I would rather not contrast two conditions normalized by two baselines. This gets really hard in interpretation (e.g. is the observed effect caused by a difference in baseline or a different in stimulus processing?). My favourite is log(Post#1/Post#2) or taking the z-score. Taking the logarithm has the advantage that extreme values get squashed nearer together, thereby reducing the influence of outliers. Z-scoring achieves a similar thing by explicitly normalizing by the variance. I would suggest for you to create some synthetic signals or values and play around with different ways of normalizing to get a feeling for what you are doing and what influence this has. I test different cases (e.g. 3: difference in prestim but no difference in poststim, no difference in prestim but difference in poststim and difference in prestim and poststim) and apply different normalizations/contrasts. Good luck :) Best, Jörn On 7/3/2013 9:35 PM, Frank Mei wrote: > Hello FieldtripList, > > I am trying to differentiate brain areas responsible for two different > conditions using the method show in the > tutorial(http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so > far I have tried to subtract condition# 1 minus the #2, and divided by > the average of the baseline period (pre-stimuli presentation), i.e., > (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this division > is for normalisation purposes. Is this the right normalsation? What > normalization do you suggest to use? Is it necessary to normalise? > > thanks > Ye > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From pgoodin at swin.edu.au Thu Jul 4 13:24:42 2013 From: pgoodin at swin.edu.au (Peter Goodin) Date: Thu, 4 Jul 2013 11:24:42 +0000 Subject: [FieldTrip] Running ICA on neuromag tsss data Message-ID: Hi Fieldtrip list, I've been using ICA (fastICA specifically) to clean blinks and cardiac artefact from my MEG data (neuromag 306 system) but find that I get some components that are "off" for a period and "on" for a period, or in other words some trials have the components "on" and others "off". I'm assuming these "off" periods are due to the differing dimensionality within the data due to the block by block rw nature of tsss, but when they're "on", they seem to contain a higher amplitude signal to the other components. My questions are: Are these on / off components due the differing dimensionality between blocks due to the tsss process? Is it more likely they contain data relating to the brain, something else such as movement, a mix of the two or it's simply impossible to tell? Thanks to anyone who can shed some light on this, Peter __________________________ Peter Goodin, BSc (Hons), Ph.D Candidate. Brain and Psychological Sciences Research Centre (BPsych) Swinburne University, Hawthorn, Vic, 3122 Monash Alfred Psychiatry Research Centre (MAPrc) Level 4, 607 St Kilda Road, Melbourne 3004 -------------- next part -------------- An HTML attachment was scrubbed... URL: From t.marshall at fcdonders.ru.nl Thu Jul 4 17:00:44 2013 From: t.marshall at fcdonders.ru.nl (Tom Marshall) Date: Thu, 04 Jul 2013 17:00:44 +0200 Subject: [FieldTrip] the right normalsation? In-Reply-To: <51D534A4.6080207@donders.ru.nl> References: <51D534A4.6080207@donders.ru.nl> Message-ID: <51D58E1C.6080002@fcdonders.ru.nl> Hi Jörn > My favourite is log(Post#1/Post#2) or taking the z-score. Could you expand on 'taking the z-score'? This could be interpreted in different ways, which might control for different sources of variance. To throw a bit more fuel on this fire... the problem with log ratios - ie log(post#1/post#2) - is that they ignore the prestimulus period altogether. That always seemed a bit funny to me. Presumably the brain response to your event of interest is somehow dependent on the brain state at the time the event happens ;) Of course one can independently test the hypothesis that the prestimulus periods differ, but how to be confident that they do not? On Thursday, July 04, 2013 10:39:00 AM, "Jörn M. Horschig" wrote: > Dear Ye, > > normalizing has different purposes. On the one hand, as Arjen pointed > out, it is necessary to normalize in source space to get rid of the > depth bias (well, alternatively you could normalize the leadfields). > On the other hand, it makes averaging over subjects reasonable - > otherwise differences in e.g. scalp conducitivity (for EEG) or > headshape and size (for MEG) might lead to biasing an average in > favour of some subjects. It is just the same reason as using a > baseline when analysing ERPs/ERFs. > Furthermore, there is no correct way of normalizing. As I said, you > could also normalize the leadfield rather than normalizing by > conditions. I think the most important thing to remember is that > a) you need some contrast or > b) you need to normalize the leadfield > > For a) it would be sufficient to use Post#1/Post#2, but I would rather > not contrast two conditions normalized by two baselines. This gets > really hard in interpretation (e.g. is the observed effect caused by a > difference in baseline or a different in stimulus processing?). My > favourite is log(Post#1/Post#2) or taking the z-score. Taking the > logarithm has the advantage that extreme values get squashed nearer > together, thereby reducing the influence of outliers. Z-scoring > achieves a similar thing by explicitly normalizing by the variance. > I would suggest for you to create some synthetic signals or values and > play around with different ways of normalizing to get a feeling for > what you are doing and what influence this has. I test different cases > (e.g. 3: difference in prestim but no difference in poststim, no > difference in prestim but difference in poststim and difference in > prestim and poststim) and apply different normalizations/contrasts. > > Good luck :) > Best, > Jörn > > > On 7/3/2013 9:35 PM, Frank Mei wrote: >> Hello FieldtripList, >> >> I am trying to differentiate brain areas responsible for two >> different conditions using the method show in the >> tutorial(http://fieldtrip.fcdonders.nl/tutorial/beamformer), and so >> far I have tried to subtract condition# 1 minus the #2, and divided >> by the average of the baseline period (pre-stimuli presentation), >> i.e., (Post#1-Post#2)./(Average of Pre#1 and Pre#2). I think this >> division is for normalisation purposes. Is this the right >> normalsation? What normalization do you suggest to use? Is it >> necessary to normalise? >> >> thanks >> Ye >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Tom Marshall, MSc. Neuronal Oscillations Group, Donders Centre for Cognitive Neuroimaging tel: +31(0)243668487 email: t.marshall at fcdonders.ru.nl postal: PO Box 9101, 6500HB, Nijmegen, The Netherlands visiting: Kapittelweg 29, 6525EN, Nijmegen, The Netherlands From aaron.schurger at gmail.com Thu Jul 4 21:33:29 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Thu, 4 Jul 2013 15:33:29 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question Message-ID: Hi, When you read in a data file using ft_preprocessing, with high-pass filtering, is the high-pass filter applied before the data are epoched (i.e. on the entire time series for the whole data file), or is the high-pass filter applied separately to each epoch? For very low frequencies (with period longer than one data epoch) this will make a difference. Thanks! Aaron -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From thomas.hartmann at th-ht.de Thu Jul 4 22:31:31 2013 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Thu, 04 Jul 2013 22:31:31 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: References: Message-ID: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> hi aaron, filtering is generally applied after the data have been epoched. to avoid the filter artifacts you are speaking about, we normally define epochs that are sufficiently larger so that these artifacts would be in data we are not interested in. about 1s at both ends of the epoch should be enough in most cases. but you better check... later you can use ft_redefinetrial to discard that extra data. hope this helps. best, thomas Aaron Schurger schrieb: >Hi, >When you read in a data file using ft_preprocessing, with high-pass >filtering, is the high-pass filter applied before the data are epoched >(i.e. on the entire time series for the whole data file), or is the >high-pass filter applied separately to each epoch? For very low >frequencies (with period longer than one data epoch) this will make a >difference. >Thanks! >Aaron > >-- >Aaron Schurger, PhD >Post-doctoral researcher >INSERM U992 / NeuroSpin >CEA - Saclay, France >+33-1-69-08-66-47 >aaron.schurger at gmail.com >http://www.unicog.org >_______________________________________________ >fieldtrip mailing list >fieldtrip at donders.ru.nl >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 5 03:51:45 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Thu, 4 Jul 2013 21:51:45 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> Message-ID: Thanks, Thomas. What if I wanted to apply the filtering to the entire time series first, and then extract the trial epochs after filtering? Is there a way to do that? Thanks, Aaron On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann wrote: > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: >> >> Hi, >> When you read in a data file using ft_preprocessing, with high-pass >> filtering, is the high-pass filter applied before the data are epoched >> (i.e. on the entire time series for the whole data file), or is the >> high-pass filter applied separately to each epoch? For very low >> frequencies (with period longer than one data epoch) this will make a >> difference. >> Thanks! >> Aaron >> >> -- >> Aaron Schurger, PhD >> Post-doctoral researcher >> INSERM U992 / NeuroSpin >> CEA - Saclay, France >> +33-1-69-08-66-47 >> aaron.schurger at gmail.com >> http://www.unicog.org >> ________________________________ >> >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From jm.horschig at donders.ru.nl Fri Jul 5 08:41:50 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 05 Jul 2013 08:41:50 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> Message-ID: <51D66AAE.70307@donders.ru.nl> Hi Aaron, in that case you need to define only one trial, going from 0 to the end of the recording and call ft_preprocessing. Not sure if this will work, but something like / cfg = [];// // ...// // hdr = ft_read_header(cfg.dataset);// // cfg.trl = [0 hdr.nSamples 0];// // data = ft_preprocessing(cfg);/ Subsequently you might want to try using ft_redefinetrial to get the epochs you are interested in. Note however that you need to have sufficient memory for reading all your data in. I am not sure how much memory you have, how long your recording is, how high your sampling rate and how many channels you have. If Matlab crashes when reading in everything, you would need to use trialpadding, or need to think of something clever yourself :) Would be great if you could let us know how you solve this in the end so that we can refer to that if someone else in future has a similar question. Best, Jörn On 7/5/2013 3:51 AM, Aaron Schurger wrote: > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: >> hi aaron, >> filtering is generally applied after the data have been epoched. to avoid >> the filter artifacts you are speaking about, we normally define epochs that >> are sufficiently larger so that these artifacts would be in data we are not >> interested in. about 1s at both ends of the epoch should be enough in most >> cases. but you better check... later you can use ft_redefinetrial to discard >> that extra data. >> hope this helps. >> best, >> thomas >> >> >> >> Aaron Schurger schrieb: >>> Hi, >>> When you read in a data file using ft_preprocessing, with high-pass >>> filtering, is the high-pass filter applied before the data are epoched >>> (i.e. on the entire time series for the whole data file), or is the >>> high-pass filter applied separately to each epoch? For very low >>> frequencies (with period longer than one data epoch) this will make a >>> difference. >>> Thanks! >>> Aaron >>> >>> -- >>> Aaron Schurger, PhD >>> Post-doctoral researcher >>> INSERM U992 / NeuroSpin >>> CEA - Saclay, France >>> +33-1-69-08-66-47 >>> aaron.schurger at gmail.com >>> http://www.unicog.org >>> ________________________________ >>> >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. Thomas Hartmann >> >> CIMeC - Center for Mind/Brain Sciences >> Università degli Studi di Trento >> via delle Regole, 101 >> 38060 Mattarello (TN) >> ITALY >> >> Tel: +39 0461 28 2779 >> Fax: +39 0461 28 3066 >> Email: thomas.hartmann at th-ht.de >> Homepage: http://sites.google.com/site/obobcimec/ >> >> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >> Doyle) >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Fri Jul 5 08:51:41 2013 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 5 Jul 2013 08:51:41 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: <46B38EE6-90F1-4B4F-8753-6F465EE39EC5@gmail.com> Hi Aaron (et al.) another way to filter the whole recording is the workaround using EEGlab. By default, you always read in the whole recording in EEGlab and apply all filters to the whole recording. After filtering, you can use eeglab2fieldtrip.m to move your filtered data from EEGlab to field trip. Note however, that Jörn's concern regarding your memory still applies. Also, filtering the whole recording takes quite some time. Best, Julian Am 05.07.2013 um 08:41 schrieb Jörn M. Horschig: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of the recording and call ft_preprocessing. Not sure if this will work, but something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs you are interested in. > > Note however that you need to have sufficient memory for reading all your data in. I am not sure how much memory you have, how long your recording is, how high your sampling rate and how many channels you have. If Matlab crashes when reading in everything, you would need to use trialpadding, or need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: >> Thanks, Thomas. What if I wanted to apply the filtering to the entire >> time series first, and then extract the trial epochs after filtering? >> Is there a way to do that? >> Thanks, >> Aaron >> >> On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann >> wrote: >>> hi aaron, >>> filtering is generally applied after the data have been epoched. to avoid >>> the filter artifacts you are speaking about, we normally define epochs that >>> are sufficiently larger so that these artifacts would be in data we are not >>> interested in. about 1s at both ends of the epoch should be enough in most >>> cases. but you better check... later you can use ft_redefinetrial to discard >>> that extra data. >>> hope this helps. >>> best, >>> thomas >>> >>> >>> >>> Aaron Schurger schrieb: >>>> Hi, >>>> When you read in a data file using ft_preprocessing, with high-pass >>>> filtering, is the high-pass filter applied before the data are epoched >>>> (i.e. on the entire time series for the whole data file), or is the >>>> high-pass filter applied separately to each epoch? For very low >>>> frequencies (with period longer than one data epoch) this will make a >>>> difference. >>>> Thanks! >>>> Aaron >>>> >>>> -- >>>> Aaron Schurger, PhD >>>> Post-doctoral researcher >>>> INSERM U992 / NeuroSpin >>>> CEA - Saclay, France >>>> +33-1-69-08-66-47 >>>> aaron.schurger at gmail.com >>>> http://www.unicog.org >>>> ________________________________ >>>> >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> Dr. Thomas Hartmann >>> >>> CIMeC - Center for Mind/Brain Sciences >>> Università degli Studi di Trento >>> via delle Regole, 101 >>> 38060 Mattarello (TN) >>> ITALY >>> >>> Tel: +39 0461 28 2779 >>> Fax: +39 0461 28 3066 >>> Email: thomas.hartmann at th-ht.de >>> Homepage: http://sites.google.com/site/obobcimec/ >>> >>> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >>> Doyle) >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.backus at donders.ru.nl Fri Jul 5 09:38:55 2013 From: a.backus at donders.ru.nl (Alexander Backus) Date: Fri, 5 Jul 2013 09:38:55 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields Message-ID: Hi, When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to covert to 3rd order gradient, it replaces the values in data.grad.chanpos and data.grad.chanori with NaNs. I assume this is done because they are no longer valid. When digging into the low-level code I found something about mismatching number of channels. Anyway, when I want to subsequently covert to planar gradient (does this actually makes sense?) or create a source model, I need these grad values. I have two questions: 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why are NaNs inserted in the grad subfields? 2) Can I still use the data for planar gradient conversion or source modeling by using the earlier stored old gradient info (pre ft_denoise_synthetic) or is this ill-advised and is there a more wise course of action? Thanks in advance, Best, Alexander Backus -- Alexander R. Backus, MSc PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Memory and Space Research Group www.doellerlab.com P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands Telephone: +31(0)24 36 10754 -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.hartmann at th-ht.de Fri Jul 5 10:16:11 2013 From: thomas.hartmann at th-ht.de (Thomas Hartmann) Date: Fri, 05 Jul 2013 10:16:11 +0200 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: <51D680CB.7040906@th-ht.de> hi, i would do this: /% do definetrial for all data...// //cfg = [];// //cfg.dataset = 'younameit.data';// //cfg.trialdef.triallength = Inf;// //cfg.trialdef.ntrials = 1;// // //cfg = ft_definetrial(cfg);// // //% preprocess all the data// //cfg.hpfilter = 'yes';// //cfg.hpfreq = 0.5;// // //alldata = ft_preprocessing(cfg);// // //% now we do definetrials for our trials...// //cfg = [];// //cfg.//trialdef.prestim = 2;// //cfg.trialdef.poststim = 2;// //cfg.trialdef.eventype = 'YourEventType';// //cfg.trialdef.eventvalue = [1 2 3 4 5];// // //cfg = ft_definetrial(cfg);// // //% now we use the trl field we just created for ft_redefinetrial...// //data_epochs = ft_redefinetrial(cfg, alldata);/ i havent tested the code but it should be more or less fine.. and the good thing is that you stay within the high level fieldtrip functions.... best, thomas On 05.07.2013 08:41, "Jörn M. Horschig" wrote: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the > end of the recording and call ft_preprocessing. Not sure if this will > work, but something like > > / cfg = [];// > // ...// > // hdr = ft_read_header(cfg.dataset);// > // cfg.trl = [0 hdr.nSamples 0];// > // data = ft_preprocessing(cfg);/ > > Subsequently you might want to try using ft_redefinetrial to get the > epochs you are interested in. > > Note however that you need to have sufficient memory for reading all > your data in. I am not sure how much memory you have, how long your > recording is, how high your sampling rate and how many channels you > have. If Matlab crashes when reading in everything, you would need to > use trialpadding, or need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end > so that we can refer to that if someone else in future has a similar > question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: >> Thanks, Thomas. What if I wanted to apply the filtering to the entire >> time series first, and then extract the trial epochs after filtering? >> Is there a way to do that? >> Thanks, >> Aaron >> >> On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann >> wrote: >>> hi aaron, >>> filtering is generally applied after the data have been epoched. to avoid >>> the filter artifacts you are speaking about, we normally define epochs that >>> are sufficiently larger so that these artifacts would be in data we are not >>> interested in. about 1s at both ends of the epoch should be enough in most >>> cases. but you better check... later you can use ft_redefinetrial to discard >>> that extra data. >>> hope this helps. >>> best, >>> thomas >>> >>> >>> >>> Aaron Schurger schrieb: >>>> Hi, >>>> When you read in a data file using ft_preprocessing, with high-pass >>>> filtering, is the high-pass filter applied before the data are epoched >>>> (i.e. on the entire time series for the whole data file), or is the >>>> high-pass filter applied separately to each epoch? For very low >>>> frequencies (with period longer than one data epoch) this will make a >>>> difference. >>>> Thanks! >>>> Aaron >>>> >>>> -- >>>> Aaron Schurger, PhD >>>> Post-doctoral researcher >>>> INSERM U992 / NeuroSpin >>>> CEA - Saclay, France >>>> +33-1-69-08-66-47 >>>> aaron.schurger at gmail.com >>>> http://www.unicog.org >>>> ________________________________ >>>> >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> Dr. Thomas Hartmann >>> >>> CIMeC - Center for Mind/Brain Sciences >>> Università degli Studi di Trento >>> via delle Regole, 101 >>> 38060 Mattarello (TN) >>> ITALY >>> >>> Tel: +39 0461 28 2779 >>> Fax: +39 0461 28 3066 >>> Email:thomas.hartmann at th-ht.de >>> Homepage:http://sites.google.com/site/obobcimec/ >>> >>> "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan >>> Doyle) >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail:jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web:http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dr. Thomas Hartmann CIMeC - Center for Mind/Brain Sciences Università degli Studi di Trento via delle Regole, 101 38060 Mattarello (TN) ITALY Tel: +39 0461 28 2779 Fax: +39 0461 28 3066 Email: thomas.hartmann at th-ht.de Homepage: http://sites.google.com/site/obobcimec/ "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan Doyle) -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 5 16:03:29 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 5 Jul 2013 10:03:29 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D66AAE.70307@donders.ru.nl> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> Message-ID: Thanks, Jörn. If memory is an issue, I suppose I could try doing the filtering one channel at a time, applying redefinetrial to each channel (one at a time), and then put the resulting epochs back together in a field-trip structure. I'll let you know what I come up with (if I find a good solution). Memory may not end up being an issue because my recording sessions were only about 5 min long each, and with 8 Gb of RAM, should be OK. Cheers, Aaron On Fri, Jul 5, 2013 at 2:41 AM, "Jörn M. Horschig" wrote: > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of > the recording and call ft_preprocessing. Not sure if this will work, but > something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs > you are interested in. > > Note however that you need to have sufficient memory for reading all your > data in. I am not sure how much memory you have, how long your recording is, > how high your sampling rate and how many channels you have. If Matlab > crashes when reading in everything, you would need to use trialpadding, or > need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so > that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: > > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: > > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: > > Hi, > When you read in a data file using ft_preprocessing, with high-pass > filtering, is the high-pass filter applied before the data are epoched > (i.e. on the entire time series for the whole data file), or is the > high-pass filter applied separately to each epoch? For very low > frequencies (with period longer than one data epoch) this will make a > difference. > Thanks! > Aaron > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > ________________________________ > > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From aaron.schurger at gmail.com Fri Jul 5 16:25:32 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 5 Jul 2013 10:25:32 -0400 Subject: [FieldTrip] ft_preprocessing high-pass filtering question In-Reply-To: <51D680CB.7040906@th-ht.de> References: <6b9df962-56b0-4f73-8ed5-cc46a71b3502@email.android.com> <51D66AAE.70307@donders.ru.nl> <51D680CB.7040906@th-ht.de> Message-ID: Hi, Thomas, Yes, this is roughly what I tried to do, but I couldn't get it to work at first. But I used ft_preprocessing instead of ft_redefinetrial, and I think that was the mistake. With ft_redefinetrial, now it works just fine. Simple - thanks! By the way, when the trials are redefined, fieldtrip always reports "found 31 events" and then "created 30 trials" (there are 30 trials in each block). Why does fieldtrip always report one extra event per run? Thanks! Aaron On Fri, Jul 5, 2013 at 4:16 AM, Thomas Hartmann wrote: > hi, > i would do this: > > % do definetrial for all data... > cfg = []; > cfg.dataset = 'younameit.data'; > cfg.trialdef.triallength = Inf; > cfg.trialdef.ntrials = 1; > > cfg = ft_definetrial(cfg); > > % preprocess all the data > cfg.hpfilter = 'yes'; > cfg.hpfreq = 0.5; > > alldata = ft_preprocessing(cfg); > > % now we do definetrials for our trials... > cfg = []; > cfg.trialdef.prestim = 2; > cfg.trialdef.poststim = 2; > cfg.trialdef.eventype = 'YourEventType'; > cfg.trialdef.eventvalue = [1 2 3 4 5]; > > cfg = ft_definetrial(cfg); > > % now we use the trl field we just created for ft_redefinetrial... > data_epochs = ft_redefinetrial(cfg, alldata); > > i havent tested the code but it should be more or less fine.. and the good > thing is that you stay within the high level fieldtrip functions.... > > best, > thomas > > > > > On 05.07.2013 08:41, "Jörn M. Horschig" wrote: > > Hi Aaron, > > in that case you need to define only one trial, going from 0 to the end of > the recording and call ft_preprocessing. Not sure if this will work, but > something like > > cfg = []; > ... > hdr = ft_read_header(cfg.dataset); > cfg.trl = [0 hdr.nSamples 0]; > data = ft_preprocessing(cfg); > > Subsequently you might want to try using ft_redefinetrial to get the epochs > you are interested in. > > Note however that you need to have sufficient memory for reading all your > data in. I am not sure how much memory you have, how long your recording is, > how high your sampling rate and how many channels you have. If Matlab > crashes when reading in everything, you would need to use trialpadding, or > need to think of something clever yourself :) > > Would be great if you could let us know how you solve this in the end so > that we can refer to that if someone else in future has a similar question. > > Best, > Jörn > On 7/5/2013 3:51 AM, Aaron Schurger wrote: > > Thanks, Thomas. What if I wanted to apply the filtering to the entire > time series first, and then extract the trial epochs after filtering? > Is there a way to do that? > Thanks, > Aaron > > On Thu, Jul 4, 2013 at 4:31 PM, Thomas Hartmann > wrote: > > hi aaron, > filtering is generally applied after the data have been epoched. to avoid > the filter artifacts you are speaking about, we normally define epochs that > are sufficiently larger so that these artifacts would be in data we are not > interested in. about 1s at both ends of the epoch should be enough in most > cases. but you better check... later you can use ft_redefinetrial to discard > that extra data. > hope this helps. > best, > thomas > > > > Aaron Schurger schrieb: > > Hi, > When you read in a data file using ft_preprocessing, with high-pass > filtering, is the high-pass filter applied before the data are epoched > (i.e. on the entire time series for the whole data file), or is the > high-pass filter applied separately to each epoch? For very low > frequencies (with period longer than one data epoch) this will make a > difference. > Thanks! > Aaron > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > ________________________________ > > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Dr. Thomas Hartmann > > CIMeC - Center for Mind/Brain Sciences > Università degli Studi di Trento > via delle Regole, 101 > 38060 Mattarello (TN) > ITALY > > Tel: +39 0461 28 2779 > Fax: +39 0461 28 3066 > Email: thomas.hartmann at th-ht.de > Homepage: http://sites.google.com/site/obobcimec/ > > "I am a brain, Watson. The rest of me is a mere appendix. " (Arthur Conan > Doyle) > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From szabbanto at gmail.com Fri Jul 5 16:51:36 2013 From: szabbanto at gmail.com (=?ISO-8859-1?Q?Szabolcs_Szeb=E9nyi?=) Date: Fri, 5 Jul 2013 16:51:36 +0200 Subject: [FieldTrip] Question about ft_freqanalysis using wavelet method Message-ID: Dear Fieldtrip developers and users, I have a question about ft_freqanalysis when I use the 'wavelet' method. When I call this fieldtrip function with the specifications below, I get an error message right at the first trial: Error using zeros Out of memory. Type HELP MEMORY for your options. Error in ft_freqanalysis (line 601) if powflg, powspctrm = nan+zeros(ntrials,nchan,nfoi,ntoi,cfg.precision); end Here are my specifications: cfg = []; cfg.trials = find(data.trialinfo(:,3) == iPhase); cfg.channel = 'MEG'; cfg.method = 'wavelet'; cfg.toi = -1.5:0.005:4; cfg.foi = 30:1:90; cfg.width = 5; cfg.keeptrials = 'yes'; cfg.output = 'pow'; cfg.pad = 'maxperlen'; cfg.padtype = 'zero'; cfg.polyremoval = 0; I tried out the wavelet approach already for lower frequencies (foi = 1:0.5:30; toi = -1.5:0.1:4; width = 7) and it worked fine for that. For the higher frequencies above, it cannot proceed further to the 2nd trial with 60GB memory either, so I think, the problem is somewhere else. The data itself consists of 275 trials, with a sampling rate of 600Hz; 273 channels CTF MEG. I would highly appreciate if you could tell me where the problem is and what I should change in order to proceed. Thank you in advance for your help, Szabolcs Szebényi -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcpiastra at libero.it Fri Jul 5 17:47:32 2013 From: mcpiastra at libero.it (mcpiastra at libero.it) Date: Fri, 5 Jul 2013 17:47:32 +0200 (CEST) Subject: [FieldTrip] source_recontruction with intracranial sensors Message-ID: <20502312.13722601373039252586.JavaMail.defaultUser@defaultHost> Dear Fieldtrip developers and users, I have some problems with source reconstruction starting with intracranial sensors. Schematic details are below. Aim: do source reconstruction using BEM for the forward problem and mne for the inverse problem. Dataset: stereoEEG recording (50 sec) Notation: I'll use the same nomenclature of the one in the tutorial Since we have intracranial sensors, our aim is to build the forward model (leadfield structure) starting from a mesh whose cortical sheet has a higher spatial resolution. To do that we approached the problem in two ways: 1) we substituted the innermost sheet, built by ft_prepare_mesh, with the Freesurfer cortical mesh (4180 vertices). We put dipoles on the mesh nodes and then we built the head model and calculate the leadfield matrices (one for each dipole). Solving the inverse problem, in source.avg.pow there were values with order of magnitude of 10^{-30}- 10^{-20}. This is due to the fact that the matrix vol.mat (one of the output of ft_prepare_headmodel) had values very different if we compared the entries in correspondence to the Fieldtrip meshes and the ones in correspondence to the Freesurfer mesh. This difference had the order of magnitude equal to 10^{9}. Due to this pathology, we tried a different way to compute the forward model (following more the tutorial). 2) we built the head model using the default Fieldtrip meshes (all of the three sheets) without substituting any sheet. (We just fixed the number of nodes for the innermost sheet equal to the Freesurfer one.) This avoided high differences in vol.mat. Freesurfer mesh vertices were used to determine dipole positions, as we did before. In this case we obtained values of source.avg.pow of the order of 10^ {-6} In both cases we preprocessed the dataset with ft_timelockanalysis and we used the regularization parameter lambda (for the mne method) equal to 0.2. Our questions are: 1) what is vol.mat? Which order of magnitude should have its values? We didn't manage to explore the building process of it. (We suppose this matrix has electrical information interpolated through the mesh vertices.) As consequences: 2) which is the order of magnitude expected for the values of source.avg.pow ? And which is its unit of measure? 3) Is it correct the interpretation of: source.avg.mom and source.avg.pow as the evolution through time of the electric dipole moment and the radiated power of the dipole, respectively? 4) In order to apply a regularization approach to solve the inverse problem we though that the best way was to introduce the noise covariation matrix built by the function ft_timelockanalysis which is subsequently controlled by the lambda parameter. Is there any criterion to choose the best lambda? Can we avoid to pass through ft_timelockanalysis to regularize the solution? Many thanks, Maria Carla Piastra PhD student in Bioengeneering c/o BioLab @ DIBRIS University of Genova, ITALY From zriouil.imane at gmail.com Fri Jul 5 21:44:41 2013 From: zriouil.imane at gmail.com (z.imane) Date: Fri, 5 Jul 2013 20:44:41 +0100 Subject: [FieldTrip] Computing the spike triggered average LFP Message-ID: Hi i would applying the paragraph "Computing the spike triggered average LFP" in tutorial "Preprocessing and analysis of spike and local field potential data" in matlab. if you explain this pocess more, because i don't understand it. -------------- next part -------------- An HTML attachment was scrubbed... URL: From baharbahar395 at yahoo.com Sat Jul 6 08:05:37 2013 From: baharbahar395 at yahoo.com (Bahar Bahar) Date: Sat, 6 Jul 2013 14:05:37 +0800 (SGT) Subject: [FieldTrip] sLORETA Message-ID: <1373090737.76319.YahooMailNeo@web192303.mail.sg3.yahoo.com> Hi dear all, I have computed sloreta from ERP data via the software, but I do not know what is the unit of the values resulted in transformation. Can any one help me about that? -------------- next part -------------- An HTML attachment was scrubbed... URL: From baharbahar395 at yahoo.com Sat Jul 6 08:15:53 2013 From: baharbahar395 at yahoo.com (Bahar Bahar) Date: Sat, 6 Jul 2013 14:15:53 +0800 (SGT) Subject: [FieldTrip] Sloreta Message-ID: <1373091353.41529.YahooMailNeo@web192306.mail.sg3.yahoo.com> Hi dear all, I have computed sloreta from ERP data via the Sloreta software, but I did not figure out the unit of the values resulted in transformation. Can any one help me about that? Thanks, Bahar -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Sat Jul 6 09:53:09 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Sat, 6 Jul 2013 09:53:09 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data Message-ID: Dear All, after running source statistics I tried to plot the result. However, I always get the error that cfg.parameter 'all' can't be used since there is "no such field". I know that I can also specify single parameters, i.e. only the ones I want to interpolate. However, I would like to know why it doesn't work for me with all the parameters... Maybe it's only a minor thing, i.e. the FT version. But I want to make sure that there is no major error in my pipeline. Any help is as always very appreciated! Thanks! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Sat Jul 6 14:19:58 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Sat, 06 Jul 2013 14:19:58 +0200 Subject: [FieldTrip] Question about ft_freqanalysis using wavelet method In-Reply-To: References: Message-ID: <51D80B6E.5040704@donders.ru.nl> Hi Szabi, That error has nothing to do with the wavelet approach but with the fact that you want to have steps of 5ms (as specified in cfg.toi) for your TFR. FieldTrip will create one big data matrin nTrials x nChannels x nSamples x nFrequencies. With the settings you specified this will be quite huge, and it does not fit into memory when Matlab tries to initiate that variable. I would suggest you use 50ms steps, that is sufficient especially given that you need some tens of milliseconds for estimating the frequency content anyway. An alternative would be to use the torque/maui cluster at the Donders and request a session with loads of memory :) Best, Jörn On 7/5/2013 4:51 PM, Szabolcs Szebényi wrote: > Dear Fieldtrip developers and users, > > I have a question about ft_freqanalysis when I use the 'wavelet' > method. When I call this fieldtrip function with the specifications > below, I get an error message right at the first trial: > > Error using zeros > Out of memory. Type HELP MEMORY for your options. > > Error in ft_freqanalysis (line 601) > if powflg, powspctrm = > nan+zeros(ntrials,nchan,nfoi,ntoi,cfg.precision); > end > > Here are my specifications: > > cfg = []; > cfg.trials = find(data.trialinfo(:,3) == iPhase); > cfg.channel = 'MEG'; > cfg.method = 'wavelet'; > cfg.toi = -1.5:0.005:4; > cfg.foi = 30:1:90; > cfg.width = 5; > cfg.keeptrials = 'yes'; > cfg.output = 'pow'; > cfg.pad = 'maxperlen'; > cfg.padtype = 'zero'; > cfg.polyremoval = 0; > > I tried out the wavelet approach already for lower frequencies (foi = > 1:0.5:30; toi = -1.5:0.1:4; width = 7) and it worked fine for that. > For the higher frequencies above, it cannot proceed further to the 2nd > trial with 60GB memory either, so I think, the problem is somewhere else. > > The data itself consists of 275 trials, with a sampling rate of 600Hz; > 273 channels CTF MEG. > > I would highly appreciate if you could tell me where the problem is > and what I should change in order to proceed. > > > Thank you in advance for your help, > > Szabolcs Szebényi > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Jul 7 19:41:51 2013 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 7 Jul 2013 19:41:51 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data Message-ID: Hi Andreas , It is annoying that it doesn't work if you specify cfg.parameter 'all' and I don't know why either. However , I have a very simple solution for this by interpolating 'stat' and 'mask' then combining afterwards when you want to plot your statistic result. The FT code is something like this: cfg = []; cfg.voxelcoord = 'no'; cfg.parameter = 'stat'; cfg.interpmethod = 'nearest'; cfg.coordsys = 'mni'; statplot = ft_sourceinterpolate(cfg, stat,mri); cfg = []; cfg.voxelcoord = 'no'; cfg.parameter = 'mask'; cfg.interpmethod = 'nearest'; cfg.coordsys = 'mni'; mask = ft_sourceinterpolate(cfg, stat,mri); statplot.mask = mask.mask; Hope this helps. Best, Haiteng > Message: 3 > Date: Sat, 6 Jul 2013 09:53:09 +0200 > From: Andreas Sauer > To: FieldTrip discussion list > Subject: [FieldTrip] ft_sourceinterpolate with stats data > Message-ID: > < > CAHLSopWD2Q-RuAMJrvwZJGAajB6aUbDyrDN6_SFMdqu7HOgZ0g at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear All, > > after running source statistics I tried to plot the result. However, I > always get the error that cfg.parameter 'all' can't be used since there is > "no such field". > > I know that I can also specify single parameters, i.e. only the ones I want > to interpolate. However, I would like to know why it doesn't work for me > with all the parameters... Maybe it's only a minor thing, i.e. the FT > version. But I want to make sure that there is no major error in my > pipeline. > > Any help is as always very appreciated! Thanks! > > Best, > > Andreas > > -- > Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstra?e 46 > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130706/b595b2e2/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 32, Issue 11 > ***************************************** > -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Sun Jul 7 20:17:58 2013 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Sun, 7 Jul 2013 20:17:58 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields Message-ID: Hi Alexander, I am not clear about what's ft_denoise_synthetic doing. However , I don't have such problem when I use . The reason you get 'mismatching number of channels' probably because you specify cfg.channel ='MEG' instead of including all channels. My FT code is something like this: % reading cfg = []; cfg.dataset = dataset; cfg.trialdef.eventtype = ''; cfg.trialdef.eventvalue = ; cfg.continuous = 'yes'; cfg.channel= 'all'; cfg.trialdef.prestim = ; cfg.trialdef.poststim = ; cfg = ft_definetrial(cfg); trl = cfg.trl; cfg.detrend ='yes'; cfg.demean = 'yes'; data= ft_preprocessing(cfg); cfg.gradient = 'G3BR'; data= ft_denoise_synthetic(cfg,data); In my pipeline , the grad changes into NAN only after I run I ICA to remove artifacts . I replace this grad with previous good gradient information and assume it is fine for the latter source reconstruction. Hope this helps. Best, Haiteng > > > Message: 2 > Date: Fri, 5 Jul 2013 09:38:55 +0200 > From: Alexander Backus > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in > grad fields > Message-ID: > < > CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to > covert to 3rd order gradient, it replaces the values in data.grad.chanpos > and data.grad.chanori with NaNs. > > I assume this is done because they are no longer valid. > When digging into the low-level code I found something about mismatching > number of channels. > > Anyway, when I want to subsequently covert to planar gradient (does this > actually makes sense?) or create a source model, I need these grad values. > > I have two questions: > > 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why > are NaNs inserted in the grad subfields? > > 2) Can I still use the data for planar gradient conversion or source > modeling by using the earlier stored old gradient info (pre > ft_denoise_synthetic) or is this ill-advised and is there a more wise > course of action? > > Thanks in advance, > Best, > Alexander Backus > -- Haiteng Jiang PhD candidate Neuronal Oscillations Group Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Visiting address Room 2.32 Donders Centre for Cognitive Neuroimaging Kapittelweg 29 6525 EN Nijmegen the Netherlands Tel.: +31 (0)243668291 Web: https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Mon Jul 8 10:34:06 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Mon, 8 Jul 2013 10:34:06 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data In-Reply-To: References: Message-ID: Thanks for your answer, Haiteng! It also works for me when I interpolate i.e. 'stat'. However, it would be good to know why 'all' does not work, since it is described in the tutorial... Best, Andreas 2013/7/7 Haiteng Jiang > Hi Andreas , > It is annoying that it doesn't work if you specify cfg.parameter > 'all' and I don't know why either. However , I have a very simple > solution for this by interpolating 'stat' and 'mask' then combining > afterwards when you want to plot your statistic result. The FT code is > something like this: > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'stat'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > statplot = ft_sourceinterpolate(cfg, stat,mri); > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'mask'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > mask = ft_sourceinterpolate(cfg, > stat,mri); > statplot.mask = mask.mask; > Hope this helps. > > Best, > Haiteng > > > > >> Message: 3 >> Date: Sat, 6 Jul 2013 09:53:09 +0200 >> From: Andreas Sauer >> To: FieldTrip discussion list >> Subject: [FieldTrip] ft_sourceinterpolate with stats data >> Message-ID: >> < >> CAHLSopWD2Q-RuAMJrvwZJGAajB6aUbDyrDN6_SFMdqu7HOgZ0g at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Dear All, >> >> after running source statistics I tried to plot the result. However, I >> always get the error that cfg.parameter 'all' can't be used since there is >> "no such field". >> > > >> >> I know that I can also specify single parameters, i.e. only the ones I >> want >> to interpolate. However, I would like to know why it doesn't work for me >> with all the parameters... Maybe it's only a minor thing, i.e. the FT >> version. But I want to make sure that there is no major error in my >> pipeline. >> >> Any help is as always very appreciated! Thanks! >> >> Best, >> >> Andreas >> >> -- >> Andreas Sauer >> Max Planck Institute for Brain Research >> Deutschordenstra?e 46 >> >> 60528 Frankfurt am Main >> Germany >> >> T: +49 69 96769 278 >> F: +49 69 96769 327 >> Email: sauer.mpih at gmail.com >> www.brain.mpg.de >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130706/b595b2e2/attachment-0001.html >> > >> >> ------------------------------ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> End of fieldtrip Digest, Vol 32, Issue 11 >> ***************************************** >> > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Dipl.-Psych. Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 8 11:30:39 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 08 Jul 2013 11:30:39 +0200 Subject: [FieldTrip] ft_sourceinterpolate with stats data In-Reply-To: References: Message-ID: <51DA86BF.3000801@donders.ru.nl> Hi Andreas, all the chiefs are on vacation right now, and I do not know if it should work or why it does not. Therefore, I created a bug on bugzilla: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2218 You can also sign up there and add yourself to the CC list to stay informed about the progress on this. In the meanwhile I would suggest to do as Haiteng proposed, as this is the only way to go right now. Thanks for reporting :) Best, Jörn On 7/8/2013 10:34 AM, Andreas Sauer wrote: > Thanks for your answer, Haiteng! It also works for me when I > interpolate i.e. 'stat'. However, it would be good to know why 'all' > does not work, since it is described in the tutorial... > > Best, > > Andreas > > > 2013/7/7 Haiteng Jiang > > > Hi Andreas , > It is annoying that it doesn't work if you > specify cfg.parameter 'all' and I don't know why either. However > , I have a very simple solution for this by interpolating 'stat' > and 'mask' then combining afterwards when you want to plot your > statistic result. The FT code is something like this: > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'stat'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > statplot = ft_sourceinterpolate(cfg, stat,mri); > > cfg = []; > cfg.voxelcoord = 'no'; > cfg.parameter = 'mask'; > cfg.interpmethod = 'nearest'; > cfg.coordsys = 'mni'; > mask = ft_sourceinterpolate(cfg, > stat,mri); > statplot.mask = mask.mask; > Hope this helps. > Best, > Haiteng > > Message: 3 > Date: Sat, 6 Jul 2013 09:53:09 +0200 > From: Andreas Sauer > > To: FieldTrip discussion list > > Subject: [FieldTrip] ft_sourceinterpolate with stats data > Message-ID: > > > > Content-Type: text/plain; charset="iso-8859-1" > > > Dear All, > > after running source statistics I tried to plot the result. > However, I > always get the error that cfg.parameter 'all' can't be used > since there is > "no such field". > > > I know that I can also specify single parameters, i.e. only > the ones I want > to interpolate. However, I would like to know why it doesn't > work for me > with all the parameters... Maybe it's only a minor thing, i.e. > the FT > version. But I want to make sure that there is no major error > in my > pipeline. > > Any help is as always very appreciated! Thanks! > > Best, > > Andreas > > -- > Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstra?e 46 > > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 32, Issue 11 > ***************************************** > > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Dipl.-Psych. Andreas Sauer > Max Planck Institute for Brain Research > Deutschordenstraße 46 > 60528 Frankfurt am Main > Germany > > T: +49 69 96769 278 > F: +49 69 96769 327 > Email: sauer.mpih at gmail.com > www.brain.mpg.de > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 8 11:33:29 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 08 Jul 2013 11:33:29 +0200 Subject: [FieldTrip] Computing the spike triggered average LFP In-Reply-To: References: Message-ID: <51DA8769.6000006@donders.ru.nl> Dear Zriouil, the problem you described is rather incomplete. If you adress certain sections in particular and state in more detail what exactly you do not understand, there might be more people abel to help you. Usually, the tutorial aim at being sufficient to get started, but if they are unclear on particular location, we would be glad to hear your thought on where they are unclear and what information needs to be added to improve them. Best, Jörn On 7/5/2013 9:44 PM, z.imane wrote: > Hi > > i would applying the paragraph "Computing the spike triggered average > LFP" in tutorial "Preprocessing and analysis of spike and local field > potential data" in matlab. if you explain this pocess more, because i > don't understand it. > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hubert.preissl at uni-tuebingen.de Mon Jul 8 11:33:59 2013 From: hubert.preissl at uni-tuebingen.de (Hubert Preissl) Date: Mon, 08 Jul 2013 11:33:59 +0200 Subject: [FieldTrip] =?windows-1252?q?6th_Autumn_School_=93Move_the_Brain?= =?windows-1252?q?=94=2C_T=FCbingen=2C_30thSeptember_-2th_October_2013?= In-Reply-To: References: Message-ID: <51DA8787.3010904@uni-tuebingen.de> Hello, we are pleased to announce the upcoming 6^th Autumn School "Move the Brain" in Tübingen. Confirmed speakers: *Douglas Cheyne, *Hospital for Sick Children, Toronto, Canada *Sarang S. Dalal, *University of Konstanz, Germany *Joachim Gross, *University of Glasgow, UK *Todd Hare, *University of Zürich, Switzerland *Floris de Lang, *Donders Institute, Nijmegen, Netherlands *Jyrki Mäkelä, *Helsinki University Central Hospital, Finland *Hilke Plassmann, *INSEAD, France *Alfons Schnitzler, *University of Düsseldorf, Germany For application and further information on the scientific program please visit our website: http://www.mp.uni-tuebingen.de/mp/index.php?id=412 We look forward meeting you in Tübingen! Best regards, Hubert Preissl -- Dr. Hubert Preissl fMEG Center phone: ++49-(0)7071-2987704 Otfried Müller Str 47 fax: ++49-(0)7071-295706 72076 Tübingen, Germany email: hubert.preissl at uni-tuebingen.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From zriouil.imane at gmail.com Mon Jul 8 12:47:03 2013 From: zriouil.imane at gmail.com (z.imane) Date: Mon, 8 Jul 2013 12:47:03 +0200 Subject: [FieldTrip] Computing the spike triggered average LFP In-Reply-To: <51DA8769.6000006@donders.ru.nl> References: <51DA8769.6000006@donders.ru.nl> Message-ID: Thank you for your response. I wish to plotting LFP based on spike using a program that I want to create. and for the obtained the same graph as in the tutorial. the problem is that I do not understand how the function ft_spiketriggeredaverage computes the avererage of the LFP around the spikes, while the spikes and LFP are recorded in the same period, and how he detect the spike? -------------- next part -------------- An HTML attachment was scrubbed... URL: From manuel.mercier at einstein.yu.edu Mon Jul 8 15:32:02 2013 From: manuel.mercier at einstein.yu.edu (Manuel Mercier) Date: Mon, 8 Jul 2013 13:32:02 +0000 Subject: [FieldTrip] ft_connectivityanalysis and PLV formula Message-ID: Dear Fieldtrip Community I am still stuck with the implementation of PLV. To be sure that I understand properly the principle of Phase Locking Value, I wrote a code to compute it. That code (see below) gave me the same results as ft_connectivityanalysis. plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)) -angle(data.fourierspctrm(:,electrode_2,:,:)))),1))); (data.fourierspctrm being produced by ft_freqanalysis). However, I then realized that the subtraction between the two angles should be done in the complex plane as in: plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)))) - exp(1i*(angle(data.fourierspctrm(:,electrode_2,:,:))))))),1))); I doubt that PLV computed through FT is wrong, but then I am circumspect since the first formula is somewhat no correct and give the same results a as ft_connectivityanalysis. I went to FT code and got confused by the way ft_connectivity_corr use the cross spectrum to compute PLV. I would greatly appreciate if someone could tell me where I am missing/misunderstanding something. Thanks you for your help, Manuel ________________________________ Manuel Mercier, PhD Research Fellow Cognitive Neurophysiology Laboratory, Children’s Evaluation and Rehabilitation Center (CERC), Departments of Pediatrics and Neuroscience Albert Einstein College of Medicine, 1225 Morris Park Avenue Bronx , NY 10461 phone: +1 (718) 862 1859 fax: +1 (718) 862 1807 ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manuel Mercier [manuel.mercier at einstein.yu.edu] Sent: Friday, June 28, 2013 4:43 PM To: fieldtrip at science.ru.nl Subject: [FieldTrip] PLV formula Dear Fieldtripers Sometime ago I wrote for myself a function that was computing PLV and some related non parametric statistics. (Phase Locking Value as define as the mean across trials of the phase angle difference recorded at two loci ; based on Lachaux et al., 1999, HBM). I implemented PLV in matlab using the following formula: plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)) ... -angle(data.fourierspctrm(:,cmb(2),:,:)))),1))); with cmb(1) and cmb(2) being the indices of the electrodes of interest (between which PLV is computed). I compared my results with the ft_connectivityanalysis function from Fieldtrip and the results were exactly the same. So far so good. But I recently went back to my code, and I was a little bit confused. Since I was dealing with angles, I though that the best way to do the subtraction should be done in the complex plane Like: plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)))) ... - exp(1i*(angle(data.fourierspctrm(:,cmb(2),:,:))))))),1))); (for instance if the two angles: pi/2 and -pi/2 the direct subtraction will give pi, whereas in the complex plan it will be pi/2 - with the norm x2). The result I got with this code is obviously different from the previous one, and what I got from Fieldtrip. I went back to the archive of the mailing list but didn't find a clear answer to my point. Does anyone can enlighten me ? Thanks ! Manuel -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Tue Jul 9 00:45:37 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Tue, 9 Jul 2013 00:45:37 +0200 Subject: [FieldTrip] sEEG Source Imaging - mne solution Message-ID: Dear FieldTrip comunity, i'm dealing with MNE source reconstruction of sEEG signals. I would like to know if it is possible to use the mesh of the source-model, obtained by MNE_Suite, as the 'brain' mesh (the inner ) of the head model prepared with ft_prepare_headmodel with the 'dipoli' method, solving the forward problem. I've tried to make this step to get a more accurate inverse solution but my results seemed completely wrong and totally different by the ones obtained using a 'traditional' head model built with ft_prepare:headmodel in the 'dipoli' case. Thanks for your attention, Alberto Ghione -------------- next part -------------- An HTML attachment was scrubbed... URL: From robince at gmail.com Tue Jul 9 18:14:40 2013 From: robince at gmail.com (Robin) Date: Tue, 9 Jul 2013 17:14:40 +0100 Subject: [FieldTrip] obtaining voxel locations Message-ID: I was wondering how to get the voxel positions (or origin and voxel size) for a fieltrip mri structure. I have an anatomical scan which I have normalised to the T1 brain: >> mrin mrin = anatomy: [181x217x181 double] transform: [4x4 double] dim: [181 217 181] params: [1x1 struct] initial: [4x4 double] coordsys: 'spm' cfg: [1x1 struct] I can I obtain the location of any voxel in MNI coordinates (mm or cm)? When loading a Nifti file (with load_nii) I can find origin and voxel_size with: voxel_size = abs(nii.hdr.dime.pixdim(2:4)); % vol in mm origin = round(abs(nii.hdr.hist.originator(1:3))); and then posmm = (vox-origin) .* voxel_size. Is there any way to do the same from the fieldtrip structure? I can't find the corresponding header information. Thanks Robin -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.backus at donders.ru.nl Tue Jul 9 18:46:40 2013 From: a.backus at donders.ru.nl (Alexander Backus) Date: Tue, 9 Jul 2013 18:46:40 +0200 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields In-Reply-To: References: Message-ID: Thanks for your answer Haiteng. To share our findings on this topic: After some more debugging, we realized that it could indeed be the ICA function that inserts NaNs into the grad info. It seems ft_denoise_synthetic only changes the grad info for some reference channels... We now use Haiteng's trick of replacing the post-ICA grad info, with the post-denoise grad info, however, it feels somewhat dangerous to perform such "dirty" fixes, since that grad info is probably removed for a certain reason. We are oblivious to its impact subsequent steps like planar transform and source reconstruction. In addition, we dug up the following page on the FieldTrip wiki which explains the denoising. http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work Thanks! Cheers, Alexander On Sun, Jul 7, 2013 at 8:17 PM, Haiteng Jiang wrote: > Hi Alexander, > I am not clear about what's ft_denoise_synthetic doing. However , I > don't have such problem when I use . The reason you get > 'mismatching number of channels' probably because you specify cfg.channel > ='MEG' instead of including all channels. My FT code is something like > this: > > % reading > cfg = []; > cfg.dataset = dataset; > cfg.trialdef.eventtype = ''; > cfg.trialdef.eventvalue = ; > cfg.continuous = 'yes'; > cfg.channel= 'all'; > cfg.trialdef.prestim = ; > cfg.trialdef.poststim = ; > cfg = ft_definetrial(cfg); > trl = cfg.trl; > cfg.detrend ='yes'; > cfg.demean = 'yes'; > data= ft_preprocessing(cfg); > cfg.gradient = 'G3BR'; > data= ft_denoise_synthetic(cfg,data); > > In my pipeline , the grad changes into NAN only after I run I ICA to > remove artifacts . I replace this grad with previous good gradient > information and assume it is fine for the latter source reconstruction. > Hope this helps. > Best, > Haiteng > > >> >> >> Message: 2 >> Date: Fri, 5 Jul 2013 09:38:55 +0200 >> From: Alexander Backus >> To: fieldtrip at science.ru.nl >> Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in >> grad fields >> Message-ID: >> < >> CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> >> Content-Type: text/plain; charset="iso-8859-1" >> >> >> Hi, >> >> When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to >> covert to 3rd order gradient, it replaces the values in data.grad.chanpos >> and data.grad.chanori with NaNs. >> >> I assume this is done because they are no longer valid. >> When digging into the low-level code I found something about mismatching >> number of channels. >> >> Anyway, when I want to subsequently covert to planar gradient (does this >> actually makes sense?) or create a source model, I need these grad values. >> >> I have two questions: >> >> 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why >> are NaNs inserted in the grad subfields? >> >> 2) Can I still use the data for planar gradient conversion or source >> modeling by using the earlier stored old gradient info (pre >> ft_denoise_synthetic) or is this ill-advised and is there a more wise >> course of action? >> >> Thanks in advance, >> Best, >> Alexander Backus >> > > > > -- > Haiteng Jiang > PhD candidate > Neuronal Oscillations Group > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > > Visiting address > Room 2.32 > Donders Centre for Cognitive Neuroimaging > Kapittelweg 29 > 6525 EN Nijmegen > the Netherlands > > Tel.: +31 (0)243668291 > Web: https://sites.google.com/site/haitengjiang/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Alexander R. Backus, MSc PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Memory and Space Research Group www.doellerlab.com P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands Telephone: +31(0)24 36 10754 -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:12:01 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:42:01 +0430 Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in grad fields In-Reply-To: References: Message-ID: *Hello,** * I am mohsen alimoradi, MSc student of artificial intelligence in Qazvin Azad University. * **I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot* On Tue, Jul 9, 2013 at 9:16 PM, Alexander Backus wrote: > Thanks for your answer Haiteng. > > To share our findings on this topic: > > After some more debugging, we realized that it could indeed be the ICA > function that inserts NaNs into the grad info. > > It seems ft_denoise_synthetic only changes the grad info for some > reference channels... > > We now use Haiteng's trick of replacing the post-ICA grad info, with the > post-denoise grad info, however, it feels somewhat dangerous to perform > such "dirty" fixes, since that grad info is probably removed for a certain > reason. We are oblivious to its impact subsequent steps like planar > transform and source reconstruction. > > In addition, we dug up the following page on the FieldTrip wiki which > explains the denoising. > > http://fieldtrip.fcdonders.nl/faq/how_does_the_ctf_higher-order_gradiometer_work > > Thanks! > > Cheers, > Alexander > > > On Sun, Jul 7, 2013 at 8:17 PM, Haiteng Jiang wrote: > >> Hi Alexander, >> I am not clear about what's ft_denoise_synthetic doing. However , >> I don't have such problem when I use . The reason you get >> 'mismatching number of channels' probably because you specify cfg.channel >> ='MEG' instead of including all channels. My FT code is something like >> this: >> >> % reading >> cfg = []; >> cfg.dataset = dataset; >> cfg.trialdef.eventtype = ''; >> cfg.trialdef.eventvalue = ; >> cfg.continuous = 'yes'; >> cfg.channel= 'all'; >> cfg.trialdef.prestim = ; >> cfg.trialdef.poststim = ; >> cfg = ft_definetrial(cfg); >> trl = cfg.trl; >> cfg.detrend ='yes'; >> cfg.demean = 'yes'; >> data= ft_preprocessing(cfg); >> cfg.gradient = 'G3BR'; >> data= ft_denoise_synthetic(cfg,data); >> >> In my pipeline , the grad changes into NAN only after I run I ICA to >> remove artifacts . I replace this grad with previous good gradient >> information and assume it is fine for the latter source reconstruction. >> Hope this helps. >> Best, >> Haiteng >> >> >>> >>> >>> Message: 2 >>> Date: Fri, 5 Jul 2013 09:38:55 +0200 >>> From: Alexander Backus >>> To: fieldtrip at science.ru.nl >>> Subject: [FieldTrip] why does ft_denoise_synthetic inserts NaNs in >>> grad fields >>> Message-ID: >>> < >>> CAEfPLbcMKmSkhak0cqQHNp-Lye8xhLJKjauN4GWupBCdVBA6cQ at mail.gmail.com> >>> Content-Type: text/plain; charset="iso-8859-1" >>> >>> >>> Hi, >>> >>> When I use ft_denoise_synthetic on my preprocessed CTF275 MEG data to >>> covert to 3rd order gradient, it replaces the values in data.grad.chanpos >>> and data.grad.chanori with NaNs. >>> >>> I assume this is done because they are no longer valid. >>> When digging into the low-level code I found something about mismatching >>> number of channels. >>> >>> Anyway, when I want to subsequently covert to planar gradient (does this >>> actually makes sense?) or create a source model, I need these grad >>> values. >>> >>> I have two questions: >>> >>> 1) What does ft_denoise_synthetic exactly do (in non-math terms) and why >>> are NaNs inserted in the grad subfields? >>> >>> 2) Can I still use the data for planar gradient conversion or source >>> modeling by using the earlier stored old gradient info (pre >>> ft_denoise_synthetic) or is this ill-advised and is there a more wise >>> course of action? >>> >>> Thanks in advance, >>> Best, >>> Alexander Backus >>> >> >> >> >> -- >> Haiteng Jiang >> PhD candidate >> Neuronal Oscillations Group >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> >> Visiting address >> Room 2.32 >> Donders Centre for Cognitive Neuroimaging >> Kapittelweg 29 >> 6525 EN Nijmegen >> the Netherlands >> >> Tel.: +31 (0)243668291 >> Web: https://sites.google.com/site/haitengjiang/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Alexander R. Backus, MSc > PhD Candidate at the Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Memory and Space Research Group > www.doellerlab.com > > P.O. Box 9101, NL-6500 HB Nijmegen , The Netherlands > Telephone: +31(0)24 36 10754 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:12:17 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:42:17 +0430 Subject: [FieldTrip] obtaining voxel locations In-Reply-To: References: Message-ID: *Hello,** * I am mohsen alimoradi, MSc student of artificial intelligence in Qazvin Azad University. * **I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot * On Tue, Jul 9, 2013 at 8:44 PM, Robin wrote: > I was wondering how to get the voxel positions (or origin and voxel size) > for a fieltrip mri structure. > > I have an anatomical scan which I have normalised to the T1 brain: > > >> mrin > > mrin = > > anatomy: [181x217x181 double] > transform: [4x4 double] > dim: [181 217 181] > params: [1x1 struct] > initial: [4x4 double] > coordsys: 'spm' > cfg: [1x1 struct] > > I can I obtain the location of any voxel in MNI coordinates (mm or cm)? > When loading a Nifti file (with load_nii) I can find origin and voxel_size > with: > > voxel_size = abs(nii.hdr.dime.pixdim(2:4)); % vol in mm > origin = round(abs(nii.hdr.hist.originator(1:3))); > > and then posmm = (vox-origin) .* voxel_size. Is there any way to do the > same from the fieldtrip structure? I can't find the corresponding header > information. > > Thanks > > Robin > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Wed Jul 10 12:14:01 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Wed, 10 Jul 2013 14:44:01 +0430 Subject: [FieldTrip] (no subject) Message-ID: *Hello,** * ***I am working on the Biomag 2012 analysis competition.** I have downloaded a .zip file from ftp://ftp.fcdonders.nl/pub/biomag2012/. ** ** I have extracted the content and I am interested in the second objective,** the one related to long-term memory representations (folder data2).** ** I was able to load the 2 mat files into Matlab workspace.** ** I was also able to use FieldTrip functions on tutorial code.** ** How could I use FieldTrip on this data? If there are more ways, which one would be the fastest/easiest?** ** Thanks a lot* -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Thu Jul 11 17:09:40 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Thu, 11 Jul 2013 17:09:40 +0200 Subject: [FieldTrip] ft_megrealign how to avoid? Message-ID: Dear all, I have CTF MEG data and I am interested in a gamma band topographies. We recorded two sessions for every subject. Now I would like to compare grand averages of these two sessions over all subjects(n=13). Without realignment these grand average topographies look ok and according to our expectation. However, I know that it would be reasonable to do realignment of all datasets (n=13x2) to common template. I have tried that with ft_megrealign which uses method suggested by Knösche, 2002 and this doesn't work. It gives me very weird results, meaning that topographies are totally changed and some new occipital activity emerges. I have plotted single subject head models(singleshell) together with sensors and they are accurately aligned. Then I tried different inwardshift options for ft_megrealign and this didn't bring so much success. So my question is, could I go without the realignment and what I need to do in order to overcome problem with realignment? -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Thu Jul 11 17:58:54 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 11 Jul 2013 17:58:54 +0200 (CEST) Subject: [FieldTrip] ft_megrealign how to avoid? In-Reply-To: Message-ID: <1783486843.2033915.1373558334245.JavaMail.root@sculptor.zimbra.ru.nl> Hi Nenad, You may want to check whether there are systematic differences (over the whole group of subjects) in head position in the first place. Here's an example page showing how to check head position/movement in MEG: http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis The same page also indicates how to 'regress out' variance accounted for by (different) head position. Applying this method on the datasets combined (trials of the two conditions for each subject) allows you to eliminate head position as a potential confound (by using ft_regressconfound prior to computing subject-level statistics). I have no first hand experience on to what extent megrealign can reduce the effects of different head position between two conditions, but from our experiences here we know that systematic differences in head position between conditions may even be noticeable at the source level. Optimally, one thus tries to minimize the influence of head movement wherever possible, i.e. already at recording. This may come in too late for your current dataset, but this online 'realignment' method may improve between- but also within-session consistency in future studies of yours involving the CTF MEG system (a Neuromag version is being developed): http://fieldtrip.fcdonders.nl/faq/how_can_i_monitor_a_subject_s_head_position_during_a_meg_session Hope these documentation pages may be of any help, Arjen ----- Oorspronkelijk bericht ----- > Van: "Nenad Polomac" > Aan: fieldtrip at science.ru.nl > Verzonden: Donderdag 11 juli 2013 17:09:40 > Onderwerp: [FieldTrip] ft_megrealign how to avoid? > Dear all, > I have CTF MEG data and I am interested in a gamma band topographies. > We recorded two sessions for every subject. Now I would like to > compare grand averages of these two sessions over all subjects(n=13). > Without realignment these grand average topographies look ok and > according to our expectation. However, I know that it would be > reasonable to do realignment of all datasets (n=13x2) to common > template. I have tried that with ft_megrealign which uses method > suggested by Knösche, 2002 and this doesn't work. It gives me very > weird results, meaning that topographies are totally changed and some > new occipital activity emerges. I have plotted single subject head > models(singleshell) together with sensors and they are accurately > aligned. Then I tried different inwardshift options for ft_megrealign > and this didn't bring so much success. So my question is, could I go > without the realignment and what I need to do in order to overcome > problem with realignment? > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Thu Jul 11 18:18:33 2013 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 11 Jul 2013 18:18:33 +0200 Subject: [FieldTrip] Fwd: 17-18 October, 2013: NatMEG inauguration conference at Karolinska Institutet, Stockholm. In-Reply-To: References: Message-ID: Dear FieldTrippers, We are very happy to announce the inauguration conference for NatMEG, the brand-new National Swedish MEG facility. Please find the invitation attached. Have a great summer, Stephen -------------- next part -------------- A non-text attachment was scrubbed... Name: Invitation to NatMEG inauguration conference.pdf Type: application/pdf Size: 228355 bytes Desc: not available URL: From ali.b.sharif at gmail.com Thu Jul 11 19:30:19 2013 From: ali.b.sharif at gmail.com (Ali Bahramisharif) Date: Thu, 11 Jul 2013 19:30:19 +0200 Subject: [FieldTrip] Fwd: 17-18 October, 2013: NatMEG inauguration conference at Karolinska Institutet, Stockholm. In-Reply-To: References: Message-ID: In the list of speakers, I see Stephen's name among the heads. Great! Ali On Thu, Jul 11, 2013 at 6:18 PM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear FieldTrippers, > > We are very happy to announce the inauguration conference for NatMEG, > the brand-new National Swedish MEG facility. Please find the > invitation attached. > > Have a great summer, > > Stephen > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamid.mohseni at eng.ox.ac.uk Fri Jul 12 15:25:29 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Fri, 12 Jul 2013 14:25:29 +0100 Subject: [FieldTrip] baseline correction Message-ID: Dear All, I am trying to do baseline correction using a specified window, e.g,: cfg.demean = 'yes'; cfg.baselinewindow = [-0.5 0]; but it seems to me fieldtrip always performs demaen in respect to the whole time window and ignores cfg.baselinewindow. I am wondering if it is a bug or I am missing something? -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Fri Jul 12 15:43:35 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Fri, 12 Jul 2013 15:43:35 +0200 Subject: [FieldTrip] ft_megrealign how to avoid? Message-ID: Dear Arjen, Thank you very much for you answer! I forgot to mention that I applied ft_megrealign on averaged single subject data since we are interested in evoked auditory early gamma response. I am familiar with the online and offline methods for removing variance which comes from head movement. These are very useful tolls. I've tested ft_regresconfound before and it worked fine. However, it will not be very helpful in this case. Because if I apply ft_regresconfound as you suggested than I will loose gradiometers information and than ft_megrealign will not work. Furthermore my evoked gamma grand average topographies (TFR of planar and axial gradiometers) look now as expected without any transformation(ft_regresconfound or ft_megrealign). So what I need is some objective evidence that condition difference is due to experiment rather than different head positions. :) Thank you and all the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From aaron.schurger at gmail.com Fri Jul 12 20:48:53 2013 From: aaron.schurger at gmail.com (Aaron Schurger) Date: Fri, 12 Jul 2013 11:48:53 -0700 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: I think you want the cfg.blc option. Demean will indeed remove the mean, as advertised! cfg.blc = ... cfg.blcwindow = [...] In general, however, I would advise against any baseline correction, unless you have a blocked design and have no choice. Best, Aaron On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni wrote: > Dear All, > > I am trying to do baseline correction using a specified window, e.g,: > > cfg.demean = 'yes'; > cfg.baselinewindow = [-0.5 0]; > > but it seems to me fieldtrip always performs demaen in respect to the whole > time window and ignores cfg.baselinewindow. > > I am wondering if it is a bug or I am missing something? > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Aaron Schurger, PhD Post-doctoral researcher INSERM U992 / NeuroSpin CEA - Saclay, France +33-1-69-08-66-47 aaron.schurger at gmail.com http://www.unicog.org From hamid.mohseni at eng.ox.ac.uk Fri Jul 12 22:12:43 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Fri, 12 Jul 2013 21:12:43 +0100 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: Thanks for your answer, but I think they are the same. On Friday, 12 July 2013, Aaron Schurger wrote: > I think you want the cfg.blc option. Demean will indeed remove the > mean, as advertised! > cfg.blc = ... > cfg.blcwindow = [...] > > In general, however, I would advise against any baseline correction, > unless you have a blocked design and have no choice. > > Best, > Aaron > > On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni > > wrote: > > Dear All, > > > > I am trying to do baseline correction using a specified window, e.g,: > > > > cfg.demean = 'yes'; > > cfg.baselinewindow = [-0.5 0]; > > > > but it seems to me fieldtrip always performs demaen in respect to the > whole > > time window and ignores cfg.baselinewindow. > > > > I am wondering if it is a bug or I am missing something? > > > > -- > > Hamid R. Mohseni, PhD > > Post-Doctoral Research Assistant > > Institute of Biomedical Engineering > > University of Oxford, OX3 7DQ, UK > > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Fri Jul 12 23:05:01 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Fri, 12 Jul 2013 23:05:01 +0200 (CEST) Subject: [FieldTrip] ft_megrealign how to avoid? In-Reply-To: Message-ID: <1979422110.2049419.1373663101977.JavaMail.root@sculptor.zimbra.ru.nl> Dear Nenad, You're welcome of course. You're right that after head movement compensation using ft_regressconfound, the sensor level data ideally is not used anymore for source modeling (see http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis -> bottom page, for why this is problematic), i.e. as is required for ft_megrealign. Optimally, ft_regressconfound is therefore used as a last step just prior to ft_XXXstatistics, whether at the sensor level (after ft_megrealign) or at the source level. To address your objective, i.e. showing that a difference is due to the experimental manipulation and not due to different head positions; using ft_regressconfound on trials of, say, condition A and B combined will remove any trial-by-trial signal variance that is due to different head positions from the mean head position of condition A and B. In other words, if a systematic difference observed between condition A and B is caused by systematically different head position between condition A and B, this difference will be removed by ft_regressconfound. If not, the difference may not be caused by different head position, and you have good indication to exclude head position as a potential confound. Yours, Arjen ----- Oorspronkelijk bericht ----- > Van: "Nenad Polomac" > Aan: fieldtrip at science.ru.nl > Verzonden: Vrijdag 12 juli 2013 15:43:35 > Onderwerp: Re: [FieldTrip] ft_megrealign how to avoid? > Dear Arjen, > Thank you very much for you answer! I forgot to mention that I applied > ft_megrealign on averaged single subject data since we are interested > in evoked auditory early gamma response. I am familiar with the online > and offline methods for removing variance which comes from head > movement. These are very useful tolls. I've tested ft_regresconfound > before and it worked fine. However, it will not be very helpful in > this case. Because if I apply ft_regresconfound as you suggested than > I will loose gradiometers information and than ft_megrealign will not > work. Furthermore my evoked gamma grand average topographies (TFR of > planar and axial gradiometers) look now as expected without any > transformation(ft_regresconfound or ft_megrealign). So what I need is > some objective evidence that condition difference is due to experiment > rather than different head positions. :) > Thank you and all the best! > Nenad > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From stidimitriadis at gmail.com Sat Jul 13 11:08:39 2013 From: stidimitriadis at gmail.com (Stavros Dimitriadis) Date: Sat, 13 Jul 2013 12:08:39 +0300 Subject: [FieldTrip] 3D spline interpolation Message-ID: Dear all I am trying to do 3D spline interpolation of a MEG dataset based on axial gradiometer according to the following methodological paper ! Bastiaansena & Thomas R. KnoÈsche."Tangential derivative mapping of axial MEG applied to event-related desynchronization research' Clinical Neurophysiology 111 (2000) 1300±1305. Is there any function in fieldtrip that do this kind of transformation ? Best Dimitriadis Stavros , PhD http://users.auth.gr/~stdimitr/index.html http://neuroinformatics.gr/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Sat Jul 13 11:48:04 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Sat, 13 Jul 2013 11:48:04 +0200 Subject: [FieldTrip] 3D spline interpolation Message-ID: Dear Stavros, You should have look on this http://fieldtrip.fcdonders.nl/tutorial/eventrelatedaveraging#calculate_the_planar_gradient. That is an explanation how to perform it on ERF data. And here you can find pipeline for time freq analysis. http://fieldtrip.fcdonders.nl/tutorial/cluster_permutation_freq#procedure The ft_megplanar and ft_combineplanar together transform axial to planar gradients. Have look in the functions help as well. The paper you mentioned is cited here in the Fildtrip documentation. All the best! Nenad -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Sun Jul 14 22:19:16 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Mon, 15 Jul 2013 00:49:16 +0430 Subject: [FieldTrip] Fwd: (no subject) In-Reply-To: References: Message-ID: Dear fieldtripers I'm going to use Fieldstrip toolbox for removing noise. but I confronted with a small problem. I was wondering if you could tell me how I could use “.mat” format in Fieldtrip's toolbox. In this regard, I want to ask you FieldTrip, if it is possible for you guide me as soon as possible. I am looking forward to hearing from you. Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From moh3nalimoradi at gmail.com Sun Jul 14 22:21:09 2013 From: moh3nalimoradi at gmail.com (Mohsen moradi) Date: Mon, 15 Jul 2013 00:51:09 +0430 Subject: [FieldTrip] How .mat format used in FieldTrip toolbox Message-ID: Dear fieldtripers I'm going to use Fieldstrip toolbox for removing noise. but I confronted with a small problem. I was wondering if you could tell me how I could use “.mat” format in Fieldtrip's toolbox. In this regard, I want to ask you FieldTrip, if it is possible for you guide me as soon as possible. I am looking forward to hearing from you. Best Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 15 10:15:14 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 15 Jul 2013 10:15:14 +0200 Subject: [FieldTrip] Fwd: Announcement of Donders Discussions 2013 In-Reply-To: <449335090.2248168.1373799535995.JavaMail.root@indus.zimbra.ru.nl> References: <449335090.2248168.1373799535995.JavaMail.root@indus.zimbra.ru.nl> Message-ID: See below; apologies for multiple postings. ---------- Forwarded message ---------- From: Vogel, S. (Susanne) Date: 14 July 2013 12:58 Subject: Announcement of Donders Discussions 2013 To: fieldtrip-owner at science.ru.nl Dear fieltrip list owner, We are happy to announce the Donders Discussions 2013 and we would be happy if you could distribute this announcement to the fieldrip list or other interested PhD students. With best regards, Susanne ---- Dear PhD student, We are pleased to announce the Donders Discussions 2013: a two-day conference for PhD students in all fields of (cognitive) neuroscience which will take place on October 31st and November 1st in Nijmegen, The Netherlands. The aim of the Donders Discussions is to bring PhD students together in an informal, interdisciplinary atmosphere. Last year we welcomed over 150 participants from all over Europe. We invite you to join us and make this year’s edition an even bigger success! Our exciting program features brains of many kinds, including baby brains, sleeping, stressed and disordered brains, linguistic, attentive and aging brains, and of course investigated brains (where we review methodological innovations). We also offer interactive workshops on science communication and career management. For more information and registration please visit www.ru.nl/dondersdiscussions. We warmly invite all participants to submit a poster abstract. Registration will open on July 15, the deadline is September 16, but registration may close earlier if the maximum number of participants has been reached. The registration fee is €45. If you have any questions, don’t hesitate to e-mail us on discussions2013 at donders.ru.nl. For the latest updates and special offers, join us on facebook (facebook.com/dondersdiscussions2013) or twitter (discussions2013). We look forward to seeing you in Nijmegen! The Donders Discussions committee 2013 From jan.schoffelen at donders.ru.nl Mon Jul 15 10:43:07 2013 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 15 Jul 2013 10:43:07 +0200 Subject: [FieldTrip] ft_connectivityanalysis and PLV formula In-Reply-To: References: Message-ID: Hi Manuel, The first formula is correct, the second isn't. Hint: when working with the complex representation in the second formula you should use a multiplication, rather than a subtraction, and take the negative angle for the second signal. In other words exp(1i.*angle(x)) .* exp(-1i.*angle(y)). This is the same as: exp(1i.*(angle(x)-angle(y))). Hope this helps, Jan-Mathijs On Jul 8, 2013, at 3:32 PM, Manuel Mercier wrote: > Dear Fieldtrip Community > I am still stuck with the implementation of PLV. To be sure that I understand properly the principle of Phase Locking Value, I wrote a code to compute it. That code (see below) gave me the same results as ft_connectivityanalysis. > plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)) -angle(data.fourierspctrm(:,electrode_2,:,:)))),1))); > (data.fourierspctrm being produced by ft_freqanalysis). > > However, I then realized that the subtraction between the two angles should be done in the complex plane as in: > plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,electrodes_1,:,:)))) - exp(1i*(angle(data.fourierspctrm(:,electrode_2,:,:))))))),1))); > > I doubt that PLV computed through FT is wrong, but then I am circumspect since the first formula is somewhat no correct and give the same results a as ft_connectivityanalysis. > I went to FT code and got confused by the way ft_connectivity_corr use the cross spectrum to compute PLV. > I would greatly appreciate if someone could tell me where I am missing/misunderstanding something. > Thanks you for your help, > > Manuel > > > > Manuel Mercier, PhD > Research Fellow > > Cognitive Neurophysiology Laboratory, > Children’s Evaluation and Rehabilitation Center (CERC), > Departments of Pediatrics and Neuroscience > Albert Einstein College of Medicine, > 1225 Morris Park Avenue > Bronx , NY 10461 > > phone: +1 (718) 862 1859 > fax: +1 (718) 862 1807 > From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Manuel Mercier [manuel.mercier at einstein.yu.edu] > Sent: Friday, June 28, 2013 4:43 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] PLV formula > > Dear Fieldtripers > Sometime ago I wrote for myself a function that was computing PLV and some related non parametric statistics. > (Phase Locking Value as define as the mean across trials of the phase angle difference recorded at two loci ; based on Lachaux et al., 1999, HBM). > I implemented PLV in matlab using the following formula: > plv = squeeze(abs(mean(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)) ... > -angle(data.fourierspctrm(:,cmb(2),:,:)))),1))); > with cmb(1) and cmb(2) being the indices of the electrodes of interest (between which PLV is computed). > I compared my results with the ft_connectivityanalysis function from Fieldtrip and the results were exactly the same. > So far so good. > > But I recently went back to my code, and I was a little bit confused. > Since I was dealing with angles, I though that the best way to do the subtraction should be done in the complex plane > Like: > plv = squeeze(abs(mean(exp(1i*(angle(exp(1i*(angle(data.fourierspctrm(:,cmb(1),:,:)))) ... > - exp(1i*(angle(data.fourierspctrm(:,cmb(2),:,:))))))),1))); > (for instance if the two angles: pi/2 and -pi/2 the direct subtraction will give pi, > whereas in the complex plan it will be pi/2 - with the norm x2). > > The result I got with this code is obviously different from the previous one, and what I got from Fieldtrip. > I went back to the archive of the mailing list but didn't find a clear answer to my point. Does anyone can enlighten me ? > Thanks ! > > Manuel > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 15 10:51:32 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 15 Jul 2013 10:51:32 +0200 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: <51E3B814.5060000@donders.ru.nl> Dear Hamid, I guess your problem is precisely this one: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2220 Will be fixed asap :) Best, Jörn On 7/12/2013 10:12 PM, Hamid Mohseni wrote: > Thanks for your answer, but I think they are the same. > > On Friday, 12 July 2013, Aaron Schurger wrote: > > I think you want the cfg.blc option. Demean will indeed remove the > mean, as advertised! > cfg.blc = ... > cfg.blcwindow = [...] > > In general, however, I would advise against any baseline correction, > unless you have a blocked design and have no choice. > > Best, > Aaron > > On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni > > wrote: > > Dear All, > > > > I am trying to do baseline correction using a specified window, > e.g,: > > > > cfg.demean = 'yes'; > > cfg.baselinewindow = [-0.5 0]; > > > > but it seems to me fieldtrip always performs demaen in respect > to the whole > > time window and ignores cfg.baselinewindow. > > > > I am wondering if it is a bug or I am missing something? > > > > -- > > Hamid R. Mohseni, PhD > > Post-Doctoral Research Assistant > > Institute of Biomedical Engineering > > University of Oxford, OX3 7DQ, UK > > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Aaron Schurger, PhD > Post-doctoral researcher > INSERM U992 / NeuroSpin > CEA - Saclay, France > +33-1-69-08-66-47 > aaron.schurger at gmail.com > http://www.unicog.org > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamid.mohseni at eng.ox.ac.uk Mon Jul 15 11:16:14 2013 From: hamid.mohseni at eng.ox.ac.uk (Hamid Mohseni) Date: Mon, 15 Jul 2013 10:16:14 +0100 Subject: [FieldTrip] baseline correction In-Reply-To: References: Message-ID: great, thanks. On 15 July 2013 09:51, "Jörn M. Horschig" wrote: > Dear Hamid, > > I guess your problem is precisely this one: > http://bugzilla.fcdonders.nl/show_bug.cgi?id=2220 > Will be fixed asap :) > > Best, > Jörn > > > On 7/12/2013 10:12 PM, Hamid Mohseni wrote: > > Thanks for your answer, but I think they are the same. > > On Friday, 12 July 2013, Aaron Schurger wrote: > >> I think you want the cfg.blc option. Demean will indeed remove the >> mean, as advertised! >> cfg.blc = ... >> cfg.blcwindow = [...] >> >> In general, however, I would advise against any baseline correction, >> unless you have a blocked design and have no choice. >> >> Best, >> Aaron >> >> On Fri, Jul 12, 2013 at 6:25 AM, Hamid Mohseni >> wrote: >> > Dear All, >> > >> > I am trying to do baseline correction using a specified window, e.g,: >> > >> > cfg.demean = 'yes'; >> > cfg.baselinewindow = [-0.5 0]; >> > >> > but it seems to me fieldtrip always performs demaen in respect to the >> whole >> > time window and ignores cfg.baselinewindow. >> > >> > I am wondering if it is a bug or I am missing something? >> > >> > -- >> > Hamid R. Mohseni, PhD >> > Post-Doctoral Research Assistant >> > Institute of Biomedical Engineering >> > University of Oxford, OX3 7DQ, UK >> > Tel: +44 (0) 1865 2 83826 >> > >> > _______________________________________________ >> > fieldtrip mailing list >> > fieldtrip at donders.ru.nl >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Aaron Schurger, PhD >> Post-doctoral researcher >> INSERM U992 / NeuroSpin >> CEA - Saclay, France >> +33-1-69-08-66-47 >> aaron.schurger at gmail.com >> http://www.unicog.org >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > -- > Hamid R. Mohseni, PhD > Post-Doctoral Research Assistant > Institute of Biomedical Engineering > University of Oxford, OX3 7DQ, UK > Tel: +44 (0) 1865 2 83826 > > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamid R. Mohseni, PhD Post-Doctoral Research Assistant Institute of Biomedical Engineering University of Oxford, OX3 7DQ, UK Tel: +44 (0) 1865 2 83826 -------------- next part -------------- An HTML attachment was scrubbed... URL: From rmontefusco at med.uchile.cl Mon Jul 15 16:04:32 2013 From: rmontefusco at med.uchile.cl (Rodrigo Montefusco) Date: Mon, 15 Jul 2013 10:04:32 -0400 Subject: [FieldTrip] Fwd: (no subject) In-Reply-To: References: Message-ID: Hi Mohsen Can you provide more details? Which is your particular question? Your help sounds a little bit general. Best Y On Sun, Jul 14, 2013 at 4:19 PM, Mohsen moradi wrote: > Dear fieldtripers > > I'm going to use Fieldstrip toolbox for removing noise. but I confronted > with a small problem. > I was wondering if you could tell me how I could use “.mat” format in > Fieldtrip's toolbox. > In this regard, I want to ask you FieldTrip, if it is possible for you > guide me as soon as possible. > I am looking forward to hearing from you. > > Best Regards > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Tue Jul 16 14:11:06 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Tue, 16 Jul 2013 13:11:06 +0100 Subject: [FieldTrip] 2D surface spline interpolation Message-ID: Dear all, I am working on spatiotemporal mapping of 2D and 3D EEG data. I want to develop the method of surface interpolation, what is the function in FieldTrip that develops this interpolation method. I hope you will send me positive and helpful response. Thanks a lot in advance! Best, ahmed -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Tue Jul 16 14:54:19 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 16 Jul 2013 14:54:19 +0200 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: Message-ID: <51E5427B.2020103@donders.ru.nl> Dear Ahmed, there are several functions making use of (spline) interpolation, e.g. ft_channelrepair for reconstructing time-courses of missing or bad channels, or ft_scalpcurrentdensity for spatial filtering of data. Also ft_megrealign is doing some interpolation magic, but I don't know what method that function is using. In case you are interested in low-level functions, they are in FieldTrip/private, called splint.m and sphericalSplineInterpolate.m (afaik both doing essentially the same, just different implementations of the same method). Best, Jörn On 7/16/2013 2:11 PM, ingenieur eniso wrote: > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the > function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > > Thanks a lot in advance! > > Best, > > ahmed > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jul 16 14:55:05 2013 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 16 Jul 2013 14:55:05 +0200 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: Message-ID: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Hi Ahmed, For the visualization of sensor topographies, fieldtrip relies on the 'griddata' function from matlab. You can type 'doc griddata' on the matlab command line for more information. Note that this is not a function that is specific to fieldtrip. For actual interpolation of data, FieldTrip has a ft_channelrepair function, which implements (among others) a spherical spline interpolation. Best wishes, Jan-Mathijs On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > Thanks a lot in advance! > Best, > ahmed > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Jan-Mathijs Schoffelen, MD PhD Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: +31-24-3614793 http://www.hettaligebrein.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jakob.wischniowski at uni-ulm.de Wed Jul 17 02:27:18 2013 From: jakob.wischniowski at uni-ulm.de (Jakob) Date: Wed, 17 Jul 2013 02:27:18 +0200 Subject: [FieldTrip] rejectvisual/summary on Mac OS X In-Reply-To: References: <51C85906.2090204@uni-konstanz.de> Message-ID: <79A73D01-FB88-41A6-A12C-70D742C68F74@uni-ulm.de> Dear all, I'm running Matlab 2013a on an Apple OSX 10.8.4 (Mountain Lion) machine. While performing the rejectvisual/summary function, dragging the mouse over the channels won't work: The "selecting box" for dragging simply won't appear while holding down the left mouse button/trackpad button. I was wondering if anyone is experiencing the same problem? Best regards! Jakob From Sara.Bogels at mpi.nl Wed Jul 17 12:30:01 2013 From: Sara.Bogels at mpi.nl (=?ISO-8859-1?Q?Sara_B=F6gels?=) Date: Wed, 17 Jul 2013 12:30:01 +0200 Subject: [FieldTrip] problem with ft_multiplotER In-Reply-To: References: Message-ID: <51E67229.8040001@mpi.nl> Hi all, I have a very specific problem with the ft_multiplotER function. For 2 of my 24 participants, the function gives an error-message when I try to plot the averages of two conditions at the same time. Plotting them one by one is not a problem. There appears to be a specific point in time (different for the two participants) when this goes wrong. If I avoid that time (by using cfg.xlim) it works fine. My trials have different lengths and I used "cfg.vartrllength = 2;" when calling ft_timelockanalysis (not sure whether this is relevant). The error message I get is "Error in ft_multiplotER (line 616) yval(i,:) = datamatrix{i}(m,:);" I cannot find out what happens in this line. Can anyone tell me what this might be referring to? Thank you, Sara From jm.horschig at donders.ru.nl Wed Jul 17 13:44:15 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 17 Jul 2013 13:44:15 +0200 Subject: [FieldTrip] problem with ft_multiplotER In-Reply-To: <51E67229.8040001@mpi.nl> References: <51E67229.8040001@mpi.nl> Message-ID: <51E6838F.3050302@donders.ru.nl> Dear Sara, What you describe sounds like a bug to me. It looks like that in these lines the averages of the two conditions should be concatenated into one matrix, and apparently something goes wrong. However, you truncated the error message a bit (you pasted the line where the error occurs, but not the error message itself). If one of us developers should look into this further, it would be great if you register and create a bugreport on bugzilla.fconders.nl. Preferably would be to upload a snippet of your data, e.g. timelockstructures of one participant, and some lines of code which reproduce the error. We can then look into this further and fix this as soon as possible :) Best, Jörn On 7/17/2013 12:30 PM, Sara Bögels wrote: > Hi all, > > I have a very specific problem with the ft_multiplotER function. For 2 > of my 24 participants, the function gives an error-message when I try > to plot the averages of two conditions at the same time. Plotting them > one by one is not a problem. There appears to be a specific point in > time (different for the two participants) when this goes wrong. If I > avoid that time (by using cfg.xlim) it works fine. My trials have > different lengths and I used "cfg.vartrllength = 2;" when calling > ft_timelockanalysis (not sure whether this is relevant). > > The error message I get is > "Error in ft_multiplotER (line 616) > yval(i,:) = datamatrix{i}(m,:);" > > I cannot find out what happens in this line. Can anyone tell me what > this might be referring to? > > Thank you, > Sara > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From christophe.grova at mcgill.ca Wed Jul 17 16:11:58 2013 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Wed, 17 Jul 2013 10:11:58 -0400 Subject: [FieldTrip] Postdoctoral Position Available et the Montreal Neurological Institute In-Reply-To: Message-ID: Postdoctoral Position Available et the Montreal Neurological Institute Multimodal Functional Imaging Laboratory, Biomedical Engineering Dpt, Montreal Neurological Institute, McGill University, Montreal, Canada The candidate will join a multidisciplinary team composed of neurologists and methodologists within the Multimodal Functional Imaging Laboratory and in close collaboration with the epilepsy group of the Montreal Neurological Institute. A brief description of the project can be found below. The main role of the candidate will be to recruit patients, to assist data acquisition and to identify epileptic events on recorded signals. (S)he will be trained to contribute to data acquisition and to use dedicated source localization and data fusion techniques developed locally. Initial appointment is for 1 year, with possibility of renewal up to 3 years. Project: Multimodal investigation of epileptic activity using simultaneous EEG/MEG and EEG/NIRS acquisitions. The proposed project aims at localizing and characterizing the generators of epileptic activity using simultaneous acquisitions of ElectroEncephaloGraphy (EEG) with Magneto-EncephaloGraphy (MEG), as well as simultaneous acquisitions of EEG with Near Infra-Red Spectroscopy (NIRS). ElectroEncephaloGraphy (EEG) and Magneto-EncephaloGraphy (MEG) are respectively measuring on the scalp electric and magnetic fields generated by neuronal activity at a millisecond scale, providing a detailed description of brain activity using 275 MEG sensors and 56 EEG electrodes. Combined with EEG measuring brain electric activity on the scalp, NIRS allows studying hemodynamic processes at the time of spontaneous epileptic activity. The specificity of NIRS data is its ability to measure local changes oxy-hemoglobin (HbO) and deoxy-hemoglobin (HbR), exploiting absorption properties of infrared light within brain tissue using optic fibers placed on the surface of the head (temporal resolution: 10 ms, 16 sources x 32 detectors, penetration: 2-3 cm from the surface of the head). The candidate will be trained to use the first Brainsight NIRS device developped by Rogue-Research Inc, with which we were able to record promising preliminary data. While methodological developpments in the lab will consist in 3D reconstruction of the generators of EEG, MEG and NIRS signals and assessing multimodal concordances between bioelectrical neuronal signals and hemodynamic processes, the purpose of this Postdoctoral project will be to assess the integrity of neurovascular coupling processes at the time of epileptic discharges, using a unique multimodal environment involving EEG/MEG, EEG/NIRS and also EEG/fMRI recordings. Close collaborations with the epilepsy group of the Montreal Neurological Institute, involving notably Dr E. Kobayashi MD-PhD, Dr F. Dubeau MD-PhD and Dr. J. Gotman PhD, will provide access to patient populations and additional clinical expertise for this project. Requirements: The candidate should be an MD (neurologist) with previous training in epileptology and neurophysiology (EEG). Expertise in analyzing MEG or NIRS signals and/or computational skills including neuroimaging softwares are appreciated additional qualification. The candidate should be fluent in English (and if possible French) due to the patient population studied. Supervisor: Christophe Grova Ph.D. Assistant Professor, Biomedical Engineering Assistant Professor, Neurology & Neurosurgery Director of the Multimodal Functional Imaging Laboratory Email: christophe.grova at mcgill.ca Multi FunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage Please send your CV, a motivation letter and reference letters to christophe.grova at mcgill.ca *************************** Christophe Grova, PhD Assistant Professor Biomedical Engineering Dpt Neurology and Neurosurgery Dpt Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute Centre de Recherches en Mathématiques Biomedical Engineering Department - Room 304 McGill University 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 email : christophe.grova at mcgill.ca tel : (514) 398 2516 fax : (514) 398 7461 web: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe http://www.bmed.mcgill.ca/ MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Wed Jul 17 17:16:14 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Wed, 17 Jul 2013 17:16:14 +0200 Subject: [FieldTrip] Error in Beamforming analysis due to units? Message-ID: Dear all, I'm having a hard time understanding my beamforming analysis/results. I set up the analysis pipeline as described in the tutorial(s). First, I create my template grid as shown below: ---------------------- % Step 1: CREATE A TEMPLATE template = ft_read_mri([TemplateDir 'T1.nii']); template.coordsys = 'spm'; % Step 2: Segment the template brain and construct a volume conduction % model (i.e. head model): this is needed for the inside/outside detection of voxels cfg = []; template_seg = ft_volumesegment(cfg,template); cfg = []; cfg.method = 'singleshell'; template_vol = ft_prepare_headmodel(cfg,template_seg); template_vol = ft_convert_units(template_vol,'cm'); % Step 3: Construct the dipole grid in the template brain coordinates. % The source units are in cm cfg = []; cfg.grid.xgrid = -20:1:20; cfg.grid.ygrid = -20:1:20; cfg.grid.zgrid = -10:1:20; cfg.unit = 'cm'; cfg.grid.tight = 'yes'; cfg.inwardshift = -1.5; % negative inwardshift leads to an outwardshift of the brain's surface cfg.reducerank = 'no'; cfg.vol = template_vol; template_grid = ft_prepare_sourcemodel(cfg); % Step 4: Make a figure with the template head model and dipole grid figure hold on; ft_plot_vol(template_vol,'facecolor','cortex','edgecolor','none'); alpha 0.5; camlight; ft_plot_mesh(template_grid.pos(template_grid.inside,:)); ---------------------- Some of my colleagues also add another step where they convert the template grid units from 'cm' to 'mm' since MNI space is in 'mm'. Since this is not mentioned in the tutorial, I skipped that step. In the next steps for creating the single subject's grid and headmodel I follow exactly the steps described in the tutorial to create single subject grids in MNI space. When I check the segmentation everything looks fine. I then of course use this grid to calculate the sources, also as described in the tutorial. At the end I put the template grid position fields onto the subject's baseline normalized source (sourceDiff_tem). ----------------------------------------------------- for k = 1:length(cond) cfg = []; eval(['cfg.frequency = freqAll.Cond_',num2str(cond(k)),'.freq;']); cfg.method = 'dics'; cfg.grid = grid; % Here it gives .pos, .inside, .outside to the structure cfg.vol = vol; cfg.dim = grid.dim; eval(['cfg.grad = Cond_',num2str(cond(k)),'.hdr.grad;']); cfg.lambda = '5%'; cfg.reducerank = 'no'; cfg.projectnoise = 'yes'; cfg.realfilter = 'yes'; cfg.keepfilter = 'yes'; % the output saves the computed inverse filter eval(['sourceAll.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqAll.Cond_',num2str(cond(k)),');']) % use the pre-calculated common filter here eval(['cfg.grid.filter = sourceAll.Cond_',num2str(cond(k)),'.avg.filter;']); eval(['sourcePre.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqPre.Cond_',num2str(cond(k)),');']) eval(['sourcePost.Cond_',num2str(cond(k)),' = ft_sourceanalysis(cfg,freqPost.Cond_',num2str(cond(k)),');']) % compute the contrast of (post-pre)/pre (normalization of the power with the baseline activity) eval(['sourceDiff.Cond_',num2str(cond(k)),' = sourcePost.Cond_',num2str(cond(k)),';']) eval(['sourceDiff.Cond_',num2str(cond(k)),'.avg.pow = (sourcePost.Cond_',num2str(cond(k)),'.avg.pow-sourcePre.Cond_',num2str(cond(k)),'.avg.pow) ./ sourcePre.Cond_',num2str(cond(k)),'.avg.pow;']); % put the template grid positions (x,y,z & pos) into the source structure eval(['sourceDiff_tem.Cond_',num2str(cond(k)),' = sourceDiff.Cond_',num2str(cond(k)),';']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.pos = template_grid.pos;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.xgrid = template_grid.xgrid;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.ygrid = template_grid.ygrid;']); eval(['sourceDiff_tem.Cond_',num2str(cond(k)),'.zgrid = template_grid.zgrid;']); end ----------------------------------------------------- If I then look at the data of this sourceDiff_tem, i.e. of condition 1, plotted on a surface file, it looks a bit strange to me (see Fig1). Also, I am not able to plot this data with cfg.method 'slice'. I get the error that the dimensions do not match. pos: [5780x3 double] dim: [17 20 17] avg: [1x1 struct] var: [1x1 struct] dimord: 'voxel' inside: [2985x1 double] outside: [2795x1 double] df: [5780x1 double] cfg: [1x1 struct] I then tried it the 'old' way and took the Diff_Source of each subject, interpolated this to the subject's anatomy and normalized it. With that I get a result that makes more sense to me (Fig2). However, also with this I am not able to plot it with cfg.method 'slice'. Actually, the slices I can only use for plotting the stats. So I guess that something is wrong here and that I have an error somewhere in my script. However, I really can't find it. Our guess is that it has something to do with the units and the conversion(s) from one space to the other. I went through all the tutorials again and again but I can't see the mistake. I am stuck and therefore would really appreciate any help on that matter! Thanks a lot! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig1.png Type: image/png Size: 295434 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Fig2.png Type: image/png Size: 291696 bytes Desc: not available URL: From mushfa.yousuf at googlemail.com Wed Jul 17 17:50:27 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Wed, 17 Jul 2013 17:50:27 +0200 Subject: [FieldTrip] Load Error Message-ID: Hello; I have a preprocessed data structure in the fieldtrip which I want to load in SPM for the 3D source reconstruction. this data Structute includes * fsample * label * trial * time * grad * elec I have converted this data structure to spm format using function spm_eeg_ft2spm. But when I try to load the converted file to SPM, it gives me the following error The requested file is not ready for source reconstruction. See matlab window for details on matlab following message appears checkmeeg: no sensor positions are defined. Please help me out to troubleshoot this problem. Any help will be appreciated. Regards; Mushfa Yousuf -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Jul 17 17:55:54 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 17 Jul 2013 17:55:54 +0200 Subject: [FieldTrip] Load Error In-Reply-To: References: Message-ID: <51E6BE8A.2000804@donders.ru.nl> Hi Mushfa, hm, you provided elec and grad information, do you indeed have combined EEG/MEG data? Maybe SPM does not like that - I know that FieldTrip would not like that ;) - so you could try with either of them and see whether that works. Best, Jörn On 7/17/2013 5:50 PM, Mushfa Yousuf wrote: > Hello; > > I have a preprocessed data structure in the fieldtrip which I want to > load in SPM for the 3D source reconstruction. > > this data Structute includes > > * fsample > * label > * trial > * time > * grad > * elec > > I have converted this data structure to spm format using function > spm_eeg_ft2spm. > > But when I try to load the converted file to SPM, it gives me the > following error > > The requested file is not ready for source reconstruction. See matlab > window for details > > on matlab following message appears > > checkmeeg: no sensor positions are defined. > > > Please help me out to troubleshoot this problem. Any help will be > appreciated. > > Regards; > > Mushfa Yousuf > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Wed Jul 17 18:00:46 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Wed, 17 Jul 2013 18:00:46 +0200 Subject: [FieldTrip] Load Error In-Reply-To: <51E6BE8A.2000804@donders.ru.nl> References: <51E6BE8A.2000804@donders.ru.nl> Message-ID: Hello Jörn; I also tried without elec and grad in the structure but it doesn't help me out. Regards, Mushfa Yousuf On Wed, Jul 17, 2013 at 5:55 PM, "Jörn M. Horschig" < jm.horschig at donders.ru.nl> wrote: > Hi Mushfa, > > hm, you provided elec and grad information, do you indeed have combined > EEG/MEG data? Maybe SPM does not like that - I know that FieldTrip would > not like that ;) - so you could try with either of them and see whether > that works. > > Best, > Jörn > > > On 7/17/2013 5:50 PM, Mushfa Yousuf wrote: > > Hello; > > I have a preprocessed data structure in the fieldtrip which I want to > load in SPM for the 3D source reconstruction. > > this data Structute includes > > * fsample > * label > * trial > * time > * grad > * elec > > I have converted this data structure to spm format using function > spm_eeg_ft2spm. > > But when I try to load the converted file to SPM, it gives me the > following error > > The requested file is not ready for source reconstruction. See matlab > window for details > > on matlab following message appears > > checkmeeg: no sensor positions are defined. > > > Please help me out to troubleshoot this problem. Any help will be > appreciated. > > Regards; > > Mushfa Yousuf > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From antony.passaro at gmail.com Wed Jul 17 19:08:41 2013 From: antony.passaro at gmail.com (Antony Passaro) Date: Wed, 17 Jul 2013 13:08:41 -0400 Subject: [FieldTrip] Error using indepsamplesZcoh with cluster statistics Message-ID: Hi all, I'm having an issue running freqstatistics using the indepsamplesZcoh and a cluster correction. The indepsamplesZcoh portion seems to run just fine but I get an error when I try to perform the cluster statistics. The first issue is error1: The error describes a dimension mismatch at line 297 of ft_statistics_montecarlo: statrand(:,:,i) = getfield(dum, 'stat'); Apparently the output (dum) from indepsamplesZcoh collapses my 100 frequencies and 100 timepoints into 10000 points (nchancmb/2 x 10000) but the dimensions of statrand are nchancmb/2 x 100 x Nrand which obviously creates a dimension mismatch. I can get past that part if I set avgovertime = 'yes' which takes me to error 2: "To RESHAPE the number of elements must not change" refers to line 202 in clusterstat.m, posclusobs = findcluster(reshape(postailobs, [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); Here, cfg.dim is nchan x 100 freq x 1 (avgtime) which obviously doesn't match postailobs dimensions of nchancmb/2 x 100. I thought perhaps the ndepsamplesZcoh function is not supposed to be used in conjunction with the cluster statistics but the Maris 2007 paper appears to use the two together. Any help with this would be much appreciated. Below is the code that that I'm using: cfg = []; %cfg.avgovertime = 'yes'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.clusterthreshold = 'parametric'; cfg.minnbchan = 2; cfg.correcttail = 'alpha'; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesZcoh'; cfg.parameter = 'fourierspctrm'; cfg.computecritval = 'yes'; cfg.neighbours = neighbours; cfg.numrandomization = 99; cfg.alpha = 0.05; cfg.tail = 0; design = ones(1, 90); design(91:180)=2; cfg.design = design; cfg.label = freqL.label; stat = ft_freqstatistics(cfg, freqL,freqR); Thanks, -Tony -------------- next part -------------- An HTML attachment was scrubbed... URL: From Natalia.Egorova at mrc-cbu.cam.ac.uk Wed Jul 17 19:11:24 2013 From: Natalia.Egorova at mrc-cbu.cam.ac.uk (Natalia Egorova) Date: Wed, 17 Jul 2013 17:11:24 +0000 Subject: [FieldTrip] neuromag - sources Message-ID: Hi, I have a question. When doing source reconstruction in the frequency domain with DICS I got a bit confused using neuromag data. Since there are both gradiometer and magnetometer sensors, which sensors are used for source reconstruction by default (if the .grad contains all 360)? Is it possible to use all MEG data, or should MEGGRAD and MEGMAG-based sources be calculated separately? Thanks in advance, Nataila -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Wed Jul 17 20:03:49 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Wed, 17 Jul 2013 19:03:49 +0100 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> References: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Message-ID: Hi Jörn and jan-mathijs, thank you very much for help. All the best Ahmed 2013/7/16 jan-mathijs schoffelen > Hi Ahmed, > > For the visualization of sensor topographies, fieldtrip relies on the > 'griddata' function from matlab. You can type 'doc griddata' on the matlab > command line for more information. Note that this is not a function that is > specific to fieldtrip. > > For actual interpolation of data, FieldTrip has a ft_channelrepair > function, which implements (among others) a spherical spline interpolation. > > > Best wishes, > Jan-Mathijs > > On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: > > Dear all, > I am working on spatiotemporal mapping of 2D and 3D EEG data. > I want to develop the method of surface interpolation, what is the > function in FieldTrip that develops this interpolation method. > > I hope you will send me positive and helpful response. > > Thanks a lot in advance! > > Best, > > ahmed > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Jan-Mathijs Schoffelen, MD PhD > > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > > Max Planck Institute for Psycholinguistics, > Nijmegen, The Netherlands > > J.Schoffelen at donders.ru.nl > Telephone: +31-24-3614793 > > http://www.hettaligebrein.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sauer.mpih at googlemail.com Thu Jul 18 12:10:00 2013 From: sauer.mpih at googlemail.com (Andreas Sauer) Date: Thu, 18 Jul 2013 12:10:00 +0200 Subject: [FieldTrip] Error in Beamforming analysis due to units? Problem solved! Message-ID: Dear all, I just solved the problem with the beamforming analysis. So please ignore my previous mail on that! Best, Andreas -- Andreas Sauer Max Planck Institute for Brain Research Deutschordenstraße 46 60528 Frankfurt am Main Germany T: +49 69 96769 278 F: +49 69 96769 327 Email: sauer.mpih at gmail.com www.brain.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From ingenieureniso at gmail.com Thu Jul 18 17:02:34 2013 From: ingenieureniso at gmail.com (ingenieur eniso) Date: Thu, 18 Jul 2013 16:02:34 +0100 Subject: [FieldTrip] 2D surface spline interpolation In-Reply-To: References: <6388792D-E3C4-45E9-9A8E-C80A6928F8D0@donders.ru.nl> Message-ID: Hi , I use the splint.m function to implement the spherical spline interpolation. But an error is occured: ??? Error using ==> rdivide Matrix dimensions must agree. Error in ==> splint at 58 elc1 = elc1 ./ repmat(sqrt(sum(elc1.^2,2)), 1, 3); Error in ==> eeg_interp_sph_spline_test at 50 [V2, L2, L1] = splint(elc1, V, elc2) I have written following program in Matlab elc1=[x y z]'; elc2=[0.430 0.050 -0.010]'; [V2, L2, L1] = splint(elc1, V, elc2) with [x y z]=[-0.0176 0.0907 0.0071 0.0024 0.0924 0.0076 0.0284 0.0879 0.0075 -0.0085 0.0903 0.0190 0.0153 0.0895 0.0189 -0.0391 0.0836 0.0089 -0.0156 0.0868 0.0286 0.0299 0.0823 0.0305 0.0559 0.0735 0.0080 -0.0329 0.0805 0.0321 -0.0043 0.0789 0.0485 0.0155 0.0785 0.0468 0.0462 0.0726 0.0344 -0.0618 0.0683 0.0105 -0.0509 0.0719 0.0289 -0.0418 0.0694 0.0451 -0.0200 0.0725 0.0542 0.0040 0.0690 0.0618 0.0332 0.0657 0.0563 0.0507 0.0593 0.0501 0.0674 0.0552 0.0315 0.0770 0.0510 0.0080 -0.0651 0.0617 0.0234 -0.0560 0.0608 0.0420 -0.0406 0.0598 0.0580 -0.0080 0.0579 0.0720 0.0196 0.0538 0.0729 0.0444 0.0515 0.0631 0.0678 0.0422 0.0471 0.0803 0.0412 0.0213 -0.0738 0.0546 -0.0128 -0.0782 0.0496 0.0047 -0.0692 0.0506 0.0353 -0.0518 0.0466 0.0611 -0.0288 0.0444 0.0761 0.0018 0.0412 0.0830 0.0296 0.0370 0.0797 0.0582 0.0294 0.0659 0.0799 0.0258 0.0392 0.0902 0.0207 0.0049 0.0842 0.0364 -0.0135 -0.0831 0.0366 0.0188 -0.0709 0.0332 0.0497 -0.0493 0.0303 0.0724 -0.0187 0.0239 0.0876 0.0157 0.0212 0.0889 0.0488 0.0165 0.0771 0.0758 0.0093 0.0526 0.0905 0.0016 0.0200 -0.0846 0.0327 -0.0191 -0.0914 0.0153 -0.0017 -0.0851 0.0124 0.0345 -0.0648 0.0150 0.0646 -0.0401 0.0047 0.0834 0.0295 -0.0054 0.0877 0.0596 -0.0112 0.0701 0.0821 -0.0158 0.0400 0.0916 -0.0140 0.0023 0.0909 0.0050 -0.0172 -0.0913 -0.0021 0.0158 -0.0805 -0.0014 0.0459 -0.0562 -0.0090 0.0732 -0.0215 -0.0170 0.0885 0.0119 -0.0205 0.0896 0.0468 -0.0289 0.0746 0.0717 -0.0317 0.0494 0.0852 -0.0321 0.0173 -0.0856 -0.0313 -0.0167 -0.0906 -0.0195 -0.0002 -0.0861 -0.0199 0.0279 -0.0681 -0.0230 0.0585 -0.0375 -0.0303 0.0791 -0.0029 -0.0388 0.0841 0.0277 -0.0432 0.0772 0.0560 -0.0450 0.0586 0.0738 -0.0459 0.0322 0.0801 -0.0466 0.0005 0.0692 -0.0591 -0.0177 -0.0828 -0.0397 0.0127 -0.0751 -0.0381 0.0389 -0.0556 -0.0426 0.0607 -0.0218 -0.0555 0.0709 0.0119 -0.0587 0.0707 0.0402 -0.0598 0.0583 0.0588 -0.0606 0.0383 0.0698 -0.0602 0.0099 -0.0681 -0.0592 -0.0211 -0.0770 -0.0512 -0.0056 -0.0725 -0.0542 0.0200 -0.0626 -0.0544 0.0415 -0.0372 -0.0663 0.0531 -0.0075 -0.0692 0.0613 0.0157 -0.0732 0.0547 0.0438 -0.0705 0.0413 0.0567 -0.0703 0.0209 0.0630 -0.0678 -0.0043 0.0545 -0.0723 -0.0201 -0.0558 -0.0683 0.0284 -0.0226 -0.0794 0.0421 0.0036 -0.0823 0.0425 0.0386 -0.0810 0.0235 -0.0654 -0.0655 0.0051 -0.0452 -0.0802 0.0113 -0.0322 -0.0824 0.0276 -0.0078 -0.0884 0.0267 0.0175 -0.0876 0.0247 0.0282 -0.0877 0.0104 0.0510 -0.0772 0.0057 -0.0193 -0.0900 0.0110 0.0060 -0.0919 0.0105 -0.0556 -0.0736 -0.0089 -0.0287 -0.0879 -0.0060 -0.0054 -0.0924 -0.0056 0.0148 -0.0913 -0.0057 0.0422 -0.0820 -0.0095 -0.0168 -0.0899 -0.0149 0.0059 -0.0913 -0.0151 -0.0258 -0.0854 -0.0253 -0.0063 -0.0889 -0.0255 0.0142 -0.0880 -0.0254 -0.0398 0.0828 -0.0126 -0.0116 0.0913 -0.0111 0.0115 0.0914 -0.0103 0.0378 0.0841 -0.0101] V = [3.3540 1.9345 0.5927 2.6217 1.3858 5.1010 3.2264 0.3127 -1.2031 4.8916 2.2626 0.7324 -0.8725 8.8664 7.1630 5.9588 3.6880 1.7445 -0.4065 -1.4554 -2.5648 -2.8607 9.7859 8.1602 5.9181 2.3645 0.3716 -1.0117 -2.4332 -3.0173 9.7933 11.8346 10.4268 7.4601 4.5098 1.8013 -0.3755 -1.7671 -2.9153 -3.5252 -3.2862 13.3333 10.0548 6.8787 3.4798 0.8774 -0.9168 -2.3297 -3.1422 11.8833 13.2409 11.6124 8.3419 4.8045 0.6147 -0.8466 -2.0623 -2.8388 -3.2469 12.1843 9.6097 6.2738 3.3943 1.4797 0.0743 -1.2483 -2.0240 8.5136 10.3840 9.7096 7.3371 4.4194 2.6834 1.0785 -0.2747 -1.3383 -1.4970 -0.4476 8.3757 7.6361 5.7288 3.4908 1.8043 0.7450 -0.1646 -0.7976 6.1441 7.2345 7.0914 6.2035 4.1770 2.5408 1.8116 0.3820 -0.1287 -0.4707 0.2793 5.3026 3.5360 2.1660 0.7409 6.1342 4.4963 3.6572 2.5199 1.7607 1.3430 0.4600 3.2784 2.1011 5.2801 3.5401 2.6195 2.0038 0.7776 3.1047 2.2821 3.3528 2.6710 1.9100 5.1250 2.9475 1.6662 0.1915] I haven't found a solution though. So, what is wrong? Thanks a lot in advance! Best, ahmed 2013/7/17 ingenieur eniso > Hi Jörn and jan-mathijs, > > > thank you very much for help. > > All the best > Ahmed > > > 2013/7/16 jan-mathijs schoffelen > >> Hi Ahmed, >> >> For the visualization of sensor topographies, fieldtrip relies on the >> 'griddata' function from matlab. You can type 'doc griddata' on the matlab >> command line for more information. Note that this is not a function that is >> specific to fieldtrip. >> >> For actual interpolation of data, FieldTrip has a ft_channelrepair >> function, which implements (among others) a spherical spline interpolation. >> >> >> Best wishes, >> Jan-Mathijs >> >> On Jul 16, 2013, at 2:11 PM, ingenieur eniso wrote: >> >> Dear all, >> I am working on spatiotemporal mapping of 2D and 3D EEG data. >> I want to develop the method of surface interpolation, what is the >> function in FieldTrip that develops this interpolation method. >> >> I hope you will send me positive and helpful response. >> >> Thanks a lot in advance! >> >> Best, >> >> ahmed >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> Jan-Mathijs Schoffelen, MD PhD >> >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> >> Max Planck Institute for Psycholinguistics, >> Nijmegen, The Netherlands >> >> J.Schoffelen at donders.ru.nl >> Telephone: +31-24-3614793 >> >> http://www.hettaligebrein.nl >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Thu Jul 18 17:23:43 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Thu, 18 Jul 2013 17:23:43 +0200 Subject: [FieldTrip] MNE source imaging - EEG Message-ID: Dear Fieldtrippers, I would like to know if it is possible to use a detailed downsampled mesh from FreeSurfer tassellation ( representing also the gyrus and the sulcus) as the 'brain' mesh in the method 'dipoli' in BEM computation (having supposed the three layers: 'scalp', 'skull' and 'brain'). I've tried to do this but vol.mat gained really high values (10^8) which led to really high values of the leadfield matrix. Thanks, Alberto Ghione University of Genoa -------------- next part -------------- An HTML attachment was scrubbed... URL: From virginie.van.wassenhove at gmail.com Thu Jul 18 20:21:49 2013 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Thu, 18 Jul 2013 20:21:49 +0200 Subject: [FieldTrip] Postdoctoral position available at Neurospin, France Message-ID: Dear all, please see below or here ( https://sites.google.com/site/virginievanwassenhove/opportunities) for a fellowship openings at NeuroSpin MEG, France! *-------**-------**-------**-------**-------**-------**-------**-------* *Postdoctoral Fellowship - *please, put *POSTDOC* in the email subject. *-------**-------**-------**-------**-------**-------**-------**-------* Due to a postdoctoral fellow having found a permanent position, we have a new opening in the group! Applications are invited from a talented, dynamic, committed, and enthusiastic researcher. The ideal applicant will have a sound experience in the analysis of MEG and/or EEG data and a strong record and research interest in cognitive neurosciences. The selected postdoctoral fellow will lead MEG studies as part of the ERC funded project “Mind Time”. A set of studies will specifically aim at using classifiers and decoding techniques with MEG data. The researcher will be expected to work closely with and supervise (master, phd) students involved in the project. Some involvement in organizational and managerial aspects specific to these projects can be expected. *Requirements:* - should hold a PhD in cognitive neurosciences, neurosciences, psychology, and/or related fields - a strong record of published work - prior experience with MEG/EEG techniques - sound signal processing skills - sound programming skills (matlab, python) Applicants from outside the European Union are welcome but must qualify for a valid visa. French speaking is not a requirement as long as the English language is mastered. * * *Starting date*: asap *Salary*: commensurate with experience. The position will be initially funded for one year (renewable for an additional 2 years).** * * *Application package* *CV* (incl. a list of publications) *Two letters of recommendation* (or contacts from which those could be obtained) *A letter of intent with a statement of research interests* *Applications will be considered until the position is filled.* * * *-------**-------**-------**-------**-------**-------**-------**-------* *Master students - p*lease, put *GRAD *in the email subject *-------**-------**-------**-------**-------**-------**-------**-------* Applications are invited from ambitious and talented students at the level of Master. The ideal applicants will have some lab experience in working with Human participants, and will be familiarized with one or several non-invasive neuroimaging techniques and/or electrophysiology. The applicant will be versed in cognitive neurosciences and demonstrate excellent scholarship. The selected candidate will show a strong academic record and interests in pursuing a PhD in cognitive neurosciences. *Requirements for the candidates:* - master level in cognitive neurosciences, neurosciences, psychology, and/or related fields - a strong academic record - some experience/familiarization with neuroimaging techniques or electrophysiology - fair understanding of signal processing - good programming skills and willingness to improve (matlab, python) Applicants from outside the European Union are welcome but they must qualify for a valid visa. French speaking is not a requirement as long as the English language is mastered. * * *Starting date*: asap and negotiable. *Application package* - *CV* - *A letter of motivation with a statement of research interests* - *Two letters of recommendation* (or contacts from which those could be obtained)*-* . Best wishes, Virginie -- Virginie van Wassenhove Exec Dir NeuroSpin MEG Group leader, Brain Dynamics CEA.DSV.I2BM.NeuroSpin - INSERM Cognitive Neuroimaging Unit Bât 145 Point Courrier 156 Gif s/ Yvette F-91191 FRANCE +33(0)1.69.08.1667 Virginie.van.Wassenhove at gmail.com https://sites.google.com/site/virginievanwassenhove/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From lei.niu at einstein.yu.edu Thu Jul 18 21:52:13 2013 From: lei.niu at einstein.yu.edu (Lei Niu) Date: Thu, 18 Jul 2013 19:52:13 +0000 Subject: [FieldTrip] question about to get the numbers of rejected trials Message-ID: Dear Fieldtrippers, I am new one to use the fieldtrip, and have a question about the rejected trials. To be simply, let we say: 1) the original data is data_org, one singal trial in 32 channel, with 2 different trigger codes and 100 trials per trigger. 2) I process the data to the data_stimulus, incuding 200 trials. Each trial has prestim = 0.1, poststim = 1; 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I get data_reject, including 190 trials. Here is the problem. I found the prestim is too short, I want to increase the prestim time to 0.5. How can I get the numbers of rejected 10 trials to do ft_redefinetrial? Thanks, Lei Niu Albert Einstein College of Medicine -------------- next part -------------- An HTML attachment was scrubbed... URL: From kyle.hird at gmail.com Fri Jul 19 00:24:48 2013 From: kyle.hird at gmail.com (Kyle Hird) Date: Thu, 18 Jul 2013 18:24:48 -0400 Subject: [FieldTrip] Peer module thinks it has too little memory Message-ID: Hi I am attempting to set up the distributed peer system on a 32-bit Linux machine, using version 20130419 from the ftp server (I'm using the shipped binaries because peerslave segfaults on receiving a job if compiled on my system). My tests involve one local slave and one local master on this four-core machine with 4GB of memory. After starting the slave peer, I attempt to run the example command peercellfun(@rand, {10, 20, 30}, 'UniformOutput', false). This fails with the message: 'there are no slave peers available that meet the memory requirements' Examining the output of the slave peer, it contains the following lines (edited for personal info): executing job 1 from myusername at HOSTNAME (jobid=672774519, memreq=2147483648, timreq=3600) executing job took 0.042167 seconds and 22957802788233216 bytes executing job 2 from myusername at HOSTNAME (jobid=1862053136, memreq=2147483648, timreq=3600) executing job took 0.001907 seconds and 22957802787971072 bytes While the times seem reasonable for such a simple problem, the memory usage does not (nearly 23,000 terabytes). The memory usage is reported by fexec, which in turn calculates it from the output of memprofile. Memprofile itself appears to discover resident and virtual size from getmem. I looked at the source for getmem and it appears that it should return -1 in my case (because the elif block for PLATFORM_LINUX is empty), causing memprofile_sample to report zeros for both. However, if I invoke memprofile_sample by using memprofile('info') at the command line, I get: ans = time: 1.3742e+09 mem: 3.6693e+18 I wonder exactly what is happening when getmem gets called. I'm not too experienced with C, but from my understanding the #if statement is evaluated at compile time, so getmem will behave according to the platform on which it was compiled, which may be different from that on which it is executed. As written, the function won't compile on my system due to the absence of . I can't actually find the binary mex getmem in the module, so although the source has mexFunction framework in it, I can't call it from MATLAB. What behaviour should I be getting from memprofile? Should I be doing something differently to get peercellfun to behave correctly? Thanks for your consideration Kyle Hird From samarakm at mail.uc.edu Fri Jul 19 02:24:32 2013 From: samarakm at mail.uc.edu (Samarasinghe, Kasun (samarakm)) Date: Fri, 19 Jul 2013 00:24:32 +0000 Subject: [FieldTrip] Using ft_sourceplot to visualize simulated dipoles Message-ID: <158540F0F1AD27479479077742EA83C5215B90A5@BY2PRD0111MB511.prod.exchangelabs.com> Hello, I am a rookie to fieldtrip, and I have a pretty basic question. I am trying to visually see what a dipole/s would look like after using the function ft_dipolesimulation(cfg). Can I use ft_sourceplot to do this. (I know the BESA_Dipole Simulator gives a nice visual description of the dipoles). My primary objective is to visually compare a simulated dipole/s with its reconstructed counterpart. The reconstruction can be done using any of the source analysis methods. I would really appreciate if anyone could assist me with this problem. Thank you, Kasun Samarasinghe -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Fri Jul 19 11:40:01 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Fri, 19 Jul 2013 11:40:01 +0200 Subject: [FieldTrip] 'ft_prepare_layout' Error Message-ID: Hello ; I am receiving the following error while using ft_prepare_layout ??? Index exceeds matrix dimensions. Error in ==> ft_prepare_layout>sens2lay at 788 mindist = mindist(1:round(numel(label)/4)); Error in ==> ft_prepare_layout at 285 lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, cfg.style); Error in ==> spm_eeg_project3D at 27 lay = ft_prepare_layout(cfg); Notice that I am using MEG channels and the above function perfectly works when I used the EEG channel. For me itt seems like there is any problem with my '.grad' structure ? Kindly please help me to toubleshoot this problem. Regards; Mushfa Yousuf -------------- next part -------------- An HTML attachment was scrubbed... URL: From mushfa.yousuf at googlemail.com Fri Jul 19 12:34:37 2013 From: mushfa.yousuf at googlemail.com (Mushfa Yousuf) Date: Fri, 19 Jul 2013 12:34:37 +0200 Subject: [FieldTrip] 'ft_prepare_layout' Error In-Reply-To: References: Message-ID: hello ; or it has something to do with layout ? because this msg appears after this line *creating layout for neuromag306 system* * * ??? Index exceeds matrix dimensions. Error in ==> ft_prepare_layout>sens2lay at 788 mindist = mindist(1:round(numel(label)/4)); Error in ==> ft_prepare_layout at 285 lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, cfg.style); Error in ==> spm_eeg_project3D at 27 lay = ft_prepare_layout(cfg); Regards; Mushfa Yousuf On Fri, Jul 19, 2013 at 11:40 AM, Mushfa Yousuf < mushfa.yousuf at googlemail.com> wrote: > Hello ; > > I am receiving the following error while using ft_prepare_layout > > > ??? Index exceeds matrix dimensions. > > Error in ==> ft_prepare_layout>sens2lay at 788 > mindist = mindist(1:round(numel(label)/4)); > > Error in ==> ft_prepare_layout at 285 > lay = sens2lay(cfg.grad, cfg.rotate, cfg.projection, > cfg.style); > > Error in ==> spm_eeg_project3D at 27 > lay = ft_prepare_layout(cfg); > > Notice that I am using MEG channels and the above function perfectly works > when I used the EEG channel. > > For me itt seems like there is any problem with my '.grad' structure ? > > > > Kindly please help me to toubleshoot this problem. > > > Regards; > > Mushfa Yousuf > -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at gmail.com Sat Jul 20 21:45:44 2013 From: johanna.zumer at gmail.com (Johanna Zumer) Date: Sat, 20 Jul 2013 21:45:44 +0200 Subject: [FieldTrip] question about to get the numbers of rejected trials In-Reply-To: References: Message-ID: Dear Lei, I think that you are asking that you want to run the steps again, with prestim =0.5 but with rejecting the same 10 trials that you already have decided to reject? If so, the numbers of rejected trials should be inside data_reject.cfg (or possibly data_reject.cfg.previous). But note that by including more prestim time, you might also find a need to reject more trials if there is an artifact in the new included prestim time-points. If you use ft_redefinetrial, I think you only would shift where the time 0.0 is, but not add more data to each trial, so it depends which you want to do. Best regards, Johanna 2013/7/18 Lei Niu > Dear Fieldtrippers, > > I am new one to use the fieldtrip, and have a question about the rejected > trials. > To be simply, let we say: > 1) the original data is data_org, one singal trial in 32 channel, with 2 > different trigger codes and 100 trials per trigger. > 2) I process the data to the data_stimulus, incuding 200 trials. Each > trial has prestim = 0.1, > poststim = 1; > 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I > get data_reject, including 190 trials. > > Here is the problem. I found the prestim is too short, I want to increase > the prestim time to 0.5. How can I get the numbers of rejected 10 trials to > do ft_redefinetrial? > > Thanks, > Lei Niu > Albert Einstein College of Medicine > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From s32334077 at gmail.com Mon Jul 22 10:35:50 2013 From: s32334077 at gmail.com (Alberto Ghione) Date: Mon, 22 Jul 2013 10:35:50 +0200 Subject: [FieldTrip] Source time series signals Message-ID: Dear Fieldtrippers, I performed the source reconstruction using the MNE method; i would like to ask what type of signal is 'source.avg.pow', is it correct to assume that it is the time series related to a specific source? Thanks for your attention, Alberto Ghione University of Genoa -------------- next part -------------- An HTML attachment was scrubbed... URL: From polomacnenad at gmail.com Mon Jul 22 10:56:30 2013 From: polomacnenad at gmail.com (Nenad Polomac) Date: Mon, 22 Jul 2013 10:56:30 +0200 Subject: [FieldTrip] Fieldtrip to SPM Message-ID: Dear all, I would like to convert my MEG CTF data analysed with Fieldtrip into the SPM format in order to do dynamic causal modeling. I am familiar with explanations from the spm manual and spm_eeg_ft2spm function. Is there any more detailed source of information about this? To make more concrete I have successfully converted my data but it seems something is missing from the structure which explains MEG header information. Thank you in advance! Nenad Polomac -------------- next part -------------- An HTML attachment was scrubbed... URL: From Johanna.Fiess at uni-konstanz.de Mon Jul 22 14:40:47 2013 From: Johanna.Fiess at uni-konstanz.de (=?iso-8859-1?Q?Johanna_Fie=DF?=) Date: Mon, 22 Jul 2013 14:40:47 +0200 Subject: [FieldTrip] different frequency bins Message-ID: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Dear all, whenever I try to compute the statistics for (MEG) time-frequency data, this error message comes up: computing statistic over the frequency range [8.000 11.000] computing statistic over the time range [0.300 1.100] Error using ft_appendfreq (line 250) the input data structures have non-unique frequency bins, concatenation across frequency is not possible Error in ft_appendfreq (line 139) freq = ft_appendfreq(tmpcfg, varargin{:}); Error in ft_freqstatistics (line 231) data = ft_appendfreq(cfg, varargin{:}); Out of 35 participants in total, (only) three show slightly different frequency bins (starting point 2.0001 instead of 1.9998) – if I remove them from the average, the error message disappears. If renaming the freq-structure of those three participants, the error message disappears, too. Could anyone tell me what causes this problem or how I should handle it? Thanks a lot in advance! Johanna PS: I'm running Matlab R2012b & fieldtrip-20130515 %% stats design=[1:10,1:10; ones(1,10),ones(1,10)*2]; cfg = []; cfg.frequency = [8 11]; cfg.latency = [.3 1.1]; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clustertail = 0; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.numrandomization = 500; cfg.alpha = 0.05; cfg.avgoverfreq = 'yes'; % cfg.avgovertime = 'yes'; cfg.design = design; cfg.neighbours = neighbours; cfg.ivar = 2; stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); cfg = []; cfg.alpha = 0.3; cfg.parameter = 'stat'; cfg.zlim = [-3 2]; cfg.layout = '4D148.lay'; ft_clusterplot(cfg, stat); -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 22 14:50:16 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 22 Jul 2013 14:50:16 +0200 Subject: [FieldTrip] different frequency bins In-Reply-To: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> References: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Message-ID: <51ED2A88.60304@donders.ru.nl> Dear Johanna, the problem is that the trial length you put into freqanalysis differed across subjects, leading to a different frequency resolution across participants. FieldTrip realizes that and errors because 1.9998 is not 2.0001 ;) I would propose you re-do the frequencyanalysis with the same time window/trial length for all participants. Maybe you should first check why your trials have different lengths and if that is desired or you did another mistake somewhere in your analysis. If you want to different trial lengths, you can use a padding cfg option in ft_freqanalysis to pad trials to a fixed length. Good luck ;) Best, Jörn On 7/22/2013 2:40 PM, Johanna Fieß wrote: > Dear all, > > whenever I try to compute the statistics for (MEG) time-frequency > data, this error message comes up: > > computing statistic over the frequency range [8.000 11.000] > computing statistic over the time range [0.300 1.100] > Error using ft_appendfreq (line 250) > the input data structures have non-unique frequency bins, > concatenation across frequency is not possible > > Error in ft_appendfreq (line 139) > freq = ft_appendfreq(tmpcfg, varargin{:}); > > Error in ft_freqstatistics (line 231) > data = ft_appendfreq(cfg, varargin{:}); > > Out of 35 participants in total, (only) three show slightly different > frequency bins (starting point 2.0001 instead of 1.9998) -- if I > remove them from the average, the error message disappears. > If renaming the freq-structure of those three participants, the error > message disappears, too. > > Could anyone tell me what causes this problem or how I should handle it? > > Thanks a lot in advance! > > Johanna > > > PS: I'm running Matlab R2012b & fieldtrip-20130515 > %% stats > design=[1:10,1:10; ones(1,10),ones(1,10)*2]; > > cfg = []; > cfg.frequency = [8 11]; > cfg.latency = [.3 1.1]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clustertail =0; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.numrandomization = 500; > cfg.alpha = 0.05; > > cfg.avgoverfreq = 'yes'; > % cfg.avgovertime = 'yes'; > cfg.design = design; > cfg.neighbours = neighbours; > cfg.ivar = 2; > > > stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); > cfg = []; > cfg.alpha = 0.3; > cfg.parameter = 'stat'; > cfg.zlim = [-3 2]; > cfg.layout = '4D148.lay'; > ft_clusterplot(cfg, stat); > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 22 14:53:27 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 22 Jul 2013 14:53:27 +0200 Subject: [FieldTrip] Source time series signals In-Reply-To: References: Message-ID: <51ED2B47.5000408@donders.ru.nl> Dear Alberto, the abbreviation stands for *pow*er of the *av*era*g*e across your observation(s) of the *source*-reconstructed data :) If I am not mistaken, there should be a .mom field (if you set cfg.keepmom = 'yes') which contains the time-resolved data rather than the power. Best, Jörn On 7/22/2013 10:35 AM, Alberto Ghione wrote: > Dear Fieldtrippers, > I performed the source reconstruction using the MNE method; i would > like to ask what type of signal is 'source.avg.pow', > is it correct to assume that it is the time series related to a > specific source? > > Thanks for your attention, > Alberto Ghione > University of Genoa > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 22 15:00:39 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 22 Jul 2013 15:00:39 +0200 Subject: [FieldTrip] different frequency bins In-Reply-To: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> References: <37D727CC-499E-4D25-B975-BAC49D255F53@uni-konstanz.de> Message-ID: Dear Johanna, The slight differences in frequency bins was probably caused by a slightly different trial length for some of your participants. When doing frequency analysis, the frequency resolution is determined by the length of your data. (You can have a look at e.g. this FAQ entry: http://fieldtrip.fcdonders.nl/faq/what_does_padding_not_sufficient_for_requested_frequency_resolution_mean for more information.) You mention that the differences in frequency bins are very small. In your case, therefore, I would solve (or 'patch' ;) ) the problem by simply doing something like: participantB.freq = participantA.freq; for all participants B with the aberrant frequency axis. Of course, this only makes sense if the frequency axes between participants A and B are actually almost identical! Hope this helps, Best regards, Eelke On 22 July 2013 14:40, Johanna Fieß wrote: > Dear all, > > whenever I try to compute the statistics for (MEG) time-frequency data, this > error message comes up: > > computing statistic over the frequency range [8.000 11.000] > computing statistic over the time range [0.300 1.100] > Error using ft_appendfreq (line 250) > the input data structures have non-unique frequency bins, concatenation > across frequency is not possible > > Error in ft_appendfreq (line 139) > freq = ft_appendfreq(tmpcfg, varargin{:}); > > Error in ft_freqstatistics (line 231) > data = ft_appendfreq(cfg, varargin{:}); > > Out of 35 participants in total, (only) three show slightly different > frequency bins (starting point 2.0001 instead of 1.9998) – if I remove them > from the average, the error message disappears. > If renaming the freq-structure of those three participants, the error > message disappears, too. > > Could anyone tell me what causes this problem or how I should handle it? > > Thanks a lot in advance! > > Johanna > > > PS: I'm running Matlab R2012b & fieldtrip-20130515 > %% stats > design=[1:10,1:10; ones(1,10),ones(1,10)*2]; > > cfg = []; > cfg.frequency = [8 11]; > cfg.latency = [.3 1.1]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clustertail = 0; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.numrandomization = 500; > cfg.alpha = 0.05; > > cfg.avgoverfreq = 'yes'; > % cfg.avgovertime = 'yes'; > cfg.design = design; > cfg.neighbours = neighbours; > cfg.ivar = 2; > > > stat = ft_freqstatistics (cfg,patUr{:}, konUr{:}); > cfg = []; > cfg.alpha = 0.3; > cfg.parameter = 'stat'; > cfg.zlim = [-3 2]; > cfg.layout = '4D148.lay'; > ft_clusterplot(cfg, stat); > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From lei.niu at einstein.yu.edu Mon Jul 22 15:11:42 2013 From: lei.niu at einstein.yu.edu (Lei Niu) Date: Mon, 22 Jul 2013 13:11:42 +0000 Subject: [FieldTrip] question about to get the numbers of rejected trials In-Reply-To: References: , Message-ID: Dear Johanna, Thank you very much for your reply. I have resolved the problem following your suggestions. Thanks, Lei ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Johanna Zumer [johanna.zumer at gmail.com] Sent: Saturday, July 20, 2013 3:45 PM To: FieldTrip discussion list Subject: Re: [FieldTrip] question about to get the numbers of rejected trials Dear Lei, I think that you are asking that you want to run the steps again, with prestim =0.5 but with rejecting the same 10 trials that you already have decided to reject? If so, the numbers of rejected trials should be inside data_reject.cfg (or possibly data_reject.cfg.previous). But note that by including more prestim time, you might also find a need to reject more trials if there is an artifact in the new included prestim time-points. If you use ft_redefinetrial, I think you only would shift where the time 0.0 is, but not add more data to each trial, so it depends which you want to do. Best regards, Johanna 2013/7/18 Lei Niu > Dear Fieldtrippers, I am new one to use the fieldtrip, and have a question about the rejected trials. To be simply, let we say: 1) the original data is data_org, one singal trial in 32 channel, with 2 different trigger codes and 100 trials per trigger. 2) I process the data to the data_stimulus, incuding 200 trials. Each trial has prestim = 0.1, poststim = 1; 3) I do ft_rejectvisual to reject 10 trials, 5 for each trigger. Then I get data_reject, including 190 trials. Here is the problem. I found the prestim is too short, I want to increase the prestim time to 0.5. How can I get the numbers of rejected 10 trials to do ft_redefinetrial? Thanks, Lei Niu Albert Einstein College of Medicine _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From kyle.hird+fieldtrip at gmail.com Mon Jul 22 18:54:38 2013 From: kyle.hird+fieldtrip at gmail.com (Kyle Hird) Date: Mon, 22 Jul 2013 12:54:38 -0400 Subject: [FieldTrip] Peer module thinks it has too little memory In-Reply-To: References: Message-ID: I've investigated my issue a bit further and found a couple of things that may be of use for anyone attempting to diagnose the problem. I mentioned previously that the instance of MATLAB which is running peerslave segfaults when it receives a job if I compile the toolbox on my system. On inspection of the stack trace, I find memprofile twice- the only file from FieldTrip to show up at all. So I run memprofile directly from the private directory with a couple of different options. With 'info', it appears to correctly measure memory usage- approximately 110MB (the distributed binary reported an unrealistically high number). However, when set up to repeatedly sample using 'on' and 'off', memprofile segfaults when 'off' is given, and returns an almost-identical stack trace as when peerslave was run. If 'off' is given to memprofile without first having given 'on', the error does not occur. Other ways to trigger the segfault are, once setting memprofile('on'), to give MATLAB the commands 'exit' or 'clear mex'. I added some mexPrintf statements to try and pinpoint what instruction is causing the segfault. Based on this, the block of code beginning with else if (strcasecmp(command, "off")==0) completes execution correctly. However, nothing in exitFun appears to be executed, not even a print statement I put on the first line. I'm not sure what could cause this problem, but hopefully someone on the list can make sense of this. Thanks for your consideration Kyle Hird From jm.horschig at donders.ru.nl Tue Jul 23 09:41:56 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Tue, 23 Jul 2013 09:41:56 +0200 Subject: [FieldTrip] Getting started with realtime EEG data In-Reply-To: References: <9EDC29E4-D79B-4777-A3C6-0C5E5E2C9E0F@donders.ru.nl> Message-ID: <51EE33C3.7020204@donders.ru.nl> Hi Eric, I was just reading up on this conversation and since you mentioned that you do not have any signal processing experience, I thought it'd be nice to point to http://www.dspguide.com/ (free online book) Good luck with oscillating in your sleep :) Best, Jörn On 3/6/2013 9:08 AM, Eelke Spaak wrote: > Hi Eric, > > Yes, FieldTrip's raw data format is the same regardless of acquisition > device, so I expect no problems switching from one device to another. > Note, though, that I have not worked with the realtime buffer, but I > think it ought to work the same as with offline data processing. > > Certain analysis pipelines (e.g. source reconstruction) require > accurate information about the electrode positions. The ease at which > you could obtain these might differ between different devices. > However, based on the info you've given so far I guess this will not > be a problem for you. > > Best, > Eelke > > On 6 March 2013 05:24, Eric Mill wrote: >> Sorry, that was a very long response on my part - but the one actual >> question I have in there is, how easy is it to switch from one EEG device to >> another? Should I expect to have to rework my code entirely, or will the >> core data format and signal processing work be the same? Is standardizing >> the data stream one of the things using an intermediary like Field Trip >> does? >> >> -- Eric >> >> >> On Sun, Mar 3, 2013 at 5:26 PM, Eric Mill wrote: >>> This is extremely helpful, and just what I was looking for, thank you >>> (both Robert and Stefan). I have a few followup questions you've inspired. >>> >>> How "swappable" is the hardware? Do all EEG's fundamentally produce the >>> same data from the same brain activity? And/or, does FieldTrip always expose >>> data in its buffer in the same format? >>> >>> For example, I would be fine investing the $750 for an Emotiv 14-channel >>> EEG, or even the $1200 for a KT88-1016, but not until after I've done some >>> development with a cheaper device first. However, I would not want to have >>> to rewrite all my code, or much of it, if I switch devices. >>> >>> I do have a requirement that I can have the same code work with either >>> live or replayed data. From how you describe its buffer approach, it sounds >>> like that's a core value of FieldTrip, and will make that requirement much >>> easier to satisfy. >>> >>> Also, I do have one peculiar requirement, which is that the hardware be >>> suitable for wearing during ordinary sleeping at home. This is more a >>> requirement for the final (potentially more expensive) device, than the >>> development device. The promotional photo for the Emotiv EEG, for example, >>> looks like it might not be so great for that. >>> >>> I think I will be using WebSockets, but there will be an intermediate >>> server. So, I will have a computer (perhaps a Raspberry Pi) receive data >>> from the EEG, and then immediately stream it up an open TCP connection to a >>> web server. This server will then stream it down to the individual browsers >>> of visiting users, and JavaScript will do the visualization, in something >>> like Three.js or Processing.js. >>> >>> So I don't think I'd be making a JavaScript implementation of FieldTrip, >>> but I believe the server software could be made to be general purpose, and >>> reusable in the work of others like yourselves. That would be a satisfying >>> byproduct. >>> >>> The idea here is that the resulting website will show fully live and real >>> time EEG data, specifically while I am sleeping. Since I only sleep for ~1/3 >>> of any given day, the ability to replay things will be helpful in giving the >>> site utility during the other 2/3. >>> >>> I've never done any signal processing before, not even so much as a fast >>> Fourier transform. But I'm willing to learn! I'll be consulting the tutorial >>> you've kindly written, but if you have any suggestions of learning material >>> I should look at when figuring out how to (for example) detect when a >>> subject has entered levels of sleep given streams of EEG data, it would be a >>> lot of help to me. >>> >>> Unfortunately, the paper you linked to >>> (http://onlinelibrary.wiley.com/doi/10.1111/j.1469-8986.2012.01471.x/full) >>> is behind a paywall and is $35, but if you recommend it highly enough, I'll >>> check it out. >>> >>> Again, thank you for being so welcome to a newbie, and for the >>> recommendations and links. >>> >>> -- Eric >>> >>> >>> On Sun, Mar 3, 2013 at 4:58 AM, Robert Oostenveld >>> wrote: >>>> Hi Eric, >>>> >>>> I think that NeuroSky renamed and discontinued some of their products >>>> since we made the initial implementation of the ThinkCap. I am still able >>>> to find documentation here >>>> http://developer.neurosky.com/docs/lib/exe/fetch.php?media=thinkcap:thinkcap_headset_user_manual.pdf >>>> and http://developer.neurosky.com/docs/doku.php?id=thinkcap. I cannot tell >>>> whether the complete sets now sold by NeuroSky still use the same software >>>> interface, but NeuroSky is rather open with their development tools. >>>> >>>> Alternatives you may consider are the Emotiv Epoc or the DIY OpenEEG. The >>>> Epoc has more channels and a head mount for the electrodes. For the Epoc you >>>> have to look into teh different SDK options, the cheapest version only gives >>>> access to processed data, not to the raw data. For both the Epoc and openeeg >>>> a implementation of a stand-allone executable is available in >>>> http://fieldtrip.fcdonders.nl/development/realtime/implementation. LIke for >>>> the ThinkCap, this copies the data to a "fieldtrip buffer", where another >>>> (c/c++/java/python/matlab) application can easily read it from and do the >>>> signal processing, not having to worry about the buffering and data >>>> representation any more. >>>> >>>> I know it falls outside your budget, but have a look at >>>> http://engineuring.wordpress.com/2009/06/15/writing-your-own-soft-for-a-really-cheap-eeg-hardware-for-brain-computer-interfacing. >>>> These KT88-1016 systems are available from ebay. >>>> >>>> Let me add a bit from the developers perspective and software design. The >>>> rationale for the fieldtrip buffer is that it allows us to develop analysis >>>> pipelines using EEG data files on disk (using ft_read_data). Once the >>>> offline analysis pipeline performs as desired, we just switch from reading >>>> to disk to reading from the buffer (also ft_read_data). We happen to do this >>>> using MATLAB for the rapid application development, but the same strategy >>>> (develop for file, run in real-time) can be used with another programming >>>> environment. >>>> >>>> I think that for signal processing you'll better off if you develop the >>>> code using some good quality data from a file on disk. You can always enact >>>> a real-time data stream by replaying data from that EEG file, or using the >>>> sine2ft GUIs (see realtime/bin). Otherwise you'll be doing all development, >>>> constantly having to wear the headset. That is fine for artefact detection >>>> (you can blink while you code), but not if the tasks get more complicated, >>>> e.g. relaxing to increase your occipital alpha/10Hz won't work well if you >>>> also have in realtime have to monitor whether your applications picks up the >>>> alpha. >>>> >>>> Some time ago we (i.e. Boris Reuderink and me) looked into the >>>> possibilities of a web-standards implementation. Web Sockets would be >>>> needed in Javascript if we want to have the browser connect to a "fieldtrip >>>> buffer" TCP server. The Web Sockets still seemed a bit risky w.r.t. it >>>> working on all platforms. A server-side implementation offers more choice, >>>> python/java/php reading the data from a FT buffer or from the device, and >>>> then pass it on in html format to the connected web ) but would not scale as >>>> easily with multiple client connections if data processing needs to be done >>>> on the server. We then considered the best option to be to implement a >>>> RESTless server implementation. The server would one the one hand contains >>>> the FT buffer (where it receives the data over low-level TCP) and on the >>>> other hand have a web server with the RESTless interface. I.e. the requests >>>> that are represented here >>>> http://fieldtrip.fcdonders.nl/development/realtime/buffer_protocol would >>>> each translate to a http call like "http://ftbuffer.donders.nl/get/hdr" and >>>> "http://ftbuffer.donders.nl/get/dat?begsample=xx&endsample=xx". You can ask >>>> Boris (CC) offline whether he has given it further thought. >>>> >>>> best regards, >>>> Robert >>>> >>>> >>>> >>>> On 2 Mar 2013, at 3:12, Eric Mill wrote: >>>> >>>>> Hi all, >>>>> >>>>> My apologies if this is off-topic here, since you all seem like very >>>>> busy experts! >>>>> >>>>> I'm trying to figure out what I need to get started with capturing >>>>> real-time EEG data using consumer-priced headsets (<$200). I don't actually >>>>> have any interest in using MATLAB, though - I just want to capture the raw >>>>> data, in real time. >>>>> >>>>> I see that FieldTrip has a realtime acquisition module for NeuroSky's >>>>> "ThinkCap", though I can't find a current product by NeuroSky called that. >>>>> Is there something else of theirs I could buy that would work with >>>>> FieldTrip? >>>>> >>>>> Or, should I be looking elsewhere entirely? What should someone who >>>>> wants real-time EEG data do? >>>>> >>>>> My plan is to stream this data and visualize it on the web in real >>>>> time. My background is in web development, not cognitive science, but I'm >>>>> willing to learn what I have to make something interesting. I'd also love to >>>>> have the project result in libraries useful for other people in the field. >>>>> >>>>> Thanks for any advice you can give on what EEG to buy, and/or where to >>>>> learn the core concepts I'll need to use the data. >>>>> >>>>> -- Eric >>>>> _______________________________________________ >>>>> fieldtrip mailing list >>>>> fieldtrip at donders.ru.nl >>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From K.Kalogianni at tudelft.nl Tue Jul 23 19:05:52 2013 From: K.Kalogianni at tudelft.nl (Konstantina Kalogianni) Date: Tue, 23 Jul 2013 17:05:52 +0000 Subject: [FieldTrip] music_SL In-Reply-To: <4DF682D3A10EAC46B462A46E16F0B049128DF845@SRV366.tudelft.net> References: <4DF682D3A10EAC46B462A46E16F0B049128DF845@SRV366.tudelft.net> Message-ID: <96D063C2-1544-4FB2-BAA6-D4DD736FD6CE@tudelft.nl> Sent from my iPhone Begin forwarded message: Dear fieldtripers, I want to use the music algorithm for source localization on SEP data(somatosensory evoked potentials) and I would like some help.: Those are my questions 1.The music algorithm needs a number of components (i.e dipoles) and I am wondering where to specify that. For the moment I ‘ve just edited the music.m file for that, but I was wondering if there is a more efficient way. 2.Does the algorithm needs a prestimulus part of the data for comparison that will be used in the covariance matrix? 3. How do I plot the results for music algorithm if I am only interested in one dipole activated? Should I set a roi before? Thanks in advance Nadia Kalogianni -------------- next part -------------- An HTML attachment was scrubbed... URL: From robince at gmail.com Wed Jul 24 10:16:02 2013 From: robince at gmail.com (Robin) Date: Wed, 24 Jul 2013 09:16:02 +0100 Subject: [FieldTrip] matlab stops showing functional images! Message-ID: Hi all, Sorry for a question which might be slightly off topic. I am plotting functional images over anatomy with the 'slice' method of ft_sourceplot. On one machine this has stopped working. The anatomy displays and the functional colorbar is displayed correctly (I can update the CData attribute and see the colorbar update) - but I do not see any part of the functional map. I think it is something related to OpenGL (the renderer for the figure is definitely set to opengl) on this particular computer (the exact same code works on other machines). The setup is CentOS 6 with Matlab R2012a. I have restarted Matlab and the machine but it still doesn't show up - I haven't changed any Matlab settings as far as I know. I am a bit stuck with this so wondered if anyone here might have seen anything like it before? Cheers Robin -------------- next part -------------- An HTML attachment was scrubbed... URL: From Yingying.Wang at cchmc.org Thu Jul 25 08:10:57 2013 From: Yingying.Wang at cchmc.org (Wang, Yingying) Date: Thu, 25 Jul 2013 06:10:57 +0000 Subject: [FieldTrip] website is down In-Reply-To: <018501ce88fd$932b3970$b981ac50$@hotmail.com> References: <018501ce88fd$932b3970$b981ac50$@hotmail.com> Message-ID: <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> http://fieldtrip.fcdonders.nl/ is down. When will it come back? Thanks. -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Thu Jul 25 08:50:25 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Thu, 25 Jul 2013 08:50:25 +0200 Subject: [FieldTrip] website is down In-Reply-To: <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> References: <018501ce88fd$932b3970$b981ac50$@hotmail.com> <67FF4A406B7F5241A042A2BE613571B90DC7C861@MCEXMB3.chmccorp.cchmc.org> Message-ID: Dear list, We apologize for the present website issues, and working as best we can to get the website up again. Most likely, it will be back up later today. Best, Eelke On 25 July 2013 08:10, Wang, Yingying wrote: > http://fieldtrip.fcdonders.nl/ is down. > > When will it come back? > > Thanks. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From constantino.mendezbertolo at ctb.upm.es Fri Jul 26 18:46:23 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Fri, 26 Jul 2013 18:46:23 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics Message-ID: Greetings, We have Timelock data (LFPs). In order to run cluster based permutation tests we generated a Template similar to a Freqdata structure, with size(Template.powspctrm) = 9 1 1 320 Template.dimord = subj_chan_freq_time We set cfg.neighbouts = [] and run ft_freqstatistics (method ='montecarlo'; correctm = 'cluster', etc) * * This way we can run permutation tests and explore the output, hence, clusters are made on time. What we would like to do is: - *Selecting a minimum amount of consecutive time-bins for a cluster to be considered.* * * For example: Only if (say) 10 consecutive time points are above threshold (whether 'maxsum' or 'wcm' criteria are being used) fieldtrip should consider it a cluster. If just one solely sample point is above clusteralpha threshold, it should not be considered. Is it possible? It would similar to cfg.minnbchan, but in time. Only a cfg.minnbtbin does not exist! As we are already tricking freqstats to believe is working with freqdata (with just one frequency) I am not sure if this is possible. If someone has got some input it would be much appreciated -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Fri Jul 26 19:54:38 2013 From: smoratti at psi.ucm.es (smoratti at psi.ucm.es) Date: Fri, 26 Jul 2013 19:54:38 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: Message-ID: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> I think cfg.minnbchan, applies also to time bins. s ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Universidad Complutense de Madrid Facultad de Psicología Departamento de Psicología Básica I Campus de Somosaguas 28223 Pozuelo de Alarcón (Madrid) Spain and Center for Biomedical Technology Laboratory for Cognitive and Computational Neuroscience Parque Científico y Tecnológico de la Universidad Politecnica de Madrid Campus Montegancedo 28223 Pozuelo de Alarcón (Madrid) Spain email: smoratti at psi.ucm.es Tel.: +34 679219982 El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > cfg.minnbchan, -------------- next part -------------- An HTML attachment was scrubbed... URL: From constantino.mendezbertolo at ctb.upm.es Fri Jul 26 20:55:36 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Fri, 26 Jul 2013 20:55:36 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> Message-ID: Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations This is the error (with neighbours) V V V Error in clusterstat>makechanneighbstructmat (line 519) [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); Error in clusterstat (line 59) channeighbstructmat = makechanneighbstructmat(cfg); Error in statistics_montecarlo (line 320) [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ft_freqstatistics (line 267) [stat, cfg] = statmethod(cfg, dat, cfg.design); While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: > > I think cfg.minnbchan, applies also to time bins. > > s > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > > cfg.minnbchan, > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN -------------- next part -------------- An HTML attachment was scrubbed... URL: From mengtongxiao at gmail.com Mon Jul 29 04:44:49 2013 From: mengtongxiao at gmail.com (=?GB2312?B?s8LRqQ==?=) Date: Mon, 29 Jul 2013 10:44:49 +0800 Subject: [FieldTrip] EEG source reconstruction Message-ID: Dear all I do EEG source analyse,But I use the method as the follow got strong function connectivity from different brain areas.（eg.correlation）and strength is similar; I want konw the code with source reconstruction is right? Or some stimulate can prove the code that is right. (the VOL and sourcemode form template) cfg = []; cfg.covariance = 'yes'; cfg.vartrllength = 2; cfg.covariancewindow = 'all'; timelock = ft_timelockanalysis(cfg, data); cfg = []; cfg.channel = {'EEG'}; cfg.vol = vol; cfg.reducerank = 3; cfg.normalize ='yes'; cfg.elec = data_org.hdr.elec; cfg.grid =sourcemodel; [grid]= ft_prepare_leadfield(cfg); cfg = []; cfg.method = 'lcmv'; cfg.vol = vol; cfg.grid = grid; cfg.lcmv.fixedori = 'yes'; cfg.elec = data.hdr.elec; cfg.lcmv.keepfilter = 'yes'; cfg.lcmv.projectnoise = 'yes'; source1 = ft_sourceanalysis(cfg, timelock); thanks in advance xiao -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Mon Jul 29 07:48:59 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 29 Jul 2013 07:48:59 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> Message-ID: <51F6024B.8070000@donders.ru.nl> Dear Constantino, I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. Best, Jörn On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: > Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no > cluster (not even with minnbchan = 1) were there was a cluster before > (without cfg.minnbchan) > > Using cfg.neighbours = 'triangulation', or 'distance', with or without > cfg.minnbchan computes the statistics but fails prior to compute the > clusters in the randomizations > > This is the error (with neighbours) V V V > > Error in clusterstat>makechanneighbstructmat (line 519) > [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); > > Error in clusterstat (line 59) > channeighbstructmat = makechanneighbstructmat(cfg); > > Error in statistics_montecarlo (line 320) > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ft_freqstatistics (line 267) > [stat, cfg] = statmethod(cfg, dat, cfg.design); > > > While it seems it is minnbchan what will be helpful, we do not come up > with an idea. Maybe, besides tricking fieldtrip to think we have > frequency data we should also trick him to believe that points in time > are channels? :) > > > El 26 de julio de 2013 19:54, smoratti at psi.ucm.es > > escribió: > > > I think cfg.minnbchan, applies also to time bins. > > s > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Universidad Complutense de Madrid > Facultad de Psicología > Departamento de Psicología Básica I > Campus de Somosaguas > 28223 Pozuelo de Alarcón (Madrid) > Spain > > and > > Center for Biomedical Technology > Laboratory for Cognitive and Computational Neuroscience > Parque Científico y Tecnológico de la Universidad Politecnica de > Madrid > Campus Montegancedo > 28223 Pozuelo de Alarcón (Madrid) > Spain > > > email: smoratti at psi.ucm.es > Tel.: +34 679219982 > > El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: > >> cfg.minnbchan, > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Constantino Méndez-Bértolo > Laboratorio de Neurociencia Clínica,Centro de Tecnología Biomédica (CTB) > > Parque Científico y Tecnológico de la UPM, Campus de Montegancedo > > 28223 Pozuelo deAlarcón, Madrid, SPAIN > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From constantino.mendezbertolo at ctb.upm.es Mon Jul 29 13:06:43 2013 From: constantino.mendezbertolo at ctb.upm.es (=?ISO-8859-1?Q?Constantino_M=E9ndez_B=E9rtolo?=) Date: Mon, 29 Jul 2013 13:06:43 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: <51F6024B.8070000@donders.ru.nl> References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> <51F6024B.8070000@donders.ru.nl> Message-ID: Dear Jörn, Thanks for your response. You are sensibly confused. It is because we wanted to do the statistics (montecarlo; correctm = cluster) with just one channel per data/individual. [As was pointed out above: size(Template.powspctrm) = 9 1 1 320; Template.dimord = subj_chan_freq_time], and ft_timelockstatistics would ask me for a neighbourstructure relenteless, while ft_freqstatistics is ok with cfg.neighbour = [] and so clusters in time. Hence the unorthodoxy. I did a function that parses the mask of the already computed stat finding '1s', determining the span and setting zeros on an arbitrary width-criteria; which serves the purpose but it is not as ellegant as it would be my own statfun. Cheers, Tino 2013/7/29 "Jörn M. Horschig" > > Dear Constantino, > > I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). > > The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. > > Best, > Jörn > > > On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: >> >> Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) >> >> Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations >> >> This is the error (with neighbours) V V V >> >> Error in clusterstat>makechanneighbstructmat (line 519) >> [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); >> >> Error in clusterstat (line 59) >> channeighbstructmat = makechanneighbstructmat(cfg); >> >> Error in statistics_montecarlo (line 320) >> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >> >> Error in ft_freqstatistics (line 267) >> [stat, cfg] = statmethod(cfg, dat, cfg.design); >> >> >> While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) >> >> >> El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: >>> >>> >>> I think cfg.minnbchan, applies also to time bins. >>> >>> s >>> >>> ________________________________________________________ >>> Stephan Moratti, PhD >>> >>> see also: http://web.me.com/smoratti/ >>> >>> Universidad Complutense de Madrid >>> Facultad de Psicología >>> Departamento de Psicología Básica I >>> Campus de Somosaguas >>> 28223 Pozuelo de Alarcón (Madrid) >>> Spain >>> >>> and >>> >>> Center for Biomedical Technology >>> Laboratory for Cognitive and Computational Neuroscience >>> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >>> Campus Montegancedo >>> 28223 Pozuelo de Alarcón (Madrid) >>> Spain >>> >>> >>> email: smoratti at psi.ucm.es >>> Tel.:    +34 679219982 >>> >>> El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: >>> >>>> cfg.minnbchan, >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> Constantino Méndez-Bértolo >> Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) >> >> Parque Científico y Tecnológico de la UPM, Campus de Montegancedo >> >> 28223 Pozuelo de Alarcón, Madrid, SPAIN >> >> >> [image] >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Jörn M. Horschig > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Radboud University Nijmegen > Neuronal Oscillations Group > FieldTrip Development Team > > P.O. Box 9101 > NL-6500 HB Nijmegen > The Netherlands > > Contact: > E-Mail: jm.horschig at donders.ru.nl > Tel: +31-(0)24-36-68493 > Web: http://www.ru.nl/donders > > Visiting address: > Trigon, room 2.30 > Kapittelweg 29 > NL-6525 EN Nijmegen > The Netherlands > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Constantino Méndez-Bértolo Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) Parque Científico y Tecnológico de la UPM, Campus de Montegancedo 28223 Pozuelo de Alarcón, Madrid, SPAIN [image] From jm.horschig at donders.ru.nl Mon Jul 29 13:54:12 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 29 Jul 2013 13:54:12 +0200 Subject: [FieldTrip] Choose minimun time-width of clusters for cluster based permutations on freq_statistics In-Reply-To: References: <0F2493B6-9C53-43FA-8DA0-B66F9936A840@psi.ucm.es> <51F6024B.8070000@donders.ru.nl> Message-ID: <51F657E4.60001@donders.ru.nl> Dear Tino, As I said, try cfg.avgoverchan='yes' with ft_timelockstatistics, then cfg.neighbours can be anything. K>> cfg.neighbours = []; K>> cfg.avgoverchan = 'yes'; K>> [stat] = ft_timelockstatistics(cfg, timelockFIC, timelockFC); [...] using a cluster-based method for multiple comparison correction the returned probabilities and the thresholded mask are corrected for multiple comparisons the call to "ft_timelockstatistics" took 2 seconds K>> You'd still require an own statfun for what you want though ;) Best, Jörn On 7/29/2013 1:06 PM, Constantino Méndez Bértolo wrote: > Dear Jörn, > > Thanks for your response. You are sensibly confused. It is because we > wanted to do the statistics (montecarlo; correctm = cluster) with just > one channel per data/individual. [As was pointed out above: > size(Template.powspctrm) = 9 1 1 320; Template.dimord = > subj_chan_freq_time], and ft_timelockstatistics would ask me for a > neighbourstructure relenteless, while ft_freqstatistics is ok with > cfg.neighbour = [] and so clusters in time. Hence the unorthodoxy. > > I did a function that parses the mask of the already computed stat > finding '1s', determining the span and setting zeros on an arbitrary > width-criteria; which serves the purpose but it is not as ellegant as > it would be my own statfun. > > Cheers, > Tino > > > 2013/7/29 "Jörn M. Horschig" >> Dear Constantino, >> >> I'm pretty confused why you want to trick FieldTrip and put timelock data into a frequency structure. You are aware that there is a ft_timelockstatistics function that can cluster in time, aren't you? Anyway, imho cfg.minnbchan defines how many neighbouring samples another samples needs to have, and a timebin can have max. two neighbouring samples, so it does not make much sense here (and I think it really applies to channels only). >> >> The error you describe is because FT wants to compute neighbouring channels, because you did not set cfg.avgoverchan='yes'. If you do that, it will run through smoothly without an error. However, the best way for you would be to write your own statfun by making a copy of the statfun of your choice and modifying stat.stat to be 1 if the clustersize is < 10. That way, you could achieve what you want. >> >> Best, >> Jörn >> >> >> On 7/26/2013 8:55 PM, Constantino Méndez Bértolo wrote: >>> Using cfg.minnbchan = 1, 5 or 40 and cfg.neighbours = [] finds no cluster (not even with minnbchan = 1) were there was a cluster before (without cfg.minnbchan) >>> >>> Using cfg.neighbours = 'triangulation', or 'distance', with or without cfg.minnbchan computes the statistics but fails prior to compute the clusters in the randomizations >>> >>> This is the error (with neighbours) V V V >>> >>> Error in clusterstat>makechanneighbstructmat (line 519) >>> [seld] = match_str(cfg.channel, cfg.neighbours(chan).label); >>> >>> Error in clusterstat (line 59) >>> channeighbstructmat = makechanneighbstructmat(cfg); >>> >>> Error in statistics_montecarlo (line 320) >>> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >>> >>> Error in ft_freqstatistics (line 267) >>> [stat, cfg] = statmethod(cfg, dat, cfg.design); >>> >>> >>> While it seems it is minnbchan what will be helpful, we do not come up with an idea. Maybe, besides tricking fieldtrip to think we have frequency data we should also trick him to believe that points in time are channels? :) >>> >>> >>> El 26 de julio de 2013 19:54, smoratti at psi.ucm.es escribió: >>>> >>>> I think cfg.minnbchan, applies also to time bins. >>>> >>>> s >>>> >>>> ________________________________________________________ >>>> Stephan Moratti, PhD >>>> >>>> see also: http://web.me.com/smoratti/ >>>> >>>> Universidad Complutense de Madrid >>>> Facultad de Psicología >>>> Departamento de Psicología Básica I >>>> Campus de Somosaguas >>>> 28223 Pozuelo de Alarcón (Madrid) >>>> Spain >>>> >>>> and >>>> >>>> Center for Biomedical Technology >>>> Laboratory for Cognitive and Computational Neuroscience >>>> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid >>>> Campus Montegancedo >>>> 28223 Pozuelo de Alarcón (Madrid) >>>> Spain >>>> >>>> >>>> email: smoratti at psi.ucm.es >>>> Tel.: +34 679219982 >>>> >>>> El 26/07/2013, a las 18:46, Constantino Méndez Bértolo escribió: >>>> >>>>> cfg.minnbchan, >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Constantino Méndez-Bértolo >>> Laboratorio de Neurociencia Clínica, Centro de Tecnología Biomédica (CTB) >>> >>> Parque Científico y Tecnológico de la UPM, Campus de Montegancedo >>> >>> 28223 Pozuelo de Alarcón, Madrid, SPAIN >>> >>> >>> [image] >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -- >> Jörn M. Horschig >> PhD Student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Radboud University Nijmegen >> Neuronal Oscillations Group >> FieldTrip Development Team >> >> P.O. Box 9101 >> NL-6500 HB Nijmegen >> The Netherlands >> >> Contact: >> E-Mail: jm.horschig at donders.ru.nl >> Tel: +31-(0)24-36-68493 >> Web: http://www.ru.nl/donders >> >> Visiting address: >> Trigon, room 2.30 >> Kapittelweg 29 >> NL-6525 EN Nijmegen >> The Netherlands >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands From alexis.makin at liverpool.ac.uk Mon Jul 29 17:33:13 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 16:33:13 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing Message-ID: Hi I already have data which has been cleaned, filtered and artefact rejected etc. It is now .mat format (trials X electrodes X time). I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields data.label % cell-array containing strings, Nchan X 1 data.fsample % sampling frequency in Hz, single number data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M but when I try to run ft_freqanalysis(cfg, data) on this I get the following error messages: ??? Error using ==> ft_checkdata at 366 This function requires raw, comp or mvar data as input. Error in ==> ft_freqanalysis at 219 data = ft_checkdata(data, 'datatype', {'raw', 'comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? cheers, Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Mon Jul 29 17:51:38 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 29 Jul 2013 17:51:38 +0200 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: Hi Alexis, How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. Best, Eelke Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected > etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which > should be compatible with ft_freqanalysis: > > Alternatively, if you already are able to read the data into Matlab, you > can reformat that data within Matlab into a datastructure that is > compatible with FieldTrip. Raw data that is comparable with the output of > preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a > simple problem? > > Is it common to use fieldtrip functions on data which has already been > preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexis.makin at liverpool.ac.uk Mon Jul 29 17:59:33 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 16:59:33 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: <3E0B8C1F-B490-48FD-A1F6-1F9209F43E14@liv.ac.uk> data = label: {64x1 cell} fsample: 128 trials: {1x60 cell} times: {1x60 cell} On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > > Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: > Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? > > Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From alexis.makin at liverpool.ac.uk Mon Jul 29 18:03:29 2013 From: alexis.makin at liverpool.ac.uk (Alexis) Date: Mon, 29 Jul 2013 17:03:29 +0100 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: Hi, thanks for your reply, so that's what my data structure looks like. Is it common to use fieldtrip functions on data which has already been cleaned and epoched elsewhere? Alexis On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > > Op 29 jul. 2013 17:36 schreef "Alexis" het volgende: > Hi > > I already have data which has been cleaned, filtered and artefact rejected etc. > > It is now .mat format (trials X electrodes X time). > > I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: > Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields > > data.label % cell-array containing strings, Nchan X 1 > data.fsample % sampling frequency in Hz, single number > data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples > data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector > data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M > > but when I try to run ft_freqanalysis(cfg, data) on this > > I get the following error messages: > > ??? Error using ==> ft_checkdata at 366 > This function requires raw, comp or mvar data as input. > > Error in ==> ft_freqanalysis at 219 > data = ft_checkdata(data, 'datatype', {'raw', 'comp', > 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); > > How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? > > Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? > > cheers, > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From max-philipp.stenner at med.ovgu.de Mon Jul 29 18:19:48 2013 From: max-philipp.stenner at med.ovgu.de (Stenner, Max-Philipp) Date: Mon, 29 Jul 2013 16:19:48 +0000 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: <16338_1375114551_51F69537_16338_213_1_D9DA6D7F-1D2F-49F7-95B1-47F3A4453A85@liv.ac.uk> References: , <16338_1375114551_51F69537_16338_213_1_D9DA6D7F-1D2F-49F7-95B1-47F3A4453A85@liv.ac.uk> Message-ID: Hi Alexis, it may just be that ft_checkdata is unhappy with the subfields '.trials' and '.times' instead of '.trial' and '.time'. Good luck, best Max ________________________________ Von: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl]" im Auftrag von "Alexis [alexis.makin at liverpool.ac.uk] Gesendet: Montag, 29. Juli 2013 18:03 Bis: FieldTrip discussion list Betreff: Re: [FieldTrip] ft_freqanalysis without ft_preprocessing Hi, thanks for your reply, so that's what my data structure looks like. Is it common to use fieldtrip functions on data which has already been cleaned and epoched elsewhere? Alexis On 29 Jul 2013, at 16:51, Eelke Spaak wrote: Hi Alexis, How does your data structure look exactly? I.e. what does matlab display when you type 'data' at the prompt? The error message suggests that it is not yet quite in the appropriate fieldtrip format. Best, Eelke Op 29 jul. 2013 17:36 schreef "Alexis" > het volgende: Hi I already have data which has been cleaned, filtered and artefact rejected etc. It is now .mat format (trials X electrodes X time). I can follow the advice from the wiki below to make a structure which should be compatible with ft_freqanalysis: Alternatively, if you already are able to read the data into Matlab, you can reformat that data within Matlab into a datastructure that is compatible with FieldTrip. Raw data that is comparable with the output of preprocessing should consist of a structure with the fields data.label % cell-array containing strings, Nchan X 1 data.fsample % sampling frequency in Hz, single number data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M but when I try to run ft_freqanalysis(cfg, data) on this I get the following error messages: ??? Error using ==> ft_checkdata at 366 This function requires raw, comp or mvar data as input. Error in ==> ft_freqanalysis at 219 data = ft_checkdata(data, 'datatype', {'raw', 'comp', 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); How to I tell the ft_checkdata function what datatype I have? Is this a simple problem? Is it common to use fieldtrip functions on data which has already been preprocessed in another way? Or is this not advisable? cheers, Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Alexis alexis.makin at liv.ac.uk Network: www.liv.ac.uk/perception-action/ From eelke.spaak at donders.ru.nl Mon Jul 29 18:22:45 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Mon, 29 Jul 2013 18:22:45 +0200 Subject: [FieldTrip] ft_freqanalysis without ft_preprocessing In-Reply-To: References: Message-ID: 'trial' and 'time' should be singular :) Eelke Op 29 jul. 2013 18:13 schreef "Alexis" het volgende: > Hi, thanks for your reply, > > so that's what my data structure looks like. > > Is it common to use fieldtrip functions on data which has already been > cleaned and epoched elsewhere? > > Alexis > > On 29 Jul 2013, at 16:51, Eelke Spaak wrote: > > Hi Alexis, > > How does your data structure look exactly? I.e. what does matlab display > when you type 'data' at the prompt? The error message suggests that it is > not yet quite in the appropriate fieldtrip format. > > Best, > Eelke > Op 29 jul. 2013 17:36 schreef "Alexis" het > volgende: > >> Hi >> >> I already have data which has been cleaned, filtered and artefact >> rejected etc. >> >> It is now .mat format (trials X electrodes X time). >> >> I can follow the advice from the wiki below to make a structure which >> should be compatible with ft_freqanalysis: >> >> Alternatively, if you already are able to read the data into Matlab, you >> can reformat that data within Matlab into a datastructure that is >> compatible with FieldTrip. Raw data that is comparable with the output of >> preprocessing should consist of a structure with the fields >> >> data.label % cell-array containing strings, Nchan X 1 >> data.fsample % sampling frequency in Hz, single number >> data.trial % cell-array containing a data matrix for each trial (1 X Ntrial), each data matrix is Nchan X Nsamples >> data.time % cell-array containing a time axis for each trial (1 X Ntrial), each time axis is a 1 X Nsamples vector >> data.trialinfo % this field is optional, but can be used to store trial-specific information, such as condition numbers, reaction times, correct responses etc. The dimensionality is N x M >> >> >> but when I try to run ft_freqanalysis(cfg, data) on this >> >> I get the following error messages: >> >> ??? Error using ==> ft_checkdata at 366 >> This function requires raw, comp or mvar data as input. >> >> Error in ==> ft_freqanalysis at 219 >> data = ft_checkdata(data, 'datatype', {'raw', 'comp', >> 'mvar'}, 'feedback', cfg.feedback, 'hassampleinfo', 'yes'); >> >> How to I tell the ft_checkdata function what datatype I have? Is this a >> simple problem? >> >> Is it common to use fieldtrip functions on data which has already been >> preprocessed in another way? Or is this not advisable? >> >> cheers, >> >> >> Alexis >> alexis.makin at liv.ac.uk >> >> Network: www.liv.ac.uk/perception-action/ >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > Alexis > alexis.makin at liv.ac.uk > > Network: www.liv.ac.uk/perception-action/ > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From johanna.zumer at donders.ru.nl Tue Jul 30 10:27:05 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 30 Jul 2013 10:27:05 +0200 Subject: [FieldTrip] EEG source reconstruction In-Reply-To: References: Message-ID: Dear Xiao, The code doesn't look wrong at first glance. However, with beamforming, the pre-processing of the 'data' is just as important of a step, so be sure you are using the optimal time windows for your research question, and optimal frequency filtering, if desired, etc. Also, check that the units of data.hdr.elec is the same as the vol and sourcemodel. Also, is there a reason you use data_org.hdr.elec in one instance, and the data.hdr.elec in another instance? Best, Johanna 2013/7/29 陈雪 > Dear all > > I do EEG source analyse,But I use the method as the follow got strong > function connectivity from different brain areas.（eg.correlation）and > strength is similar; > I want konw the code with source reconstruction is right? > Or some stimulate can prove the code that is right. > (the VOL and sourcemode form template) > > > cfg = []; > cfg.covariance = 'yes'; > cfg.vartrllength = 2; > cfg.covariancewindow = 'all'; > timelock = ft_timelockanalysis(cfg, data); > > cfg = []; > cfg.channel = {'EEG'}; > cfg.vol = vol; > cfg.reducerank = 3; > cfg.normalize ='yes'; > cfg.elec = data_org.hdr.elec; > cfg.grid =sourcemodel; > [grid]= ft_prepare_leadfield(cfg); > > > cfg = []; > cfg.method = 'lcmv'; > cfg.vol = vol; > cfg.grid = grid; > cfg.lcmv.fixedori = 'yes'; > cfg.elec = data.hdr.elec; > cfg.lcmv.keepfilter = 'yes'; > cfg.lcmv.projectnoise = 'yes'; > source1 = ft_sourceanalysis(cfg, timelock); > > thanks in advance > xiao > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erica.boschin at queens.ox.ac.uk Tue Jul 30 16:29:27 2013 From: erica.boschin at queens.ox.ac.uk (Erica Boschin) Date: Tue, 30 Jul 2013 15:29:27 +0100 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script Message-ID: Dear Fieldtrip users, In trying to run ft_timelockanalysis I keep getting the following error: ??? Error using ==> CalcMD5 at 70 Cannot find MEX script This error should allegedly occur when the path is the same as the parent folder for the script, which is not my case. I have tried recompiling the mex files in private and src, with no luck. Has anyone ever experienced this error and if so, could point me towards a solution? I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS 10.6.8. I do not get the error if I try to run the exact same script in Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not sure whether it might be a specs issue or something else. Many thanks, Erica From johanna.zumer at donders.ru.nl Tue Jul 30 16:40:43 2013 From: johanna.zumer at donders.ru.nl (Johanna Zumer) Date: Tue, 30 Jul 2013 16:40:43 +0200 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script In-Reply-To: References: Message-ID: Dear Erica, Is the computer on which it fails a 32-bit? If so, this is a known problem: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2010 Feel free to 'cc' yourself onto this bug report. Best, Johanna 2013/7/30 Erica Boschin > Dear Fieldtrip users, > > In trying to run ft_timelockanalysis I keep getting the following error: > > ??? Error using ==> CalcMD5 at 70 > Cannot find MEX script > > This error should allegedly occur when the path is the same as the parent > folder for the script, which is not my case. I have tried recompiling the > mex files in private and src, with no luck. > > Has anyone ever experienced this error and if so, could point me towards a > solution? > > I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS > 10.6.8. I do not get the error if I try to run the exact same script in > Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not > sure whether it might be a specs issue or something else. > > Many thanks, > Erica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From erica.boschin at queens.ox.ac.uk Tue Jul 30 17:09:29 2013 From: erica.boschin at queens.ox.ac.uk (Erica Boschin) Date: Tue, 30 Jul 2013 16:09:29 +0100 Subject: [FieldTrip] Error in ft_timelockanalysis: Cannot find MEX Script In-Reply-To: References: Message-ID: <1800336A-B1AB-4093-9168-84DFA73BD82C@queens.ox.ac.uk> Dear Johanna, it is indeed a 32-bit, thanks for letting me know it's a bug. Best wishes, Erica On Jul 30, 2013, at 3:40 PM, Johanna Zumer wrote: > Dear Erica, > > Is the computer on which it fails a 32-bit? If so, this is a known problem: http://bugzilla.fcdonders.nl/show_bug.cgi?id=2010 Feel free to 'cc' yourself onto this bug report. > > Best, > Johanna > > > 2013/7/30 Erica Boschin > Dear Fieldtrip users, > > In trying to run ft_timelockanalysis I keep getting the following error: > > ??? Error using ==> CalcMD5 at 70 > Cannot find MEX script > > This error should allegedly occur when the path is the same as the parent folder for the script, which is not my case. I have tried recompiling the mex files in private and src, with no luck. > > Has anyone ever experienced this error and if so, could point me towards a solution? > > I am running Fieldtrip in Matlab 2010a, on a Mac Intel Core Duo running OS 10.6.8. I do not get the error if I try to run the exact same script in Matlab2012b on a Quad-Core Intel Xeon Mac running Mac OS 10.6.8. I'm not sure whether it might be a specs issue or something else. > > Many thanks, > Erica > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From ggonesc at upo.es Wed Jul 31 09:05:34 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 09:05:34 +0200 Subject: [FieldTrip] ancova for sources analysis Message-ID: <167095db43e3fd69.51f8d35e@upo.es> Dear fieldtrip experts, I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? Many thanks in advanced, Gabriel -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Wed Jul 31 09:55:58 2013 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Wed, 31 Jul 2013 09:55:58 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> References: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: <51F8C30E.8010004@donders.ru.nl> Hi Gabriel, hmm, you could try to use ft_regressconfound, see http://www.ncbi.nlm.nih.gov/pubmed/23246857 I am not aware of other functionality in FT, but that should do pretty much what you want . Best, Jörn On 7/31/2013 9:05 AM, Gabriel Gonzalez Escamilla wrote: > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the > effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Jörn M. Horschig PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen Neuronal Oscillations Group FieldTrip Development Team P.O. Box 9101 NL-6500 HB Nijmegen The Netherlands Contact: E-Mail: jm.horschig at donders.ru.nl Tel: +31-(0)24-36-68493 Web: http://www.ru.nl/donders Visiting address: Trigon, room 2.30 Kapittelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Wed Jul 31 09:56:02 2013 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Wed, 31 Jul 2013 09:56:02 +0200 (CEST) Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Dear Gabriel, This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? Yours, Arjen ----- Oorspronkelijk bericht ----- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > Dear fieldtrip experts, > I'm wondering if it is possible to perform an ancova or to remove the > effect of a covariate in a source analysis? > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Wed Jul 31 09:58:39 2013 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Wed, 31 Jul 2013 09:58:39 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <167095db43e3fd69.51f8d35e@upo.es> References: <167095db43e3fd69.51f8d35e@upo.es> Message-ID: Dear Gabriel, To do a full ANCOVA, you would have to write your own 'statfun' to use in the statistics routines. This is not super-hard to do, but is also far from trivial. However, there might be a much easier solution. There is a function called ft_regressconfound which linearly regresses out a 'confound' or covariate from raw, freq, or source data. Would it be an option to use this function first, and then do ft_sourcestatistics on the cleaned data? Note that ft_regressconfound only supports one value per trial, per confound; so the covariates cannot be fully time-resolved. Best, Eelke On 31 July 2013 09:05, Gabriel Gonzalez Escamilla wrote: > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect > of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From ggonesc at upo.es Wed Jul 31 10:55:44 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 10:55:44 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> References: <167095db43e3fd69.51f8d35e@upo.es> <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <23400797220a159c.51f8ed30@upo.es> Thanks for your quick ans Arjen, It seems to do what I want, I'm trying to correct grandaveraged source data in which my data is a 1xNsubjs structure, each subject containing 29232 positions. I'm wondering how would be the correct way to input the age of each subject as a counfound. I have tried to set a structure, were each field was the age of each subject, but the ft_regressconfound seems not to work with structures, so I change it. I've also tried to set as a double array (1xNsubjects), but says that "the number of my confound matrix does not match with the number of trials/subjects"; to which I have input the cfg.counfound as a double array (Nsubjsx1), but now I'm getting an error saying that there is not an existing field in the data.trial structure called "pow". Is there something missing on my data? How can I get that pow field into my data comming from ft_grandaverage? Best Regards, Gabriel ----- Mensaje original ----- De: "Stolk, A." Fecha: Miércoles, 31 de Julio de 2013, 10:04 am Asunto: Re: [FieldTrip] ancova for sources analysis A: FieldTrip discussion list p { margin: 0; } > Dear Gabriel, > > This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). > > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? > > Yours, > Arjen > ----------------------------------------------------------- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip --------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggonesc at upo.es
http://www.upo.es/neuroaging/es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From ggonesc at upo.es Wed Jul 31 11:56:33 2013 From: ggonesc at upo.es (Gabriel Gonzalez Escamilla) Date: Wed, 31 Jul 2013 11:56:33 +0200 Subject: [FieldTrip] ancova for sources analysis In-Reply-To: <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> References: <167095db43e3fd69.51f8d35e@upo.es> <1763660954.2174368.1375257362812.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <2264a36963356fbe.51f8fb71@upo.es> Thank you all for your responses. The last problem I did wrote is now solved, see below. I had a field called 'stat' instead of the 'pow', I'm guessing this field was set before, so, now i'm using this field as if it was the 'pow' I needed and it's working, Is that OK?  Now it takes me to the next question, my data has the avg field, and it says that will update the descriptives but that the 'method' is missing, is this update necessary? or can I just skeep it? Many thanks in advanced, Gabriel ----- Mensaje original ----- De: "Stolk, A." Fecha: Miércoles, 31 de Julio de 2013, 10:04 am Asunto: Re: [FieldTrip] ancova for sources analysis A: FieldTrip discussion list p { margin: 0; } > Dear Gabriel, > > This page demonstrates how to remove contributions to the data originating from head movement, but one could as well follow the same principle for any other type of covariate (e.g. eye movement related activity). > > http://fieldtrip.fcdonders.nl/example/how_to_incorporate_head_movements_in_meg_analysis? > > Yours, > Arjen > ----------------------------------------------------------- > Van: "Gabriel Gonzalez Escamilla" > Aan: "fieFieldTrip discussion list" > Verzonden: Woensdag 31 juli 2013 09:05:34 > Onderwerp: [FieldTrip] ancova for sources analysis > > Dear fieldtrip experts, > > I'm wondering if it is possible to perform an ancova or to remove the effect of a covariate in a source analysis? > > Many thanks in advanced, > Gabriel > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip --------------------------
PhD. student Gabriel González-Escamilla
Laboratory of Functional Neuroscience
Department of Physiology, Anatomy, and Cell Biology
University Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Seville
- Spain -

Email: ggonesc at upo.es
http://www.upo.es/neuroaging/es/ -------------- next part -------------- An HTML attachment was scrubbed... URL: