From max.taubert at gmail.com Sun May 1 15:48:13 2011 From: max.taubert at gmail.com (Max T.) Date: Sun, 1 May 2011 15:48:13 +0200 Subject: [FieldTrip] Plotting Dipoles Message-ID: Dear all, I'd like to visualize the results of ft_dipolefitting, sadly I've got no individual MRIs. Is there any function like ft_sourceplot that can handle ft_dipolefitting-results, maybe using a template brain? Besides this, is there any function that can transform my Unit Sphere-coordinates into Talairach space? And is it possible to apply the 'adaptive spatial filter' if I dont want to use a Beamformer? Thanks in advance Max Taubert From m.severens at maartenskliniek.nl Mon May 2 13:57:17 2011 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 2 May 2011 13:57:17 +0200 Subject: [FieldTrip] adding lines in multiplot TFR Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> Dear fieldtrippers I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? Thanks in advance Best Marianne Severens Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3 6522 JV NIJMEGEN Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From jm.horschig at donders.ru.nl Mon May 2 14:10:11 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 May 2011 14:10:11 +0200 Subject: [FieldTrip] adding lines in multiplot TFR In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> Message-ID: <4DBE9F23.8070600@donders.ru.nl> Hi Marianne, Adding vertical lines to annotate, for example, events is not possible using ft_multiplot_XXX afaik. A similar feature is added in ft_databrowser, which however does only work for two-dimensional data (amplitude x time). One way around would be to filter your data in the desired frequency range and then use ft_databrowser. The function, however, still lacks some functionality and compatibility. Should you encounter any strange problems, feel free to contact me and we (the FT developer team) will try to improve the databrowser according to your experiences and wishes. Another, slightly less elegant way to answer your question is the following: Rutger from your group changed a fieldtrip method for his personal purposes. Unselfishly, he called the function rutgerplot_TFR. In this function, he added horizontal lines to annotate specific frequency bands. You can maybe ask him to re-write this hack to add vertical lines to annotate the events you are interested in. Hope this helps! Best, Jörn On 5/2/2011 1:57 PM, Severens, Marianne wrote: > Dear fieldtrippers > > I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. > I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? > > Thanks in advance > Best Marianne Severens > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3 > 6522 JV NIJMEGEN > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands From m.severens at maartenskliniek.nl Mon May 2 14:34:56 2011 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 2 May 2011 14:34:56 +0200 Subject: [FieldTrip] adding lines in multiplot TFR In-Reply-To: <4DBE9F23.8070600@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl>, <4DBE9F23.8070600@donders.ru.nl> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B71@smkexch02.maartenskliniek.nl> Hi Jörn Thanks for your quick reply! The plots need to be TFR plots, with several frequency bins, so I think the databrowser is not really appropriate for this. I'll try to modify Rutger's solution to make the lines vertical! Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Jörn M. Horschig [jm.horschig at donders.ru.nl] Sent: Monday, May 02, 2011 2:10 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] adding lines in multiplot TFR Hi Marianne, Adding vertical lines to annotate, for example, events is not possible using ft_multiplot_XXX afaik. A similar feature is added in ft_databrowser, which however does only work for two-dimensional data (amplitude x time). One way around would be to filter your data in the desired frequency range and then use ft_databrowser. The function, however, still lacks some functionality and compatibility. Should you encounter any strange problems, feel free to contact me and we (the FT developer team) will try to improve the databrowser according to your experiences and wishes. Another, slightly less elegant way to answer your question is the following: Rutger from your group changed a fieldtrip method for his personal purposes. Unselfishly, he called the function rutgerplot_TFR. In this function, he added horizontal lines to annotate specific frequency bands. You can maybe ask him to re-write this hack to add vertical lines to annotate the events you are interested in. Hope this helps! Best, Jörn On 5/2/2011 1:57 PM, Severens, Marianne wrote: > Dear fieldtrippers > > I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. > I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? > > Thanks in advance > Best Marianne Severens > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3 > 6522 JV NIJMEGEN > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3 6522 JV NIJMEGEN Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From andrecravo at gmail.com Mon May 2 14:38:37 2011 From: andrecravo at gmail.com (Andre Cravo) Date: Mon, 2 May 2011 09:38:37 -0300 Subject: [FieldTrip] QuikCap 128 NSL layout In-Reply-To: References: Message-ID: Hello, I am collecting EEG data from a SynAmps RT 128 channels. I am using a QuikCap NSL, which although has 128 electrodes, does not follow standard 10-20 localisation. I'm trying to create a layout to visualise my data using the template fiducials of the cap. My script currently looks something like this: cfg =[]; cfg.elecfile='QuikCap_128_NSL.sfp' cfg.rotate=0; cfg.projection='polar' lay=ft_prepare_layout(cfg); ft_layoutplot(cfg) However, the electrodes seems to be shifted towards the back of the head. The layout I get can be seen in the FieldTrip_Layout figure attached. I have tried to realign the electrodes (using ft_electroderealign), but I get similar results. Has anyone ever had a similar problem? Please find attached the 'QuikCap_128_NSL.sfp' file with the fiducials and a .png figure of the electrode positions taken from NeuroScan's website. Thanks in advance for the help. Andre Cravo --- University of Sao Paulo-Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QuikCap_128_NSL.sfp Type: application/octet-stream Size: 3888 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: neuroscan.png Type: image/png Size: 282038 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FieldTrip_Layout.png Type: image/png Size: 12814 bytes Desc: not available URL: From cmuehl at gmail.com Mon May 2 17:48:42 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Mon, 2 May 2011 17:48:42 +0200 Subject: [FieldTrip] Call for Papers: Affective BCI Workshop, Memphis, USA Message-ID: ** Call for Papers ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuroergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 15th of June: Workshop papers due 1st of July: Notification of Acceptance 18th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From r.oostenveld at donders.ru.nl Tue May 3 10:20:05 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 3 May 2011 10:20:05 +0200 Subject: [FieldTrip] changed channel names for EGI data format from 'e' to 'E' Message-ID: <4522B5B9-579C-4AFF-A2CF-449420DAFFAF@donders.ru.nl> Dear fieldtrip users working on EGI data, The EGI system does not have well described channel names, but most software deals with it by prefixing the EGI channel names with an 'E', e.g. E1, E2 ... E256 It turned out that there were some inconsistent definitions whether it should be a lowercase 'e' or an uppercase 'E'. After consulting with some EGI experts (Joseph Dien, Catherine Poulsen, Ingrid Nieuwenhuis), I have just changed fieldtrip to use an uppercase 'E' consistently throughout the code. The EGI layouts (*.sfp files) also use this uppercase definition. The consequence is that string comparisons between channels like 'e1' and 'E1' might fail and that in the analysis (e.g. grandaveraging data with mixed case labels) the identical channels are not recognized/matched to each other. If you encounter problems like these, you should fix them by converting the channel labels for data that you have stored on disk in *.mat files to uppercase. That can be easily done with the "upper" function in MATLAB for example like this: data.label = upper(data.label); timelock.label = upper(timelock.label); freq.label = upper(freq.label); freq.labelcmb = upper(freq.labelcmb); Sorry for the inconvenience that this causes, hopefully in the future with the consistent definition of the channel labels we won't have problems like this any more. best regards, Robert From annajafarpour at gmail.com Tue May 3 19:40:20 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 18:40:20 +0100 Subject: [FieldTrip] tf online tutorial is missed Message-ID: Hello all, In the Fieldtrip online documentation, the tutorial about tf analysis is missed. Where else can I find a copy of the tutorial? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue May 3 19:55:44 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 3 May 2011 19:55:44 +0200 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Hello Anna, To be honest, I have no idea what happened, or why the time-frequency tutorial page was suddenly blank. However, I seem to have fixed the issue by clearing the page's contents, and re-adding it. I'll look into the issue further; but for now, your problem is solved. Best, Eelke 2011/5/3 Anna Jafarpour : > Hello all, > > In the Fieldtrip online documentation, the tutorial about tf analysis is > missed. Where else can I find a copy of the tutorial? > > Best, > Anna > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From annajafarpour at gmail.com Tue May 3 20:04:57 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 19:04:57 +0100 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Thank you :) On Tue, May 3, 2011 at 6:55 PM, Eelke Spaak wrote: > Hello Anna, > > To be honest, I have no idea what happened, or why the time-frequency > tutorial page was suddenly blank. However, I seem to have fixed the > issue by clearing the page's contents, and re-adding it. I'll look > into the issue further; but for now, your problem is solved. > > Best, > Eelke > > 2011/5/3 Anna Jafarpour : > > Hello all, > > > > In the Fieldtrip online documentation, the tutorial about tf analysis is > > missed. Where else can I find a copy of the tutorial? > > > > Best, > > Anna > > > > _______________________________________________ > > 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 annajafarpour at gmail.com Tue May 3 21:10:48 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 20:10:48 +0100 Subject: [FieldTrip] trial selection Message-ID: Dear All, I am sorry if this is an FAQ; the online FAQ is not accessible. Is there any function for selecting trials according to the trialinfo? Or is there any function for copying specific trials (with its configuration) into a new variable? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue May 3 21:39:15 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 3 May 2011 21:39:15 +0200 (CEST) Subject: [FieldTrip] trial selection In-Reply-To: Message-ID: <1167814753.23605.1304451555946.JavaMail.root@sculptor.zimbra.ru.nl> Hi Anna, Have a look at the help of ft_redefinetrial. Possibly the configuration option cfg.trials is the one you're looking for. Yours, Arjen   ----- "Anna Jafarpour" schreef: > Van: "Anna Jafarpour" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 3 mei 2011 21:10:48 > Onderwerp: [FieldTrip] trial selection > > Dear All, > I am sorry if this is an FAQ; the online FAQ is not accessible. > Is there any function for selecting trials according to the trialinfo? Or is there any function for copying specific trials (with its configuration) into a new variable? > > Best, > Anna > > _______________________________________________ > 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 inbalots at gmail.com Wed May 4 14:25:30 2011 From: inbalots at gmail.com (Inbal Lots) Date: Wed, 4 May 2011 15:25:30 +0300 Subject: [FieldTrip] Question about trl Message-ID: Hello my name is Inbal and I wanted to ask about trl. Say I define trl myself, as following: trl = [1000 , 1600 , -100]; Lets assume that the sampling rate is 1000Hz trl defines, as far as I understand, the onset at sample #1000, the data start of the data to analyze , before onset, at sample #900 and the end of the data to analyze at sample # 1500. Is that so? Thanks Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Wed May 4 14:56:59 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Wed, 4 May 2011 14:56:59 +0200 (CEST) Subject: [FieldTrip] Question about trl In-Reply-To: <244f01cc0a5a$2d05a1e0$8710e5a0$@vanpelt@fcdonders.ru.nl> Message-ID: <915523278.28822.1304513819890.JavaMail.root@sculptor.zimbra.ru.nl> Hello Inbal, That is not quite correct. Say you define a trial as cfg.trl=[1000 1600 -100], then “-100” is the offset (in samples) of your time axis. So, for this trial, you will get a dataset of 600 samples (or also ms in your example case) length (=1600-1000), of which sample 101 will be defined as t=0s (-100 meaning that the 1 st sample of your trial is -100 samples from t=0). So, the third column in cfg.trl doesn’t affect which part of the data will de used to define the trial (samples 1000 to 1600 will always be read from your data), but only affects the position of t=0 on the time-axis of your trial (data.time). Best, Stan Stan van Pelt, PhD Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 68495 Fax: (+31) (0)24 36 10989 > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Inbal Lots > Sent: Wednesday, May 04, 2011 2:26 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Question about trl Hello > my name is Inbal and I wanted to ask about trl. > Say I define trl myself, as following: > trl = [1000 , 1600 , -100]; > Lets assume that the sampling rate is 1000Hz > trl defines, as far as I understand, the onset at sample #1000, the data start of the data to analyze , before onset, at sample #900 and the end of the data to analyze at sample # 1500. Is that so? > > Thanks > Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko at nyu.edu Wed May 4 15:17:49 2011 From: akiko at nyu.edu (Akiko Ikkai) Date: Wed, 04 May 2011 09:17:49 -0400 Subject: [FieldTrip] overlaying beamformer results to native/normalized space Message-ID: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> I sent a below message to the list last night, but it was bounced back. I'm trying from another email account. My apologies if this was duplicate... I'm trying to run beamformer analysis on my MEG data, using DICS, and having difficulty visualizing meaningful results. I was able to align MRI image to MEG sensors; after segmentation, ft_prepare_singleshell and ft_prepare_leadfield, plotting ft_data.grad and volume model confirms that they align reasonably. However, using data.grad, grid, and vol to run ft_sourceanalysis, and ft_sourceinterpolate with MRI (in ctf coordinate system and aligned to MEG sensors) somehow distorts the alignment, and the new volume model does not resemble the original. I'm assuming that, after ft_sourceinterpolate, if I segment source_interpolated.anatomy and run ft_prepare_singleshell and ft_prepare_leadfield, it should align with MEG sensors, just as the initial volume model aligned with MEG sensors... or am I making too much of an assumption here? Because of the misalignment, output data of ft_sourceinterpolate with "anatomy" and "avg.pow" does not agree with topoplot (run ft_freqanalysis on the same dataset). If anyone could explain why this alignment distortion might be happening during ft_sourceanalysis and/or ft_sourceinterpolate, I'd really appreciate it. Thanks in advance, Akiko -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 From ting.ac at gmail.com Wed May 4 15:56:57 2011 From: ting.ac at gmail.com (Allison Connolly) Date: Wed, 4 May 2011 08:56:57 -0500 Subject: [FieldTrip] error using spm_slice_vol Message-ID: Hi all, I am trying to segment an mri volume using. When I call ft_read_mri('filename'), I get an error that says: ??? Error using ==> spm_slice_vol at 28 spm_slice_vol.c not compiled - see spm_MAKE.sh Error in ==> spm_read_vols at 35 Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 p]),V(i).dim(1:2),0); Error in ==> ft_read_mri at 97 img = spm_read_vols(hdr); I tried installing the most up to date version of fieldtrip and I still get the same error. Can someone help me? -Allison -------------- next part -------------- An HTML attachment was scrubbed... URL: From annajafarpour at gmail.com Wed May 4 16:03:18 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Wed, 4 May 2011 15:03:18 +0100 Subject: [FieldTrip] Multivariate analysis of MEG data Message-ID: Hi, I am trying to run an SVM on a data (2 X 60 rpt 274 chan 1 freq 41 timep) using Fieltrip 20110420. But it gives an error and looks for ft_mv_standardizer. I cannot find this function anywhere (I set-pathed the multivariate folder as well). What is the problem? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed May 4 22:24:40 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 May 2011 22:24:40 +0200 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Dear wiki visitors, There were some issues on the fieldtrip wiki with pages suddenly displaying as empty. It turned out that it was due to a full hard-disk in our webserver. The problem has been resolved and now everything should work smoothly again. best regards, Robert On 3 May 2011, at 20:04, Anna Jafarpour wrote: > Thank you :) > > On Tue, May 3, 2011 at 6:55 PM, Eelke Spaak wrote: > Hello Anna, > > To be honest, I have no idea what happened, or why the time-frequency > tutorial page was suddenly blank. However, I seem to have fixed the > issue by clearing the page's contents, and re-adding it. I'll look > into the issue further; but for now, your problem is solved. > > Best, > Eelke > > 2011/5/3 Anna Jafarpour : > > Hello all, > > > > In the Fieldtrip online documentation, the tutorial about tf analysis is > > missed. Where else can I find a copy of the tutorial? > > > > Best, > > Anna > > > > _______________________________________________ > > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekanal at cmu.edu Thu May 5 00:05:54 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Wed, 4 May 2011 18:05:54 -0400 Subject: [FieldTrip] ft_channelselection fails with negation and regex matching Message-ID: <710C0AC3-5C40-4746-96FC-FBB2D5D1979F@cmu.edu> Hello fieldtrip - We have a Elekta Neuromag 306 scanner, and I'm trying to select only the gradiometers. The magnetometers are labeled 'MEGxxx1', where x can be any number, and the gradiometers are either 'MEGxxx2' or 'MEGxxx3'. However, using ft_channelselection results in the following error: ~~~~ >> ft_channelselection({'all','-STI*','-MEG*1'}, cfg.hdr.label) ??? Matrix index is out of range for deletion. Error in ==> ft_channelselection at 287 channel([ ~~~~ This error is somewhat complex, as I was able to determine that ft_channelselection recursively calls itself a number of times while running, and I was unable to figure out what is causing this problem. Any help would be appreciated. Thanks! Eliezer Kanal -------------------- Eliezer Kanal, Ph.D. Postdoctoral Fellow Center for the Neural Basis of Cognition Carnegie Mellon University 4400 Fifth Ave, Suite 110A Pittsburgh PA 15213 P: 412-268-4115 F: 412-268-5060 From a.stolk at fcdonders.ru.nl Thu May 5 09:54:53 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 5 May 2011 09:54:53 +0200 (CEST) Subject: [FieldTrip] ft_channelselection fails with negation and regex matching In-Reply-To: <710C0AC3-5C40-4746-96FC-FBB2D5D1979F@cmu.edu> Message-ID: <543079.33508.1304582093866.JavaMail.root@sculptor.zimbra.ru.nl> Hi Kanal, I've managed to replicate your bug with MEG data and we will try to sort this out. Yours, Arjen ----- "Kanal Eliezer" schreef: > Van: "Kanal Eliezer" > Aan: "Email FieldTrip project discussion list for the" > Verzonden: Donderdag 5 mei 2011 00:05:54 > Onderwerp: [FieldTrip] ft_channelselection fails with negation and regex matching > > Hello fieldtrip - > > We have a Elekta Neuromag 306 scanner, and I'm trying to select only > the gradiometers. The magnetometers are labeled 'MEGxxx1', where x can > be any number, and the gradiometers are either 'MEGxxx2' or 'MEGxxx3'. > However, using ft_channelselection results in the following error: > > ~~~~ > >> ft_channelselection({'all','-STI*','-MEG*1'}, cfg.hdr.label) > ??? Matrix index is out of range for deletion. > > Error in ==> ft_channelselection at 287 > channel([ > ~~~~ > > This error is somewhat complex, as I was able to determine that > ft_channelselection recursively calls itself a number of times while > running, and I was unable to figure out what is causing this problem. > Any help would be appreciated. Thanks! > > Eliezer Kanal > > > -------------------- > Eliezer Kanal, Ph.D. > Postdoctoral Fellow > Center for the Neural Basis of Cognition > Carnegie Mellon University > 4400 Fifth Ave, Suite 110A > Pittsburgh PA 15213 > P: 412-268-4115 > F: 412-268-5060 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From julian.keil at gmail.com Thu May 5 14:15:02 2011 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 5 May 2011 14:15:02 +0200 Subject: [FieldTrip] cfg.maskparameter in ft_multiplotER Message-ID: <06AC35D0-BE3D-4B96-B67F-3E1B64DBAE22@gmail.com> Hi all, i have a question regarding the mask-option in ft_multiplotER (and singleplotER). After the montecarlo statistic with holm-correction, I get the following data structure: stats = prob: [145x679 double] mask: [145x679 double] stat: [145x679 double] ref: [145x679 double] dimord: 'chan_time' label: {145x1 cell} time: [1x679 double] cfg: [1x1 struct] I then use these options to plot the results: cfg=[]; cfg.interactive='yes'; cfg.layout='4D148.lay'; cfg.zparam='stat'; cfg.maskparameter='mask'; figure;ft_multiplotER(cfg,stats); Unfortunately, I get the error message: ??? Error using ==> ft_multiplotER at 528 data in cfg.maskparameter should be vector with one value per channel I am a bit confused, as this used to work fine with an older version of fieldtrip (fieldtrip-20110113). Can anyone explain to me how to handle the mask-option. I already tried to reduce the mask-matrix to a one-value-per channel vector, but this produces the error: ??? Attempt to reference field of non-structure array. Error in ==> ft_multiplotER at 527 if min(size(datmask)) ~= 1 || max(size(datmask)) ~= length(data.label) Maybe I missed some important changes in a recent fieldtrip-update.... Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Thu May 5 23:55:32 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Thu, 05 May 2011 14:55:32 -0700 Subject: [FieldTrip] fieldtrip2eeglab Message-ID: <4DC31CD4.6070508@berkeley.edu> Hi, Does a fieldtrip2eeglab script exist, to transform a Matlab structure generated by FieldTrip into a Matlab struct that EEGlab can swallow? I know the reverse does exist (eeglab2fieldtrip). I need to get some raw data (egi_mff dataformat, which is not implemented in EEGlab yet as far as I know) into EEGlab. Or if anyone has written some code that might do the trick, that would be very much appreciated as well! Thanks! Ingrid -- Ingrid Nieuwenhuis PhD Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From Maarten.van-Casteren at mrc-cbu.cam.ac.uk Fri May 6 14:10:13 2011 From: Maarten.van-Casteren at mrc-cbu.cam.ac.uk (Maarten van-Casteren) Date: Fri, 6 May 2011 12:10:13 +0000 Subject: [FieldTrip] Problem with user specified trial function Message-ID: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> Hi, I've just started to use Fieldtrip and I don't have much experience with Matlab, so I could just be making a stupid mistake, but I found some very strange behavious when I tried to specify my own trailfunction. I started from the example given on the tutorial pages of the wiki. I've indicated the line of interest with an additional '->'. This is what I used: for i=1:length(event) if strcmp(event(i).type, cfg.trialdef.eventtype) % it is a trigger, see whether it has the right value if ismember(event(i).value, cfg.trialdef.eventvalue) % add this to the trl definition begsample = event(i).sample - cfg.trialdef.prestim*hdr.Fs; endsample = event(i).sample + cfg.trialdef.poststim*hdr.Fs - 1; offset = -cfg.trialdef.prestim*hdr.Fs; trigger = event(i).value; % remember the trigger (=condition) for each trial -> trl(end+1, :) = [round([begsample endsample offset]) trigger]; end end end When I use it like this it will clip all sample and offset values at 0 - 65536, that is the limits of an unsigned integer. I had to change the actual line that appends the trial to this to make it work: trl(end+1, :) = [double(begsample) double(endsample) double(offset) double(trigger)]; All values are shown by the debugger as doubles anyway, so why this explicit conversion is needed is completely beyond me. Does anyone of you know what is going on? I already asked one of the local Matlab gurus, but he was even more amazed than me... Thanks, Maarten -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri May 6 14:31:24 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 06 May 2011 14:31:24 +0200 Subject: [FieldTrip] Problem with user specified trial function In-Reply-To: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> References: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> Message-ID: <4DC3EA1C.4080606@donders.ru.nl> Hi Maarten, no idea what might go wrong there (for me your code snippet works fine). Anyway, you could try to first round cfg.trialdef.prestim*hdr.Fs (same for poststim) outside the loop and store them as local variables and then continue without having to round in every single iteration for every single trial-def, e.g.: trloff = round(-cfg.trialdef.prestim*hdr.Fs); trldur = round((cfg.trialdef.poststim+cfg.trialdef.prestim)*hdr.Fs) - 1; % that's from trialfun_general I bet this will make a difference, although it should of course not. Maybe someone else can confirm the error with your code snippet... Best, Jörn On 5/6/2011 2:10 PM, Maarten van-Casteren wrote: > > Hi, > > I've just started to use Fieldtrip and I don't > > have much experience with Matlab, so I could > > just be making a stupid mistake, but I found > > some very strange behavious when I tried to > > specify my own trailfunction. > > I started from the example given on the tutorial > > pages of the wiki. I've indicated the line of interest > > with an additional '->'. This is what I used: > > for i=1:length(event) > > if strcmp(event(i).type, cfg.trialdef.eventtype) > > % it is a trigger, see whether it has the right value > > if ismember(event(i).value, cfg.trialdef.eventvalue) > > % add this to the trl definition > > begsample = event(i).sample - cfg.trialdef.prestim*hdr.Fs; > > endsample = event(i).sample + cfg.trialdef.poststim*hdr.Fs - 1; > > offset = -cfg.trialdef.prestim*hdr.Fs; > > trigger = event(i).value; % remember the trigger > (=condition) for each trial > > -> trl(end+1, :) = [round([begsample endsample offset]) trigger]; > > end > > end > > end > > When I use it like this it will clip all sample and > > offset values at 0 -- 65536, that is the limits of an > > unsigned integer. I had to change the actual line > > that appends the trial to this to make it work: > > trl(end+1, :) = [double(begsample) double(endsample) double(offset) > double(trigger)]; > > All values are shown by the debugger as doubles > > anyway, so why this explicit conversion is needed > > is completely beyond me. > > Does anyone of you know what is going on? > > I already asked one of the local Matlab gurus, > > but he was even more amazed than me... > > Thanks, > > Maarten > > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From fedeletommaso at yahoo.it Fri May 6 17:28:48 2011 From: fedeletommaso at yahoo.it (tommaso fedele) Date: Fri, 6 May 2011 16:28:48 +0100 (BST) Subject: [FieldTrip] FT_analysis of the average vs average(FT_analysis(single trials)) Message-ID: <686364.21106.qm@web28608.mail.ukl.yahoo.com> Hi all, I want to test if some component that I observe in the average of my ERP signal are phase locked to the stimulus. In oder to do so I compare 1. TFR_averaged_signal = ft_freqanalysis(cfg, averaged_signal) 2. TFR_singletrials_signal = ft_freqanalysis(cfg, singletrials_signal) with the first structure TFR_averaged_signal everything is fine, and I get my nice TF plot. with the second I should average through "trials". Is there a function for that? Or, is it correct to proceed plotting the average of TFR_singletrials_signal.powspctrm through the "trials-matrix dimension"? Thanks Tommaso -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon May 9 12:13:40 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 May 2011 12:13:40 +0200 Subject: [FieldTrip] fieldtrip2eeglab In-Reply-To: <4DC31CD4.6070508@berkeley.edu> References: <4DC31CD4.6070508@berkeley.edu> Message-ID: <45F6D404-F8C3-4339-AE25-25E52C8D2598@donders.ru.nl> Hi Ingrid, I searched my hard disk and found the attached file. Note that it is a very old file (last modified 2006) and I don't know whether the "EEG" structure is still like this, but it may help you get started. best, Robert On 5 May 2011, at 23:55, Ingrid Nieuwenhuis wrote: > Hi, > > Does a fieldtrip2eeglab script exist, to transform a Matlab > structure generated by FieldTrip into a Matlab struct that EEGlab > can swallow? I know the reverse does exist (eeglab2fieldtrip). I > need to get some raw data (egi_mff dataformat, which is not > implemented in EEGlab yet as far as I know) into EEGlab. Or if > anyone has written some code that might do the trick, that would be > very much appreciated as well! > > Thanks! > Ingrid -------------- next part -------------- A non-text attachment was scrubbed... Name: fieldtrip2eeglab.m Type: application/octet-stream Size: 1094 bytes Desc: not available URL: -------------- next part -------------- From jstout211 at yahoo.com Mon May 9 22:12:15 2011 From: jstout211 at yahoo.com (Jeff Stout) Date: Mon, 9 May 2011 13:12:15 -0700 (PDT) Subject: [FieldTrip] Leadfield calculations result in NaNs Message-ID: <102170.78349.qm@web113519.mail.gq1.yahoo.com> Hi,  I am having trouble generating leadfields for source analysis.  I am using data from a 4D magnetometer system (Magnes 3600), at St. Louis University. The data is averged time domain data.  The volume conductor is a single shell model generated from the headshape file(~4000 vert. and 8000 triangles).  I have vizualized the volume conductor, sensors, and "inside" grid and they appear to be in the correct locations relative to each other.  I have performed this analysis using the default source space for 4D ('m') and I have tried it scaling the headshape and sensors into cm to conform with the ctf source space.   Below is part of my code and the warning thrown by matlab.  After the calculation of the leadfields, it is apparent that they are all NaN's, so I am unable to generate source activations. cfg = [];cfg.headshape = shape;shape.pnt = shape.pnt*100;shape.unit  = 'cm';[vol,cfg] = ft_prepare_singleshell(cfg) cfg                 = [];cfg.grad            = avg.grad; cfg.grad.pnt = cfg.grad.pnt*100;cfg.grad.unit  = 'cm';cfg.vol             = vol;cfg.sourceunits = 'cm';cfg.coordsys   = 'ctf';cfg.reducerank      ='no';  cfg.channel         = {'MEG'};cfg.grid.resolution = 2[vol, sens] = ft_prepare_vol_sens(vol, cfg.grad)[grid] = ft_prepare_leadfield(cfg)    >> [grid] = ft_prepare_leadfield(cfg)using headmodel specified in the configurationusing gradiometers specified in the configurationcomputing surface normalsWarning: Matrix is singular, close to singular or badly scaled.   <<<<<<<<<<         Results may be inaccurate. RCOND = NaN. > In forward/private/meg_ini>getcoeffs at 111  In forward/private/meg_ini at 53  In ft_prepare_vol_sens at 275  In fieldtrip-20110507/private/prepare_headmodel at 114  In ft_prepare_leadfield at 150creating dipole grid based on automatic 3D grid with specified resolution3528 dipoles inside, 0 dipoles outside brainmaking tight grid3528 dipoles inside, 0 dipoles outside braincomputing leadfieldcomputing leadfield 1/3528computing leadfield 2/3528computing leadfield 3/3528computing leadfield 4/3528 ...... The leadfield data generated is a matrix of NaN's, which appear to be an issue when evaluating bas and gradbas in the get_coeffs subfunction  [bas,gradbas]=legs(x1,n1,order,scale). Does anyone know how to resolve this issue? Any help will be greatly appreciated. Thanks, Jeff Stout Open in Google Docs ViewerOpen link in new tabOpen link in new windowOpen link in new incognito windowDownload fileCopy link addressEdit PDF File on PDFescape.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew at psych.columbia.edu Tue May 10 00:37:39 2011 From: matthew at psych.columbia.edu (Matthew Davidson) Date: Mon, 9 May 2011 18:37:39 -0400 Subject: [FieldTrip] Human neurophysiology analysis tech posting in San Diego Message-ID: Human Neurophysiology Analysis Technician – To assist a team of experienced neurophysiologists conduct language, memory, sleep and developmental studies in humans with MEG and intracranial recordings. MEG localization will use structural MRI constraints and functional MRI bias. Intracranial recordings include microelectrode arrays, unit-recordings, and laminar current source density analysis. The candidate must have high abstract intelligence in order to rapidly acquire different techniques, modify them as necessary, and recognize inconsistent results. Prior expertise with MatLab would be very useful, and some knowledge of neuroscience is expected. Collaborate with a large, talented and friendly group of scientists, programmers and technicians engaged in multimodal brain research. The position is available starting immediately, with the expectation that you would remain for at least 2 years, but it is subject to annual review and continuation of grant funding. Everyone is welcome to apply regardless of gender, ethnicity, or other irrelevancies. Please contact Eric Halgren, Ph.D., Multimodal Imaging Laboratory, University of California at San Diego,ehalgren at ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 10 08:36:51 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 10 May 2011 08:36:51 +0200 Subject: [FieldTrip] Leadfield calculations result in NaNs In-Reply-To: <102170.78349.qm@web113519.mail.gq1.yahoo.com> References: <102170.78349.qm@web113519.mail.gq1.yahoo.com> Message-ID: Dear Jeff, From what you describe I don't really know what's going wrong. Are you using the headsurface file generated with the polhemus? It could be that this causes the problem. For the singleshell model to work, you need a triangulated surface. The headsurface file contains only a point cloud. Matlab tries to create a triangulation from this point cloud, and I could imagine that this triangulation misbehaves here, leading some nans here and there (judging from your message this happens when the normals to the triangles are computed), which eventually cause nans all over the place. For the time being you could try to use a different volume conductor model (localspheres), or you may want to use a structural MRI for the singleshell creation (if available), to verify that the problem is caused by the headsurface file and not by fieldtrip. Best, Jan-Mathijs On May 9, 2011, at 10:12 PM, Jeff Stout wrote: > > Hi, > > I am having trouble generating leadfields for source analysis. I am > using data from a 4D magnetometer system (Magnes 3600), at St. Louis > University. > > The data is averged time domain data. The volume conductor is a > single shell model generated from the headshape file(~4000 vert. and > 8000 triangles). I have vizualized the volume conductor, sensors, > and "inside" grid and they appear to be in the correct locations > relative to each other. I have performed this analysis using the > default source space for 4D ('m') and I have tried it scaling the > headshape and sensors into cm to conform with the ctf source > space. Below is part of my code and the warning thrown by matlab. > After the calculation of the leadfields, it is apparent that they > are all NaN's, so I am unable to generate source activations. > > cfg = []; > cfg.headshape = shape; > shape.pnt = shape.pnt*100; > shape.unit = 'cm'; > [vol,cfg] = ft_prepare_singleshell(cfg) > > cfg = []; > cfg.grad = avg.grad; > cfg.grad.pnt = cfg.grad.pnt*100; > cfg.grad.unit = 'cm'; > cfg.vol = vol; > cfg.sourceunits = 'cm'; > cfg.coordsys = 'ctf'; > cfg.reducerank ='no'; > cfg.channel = {'MEG'}; > cfg.grid.resolution = 2 > [vol, sens] = ft_prepare_vol_sens(vol, cfg.grad) > [grid] = ft_prepare_leadfield(cfg) > > >> [grid] = ft_prepare_leadfield(cfg) > using headmodel specified in the configuration > using gradiometers specified in the configuration > computing surface normals > Warning: Matrix is singular, close to singular or badly scaled. > <<<<<<<<<< > Results may be inaccurate. RCOND = NaN. > > In forward/private/meg_ini>getcoeffs at 111 > In forward/private/meg_ini at 53 > In ft_prepare_vol_sens at 275 > In fieldtrip-20110507/private/prepare_headmodel at 114 > In ft_prepare_leadfield at 150 > creating dipole grid based on automatic 3D grid with specified > resolution > 3528 dipoles inside, 0 dipoles outside brain > making tight grid > 3528 dipoles inside, 0 dipoles outside brain > computing leadfield > computing leadfield 1/3528 > computing leadfield 2/3528 > computing leadfield 3/3528 > computing leadfield 4/3528 ...... > > > The leadfield data generated is a matrix of NaN's, which appear to > be an issue when evaluating bas and gradbas in the get_coeffs > subfunction [bas,gradbas]=legs(x1,n1,order,scale). > > Does anyone know how to resolve this issue? Any help will be greatly > appreciated. > > Thanks, > Jeff Stout > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan.debener at uni-oldenburg.de Tue May 10 09:04:47 2011 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Tue, 10 May 2011 09:04:47 +0200 Subject: [FieldTrip] Auditory BCI post-doc posting Message-ID: <4DC8E38F.5050902@uni-oldenburg.de> Dear all, We are seeking a scientist/post-doc who is interested in developing an auditiry brain computer interface. Please visit: http://www.hearingresearch.uni-oldenburg.de/52922.html (job offer #4), and feel free to contact me via email for further information. Thanks much, Stefan -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de From jan.schoffelen at donders.ru.nl Wed May 11 08:35:19 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 08:35:19 +0200 Subject: [FieldTrip] ft_freqstatistics Message-ID: <4EE8E6A8-5C67-45A6-A6CE-7D6FFA5C3D64@donders.ru.nl> Dear all, I just committed to the svn-repository a revamped version of ft_freqstatistics, the function which does channel-level statistics on frequency domain data. This was a necessary cleaning operation to keep the code up-to-date. Important for you to know is that nothing has changed in the handling of good old-fashioned (time-frequency) power. The new thing is that you don't need to hack your way into the function anymore in order to do group level statistics on connectivity data. Things should just run fine, but although I extensively tested the code (to my best knowledge) on plausible scenarios, please keep your eyes open. Best, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From ndavid at uke.de Wed May 11 10:45:32 2011 From: ndavid at uke.de (Nicole David) Date: Wed, 11 May 2011 10:45:32 +0200 Subject: [FieldTrip] Job Announcement (PhD Position) In-Reply-To: <03750F99-88BD-42D6-9133-8E4B4814E133@uke.de> References: <03750F99-88BD-42D6-9133-8E4B4814E133@uke.de> Message-ID: Dear FieldTrip list, I would like to announce an open PhD position with Prof. Andreas Engel at the Dept. of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf. For details, see below. Best, Nicole David ------------------------------- The Department of Neurophysiology and Pathophysiology at the University Medical Center Hamburg-Eppendorf (Director: Prof. Dr. Andreas K. Engel) invites applications for a PhD student position. The position is available with immediate start. The appointment will be for 3 years. The position is at the intersection of psychology, cognitive neuroscience and philosophy. More specifically, experiments investigating the sense of agency shall be carried out, using neuroscience techniques such as magnetoencephalography (MEG). The sense of agency refers to the monitoring of actions and the experience, or awareness, of such as self- or other-generated. Applicants should have experience in analyzing human EEG or MEG studies. Programming experience (Matlab) as well as fluent written and spoken English is considered mandatory. Applicants will be responsible for the management and implementation of research paradigms, data acquisition and analysis. Knowledge in theories of action and perception, multisensory processing, self-awareness and a basic understanding of information processing in the human brain would be preferred. The successful candidate will be member of the European collaborative project “Extending Sensorimotor Contingencies to Cognition – eSMCs” that has started in January 2011. The main objective of the project is to extend the Sensorimotor Contingency Theory as an action-based approach to perception and cognition, and to investigate its implications in studies of natural and artificial agents. More information on the project is to appear at http://eSMCs.eu. Information on the Dept. of Neurophysiology and Pathophysiology is available at http://www.uke.de/neurophysiologie and at http://www.40hz.de . Please send your application (including a CV) to Dr. Nicole David or Prof. Dr. Andreas K. Engel Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistrasse 52 20246 Hamburg Germany Submission of applications through email (ndavid at uke.de, ak.engel at uke.de) is encouraged. -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Joachim Prölß Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 11 10:56:10 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 10:56:10 +0200 Subject: [FieldTrip] FT_analysis of the average vs average(FT_analysis(single trials)) In-Reply-To: <686364.21106.qm@web28608.mail.ukl.yahoo.com> References: <686364.21106.qm@web28608.mail.ukl.yahoo.com> Message-ID: Dear Tommaso, Yes, if you average across the trial-dimension you will obtain the TFR you're after. Best, JM On May 6, 2011, at 5:28 PM, tommaso fedele wrote: > Hi all, > I want to test if some component that I observe in the average of my > ERP signal are phase locked to the stimulus. > In oder to do so I compare > 1. TFR_averaged_signal = ft_freqanalysis(cfg, averaged_signal) > 2. TFR_singletrials_signal = ft_freqanalysis(cfg, > singletrials_signal) > > with the first structure TFR_averaged_signal everything is fine, and > I get my nice TF plot. > with the second I should average through "trials". Is there a > function for that? Or, is it correct to proceed plotting > the average of TFR_singletrials_signal.powspctrm through the > "trials-matrix dimension"? > > Thanks > Tommaso > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 11 10:59:06 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 10:59:06 +0200 Subject: [FieldTrip] error using spm_slice_vol In-Reply-To: References: Message-ID: Hi Allison, This looks like an SPM-related error to me, or it is operating system related. Can you check which spm-version you are using, in other words: is it the fieldtrip/external/spmXXX directory, or do you have spm somewhere else on your matlab-path? If it is the former, then it is a potential bug which needs fixing by us. Otherwise we cannot help it. What kind of operating system are you using? Best, Jan-Mathijs On May 4, 2011, at 3:56 PM, Allison Connolly wrote: > Hi all, > > I am trying to segment an mri volume using. When I call > ft_read_mri('filename'), I get an error that says: > > ??? Error using ==> spm_slice_vol at 28 > spm_slice_vol.c not compiled - see spm_MAKE.sh > > Error in ==> spm_read_vols at 35 > Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 > p]),V(i).dim(1:2),0); > > Error in ==> ft_read_mri at 97 > img = spm_read_vols(hdr); > > I tried installing the most up to date version of fieldtrip and I > still get the same error. Can someone help me? > > -Allison > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Wed May 11 11:02:49 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 11:02:49 +0200 Subject: [FieldTrip] overlaying beamformer results to native/normalized space In-Reply-To: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> References: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> Message-ID: Dear Akiko, On May 4, 2011, at 3:17 PM, Akiko Ikkai wrote: > I sent a below message to the list last night, but it was bounced > back. I'm trying from another email account. My apologies if this > was duplicate... > > > > I'm trying to run beamformer analysis on my MEG data, using DICS, > and having difficulty visualizing meaningful results. > > I was able to align MRI image to MEG sensors; after segmentation, > ft_prepare_singleshell and ft_prepare_leadfield, plotting > ft_data.grad and volume model confirms that they align reasonably. > However, using data.grad, grid, and vol to run ft_sourceanalysis, > and ft_sourceinterpolate with MRI (in ctf coordinate system and > aligned to MEG sensors) somehow distorts the alignment, and the new > volume model does not resemble the original. So, the problem is that ft_sourceinterpolate does not behave as expected? > I'm assuming that, after ft_sourceinterpolate, if I segment > source_interpolated.anatomy and run ft_prepare_singleshell and > ft_prepare_leadfield, it should align with MEG sensors, just as the > initial volume model aligned with MEG sensors... or am I making too > much of an assumption here? Why would you want to do this? > Because of the misalignment, output data of ft_sourceinterpolate > with "anatomy" and "avg.pow" does not agree with topoplot (run > ft_freqanalysis on the same dataset). > If anyone could explain why this alignment distortion might be > happening during ft_sourceanalysis and/or ft_sourceinterpolate, I'd > really appreciate it. > I am afraid you need to be a bit more specific in order for us to understand what may be going wrong here. Best, Jan-Mathijs > Thanks in advance, Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ting.ac at gmail.com Wed May 11 19:30:14 2011 From: ting.ac at gmail.com (Allison Connolly) Date: Wed, 11 May 2011 12:30:14 -0500 Subject: [FieldTrip] channelcmb with removed channels Message-ID: I am trying to do beamforming on some MEG data. However, some of the sensors railed during the recordings, so I want to remove them from the analysis. I declare the channels I want to use during import with ft_preprocessing by saying: cfg.channel = {'MEG','-TRIGGER','-RESPONSE',... '-UACurrent','-MxA','-MyA','-MzA','-GxxA','-GyxA','-GyyA',... '-GzyA','-GzxA','-MxaA','-MyaA','-MzaA','-E1','-E2','-E3','-E4',... '-A40','-A57','-A76','-A77','-A79','-A81','-A88','-A89','-A96',... '-A100','-A102','-A103','-A108','-A112','-A113','-A114','-A116',... '-A120','-A121','-A123','-A124','-A125','-A126','-A127','-A128',... '-A129','-A130','-A131','-A124','-A139','-A140','-A141','-A142',... '-A144','-A145','-A146','-A147','-A148'}; Then I use ft_freqanalysis to calculate the cross spectral density and ft_prepare_leadfield to create the brain grid. When I try to run ft_sourceanalysis, I get this error: creating dipole grid based on user specified dipole positions 13718 dipoles inside, 144943 dipoles outside brain ??? In an assignment A(I) = B, a matrix A cannot be resized. Error in ==> prepare_freq_matrices at 115 Cf(find(crsspctrmindx)) = freq.crsspctrm(crsspctrmindx(find(crsspctrmindx)), fbin); Error in ==> ft_sourceanalysis at 461 [Cf, Cr, Pr, Ntrials, cfg] = prepare_freq_matrices(cfg, data); I think it is because I have removed channels. When I try to run ft_freqanalysis while specifying the channels in cfg.channel, i get this error: the input is raw data with 111 channels and 60 trials ??? Error using ==> ft_freqanalysis at 352 *channels in cfg.channelcmb not present in cfg.channel* * *I think I need to explicitly define cfg.channelcmb, but I don't know how to do this if I have removed channels. -Allison -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpoll at ugr.es Thu May 12 14:10:46 2011 From: jpoll at ugr.es (JOAN PAUL POZUELOS LOPEZ) Date: Thu, 12 May 2011 14:10:46 +0200 Subject: [FieldTrip] Problems with the Buffer Message-ID: Hello everyone, Im new using the matlab for analyzing ERP´s. I have been using the FASTER program (Nolan, Whelan &Reilly, 2010, Journal of Neuroscience Methods) and i have encounter a problem with some files contained in the filedtrip toolbox. The problem its that when it is computing the ICA the process is not finished because theres an error that says: "error - invalid MEX_file 'c: Users\....\Matlab\external\fieldtrip-20110320\realtime\buffer\matlab\buffer.mexw32': could not find the specified module. When i check the folder containing the Buffer.mexw32 file, it is in the folder that the Filepath looks. Any suggestions on how to solve this problem?. Thank you very much for your help JOAN PAUL POZUELOS LOPEZ Departamento de Psicología Experimental y Fisiología del Comportamiento Universidad de Granada jpoll at ugr.es From nuria.donamayor at neuro.uni-luebeck.de Fri May 13 10:42:05 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Fri, 13 May 2011 10:42:05 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> Dear fieltrip users, I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a 64-bit Matlab version and I am getting an error I don't know how to solve: hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); ??? SWITCH expression must be a scalar or string constant. Error in ==> read_4d_hdr at 60 switch format Error in ==> ft_read_header at 153 orig = read_4d_hdr(datafile); If I try to read the same data on my Windows PC with 32-bit Matlab I have no problem reading the header file (but I can't even finish the preprocessing before it runs out of memory, therefore the switch to the Linux machine), so I'm pretty clueless here... Can any of you help me? Thanks, Nuria Nuria Doñamayor Alonso, MSc Universitätsklinikum Schleswig-Holstein Campus Lübeck Klinik für Neurologie Ratzeburger Allee 160 23538 Lübeck From paul_c at gmx.de Fri May 13 11:27:01 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Fri, 13 May 2011 11:27:01 +0200 Subject: [FieldTrip] Systematic electrode displacement Message-ID: <4DCCF965.4050408@gmx.de> Dear fieldtrippers, I've got an issue with electrode placement and I hope that someone has any idea how to tackle those issues. For research on my diploma thesis I am fitting simulated data with the realistic brain shape I used to simulate the data as well as a icbm model (BEM models). I used the electrode system for the icbm152 brain provided by Robert Oostenveld and did some manual correction to the realistic brains (which were normalised to icbm brain) with the ft_electroderealign function. I simulated the data in a position near the auditory cortex, since this is the location where we assume our real ERP. In my fitted data I encountered strange systematic errors (especially some kind of bias on the z-axis), as seen on the boxplot_coord_20110407.png file (note that it's both age groups: 1 for old and 2 for young, scale is meters). While investigating on the origin of this bias, I made a box plot of the distance of the electrodes in the icbm model and the electrodes in each of the realistic models (dist_electrodes.png). Obviously there already is an bias in the electrodes placement. First I assumed this was caused my the manual correction of the electrodes I performed. To check this out, I fitted the very data with the manually corrected electrodes on the icbm brain. Still I found that there was a bias, mainly on the z-axis and - what astonished me even more, there was still a bias in the electrodes. This is observable in the boxplot_20110512_electrode_locations_matched.png (sorry for the German captions), x-Axis is coordinate and y-axis is the deviation of the electrode's positions. Furthermore I simulated and fitted a position near the vertex (though still in the brain ;) ). There was not so much of a bias there, therefore I assume it's mainly the lateral and maybe posterior electrodes causing the bias, not that much the superior. Due to those results I assumed that it's got something to do with the automatic projection of the electrodes on the head surface. I had no time yet to compare those electrode positions manually (or better visually), but this is definitely on my agenda. I wondered, if anyone had an idea, how to improve this, for electrode deviations up to ~10 cm is way to much, asking me. I already checked if there maybe was any confusion in the order of the electrodes, but I just checked the labels and this does not support it. Thanks in advance and best regards, Paul Czienskowski -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_coord_20110407.jpg Type: image/jpeg Size: 17510 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dist_electrodes.png Type: image/png Size: 8323 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_20110512_electrode_locations_matched.png Type: image/png Size: 6945 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_20110512_coordinates.png Type: image/png Size: 8841 bytes Desc: not available URL: From yuvharpaz at gmail.com Fri May 13 13:39:29 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 13 May 2011 14:39:29 +0300 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> Message-ID: Dear Nuria Is it exactly the same fieldtrip version? I hope someone will solve this. as temporary work around you can read the header on windows and then move to linux yuval On 13 May 2011 11:42, Nuria Donamayor Alonso < nuria.donamayor at neuro.uni-luebeck.de> wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a > 64-bit Matlab version and I am getting an error I don't know how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I have > no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to the > Linux machine), so I'm pretty clueless here... Can any of you help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuria.donamayor at neuro.uni-luebeck.de Fri May 13 14:34:36 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Fri, 13 May 2011 14:34:36 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> Yes, it is exectly the same version. Better said, versions, because I tried both 20110413 and 20110512.... ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com] Gesendet: Freitag, 13. Mai 2011 13:39 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Dear Nuria Is it exactly the same fieldtrip version? I hope someone will solve this. as temporary work around you can read the header on windows and then move to linux yuval On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: Dear fieltrip users, I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a 64-bit Matlab version and I am getting an error I don't know how to solve: hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); ??? SWITCH expression must be a scalar or string constant. Error in ==> read_4d_hdr at 60 switch format Error in ==> ft_read_header at 153 orig = read_4d_hdr(datafile); If I try to read the same data on my Windows PC with 32-bit Matlab I have no problem reading the header file (but I can't even finish the preprocessing before it runs out of memory, therefore the switch to the Linux machine), so I'm pretty clueless here... Can any of you help me? Thanks, Nuria Nuria Doñamayor Alonso, MSc Universitätsklinikum Schleswig-Holstein Campus Lübeck Klinik für Neurologie Ratzeburger Allee 160 23538 Lübeck _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html "Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams From jan.schoffelen at donders.ru.nl Fri May 13 16:43:41 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 May 2011 16:43:41 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> Message-ID: Hi Nuria, Could you type dbstop if error on the command line, and evaluate what the variable 'format' is in your case? Thanks, Jan-Mathijs On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > Yes, it is exectly the same version. Better said, versions, because > I tried both 20110413 and 20110512.... > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com > ] > Gesendet: Freitag, 13. Mai 2011 13:39 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Dear Nuria > Is it exactly the same fieldtrip version? > I hope someone will solve this. > as temporary work around you can read the header on windows and then > move to linux > > yuval > > On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine > with a 64-bit Matlab version and I am getting an error I don't know > how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I > have no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to > the Linux machine), so I'm pretty clueless here... Can any of you > help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > > "Many were increasingly of the opinion that they'd all made a big > mistake in coming down from the trees in the first place. And some > said that even the trees had been a bad move, and that no one should > ever have left the oceans". Douglas Adams > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From anokhina at psychiatry.wustl.edu Sat May 14 17:10:43 2011 From: anokhina at psychiatry.wustl.edu (Anokhin, Andrey) Date: Sat, 14 May 2011 10:10:43 -0500 Subject: [FieldTrip] job announcement Message-ID: <86712757862F3640B2F4BB5C14D8EDC4090EF4A245@wusmexmbx2.medpriv.wucon.wustl.edu> An HTML attachment was scrubbed... URL: From l.frei at psy.gla.ac.uk Sat May 14 22:37:45 2011 From: l.frei at psy.gla.ac.uk (Luisa Frei) Date: Sat, 14 May 2011 21:37:45 +0100 Subject: [FieldTrip] stats on planar gradient topographies Message-ID: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Hi there, I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. This the code I used: %%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.001; cfg.clusterstatistic = 'maxsize'; cfg.minnbchan = 4; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.005; cfg.numrandomization = 500; design = [ones(1,13) ones(1,13)+1]; cfg.design = design; cfg.ivar = 1; cfg.channel = {'MEG',sub(1).allbadchan{:}}; cfg.latency = [.15 .2]; [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? Thanks, Luisa Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change.  -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 2.png Type: application/applefile Size: 73 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 2.png Type: image/png Size: 105588 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon May 16 14:32:07 2011 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 16 May 2011 14:32:07 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Message-ID: Hi Luisa, schnell from the top of my head: wie definierst du denn deine neighbors? Ich seh nirgendwo ein Feld cfg.neighbors.... Ich muss das bei unserem 4D-System immer angeben.... Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind falsch definierst, so könntest du zu deinen "random" Clustern kommen. Ich mache diese Neighbor-Struktur folgendermaßen: cfg=[]; cfg.neighbourdist=0.1; %cfg.grad=Comb_AV1_1{1}.grad; cfg.layout='4D148.lay'; cfg.channel={'all'}; %cfg.grad.pnt=cfg.grad.pnt*100; dummy=neighbourselection(cfg); Da bekomme ich auch immer einen Output, wie viele Channels so in der Umgebung sind (sollten in etwa 5 sein). Hoffe das hilft dir weiter Viele Grüße Julian Am 14.05.2011 um 22:37 schrieb Luisa Frei: > Hi there, > I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. > This the code I used: > > %%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.001; > cfg.clusterstatistic = 'maxsize'; > cfg.minnbchan = 4; > > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.005; > cfg.numrandomization = 500; > > design = [ones(1,13) ones(1,13)+1]; > > cfg.design = design; > cfg.ivar = 1; > > cfg.channel = {'MEG',sub(1).allbadchan{:}}; > cfg.latency = [.15 .2]; > > [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? > > Thanks, > Luisa > > Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change. > > _______________________________________________ > 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 jm.horschig at donders.ru.nl Mon May 16 14:52:24 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 16 May 2011 14:52:24 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Message-ID: <4DD11E08.6050207@donders.ru.nl> Hi all, First of all, @julian: It would be nice if you wrote in English so that all people can understand what you are saying :) Second, I would like to mention ft_neighbourplot, which is a relative new function and plots sensors and its' neighbours in 2D or 3D, depending on whether you got 2D or 3D coordinates. Using that function, you can verify whether your neighbourselection looks meaningful and makes sense. Finally, we are currently working on changing/improving the neighbourselecion function. There will be different methods to choose from, and we (me) will create templates for the most common systems that can be used instead of relying on a particular mathematical selection method. We will announce this when it's done (probably soon). Maybe Julian is right and Luisa's problem is due to a 'wrong' neighbourselection. Given that cfg.minnbhchan is set to 4, this might be likely, because not all of the found clusters consist of 4 or more channels. What system are you using? Best, Jörn On 5/16/2011 2:32 PM, Julian Keil wrote: > Hi Luisa, > > schnell from the top of my head: wie definierst du denn deine neighbors? > Ich seh nirgendwo ein Feld cfg.neighbors.... > Ich muss das bei unserem 4D-System immer angeben.... > Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind > falsch definierst, so könntest du zu deinen "random" Clustern kommen. > > Ich mache diese Neighbor-Struktur folgendermaßen: > > cfg=[]; > cfg.neighbourdist=0.1; > %cfg.grad=Comb_AV1_1{1}.grad; > cfg.layout='4D148.lay'; > cfg.channel={'all'}; > %cfg.grad.pnt=cfg.grad.pnt*100; > dummy=neighbourselection(cfg); > > Da bekomme ich auch immer einen Output, wie viele Channels so in der > Umgebung sind (sollten in etwa 5 sein). > > Hoffe das hilft dir weiter > > Viele Grüße > > Julian > > Am 14.05.2011 um 22:37 schrieb Luisa Frei: > >> Hi there, >> I am trying to compute a simple cluster-based statistic in a between >> subjects design. I have followed the steps in the respective tutorial >> very closely. >> This the code I used: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'indepsamplesT'; >> >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.001; >> cfg.clusterstatistic = 'maxsize'; >> cfg.minnbchan = 4; >> >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.005; >> cfg.numrandomization = 500; >> >> design = [ones(1,13) ones(1,13)+1]; >> >> cfg.design = design; >> cfg.ivar = 1; >> >> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >> cfg.latency = [.15 .2]; >> >> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % >> individuals kept >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> My problem is, that I'm not sure which time resolution to use. I >> would like to use a small resolution of 10 ms, but this leads to a >> fairly random pattern of significant sensors (see attached figure, on >> the right). Of course, the more time points I include, the less >> significant sensors are left over. However, another problem is, that >> the ones that are left (figure, left), are not related to big >> differences in the activation pattern at all. How is it possible that >> my significant sensors end up being so randomly distributed? Also, >> ft_timelockstatistics only comes up with one positive and one >> negative cluster., but the sign. sensors are not always connected. >> Could anyone give some helpful input here? >> >> Thanks, >> Luisa >> >> Fyi: I have tried different thresholds and different numbers of >> neighbourhood channels, but there's not much of a change. >> _______________________________________________ >> 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon May 16 14:58:35 2011 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 16 May 2011 14:58:35 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: <4DD11E08.6050207@donders.ru.nl> References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> <4DD11E08.6050207@donders.ru.nl> Message-ID: Hi all, sorry, I thought the answer would only go to Luisa. Apologies, Julian Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig: > Hi all, > > First of all, @julian: It would be nice if you wrote in English so that all people can understand what you are saying :) > > Second, I would like to mention ft_neighbourplot, which is a relative new function and plots sensors and its' neighbours in 2D or 3D, depending on whether you got 2D or 3D coordinates. Using that function, you can verify whether your neighbourselection looks meaningful and makes sense. > > Finally, we are currently working on changing/improving the neighbourselecion function. There will be different methods to choose from, and we (me) will create templates for the most common systems that can be used instead of relying on a particular mathematical selection method. We will announce this when it's done (probably soon). > > Maybe Julian is right and Luisa's problem is due to a 'wrong' neighbourselection. Given that cfg.minnbhchan is set to 4, this might be likely, because not all of the found clusters consist of 4 or more channels. What system are you using? > > Best, > Jörn > > > On 5/16/2011 2:32 PM, Julian Keil wrote: >> >> Hi Luisa, >> >> schnell from the top of my head: wie definierst du denn deine neighbors? >> Ich seh nirgendwo ein Feld cfg.neighbors.... >> Ich muss das bei unserem 4D-System immer angeben.... >> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind falsch definierst, so könntest du zu deinen "random" Clustern kommen. >> >> Ich mache diese Neighbor-Struktur folgendermaßen: >> >> cfg=[]; >> cfg.neighbourdist=0.1; >> %cfg.grad=Comb_AV1_1{1}.grad; >> cfg.layout='4D148.lay'; >> cfg.channel={'all'}; >> %cfg.grad.pnt=cfg.grad.pnt*100; >> dummy=neighbourselection(cfg); >> >> Da bekomme ich auch immer einen Output, wie viele Channels so in der Umgebung sind (sollten in etwa 5 sein). >> >> Hoffe das hilft dir weiter >> >> Viele Grüße >> >> Julian >> >> Am 14.05.2011 um 22:37 schrieb Luisa Frei: >> >>> Hi there, >>> I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. >>> This the code I used: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'indepsamplesT'; >>> >>> cfg.correctm = 'cluster'; >>> cfg.clusteralpha = 0.001; >>> cfg.clusterstatistic = 'maxsize'; >>> cfg.minnbchan = 4; >>> >>> cfg.tail = 0; >>> cfg.clustertail = 0; >>> cfg.alpha = 0.005; >>> cfg.numrandomization = 500; >>> >>> design = [ones(1,13) ones(1,13)+1]; >>> >>> cfg.design = design; >>> cfg.ivar = 1; >>> >>> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >>> cfg.latency = [.15 .2]; >>> >>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? >>> >>> Thanks, >>> Luisa >>> >>> Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change. >>> _______________________________________________ >>> 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 > > 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 > Kapitelweg 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 l.frei at psy.gla.ac.uk Mon May 16 15:10:27 2011 From: l.frei at psy.gla.ac.uk (Luisa Frei) Date: Mon, 16 May 2011 14:10:27 +0100 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> <4DD11E08.6050207@donders.ru.nl> Message-ID: <95704E05-6DEC-4B66-A9EA-381B9C88CA12@psy.gla.ac.uk> Thanks for all the answers, I'll try Julian's suggestion and let you know what happens. Luisa On 16 May 2011, at 13:58, Julian Keil wrote: > Hi all, > > sorry, I thought the answer would only go to Luisa. > > Apologies, > Julian > > Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig: > >> Hi all, >> >> First of all, @julian: It would be nice if you wrote in English so >> that all people can understand what you are saying :) >> >> Second, I would like to mention ft_neighbourplot, which is a >> relative new function and plots sensors and its' neighbours in 2D >> or 3D, depending on whether you got 2D or 3D coordinates. Using >> that function, you can verify whether your neighbourselection >> looks meaningful and makes sense. >> >> Finally, we are currently working on changing/improving the >> neighbourselecion function. There will be different methods to >> choose from, and we (me) will create templates for the most common >> systems that can be used instead of relying on a particular >> mathematical selection method. We will announce this when it's >> done (probably soon). >> >> Maybe Julian is right and Luisa's problem is due to a 'wrong' >> neighbourselection. Given that cfg.minnbhchan is set to 4, this >> might be likely, because not all of the found clusters consist of >> 4 or more channels. What system are you using? >> >> Best, >> Jörn >> >> >> On 5/16/2011 2:32 PM, Julian Keil wrote: >>> >>> Hi Luisa, >>> >>> schnell from the top of my head: wie definierst du denn deine >>> neighbors? >>> Ich seh nirgendwo ein Feld cfg.neighbors.... >>> Ich muss das bei unserem 4D-System immer angeben.... >>> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen >>> sind falsch definierst, so könntest du zu deinen "random" >>> Clustern kommen. >>> >>> Ich mache diese Neighbor-Struktur folgendermaßen: >>> >>> cfg=[]; >>> cfg.neighbourdist=0.1; >>> %cfg.grad=Comb_AV1_1{1}.grad; >>> cfg.layout='4D148.lay'; >>> cfg.channel={'all'}; >>> %cfg.grad.pnt=cfg.grad.pnt*100; >>> dummy=neighbourselection(cfg); >>> >>> Da bekomme ich auch immer einen Output, wie viele Channels so in >>> der Umgebung sind (sollten in etwa 5 sein). >>> >>> Hoffe das hilft dir weiter >>> >>> Viele Grüße >>> >>> Julian >>> >>> Am 14.05.2011 um 22:37 schrieb Luisa Frei: >>> >>>> Hi there, >>>> I am trying to compute a simple cluster-based statistic in a >>>> between subjects design. I have followed the steps in the >>>> respective tutorial very closely. >>>> This the code I used: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.method = 'montecarlo'; >>>> cfg.statistic = 'indepsamplesT'; >>>> >>>> cfg.correctm = 'cluster'; >>>> cfg.clusteralpha = 0.001; >>>> cfg.clusterstatistic = 'maxsize'; >>>> cfg.minnbchan = 4; >>>> >>>> cfg.tail = 0; >>>> cfg.clustertail = 0; >>>> cfg.alpha = 0.005; >>>> cfg.numrandomization = 500; >>>> >>>> design = [ones(1,13) ones(1,13)+1]; >>>> >>>> cfg.design = design; >>>> cfg.ivar = 1; >>>> >>>> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >>>> cfg.latency = [.15 .2]; >>>> >>>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % >>>> individuals kept >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> >>>> My problem is, that I'm not sure which time resolution to use. I >>>> would like to use a small resolution of 10 ms, but this leads to >>>> a fairly random pattern of significant sensors (see attached >>>> figure, on the right). Of course, the more time points I >>>> include, the less significant sensors are left over. However, >>>> another problem is, that the ones that are left (figure, left), >>>> are not related to big differences in the activation pattern at >>>> all. How is it possible that my significant sensors end up being >>>> so randomly distributed? Also, ft_timelockstatistics only comes >>>> up with one positive and one negative cluster., but the sign. >>>> sensors are not always connected. Could anyone give some helpful >>>> input here? >>>> >>>> Thanks, >>>> Luisa >>>> >>>> Fyi: I have tried different thresholds and different numbers of >>>> neighbourhood channels, but there's not much of a change. >>>> _______________________________________________ >>>> 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 >> >> 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 >> Kapitelweg 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Mon May 16 15:59:36 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 16 May 2011 15:59:36 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection Message-ID: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> Dear Fieldtrippers, I'm using ft_rejectvisual function to reject visually EOG artifacts of epoched trials. My problem consist that I'm not able to plot only the EOG channels even when I explicitly select them ignoring the 'MEG' channels (I get a plot with all channels MEG + EOG). I directly used rejectvisual_channel (used in line 263 offt_rejectvisual) function selecting the EOG channels but I'm getting again all channels. Somebody could tell me what I'm doing wrong? Thanks in advance, Diego PS: Code %epoching cfg = []; cfg.dataset = [direc d(rr,1).name]; cfg.trialdef.eventtype = 'frontpanel trigger'; cfg.trialdef.eventvalue = 4; cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 4; % in seconds cfg.trialdef.epochmoving = 'inbackward'; cfg.trialdef.pivoteventvalue = 2;% cue stimulus cfg.trialdef.jumps = 1; cfg.trialfun = 'trialselec'; cfg = ft_definetrial(cfg); cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.lpfilter = 'yes'; cfg.lpfreq = 250; cfg.baselinewindow = [-1 0]; cfg.keeptrials = 'yes'; cfg.demean = 'yes'; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); %.............. %visual data rejection cfg = []; cfg.channel = {'EEG057' 'EEG058'}; cfg.method = 'channel'; cfg.keepchannel = 'yes'; data_c = ft_rejectvisual(cfg,data); -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From stan.vanpelt at fcdonders.ru.nl Mon May 16 16:16:16 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 May 2011 16:16:16 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> References: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> Hi Diego, You could try using ft_databrowser instead of ft_rejectvisual (followed by ft_rejectartifact), so: cfg = []; cfg.continuous = 'no'; cfg.channel = {'EEG057','EEG058'}; cfg = ft_databrowser(cfg,data); I think it should work like this. Best, Stan -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano Soldevilla, D. (Diego) Sent: Monday, May 16, 2011 4:00 PM To: fieldtrip at donders.ru.nl Subject: [FieldTrip] ft_rejectvisual channel selection Dear Fieldtrippers, I'm using ft_rejectvisual function to reject visually EOG artifacts of epoched trials. My problem consist that I'm not able to plot only the EOG channels even when I explicitly select them ignoring the 'MEG' channels (I get a plot with all channels MEG + EOG). I directly used rejectvisual_channel (used in line 263 offt_rejectvisual) function selecting the EOG channels but I'm getting again all channels. Somebody could tell me what I'm doing wrong? Thanks in advance, Diego PS: Code %epoching cfg = []; cfg.dataset = [direc d(rr,1).name]; cfg.trialdef.eventtype = 'frontpanel trigger'; cfg.trialdef.eventvalue = 4; cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 4; % in seconds cfg.trialdef.epochmoving = 'inbackward'; cfg.trialdef.pivoteventvalue = 2;% cue stimulus cfg.trialdef.jumps = 1; cfg.trialfun = 'trialselec'; cfg = ft_definetrial(cfg); cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.lpfilter = 'yes'; cfg.lpfreq = 250; cfg.baselinewindow = [-1 0]; cfg.keeptrials = 'yes'; cfg.demean = 'yes'; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); %.............. %visual data rejection cfg = []; cfg.channel = {'EEG057' 'EEG058'}; cfg.method = 'channel'; cfg.keepchannel = 'yes'; data_c = ft_rejectvisual(cfg,data); -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.lozanosoldevilla at fcdonders.ru.nl Mon May 16 16:24:38 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 16 May 2011 16:24:38 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> Message-ID: <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> Hi Stan, Thanks for your quickly answer. I get this error: Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording > In utilities/private/warning_once at 81 In utilities/private/fixtrialdef at 52 In ft_datatype_raw at 91 In ft_checkdata at 161 In ft_databrowser at 120 redrawing with viewmode butterfly ??? Improper index matrix reference. Error in ==> ft_databrowser>redraw_cb at 910 evtsample = [event(:).sample]; Error in ==> ft_databrowser at 419 redraw_cb(h); I don't know why my data have no trial definition when I'm sure that is epoched... Any ideas? Thanks in advance, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 4:16:16 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > You could try using ft_databrowser instead of ft_rejectvisual > (followed by > ft_rejectartifact), so: > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = {'EEG057','EEG058'}; > cfg = ft_databrowser(cfg,data); > > I think it should work like this. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:00 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] ft_rejectvisual channel selection > > Dear Fieldtrippers, > > I'm using ft_rejectvisual function to reject visually EOG artifacts > of > epoched trials. My problem consist that I'm not able to plot only the > EOG > channels even when I explicitly select them ignoring the 'MEG' > channels (I > get a plot with all channels MEG + EOG). > > I directly used rejectvisual_channel (used in line 263 > offt_rejectvisual) > function selecting the EOG channels but I'm getting again all > channels. > Somebody could tell me what I'm doing wrong? > > Thanks in advance, > > Diego > > > > PS: Code > > %epoching > cfg = []; > cfg.dataset = [direc d(rr,1).name]; > cfg.trialdef.eventtype = 'frontpanel trigger'; > cfg.trialdef.eventvalue = 4; > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 4; % in seconds > cfg.trialdef.epochmoving = 'inbackward'; > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > cfg.trialdef.jumps = 1; > cfg.trialfun = 'trialselec'; > > cfg = ft_definetrial(cfg); > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.lpfilter = 'yes'; > cfg.lpfreq = 250; > cfg.baselinewindow = [-1 0]; > cfg.keeptrials = 'yes'; > cfg.demean = 'yes'; > cfg.continuous = 'yes'; > > data = ft_preprocessing(cfg); > > %.............. > > > %visual data rejection > cfg = []; > cfg.channel = {'EEG057' 'EEG058'}; > cfg.method = 'channel'; > cfg.keepchannel = 'yes'; > data_c = ft_rejectvisual(cfg,data); > > > > -- > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > _______________________________________________ > 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 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From stan.vanpelt at fcdonders.ru.nl Mon May 16 21:40:11 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 May 2011 21:40:11 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> References: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <024701cc1401$122fb120$368f1360$@vanpelt@fcdonders.ru.nl> Hi Diego, Hm, sounds odd to me. Is your trial-definition output from ft_definetrial correct? So a cfg.trl that is not empty? Otherwise, you might try starting with an empty cfg again before calling ft_preprocessing? cfg=ft_definetrial(cfg); trials=cfg.trl; cfg=[]; cfg.trl=trials; cfg.dataset = [direc d(rr,1).name]; cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.continuous = 'yes'; etc.. data = ft_preprocessing(cfg); That should give you an output with a trial-structure, I'd say. Best, Stan -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano Soldevilla, D. (Diego) Sent: Monday, May 16, 2011 4:25 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] ft_rejectvisual channel selection Hi Stan, Thanks for your quickly answer. I get this error: Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording > In utilities/private/warning_once at 81 In utilities/private/fixtrialdef at 52 In ft_datatype_raw at 91 In ft_checkdata at 161 In ft_databrowser at 120 redrawing with viewmode butterfly ??? Improper index matrix reference. Error in ==> ft_databrowser>redraw_cb at 910 evtsample = [event(:).sample]; Error in ==> ft_databrowser at 419 redraw_cb(h); I don't know why my data have no trial definition when I'm sure that is epoched... Any ideas? Thanks in advance, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 4:16:16 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > You could try using ft_databrowser instead of ft_rejectvisual > (followed by > ft_rejectartifact), so: > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = {'EEG057','EEG058'}; > cfg = ft_databrowser(cfg,data); > > I think it should work like this. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:00 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] ft_rejectvisual channel selection > > Dear Fieldtrippers, > > I'm using ft_rejectvisual function to reject visually EOG artifacts > of > epoched trials. My problem consist that I'm not able to plot only the > EOG > channels even when I explicitly select them ignoring the 'MEG' > channels (I > get a plot with all channels MEG + EOG). > > I directly used rejectvisual_channel (used in line 263 > offt_rejectvisual) > function selecting the EOG channels but I'm getting again all > channels. > Somebody could tell me what I'm doing wrong? > > Thanks in advance, > > Diego > > > > PS: Code > > %epoching > cfg = []; > cfg.dataset = [direc d(rr,1).name]; > cfg.trialdef.eventtype = 'frontpanel trigger'; > cfg.trialdef.eventvalue = 4; > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 4; % in seconds > cfg.trialdef.epochmoving = 'inbackward'; > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > cfg.trialdef.jumps = 1; > cfg.trialfun = 'trialselec'; > > cfg = ft_definetrial(cfg); > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.lpfilter = 'yes'; > cfg.lpfreq = 250; > cfg.baselinewindow = [-1 0]; > cfg.keeptrials = 'yes'; > cfg.demean = 'yes'; > cfg.continuous = 'yes'; > > data = ft_preprocessing(cfg); > > %.............. > > > %visual data rejection > cfg = []; > cfg.channel = {'EEG057' 'EEG058'}; > cfg.method = 'channel'; > cfg.keepchannel = 'yes'; > data_c = ft_rejectvisual(cfg,data); > > > > -- > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > _______________________________________________ > 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 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.lozanosoldevilla at fcdonders.ru.nl Tue May 17 00:19:50 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Tue, 17 May 2011 00:19:50 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <940868980.135061.1305583605111.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> Hi Stan, You're right. It seems that my problem lies in the lack of trl because I previously resample my data and this last function do not creates a new trl with the updated begin and end samples. If I create a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) *data.fsample);, I get the same error but not with the original data (without resampling). Then I'll use data without resampling to check my artifacts. Thanks again, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 9:40:11 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > Hm, sounds odd to me. Is your trial-definition output from > ft_definetrial > correct? So a cfg.trl that is not empty? > > Otherwise, you might try starting with an empty cfg again before > calling > ft_preprocessing? > > cfg=ft_definetrial(cfg); > trials=cfg.trl; > > cfg=[]; > cfg.trl=trials; > cfg.dataset = [direc d(rr,1).name]; > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.continuous = 'yes'; > etc.. > data = ft_preprocessing(cfg); > > That should give you an output with a trial-structure, I'd say. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:25 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Stan, > > Thanks for your quickly answer. I get this error: > > Warning: the data does not contain a trial definition, assuming that > the > trials are consecutive segments of a continuous recording > > In utilities/private/warning_once at 81 > In utilities/private/fixtrialdef at 52 > In ft_datatype_raw at 91 > In ft_checkdata at 161 > In ft_databrowser at 120 > redrawing with viewmode butterfly > ??? Improper index matrix reference. > > Error in ==> ft_databrowser>redraw_cb at 910 > evtsample = [event(:).sample]; > > Error in ==> ft_databrowser at 419 > redraw_cb(h); > > I don't know why my data have no trial definition when I'm sure that > is > epoched... Any ideas? > > Thanks in advance, > > Diego > > > > ----- "Stan van Pelt" wrote: > > > From: "Stan van Pelt" > > To: "Email discussion list for the FieldTrip project" > > > Sent: Monday, 16 May, 2011 4:16:16 PM > > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > > > Hi Diego, > > > > You could try using ft_databrowser instead of ft_rejectvisual > > (followed by > > ft_rejectartifact), so: > > > > cfg = []; > > cfg.continuous = 'no'; > > cfg.channel = {'EEG057','EEG058'}; > > cfg = ft_databrowser(cfg,data); > > > > I think it should work like this. > > > > Best, > > Stan > > > > -----Original Message----- > > From: fieldtrip-bounces at donders.ru.nl > > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > > Soldevilla, > > D. (Diego) > > Sent: Monday, May 16, 2011 4:00 PM > > To: fieldtrip at donders.ru.nl > > Subject: [FieldTrip] ft_rejectvisual channel selection > > > > Dear Fieldtrippers, > > > > I'm using ft_rejectvisual function to reject visually EOG artifacts > > of > > epoched trials. My problem consist that I'm not able to plot only > the > > EOG > > channels even when I explicitly select them ignoring the 'MEG' > > channels (I > > get a plot with all channels MEG + EOG). > > > > I directly used rejectvisual_channel (used in line 263 > > offt_rejectvisual) > > function selecting the EOG channels but I'm getting again all > > channels. > > Somebody could tell me what I'm doing wrong? > > > > Thanks in advance, > > > > Diego > > > > > > > > PS: Code > > > > %epoching > > cfg = []; > > cfg.dataset = [direc d(rr,1).name]; > > cfg.trialdef.eventtype = 'frontpanel trigger'; > > cfg.trialdef.eventvalue = 4; > > cfg.trialdef.prestim = 1; % in seconds > > cfg.trialdef.poststim = 4; % in seconds > > cfg.trialdef.epochmoving = 'inbackward'; > > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > > cfg.trialdef.jumps = 1; > > cfg.trialfun = 'trialselec'; > > > > cfg = ft_definetrial(cfg); > > > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > > cfg.lpfilter = 'yes'; > > cfg.lpfreq = 250; > > cfg.baselinewindow = [-1 0]; > > cfg.keeptrials = 'yes'; > > cfg.demean = 'yes'; > > cfg.continuous = 'yes'; > > > > data = ft_preprocessing(cfg); > > > > %.............. > > > > > > %visual data rejection > > cfg = []; > > cfg.channel = {'EEG057' 'EEG058'}; > > cfg.method = 'channel'; > > cfg.keepchannel = 'yes'; > > data_c = ft_rejectvisual(cfg,data); > > > > > > > > -- > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Trigon, room 0.83 > > Kapittelweg 29 > > Radboud University Nijmegen > > NL-6500 HB Nijmegen > > The Netherlands > > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > > Tel: +31-(0)24-36-66274 > > Web: http://www.neuosc.com/ > > _______________________________________________ > > 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 > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > > > _______________________________________________ > 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 From younes_zerouali at hotmail.com Tue May 17 00:25:25 2011 From: younes_zerouali at hotmail.com (Younes Zerouali) Date: Mon, 16 May 2011 18:25:25 -0400 Subject: [FieldTrip] Segment anatomy from MRI (spm8) Message-ID: Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 17 08:18:39 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 17 May 2011 08:18:39 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: References: Message-ID: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit, skin_a = imerode(skin, s); brain_a = imdilate(brain, s); skull = (brain_a & skin_a); Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 17 08:42:22 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 17 May 2011 08:42:22 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> References: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> Message-ID: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote: > Hi Younes, > > this is actually not a problem with the function. The > "ft_volumesegment" will only return segmentations of the anatomical > mri with respect to three tissue types: grey matter, white matter, > and csf. You can use gray and white matter segmentations to > construct your brain compartement by typing e. g. "brain = > (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order > to get skull and skin compartements, you need your original > mri.anatomy which holds the image intensity on a black-to-white > scale. You can threshold the white values to segment the head from > the background, and this is then your skin compartement (e. g., > "skin = (mri.anatomy>300);" as shown in the tutorial). The skull > compartement is the oversection of the skin compartement and the > brain compartement after you blew up those compartements a bit, > skin_a = imerode(skin, s); > brain_a = imdilate(brain, s); > skull = (brain_a & skin_a); > Especially the construction of the skin is a lot of work, as you > need the wholes in the anatomical mri (eyes, ear, inhomogeneities) > by hand. > > Best regards and good luck, > Gregor > > > > > -- > Dr. rer. nat. Gregor Volberg > ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) > University of Regensburg > Institute for Experimental Psychology > 93040 Regensburg, Germany > Tel: +49 941 943 3862 > Fax: +49 941 943 3233 > http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html > > > >>> Younes Zerouali 5/17/2011 12:25 AM > >>> > Hi all, > > I'm trying to segment head anatomical surfaces (scalp, skull) using > the mri scan from patient Colin27 (MNI, Montreal) following the > steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel > ). > My problem is that the function "ft_volumesegment" doesn't return > all the variables that are mentionned in the tutorial. For example, > there is no field named "skull" or "scalp" in the argument returned > by this function. Anyone had this problem before? > > Best, > > > Younes > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 17 09:14:54 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 17 May 2011 09:14:54 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> References: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Message-ID: <4DD23C8E02000057000096DB@gwsmtp1.uni-regensburg.de> Dear Jan-Matthijs, I wasn't aware of this! Thanks a lot dear fieldtrippers, this is surely a helpful addition to ft_volumesegment. Best regards, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> jan-mathijs schoffelen 5/17/2011 8:42 AM >>> Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote: Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit, skin_a = imerode(skin, s); brain_a = imdilate(brain, s); skull = (brain_a & skin_a); Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue May 17 09:28:36 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 17 May 2011 09:28:36 +0200 Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> References: <940868980.135061.1305583605111.JavaMail.root@sculptor.zimbra.ru.nl> <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Hi Diego, Indeed, it is probably a good idea to check for artifacts before performing any resampling. The sample indices that are stored in trl (or sampleinfo) matrices, should always correspond to sample indices in the *original* dataset (on disk), and do not necessarily have any direct relation to sample indices in the data you have in memory. Therefore, if you resample the data, the samples in your data in memory do not directly correspond to samples in the dataset on disk anymore; so therefore trl or sampleinfo fields would not make sense, and might even lead to inconsistencies. This is the reason that ft_resampledata removes any such fields, if present, from your (in-memory) dataset. We are currently in the process of thinking hard about the trl and sampleinfo matrices, and might revise how these are handled in the future. In any case, it should become possible (already on our todo-list) to use the artifact detection functions on in-data memory without explicit sample indices. But, for now, your solution is the quickest one :) Best, Eelke 2011/5/17 Lozano Soldevilla, D. (Diego) : > Hi Stan, > > You're right. It seems that my problem lies in the lack of trl because I previously resample my data and this last function do not creates a new trl with the updated begin and end samples. If I create a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) *data.fsample);, I get the same error but not with the original data (without resampling). Then I'll use data without resampling to check my artifacts. > > Thanks again, > > Diego > > > > ----- "Stan van Pelt" wrote: > >> From: "Stan van Pelt" >> To: "Email discussion list for the FieldTrip project" >> Sent: Monday, 16 May, 2011 9:40:11 PM >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> >> Hi Diego, >> >> Hm, sounds odd to me. Is your trial-definition output from >> ft_definetrial >> correct? So a cfg.trl that is not empty? >> >> Otherwise, you might try starting with an empty cfg again before >> calling >> ft_preprocessing? >> >> cfg=ft_definetrial(cfg); >> trials=cfg.trl; >> >> cfg=[]; >> cfg.trl=trials; >> cfg.dataset                     = [direc d(rr,1).name]; >> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; >> cfg.continuous                  = 'yes'; >> etc.. >> data                            = ft_preprocessing(cfg); >> >> That should give you an output with a trial-structure, I'd say. >> >> Best, >> Stan >> >> -----Original Message----- >> From: fieldtrip-bounces at donders.ru.nl >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano >> Soldevilla, >> D. (Diego) >> Sent: Monday, May 16, 2011 4:25 PM >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> >> Hi Stan, >> >> Thanks for your quickly answer. I get this error: >> >> Warning: the data does not contain a trial definition, assuming that >> the >> trials are consecutive segments of a continuous recording >> > In utilities/private/warning_once at 81 >>   In utilities/private/fixtrialdef at 52 >>   In ft_datatype_raw at 91 >>   In ft_checkdata at 161 >>   In ft_databrowser at 120 >> redrawing with viewmode butterfly >> ??? Improper index matrix reference. >> >> Error in ==> ft_databrowser>redraw_cb at 910 >>   evtsample = [event(:).sample]; >> >> Error in ==> ft_databrowser at 419 >> redraw_cb(h); >> >> I don't know why my data have no trial definition when I'm sure that >> is >> epoched... Any ideas? >> >> Thanks in advance, >> >> Diego >> >> >> >> ----- "Stan van Pelt" wrote: >> >> > From: "Stan van Pelt" >> > To: "Email discussion list for the FieldTrip project" >> >> > Sent: Monday, 16 May, 2011 4:16:16 PM >> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> > >> > Hi Diego, >> > >> > You could try using ft_databrowser instead of ft_rejectvisual >> > (followed by >> > ft_rejectartifact), so: >> > >> > cfg            = []; >> > cfg.continuous = 'no'; >> > cfg.channel    = {'EEG057','EEG058'}; >> > cfg            = ft_databrowser(cfg,data); >> > >> > I think it should work like this. >> > >> > Best, >> > Stan >> > >> > -----Original Message----- >> > From: fieldtrip-bounces at donders.ru.nl >> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano >> > Soldevilla, >> > D. (Diego) >> > Sent: Monday, May 16, 2011 4:00 PM >> > To: fieldtrip at donders.ru.nl >> > Subject: [FieldTrip] ft_rejectvisual channel selection >> > >> > Dear Fieldtrippers, >> > >> > I'm using ft_rejectvisual function to reject visually EOG artifacts >> > of >> > epoched trials. My problem consist that I'm not able to plot only >> the >> > EOG >> > channels even when I explicitly select them ignoring the 'MEG' >> > channels (I >> > get a plot with all channels MEG + EOG). >> > >> > I directly used rejectvisual_channel (used in line 263 >> > offt_rejectvisual) >> > function selecting the EOG channels but I'm getting again all >> > channels. >> > Somebody could tell me what I'm doing wrong? >> > >> > Thanks in advance, >> > >> > Diego >> > >> > >> > >> > PS: Code >> > >> > %epoching >> > cfg = []; >> > cfg.dataset                     = [direc d(rr,1).name]; >> > cfg.trialdef.eventtype          = 'frontpanel trigger'; >> > cfg.trialdef.eventvalue         = 4; >> > cfg.trialdef.prestim            = 1; % in seconds >> > cfg.trialdef.poststim           = 4; % in seconds >> > cfg.trialdef.epochmoving        = 'inbackward'; >> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus >> > cfg.trialdef.jumps              = 1; >> > cfg.trialfun                    = 'trialselec'; >> > >> > cfg = ft_definetrial(cfg); >> > >> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; >> > cfg.lpfilter                    = 'yes'; >> > cfg.lpfreq                      = 250; >> > cfg.baselinewindow              = [-1 0]; >> > cfg.keeptrials                  = 'yes'; >> > cfg.demean                      = 'yes'; >> > cfg.continuous                  = 'yes'; >> > >> > data    = ft_preprocessing(cfg); >> > >> > %.............. >> > >> > >> > %visual data rejection >> > cfg             = []; >> > cfg.channel     = {'EEG057' 'EEG058'}; >> > cfg.method      = 'channel'; >> > cfg.keepchannel = 'yes'; >> > data_c          = ft_rejectvisual(cfg,data); >> > >> > >> > >> > -- >> > PhD Student >> > Donders Institute for Brain, Cognition and Behaviour >> > Centre for Cognitive Neuroimaging >> > Trigon, room 0.83 >> > Kapittelweg 29 >> > Radboud University Nijmegen >> > NL-6500 HB Nijmegen >> > The Netherlands >> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl >> > Tel:      +31-(0)24-36-66274 >> > Web:    http://www.neuosc.com/ >> > _______________________________________________ >> > 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 >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Trigon, room 0.83 >> Kapittelweg 29 >> Radboud University Nijmegen >> NL-6500 HB Nijmegen >> The Netherlands >> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl >> Tel:      +31-(0)24-36-66274 >> Web:    http://www.neuosc.com/ >> >> >> _______________________________________________ >> 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 > From d.lozanosoldevilla at fcdonders.ru.nl Tue May 17 09:37:09 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Tue, 17 May 2011 09:37:09 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <1942589717.137158.1305617671275.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <1909529539.137200.1305617829447.JavaMail.root@sculptor.zimbra.ru.nl> Thanks for your explanation Eelke ;). Now all makes sense. Diego ----- "Eelke Spaak" wrote: > From: "Eelke Spaak" > To: "Email discussion list for the FieldTrip project" > Sent: Tuesday, 17 May, 2011 9:28:36 AM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > Indeed, it is probably a good idea to check for artifacts before > performing any resampling. The sample indices that are stored in trl > (or sampleinfo) matrices, should always correspond to sample indices > in the *original* dataset (on disk), and do not necessarily have any > direct relation to sample indices in the data you have in memory. > Therefore, if you resample the data, the samples in your data in > memory do not directly correspond to samples in the dataset on disk > anymore; so therefore trl or sampleinfo fields would not make sense, > and might even lead to inconsistencies. This is the reason that > ft_resampledata removes any such fields, if present, from your > (in-memory) dataset. > > We are currently in the process of thinking hard about the trl and > sampleinfo matrices, and might revise how these are handled in the > future. In any case, it should become possible (already on our > todo-list) to use the artifact detection functions on in-data memory > without explicit sample indices. > > But, for now, your solution is the quickest one :) > > Best, > Eelke > > 2011/5/17 Lozano Soldevilla, D. (Diego) > : > > Hi Stan, > > > > You're right. It seems that my problem lies in the lack of trl > because I previously resample my data and this last function do not > creates a new trl with the updated begin and end samples. If I create > a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) > *data.fsample);, I get the same error but not with the original data > (without resampling). Then I'll use data without resampling to check > my artifacts. > > > > Thanks again, > > > > Diego > > > > > > > > ----- "Stan van Pelt" wrote: > > > >> From: "Stan van Pelt" > >> To: "Email discussion list for the FieldTrip project" > > >> Sent: Monday, 16 May, 2011 9:40:11 PM > >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > >> Hi Diego, > >> > >> Hm, sounds odd to me. Is your trial-definition output from > >> ft_definetrial > >> correct? So a cfg.trl that is not empty? > >> > >> Otherwise, you might try starting with an empty cfg again before > >> calling > >> ft_preprocessing? > >> > >> cfg=ft_definetrial(cfg); > >> trials=cfg.trl; > >> > >> cfg=[]; > >> cfg.trl=trials; > >> cfg.dataset                     = [direc d(rr,1).name]; > >> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; > >> cfg.continuous                  = 'yes'; > >> etc.. > >> data                            = ft_preprocessing(cfg); > >> > >> That should give you an output with a trial-structure, I'd say. > >> > >> Best, > >> Stan > >> > >> -----Original Message----- > >> From: fieldtrip-bounces at donders.ru.nl > >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > >> Soldevilla, > >> D. (Diego) > >> Sent: Monday, May 16, 2011 4:25 PM > >> To: Email discussion list for the FieldTrip project > >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > >> Hi Stan, > >> > >> Thanks for your quickly answer. I get this error: > >> > >> Warning: the data does not contain a trial definition, assuming > that > >> the > >> trials are consecutive segments of a continuous recording > >> > In utilities/private/warning_once at 81 > >>   In utilities/private/fixtrialdef at 52 > >>   In ft_datatype_raw at 91 > >>   In ft_checkdata at 161 > >>   In ft_databrowser at 120 > >> redrawing with viewmode butterfly > >> ??? Improper index matrix reference. > >> > >> Error in ==> ft_databrowser>redraw_cb at 910 > >>   evtsample = [event(:).sample]; > >> > >> Error in ==> ft_databrowser at 419 > >> redraw_cb(h); > >> > >> I don't know why my data have no trial definition when I'm sure > that > >> is > >> epoched... Any ideas? > >> > >> Thanks in advance, > >> > >> Diego > >> > >> > >> > >> ----- "Stan van Pelt" wrote: > >> > >> > From: "Stan van Pelt" > >> > To: "Email discussion list for the FieldTrip project" > >> > >> > Sent: Monday, 16 May, 2011 4:16:16 PM > >> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > > >> > Hi Diego, > >> > > >> > You could try using ft_databrowser instead of ft_rejectvisual > >> > (followed by > >> > ft_rejectartifact), so: > >> > > >> > cfg            = []; > >> > cfg.continuous = 'no'; > >> > cfg.channel    = {'EEG057','EEG058'}; > >> > cfg            = ft_databrowser(cfg,data); > >> > > >> > I think it should work like this. > >> > > >> > Best, > >> > Stan > >> > > >> > -----Original Message----- > >> > From: fieldtrip-bounces at donders.ru.nl > >> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > >> > Soldevilla, > >> > D. (Diego) > >> > Sent: Monday, May 16, 2011 4:00 PM > >> > To: fieldtrip at donders.ru.nl > >> > Subject: [FieldTrip] ft_rejectvisual channel selection > >> > > >> > Dear Fieldtrippers, > >> > > >> > I'm using ft_rejectvisual function to reject visually EOG > artifacts > >> > of > >> > epoched trials. My problem consist that I'm not able to plot > only > >> the > >> > EOG > >> > channels even when I explicitly select them ignoring the 'MEG' > >> > channels (I > >> > get a plot with all channels MEG + EOG). > >> > > >> > I directly used rejectvisual_channel (used in line 263 > >> > offt_rejectvisual) > >> > function selecting the EOG channels but I'm getting again all > >> > channels. > >> > Somebody could tell me what I'm doing wrong? > >> > > >> > Thanks in advance, > >> > > >> > Diego > >> > > >> > > >> > > >> > PS: Code > >> > > >> > %epoching > >> > cfg = []; > >> > cfg.dataset                     = [direc d(rr,1).name]; > >> > cfg.trialdef.eventtype          = 'frontpanel trigger'; > >> > cfg.trialdef.eventvalue         = 4; > >> > cfg.trialdef.prestim            = 1; % in seconds > >> > cfg.trialdef.poststim           = 4; % in seconds > >> > cfg.trialdef.epochmoving        = 'inbackward'; > >> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus > >> > cfg.trialdef.jumps              = 1; > >> > cfg.trialfun                    = 'trialselec'; > >> > > >> > cfg = ft_definetrial(cfg); > >> > > >> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; > >> > cfg.lpfilter                    = 'yes'; > >> > cfg.lpfreq                      = 250; > >> > cfg.baselinewindow              = [-1 0]; > >> > cfg.keeptrials                  = 'yes'; > >> > cfg.demean                      = 'yes'; > >> > cfg.continuous                  = 'yes'; > >> > > >> > data    = ft_preprocessing(cfg); > >> > > >> > %.............. > >> > > >> > > >> > %visual data rejection > >> > cfg             = []; > >> > cfg.channel     = {'EEG057' 'EEG058'}; > >> > cfg.method      = 'channel'; > >> > cfg.keepchannel = 'yes'; > >> > data_c          = ft_rejectvisual(cfg,data); > >> > > >> > > >> > > >> > -- > >> > PhD Student > >> > Donders Institute for Brain, Cognition and Behaviour > >> > Centre for Cognitive Neuroimaging > >> > Trigon, room 0.83 > >> > Kapittelweg 29 > >> > Radboud University Nijmegen > >> > NL-6500 HB Nijmegen > >> > The Netherlands > >> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > >> > Tel:      +31-(0)24-36-66274 > >> > Web:    http://www.neuosc.com/ > >> > _______________________________________________ > >> > 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 > >> Donders Institute for Brain, Cognition and Behaviour > >> Centre for Cognitive Neuroimaging > >> Trigon, room 0.83 > >> Kapittelweg 29 > >> Radboud University Nijmegen > >> NL-6500 HB Nijmegen > >> The Netherlands > >> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > >> Tel:      +31-(0)24-36-66274 > >> Web:    http://www.neuosc.com/ > >> > >> > >> _______________________________________________ > >> 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 -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From nuria.donamayor at neuro.uni-luebeck.de Tue May 17 10:03:50 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Tue, 17 May 2011 10:03:50 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, sorry it took me this long to answer. The variable format seems to be empty.... Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Freitag, 13. Mai 2011 16:43 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, Could you type dbstop if error on the command line, and evaluate what the variable 'format' is in your case? Thanks, Jan-Mathijs On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > Yes, it is exectly the same version. Better said, versions, because > I tried both 20110413 and 20110512.... > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com > ] > Gesendet: Freitag, 13. Mai 2011 13:39 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Dear Nuria > Is it exactly the same fieldtrip version? > I hope someone will solve this. > as temporary work around you can read the header on windows and then > move to linux > > yuval > > On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine > with a 64-bit Matlab version and I am getting an error I don't know > how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I > have no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to > the Linux machine), so I'm pretty clueless here... Can any of you > help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > > "Many were increasingly of the opinion that they'd all made a big > mistake in coming down from the trees in the first place. And some > said that even the trees had been a bad move, and that no one should > ever have left the oceans". Douglas Adams > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From amelie.serpollet at cea.fr Tue May 17 15:58:49 2011 From: amelie.serpollet at cea.fr (=?iso-8859-1?Q?SERPOLLET_Am=E9lie_228173?=) Date: Tue, 17 May 2011 15:58:49 +0200 Subject: [FieldTrip] questions about realtime buffer Message-ID: Dear Fieldtrip users, I'm implementing a realtime buffer in C++ pretty much like in "demo_combined" : my application creates a buffer server and an acquisition client. I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. If these modifications can be useful for other users and do not create other problems, I will share them. I encounter now a new problem : what if there are several acquisition clients ? I tried to create several couples "buffer-server + acquisition client" in different threads in my application, but it does not work at all, because of global variables (I suppose). It seems that one buffer server can not manage several acquisition clients, but I'm not sure of this point. Did anyone encounter this problem (or solve it) ? Or do anyone have an idea ? Best regards, Amelie Serpollet -------------- next part -------------- An HTML attachment was scrubbed... URL: From younes_zerouali at hotmail.com Tue May 17 16:11:36 2011 From: younes_zerouali at hotmail.com (Younes Zerouali) Date: Tue, 17 May 2011 10:11:36 -0400 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> References: , <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de>, <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Message-ID: Dear Gregor and Jan-Mathijs, Thank you both for prompt answers, I'll get to work and try that! Best, Younes From: jan.schoffelen at donders.ru.nl To: fieldtrip at donders.ru.nl Date: Tue, 17 May 2011 08:42:22 +0200 Subject: Re: [FieldTrip] Antw: Segment anatomy from MRI (spm8) Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote:Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit,skin_a = imerode(skin, s);brain_a = imdilate(brain, s);skull = (brain_a & skin_a);Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck,Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The NetherlandsJ.Schoffelen at donders.ru.nlTelephone: 0031-24-3614793 _______________________________________________ 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 jan.schoffelen at donders.ru.nl Tue May 17 16:24:21 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 17 May 2011 16:24:21 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> Message-ID: <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> Hi Nuria, Strange. Format should contain a number. What matlab version are you running on the Linux machine? Best, Jan-Mathijs On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > sorry it took me this long to answer. The variable format seems to > be empty.... > Nuria > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Freitag, 13. Mai 2011 16:43 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Could you type dbstop if error on the command line, and evaluate what > the variable 'format' is in your case? > > Thanks, > > Jan-Mathijs > > On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > >> Yes, it is exectly the same version. Better said, versions, because >> I tried both 20110413 and 20110512.... >> >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >> ] >> Gesendet: Freitag, 13. Mai 2011 13:39 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Dear Nuria >> Is it exactly the same fieldtrip version? >> I hope someone will solve this. >> as temporary work around you can read the header on windows and then >> move to linux >> >> yuval >> >> On 13 May 2011 11:42, Nuria Donamayor Alonso > > wrote: >> Dear fieltrip users, >> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >> with a 64-bit Matlab version and I am getting an error I don't know >> how to solve: >> >> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >> ??? SWITCH expression must be a scalar or string constant. >> >> Error in ==> read_4d_hdr at 60 >> switch format >> >> Error in ==> ft_read_header at 153 >> orig = read_4d_hdr(datafile); >> >> If I try to read the same data on my Windows PC with 32-bit Matlab I >> have no problem reading the header file (but I can't even finish the >> preprocessing before it runs out of memory, therefore the switch to >> the Linux machine), so I'm pretty clueless here... Can any of you >> help me? >> Thanks, >> Nuria >> >> >> >> Nuria Doñamayor Alonso, MSc >> Universitätsklinikum Schleswig-Holstein >> Campus Lübeck >> Klinik für Neurologie >> Ratzeburger Allee 160 >> 23538 Lübeck >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Y.Harpaz >> >> a link to the BIU MEG lab: >> http://faculty.biu.ac.il/~goldsa/index.html>> >> >> "Many were increasingly of the opinion that they'd all made a big >> mistake in coming down from the trees in the first place. And some >> said that even the trees had been a bad move, and that no one should >> ever have left the oceans". Douglas Adams >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From nuria.donamayor at neuro.uni-luebeck.de Tue May 17 16:49:17 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Tue, 17 May 2011 16:49:17 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, I'm using Matlab 7.11.0 (R2010b). Best, Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Dienstag, 17. Mai 2011 16:24 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, Strange. Format should contain a number. What matlab version are you running on the Linux machine? Best, Jan-Mathijs On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > sorry it took me this long to answer. The variable format seems to > be empty.... > Nuria > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Freitag, 13. Mai 2011 16:43 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Could you type dbstop if error on the command line, and evaluate what > the variable 'format' is in your case? > > Thanks, > > Jan-Mathijs > > On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > >> Yes, it is exectly the same version. Better said, versions, because >> I tried both 20110413 and 20110512.... >> >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >> ] >> Gesendet: Freitag, 13. Mai 2011 13:39 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Dear Nuria >> Is it exactly the same fieldtrip version? >> I hope someone will solve this. >> as temporary work around you can read the header on windows and then >> move to linux >> >> yuval >> >> On 13 May 2011 11:42, Nuria Donamayor Alonso > > wrote: >> Dear fieltrip users, >> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >> with a 64-bit Matlab version and I am getting an error I don't know >> how to solve: >> >> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >> ??? SWITCH expression must be a scalar or string constant. >> >> Error in ==> read_4d_hdr at 60 >> switch format >> >> Error in ==> ft_read_header at 153 >> orig = read_4d_hdr(datafile); >> >> If I try to read the same data on my Windows PC with 32-bit Matlab I >> have no problem reading the header file (but I can't even finish the >> preprocessing before it runs out of memory, therefore the switch to >> the Linux machine), so I'm pretty clueless here... Can any of you >> help me? >> Thanks, >> Nuria >> >> >> >> Nuria Doñamayor Alonso, MSc >> Universitätsklinikum Schleswig-Holstein >> Campus Lübeck >> Klinik für Neurologie >> Ratzeburger Allee 160 >> 23538 Lübeck >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Y.Harpaz >> >> a link to the BIU MEG lab: >> http://faculty.biu.ac.il/~goldsa/index.html>> >> >> "Many were increasingly of the opinion that they'd all made a big >> mistake in coming down from the trees in the first place. And some >> said that even the trees had been a bad move, and that no one should >> ever have left the oceans". Douglas Adams >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From batrod at gmail.com Tue May 17 20:50:43 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 17 May 2011 13:50:43 -0500 Subject: [FieldTrip] Problem with recent version of eeglab2fieldtrip Message-ID: Dear Fieldtrip users, Recently i experienced problems doing sone Time-freq analysis and i realized it's coming from the eeglab2fieldtrip function and more precisely one line that has been changed, apparently without being reported on the eeglab revision history and neither in fieldtrip revision history (but i may be wrong with this last one, i checked very quickly on google code) The problem occurs at the Line 47: data.label = { EEG.chanlocs(1:EEG.nbchan).labels }; % Eeglab version 9.0.2.3 data.label = { EEG.chanlocs(EEG.icachansind).labels }; % Eeglab verion 9.0.4.4 The old version works, whereas the new version will cause problem if you dont perform an ICA with eeglab, prior to the conversion. Hope this helps, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arno at cerco.ups-tlse.fr Wed May 18 00:08:36 2011 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Tue, 17 May 2011 15:08:36 -0700 Subject: [FieldTrip] Problem with recent version of eeglab2fieldtrip In-Reply-To: References: Message-ID: <07D46921-50BF-4C27-AA81-E4E96FD49698@cerco.ups-tlse.fr> Dear Rodolphe, I had changed that line because I could not fit dipoles for some ICA components (which is the main reason this function was originally designed for). The attached function should work for both components and channel data. Let me know if it does not. Best, Arno ps: the change was actually documented on the web (http://sccn.ucsd.edu/wiki/EEGLAB_revision_history_version_9) as "eeglab2fieldtrip.m, fix performing dipole fitting on subset of channels (SVN 9092 - Arno)" On May 17, 2011, at 11:50 AM, Rodolphe Nenert wrote: > Dear Fieldtrip users, > > Recently i experienced problems doing sone Time-freq analysis and i realized it's coming from the eeglab2fieldtrip function and more precisely one line that has been changed, apparently without being reported on the eeglab revision history and neither in fieldtrip revision history (but i may be wrong with this last one, i checked very quickly on google code) > > The problem occurs at the Line 47: > > data.label = { EEG.chanlocs(1:EEG.nbchan).labels }; % Eeglab version 9.0.2.3 > > data.label = { EEG.chanlocs(EEG.icachansind).labels }; % Eeglab verion 9.0.4.4 > > The old version works, whereas the new version will cause problem if you dont perform an ICA with eeglab, prior to the conversion. > > Hope this helps, > > Rodolphe. > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eeglab2fieldtrip.m Type: application/octet-stream Size: 5887 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed May 18 10:51:14 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 18 May 2011 10:51:14 +0200 Subject: [FieldTrip] Tutorial error Message-ID: Dear all, I am a very beginner with fieldtrip. I have tried to run the tutorial a couple of weeks ago, and it worked smoothly. Yesterday I have tried again, but surprisngly I got anerror message, as soon as I started the tutorial (the first step entitled: "reading and processing the interesting trials"): cfg = []; cfg.dataset = 'Subject01.ds'; cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for fully incongruent (FIC). cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 2; % in seconds cfg = ft_definetrial(cfg); ??? Attempt to reference field of non-structure array Error in ==> trialfun_general at 117 for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) This sounds really weird since it worked 2 weeks ago on the same machine and with the same version of Fieldtrip. Any advice would be very appreciated. Best wishes, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 18 11:02:29 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 18 May 2011 11:02:29 +0200 Subject: [FieldTrip] Tutorial error In-Reply-To: References: Message-ID: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> Dear Davide, I am not sure whether you are using the same fieldtrip version. There has been a glitch recently with the trialfun_general, but this should be fixed by now. Could you update to a superrecent version of fieldtrip and try again? Thanks, Jan-Mathijs PS: I cannot reproduce your error so I expect it to go away if you update. On May 18, 2011, at 10:51 AM, Davide Rivolta wrote: > Dear all, > > I am a very beginner with fieldtrip. > > I have tried to run the tutorial a couple of weeks ago, and it > worked smoothly. > > Yesterday I have tried again, but surprisngly I got anerror message, > as soon as I started the tutorial (the first step entitled: "reading > and processing the interesting trials"): > > > cfg = []; > cfg.dataset = 'Subject01.ds'; > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger > for fully incongruent (FIC). > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 2; % in seconds > > cfg = ft_definetrial(cfg); > > > ??? Attempt to reference field of non-structure array > > Error in ==> trialfun_general at 117 > for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) > > > > > This sounds really weird since it worked 2 weeks ago on the same > machine and with the same version of Fieldtrip. > > Any advice would be very appreciated. > > Best wishes, > > Davide > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Wed May 18 12:13:27 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 18 May 2011 12:13:27 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> Message-ID: <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> Hi Nuria, I cannot reproduce your problem on a linux machine we have here, running matlab 2010b (64-bit). Either there is something wrong with your dataset (does it happen as well for another dataset?), or there is something different with respect to the configuration of your Linux machine. Best, Jan-Mathijs On May 17, 2011, at 4:49 PM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > I'm using Matlab 7.11.0 (R2010b). > Best, > Nuria > > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Dienstag, 17. Mai 2011 16:24 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Strange. Format should contain a number. What matlab version are you > running on the Linux machine? > > Best, > > Jan-Mathijs > > > On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > >> Hi Jan-Mathijs, >> sorry it took me this long to answer. The variable format seems to >> be empty.... >> Nuria >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl >> ] >> Gesendet: Freitag, 13. Mai 2011 16:43 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Hi Nuria, >> >> Could you type dbstop if error on the command line, and evaluate what >> the variable 'format' is in your case? >> >> Thanks, >> >> Jan-Mathijs >> >> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: >> >>> Yes, it is exectly the same version. Better said, versions, because >>> I tried both 20110413 and 20110512.... >>> >>> ________________________________________ >>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >>> ] >>> Gesendet: Freitag, 13. Mai 2011 13:39 >>> An: Email discussion list for the FieldTrip project >>> Betreff: Re: [FieldTrip] problem reading 4d header >>> >>> Dear Nuria >>> Is it exactly the same fieldtrip version? >>> I hope someone will solve this. >>> as temporary work around you can read the header on windows and then >>> move to linux >>> >>> yuval >>> >>> On 13 May 2011 11:42, Nuria Donamayor Alonso >> > wrote: >>> Dear fieltrip users, >>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >>> with a 64-bit Matlab version and I am getting an error I don't know >>> how to solve: >>> >>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >>> ??? SWITCH expression must be a scalar or string constant. >>> >>> Error in ==> read_4d_hdr at 60 >>> switch format >>> >>> Error in ==> ft_read_header at 153 >>> orig = read_4d_hdr(datafile); >>> >>> If I try to read the same data on my Windows PC with 32-bit Matlab I >>> have no problem reading the header file (but I can't even finish the >>> preprocessing before it runs out of memory, therefore the switch to >>> the Linux machine), so I'm pretty clueless here... Can any of you >>> help me? >>> Thanks, >>> Nuria >>> >>> >>> >>> Nuria Doñamayor Alonso, MSc >>> Universitätsklinikum Schleswig-Holstein >>> Campus Lübeck >>> Klinik für Neurologie >>> Ratzeburger Allee 160 >>> 23538 Lübeck >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Y.Harpaz >>> >>> a link to the BIU MEG lab: >>> http://faculty.biu.ac.il/~goldsa/index.html>>> >>> >>> "Many were increasingly of the opinion that they'd all made a big >>> mistake in coming down from the trees in the first place. And some >>> said that even the trees had been a bad move, and that no one should >>> ever have left the oceans". Douglas Adams >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> >> _______________________________________________ >> 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 > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From drivolta81 at gmail.com Wed May 18 13:40:11 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 18 May 2011 13:40:11 +0200 Subject: [FieldTrip] Tutorial error In-Reply-To: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> References: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> Message-ID: Dear Jan-Mathijs This is the funny part. I run it (and worked) on the 201105053 version two weeks ago. Yesterday it did not work on the same version. So, I have downloaded the most recent version 20110516, but it is still not working. I do not really know what to do with it. Thanks for your kind help, Davide On Wed, May 18, 2011 at 11:02 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Davide, > > I am not sure whether you are using the same fieldtrip version. There has > been a glitch recently with the trialfun_general, but this should be fixed > by now. Could you update to a superrecent version of fieldtrip and try > again? > > Thanks, > > Jan-Mathijs > > PS: I cannot reproduce your error so I expect it to go away if you update. > > > On May 18, 2011, at 10:51 AM, Davide Rivolta wrote: > > Dear all, >> >> I am a very beginner with fieldtrip. >> >> I have tried to run the tutorial a couple of weeks ago, and it worked >> smoothly. >> >> Yesterday I have tried again, but surprisngly I got anerror message, as >> soon as I started the tutorial (the first step entitled: "reading and >> processing the interesting trials"): >> >> >> cfg = []; >> cfg.dataset = 'Subject01.ds'; >> cfg.trialdef.eventtype = 'backpanel trigger'; >> cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for >> fully incongruent (FIC). >> cfg.trialdef.prestim = 1; % in seconds >> cfg.trialdef.poststim = 2; % in seconds >> >> cfg = ft_definetrial(cfg); >> >> >> ??? Attempt to reference field of non-structure array >> >> Error in ==> trialfun_general at 117 >> for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) >> >> >> >> >> This sounds really weird since it worked 2 weeks ago on the same machine >> and with the same version of Fieldtrip. >> >> Any advice would be very appreciated. >> >> Best wishes, >> >> Davide >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuria.donamayor at neuro.uni-luebeck.de Wed May 18 15:00:33 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Wed, 18 May 2011 15:00:33 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de>, <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F903D@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, I get the same error message with all my datasets. Maybe it does have to do with my Linux machine... Any idea what I should look for to fix it? Thanks, Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Mittwoch, 18. Mai 2011 12:13 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, I cannot reproduce your problem on a linux machine we have here, running matlab 2010b (64-bit). Either there is something wrong with your dataset (does it happen as well for another dataset?), or there is something different with respect to the configuration of your Linux machine. Best, Jan-Mathijs On May 17, 2011, at 4:49 PM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > I'm using Matlab 7.11.0 (R2010b). > Best, > Nuria > > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Dienstag, 17. Mai 2011 16:24 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Strange. Format should contain a number. What matlab version are you > running on the Linux machine? > > Best, > > Jan-Mathijs > > > On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > >> Hi Jan-Mathijs, >> sorry it took me this long to answer. The variable format seems to >> be empty.... >> Nuria >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl >> ] >> Gesendet: Freitag, 13. Mai 2011 16:43 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Hi Nuria, >> >> Could you type dbstop if error on the command line, and evaluate what >> the variable 'format' is in your case? >> >> Thanks, >> >> Jan-Mathijs >> >> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: >> >>> Yes, it is exectly the same version. Better said, versions, because >>> I tried both 20110413 and 20110512.... >>> >>> ________________________________________ >>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >>> ] >>> Gesendet: Freitag, 13. Mai 2011 13:39 >>> An: Email discussion list for the FieldTrip project >>> Betreff: Re: [FieldTrip] problem reading 4d header >>> >>> Dear Nuria >>> Is it exactly the same fieldtrip version? >>> I hope someone will solve this. >>> as temporary work around you can read the header on windows and then >>> move to linux >>> >>> yuval >>> >>> On 13 May 2011 11:42, Nuria Donamayor Alonso >> > wrote: >>> Dear fieltrip users, >>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >>> with a 64-bit Matlab version and I am getting an error I don't know >>> how to solve: >>> >>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >>> ??? SWITCH expression must be a scalar or string constant. >>> >>> Error in ==> read_4d_hdr at 60 >>> switch format >>> >>> Error in ==> ft_read_header at 153 >>> orig = read_4d_hdr(datafile); >>> >>> If I try to read the same data on my Windows PC with 32-bit Matlab I >>> have no problem reading the header file (but I can't even finish the >>> preprocessing before it runs out of memory, therefore the switch to >>> the Linux machine), so I'm pretty clueless here... Can any of you >>> help me? >>> Thanks, >>> Nuria >>> >>> >>> >>> Nuria Doñamayor Alonso, MSc >>> Universitätsklinikum Schleswig-Holstein >>> Campus Lübeck >>> Klinik für Neurologie >>> Ratzeburger Allee 160 >>> 23538 Lübeck >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Y.Harpaz >>> >>> a link to the BIU MEG lab: >>> http://faculty.biu.ac.il/~goldsa/index.html>>> >>> >>> "Many were increasingly of the opinion that they'd all made a big >>> mistake in coming down from the trees in the first place. And some >>> said that even the trees had been a bad move, and that no one should >>> ever have left the oceans". Douglas Adams >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> >> _______________________________________________ >> 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 > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From michael.hanke at gmail.com Wed May 18 15:10:26 2011 From: michael.hanke at gmail.com (Michael Hanke) Date: Wed, 18 May 2011 09:10:26 -0400 Subject: [FieldTrip] Neuroscience software survey: What is popular, what has problems? Immediate results Message-ID: <20110518131026.GD19084@meiner> [Apologies for cross-posting] Dear neuroscience researchers and their IT staff We invite you to participate in a survey on software usage and computing environments in neuroscience research. It will take no more than five minutes to fill it out. Immediately after sending your answers you will get to see a summary of how other participants have responded before. This data will eventually be made available to software vendors and distributors to determine advantages and issue of popular computing environments in neuroscience research. Learn about what fellow neuroscientists are doing to address their computing demands -- take the survey! http://goo.gl/euIMc Thanks, -- PyMVPA/NeuroDebian Team: Yaroslav O. Halchenko & Michael Hanke Postdoctoral Fellows, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 From jdien07 at mac.com Fri May 20 04:30:59 2011 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 19 May 2011 22:30:59 -0400 Subject: [FieldTrip] problems using ft_freqanalysis Message-ID: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> Hi, I'm just starting to get up to speed on spectral analysis (I'm an ERPer). I'm using the following set-up: I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): cfg.method='mtmwelch'; cfg.output='pow'; [freq] = ft_freqanalysis(cfg, data); I got the error message: ------------------------- the input is raw data with 128 channels and 160 trials 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used taking every sample as time of interest the input is raw data with 128 channels and 160 trials ??? Error using ==> ft_freqanalysis at 216 you must specify a smoothing parameter with taper = dpss Error in ==> ft_freqanalysis_mtmwelch at 107 freq = ft_freqanalysis(cfgconvol, data); Error in ==> ft_freqanalysis at 271 [freq] = feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, data); ----------------------- Two things: 1) What would be an appropriate smoothing parameter? 2) Is this a bug? It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: cfg.foi=[1:1:30]; cfg.taper='hanning'; which resulted in: -------------------------- >> [freq] = ft_freqanalysis(cfg, data); the input is raw data with 128 channels and 160 trials 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used taking every sample as time of interest the input is raw data with 128 channels and 160 trials processing trials ??? Reference to non-existent field 't_ftimwin'. Error in ==> ft_freqanalysis at 454 [spectrum_mtmconvol,ntaper,foi,toi] = ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, 'timwin', cfg.t_ftimwin, 'taper', ... Error in ==> ft_freqanalysis_mtmwelch at 107 freq = ft_freqanalysis(cfgconvol, data); Error in ==> ft_freqanalysis at 271 [freq] = feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, data); -------------------- What am I doing wrong? I looked through the code but couldn't figure out what the problem was. I am very confused... fieldtrip-20110519 MATLAB Version 7.11.0.584 (R2010b) Operating System: Mac OS X Version: 10.6.7 Build: 10J869 >> cfg cfg = dataset: 'SLI_3011m_40m_POA.egis' method: 'mtmwelch' output: 'pow' taper: 'hanning' tapsmofrq: 4 foi: [1x30 double] >> data data = hdr: [1x1 struct] label: {128x1 cell} time: {1x160 cell} trial: {1x160 cell} fsample: 250 sampleinfo: [160x2 double] cfg: [1x1 struct] Thanks for any help you can give! Joe From jan.schoffelen at donders.ru.nl Fri May 20 07:36:03 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 20 May 2011 07:36:03 +0200 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> Message-ID: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Dear Joe, To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. Cheers, Jan-Mathijs On May 20, 2011, at 4:30 AM, Joseph Dien wrote: > Hi, > I'm just starting to get up to speed on spectral analysis (I'm an > ERPer). > I'm using the following set-up: > > I tried the following (for one second long trials with an Fs of > 250Hz and interest in frequencies below 30Hz): > > cfg.method='mtmwelch'; > cfg.output='pow'; > [freq] = ft_freqanalysis(cfg, data); > > I got the error message: > > ------------------------- > the input is raw data with 128 channels and 160 trials > 'mtmwelch' has not been implemented yet in the specest toolbox, the > old implementation is being used > taking every sample as time of interest > the input is raw data with 128 channels and 160 trials > ??? Error using ==> ft_freqanalysis at 216 > you must specify a smoothing parameter with taper = dpss > > Error in ==> ft_freqanalysis_mtmwelch at 107 > freq = ft_freqanalysis(cfgconvol, data); > > Error in ==> ft_freqanalysis at 271 > [freq] = > feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, > data); > > ----------------------- > Two things: > > 1) What would be an appropriate smoothing parameter? > > 2) Is this a bug? It defaulted to dpss as specified by the > documentation but it didn't provide a default smoothing parameter so > the default still resulted in a crash. > > Anyway, given the advice in the tutlrial to use a hanning window > rather than a multi-taper like dpss for frequencies below 30, I > tried the following: > > cfg.foi=[1:1:30]; > cfg.taper='hanning'; > > which resulted in: > > -------------------------- >>> [freq] = ft_freqanalysis(cfg, data); > the input is raw data with 128 channels and 160 trials > 'mtmwelch' has not been implemented yet in the specest toolbox, the > old implementation is being used > taking every sample as time of interest > the input is raw data with 128 channels and 160 trials > processing trials > ??? Reference to non-existent field 't_ftimwin'. > > Error in ==> ft_freqanalysis at 454 > [spectrum_mtmconvol,ntaper,foi,toi] = > ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, > 'timwin', cfg.t_ftimwin, 'taper', ... > > Error in ==> ft_freqanalysis_mtmwelch at 107 > freq = ft_freqanalysis(cfgconvol, data); > > Error in ==> ft_freqanalysis at 271 > [freq] = > feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, > data); > > > -------------------- > What am I doing wrong? I looked through the code but couldn't > figure out what the problem was. I am very confused... > > fieldtrip-20110519 > MATLAB Version 7.11.0.584 (R2010b) > Operating System: Mac OS X Version: 10.6.7 Build: 10J869 > > >>> cfg > > cfg = > > dataset: 'SLI_3011m_40m_POA.egis' > method: 'mtmwelch' > output: 'pow' > taper: 'hanning' > tapsmofrq: 4 > foi: [1x30 double] > >>> data > > data = > > hdr: [1x1 struct] > label: {128x1 cell} > time: {1x160 cell} > trial: {1x160 cell} > fsample: 250 > sampleinfo: [160x2 double] > cfg: [1x1 struct] > > > Thanks for any help you can give! > > Joe > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From Elena.Orekhova at neuro.gu.se Fri May 20 14:00:40 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 20 May 2011 12:00:40 +0000 Subject: [FieldTrip] ft_read_vol with Neuromag Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> Hi, I try to read volume from the Neuromag .fif file using vol = ft_read_vol(NEUROMAG_FIF_FILE_NAME, 'fileformat', 'neuromag_fif') I get the error: *********************** ??? Undefined variable "cfg" or class "cfg.gradfile". Error in ==> ft_read_vol at 77 fprintf('using Neuromag gradiometer definition from %s\n', cfg.gradfile); Any advice? Elena ________________________________ Elena V Orekhova, Ph.D. Inst. Neuroscience and Physiology University of Gothenburg S-413 45 Gothenburg, Sweden phone: +46 31 342 48 02 elena at neuro.gu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri May 20 16:54:16 2011 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 20 May 2011 10:54:16 -0400 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> Thanks for this helpful explanation! Can you provide me with guidance on what is involved in deciding the setting for the spectral smoothing parameter 'tapsmofrq' for dpss? Or where to look for information on this issue? Thanks again! Joe On May 20, 2011, at 1:36 AM, jan-mathijs schoffelen wrote: > Dear Joe, > > To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. > Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). > In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. > > Cheers, > > Jan-Mathijs > > > > On May 20, 2011, at 4:30 AM, Joseph Dien wrote: > >> Hi, >> I'm just starting to get up to speed on spectral analysis (I'm an ERPer). >> I'm using the following set-up: >> >> I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): >> >> cfg.method='mtmwelch'; >> cfg.output='pow'; >> [freq] = ft_freqanalysis(cfg, data); >> >> I got the error message: >> >> ------------------------- >> the input is raw data with 128 channels and 160 trials >> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >> taking every sample as time of interest >> the input is raw data with 128 channels and 160 trials >> ??? Error using ==> ft_freqanalysis at 216 >> you must specify a smoothing parameter with taper = dpss >> >> Error in ==> ft_freqanalysis_mtmwelch at 107 >> freq = ft_freqanalysis(cfgconvol, data); >> >> Error in ==> ft_freqanalysis at 271 >> [freq] = >> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >> data); >> >> ----------------------- >> Two things: >> >> 1) What would be an appropriate smoothing parameter? >> >> 2) Is this a bug? It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. >> >> Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: >> >> cfg.foi=[1:1:30]; >> cfg.taper='hanning'; >> >> which resulted in: >> >> -------------------------- >>>> [freq] = ft_freqanalysis(cfg, data); >> the input is raw data with 128 channels and 160 trials >> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >> taking every sample as time of interest >> the input is raw data with 128 channels and 160 trials >> processing trials >> ??? Reference to non-existent field 't_ftimwin'. >> >> Error in ==> ft_freqanalysis at 454 >> [spectrum_mtmconvol,ntaper,foi,toi] = >> ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, >> 'timwin', cfg.t_ftimwin, 'taper', ... >> >> Error in ==> ft_freqanalysis_mtmwelch at 107 >> freq = ft_freqanalysis(cfgconvol, data); >> >> Error in ==> ft_freqanalysis at 271 >> [freq] = >> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >> data); >> >> >> -------------------- >> What am I doing wrong? I looked through the code but couldn't figure out what the problem was. I am very confused... >> >> fieldtrip-20110519 >> MATLAB Version 7.11.0.584 (R2010b) >> Operating System: Mac OS X Version: 10.6.7 Build: 10J869 >> >> >>>> cfg >> >> cfg = >> >> dataset: 'SLI_3011m_40m_POA.egis' >> method: 'mtmwelch' >> output: 'pow' >> taper: 'hanning' >> tapsmofrq: 4 >> foi: [1x30 double] >> >>>> data >> >> data = >> >> hdr: [1x1 struct] >> label: {128x1 cell} >> time: {1x160 cell} >> trial: {1x160 cell} >> fsample: 250 >> sampleinfo: [160x2 double] >> cfg: [1x1 struct] >> >> >> Thanks for any help you can give! >> >> Joe >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From dgroppe at cogsci.ucsd.edu Fri May 20 17:38:50 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 20 May 2011 08:38:50 -0700 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> Message-ID: Hi Joe, David Kleinfeld and Partha Mitra have an excellent tutorial on multitaper spectral analysis that should help: http://www-physics.ucsd.edu/neurophysics/publications/CSHL_2009_SPECTRA_4.pdf -D On Fri, May 20, 2011 at 7:54 AM, Joseph Dien wrote: > Thanks for this helpful explanation!  Can you provide me with guidance on what is involved in deciding the setting for the spectral smoothing parameter 'tapsmofrq' for dpss?  Or where to look for information on this issue? > > Thanks again! > > Joe > > > On May 20, 2011, at 1:36 AM, jan-mathijs schoffelen wrote: > >> Dear Joe, >> >> To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. >> Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). >> In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. >> >> Cheers, >> >> Jan-Mathijs >> >> >> >> On May 20, 2011, at 4:30 AM, Joseph Dien wrote: >> >>> Hi, >>> I'm just starting to get up to speed on spectral analysis (I'm an ERPer). >>> I'm using the following set-up: >>> >>> I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): >>> >>> cfg.method='mtmwelch'; >>> cfg.output='pow'; >>> [freq] = ft_freqanalysis(cfg, data); >>> >>> I got the error message: >>> >>> ------------------------- >>> the input is raw data with 128 channels and 160 trials >>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >>> taking every sample as time of interest >>> the input is raw data with 128 channels and 160 trials >>> ??? Error using ==> ft_freqanalysis at 216 >>> you must specify a smoothing parameter with taper = dpss >>> >>> Error in ==> ft_freqanalysis_mtmwelch at 107 >>> freq = ft_freqanalysis(cfgconvol, data); >>> >>> Error in ==> ft_freqanalysis at 271 >>> [freq] = >>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >>> data); >>> >>> ----------------------- >>> Two things: >>> >>> 1) What would be an appropriate smoothing parameter? >>> >>> 2) Is this a bug?  It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. >>> >>> Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: >>> >>> cfg.foi=[1:1:30]; >>> cfg.taper='hanning'; >>> >>> which resulted in: >>> >>> -------------------------- >>>>> [freq] = ft_freqanalysis(cfg, data); >>> the input is raw data with 128 channels and 160 trials >>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >>> taking every sample as time of interest >>> the input is raw data with 128 channels and 160 trials >>> processing trials >>> ??? Reference to non-existent field 't_ftimwin'. >>> >>> Error in ==> ft_freqanalysis at 454 >>>     [spectrum_mtmconvol,ntaper,foi,toi] = >>>     ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, >>>     'timwin', cfg.t_ftimwin, 'taper', ... >>> >>> Error in ==> ft_freqanalysis_mtmwelch at 107 >>> freq = ft_freqanalysis(cfgconvol, data); >>> >>> Error in ==> ft_freqanalysis at 271 >>> [freq] = >>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >>> data); >>> >>> >>> -------------------- >>> What am I doing wrong?  I looked through the code but couldn't figure out what the problem was.  I am very confused... >>> >>> fieldtrip-20110519 >>> MATLAB Version 7.11.0.584 (R2010b) >>> Operating System: Mac OS X  Version: 10.6.7 Build: 10J869 >>> >>> >>>>> cfg >>> >>> cfg = >>> >>>   dataset: 'SLI_3011m_40m_POA.egis' >>>    method: 'mtmwelch' >>>    output: 'pow' >>>     taper: 'hanning' >>> tapsmofrq: 4 >>>       foi: [1x30 double] >>> >>>>> data >>> >>> data = >>> >>>        hdr: [1x1 struct] >>>      label: {128x1 cell} >>>       time: {1x160 cell} >>>      trial: {1x160 cell} >>>    fsample: 250 >>> sampleinfo: [160x2 double] >>>        cfg: [1x1 struct] >>> >>> >>> Thanks for any help you can give! >>> >>> Joe >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> _______________________________________________ >> 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 > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From Elena.Orekhova at neuro.gu.se Sat May 21 14:11:41 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Sat, 21 May 2011 12:11:41 +0000 Subject: [FieldTrip] rpa/nas/lpa coordinates Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> Hi I Just started to use Fieldtrip with my Neuromag MEG data and try to follow the example script ‘read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space’ The instruction suggests to take voxel coordinates of fiduscials from the Neuromag GUI for MRI-MEG Integration. I have already performed this step and saved the transformed mri in the /sets/XXX.fif file. Should I write any rpa/nas/lpa coordinates in this case? cfg.fiducial.rpa = [y x z]; cfg.fiducial.nas = [y x z]; cfg.fiducial.lpa = [y x z]; I have 2 4X4 transformations in the .fif file, not sure what they mean. mri.hdr.trans.trans 0.9913 0.1210 0.0518 -0.0032 -0.0948 0.9291 -0.3574 0.0254 -0.0914 0.3494 0.9325 -0.0519 0 0 0 1.0000 mri.hdr.voxel_trans.trans -0.0000 -0.0000 -0.0010 0.1058 -0.0005 0.0000 0.0000 0.1597 0 -0.0005 0.0001 0.1058 0 0 0 1.0000 I'll be most grateful for the help! Regards, Elena ________________________________ Elena V Orekhova, Ph.D. Inst. Neuroscience and Physiology University of Gothenburg S-413 45 Gothenburg, Sweden phone: +46 31 342 48 02 elena at neuro.gu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon May 23 09:33:34 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 23 May 2011 09:33:34 +0200 Subject: [FieldTrip] rpa/nas/lpa coordinates In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> Message-ID: Dear Elena > On 21 May 2011, at 14:11, Elena Orekhova wrote: > >> Hi >> I Just started to use Fieldtrip with my Neuromag MEG data and try >> to follow the example script >> ‘read_neuromag_mri_and_create_single- >> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space >> ’ I don't know all details of the Neuromag system, but recently we did add the http://fieldtrip.fcdonders.nl/getting_started/yokogawa documentation that explains reasonably general how coordinate system coregistration works. We also added a new function (FT_SENSORREALIGN) to ease the coregistration and we are working towards a more consistent representation of the corodinate systems in the relevant fieldtrip data structures. Although the details for your system are different (see http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined) , you might get a better overview of the steps that are involved by reading the yokogawa getting started. > The instruction suggests to take voxel coordinates of fiduscials > from the Neuromag > GUI for MRI-MEG Integration. I have already performed this step and > saved the > transformed mri in the /sets/XXX.fif file. I suggest you use the FT_DETERMINE_COORDSYS to perform a visual inspection of the coordinate systems of your anatomical MRI and of your sensor positions (data.grad, or you can use FT_READ_SENS to read them directly from the MEG fif file). Note that you have to use the function twice (on the mri and on the grad) and compare the figures yourself. > Should I write any rpa/nas/lpa coordinates in this case? > cfg.fiducial.rpa = [y x z]; > cfg.fiducial.nas = [y x z]; > cfg.fiducial.lpa = [y x z]; if you need them (see above), then these should be [x y z] and not [y x z]. > > I have 2 4X4 transformations in the .fif file, not sure what they > mean. Please read this page, which is a general introduction. > > mri.hdr.trans.trans > > 0.9913 0.1210 0.0518 -0.0032 > -0.0948 0.9291 -0.3574 0.0254 > -0.0914 0.3494 0.9325 -0.0519 > 0 0 0 1.0000 > mri.hdr.voxel_trans.trans > > -0.0000 -0.0000 -0.0010 0.1058 > -0.0005 0.0000 0.0000 0.1597 > 0 -0.0005 0.0001 0.1058 > 0 0 0 1.0000 the mri header is system specific, so I am not sure. But I guess that the first is the homogenous transformation matrix in head coordinates (linked to the fiducials) and the second is the homogenous transformation matrix in MRI coordinates. The first one appears to be in mm, the second one in meter. Please try mri.transform = mri.hdr.voxel_trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c mri.transform = mri.hdr.trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c The two figures will show you the origin, the direction of axes of the coordinate system and the scale. best regards, Robert From r.oostenveld at donders.ru.nl Mon May 23 09:41:17 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 23 May 2011 09:41:17 +0200 Subject: [FieldTrip] ft_read_vol with Neuromag In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> Message-ID: <4BFE3CE0-268F-4ACC-8863-5017DC5957AF@donders.ru.nl> Hi Elena Although some years ago FieldTrip was supporting volume conduction models from Neuromag using the meg-pd and the (closed source) meg-calc toolboxes from the company itself, I suspect that nobody has been using them the last few years. The mex files in meg-pd and meg-calc were often problematic to work with due to platform and library issues. The single-shell volume conduction model that is avaialble in Fieldtrip is currently the preferred volume model. Looking at the code, there is indeed a bug since cfg.gradfile is not defined. If you want to continue along the path of meg-pd and meg- calc, you could hardcode the filename and see how far you get. But I'd suspect that you don't have the required (commercial) mex files from meg-calc anyway. best regards Robert On 20 May 2011, at 14:00, Elena Orekhova wrote: > Hi, > I try to read volume from the Neuromag .fif file using > > vol = ft_read_vol(NEUROMAG_FIF_FILE_NAME, 'fileformat', > 'neuromag_fif') > > I get the error: > *********************** > ??? Undefined variable "cfg" or class "cfg.gradfile". > > Error in ==> ft_read_vol at 77 > fprintf('using Neuromag gradiometer definition from %s\n', > cfg.gradfile); > > Any advice? > > Elena > > Elena V Orekhova, Ph.D. > Inst. Neuroscience and Physiology > University of Gothenburg > S-413 45 Gothenburg, Sweden > phone: +46 31 342 48 02 > elena at neuro.gu.se > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Elena.Orekhova at neuro.gu.se Mon May 23 10:00:15 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 23 May 2011 08:00:15 +0000 Subject: [FieldTrip] segmentation problem with Neuromag Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC7CC3@exchccr1.neuro.gu.se> Dear Fieldtrip users and developers, I would like to start using Fieldtrip for the source analysis of the MEG data, but I have some problem with mri segmentation using Neuromag-306 .fif MRI file. I do: 1) import .fif, (Coordinate alignment was already done in Neuromag). mriname = 'NEUROMAGxxx.fif' [mri] = ft_read_mri(mriname) cfg = []; ft_sourceplot(cfg,mri); ***** attachment: mri.jpg ****** 2) do segmentation cfg = []; cfg.template = 'T1.nii'; %spm8 cfg.coordsys = 'neuromag'; cfg.write = 'no'; cfg.name = 'temp'; cfg.interactive = 'yes'; [segmentedmri] = ft_volumesegment(cfg, mri) 3) plot the original and segmented mri cfg = []; test.dim = [512 512 180]; test = segmentedmri; test.avg.pow = test.gray+test.white; test.anatomy = mri.anatomy; cfg.funparameter = 'avg.pow'; cfg.interactive = 'yes'; ft_sourceplot(cfg,test); ***** attachment : mri_segmented.jpg ****** Apparently, there is a displacement of the segmented mri image. It seems also that the segmented mri is bigger then the original mri. The similar (although not the same) picture is observed when I do coordinate alignment in the MNE and use the /sets/CORxxx.fif saved from the MNE sohtware. I have seen some discussions on this topic, but I have not found the solution. Should I swap x and y coordinates? How can I do it? I would be most grateful for help! Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mri.jpg Type: image/jpeg Size: 20047 bytes Desc: mri.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mri_segmented.jpg Type: image/jpeg Size: 59004 bytes Desc: mri_segmented.jpg URL: From odidodi at hotmail.com Mon May 23 10:44:31 2011 From: odidodi at hotmail.com (odelia nakar) Date: Mon, 23 May 2011 08:44:31 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Mon May 23 12:03:11 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 23 May 2011 10:03:11 +0000 Subject: [FieldTrip] rpa/nas/lpa coordinates In-Reply-To: References: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se>, Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC8D07@exchccr1.neuro.gu.se> Dear Robert, As you advised, I tried to use 'ft_determine_coordsys' to look at my non-segmented MRI, but got the error (see below). What can be the reason? /Elena >> >> mri mri = dim: [512 512 180] anatomy: [512x512x180 int16] hdr: [1x1 struct] transform: [4x4 double] unit: 'm' >> [dataout] = ft_determine_coordsys(mri) ??? Error using ==> surface Z must be a matrix, not a scalar or vector Error in ==> ft_plot_slice at 184 h = surface(Xh, Yh, Zh, V); Error in ==> ft_plot_ortho at 94 hx = ft_plot_slice(dat, varargin{:}); Error in ==> ft_determine_coordsys at 192 ft_plot_ortho(data.(funparam), 'transform', data.transform, 'resolution', 1, 'style', 'intersect'); >> ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Robert Oostenveld [r.oostenveld at donders.ru.nl] Sent: Monday, May 23, 2011 9:33 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] rpa/nas/lpa coordinates Dear Elena > On 21 May 2011, at 14:11, Elena Orekhova wrote: > >> Hi >> I Just started to use Fieldtrip with my Neuromag MEG data and try >> to follow the example script >> ‘read_neuromag_mri_and_create_single- >> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space >> ’ I don't know all details of the Neuromag system, but recently we did add the http://fieldtrip.fcdonders.nl/getting_started/yokogawa documentation that explains reasonably general how coordinate system coregistration works. We also added a new function (FT_SENSORREALIGN) to ease the coregistration and we are working towards a more consistent representation of the corodinate systems in the relevant fieldtrip data structures. Although the details for your system are different (see http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined) , you might get a better overview of the steps that are involved by reading the yokogawa getting started. > The instruction suggests to take voxel coordinates of fiduscials > from the Neuromag > GUI for MRI-MEG Integration. I have already performed this step and > saved the > transformed mri in the /sets/XXX.fif file. I suggest you use the FT_DETERMINE_COORDSYS to perform a visual inspection of the coordinate systems of your anatomical MRI and of your sensor positions (data.grad, or you can use FT_READ_SENS to read them directly from the MEG fif file). Note that you have to use the function twice (on the mri and on the grad) and compare the figures yourself. > Should I write any rpa/nas/lpa coordinates in this case? > cfg.fiducial.rpa = [y x z]; > cfg.fiducial.nas = [y x z]; > cfg.fiducial.lpa = [y x z]; if you need them (see above), then these should be [x y z] and not [y x z]. > > I have 2 4X4 transformations in the .fif file, not sure what they > mean. Please read this page, which is a general introduction. > > mri.hdr.trans.trans > > 0.9913 0.1210 0.0518 -0.0032 > -0.0948 0.9291 -0.3574 0.0254 > -0.0914 0.3494 0.9325 -0.0519 > 0 0 0 1.0000 > mri.hdr.voxel_trans.trans > > -0.0000 -0.0000 -0.0010 0.1058 > -0.0005 0.0000 0.0000 0.1597 > 0 -0.0005 0.0001 0.1058 > 0 0 0 1.0000 the mri header is system specific, so I am not sure. But I guess that the first is the homogenous transformation matrix in head coordinates (linked to the fiducials) and the second is the homogenous transformation matrix in MRI coordinates. The first one appears to be in mm, the second one in meter. Please try mri.transform = mri.hdr.voxel_trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c mri.transform = mri.hdr.trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c The two figures will show you the origin, the direction of axes of the coordinate system and the scale. best regards, Robert _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jinyinz at ece.cmu.edu Mon May 23 15:46:20 2011 From: jinyinz at ece.cmu.edu (jinyinz at ece.cmu.edu) Date: Mon, 23 May 2011 09:46:20 -0400 (EDT) Subject: [FieldTrip] the source space for MEG/EEG source localization Message-ID: <4412.128.2.133.95.1306158380.squirrel@webmail.ece.cmu.edu> Dear Fieldtrippers, I have a question about the source space selection for MEG/EEG source localization. Some source localization algorithms restrict the reconstruction to sources located on cortical surface. To implement such kind of algorithm, I used mne_setup_source_space to create a source space on cortical surface. By default mne_setup_source_space creates a decimated dipole grid on the white matter surface. Although this setting is widely used, some papers create a source space on the gray matter surface instead. Are there any specific reasons for selecting any of the two options? Thanks, Jinyin From dgroppe at cogsci.ucsd.edu Mon May 23 17:57:25 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Mon, 23 May 2011 08:57:25 -0700 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: > Hi all, > > I'm troubled by the fact that when I use ICA for blinks\eyes movements > removal, I remove the relevant components also from trials that do not > contain blinks\eyes movements. In order to avoid this bias we thought to > combine the data before ICA ("data" structure) with the data after ICA > ("dataica" structure), only in specific trials, as follows: > > datall=dataica; > datall.trial=data.trial; > datall.time=data.time; > blinks=[2 4 5 8 bla bla 156]; > for ind=1:length(blinks) >      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; > end > > To my first question: I just wanted to check that there is no problem with > that, or any reason not to use it. > > Another issue- I use motor learning task, and I'm trying to understand what > happens through the process, in terms of power-frequency changes through the > process. How would you recommend that I'd use the ft_freqanalysis function? > What method to use (or what do I need to consider when choosing the method > field)? > > > Thanks a lot, > Odelia. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From jdien07 at mac.com Tue May 24 03:07:57 2011 From: jdien07 at mac.com (Joseph Dien) Date: Mon, 23 May 2011 21:07:57 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote: > Hi Odelia, > When you use ICA (or any other spatial filter) to correct for EEG > artifacts, you're going to distort your data some by removing true EEG > activity in addition to the artifact (for an explanation, see: > http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). > So to minimize distortion, it would be better not to apply ICA > artifact correction to artifact-free data. However, if the frequency > of the artifact differs across experimental conditions, it could > confound your analysis. For example, I suspect people blink more > often to targets in an oddball experiment than standards. Thus if you > apply ICA only to blinky trials, you could find a difference between > the EEG response to standards and targets that simply reflects the > fact ICA removed more EEG activity in the target trials (i.e., it > wouldn't reflect a true difference in neural processing). > hope this helps, > -David > > On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: >> Hi all, >> >> I'm troubled by the fact that when I use ICA for blinks\eyes movements >> removal, I remove the relevant components also from trials that do not >> contain blinks\eyes movements. In order to avoid this bias we thought to >> combine the data before ICA ("data" structure) with the data after ICA >> ("dataica" structure), only in specific trials, as follows: >> >> datall=dataica; >> datall.trial=data.trial; >> datall.time=data.time; >> blinks=[2 4 5 8 bla bla 156]; >> for ind=1:length(blinks) >> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >> end >> >> To my first question: I just wanted to check that there is no problem with >> that, or any reason not to use it. >> >> Another issue- I use motor learning task, and I'm trying to understand what >> happens through the process, in terms of power-frequency changes through the >> process. How would you recommend that I'd use the ft_freqanalysis function? >> What method to use (or what do I need to consider when choosing the method >> field)? >> >> >> Thanks a lot, >> Odelia. >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From shackman at wisc.edu Tue May 24 04:00:34 2011 From: shackman at wisc.edu (Alexander J. Shackman) Date: Mon, 23 May 2011 21:00:34 -0500 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: And for a related perspective, see McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, *Neuroimage**, 54*, 4-9. http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: > I agree with David's reasoning. You may find the following article to be > of help as well in understanding the issues involved: > > Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of > simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping*, 28 > (8), 742-763. > > Cheers! > > Joe > > On May 23, 2011, at 11:57 AM, David Groppe wrote: > > Hi Odelia, > When you use ICA (or any other spatial filter) to correct for EEG > artifacts, you're going to distort your data some by removing true EEG > activity in addition to the artifact (for an explanation, see: > http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). > So to minimize distortion, it would be better not to apply ICA > artifact correction to artifact-free data. However, if the frequency > of the artifact differs across experimental conditions, it could > confound your analysis. For example, I suspect people blink more > often to targets in an oddball experiment than standards. Thus if you > apply ICA only to blinky trials, you could find a difference between > the EEG response to standards and targets that simply reflects the > fact ICA removed more EEG activity in the target trials (i.e., it > wouldn't reflect a true difference in neural processing). > hope this helps, > -David > > On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: > > Hi all, > > > I'm troubled by the fact that when I use ICA for blinks\eyes movements > > removal, I remove the relevant components also from trials that do not > > contain blinks\eyes movements. In order to avoid this bias we thought to > > combine the data before ICA ("data" structure) with the data after ICA > > ("dataica" structure), only in specific trials, as follows: > > > datall=dataica; > > datall.trial=data.trial; > > datall.time=data.time; > > blinks=[2 4 5 8 bla bla 156]; > > for ind=1:length(blinks) > > datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; > > end > > > To my first question: I just wanted to check that there is no problem with > > that, or any reason not to use it. > > > Another issue- I use motor learning task, and I'm trying to understand what > > happens through the process, in terms of power-frequency changes through > the > > process. How would you recommend that I'd use the ft_freqanalysis function? > > What method to use (or what do I need to consider when choosing the method > > field)? > > > > Thanks a lot, > > Odelia. > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://homepage.mac.com/jdien07/ > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Alexander J. Shackman, Ph.D. Wisconsin Psychiatric Institute & Clinics and Department of Psychology University of Wisconsin-Madison 1202 West Johnson Street Madison, Wisconsin 53706 Telephone: +1 (608) 358-5025 Fax: +1 (608) 265-2875 Email: shackman at wisc.edu http://psyphz.psych.wisc.edu/~shackman -------------- next part -------------- An HTML attachment was scrubbed... URL: From odidodi at hotmail.com Tue May 24 08:46:55 2011 From: odidodi at hotmail.com (odelia nakar) Date: Tue, 24 May 2011 06:46:55 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>, , , <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: Thank you all- Joe, Alexander and David, it is indeed very helpful and enlightening. I actually don't have any stimulus, but I wasn't aware of the hidden EMG. Have a good day (or night :))! Odelia. From: jdien07 at mac.com Date: Mon, 23 May 2011 21:07:57 -0400 To: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] ICA+frqanalysis questions I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote:Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph DienE-mail: jdien07 at mac.comPhone: 301-226-8848Fax: 301-226-8811http://homepage.mac.com/jdien07/ _______________________________________________ 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 stefan.debener at uni-oldenburg.de Tue May 24 09:11:16 2011 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Tue, 24 May 2011 09:11:16 +0200 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: <4DDB5A14.3090102@uni-oldenburg.de> Hi Odelia, I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... Best, Stefan Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: > And for a related perspective, see > > McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. > J. (2011). Electromyogenic artifacts and electroencephalographic > inferences revisited, */Neuroimage/*/, 54/, 4-9. > > http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf > > > > On Mon, May 23, 2011 at 8:07 PM, Joseph Dien > wrote: > > I agree with David's reasoning. You may find the following > article to be of help as well in understanding the issues involved: > > Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and > ICA of simulated ERPs: Promax versus Infomax rotations. /Human > Brain Mapping/, 28(8), 742-763. > > Cheers! > > Joe > > On May 23, 2011, at 11:57 AM, David Groppe wrote: > >> Hi Odelia, >> When you use ICA (or any other spatial filter) to correct for EEG >> artifacts, you're going to distort your data some by removing >> true EEG >> activity in addition to the artifact (for an explanation, see: >> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >> So to minimize distortion, it would be better not to apply ICA >> artifact correction to artifact-free data. However, if the frequency >> of the artifact differs across experimental conditions, it could >> confound your analysis. For example, I suspect people blink more >> often to targets in an oddball experiment than standards. Thus >> if you >> apply ICA only to blinky trials, you could find a difference between >> the EEG response to standards and targets that simply reflects the >> fact ICA removed more EEG activity in the target trials (i.e., it >> wouldn't reflect a true difference in neural processing). >> hope this helps, >> -David >> >> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >> > wrote: >>> Hi all, >>> >>> I'm troubled by the fact that when I use ICA for blinks\eyes >>> movements >>> removal, I remove the relevant components also from trials that >>> do not >>> contain blinks\eyes movements. In order to avoid this bias we >>> thought to >>> combine the data before ICA ("data" structure) with the data >>> after ICA >>> ("dataica" structure), only in specific trials, as follows: >>> >>> datall=dataica; >>> datall.trial=data.trial; >>> datall.time=data.time; >>> blinks=[2 4 5 8 bla bla 156]; >>> for ind=1:length(blinks) >>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>> end >>> >>> To my first question: I just wanted to check that there is no >>> problem with >>> that, or any reason not to use it. >>> >>> Another issue- I use motor learning task, and I'm trying to >>> understand what >>> happens through the process, in terms of power-frequency changes >>> through the >>> process. How would you recommend that I'd use the >>> ft_freqanalysis function? >>> What method to use (or what do I need to consider when choosing >>> the method >>> field)? >>> >>> >>> Thanks a lot, >>> Odelia. >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> David Groppe, Ph.D. >> Postdoctoral Researcher >> Kutaslab >> Dept. of Cognitive Science >> University of California, San Diego >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://homepage.mac.com/jdien07/ > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Alexander J. Shackman, Ph.D. > Wisconsin Psychiatric Institute & Clinics and > Department of Psychology > University of Wisconsin-Madison > 1202 West Johnson Street > Madison, Wisconsin 53706 > > Telephone: +1 (608) 358-5025 > Fax: +1 (608) 265-2875 > Email: shackman at wisc.edu > http://psyphz.psych.wisc.edu/~shackman > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Tue May 24 23:47:39 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Tue, 24 May 2011 14:47:39 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine Message-ID: Hi there, My lab is running MATLAB 7.8 on a Linux network and when we plot spectrograms using ft_multiplotTFR.m the computer we're using will often reboot. It appears to happen most often (if not exclusively), when we close the figure window produced by ft_multiplotTFR.m. The problem happens even if we create non-interactive figures (i.e., we set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., Java disabled). Has anyone else had this problem? Does anyone have an idea as to what a solution might be? Puzzlingly, we don't have this problem when running MATLAB on a Mac. much appreciated, -David -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From r.vandermeij at donders.ru.nl Wed May 25 00:23:58 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 24 May 2011 15:23:58 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: References: Message-ID: <4DDC2FFE.9000600@donders.ru.nl> Hi David, Depending on what you mean by crashing, it could be the opengl drivers. I've experienced similar issues with complex plotting functions. Try creating the figure-window (note, not the plot) using the zbuffer to circumvent it by figure('renderer','zbuffer') Hope it helps, Roemer On 24-May-11 14:47, David Groppe wrote: > Hi there, > My lab is running MATLAB 7.8 on a Linux network and when we plot > spectrograms using ft_multiplotTFR.m the computer we're using will > often reboot. It appears to happen most often (if not exclusively), > when we close the figure window produced by ft_multiplotTFR.m. The > problem happens even if we create non-interactive figures (i.e., we > set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., > Java disabled). Has anyone else had this problem? Does anyone have > an idea as to what a solution might be? Puzzlingly, we don't have > this problem when running MATLAB on a Mac. > much appreciated, > -David > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Radboud University Nijmegen P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Wed May 25 02:10:02 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Tue, 24 May 2011 17:10:02 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: <4DDC2FFE.9000600@donders.ru.nl> References: <4DDC2FFE.9000600@donders.ru.nl> Message-ID: Thanks very much for the response Roemer. By "crashing," I mean the screen suddenly goes blank and the machine reverts to the login screen. I've tried your suggestion and so far it looks like it's working! I'll let you know if the problem returns. greatly appreciated, -David On Tue, May 24, 2011 at 3:23 PM, Roemer van der Meij wrote: > Hi David, > > Depending on what you mean by crashing, it could be the opengl drivers. I've > experienced similar issues with complex plotting functions. Try creating the > figure-window (note, not the plot) using the zbuffer to circumvent it by > figure('renderer','zbuffer') > > Hope it helps, > Roemer > > > > On 24-May-11 14:47, David Groppe wrote: > > Hi there, > My lab is running MATLAB 7.8 on a Linux network and when we plot > spectrograms using ft_multiplotTFR.m the computer we're using will > often reboot. It appears to happen most often (if not exclusively), > when we close the figure window produced by ft_multiplotTFR.m. The > problem happens even if we create non-interactive figures (i.e., we > set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., > Java disabled). Has anyone else had this problem? Does anyone have > an idea as to what a solution might be? Puzzlingly, we don't have > this problem when running MATLAB on a Mac. > much appreciated, > -David > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > Radboud University Nijmegen > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From g.piantoni at nin.knaw.nl Wed May 25 08:59:20 2011 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Wed, 25 May 2011 08:59:20 +0200 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: References: <4DDC2FFE.9000600@donders.ru.nl> Message-ID: Hi David, I also had similar problems, such as crashing of the VNC window on a remote server. I agree with Roemer that it's probably due to buggy opengl drivers. More information at: http://www.mathworks.com/support/tech-notes/1200/1201.html#Section_4 Briefly, you can run as first command: >> opengl software to force matlab to use the (less buggy) software implementation of opengl. Then the trick "figure('renderer','zbuffer')" should not be necessary. Hope this helps. Gio -- Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.giovannipiantoni.com On Wed, May 25, 2011 at 02:10, David Groppe wrote: > Thanks very much for the response Roemer.  By "crashing," I mean the > screen suddenly goes blank and the machine reverts to the login > screen.  I've tried your suggestion and so far it looks like it's > working!  I'll let you know if the problem returns. >     greatly appreciated, >          -David > > On Tue, May 24, 2011 at 3:23 PM, Roemer van der Meij > wrote: >> Hi David, >> >> Depending on what you mean by crashing, it could be the opengl drivers. I've >> experienced similar issues with complex plotting functions. Try creating the >> figure-window (note, not the plot) using the zbuffer to circumvent it by >> figure('renderer','zbuffer') >> >> Hope it helps, >> Roemer >> >> >> >> On 24-May-11 14:47, David Groppe wrote: >> >> Hi there, >>    My lab is running MATLAB 7.8 on a Linux network and when we plot >> spectrograms using ft_multiplotTFR.m the computer we're using will >> often reboot.  It appears to happen most often (if not exclusively), >> when we close the figure window produced by ft_multiplotTFR.m.  The >> problem happens even if we create non-interactive figures (i.e., we >> set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., >> Java disabled).  Has anyone else had this problem?   Does anyone have >> an idea as to what a solution might be?  Puzzlingly, we don't have >> this problem when running MATLAB on a Mac. >>           much appreciated, >>                 -David >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> Radboud University Nijmegen >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From g.dimitriadis at donders.ru.nl Wed May 25 09:48:49 2011 From: g.dimitriadis at donders.ru.nl (George Dimitriadis) Date: Wed, 25 May 2011 09:48:49 +0200 Subject: [FieldTrip] (no subject) Message-ID: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> Hello guys, I just run an ft_freqanalysis using cfg.taper='dssp'. By mistake I took the cfg. tapsmofrq to be too small resulting in a single taper. This was fine, but when I run freqanalysis I got an error saying that the warning_once (ft_specest_mtmfft at 89) was not found. Apparently it was there to warn me about using only 1 tapper for smoothing with 'dssp'. I am just letting you know that for some reason the warning_once(char) function couldn't be found. Thanks George -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 25 10:10:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 25 May 2011 10:10:02 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> References: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> Message-ID: <6F47EF43-DE4D-4031-8BCC-F5C9D9AA13D3@donders.ru.nl> Hi George, Sorry about this. If you are running a local copy of fieldtrip, you can copy warning_once.m from fieldtrip/private into fieldtrip/specest/ private. It should work then. I'll fix it in the release version asap. Cheers, JM On May 25, 2011, at 9:48 AM, George Dimitriadis wrote: > Hello guys, > > I just run an ft_freqanalysis using cfg.taper=’dssp’. By mistake I > took the cfg. tapsmofrq to be too small resulting in a single taper. > This was fine, but when I run freqanalysis I got an error saying > that the warning_once (ft_specest_mtmfft at 89) was not found. > Apparently it was there to warn me about using only 1 tapper for > smoothing with ‘dssp’. I am just letting you know that for some > reason the warning_once(char) function couldn’t be found. > > Thanks > > George > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.N.Maijers at student.ru.nl Wed May 25 11:50:16 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Wed, 25 May 2011 11:50:16 +0200 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? Message-ID: <20110525115016.0fc02ea6@thuisrekenaar> Dear readers, I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit (Linux thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux). When I call "ft_timelockstatistics()" with "cfg.mva ={ft_mv_standardizer() ft_mv_svm()};" It fails: "selected 60 channels selected 351 time bins selected 1 frequency bins using "statistics_crossvalidate" for the statistical testing initializing random number generator with seed 1 validating 1 dataset(s) input 1 consists of 439 examples and 21060 features output 1 consists of 439 examples and 1 features validating using 5-fold cross-validation using 5 folds for 1 datasets dataset 1: validating fold 1 of 5 using 351 training samples and 88 test samples Compiling tprod for first use /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching for -lstdc++ /usr/bin/ld: cannot find -lstdc++ collect2: ld returned 1 exit status mex: link of ' "tprod.mexglx"' failed. ??? Error using ==> tprod at 132 unable to compile MEX version of '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', please make sure your MEX compiler is set up correctly (try 'mex -setup')." I have followed the instructions on https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX compiling but it was not successful. -> Before I singlehandedly bring my operating system configuration into disarray, I would like to learn from you the following. Do you know of ways to use a gcc to compile code written for a 32-bit architecture ona 64-bit machine? Or if necessary another compiler that works under Linux? -> If such a thing is certainly impossible, are there ways to avoid MEX compiling? Or could someone provide precompiled MEX files that would suit my configuration? [*] I have installed the Ubuntu package "ia32-libs" (version 20090808ubuntu9.1) [*] It seems that the only thing I need is 32-bit binaries for libstdc++. Perhaps I can introduce these in some creative way, but I would like to check with you all first. I hope you are willing to help me. As a novice to FieldTrip and even MATLAB, I have encountered many obstacles but I am determined to surmount them. Kind regards, Sander Maijers (BA Linguistics student) From S.N.Maijers at student.ru.nl Wed May 25 12:13:01 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Wed, 25 May 2011 12:13:01 +0200 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory Message-ID: <20110525121301.2f896b3e@thuisrekenaar> Dear readers, While all other functional subdirectories do get included after an "addpath" of the FieldTrip root directory, the "multivariate" subdirectories does not get included. It assume this is because of automatical detection that requirements of the FieldTrip multivariate module were not met. Yet while some parts of the multivariate module seem to rely on features exclusive to MATLAB 64-bit editions, others (like the ridge regression functionality) do not. >From my (tentative) investigation it appears that there is no standard way to add a path recursively from a startup.m file, even though that can be done with the graphical interface of MATLAB. What are your thoughts about this? Can anyone offer a method to automatically add FieldTrip including the multivariate module to the path upon startup of MATLAB that works in my situation? Kind regards, Sander Maijers P.S.: In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit Linux. From ekanal at cmu.edu Wed May 25 14:53:53 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Wed, 25 May 2011 08:53:53 -0400 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory In-Reply-To: <20110525121301.2f896b3e@thuisrekenaar> References: <20110525121301.2f896b3e@thuisrekenaar> Message-ID: <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> Hello Sander - Just so you know, there is a way to recursively add folders to a path, using the `genpath` command: addpath(genpath(path/to/folder)) However, as you said, it's probably just a better idea to add it to the `ft_defaults` file so it's added automatically, as you suggested. Elli On May 25, 2011, at 6:13 AM, Sander Maijers wrote: > Dear readers, > > While all other functional subdirectories do get included after an > "addpath" of the FieldTrip root directory, the "multivariate" > subdirectories does not get included. > > It assume this is because of automatical detection that requirements of > the FieldTrip multivariate module were not met. > > Yet while some parts of the multivariate module seem to rely on > features exclusive to MATLAB 64-bit editions, others (like the ridge > regression functionality) do not. > >> From my (tentative) investigation it appears that there is no standard > way to add a path recursively from a startup.m file, even though that > can be done with the graphical interface of MATLAB. > > What are your thoughts about this? > > Can anyone offer a method to automatically add FieldTrip including the > multivariate module to the path upon startup of MATLAB that works in > my situation? > > Kind regards, > Sander Maijers > > P.S.: > In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit > Linux. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From batrod at gmail.com Wed May 25 17:39:02 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Wed, 25 May 2011 10:39:02 -0500 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory In-Reply-To: <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> References: <20110525121301.2f896b3e@thuisrekenaar> <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> Message-ID: Hello Sander, Elli's suggestion is right. As you apparently want to do that on matlab startup and using Linux, you can add a matlab shortcut on your panel with the following instructions : matlab -r "yourinstructions" "yourinstructions" can be an addpath or wathever you want. I often use this initialization to avoid default path conflicts between spm, fieldtrip, eeglab, etc... Hope this helps, Rodolphe On Wed, May 25, 2011 at 7:53 AM, Kanal Eliezer wrote: > Hello Sander - > > Just so you know, there is a way to recursively add folders to a path, > using the `genpath` command: > > addpath(genpath(path/to/folder)) > > However, as you said, it's probably just a better idea to add it to the > `ft_defaults` file so it's added automatically, as you suggested. > > Elli > > > On May 25, 2011, at 6:13 AM, Sander Maijers wrote: > > > Dear readers, > > > > While all other functional subdirectories do get included after an > > "addpath" of the FieldTrip root directory, the "multivariate" > > subdirectories does not get included. > > > > It assume this is because of automatical detection that requirements of > > the FieldTrip multivariate module were not met. > > > > Yet while some parts of the multivariate module seem to rely on > > features exclusive to MATLAB 64-bit editions, others (like the ridge > > regression functionality) do not. > > > >> From my (tentative) investigation it appears that there is no standard > > way to add a path recursively from a startup.m file, even though that > > can be done with the graphical interface of MATLAB. > > > > What are your thoughts about this? > > > > Can anyone offer a method to automatically add FieldTrip including the > > multivariate module to the path upon startup of MATLAB that works in > > my situation? > > > > Kind regards, > > Sander Maijers > > > > P.S.: > > In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit > > Linux. > > > > _______________________________________________ > > 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 batrod at gmail.com Wed May 25 18:32:19 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Wed, 25 May 2011 11:32:19 -0500 Subject: [FieldTrip] Filtering and oscillations Message-ID: Dear Fieldtrippers, i have a theoretical question. Im interested into phase-lock analysis between sensors in alpha oscillations. Prior to do so, my data were bandpassed between 2 and 30 Hz. However, i heard that such a low-pass filter can alter informations usefull to phase-lock analysis. Any suggestions on that? Best regards, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jenwhitman at gmail.com Wed May 25 19:53:28 2011 From: jenwhitman at gmail.com (Jen Whitman) Date: Wed, 25 May 2011 10:53:28 -0700 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? In-Reply-To: <20110525115016.0fc02ea6@thuisrekenaar> References: <20110525115016.0fc02ea6@thuisrekenaar> Message-ID: As another ubuntu 64-bit user, I'd say your problem is with your matlab install rather than with fieldtrip. You may have inadvertently specified 32-bit instead of 64-bit when you installed matlab. If you type "computer" at the matlab prompt, it should say "GLNXA64". If not, I recommend redoing the matlab installation and making sure you specify your OS as 64-bit. If you still get error message about libstdc++.so, you may need to install that library using the 'synaptic package manger' (in your system menu under administration). A good resource for help if you have further difficulty may be linuxquestions.org. Best of luck! On Wed, May 25, 2011 at 2:50 AM, Sander Maijers wrote: > Dear readers, > > I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit (Linux > thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 > x86_64 GNU/Linux). > > When I call "ft_timelockstatistics()" with "cfg.mva ={ft_mv_standardizer() > ft_mv_svm()};" > > It fails: > > "selected 60 channels > selected 351 time bins > selected 1 frequency bins > using "statistics_crossvalidate" for the statistical testing > initializing random number generator with seed 1 > validating 1 dataset(s) > input 1 consists of 439 examples and 21060 features > output 1 consists of 439 examples and 1 features > validating using 5-fold cross-validation > using 5 folds for 1 datasets > dataset 1: validating fold 1 of 5 using 351 training samples and 88 test > samples Compiling tprod for first use > /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > searching for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching > for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > searching for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching > for -lstdc++ /usr/bin/ld: > cannot find -lstdc++ collect2: ld returned 1 exit status > > mex: link of ' "tprod.mexglx"' failed. > > ??? Error using ==> tprod at 132 unable to compile MEX version of > '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', > please make sure your MEX compiler is set up correctly (try 'mex -setup')." > > > I have followed the instructions on > https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX > compiling but it was not successful. > > -> Before I singlehandedly bring my operating system configuration into > disarray, I would like to learn from you the following. Do you know of ways > to use a gcc to compile code written for a 32-bit architecture ona 64-bit > machine? Or if necessary another compiler that works under Linux? > -> If such a thing is certainly impossible, are there ways to avoid MEX > compiling? Or could someone provide precompiled MEX files that would suit my > configuration? > > [*] I have installed the Ubuntu package "ia32-libs" (version > 20090808ubuntu9.1) > [*] It seems that the only thing I need is 32-bit binaries for libstdc++. > Perhaps I can introduce these in some creative way, but I would like to > check with you all first. > > I hope you are willing to help me. As a novice to FieldTrip and even > MATLAB, I have encountered many obstacles but I am determined to surmount > them. > > Kind regards, > Sander Maijers (BA Linguistics student) > _______________________________________________ > 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 S.N.Maijers at student.ru.nl Thu May 26 16:23:39 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Thu, 26 May 2011 16:23:39 +0200 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? In-Reply-To: References: <20110525115016.0fc02ea6@thuisrekenaar> Message-ID: <20110526162339.65dd030c@thuisrekenaar> Jen, thanks for your suggestion. That problem I had fixed before. I am among those who could not even get a 64-bit install if they wished so, because the Student edition of MATLAB is still 32-bit-only. This problem will occur later on, in case some MEX-compilation needs to be done, in my case with the multivariate module! I have succeeded in fixing the problem however. Those who are confronted with it as well, can read: http://fieldtrip.fcdonders.nl/faq/compile?&#fixing_mex-compilation_with_32-bit_variants_of_matlab_running_under_64-bit_linux . On Wed, 25 May 2011 10:53:28 -0700 Jen Whitman wrote: > As another ubuntu 64-bit user, I'd say your problem is with your > matlab install rather than with fieldtrip. You may have inadvertently > specified 32-bit instead of 64-bit when you installed matlab. If you > type "computer" at the matlab prompt, it should say "GLNXA64". If > not, I recommend redoing the matlab installation and making sure you > specify your OS as 64-bit. If you still get error message about > libstdc++.so, you may need to install that library using the > 'synaptic package manger' (in your system menu under administration). > A good resource for help if you have further difficulty may be > linuxquestions.org. > > Best of luck! > > On Wed, May 25, 2011 at 2:50 AM, Sander Maijers > wrote: > > > Dear readers, > > > > I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit > > (Linux thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 > > 18:42:20 UTC 2011 x86_64 GNU/Linux). > > > > When I call "ft_timelockstatistics()" with "cfg.mva > > ={ft_mv_standardizer() ft_mv_svm()};" > > > > It fails: > > > > "selected 60 channels > > selected 351 time bins > > selected 1 frequency bins > > using "statistics_crossvalidate" for the statistical testing > > initializing random number generator with seed 1 > > validating 1 dataset(s) > > input 1 consists of 439 examples and 21060 features > > output 1 consists of 439 examples and 1 features > > validating using 5-fold cross-validation > > using 5 folds for 1 datasets > > dataset 1: validating fold 1 of 5 using 351 training samples and 88 > > test samples Compiling tprod for first use > > /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when > > searching for -lstdc++ /usr/bin/ld: > > cannot find -lstdc++ collect2: ld returned 1 exit status > > > > mex: link of ' "tprod.mexglx"' failed. > > > > ??? Error using ==> tprod at 132 unable to compile MEX version of > > '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', > > please make sure your MEX compiler is set up correctly (try 'mex > > -setup')." > > > > > > I have followed the instructions on > > https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX > > compiling but it was not successful. > > > > -> Before I singlehandedly bring my operating system configuration > > into disarray, I would like to learn from you the following. Do you > > know of ways to use a gcc to compile code written for a 32-bit > > architecture ona 64-bit machine? Or if necessary another compiler > > that works under Linux? -> If such a thing is certainly impossible, > > are there ways to avoid MEX compiling? Or could someone provide > > precompiled MEX files that would suit my configuration? > > > > [*] I have installed the Ubuntu package "ia32-libs" (version > > 20090808ubuntu9.1) > > [*] It seems that the only thing I need is 32-bit binaries for > > libstdc++. Perhaps I can introduce these in some creative way, but > > I would like to check with you all first. > > > > I hope you are willing to help me. As a novice to FieldTrip and even > > MATLAB, I have encountered many obstacles but I am determined to > > surmount them. > > > > Kind regards, > > Sander Maijers (BA Linguistics student) > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > From dgroppe at cogsci.ucsd.edu Fri May 27 03:54:35 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Thu, 26 May 2011 18:54:35 -0700 Subject: [FieldTrip] duplicate spm directories Message-ID: Hi again, I'm running the March 28th version of Fieldtrip and am getting the following warning: Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20110328/private/warning_once at 75 In ft_defaults at 45 In ft_preprocessing at 179 Warning: one version of SPM is found here: /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm2/spm.m > In ft_defaults at 48 In ft_preprocessing at 179 Warning: one version of SPM is found here: /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm8/spm.m Can I simply remove the spm2 directory? thanks in advance, -D -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From jdien07 at mac.com Fri May 27 05:16:03 2011 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 26 May 2011 23:16:03 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <4DDB5A14.3090102@uni-oldenburg.de> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> Message-ID: <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Stefan, just to be clear, I don't think any of us were saying not to use ICA to correct blinks. David was just saying that there are potential concerns when one only applies the ICA to the blink trials rather than to all the trials. I myself use EEGlab's infomax implementation in the automatic eyeblink correction tool of my EP Toolkit (http://sourceforge.net/projects/erppcatoolkit/). Now that said, I should add a little more nuance to my response. One of the things I observed (or rather, that Tim Curran pointed out to me) is that when you apply ICA to remove eyeblink artifacts in this manner, it can actually substantially increase the noise level in the data, so for the trials without eyeblinks it can have a considerable cost. So in order to balance the cost/benefit ratio, what I did was to include a trial by trial criterion that the putative eyeblink factors would only be removed if doing so reduced the overall variance of the trial. This approach does still have some potential for causing the concerns that David raises but not as much as only applying the ICA to blink trials since it does end up getting applied to non-blink trials too. This does mean that one should be cautious about any apparent effects in the artifact corrected data that are centered around the eyes (that have a blink topography) but that goes without saying in any case. So anyway, I agree, it's not perfect but seems to be the best available option. Cheers! Joe On May 24, 2011, at 3:11 AM, Stefan Debener wrote: > Hi Odelia, > > I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... > > For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... > > Best, > Stefan > > > Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: >> >> And for a related perspective, see >> >> McMenamin, B. W., Shackman, A. J., Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, Neuroimage, 54, 4-9. >> >> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf >> >> >> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: >> I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: >> >> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. >> >> Cheers! >> >> Joe >> >> On May 23, 2011, at 11:57 AM, David Groppe wrote: >> >>> Hi Odelia, >>> When you use ICA (or any other spatial filter) to correct for EEG >>> artifacts, you're going to distort your data some by removing true EEG >>> activity in addition to the artifact (for an explanation, see: >>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >>> So to minimize distortion, it would be better not to apply ICA >>> artifact correction to artifact-free data. However, if the frequency >>> of the artifact differs across experimental conditions, it could >>> confound your analysis. For example, I suspect people blink more >>> often to targets in an oddball experiment than standards. Thus if you >>> apply ICA only to blinky trials, you could find a difference between >>> the EEG response to standards and targets that simply reflects the >>> fact ICA removed more EEG activity in the target trials (i.e., it >>> wouldn't reflect a true difference in neural processing). >>> hope this helps, >>> -David >>> >>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: >>>> Hi all, >>>> >>>> I'm troubled by the fact that when I use ICA for blinks\eyes movements >>>> removal, I remove the relevant components also from trials that do not >>>> contain blinks\eyes movements. In order to avoid this bias we thought to >>>> combine the data before ICA ("data" structure) with the data after ICA >>>> ("dataica" structure), only in specific trials, as follows: >>>> >>>> datall=dataica; >>>> datall.trial=data.trial; >>>> datall.time=data.time; >>>> blinks=[2 4 5 8 bla bla 156]; >>>> for ind=1:length(blinks) >>>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>>> end >>>> >>>> To my first question: I just wanted to check that there is no problem with >>>> that, or any reason not to use it. >>>> >>>> Another issue- I use motor learning task, and I'm trying to understand what >>>> happens through the process, in terms of power-frequency changes through the >>>> process. How would you recommend that I'd use the ft_freqanalysis function? >>>> What method to use (or what do I need to consider when choosing the method >>>> field)? >>>> >>>> >>>> Thanks a lot, >>>> Odelia. >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> David Groppe, Ph.D. >>> Postdoctoral Researcher >>> Kutaslab >>> Dept. of Cognitive Science >>> University of California, San Diego >>> http://www.cogsci.ucsd.edu/~dgroppe/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://homepage.mac.com/jdien07/ >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> Alexander J. Shackman, Ph.D. >> Wisconsin Psychiatric Institute & Clinics and >> Department of Psychology >> University of Wisconsin-Madison >> 1202 West Johnson Street >> Madison, Wisconsin 53706 >> >> Telephone: +1 (608) 358-5025 >> Fax: +1 (608) 265-2875 >> Email: shackman at wisc.edu >> http://psyphz.psych.wisc.edu/~shackman >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email: stefan.debener at uni-oldenburg.de > _______________________________________________ > 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 yuvharpaz at gmail.com Fri May 27 05:40:14 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 27 May 2011 06:40:14 +0300 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Message-ID: Dear discussion group Did anybody consider smoothing or filtering the component trace before rejecting it? it seems that the added noise to no-blink trials is in a frequency higher than that typical to blinks. what if we evaluate the component weight, creating a trace for the eyeblink component for every trial, then bandpass filter the blink trace , say 0.1-25Hz, and only then remove the component from the data? yuval On 27 May 2011 06:16, Joseph Dien wrote: > Stefan, just to be clear, I don't think any of us were saying not to use > ICA to correct blinks. David was just saying that there are potential > concerns when one only applies the ICA to the blink trials rather than to > all the trials. I myself use EEGlab's infomax implementation in the > automatic eyeblink correction tool of my EP Toolkit ( > http://sourceforge.net/projects/erppcatoolkit/). > > Now that said, I should add a little more nuance to my response. One of > the things I observed (or rather, that Tim Curran pointed out to me) is that > when you apply ICA to remove eyeblink artifacts in this manner, it can > actually substantially increase the noise level in the data, so for the > trials without eyeblinks it can have a considerable cost. So in order to > balance the cost/benefit ratio, what I did was to include a trial by trial > criterion that the putative eyeblink factors would only be removed if doing > so reduced the overall variance of the trial. This approach does still have > some potential for causing the concerns that David raises but not as much as > only applying the ICA to blink trials since it does end up getting applied > to non-blink trials too. This does mean that one should be cautious about > any apparent effects in the artifact corrected data that are centered around > the eyes (that have a blink topography) but that goes without saying in any > case. So anyway, I agree, it's not perfect but seems to be the best > available option. > > Cheers! > > Joe > > On May 24, 2011, at 3:11 AM, Stefan Debener wrote: > > Hi Odelia, > > I have a slightly different opinion here. It is certainly true that any > filter has the tendency to distort data (with distortion I mean that data > consists of a mixture of some wanted, true signal and some unwanted signal, > and that the removal of the unwanted part of the signal is neither complete > nor specific). In our lab we regularly use ICA for artefact removal (and > more), and the benefit/gain is clearly are much larger than the distortion. > In fact there are a number of examples out showing that currently only ICA > (or related tools) can recover the study of (a substantial fraction of the > wanted) EEG signal (but again, it is NOT a perfect tool at all), in > particular in cases where other means of SNR enhancement don't work well > (averaging, spectral analysis). I am happy to provide references if you are > interested... > > For the evaluation of outcome it would be reasonable to not evaluate the > ERP alone, as this could be misleading. Better evaluate the sensitivity and > specificity of an eye blink attentuation approach on the single trial (and > single subject) level, this will give you good insight. And it is worth > keeping in mind that the preprocessing of the data (among other issues, like > the quality of the recording and so on) largely determines the quality of > the output (for some introduction you may look up chapter 3.1 in Ullsperger > & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just > by a different preprocessing ICA output could vary between crap and > excellent unmixing. Thus a poor ICA eye blink attenuation would make me a > bit suspicious... > > Best, > Stefan > > > Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: > > And for a related perspective, see > > McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. > (2011). Electromyogenic artifacts and electroencephalographic inferences > revisited, *Neuroimage**, 54*, 4-9. > > http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf > > > On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: > >> I agree with David's reasoning. You may find the following article to >> be of help as well in understanding the issues involved: >> >> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of >> simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping*, >> 28(8), 742-763. >> >> Cheers! >> >> Joe >> >> On May 23, 2011, at 11:57 AM, David Groppe wrote: >> >> Hi Odelia, >> When you use ICA (or any other spatial filter) to correct for EEG >> artifacts, you're going to distort your data some by removing true EEG >> activity in addition to the artifact (for an explanation, see: >> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >> So to minimize distortion, it would be better not to apply ICA >> artifact correction to artifact-free data. However, if the frequency >> of the artifact differs across experimental conditions, it could >> confound your analysis. For example, I suspect people blink more >> often to targets in an oddball experiment than standards. Thus if you >> apply ICA only to blinky trials, you could find a difference between >> the EEG response to standards and targets that simply reflects the >> fact ICA removed more EEG activity in the target trials (i.e., it >> wouldn't reflect a true difference in neural processing). >> hope this helps, >> -David >> >> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >> wrote: >> >> Hi all, >> >> >> I'm troubled by the fact that when I use ICA for blinks\eyes movements >> >> removal, I remove the relevant components also from trials that do not >> >> contain blinks\eyes movements. In order to avoid this bias we thought to >> >> combine the data before ICA ("data" structure) with the data after ICA >> >> ("dataica" structure), only in specific trials, as follows: >> >> >> datall=dataica; >> >> datall.trial=data.trial; >> >> datall.time=data.time; >> >> blinks=[2 4 5 8 bla bla 156]; >> >> for ind=1:length(blinks) >> >> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >> >> end >> >> >> To my first question: I just wanted to check that there is no problem >> with >> >> that, or any reason not to use it. >> >> >> Another issue- I use motor learning task, and I'm trying to understand >> what >> >> happens through the process, in terms of power-frequency changes through >> the >> >> process. How would you recommend that I'd use the ft_freqanalysis >> function? >> >> What method to use (or what do I need to consider when choosing the method >> >> field)? >> >> >> >> Thanks a lot, >> >> Odelia. >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> >> -- >> David Groppe, Ph.D. >> Postdoctoral Researcher >> Kutaslab >> Dept. of Cognitive Science >> University of California, San Diego >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://homepage.mac.com/jdien07/ >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> > > > -- > Alexander J. Shackman, Ph.D. > Wisconsin Psychiatric Institute & Clinics and > Department of Psychology > University of Wisconsin-Madison > 1202 West Johnson Street > Madison, Wisconsin 53706 > > Telephone: +1 (608) 358-5025 > Fax: +1 (608) 265-2875 > Email: shackman at wisc.edu > http://psyphz.psych.wisc.edu/~shackman > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email: stefan.debener at uni-oldenburg.de > > _______________________________________________ > 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 > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahesh.casiraghi at gmail.com Fri May 27 06:32:01 2011 From: mahesh.casiraghi at gmail.com (Mahesh Casiraghi) Date: Fri, 27 May 2011 00:32:01 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Message-ID: Dear Yuval and discussion group, it seems to me that what you are proposing is getting close to what proposed by the hybrid approach of regica described here: *Manousos A. Klados, Christos Papadelis, Christoph Braun, Panagiotis D. Bamidis, REG-ICA: A hybrid methodology combining Blind Source Separation and regression techniques for the rejection of ocular artifacts, Biomedical Signal Processing and Control, In Press, Corrected Proof, Available online 16 March 2011, ISSN 1746-8094, DOI: 10.1016/j.bspc.2011.02.001.* They suggest to selectively run regression based AR only on those components which correlate with EOG signals. This makes sense to me and I have been trying to experiment that on some old data, although with no clear conclusions yet. It may be worth a try for Odelia: Anybody out there with some insights for this - or maybe a similar - approach? Cheers, Mahesh Mahesh M. Casiraghi PhD candidate - Cognitive Sciences Roberto Dell'Acqua Lab, University of Padova Pierre Jolicoeur Lab, Univesité de Montréal mahesh.casiraghi at umontreal.ca I have the conviction that when Physiology will be far enough advanced, the poet, the philosopher, and the physiologist will all understand each other. Claude Bernard On Thu, May 26, 2011 at 11:40 PM, Yuval Harpaz wrote: > Dear discussion group > Did anybody consider smoothing or filtering the component trace before > rejecting it? > it seems that the added noise to no-blink trials is in a frequency higher > than that typical to blinks. what if we evaluate the component weight, > creating a trace for the eyeblink component for every trial, then bandpass > filter the blink trace , say 0.1-25Hz, and only then remove the component > from the data? > yuval > > On 27 May 2011 06:16, Joseph Dien wrote: > >> Stefan, just to be clear, I don't think any of us were saying not to use >> ICA to correct blinks. David was just saying that there are potential >> concerns when one only applies the ICA to the blink trials rather than to >> all the trials. I myself use EEGlab's infomax implementation in the >> automatic eyeblink correction tool of my EP Toolkit ( >> http://sourceforge.net/projects/erppcatoolkit/). >> >> Now that said, I should add a little more nuance to my response. One of >> the things I observed (or rather, that Tim Curran pointed out to me) is that >> when you apply ICA to remove eyeblink artifacts in this manner, it can >> actually substantially increase the noise level in the data, so for the >> trials without eyeblinks it can have a considerable cost. So in order to >> balance the cost/benefit ratio, what I did was to include a trial by trial >> criterion that the putative eyeblink factors would only be removed if doing >> so reduced the overall variance of the trial. This approach does still have >> some potential for causing the concerns that David raises but not as much as >> only applying the ICA to blink trials since it does end up getting applied >> to non-blink trials too. This does mean that one should be cautious about >> any apparent effects in the artifact corrected data that are centered around >> the eyes (that have a blink topography) but that goes without saying in any >> case. So anyway, I agree, it's not perfect but seems to be the best >> available option. >> >> Cheers! >> >> Joe >> >> On May 24, 2011, at 3:11 AM, Stefan Debener wrote: >> >> Hi Odelia, >> >> I have a slightly different opinion here. It is certainly true that any >> filter has the tendency to distort data (with distortion I mean that data >> consists of a mixture of some wanted, true signal and some unwanted signal, >> and that the removal of the unwanted part of the signal is neither complete >> nor specific). In our lab we regularly use ICA for artefact removal (and >> more), and the benefit/gain is clearly are much larger than the distortion. >> In fact there are a number of examples out showing that currently only ICA >> (or related tools) can recover the study of (a substantial fraction of the >> wanted) EEG signal (but again, it is NOT a perfect tool at all), in >> particular in cases where other means of SNR enhancement don't work well >> (averaging, spectral analysis). I am happy to provide references if you are >> interested... >> >> For the evaluation of outcome it would be reasonable to not evaluate the >> ERP alone, as this could be misleading. Better evaluate the sensitivity and >> specificity of an eye blink attentuation approach on the single trial (and >> single subject) level, this will give you good insight. And it is worth >> keeping in mind that the preprocessing of the data (among other issues, like >> the quality of the recording and so on) largely determines the quality of >> the output (for some introduction you may look up chapter 3.1 in Ullsperger >> & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just >> by a different preprocessing ICA output could vary between crap and >> excellent unmixing. Thus a poor ICA eye blink attenuation would make me a >> bit suspicious... >> >> Best, >> Stefan >> >> >> Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: >> >> And for a related perspective, see >> >> McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. >> (2011). Electromyogenic artifacts and electroencephalographic inferences >> revisited, *Neuroimage**, 54*, 4-9. >> >> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf >> >> >> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: >> >>> I agree with David's reasoning. You may find the following article to >>> be of help as well in understanding the issues involved: >>> >>> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA >>> of simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping >>> *, 28(8), 742-763. >>> >>> Cheers! >>> >>> Joe >>> >>> On May 23, 2011, at 11:57 AM, David Groppe wrote: >>> >>> Hi Odelia, >>> When you use ICA (or any other spatial filter) to correct for EEG >>> artifacts, you're going to distort your data some by removing true EEG >>> activity in addition to the artifact (for an explanation, see: >>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >>> So to minimize distortion, it would be better not to apply ICA >>> artifact correction to artifact-free data. However, if the frequency >>> of the artifact differs across experimental conditions, it could >>> confound your analysis. For example, I suspect people blink more >>> often to targets in an oddball experiment than standards. Thus if you >>> apply ICA only to blinky trials, you could find a difference between >>> the EEG response to standards and targets that simply reflects the >>> fact ICA removed more EEG activity in the target trials (i.e., it >>> wouldn't reflect a true difference in neural processing). >>> hope this helps, >>> -David >>> >>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >>> wrote: >>> >>> Hi all, >>> >>> >>> I'm troubled by the fact that when I use ICA for blinks\eyes movements >>> >>> removal, I remove the relevant components also from trials that do not >>> >>> contain blinks\eyes movements. In order to avoid this bias we thought to >>> >>> combine the data before ICA ("data" structure) with the data after ICA >>> >>> ("dataica" structure), only in specific trials, as follows: >>> >>> >>> datall=dataica; >>> >>> datall.trial=data.trial; >>> >>> datall.time=data.time; >>> >>> blinks=[2 4 5 8 bla bla 156]; >>> >>> for ind=1:length(blinks) >>> >>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>> >>> end >>> >>> >>> To my first question: I just wanted to check that there is no problem >>> with >>> >>> that, or any reason not to use it. >>> >>> >>> Another issue- I use motor learning task, and I'm trying to understand >>> what >>> >>> happens through the process, in terms of power-frequency changes through >>> the >>> >>> process. How would you recommend that I'd use the ft_freqanalysis >>> function? >>> >>> What method to use (or what do I need to consider when choosing the >>> method >>> >>> field)? >>> >>> >>> >>> Thanks a lot, >>> >>> Odelia. >>> >>> >>> _______________________________________________ >>> >>> fieldtrip mailing list >>> >>> fieldtrip at donders.ru.nl >>> >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> >>> -- >>> David Groppe, Ph.D. >>> Postdoctoral Researcher >>> Kutaslab >>> Dept. of Cognitive Science >>> University of California, San Diego >>> http://www.cogsci.ucsd.edu/~dgroppe/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://homepage.mac.com/jdien07/ >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >> >> >> -- >> Alexander J. Shackman, Ph.D. >> Wisconsin Psychiatric Institute & Clinics and >> Department of Psychology >> University of Wisconsin-Madison >> 1202 West Johnson Street >> Madison, Wisconsin 53706 >> >> Telephone: +1 (608) 358-5025 >> Fax: +1 (608) 265-2875 >> Email: shackman at wisc.edu >> http://psyphz.psych.wisc.edu/~shackman >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Prof. Dr. Stefan Debener >> Neuropsychology Lab >> Department of Psychology >> University of Oldenburg >> D-26111 Oldenburg >> Germany >> >> Office: A7 0-038 >> Phone: +49-441-798-4271 >> Fax: +49-441-798-5522 >> Email: stefan.debener at uni-oldenburg.de >> >> _______________________________________________ >> 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 >> > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > *"Many were increasingly of the opinion that they'd all made a big mistake > in coming down from the trees in the first place. And some said that even > the trees had been a bad move, and that no one should ever have left the > oceans". Douglas Adams > * > > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri May 27 08:19:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 27 May 2011 08:19:02 +0200 Subject: [FieldTrip] duplicate spm directories In-Reply-To: References: Message-ID: <6BA914CC-EDD4-4D85-BC49-B790FD08447E@donders.ru.nl> Dear David, Yes, you can safely remove the spm2 directory. Unless you rely in your analysis pipeline on spm2-specific stuff. The only thing I can think of here would be to read in .mnc files. Cheers, Jan-Mathijs On May 27, 2011, at 3:54 AM, David Groppe wrote: > Hi again, > I'm running the March 28th version of Fieldtrip and am getting the > following warning: > > Warning: multiple versions of SPM on your path will confuse FieldTrip >> In fieldtrip-20110328/private/warning_once at 75 > In ft_defaults at 45 > In ft_preprocessing at 179 > Warning: one version of SPM is found here: > /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm2/spm.m >> In ft_defaults at 48 > In ft_preprocessing at 179 > Warning: one version of SPM is found here: > /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm8/spm.m > > > Can I simply remove the spm2 directory? > thanks in advance, > -D > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From akademonbrain at gmail.com Fri May 27 10:43:11 2011 From: akademonbrain at gmail.com (Aka Demon) Date: Fri, 27 May 2011 11:43:11 +0300 Subject: [FieldTrip] influences between the regions In-Reply-To: References: Message-ID: Dear experts After analyzing memory experiment EEG/MEG and source localization data, i figured out that there is little I can say about the interactions between the activated regions as I don’t have any information about the connection between the activated areas. So I was wondering if there are some useful works/tools that I can use to explorer the influences between the regions (such as information transfer from one region to the other). Thanks a lot Aka -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Fri May 27 14:26:28 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Fri, 27 May 2011 14:26:28 +0200 Subject: [FieldTrip] tutorial - ft_volumenormalise Message-ID: Dear Fieldtrippers, I am running the tutorial on how to localize oscillatory sources using beamformer techniques. It works smooth until I have to normalize the anatomical mri to the template. When, after I load the already-segmented subject file, I run ft_volumenormalise it says the following: ??? Attempted to access V.dim(4); index out of bounds because numel(V.dim)=3. Error in ==> spm_create_vol>create_vol at 94 swapped = spm_type(V.dim(4),'swapped'); Interestingly this is the same error I get when I try to run ft_volumesegment both using the tutorial and my anatomical MRIs. Has someone any idea? Am I doing something silly? Thank you so much, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Sat May 28 01:13:43 2011 From: rapela at ucsd.edu (=?iso-8859-1?Q?Joaqu=EDn_Rapela?=) Date: Fri, 27 May 2011 16:13:43 -0700 (PDT) Subject: [FieldTrip] lead field without with no MRI Message-ID: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> Dear all, I want to compute a lead field matrix but I have no MRI scan of my subjects. I would be happy with a concentric spheres model, or similar, adjusted to the electrodes locations (modified 10 20 system). I would be very grateful if somebody directs me to the appropriate functions in FieldTrip. My apologizes if this is a naive question. I am new to FieldTrip. Thanks in advance, Joaquin -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel/fax: (858) 822-7536 http://www-scf.usc.edu/~rapela ---------------------------------- There are men who struggle for a day and they are good. There are men who struggle for a year and they are better. There are men who struggle many years, and they are better still. But there are those who struggle all their lives: These are the indispensable ones. Bertolt Brecht From michael.wibral at web.de Sun May 29 09:26:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Sun, 29 May 2011 09:26:47 +0200 (CEST) Subject: [FieldTrip] influences between the regions Message-ID: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Sun May 29 21:38:50 2011 From: rapela at ucsd.edu (=?iso-8859-1?Q?Joaqu=EDn_Rapela?=) Date: Sun, 29 May 2011 12:38:50 -0700 (PDT) Subject: [FieldTrip] lead field with no MRI In-Reply-To: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> References: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> Message-ID: <46100.137.110.37.196.1306697930.squirrel@acs-webmail.ucsd.edu> Below I describe how to compute the leadfield matrix adjusted to a set of electrodes in an extended 10-20 system, without having an MRI image. Besides, I have a question: why in the help of the fieldtrip functions their output is not described? Cordially, Joaquin I had to dig into the EEGLAB Dipfit plugin to learn how to do this. I used the function ft_prepare_leadfield. It requires a head model and the channel locations. Since I have an extended 10-20 electrode system, I used a BEM head model that comes with Dipfit, and also uses an extended 10-20 system. This head model is in the plugins directory of dipfit2.2: hdmFile=/usr/local/eeglab/plugins/dipfit2.2/standard_BEM/standard_vol.mat and the channel locations for this head model are also in the dipfit2.2 directory: hmChanfile=/usr/local/eeglab/plugins/dipfit2.2/standard_BEM/elec/standard_1005.elc It turns out that the previous head model is not ready for ft_prepare_leadfield, and I had to use the function ft_prepare_vol_sens to prepare it. Also, I wanted to compute the leadfield matrix only for the channels in my data set, whose labels are in the variable dsChanlabels, so I passed dsChanlabels as the argument 'channel' of ft_prepare_vol_sens. Finally, I used the head model and sensors prepared by ft_prepare_vol_sens as input to ft_prepare_headmodel. I append the code that does the job. If you see any bug, please let me know. Warmly, Joaquin ### function grid = joacosPrepareLeadfield(dsChanlabels, hmChanfile, hdmFile) cfg = []; vol = ft_read_vol(hdmFile); sens = ft_read_sens(hmChanfile); [vol, sens] = ft_prepare_vol_sens(vol, sens, 'channel', dsChanlabels); cfg = []; cfg.elec = sens; cfg.vol = vol; cfg.grid.resolution = 20; data = []; grid = ft_prepare_leadfield(cfg, data); ### > Dear all, > > I want to compute a lead field matrix but I have no MRI scan of my > subjects. I would be happy with a concentric spheres model, or similar, > adjusted to the electrodes locations (modified 10 20 system). I would be > very grateful if somebody directs me to the appropriate functions in > FieldTrip. My apologizes if this is a naive question. I am new to > FieldTrip. > > Thanks in advance, Joaquin > > -- > Joaquin Rapela, PhD > Swartz Center for Computational Neuroscience > University of California San Diego > 9500 Gilman Drive, > San Diego, CA 92093-0559 > tel/fax: (858) 822-7536 > http://www-scf.usc.edu/~rapela > ---------------------------------- > > There are men who struggle for a day and they are good. > There are men who struggle for a year and they are better. > There are men who struggle many years, and they are better still. > But there are those who struggle all their lives: > These are the indispensable ones. > > Bertolt > Brecht > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel/fax: (858) 822-7536 http://www-scf.usc.edu/~rapela ---------------------------------- There are men who struggle for a day and they are good. There are men who struggle for a year and they are better. There are men who struggle many years, and they are better still. But there are those who struggle all their lives: These are the indispensable ones. Bertolt Brecht From Elena.Orekhova at neuro.gu.se Mon May 30 13:08:29 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 30 May 2011 11:08:29 +0000 Subject: [FieldTrip] SAM beamformeing on Neuromag data Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA679@exchccr1.neuro.gu.se> Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Mon May 30 14:08:08 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 30 May 2011 14:08:08 +0200 (CEST) Subject: [FieldTrip] SAM beamformeing on Neuromag data Message-ID: <1443619351.1500061.1306757288215.JavaMail.fmail@mwmweb072> An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Mon May 30 16:30:34 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 30 May 2011 14:30:34 +0000 Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA6D6@exchccr1.neuro.gu.se> Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From tobiasnavarroschroeder at googlemail.com Mon May 30 17:58:32 2011 From: tobiasnavarroschroeder at googlemail.com (Tobias Navarro Schroeder) Date: Mon, 30 May 2011 17:58:32 +0200 Subject: [FieldTrip] Beamforming on resting state data In-Reply-To: References: Message-ID: Hi Fieldtrippers, I performed DICS beamforming on resting-state data (i.e. no task, no baseline, eyes closed) of a clinical population and controls. According to the sensor data the patients have more gamma-band (60-90 Hz) activity over temporal areas (somewhat spread-out). Curiously, after beamforming and group comparisons with 'indepsamplesT' permutation statistics the difference map shows more gamma-band (60-90 Hz) activity for controls in the left, middle-temporal gyrus. Hence, the source-level results are opposite to the sensor-level results (although more spatially confined). This is *not* a problem of the design matrix, or confusing the groups. Question 1: Does anybody have experience with opposite results on source and sensor level? The individual raw beamforming results (interpolated on the subjects' MRIs) look suspicios as well. Due to the 'unit gain constraint' there should be an overestimation of power in the center of the head, but only a minority of subjects show that. Often I see temporal or parietal activity. Question 2: Would a lack of a blob in the center of the head in individual, raw, beamforming data indicate an erroneous source analysis? Thanks a lot for help and suggestions. Best, Tobias Navarro Schröder ps: The configurations for calculating the covariance and the beamforming is added below: 1) % Compute the covariance matrices cfg.output = 'powandcsd'; cfg.foi = 75; cfg.foilim = [75 75]; cfg.tapsmofrq = 15; % 75 +- 15 = 60 - 90 Hz cfg.pad = 'maxperlen'; % default cfg.method = 'wltconvol'; % wavelet analysis cfg.width = 5; % Width of the wavelet. Determines the temporal and spectral resolution of the analysis constant. 2) % Perform the actual beamforming % load grids of MRI volume fullnameGrid = [ CurSubject.mripath CurSubject.MRIModel]; cfg = load(fullnameGrid); cfg.vol = cfg.hdm; cfg.frequency = 75; cfg.method = 'dics'; cfg.keepfilter = 'yes'; % keep the beamformer filters (virtual electrodes) for later use cfg.keeptrial = 'no'; cfg.keepmom = 'yes'; % useful for connectivity calculations. Dipole moments.. cfg.projectmom = 'yes'; cfg.projectnoise = 'yes'; cfg.latency = 1; -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Mon May 30 17:58:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 30 May 2011 17:58:47 +0200 (CEST) Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> An HTML attachment was scrubbed... URL: From Tim.Bardouille at nrc-cnrc.gc.ca Mon May 30 18:23:22 2011 From: Tim.Bardouille at nrc-cnrc.gc.ca (Bardouille, Tim) Date: Mon, 30 May 2011 12:23:22 -0400 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: Hi Michael, Elena, If it becomes a sticking point, you could also run MaxFilter with the -nosss option. I don't have any experience with how this would affect the beamformer output, but it would at least resolve the rank issue. Tim. --------------------------------------------------------- Timothy Bardouille, PhD, Research Officer Laboratory for Clinical MEG NRC Institute for Biodiagnostics (Atlantic) Office: Halifax Infirmary 3900 - 1796 Summer Street Halifax, Nova Scotia B3H 3A7 Phone: 902-473-1865 Lab: 902-470-3936 Fax: 902-473-1851 --------------------------------------------------------- ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Michael Wibral [michael.wibral at web.de] Sent: May 30, 2011 12:58 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon May 30 21:27:13 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 30 May 2011 21:27:13 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> Hi Michael, Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? Best, Stephan El 30/05/2011, a las 17:58, Michael Wibral escribió: > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the > maxfilter papers the properties of the components removed by the > maxfilter do not require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a > tiny amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please > let me know!) > > > Michael > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 4:30:34 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since > MaxFilter reduces the rank of the covariance matrix by removing > noisy components, it may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de > ] > Sent: Monday, May 30, 2011 2:08 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the > different UNITS (not only scales) of gradiometers and magnetometers. > There was a problem with the sign of the leadfields but that should > have been fixed. > > There is one more fundamental problem however, that you should be > aware of (doesn't invalidate your source analysis but bears > potential for fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your > source signal back with unit gain. Added on top however is > neurophysiological crosstalk (minimized) and sensor noise of the > sensors with the largest weights in your Beamformer (not reducible). > So different sensor types willhave different (inverse) leadfield > strengths, theerfore also fiofefrent source noise levels. the > relative benefits of each sensor type changes from location to > location, so a location (and data) dependend weighting would in > principle be best. > I am not sure if and how this is implemented if FT (Bayesian > weighting would be optimal here..) > > What you could do as a first step is to beam separately and compare > the results. > > Michael > > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 1:08:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face > { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font- > family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal > { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: > Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font- > family: Courier; }span.HTMLPreformattedChar { font-family: > Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 > { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E > \671D "; }@font-face { font-family: "Cambria Math"; }@font-face > { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal > { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: > Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font- > family: Courier; }span.HTMLPreformattedChar { font-family: > Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 > { page: WordSection1; } > Dear All, > > I try to run beamformer analysis on the auditory MEG data (Neuromag) > and have basic questions. > > > 1.Magnetometers and gradiometers Neuromag sensors have different > scales. Does the Fieldtrip take care of this difference or should I > normalize the data? It yes, how to normalize? > > > 2. I would like to do SAM analysis of evoked field and look at the > time courses at ROIs (virtual channels). The only tutorial example > I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer) > . I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method > = 'sam'. > > > I would be most grateful for any example script of this type analysis! > > Regards, > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jstout211 at yahoo.com Mon May 30 23:28:16 2011 From: jstout211 at yahoo.com (Jeff Stout) Date: Mon, 30 May 2011 14:28:16 -0700 (PDT) Subject: [FieldTrip] MEGRealign channel Message-ID: <365289.7941.qm@web113516.mail.gq1.yahoo.com> Hi All, I am having trouble using the ft_megrealign command with a 4D Magnes 3600 system.  I am trying to use this command to interpolate bad channels that have been removed in preprocessing.  When I view the output of megrealign using ft_plot_sens, sensor 'A229' is badly misplaced (approximately 10 cm above the top of the sensor array), but all the other sensors appear appropriate.  In the dataset A229 has not been labelled as a bad channel, nor any of its neighboring channels. The location of A229 is significant in that it is the most inferior/anterior channel on the left side.  I am using the original grad file as a template input using ft_read_sens('c,rfDC') and scaling the MEG channels to cm.  I am not sure how helpful the code is - below is my input and some of the output.  I can provide an image if this would be helpful. temp = ft_read_sens(subjectdata.FA_dataset); temp.pnt = temp.pnt*100; temp.unit  = 'cm'; cfg = []; cfg.inwardshift = 1; cfg.vol=vol; cfg.template{1}= temp; cfg.channel={'MEG'}; con.grad.pnt = con.grad.pnt*100; con.grad.unit = 'cm'; con = ft_megrealign(cfg, con) computing surface normals mean distance towards template gradiometers is 0.00 cm creating dipole grid based on inward-shifted brain surface from volume conductor model Warning: the normals of the surface triangulation are inward oriented  > In fieldtrip-20110507/private/headsurface at 211   In ft_prepare_sourcemodel at 492   In ft_megrealign at 245 642 dipoles inside, 0 dipoles outside brain computing forward model for 642 dipoles pruning 122 from 246, i.e. removing the 122 smallest spatial components computing interpolation matrix #1 computing interpolation matrix #2 computing interpolation matrix #3 pruning 124 from 248, i.e. removing the 124 smallest spatial components realigning trial 1 original -> template             RV 14.42 % original             -> original RV 14.42 % original -> template -> original RV 14.44 % .................... Does anyone know why this would be occurring and how to fix it? Thanks, Jeff Stout -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 31 09:04:26 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 31 May 2011 09:04:26 +0200 Subject: [FieldTrip] MEGRealign channel In-Reply-To: <365289.7941.qm@web113516.mail.gq1.yahoo.com> References: <365289.7941.qm@web113516.mail.gq1.yahoo.com> Message-ID: <012FDE87-5002-4626-B821-D83AAC043C59@donders.ru.nl> Hi Jeff, Thanks for reporting this. We'll look into it as soon as possible. Best wishes, Jan-Mathijs On May 30, 2011, at 11:28 PM, Jeff Stout wrote: > > Hi All, > > I am having trouble using the ft_megrealign command with a 4D Magnes > 3600 system. I am trying to use this command to interpolate bad > channels that have been removed in preprocessing. When I view the > output of megrealign using ft_plot_sens, sensor 'A229' is badly > misplaced (approximately 10 cm above the top of the sensor array), > but all the other sensors appear appropriate. In the dataset A229 > has not been labelled as a bad channel, nor any of its neighboring > channels. The location of A229 is significant in that it is the most > inferior/anterior channel on the left side. I am using the original > grad file as a template input using ft_read_sens('c,rfDC') and > scaling the MEG channels to cm. I am not sure how helpful the code > is - below is my input and some of the output. I can provide an > image if this would be helpful. > > > temp = ft_read_sens(subjectdata.FA_dataset); > temp.pnt = temp.pnt*100; > temp.unit = 'cm'; > > cfg = []; > cfg.inwardshift = 1; > cfg.vol=vol; > cfg.template{1}= temp; > cfg.channel={'MEG'}; > con.grad.pnt = con.grad.pnt*100; > con.grad.unit = 'cm'; > con = ft_megrealign(cfg, con) > > computing surface normals > mean distance towards template gradiometers is 0.00 cm > creating dipole grid based on inward-shifted brain surface from > volume conductor model > Warning: the normals of the surface triangulation are inward oriented > > In fieldtrip-20110507/private/headsurface at 211 > In ft_prepare_sourcemodel at 492 > In ft_megrealign at 245 > 642 dipoles inside, 0 dipoles outside brain > computing forward model for 642 dipoles > pruning 122 from 246, i.e. removing the 122 smallest spatial > components > computing interpolation matrix #1 > computing interpolation matrix #2 > computing interpolation matrix #3 > pruning 124 from 248, i.e. removing the 124 smallest spatial > components > realigning trial 1 > original -> template RV 14.42 % > original -> original RV 14.42 % > original -> template -> original RV 14.44 % .................... > > > Does anyone know why this would be occurring and how to fix it? > > Thanks, > Jeff Stout > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Nina.Kahlbrock at uni-duesseldorf.de Tue May 31 09:23:51 2011 From: Nina.Kahlbrock at uni-duesseldorf.de (Nina Kahlbrock) Date: Tue, 31 May 2011 09:23:51 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> Message-ID: <001301cc1f63$b0faedc0$cd136386@VMED.UKD> Hi Stephan, you can find the discussion list at: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG Best, Nina _____ Von: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] Im Auftrag von Stephan Moratti Gesendet: Montag, 30. Mai 2011 21:27 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Michael, Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? Best, Stephan El 30/05/2011, a las 17:58, Michael Wibral escribió: Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael _____ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena _____ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael _____ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Tue May 31 11:42:21 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Tue, 31 May 2011 11:42:21 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <001301cc1f63$b0faedc0$cd136386@VMED.UKD> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> <001301cc1f63$b0faedc0$cd136386@VMED.UKD> Message-ID: Hallo Nina, Vielen Dank !!! Stephan El 31/05/2011, a las 09:23, Nina Kahlbrock escribió: > Hi Stephan, > > you can find the discussion list at: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG > > Best, > Nina > > Von: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] Im Auftrag von Stephan Moratti > Gesendet: Montag, 30. Mai 2011 21:27 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Hi Michael, > > Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? > > Best, > > Stephan > > El 30/05/2011, a las 17:58, Michael Wibral escribió: > > > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please let me know!) > > > Michael > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 4:30:34 PM > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] > Sent: Monday, May 30, 2011 2:08 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. > > There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. > I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) > > What you could do as a first step is to beam separately and compare the results. > > Michael > > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 1:08:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear All, > I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. > > 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? > > 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. > > > I would be most grateful for any example script of this type analysis! > > Regards, > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Department of Basic Psychology > Universidad Complutense de Madrid > > Centro de Tecnología Biomédica CBT, > Universidad Politécnica de Madrid, > > en la actualidad (currently at) en el > Centro de Magnetoencefalografía Dr. Perez Modrego, > Universidad Complutense de Madrid, > Faculdad de Medicina, > Pabellón 8, > Avda. Complutense, s/n, > 28040 Madrid, > Spain, > > email: smoratti at psi.ucm.es > Tel.: +34 91 394 2186 > Fax.: +34 91 394 2294 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Tue May 31 12:06:40 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Tue, 31 May 2011 10:06:40 +0000 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> Hi Michael, > If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. What lambda you would recommend? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 5:58 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuvharpaz at gmail.com Tue May 31 12:42:53 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Tue, 31 May 2011 13:42:53 +0300 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> Message-ID: Dear Elena and group it basically depends on how much co-variability there is. if you use a large frequency range and a large strech of time you need to correct little if any. if you use averaged data and say from 50 to 120ms from target onset you need more regularization. I used 5% even for relatively short time interval (but large freq. range) and found it reasonable. yuval On 31 May 2011 13:06, Elena Orekhova wrote: > Hi Michael, > > > > If you run into rank-deficiency issue with the covariance matrix a tiny > amount of regularization should fix this. > > What lambda you would recommend? > > Elena > > > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Michael Wibral [michael.wibral at web.de] > *Sent:* Monday, May 30, 2011 5:58 PM > > *To:* Email discussion list for the FieldTrip project > *Subject:* Re: [FieldTrip] SAM beamforming on Neuromag data > > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the maxfilter > papers the properties of the components removed by the maxfilter do not > require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a tiny > amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please let me > know!) > > > Michael > > ------------------------------ > *Von:* "Elena Orekhova" > *Gesendet:* May 30, 2011 4:30:34 PM > *An:* "Email discussion list for the FieldTrip project" < > fieldtrip at donders.ru.nl> > *Betreff:* Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since MaxFilter > reduces the rank of the covariance matrix by removing noisy components, it > may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Michael Wibral [michael.wibral at web.de] > *Sent:* Monday, May 30, 2011 2:08 PM > *To:* Email discussion list for the FieldTrip project > *Subject:* Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the > different UNITS (not only scales) of gradiometers and magnetometers. There > was a problem with the sign of the leadfields but that should have been > fixed. > > There is one more fundamental problem however, that you should be aware of > (doesn't invalidate your source analysis but bears potential for > fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your source > signal back with unit gain. Added on top however is neurophysiological > crosstalk (minimized) and sensor noise of the sensors with the largest > weights in your Beamformer (not reducible). So different sensor types > willhave different (inverse) leadfield strengths, theerfore also fiofefrent > source noise levels. the relative benefits of each sensor type changes from > location to location, so a location (and data) dependend weighting would in > principle be best. > I am not sure if and how this is implemented if FT (Bayesian weighting > would be optimal here..) > > What you could do as a first step is to beam separately and compare the > results. > > Michael > > > ------------------------------ > *Von:* "Elena Orekhova" > *Gesendet:* May 30, 2011 1:08:29 PM > *An:* "fieldtrip at donders.ru.nl" > *Betreff:* [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { > font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: > "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm > 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm > 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar > { font-family: Courier; }.MsoChpDefault { font-family: Cambria; > }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D > \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face > { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { > margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { > margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; > }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { > font-family: Cambria; }div.WordSection1 { page: WordSection1; } > > Dear All, > > I try to run beamformer analysis on the auditory MEG data (Neuromag) and > have basic questions. > > > > 1.Magnetometers and gradiometers Neuromag sensors have different scales. > Does the Fieldtrip take care of this difference or should I normalize the > data? It yes, how to normalize? > > > > 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. > > > > I would be most grateful for any example script of this type analysis! > > > > Regards, > > Elena > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- sent from my 4-year-old PC. poor fellow, only ipod classic, no mail there. Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Tue May 31 12:44:50 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 31 May 2011 12:44:50 +0200 (CEST) Subject: [FieldTrip] Beamforming on resting state data Message-ID: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> An HTML attachment was scrubbed... URL: From tobiasnavarroschroeder at googlemail.com Tue May 31 14:12:48 2011 From: tobiasnavarroschroeder at googlemail.com (Tobias Navarro Schroeder) Date: Tue, 31 May 2011 14:12:48 +0200 Subject: [FieldTrip] Beamforming on resting state data In-Reply-To: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> References: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> Message-ID: Hi Michael, thanks a lot for that suggestion. The gamma activity at the sensor level might indeed be of muscular origin and this would explain why it doesn't show up inside the head. Even after automatic & manual artifact rejection the patients were left with more gamma activity. To my 'untrained eye' the sensor topographies suggested that the activity would come from the brain. It didn't extend to the boundaries of the Topoplot, at least in the 60-90 Hz range. However, this was the case for other parts of the gamma-band. Greetings, Tobias On Tue, May 31, 2011 at 12:44 PM, Michael Wibral wrote: > Hi Tobias, > > it could be that the temporal activity at the sensor level is of muscular > origin. Given all runs well in beamforming you shouldn't see too much of > that insode the head - have you considered this possibility? > > Michael > > > > ------------------------------ > *Von:* "Tobias Navarro Schroeder" > *Gesendet:* May 30, 2011 5:58:32 PM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] Beamforming on resting state data > > > Hi Fieldtrippers, > > I performed DICS beamforming on resting-state data (i.e. no task, no > baseline, eyes closed) of a clinical population and controls. > According to the sensor data the patients have more gamma-band (60-90 > Hz) activity over temporal areas (somewhat spread-out). > Curiously, after beamforming and group comparisons with 'indepsamplesT' > permutation statistics the difference map shows more gamma-band (60-90 > Hz) activity for controls in the left, middle-temporal gyrus. > Hence, the source-level results are opposite to the sensor-level results > (although more spatially confined). This is *not* a problem of the design > matrix, or confusing the groups. > > Question 1: Does anybody have experience with opposite results on source > and sensor level? > > The individual raw beamforming results (interpolated on the subjects' MRIs) > look suspicios as well. Due to the 'unit gain constraint' there should be an > overestimation of power in the center of the head, but only a minority of > subjects show that. Often I see temporal or parietal activity. > > Question 2: > > Would a lack of a blob in the center of the head in individual, > raw, beamforming data indicate an erroneous source analysis? > > Thanks a lot for help and suggestions. > > Best, Tobias Navarro Schröder > > ps: The configurations for calculating the covariance and the beamforming > is added below: > > > > 1) % Compute the covariance matrices > > > > cfg.output = > 'powandcsd'; > > cfg.foi = 75; > > cfg.foilim = [75 75]; > > cfg.tapsmofrq = 15; % 75 +- 15 = 60 - 90 Hz > > cfg.pad = > 'maxperlen'; % default > > cfg.method = > 'wltconvol'; % wavelet analysis > > cfg.width = 5; > % Width of the wavelet. Determines the temporal and spectral resolution of > the analysis constant. > > > > 2) % Perform the actual beamforming > > % load grids of MRI volume > > fullnameGrid = [ CurSubject.mripath CurSubject.MRIModel]; > > cfg = load(fullnameGrid); > > cfg.vol = cfg.hdm; > > > > > > cfg.frequency = 75; > > cfg.method = > 'dics'; > > cfg.keepfilter = > 'yes'; % keep the beamformer filters (virtual electrodes) for later use > > cfg.keeptrial = > 'no'; > > cfg.keepmom = > 'yes'; % useful for connectivity calculations. Dipole moments.. > > cfg.projectmom = > 'yes'; > > cfg.projectnoise = > 'yes'; > > cfg.latency = 1; > > > _______________________________________________ > 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 michael.wibral at web.de Tue May 31 15:36:46 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 31 May 2011 15:36:46 +0200 (CEST) Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <1271334421.1768792.1306849006599.JavaMail.fmail@mwmweb074> An HTML attachment was scrubbed... URL: From valentin.umbach at hu-berlin.de Tue May 31 18:51:17 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Tue, 31 May 2011 18:51:17 +0200 Subject: [FieldTrip] Emotiv headset realtime capture Message-ID: Hi, I'm new to FieldTrip and I'm interested in using it to capture realtime data from the Emotiv headset using this interface: http://fieldtrip.fcdonders.nl/development/realtime/emotiv I'm not clear about how to make calls to this interface from within Matlab. Also, I would like to know if it's possible to access not just the raw EEG, but also the API output of the detection libraries (Affectiv Suite...). Any help is greatly appreciated! Best, Valentin -- Dipl.-Psych. Valentin J. Umbach Institut für Psychologie Humboldt-Universität zu Berlin Rudower Chaussee 18 12489 Berlin Tel. +49 30 2093 9438 E-Mail: valentin.umbach at hu-berlin.de From mcoskun at mail.uh.edu Tue May 31 23:09:13 2011 From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun) Date: Tue, 31 May 2011 16:09:13 -0500 Subject: [FieldTrip] Dipole Fitting Algorithm Message-ID: <726086fb76fc3.4de512a9@mail.uh.edu> Dear Fieldtrippers, I am having little trouble understanding the dipole fitting algorithm. Any comments will be greatly appreciated. 1) During dipole fitting, a model data (Vmodel) is created using the computed leadfield. How exactly this model data is computed? Is it simply the projection of the pinv'ed leadfield to the true data (Vdata)?  2) The error is computed between the model data and true data for the best dipole. Is this RMS error? 3) The last part of dipole fitting is a non-linear search. I really wonder what is the algorithm, what exactly non-linear search is doing? Thanks in advance Mehmet -------------- next part -------------- An HTML attachment was scrubbed... URL: From max.taubert at gmail.com Sun May 1 15:48:13 2011 From: max.taubert at gmail.com (Max T.) Date: Sun, 1 May 2011 15:48:13 +0200 Subject: [FieldTrip] Plotting Dipoles Message-ID: Dear all, I'd like to visualize the results of ft_dipolefitting, sadly I've got no individual MRIs. Is there any function like ft_sourceplot that can handle ft_dipolefitting-results, maybe using a template brain? Besides this, is there any function that can transform my Unit Sphere-coordinates into Talairach space? And is it possible to apply the 'adaptive spatial filter' if I dont want to use a Beamformer? Thanks in advance Max Taubert From m.severens at maartenskliniek.nl Mon May 2 13:57:17 2011 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 2 May 2011 13:57:17 +0200 Subject: [FieldTrip] adding lines in multiplot TFR Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> Dear fieldtrippers I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? Thanks in advance Best Marianne Severens Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3 6522 JV NIJMEGEN Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From jm.horschig at donders.ru.nl Mon May 2 14:10:11 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 May 2011 14:10:11 +0200 Subject: [FieldTrip] adding lines in multiplot TFR In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> Message-ID: <4DBE9F23.8070600@donders.ru.nl> Hi Marianne, Adding vertical lines to annotate, for example, events is not possible using ft_multiplot_XXX afaik. A similar feature is added in ft_databrowser, which however does only work for two-dimensional data (amplitude x time). One way around would be to filter your data in the desired frequency range and then use ft_databrowser. The function, however, still lacks some functionality and compatibility. Should you encounter any strange problems, feel free to contact me and we (the FT developer team) will try to improve the databrowser according to your experiences and wishes. Another, slightly less elegant way to answer your question is the following: Rutger from your group changed a fieldtrip method for his personal purposes. Unselfishly, he called the function rutgerplot_TFR. In this function, he added horizontal lines to annotate specific frequency bands. You can maybe ask him to re-write this hack to add vertical lines to annotate the events you are interested in. Hope this helps! Best, Jörn On 5/2/2011 1:57 PM, Severens, Marianne wrote: > Dear fieldtrippers > > I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. > I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? > > Thanks in advance > Best Marianne Severens > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3 > 6522 JV NIJMEGEN > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands From m.severens at maartenskliniek.nl Mon May 2 14:34:56 2011 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 2 May 2011 14:34:56 +0200 Subject: [FieldTrip] adding lines in multiplot TFR In-Reply-To: <4DBE9F23.8070600@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl>, <4DBE9F23.8070600@donders.ru.nl> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B71@smkexch02.maartenskliniek.nl> Hi Jörn Thanks for your quick reply! The plots need to be TFR plots, with several frequency bins, so I think the databrowser is not really appropriate for this. I'll try to modify Rutger's solution to make the lines vertical! Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Jörn M. Horschig [jm.horschig at donders.ru.nl] Sent: Monday, May 02, 2011 2:10 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] adding lines in multiplot TFR Hi Marianne, Adding vertical lines to annotate, for example, events is not possible using ft_multiplot_XXX afaik. A similar feature is added in ft_databrowser, which however does only work for two-dimensional data (amplitude x time). One way around would be to filter your data in the desired frequency range and then use ft_databrowser. The function, however, still lacks some functionality and compatibility. Should you encounter any strange problems, feel free to contact me and we (the FT developer team) will try to improve the databrowser according to your experiences and wishes. Another, slightly less elegant way to answer your question is the following: Rutger from your group changed a fieldtrip method for his personal purposes. Unselfishly, he called the function rutgerplot_TFR. In this function, he added horizontal lines to annotate specific frequency bands. You can maybe ask him to re-write this hack to add vertical lines to annotate the events you are interested in. Hope this helps! Best, Jörn On 5/2/2011 1:57 PM, Severens, Marianne wrote: > Dear fieldtrippers > > I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. > I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? > > Thanks in advance > Best Marianne Severens > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3 > 6522 JV NIJMEGEN > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3 6522 JV NIJMEGEN Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From andrecravo at gmail.com Mon May 2 14:38:37 2011 From: andrecravo at gmail.com (Andre Cravo) Date: Mon, 2 May 2011 09:38:37 -0300 Subject: [FieldTrip] QuikCap 128 NSL layout In-Reply-To: References: Message-ID: Hello, I am collecting EEG data from a SynAmps RT 128 channels. I am using a QuikCap NSL, which although has 128 electrodes, does not follow standard 10-20 localisation. I'm trying to create a layout to visualise my data using the template fiducials of the cap. My script currently looks something like this: cfg =[]; cfg.elecfile='QuikCap_128_NSL.sfp' cfg.rotate=0; cfg.projection='polar' lay=ft_prepare_layout(cfg); ft_layoutplot(cfg) However, the electrodes seems to be shifted towards the back of the head. The layout I get can be seen in the FieldTrip_Layout figure attached. I have tried to realign the electrodes (using ft_electroderealign), but I get similar results. Has anyone ever had a similar problem? Please find attached the 'QuikCap_128_NSL.sfp' file with the fiducials and a .png figure of the electrode positions taken from NeuroScan's website. Thanks in advance for the help. Andre Cravo --- University of Sao Paulo-Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QuikCap_128_NSL.sfp Type: application/octet-stream Size: 3888 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: neuroscan.png Type: image/png Size: 282038 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FieldTrip_Layout.png Type: image/png Size: 12814 bytes Desc: not available URL: From cmuehl at gmail.com Mon May 2 17:48:42 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Mon, 2 May 2011 17:48:42 +0200 Subject: [FieldTrip] Call for Papers: Affective BCI Workshop, Memphis, USA Message-ID: ** Call for Papers ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuroergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 15th of June: Workshop papers due 1st of July: Notification of Acceptance 18th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From r.oostenveld at donders.ru.nl Tue May 3 10:20:05 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 3 May 2011 10:20:05 +0200 Subject: [FieldTrip] changed channel names for EGI data format from 'e' to 'E' Message-ID: <4522B5B9-579C-4AFF-A2CF-449420DAFFAF@donders.ru.nl> Dear fieldtrip users working on EGI data, The EGI system does not have well described channel names, but most software deals with it by prefixing the EGI channel names with an 'E', e.g. E1, E2 ... E256 It turned out that there were some inconsistent definitions whether it should be a lowercase 'e' or an uppercase 'E'. After consulting with some EGI experts (Joseph Dien, Catherine Poulsen, Ingrid Nieuwenhuis), I have just changed fieldtrip to use an uppercase 'E' consistently throughout the code. The EGI layouts (*.sfp files) also use this uppercase definition. The consequence is that string comparisons between channels like 'e1' and 'E1' might fail and that in the analysis (e.g. grandaveraging data with mixed case labels) the identical channels are not recognized/matched to each other. If you encounter problems like these, you should fix them by converting the channel labels for data that you have stored on disk in *.mat files to uppercase. That can be easily done with the "upper" function in MATLAB for example like this: data.label = upper(data.label); timelock.label = upper(timelock.label); freq.label = upper(freq.label); freq.labelcmb = upper(freq.labelcmb); Sorry for the inconvenience that this causes, hopefully in the future with the consistent definition of the channel labels we won't have problems like this any more. best regards, Robert From annajafarpour at gmail.com Tue May 3 19:40:20 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 18:40:20 +0100 Subject: [FieldTrip] tf online tutorial is missed Message-ID: Hello all, In the Fieldtrip online documentation, the tutorial about tf analysis is missed. Where else can I find a copy of the tutorial? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue May 3 19:55:44 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 3 May 2011 19:55:44 +0200 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Hello Anna, To be honest, I have no idea what happened, or why the time-frequency tutorial page was suddenly blank. However, I seem to have fixed the issue by clearing the page's contents, and re-adding it. I'll look into the issue further; but for now, your problem is solved. Best, Eelke 2011/5/3 Anna Jafarpour : > Hello all, > > In the Fieldtrip online documentation, the tutorial about tf analysis is > missed. Where else can I find a copy of the tutorial? > > Best, > Anna > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From annajafarpour at gmail.com Tue May 3 20:04:57 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 19:04:57 +0100 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Thank you :) On Tue, May 3, 2011 at 6:55 PM, Eelke Spaak wrote: > Hello Anna, > > To be honest, I have no idea what happened, or why the time-frequency > tutorial page was suddenly blank. However, I seem to have fixed the > issue by clearing the page's contents, and re-adding it. I'll look > into the issue further; but for now, your problem is solved. > > Best, > Eelke > > 2011/5/3 Anna Jafarpour : > > Hello all, > > > > In the Fieldtrip online documentation, the tutorial about tf analysis is > > missed. Where else can I find a copy of the tutorial? > > > > Best, > > Anna > > > > _______________________________________________ > > 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 annajafarpour at gmail.com Tue May 3 21:10:48 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 20:10:48 +0100 Subject: [FieldTrip] trial selection Message-ID: Dear All, I am sorry if this is an FAQ; the online FAQ is not accessible. Is there any function for selecting trials according to the trialinfo? Or is there any function for copying specific trials (with its configuration) into a new variable? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue May 3 21:39:15 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 3 May 2011 21:39:15 +0200 (CEST) Subject: [FieldTrip] trial selection In-Reply-To: Message-ID: <1167814753.23605.1304451555946.JavaMail.root@sculptor.zimbra.ru.nl> Hi Anna, Have a look at the help of ft_redefinetrial. Possibly the configuration option cfg.trials is the one you're looking for. Yours, Arjen   ----- "Anna Jafarpour" schreef: > Van: "Anna Jafarpour" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 3 mei 2011 21:10:48 > Onderwerp: [FieldTrip] trial selection > > Dear All, > I am sorry if this is an FAQ; the online FAQ is not accessible. > Is there any function for selecting trials according to the trialinfo? Or is there any function for copying specific trials (with its configuration) into a new variable? > > Best, > Anna > > _______________________________________________ > 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 inbalots at gmail.com Wed May 4 14:25:30 2011 From: inbalots at gmail.com (Inbal Lots) Date: Wed, 4 May 2011 15:25:30 +0300 Subject: [FieldTrip] Question about trl Message-ID: Hello my name is Inbal and I wanted to ask about trl. Say I define trl myself, as following: trl = [1000 , 1600 , -100]; Lets assume that the sampling rate is 1000Hz trl defines, as far as I understand, the onset at sample #1000, the data start of the data to analyze , before onset, at sample #900 and the end of the data to analyze at sample # 1500. Is that so? Thanks Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Wed May 4 14:56:59 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Wed, 4 May 2011 14:56:59 +0200 (CEST) Subject: [FieldTrip] Question about trl In-Reply-To: <244f01cc0a5a$2d05a1e0$8710e5a0$@vanpelt@fcdonders.ru.nl> Message-ID: <915523278.28822.1304513819890.JavaMail.root@sculptor.zimbra.ru.nl> Hello Inbal, That is not quite correct. Say you define a trial as cfg.trl=[1000 1600 -100], then “-100” is the offset (in samples) of your time axis. So, for this trial, you will get a dataset of 600 samples (or also ms in your example case) length (=1600-1000), of which sample 101 will be defined as t=0s (-100 meaning that the 1 st sample of your trial is -100 samples from t=0). So, the third column in cfg.trl doesn’t affect which part of the data will de used to define the trial (samples 1000 to 1600 will always be read from your data), but only affects the position of t=0 on the time-axis of your trial (data.time). Best, Stan Stan van Pelt, PhD Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 68495 Fax: (+31) (0)24 36 10989 > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Inbal Lots > Sent: Wednesday, May 04, 2011 2:26 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Question about trl Hello > my name is Inbal and I wanted to ask about trl. > Say I define trl myself, as following: > trl = [1000 , 1600 , -100]; > Lets assume that the sampling rate is 1000Hz > trl defines, as far as I understand, the onset at sample #1000, the data start of the data to analyze , before onset, at sample #900 and the end of the data to analyze at sample # 1500. Is that so? > > Thanks > Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko at nyu.edu Wed May 4 15:17:49 2011 From: akiko at nyu.edu (Akiko Ikkai) Date: Wed, 04 May 2011 09:17:49 -0400 Subject: [FieldTrip] overlaying beamformer results to native/normalized space Message-ID: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> I sent a below message to the list last night, but it was bounced back. I'm trying from another email account. My apologies if this was duplicate... I'm trying to run beamformer analysis on my MEG data, using DICS, and having difficulty visualizing meaningful results. I was able to align MRI image to MEG sensors; after segmentation, ft_prepare_singleshell and ft_prepare_leadfield, plotting ft_data.grad and volume model confirms that they align reasonably. However, using data.grad, grid, and vol to run ft_sourceanalysis, and ft_sourceinterpolate with MRI (in ctf coordinate system and aligned to MEG sensors) somehow distorts the alignment, and the new volume model does not resemble the original. I'm assuming that, after ft_sourceinterpolate, if I segment source_interpolated.anatomy and run ft_prepare_singleshell and ft_prepare_leadfield, it should align with MEG sensors, just as the initial volume model aligned with MEG sensors... or am I making too much of an assumption here? Because of the misalignment, output data of ft_sourceinterpolate with "anatomy" and "avg.pow" does not agree with topoplot (run ft_freqanalysis on the same dataset). If anyone could explain why this alignment distortion might be happening during ft_sourceanalysis and/or ft_sourceinterpolate, I'd really appreciate it. Thanks in advance, Akiko -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 From ting.ac at gmail.com Wed May 4 15:56:57 2011 From: ting.ac at gmail.com (Allison Connolly) Date: Wed, 4 May 2011 08:56:57 -0500 Subject: [FieldTrip] error using spm_slice_vol Message-ID: Hi all, I am trying to segment an mri volume using. When I call ft_read_mri('filename'), I get an error that says: ??? Error using ==> spm_slice_vol at 28 spm_slice_vol.c not compiled - see spm_MAKE.sh Error in ==> spm_read_vols at 35 Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 p]),V(i).dim(1:2),0); Error in ==> ft_read_mri at 97 img = spm_read_vols(hdr); I tried installing the most up to date version of fieldtrip and I still get the same error. Can someone help me? -Allison -------------- next part -------------- An HTML attachment was scrubbed... URL: From annajafarpour at gmail.com Wed May 4 16:03:18 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Wed, 4 May 2011 15:03:18 +0100 Subject: [FieldTrip] Multivariate analysis of MEG data Message-ID: Hi, I am trying to run an SVM on a data (2 X 60 rpt 274 chan 1 freq 41 timep) using Fieltrip 20110420. But it gives an error and looks for ft_mv_standardizer. I cannot find this function anywhere (I set-pathed the multivariate folder as well). What is the problem? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed May 4 22:24:40 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 May 2011 22:24:40 +0200 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Dear wiki visitors, There were some issues on the fieldtrip wiki with pages suddenly displaying as empty. It turned out that it was due to a full hard-disk in our webserver. The problem has been resolved and now everything should work smoothly again. best regards, Robert On 3 May 2011, at 20:04, Anna Jafarpour wrote: > Thank you :) > > On Tue, May 3, 2011 at 6:55 PM, Eelke Spaak wrote: > Hello Anna, > > To be honest, I have no idea what happened, or why the time-frequency > tutorial page was suddenly blank. However, I seem to have fixed the > issue by clearing the page's contents, and re-adding it. I'll look > into the issue further; but for now, your problem is solved. > > Best, > Eelke > > 2011/5/3 Anna Jafarpour : > > Hello all, > > > > In the Fieldtrip online documentation, the tutorial about tf analysis is > > missed. Where else can I find a copy of the tutorial? > > > > Best, > > Anna > > > > _______________________________________________ > > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekanal at cmu.edu Thu May 5 00:05:54 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Wed, 4 May 2011 18:05:54 -0400 Subject: [FieldTrip] ft_channelselection fails with negation and regex matching Message-ID: <710C0AC3-5C40-4746-96FC-FBB2D5D1979F@cmu.edu> Hello fieldtrip - We have a Elekta Neuromag 306 scanner, and I'm trying to select only the gradiometers. The magnetometers are labeled 'MEGxxx1', where x can be any number, and the gradiometers are either 'MEGxxx2' or 'MEGxxx3'. However, using ft_channelselection results in the following error: ~~~~ >> ft_channelselection({'all','-STI*','-MEG*1'}, cfg.hdr.label) ??? Matrix index is out of range for deletion. Error in ==> ft_channelselection at 287 channel([ ~~~~ This error is somewhat complex, as I was able to determine that ft_channelselection recursively calls itself a number of times while running, and I was unable to figure out what is causing this problem. Any help would be appreciated. Thanks! Eliezer Kanal -------------------- Eliezer Kanal, Ph.D. Postdoctoral Fellow Center for the Neural Basis of Cognition Carnegie Mellon University 4400 Fifth Ave, Suite 110A Pittsburgh PA 15213 P: 412-268-4115 F: 412-268-5060 From a.stolk at fcdonders.ru.nl Thu May 5 09:54:53 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 5 May 2011 09:54:53 +0200 (CEST) Subject: [FieldTrip] ft_channelselection fails with negation and regex matching In-Reply-To: <710C0AC3-5C40-4746-96FC-FBB2D5D1979F@cmu.edu> Message-ID: <543079.33508.1304582093866.JavaMail.root@sculptor.zimbra.ru.nl> Hi Kanal, I've managed to replicate your bug with MEG data and we will try to sort this out. Yours, Arjen ----- "Kanal Eliezer" schreef: > Van: "Kanal Eliezer" > Aan: "Email FieldTrip project discussion list for the" > Verzonden: Donderdag 5 mei 2011 00:05:54 > Onderwerp: [FieldTrip] ft_channelselection fails with negation and regex matching > > Hello fieldtrip - > > We have a Elekta Neuromag 306 scanner, and I'm trying to select only > the gradiometers. The magnetometers are labeled 'MEGxxx1', where x can > be any number, and the gradiometers are either 'MEGxxx2' or 'MEGxxx3'. > However, using ft_channelselection results in the following error: > > ~~~~ > >> ft_channelselection({'all','-STI*','-MEG*1'}, cfg.hdr.label) > ??? Matrix index is out of range for deletion. > > Error in ==> ft_channelselection at 287 > channel([ > ~~~~ > > This error is somewhat complex, as I was able to determine that > ft_channelselection recursively calls itself a number of times while > running, and I was unable to figure out what is causing this problem. > Any help would be appreciated. Thanks! > > Eliezer Kanal > > > -------------------- > Eliezer Kanal, Ph.D. > Postdoctoral Fellow > Center for the Neural Basis of Cognition > Carnegie Mellon University > 4400 Fifth Ave, Suite 110A > Pittsburgh PA 15213 > P: 412-268-4115 > F: 412-268-5060 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From julian.keil at gmail.com Thu May 5 14:15:02 2011 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 5 May 2011 14:15:02 +0200 Subject: [FieldTrip] cfg.maskparameter in ft_multiplotER Message-ID: <06AC35D0-BE3D-4B96-B67F-3E1B64DBAE22@gmail.com> Hi all, i have a question regarding the mask-option in ft_multiplotER (and singleplotER). After the montecarlo statistic with holm-correction, I get the following data structure: stats = prob: [145x679 double] mask: [145x679 double] stat: [145x679 double] ref: [145x679 double] dimord: 'chan_time' label: {145x1 cell} time: [1x679 double] cfg: [1x1 struct] I then use these options to plot the results: cfg=[]; cfg.interactive='yes'; cfg.layout='4D148.lay'; cfg.zparam='stat'; cfg.maskparameter='mask'; figure;ft_multiplotER(cfg,stats); Unfortunately, I get the error message: ??? Error using ==> ft_multiplotER at 528 data in cfg.maskparameter should be vector with one value per channel I am a bit confused, as this used to work fine with an older version of fieldtrip (fieldtrip-20110113). Can anyone explain to me how to handle the mask-option. I already tried to reduce the mask-matrix to a one-value-per channel vector, but this produces the error: ??? Attempt to reference field of non-structure array. Error in ==> ft_multiplotER at 527 if min(size(datmask)) ~= 1 || max(size(datmask)) ~= length(data.label) Maybe I missed some important changes in a recent fieldtrip-update.... Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Thu May 5 23:55:32 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Thu, 05 May 2011 14:55:32 -0700 Subject: [FieldTrip] fieldtrip2eeglab Message-ID: <4DC31CD4.6070508@berkeley.edu> Hi, Does a fieldtrip2eeglab script exist, to transform a Matlab structure generated by FieldTrip into a Matlab struct that EEGlab can swallow? I know the reverse does exist (eeglab2fieldtrip). I need to get some raw data (egi_mff dataformat, which is not implemented in EEGlab yet as far as I know) into EEGlab. Or if anyone has written some code that might do the trick, that would be very much appreciated as well! Thanks! Ingrid -- Ingrid Nieuwenhuis PhD Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From Maarten.van-Casteren at mrc-cbu.cam.ac.uk Fri May 6 14:10:13 2011 From: Maarten.van-Casteren at mrc-cbu.cam.ac.uk (Maarten van-Casteren) Date: Fri, 6 May 2011 12:10:13 +0000 Subject: [FieldTrip] Problem with user specified trial function Message-ID: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> Hi, I've just started to use Fieldtrip and I don't have much experience with Matlab, so I could just be making a stupid mistake, but I found some very strange behavious when I tried to specify my own trailfunction. I started from the example given on the tutorial pages of the wiki. I've indicated the line of interest with an additional '->'. This is what I used: for i=1:length(event) if strcmp(event(i).type, cfg.trialdef.eventtype) % it is a trigger, see whether it has the right value if ismember(event(i).value, cfg.trialdef.eventvalue) % add this to the trl definition begsample = event(i).sample - cfg.trialdef.prestim*hdr.Fs; endsample = event(i).sample + cfg.trialdef.poststim*hdr.Fs - 1; offset = -cfg.trialdef.prestim*hdr.Fs; trigger = event(i).value; % remember the trigger (=condition) for each trial -> trl(end+1, :) = [round([begsample endsample offset]) trigger]; end end end When I use it like this it will clip all sample and offset values at 0 - 65536, that is the limits of an unsigned integer. I had to change the actual line that appends the trial to this to make it work: trl(end+1, :) = [double(begsample) double(endsample) double(offset) double(trigger)]; All values are shown by the debugger as doubles anyway, so why this explicit conversion is needed is completely beyond me. Does anyone of you know what is going on? I already asked one of the local Matlab gurus, but he was even more amazed than me... Thanks, Maarten -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri May 6 14:31:24 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 06 May 2011 14:31:24 +0200 Subject: [FieldTrip] Problem with user specified trial function In-Reply-To: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> References: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> Message-ID: <4DC3EA1C.4080606@donders.ru.nl> Hi Maarten, no idea what might go wrong there (for me your code snippet works fine). Anyway, you could try to first round cfg.trialdef.prestim*hdr.Fs (same for poststim) outside the loop and store them as local variables and then continue without having to round in every single iteration for every single trial-def, e.g.: trloff = round(-cfg.trialdef.prestim*hdr.Fs); trldur = round((cfg.trialdef.poststim+cfg.trialdef.prestim)*hdr.Fs) - 1; % that's from trialfun_general I bet this will make a difference, although it should of course not. Maybe someone else can confirm the error with your code snippet... Best, Jörn On 5/6/2011 2:10 PM, Maarten van-Casteren wrote: > > Hi, > > I've just started to use Fieldtrip and I don't > > have much experience with Matlab, so I could > > just be making a stupid mistake, but I found > > some very strange behavious when I tried to > > specify my own trailfunction. > > I started from the example given on the tutorial > > pages of the wiki. I've indicated the line of interest > > with an additional '->'. This is what I used: > > for i=1:length(event) > > if strcmp(event(i).type, cfg.trialdef.eventtype) > > % it is a trigger, see whether it has the right value > > if ismember(event(i).value, cfg.trialdef.eventvalue) > > % add this to the trl definition > > begsample = event(i).sample - cfg.trialdef.prestim*hdr.Fs; > > endsample = event(i).sample + cfg.trialdef.poststim*hdr.Fs - 1; > > offset = -cfg.trialdef.prestim*hdr.Fs; > > trigger = event(i).value; % remember the trigger > (=condition) for each trial > > -> trl(end+1, :) = [round([begsample endsample offset]) trigger]; > > end > > end > > end > > When I use it like this it will clip all sample and > > offset values at 0 -- 65536, that is the limits of an > > unsigned integer. I had to change the actual line > > that appends the trial to this to make it work: > > trl(end+1, :) = [double(begsample) double(endsample) double(offset) > double(trigger)]; > > All values are shown by the debugger as doubles > > anyway, so why this explicit conversion is needed > > is completely beyond me. > > Does anyone of you know what is going on? > > I already asked one of the local Matlab gurus, > > but he was even more amazed than me... > > Thanks, > > Maarten > > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From fedeletommaso at yahoo.it Fri May 6 17:28:48 2011 From: fedeletommaso at yahoo.it (tommaso fedele) Date: Fri, 6 May 2011 16:28:48 +0100 (BST) Subject: [FieldTrip] FT_analysis of the average vs average(FT_analysis(single trials)) Message-ID: <686364.21106.qm@web28608.mail.ukl.yahoo.com> Hi all, I want to test if some component that I observe in the average of my ERP signal are phase locked to the stimulus. In oder to do so I compare 1. TFR_averaged_signal = ft_freqanalysis(cfg, averaged_signal) 2. TFR_singletrials_signal = ft_freqanalysis(cfg, singletrials_signal) with the first structure TFR_averaged_signal everything is fine, and I get my nice TF plot. with the second I should average through "trials". Is there a function for that? Or, is it correct to proceed plotting the average of TFR_singletrials_signal.powspctrm through the "trials-matrix dimension"? Thanks Tommaso -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon May 9 12:13:40 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 May 2011 12:13:40 +0200 Subject: [FieldTrip] fieldtrip2eeglab In-Reply-To: <4DC31CD4.6070508@berkeley.edu> References: <4DC31CD4.6070508@berkeley.edu> Message-ID: <45F6D404-F8C3-4339-AE25-25E52C8D2598@donders.ru.nl> Hi Ingrid, I searched my hard disk and found the attached file. Note that it is a very old file (last modified 2006) and I don't know whether the "EEG" structure is still like this, but it may help you get started. best, Robert On 5 May 2011, at 23:55, Ingrid Nieuwenhuis wrote: > Hi, > > Does a fieldtrip2eeglab script exist, to transform a Matlab > structure generated by FieldTrip into a Matlab struct that EEGlab > can swallow? I know the reverse does exist (eeglab2fieldtrip). I > need to get some raw data (egi_mff dataformat, which is not > implemented in EEGlab yet as far as I know) into EEGlab. Or if > anyone has written some code that might do the trick, that would be > very much appreciated as well! > > Thanks! > Ingrid -------------- next part -------------- A non-text attachment was scrubbed... Name: fieldtrip2eeglab.m Type: application/octet-stream Size: 1094 bytes Desc: not available URL: -------------- next part -------------- From jstout211 at yahoo.com Mon May 9 22:12:15 2011 From: jstout211 at yahoo.com (Jeff Stout) Date: Mon, 9 May 2011 13:12:15 -0700 (PDT) Subject: [FieldTrip] Leadfield calculations result in NaNs Message-ID: <102170.78349.qm@web113519.mail.gq1.yahoo.com> Hi,  I am having trouble generating leadfields for source analysis.  I am using data from a 4D magnetometer system (Magnes 3600), at St. Louis University. The data is averged time domain data.  The volume conductor is a single shell model generated from the headshape file(~4000 vert. and 8000 triangles).  I have vizualized the volume conductor, sensors, and "inside" grid and they appear to be in the correct locations relative to each other.  I have performed this analysis using the default source space for 4D ('m') and I have tried it scaling the headshape and sensors into cm to conform with the ctf source space.   Below is part of my code and the warning thrown by matlab.  After the calculation of the leadfields, it is apparent that they are all NaN's, so I am unable to generate source activations. cfg = [];cfg.headshape = shape;shape.pnt = shape.pnt*100;shape.unit  = 'cm';[vol,cfg] = ft_prepare_singleshell(cfg) cfg                 = [];cfg.grad            = avg.grad; cfg.grad.pnt = cfg.grad.pnt*100;cfg.grad.unit  = 'cm';cfg.vol             = vol;cfg.sourceunits = 'cm';cfg.coordsys   = 'ctf';cfg.reducerank      ='no';  cfg.channel         = {'MEG'};cfg.grid.resolution = 2[vol, sens] = ft_prepare_vol_sens(vol, cfg.grad)[grid] = ft_prepare_leadfield(cfg)    >> [grid] = ft_prepare_leadfield(cfg)using headmodel specified in the configurationusing gradiometers specified in the configurationcomputing surface normalsWarning: Matrix is singular, close to singular or badly scaled.   <<<<<<<<<<         Results may be inaccurate. RCOND = NaN. > In forward/private/meg_ini>getcoeffs at 111  In forward/private/meg_ini at 53  In ft_prepare_vol_sens at 275  In fieldtrip-20110507/private/prepare_headmodel at 114  In ft_prepare_leadfield at 150creating dipole grid based on automatic 3D grid with specified resolution3528 dipoles inside, 0 dipoles outside brainmaking tight grid3528 dipoles inside, 0 dipoles outside braincomputing leadfieldcomputing leadfield 1/3528computing leadfield 2/3528computing leadfield 3/3528computing leadfield 4/3528 ...... The leadfield data generated is a matrix of NaN's, which appear to be an issue when evaluating bas and gradbas in the get_coeffs subfunction  [bas,gradbas]=legs(x1,n1,order,scale). Does anyone know how to resolve this issue? Any help will be greatly appreciated. Thanks, Jeff Stout Open in Google Docs ViewerOpen link in new tabOpen link in new windowOpen link in new incognito windowDownload fileCopy link addressEdit PDF File on PDFescape.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew at psych.columbia.edu Tue May 10 00:37:39 2011 From: matthew at psych.columbia.edu (Matthew Davidson) Date: Mon, 9 May 2011 18:37:39 -0400 Subject: [FieldTrip] Human neurophysiology analysis tech posting in San Diego Message-ID: Human Neurophysiology Analysis Technician – To assist a team of experienced neurophysiologists conduct language, memory, sleep and developmental studies in humans with MEG and intracranial recordings. MEG localization will use structural MRI constraints and functional MRI bias. Intracranial recordings include microelectrode arrays, unit-recordings, and laminar current source density analysis. The candidate must have high abstract intelligence in order to rapidly acquire different techniques, modify them as necessary, and recognize inconsistent results. Prior expertise with MatLab would be very useful, and some knowledge of neuroscience is expected. Collaborate with a large, talented and friendly group of scientists, programmers and technicians engaged in multimodal brain research. The position is available starting immediately, with the expectation that you would remain for at least 2 years, but it is subject to annual review and continuation of grant funding. Everyone is welcome to apply regardless of gender, ethnicity, or other irrelevancies. Please contact Eric Halgren, Ph.D., Multimodal Imaging Laboratory, University of California at San Diego,ehalgren at ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 10 08:36:51 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 10 May 2011 08:36:51 +0200 Subject: [FieldTrip] Leadfield calculations result in NaNs In-Reply-To: <102170.78349.qm@web113519.mail.gq1.yahoo.com> References: <102170.78349.qm@web113519.mail.gq1.yahoo.com> Message-ID: Dear Jeff, From what you describe I don't really know what's going wrong. Are you using the headsurface file generated with the polhemus? It could be that this causes the problem. For the singleshell model to work, you need a triangulated surface. The headsurface file contains only a point cloud. Matlab tries to create a triangulation from this point cloud, and I could imagine that this triangulation misbehaves here, leading some nans here and there (judging from your message this happens when the normals to the triangles are computed), which eventually cause nans all over the place. For the time being you could try to use a different volume conductor model (localspheres), or you may want to use a structural MRI for the singleshell creation (if available), to verify that the problem is caused by the headsurface file and not by fieldtrip. Best, Jan-Mathijs On May 9, 2011, at 10:12 PM, Jeff Stout wrote: > > Hi, > > I am having trouble generating leadfields for source analysis. I am > using data from a 4D magnetometer system (Magnes 3600), at St. Louis > University. > > The data is averged time domain data. The volume conductor is a > single shell model generated from the headshape file(~4000 vert. and > 8000 triangles). I have vizualized the volume conductor, sensors, > and "inside" grid and they appear to be in the correct locations > relative to each other. I have performed this analysis using the > default source space for 4D ('m') and I have tried it scaling the > headshape and sensors into cm to conform with the ctf source > space. Below is part of my code and the warning thrown by matlab. > After the calculation of the leadfields, it is apparent that they > are all NaN's, so I am unable to generate source activations. > > cfg = []; > cfg.headshape = shape; > shape.pnt = shape.pnt*100; > shape.unit = 'cm'; > [vol,cfg] = ft_prepare_singleshell(cfg) > > cfg = []; > cfg.grad = avg.grad; > cfg.grad.pnt = cfg.grad.pnt*100; > cfg.grad.unit = 'cm'; > cfg.vol = vol; > cfg.sourceunits = 'cm'; > cfg.coordsys = 'ctf'; > cfg.reducerank ='no'; > cfg.channel = {'MEG'}; > cfg.grid.resolution = 2 > [vol, sens] = ft_prepare_vol_sens(vol, cfg.grad) > [grid] = ft_prepare_leadfield(cfg) > > >> [grid] = ft_prepare_leadfield(cfg) > using headmodel specified in the configuration > using gradiometers specified in the configuration > computing surface normals > Warning: Matrix is singular, close to singular or badly scaled. > <<<<<<<<<< > Results may be inaccurate. RCOND = NaN. > > In forward/private/meg_ini>getcoeffs at 111 > In forward/private/meg_ini at 53 > In ft_prepare_vol_sens at 275 > In fieldtrip-20110507/private/prepare_headmodel at 114 > In ft_prepare_leadfield at 150 > creating dipole grid based on automatic 3D grid with specified > resolution > 3528 dipoles inside, 0 dipoles outside brain > making tight grid > 3528 dipoles inside, 0 dipoles outside brain > computing leadfield > computing leadfield 1/3528 > computing leadfield 2/3528 > computing leadfield 3/3528 > computing leadfield 4/3528 ...... > > > The leadfield data generated is a matrix of NaN's, which appear to > be an issue when evaluating bas and gradbas in the get_coeffs > subfunction [bas,gradbas]=legs(x1,n1,order,scale). > > Does anyone know how to resolve this issue? Any help will be greatly > appreciated. > > Thanks, > Jeff Stout > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan.debener at uni-oldenburg.de Tue May 10 09:04:47 2011 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Tue, 10 May 2011 09:04:47 +0200 Subject: [FieldTrip] Auditory BCI post-doc posting Message-ID: <4DC8E38F.5050902@uni-oldenburg.de> Dear all, We are seeking a scientist/post-doc who is interested in developing an auditiry brain computer interface. Please visit: http://www.hearingresearch.uni-oldenburg.de/52922.html (job offer #4), and feel free to contact me via email for further information. Thanks much, Stefan -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de From jan.schoffelen at donders.ru.nl Wed May 11 08:35:19 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 08:35:19 +0200 Subject: [FieldTrip] ft_freqstatistics Message-ID: <4EE8E6A8-5C67-45A6-A6CE-7D6FFA5C3D64@donders.ru.nl> Dear all, I just committed to the svn-repository a revamped version of ft_freqstatistics, the function which does channel-level statistics on frequency domain data. This was a necessary cleaning operation to keep the code up-to-date. Important for you to know is that nothing has changed in the handling of good old-fashioned (time-frequency) power. The new thing is that you don't need to hack your way into the function anymore in order to do group level statistics on connectivity data. Things should just run fine, but although I extensively tested the code (to my best knowledge) on plausible scenarios, please keep your eyes open. Best, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From ndavid at uke.de Wed May 11 10:45:32 2011 From: ndavid at uke.de (Nicole David) Date: Wed, 11 May 2011 10:45:32 +0200 Subject: [FieldTrip] Job Announcement (PhD Position) In-Reply-To: <03750F99-88BD-42D6-9133-8E4B4814E133@uke.de> References: <03750F99-88BD-42D6-9133-8E4B4814E133@uke.de> Message-ID: Dear FieldTrip list, I would like to announce an open PhD position with Prof. Andreas Engel at the Dept. of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf. For details, see below. Best, Nicole David ------------------------------- The Department of Neurophysiology and Pathophysiology at the University Medical Center Hamburg-Eppendorf (Director: Prof. Dr. Andreas K. Engel) invites applications for a PhD student position. The position is available with immediate start. The appointment will be for 3 years. The position is at the intersection of psychology, cognitive neuroscience and philosophy. More specifically, experiments investigating the sense of agency shall be carried out, using neuroscience techniques such as magnetoencephalography (MEG). The sense of agency refers to the monitoring of actions and the experience, or awareness, of such as self- or other-generated. Applicants should have experience in analyzing human EEG or MEG studies. Programming experience (Matlab) as well as fluent written and spoken English is considered mandatory. Applicants will be responsible for the management and implementation of research paradigms, data acquisition and analysis. Knowledge in theories of action and perception, multisensory processing, self-awareness and a basic understanding of information processing in the human brain would be preferred. The successful candidate will be member of the European collaborative project “Extending Sensorimotor Contingencies to Cognition – eSMCs” that has started in January 2011. The main objective of the project is to extend the Sensorimotor Contingency Theory as an action-based approach to perception and cognition, and to investigate its implications in studies of natural and artificial agents. More information on the project is to appear at http://eSMCs.eu. Information on the Dept. of Neurophysiology and Pathophysiology is available at http://www.uke.de/neurophysiologie and at http://www.40hz.de . Please send your application (including a CV) to Dr. Nicole David or Prof. Dr. Andreas K. Engel Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistrasse 52 20246 Hamburg Germany Submission of applications through email (ndavid at uke.de, ak.engel at uke.de) is encouraged. -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Joachim Prölß Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 11 10:56:10 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 10:56:10 +0200 Subject: [FieldTrip] FT_analysis of the average vs average(FT_analysis(single trials)) In-Reply-To: <686364.21106.qm@web28608.mail.ukl.yahoo.com> References: <686364.21106.qm@web28608.mail.ukl.yahoo.com> Message-ID: Dear Tommaso, Yes, if you average across the trial-dimension you will obtain the TFR you're after. Best, JM On May 6, 2011, at 5:28 PM, tommaso fedele wrote: > Hi all, > I want to test if some component that I observe in the average of my > ERP signal are phase locked to the stimulus. > In oder to do so I compare > 1. TFR_averaged_signal = ft_freqanalysis(cfg, averaged_signal) > 2. TFR_singletrials_signal = ft_freqanalysis(cfg, > singletrials_signal) > > with the first structure TFR_averaged_signal everything is fine, and > I get my nice TF plot. > with the second I should average through "trials". Is there a > function for that? Or, is it correct to proceed plotting > the average of TFR_singletrials_signal.powspctrm through the > "trials-matrix dimension"? > > Thanks > Tommaso > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 11 10:59:06 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 10:59:06 +0200 Subject: [FieldTrip] error using spm_slice_vol In-Reply-To: References: Message-ID: Hi Allison, This looks like an SPM-related error to me, or it is operating system related. Can you check which spm-version you are using, in other words: is it the fieldtrip/external/spmXXX directory, or do you have spm somewhere else on your matlab-path? If it is the former, then it is a potential bug which needs fixing by us. Otherwise we cannot help it. What kind of operating system are you using? Best, Jan-Mathijs On May 4, 2011, at 3:56 PM, Allison Connolly wrote: > Hi all, > > I am trying to segment an mri volume using. When I call > ft_read_mri('filename'), I get an error that says: > > ??? Error using ==> spm_slice_vol at 28 > spm_slice_vol.c not compiled - see spm_MAKE.sh > > Error in ==> spm_read_vols at 35 > Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 > p]),V(i).dim(1:2),0); > > Error in ==> ft_read_mri at 97 > img = spm_read_vols(hdr); > > I tried installing the most up to date version of fieldtrip and I > still get the same error. Can someone help me? > > -Allison > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Wed May 11 11:02:49 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 11:02:49 +0200 Subject: [FieldTrip] overlaying beamformer results to native/normalized space In-Reply-To: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> References: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> Message-ID: Dear Akiko, On May 4, 2011, at 3:17 PM, Akiko Ikkai wrote: > I sent a below message to the list last night, but it was bounced > back. I'm trying from another email account. My apologies if this > was duplicate... > > > > I'm trying to run beamformer analysis on my MEG data, using DICS, > and having difficulty visualizing meaningful results. > > I was able to align MRI image to MEG sensors; after segmentation, > ft_prepare_singleshell and ft_prepare_leadfield, plotting > ft_data.grad and volume model confirms that they align reasonably. > However, using data.grad, grid, and vol to run ft_sourceanalysis, > and ft_sourceinterpolate with MRI (in ctf coordinate system and > aligned to MEG sensors) somehow distorts the alignment, and the new > volume model does not resemble the original. So, the problem is that ft_sourceinterpolate does not behave as expected? > I'm assuming that, after ft_sourceinterpolate, if I segment > source_interpolated.anatomy and run ft_prepare_singleshell and > ft_prepare_leadfield, it should align with MEG sensors, just as the > initial volume model aligned with MEG sensors... or am I making too > much of an assumption here? Why would you want to do this? > Because of the misalignment, output data of ft_sourceinterpolate > with "anatomy" and "avg.pow" does not agree with topoplot (run > ft_freqanalysis on the same dataset). > If anyone could explain why this alignment distortion might be > happening during ft_sourceanalysis and/or ft_sourceinterpolate, I'd > really appreciate it. > I am afraid you need to be a bit more specific in order for us to understand what may be going wrong here. Best, Jan-Mathijs > Thanks in advance, Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ting.ac at gmail.com Wed May 11 19:30:14 2011 From: ting.ac at gmail.com (Allison Connolly) Date: Wed, 11 May 2011 12:30:14 -0500 Subject: [FieldTrip] channelcmb with removed channels Message-ID: I am trying to do beamforming on some MEG data. However, some of the sensors railed during the recordings, so I want to remove them from the analysis. I declare the channels I want to use during import with ft_preprocessing by saying: cfg.channel = {'MEG','-TRIGGER','-RESPONSE',... '-UACurrent','-MxA','-MyA','-MzA','-GxxA','-GyxA','-GyyA',... '-GzyA','-GzxA','-MxaA','-MyaA','-MzaA','-E1','-E2','-E3','-E4',... '-A40','-A57','-A76','-A77','-A79','-A81','-A88','-A89','-A96',... '-A100','-A102','-A103','-A108','-A112','-A113','-A114','-A116',... '-A120','-A121','-A123','-A124','-A125','-A126','-A127','-A128',... '-A129','-A130','-A131','-A124','-A139','-A140','-A141','-A142',... '-A144','-A145','-A146','-A147','-A148'}; Then I use ft_freqanalysis to calculate the cross spectral density and ft_prepare_leadfield to create the brain grid. When I try to run ft_sourceanalysis, I get this error: creating dipole grid based on user specified dipole positions 13718 dipoles inside, 144943 dipoles outside brain ??? In an assignment A(I) = B, a matrix A cannot be resized. Error in ==> prepare_freq_matrices at 115 Cf(find(crsspctrmindx)) = freq.crsspctrm(crsspctrmindx(find(crsspctrmindx)), fbin); Error in ==> ft_sourceanalysis at 461 [Cf, Cr, Pr, Ntrials, cfg] = prepare_freq_matrices(cfg, data); I think it is because I have removed channels. When I try to run ft_freqanalysis while specifying the channels in cfg.channel, i get this error: the input is raw data with 111 channels and 60 trials ??? Error using ==> ft_freqanalysis at 352 *channels in cfg.channelcmb not present in cfg.channel* * *I think I need to explicitly define cfg.channelcmb, but I don't know how to do this if I have removed channels. -Allison -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpoll at ugr.es Thu May 12 14:10:46 2011 From: jpoll at ugr.es (JOAN PAUL POZUELOS LOPEZ) Date: Thu, 12 May 2011 14:10:46 +0200 Subject: [FieldTrip] Problems with the Buffer Message-ID: Hello everyone, Im new using the matlab for analyzing ERP´s. I have been using the FASTER program (Nolan, Whelan &Reilly, 2010, Journal of Neuroscience Methods) and i have encounter a problem with some files contained in the filedtrip toolbox. The problem its that when it is computing the ICA the process is not finished because theres an error that says: "error - invalid MEX_file 'c: Users\....\Matlab\external\fieldtrip-20110320\realtime\buffer\matlab\buffer.mexw32': could not find the specified module. When i check the folder containing the Buffer.mexw32 file, it is in the folder that the Filepath looks. Any suggestions on how to solve this problem?. Thank you very much for your help JOAN PAUL POZUELOS LOPEZ Departamento de Psicología Experimental y Fisiología del Comportamiento Universidad de Granada jpoll at ugr.es From nuria.donamayor at neuro.uni-luebeck.de Fri May 13 10:42:05 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Fri, 13 May 2011 10:42:05 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> Dear fieltrip users, I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a 64-bit Matlab version and I am getting an error I don't know how to solve: hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); ??? SWITCH expression must be a scalar or string constant. Error in ==> read_4d_hdr at 60 switch format Error in ==> ft_read_header at 153 orig = read_4d_hdr(datafile); If I try to read the same data on my Windows PC with 32-bit Matlab I have no problem reading the header file (but I can't even finish the preprocessing before it runs out of memory, therefore the switch to the Linux machine), so I'm pretty clueless here... Can any of you help me? Thanks, Nuria Nuria Doñamayor Alonso, MSc Universitätsklinikum Schleswig-Holstein Campus Lübeck Klinik für Neurologie Ratzeburger Allee 160 23538 Lübeck From paul_c at gmx.de Fri May 13 11:27:01 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Fri, 13 May 2011 11:27:01 +0200 Subject: [FieldTrip] Systematic electrode displacement Message-ID: <4DCCF965.4050408@gmx.de> Dear fieldtrippers, I've got an issue with electrode placement and I hope that someone has any idea how to tackle those issues. For research on my diploma thesis I am fitting simulated data with the realistic brain shape I used to simulate the data as well as a icbm model (BEM models). I used the electrode system for the icbm152 brain provided by Robert Oostenveld and did some manual correction to the realistic brains (which were normalised to icbm brain) with the ft_electroderealign function. I simulated the data in a position near the auditory cortex, since this is the location where we assume our real ERP. In my fitted data I encountered strange systematic errors (especially some kind of bias on the z-axis), as seen on the boxplot_coord_20110407.png file (note that it's both age groups: 1 for old and 2 for young, scale is meters). While investigating on the origin of this bias, I made a box plot of the distance of the electrodes in the icbm model and the electrodes in each of the realistic models (dist_electrodes.png). Obviously there already is an bias in the electrodes placement. First I assumed this was caused my the manual correction of the electrodes I performed. To check this out, I fitted the very data with the manually corrected electrodes on the icbm brain. Still I found that there was a bias, mainly on the z-axis and - what astonished me even more, there was still a bias in the electrodes. This is observable in the boxplot_20110512_electrode_locations_matched.png (sorry for the German captions), x-Axis is coordinate and y-axis is the deviation of the electrode's positions. Furthermore I simulated and fitted a position near the vertex (though still in the brain ;) ). There was not so much of a bias there, therefore I assume it's mainly the lateral and maybe posterior electrodes causing the bias, not that much the superior. Due to those results I assumed that it's got something to do with the automatic projection of the electrodes on the head surface. I had no time yet to compare those electrode positions manually (or better visually), but this is definitely on my agenda. I wondered, if anyone had an idea, how to improve this, for electrode deviations up to ~10 cm is way to much, asking me. I already checked if there maybe was any confusion in the order of the electrodes, but I just checked the labels and this does not support it. Thanks in advance and best regards, Paul Czienskowski -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_coord_20110407.jpg Type: image/jpeg Size: 17510 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dist_electrodes.png Type: image/png Size: 8323 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_20110512_electrode_locations_matched.png Type: image/png Size: 6945 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_20110512_coordinates.png Type: image/png Size: 8841 bytes Desc: not available URL: From yuvharpaz at gmail.com Fri May 13 13:39:29 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 13 May 2011 14:39:29 +0300 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> Message-ID: Dear Nuria Is it exactly the same fieldtrip version? I hope someone will solve this. as temporary work around you can read the header on windows and then move to linux yuval On 13 May 2011 11:42, Nuria Donamayor Alonso < nuria.donamayor at neuro.uni-luebeck.de> wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a > 64-bit Matlab version and I am getting an error I don't know how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I have > no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to the > Linux machine), so I'm pretty clueless here... Can any of you help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuria.donamayor at neuro.uni-luebeck.de Fri May 13 14:34:36 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Fri, 13 May 2011 14:34:36 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> Yes, it is exectly the same version. Better said, versions, because I tried both 20110413 and 20110512.... ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com] Gesendet: Freitag, 13. Mai 2011 13:39 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Dear Nuria Is it exactly the same fieldtrip version? I hope someone will solve this. as temporary work around you can read the header on windows and then move to linux yuval On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: Dear fieltrip users, I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a 64-bit Matlab version and I am getting an error I don't know how to solve: hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); ??? SWITCH expression must be a scalar or string constant. Error in ==> read_4d_hdr at 60 switch format Error in ==> ft_read_header at 153 orig = read_4d_hdr(datafile); If I try to read the same data on my Windows PC with 32-bit Matlab I have no problem reading the header file (but I can't even finish the preprocessing before it runs out of memory, therefore the switch to the Linux machine), so I'm pretty clueless here... Can any of you help me? Thanks, Nuria Nuria Doñamayor Alonso, MSc Universitätsklinikum Schleswig-Holstein Campus Lübeck Klinik für Neurologie Ratzeburger Allee 160 23538 Lübeck _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html "Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams From jan.schoffelen at donders.ru.nl Fri May 13 16:43:41 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 May 2011 16:43:41 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> Message-ID: Hi Nuria, Could you type dbstop if error on the command line, and evaluate what the variable 'format' is in your case? Thanks, Jan-Mathijs On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > Yes, it is exectly the same version. Better said, versions, because > I tried both 20110413 and 20110512.... > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com > ] > Gesendet: Freitag, 13. Mai 2011 13:39 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Dear Nuria > Is it exactly the same fieldtrip version? > I hope someone will solve this. > as temporary work around you can read the header on windows and then > move to linux > > yuval > > On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine > with a 64-bit Matlab version and I am getting an error I don't know > how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I > have no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to > the Linux machine), so I'm pretty clueless here... Can any of you > help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > > "Many were increasingly of the opinion that they'd all made a big > mistake in coming down from the trees in the first place. And some > said that even the trees had been a bad move, and that no one should > ever have left the oceans". Douglas Adams > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From anokhina at psychiatry.wustl.edu Sat May 14 17:10:43 2011 From: anokhina at psychiatry.wustl.edu (Anokhin, Andrey) Date: Sat, 14 May 2011 10:10:43 -0500 Subject: [FieldTrip] job announcement Message-ID: <86712757862F3640B2F4BB5C14D8EDC4090EF4A245@wusmexmbx2.medpriv.wucon.wustl.edu> An HTML attachment was scrubbed... URL: From l.frei at psy.gla.ac.uk Sat May 14 22:37:45 2011 From: l.frei at psy.gla.ac.uk (Luisa Frei) Date: Sat, 14 May 2011 21:37:45 +0100 Subject: [FieldTrip] stats on planar gradient topographies Message-ID: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Hi there, I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. This the code I used: %%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.001; cfg.clusterstatistic = 'maxsize'; cfg.minnbchan = 4; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.005; cfg.numrandomization = 500; design = [ones(1,13) ones(1,13)+1]; cfg.design = design; cfg.ivar = 1; cfg.channel = {'MEG',sub(1).allbadchan{:}}; cfg.latency = [.15 .2]; [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? Thanks, Luisa Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change.  -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 2.png Type: application/applefile Size: 73 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 2.png Type: image/png Size: 105588 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon May 16 14:32:07 2011 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 16 May 2011 14:32:07 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Message-ID: Hi Luisa, schnell from the top of my head: wie definierst du denn deine neighbors? Ich seh nirgendwo ein Feld cfg.neighbors.... Ich muss das bei unserem 4D-System immer angeben.... Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind falsch definierst, so könntest du zu deinen "random" Clustern kommen. Ich mache diese Neighbor-Struktur folgendermaßen: cfg=[]; cfg.neighbourdist=0.1; %cfg.grad=Comb_AV1_1{1}.grad; cfg.layout='4D148.lay'; cfg.channel={'all'}; %cfg.grad.pnt=cfg.grad.pnt*100; dummy=neighbourselection(cfg); Da bekomme ich auch immer einen Output, wie viele Channels so in der Umgebung sind (sollten in etwa 5 sein). Hoffe das hilft dir weiter Viele Grüße Julian Am 14.05.2011 um 22:37 schrieb Luisa Frei: > Hi there, > I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. > This the code I used: > > %%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.001; > cfg.clusterstatistic = 'maxsize'; > cfg.minnbchan = 4; > > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.005; > cfg.numrandomization = 500; > > design = [ones(1,13) ones(1,13)+1]; > > cfg.design = design; > cfg.ivar = 1; > > cfg.channel = {'MEG',sub(1).allbadchan{:}}; > cfg.latency = [.15 .2]; > > [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? > > Thanks, > Luisa > > Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change. > > _______________________________________________ > 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 jm.horschig at donders.ru.nl Mon May 16 14:52:24 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 16 May 2011 14:52:24 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Message-ID: <4DD11E08.6050207@donders.ru.nl> Hi all, First of all, @julian: It would be nice if you wrote in English so that all people can understand what you are saying :) Second, I would like to mention ft_neighbourplot, which is a relative new function and plots sensors and its' neighbours in 2D or 3D, depending on whether you got 2D or 3D coordinates. Using that function, you can verify whether your neighbourselection looks meaningful and makes sense. Finally, we are currently working on changing/improving the neighbourselecion function. There will be different methods to choose from, and we (me) will create templates for the most common systems that can be used instead of relying on a particular mathematical selection method. We will announce this when it's done (probably soon). Maybe Julian is right and Luisa's problem is due to a 'wrong' neighbourselection. Given that cfg.minnbhchan is set to 4, this might be likely, because not all of the found clusters consist of 4 or more channels. What system are you using? Best, Jörn On 5/16/2011 2:32 PM, Julian Keil wrote: > Hi Luisa, > > schnell from the top of my head: wie definierst du denn deine neighbors? > Ich seh nirgendwo ein Feld cfg.neighbors.... > Ich muss das bei unserem 4D-System immer angeben.... > Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind > falsch definierst, so könntest du zu deinen "random" Clustern kommen. > > Ich mache diese Neighbor-Struktur folgendermaßen: > > cfg=[]; > cfg.neighbourdist=0.1; > %cfg.grad=Comb_AV1_1{1}.grad; > cfg.layout='4D148.lay'; > cfg.channel={'all'}; > %cfg.grad.pnt=cfg.grad.pnt*100; > dummy=neighbourselection(cfg); > > Da bekomme ich auch immer einen Output, wie viele Channels so in der > Umgebung sind (sollten in etwa 5 sein). > > Hoffe das hilft dir weiter > > Viele Grüße > > Julian > > Am 14.05.2011 um 22:37 schrieb Luisa Frei: > >> Hi there, >> I am trying to compute a simple cluster-based statistic in a between >> subjects design. I have followed the steps in the respective tutorial >> very closely. >> This the code I used: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'indepsamplesT'; >> >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.001; >> cfg.clusterstatistic = 'maxsize'; >> cfg.minnbchan = 4; >> >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.005; >> cfg.numrandomization = 500; >> >> design = [ones(1,13) ones(1,13)+1]; >> >> cfg.design = design; >> cfg.ivar = 1; >> >> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >> cfg.latency = [.15 .2]; >> >> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % >> individuals kept >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> My problem is, that I'm not sure which time resolution to use. I >> would like to use a small resolution of 10 ms, but this leads to a >> fairly random pattern of significant sensors (see attached figure, on >> the right). Of course, the more time points I include, the less >> significant sensors are left over. However, another problem is, that >> the ones that are left (figure, left), are not related to big >> differences in the activation pattern at all. How is it possible that >> my significant sensors end up being so randomly distributed? Also, >> ft_timelockstatistics only comes up with one positive and one >> negative cluster., but the sign. sensors are not always connected. >> Could anyone give some helpful input here? >> >> Thanks, >> Luisa >> >> Fyi: I have tried different thresholds and different numbers of >> neighbourhood channels, but there's not much of a change. >> _______________________________________________ >> 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon May 16 14:58:35 2011 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 16 May 2011 14:58:35 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: <4DD11E08.6050207@donders.ru.nl> References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> <4DD11E08.6050207@donders.ru.nl> Message-ID: Hi all, sorry, I thought the answer would only go to Luisa. Apologies, Julian Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig: > Hi all, > > First of all, @julian: It would be nice if you wrote in English so that all people can understand what you are saying :) > > Second, I would like to mention ft_neighbourplot, which is a relative new function and plots sensors and its' neighbours in 2D or 3D, depending on whether you got 2D or 3D coordinates. Using that function, you can verify whether your neighbourselection looks meaningful and makes sense. > > Finally, we are currently working on changing/improving the neighbourselecion function. There will be different methods to choose from, and we (me) will create templates for the most common systems that can be used instead of relying on a particular mathematical selection method. We will announce this when it's done (probably soon). > > Maybe Julian is right and Luisa's problem is due to a 'wrong' neighbourselection. Given that cfg.minnbhchan is set to 4, this might be likely, because not all of the found clusters consist of 4 or more channels. What system are you using? > > Best, > Jörn > > > On 5/16/2011 2:32 PM, Julian Keil wrote: >> >> Hi Luisa, >> >> schnell from the top of my head: wie definierst du denn deine neighbors? >> Ich seh nirgendwo ein Feld cfg.neighbors.... >> Ich muss das bei unserem 4D-System immer angeben.... >> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind falsch definierst, so könntest du zu deinen "random" Clustern kommen. >> >> Ich mache diese Neighbor-Struktur folgendermaßen: >> >> cfg=[]; >> cfg.neighbourdist=0.1; >> %cfg.grad=Comb_AV1_1{1}.grad; >> cfg.layout='4D148.lay'; >> cfg.channel={'all'}; >> %cfg.grad.pnt=cfg.grad.pnt*100; >> dummy=neighbourselection(cfg); >> >> Da bekomme ich auch immer einen Output, wie viele Channels so in der Umgebung sind (sollten in etwa 5 sein). >> >> Hoffe das hilft dir weiter >> >> Viele Grüße >> >> Julian >> >> Am 14.05.2011 um 22:37 schrieb Luisa Frei: >> >>> Hi there, >>> I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. >>> This the code I used: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'indepsamplesT'; >>> >>> cfg.correctm = 'cluster'; >>> cfg.clusteralpha = 0.001; >>> cfg.clusterstatistic = 'maxsize'; >>> cfg.minnbchan = 4; >>> >>> cfg.tail = 0; >>> cfg.clustertail = 0; >>> cfg.alpha = 0.005; >>> cfg.numrandomization = 500; >>> >>> design = [ones(1,13) ones(1,13)+1]; >>> >>> cfg.design = design; >>> cfg.ivar = 1; >>> >>> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >>> cfg.latency = [.15 .2]; >>> >>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? >>> >>> Thanks, >>> Luisa >>> >>> Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change. >>> _______________________________________________ >>> 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 > > 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 > Kapitelweg 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 l.frei at psy.gla.ac.uk Mon May 16 15:10:27 2011 From: l.frei at psy.gla.ac.uk (Luisa Frei) Date: Mon, 16 May 2011 14:10:27 +0100 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> <4DD11E08.6050207@donders.ru.nl> Message-ID: <95704E05-6DEC-4B66-A9EA-381B9C88CA12@psy.gla.ac.uk> Thanks for all the answers, I'll try Julian's suggestion and let you know what happens. Luisa On 16 May 2011, at 13:58, Julian Keil wrote: > Hi all, > > sorry, I thought the answer would only go to Luisa. > > Apologies, > Julian > > Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig: > >> Hi all, >> >> First of all, @julian: It would be nice if you wrote in English so >> that all people can understand what you are saying :) >> >> Second, I would like to mention ft_neighbourplot, which is a >> relative new function and plots sensors and its' neighbours in 2D >> or 3D, depending on whether you got 2D or 3D coordinates. Using >> that function, you can verify whether your neighbourselection >> looks meaningful and makes sense. >> >> Finally, we are currently working on changing/improving the >> neighbourselecion function. There will be different methods to >> choose from, and we (me) will create templates for the most common >> systems that can be used instead of relying on a particular >> mathematical selection method. We will announce this when it's >> done (probably soon). >> >> Maybe Julian is right and Luisa's problem is due to a 'wrong' >> neighbourselection. Given that cfg.minnbhchan is set to 4, this >> might be likely, because not all of the found clusters consist of >> 4 or more channels. What system are you using? >> >> Best, >> Jörn >> >> >> On 5/16/2011 2:32 PM, Julian Keil wrote: >>> >>> Hi Luisa, >>> >>> schnell from the top of my head: wie definierst du denn deine >>> neighbors? >>> Ich seh nirgendwo ein Feld cfg.neighbors.... >>> Ich muss das bei unserem 4D-System immer angeben.... >>> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen >>> sind falsch definierst, so könntest du zu deinen "random" >>> Clustern kommen. >>> >>> Ich mache diese Neighbor-Struktur folgendermaßen: >>> >>> cfg=[]; >>> cfg.neighbourdist=0.1; >>> %cfg.grad=Comb_AV1_1{1}.grad; >>> cfg.layout='4D148.lay'; >>> cfg.channel={'all'}; >>> %cfg.grad.pnt=cfg.grad.pnt*100; >>> dummy=neighbourselection(cfg); >>> >>> Da bekomme ich auch immer einen Output, wie viele Channels so in >>> der Umgebung sind (sollten in etwa 5 sein). >>> >>> Hoffe das hilft dir weiter >>> >>> Viele Grüße >>> >>> Julian >>> >>> Am 14.05.2011 um 22:37 schrieb Luisa Frei: >>> >>>> Hi there, >>>> I am trying to compute a simple cluster-based statistic in a >>>> between subjects design. I have followed the steps in the >>>> respective tutorial very closely. >>>> This the code I used: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.method = 'montecarlo'; >>>> cfg.statistic = 'indepsamplesT'; >>>> >>>> cfg.correctm = 'cluster'; >>>> cfg.clusteralpha = 0.001; >>>> cfg.clusterstatistic = 'maxsize'; >>>> cfg.minnbchan = 4; >>>> >>>> cfg.tail = 0; >>>> cfg.clustertail = 0; >>>> cfg.alpha = 0.005; >>>> cfg.numrandomization = 500; >>>> >>>> design = [ones(1,13) ones(1,13)+1]; >>>> >>>> cfg.design = design; >>>> cfg.ivar = 1; >>>> >>>> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >>>> cfg.latency = [.15 .2]; >>>> >>>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % >>>> individuals kept >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> >>>> My problem is, that I'm not sure which time resolution to use. I >>>> would like to use a small resolution of 10 ms, but this leads to >>>> a fairly random pattern of significant sensors (see attached >>>> figure, on the right). Of course, the more time points I >>>> include, the less significant sensors are left over. However, >>>> another problem is, that the ones that are left (figure, left), >>>> are not related to big differences in the activation pattern at >>>> all. How is it possible that my significant sensors end up being >>>> so randomly distributed? Also, ft_timelockstatistics only comes >>>> up with one positive and one negative cluster., but the sign. >>>> sensors are not always connected. Could anyone give some helpful >>>> input here? >>>> >>>> Thanks, >>>> Luisa >>>> >>>> Fyi: I have tried different thresholds and different numbers of >>>> neighbourhood channels, but there's not much of a change. >>>> _______________________________________________ >>>> 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 >> >> 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 >> Kapitelweg 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Mon May 16 15:59:36 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 16 May 2011 15:59:36 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection Message-ID: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> Dear Fieldtrippers, I'm using ft_rejectvisual function to reject visually EOG artifacts of epoched trials. My problem consist that I'm not able to plot only the EOG channels even when I explicitly select them ignoring the 'MEG' channels (I get a plot with all channels MEG + EOG). I directly used rejectvisual_channel (used in line 263 offt_rejectvisual) function selecting the EOG channels but I'm getting again all channels. Somebody could tell me what I'm doing wrong? Thanks in advance, Diego PS: Code %epoching cfg = []; cfg.dataset = [direc d(rr,1).name]; cfg.trialdef.eventtype = 'frontpanel trigger'; cfg.trialdef.eventvalue = 4; cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 4; % in seconds cfg.trialdef.epochmoving = 'inbackward'; cfg.trialdef.pivoteventvalue = 2;% cue stimulus cfg.trialdef.jumps = 1; cfg.trialfun = 'trialselec'; cfg = ft_definetrial(cfg); cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.lpfilter = 'yes'; cfg.lpfreq = 250; cfg.baselinewindow = [-1 0]; cfg.keeptrials = 'yes'; cfg.demean = 'yes'; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); %.............. %visual data rejection cfg = []; cfg.channel = {'EEG057' 'EEG058'}; cfg.method = 'channel'; cfg.keepchannel = 'yes'; data_c = ft_rejectvisual(cfg,data); -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From stan.vanpelt at fcdonders.ru.nl Mon May 16 16:16:16 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 May 2011 16:16:16 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> References: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> Hi Diego, You could try using ft_databrowser instead of ft_rejectvisual (followed by ft_rejectartifact), so: cfg = []; cfg.continuous = 'no'; cfg.channel = {'EEG057','EEG058'}; cfg = ft_databrowser(cfg,data); I think it should work like this. Best, Stan -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano Soldevilla, D. (Diego) Sent: Monday, May 16, 2011 4:00 PM To: fieldtrip at donders.ru.nl Subject: [FieldTrip] ft_rejectvisual channel selection Dear Fieldtrippers, I'm using ft_rejectvisual function to reject visually EOG artifacts of epoched trials. My problem consist that I'm not able to plot only the EOG channels even when I explicitly select them ignoring the 'MEG' channels (I get a plot with all channels MEG + EOG). I directly used rejectvisual_channel (used in line 263 offt_rejectvisual) function selecting the EOG channels but I'm getting again all channels. Somebody could tell me what I'm doing wrong? Thanks in advance, Diego PS: Code %epoching cfg = []; cfg.dataset = [direc d(rr,1).name]; cfg.trialdef.eventtype = 'frontpanel trigger'; cfg.trialdef.eventvalue = 4; cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 4; % in seconds cfg.trialdef.epochmoving = 'inbackward'; cfg.trialdef.pivoteventvalue = 2;% cue stimulus cfg.trialdef.jumps = 1; cfg.trialfun = 'trialselec'; cfg = ft_definetrial(cfg); cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.lpfilter = 'yes'; cfg.lpfreq = 250; cfg.baselinewindow = [-1 0]; cfg.keeptrials = 'yes'; cfg.demean = 'yes'; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); %.............. %visual data rejection cfg = []; cfg.channel = {'EEG057' 'EEG058'}; cfg.method = 'channel'; cfg.keepchannel = 'yes'; data_c = ft_rejectvisual(cfg,data); -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.lozanosoldevilla at fcdonders.ru.nl Mon May 16 16:24:38 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 16 May 2011 16:24:38 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> Message-ID: <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> Hi Stan, Thanks for your quickly answer. I get this error: Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording > In utilities/private/warning_once at 81 In utilities/private/fixtrialdef at 52 In ft_datatype_raw at 91 In ft_checkdata at 161 In ft_databrowser at 120 redrawing with viewmode butterfly ??? Improper index matrix reference. Error in ==> ft_databrowser>redraw_cb at 910 evtsample = [event(:).sample]; Error in ==> ft_databrowser at 419 redraw_cb(h); I don't know why my data have no trial definition when I'm sure that is epoched... Any ideas? Thanks in advance, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 4:16:16 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > You could try using ft_databrowser instead of ft_rejectvisual > (followed by > ft_rejectartifact), so: > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = {'EEG057','EEG058'}; > cfg = ft_databrowser(cfg,data); > > I think it should work like this. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:00 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] ft_rejectvisual channel selection > > Dear Fieldtrippers, > > I'm using ft_rejectvisual function to reject visually EOG artifacts > of > epoched trials. My problem consist that I'm not able to plot only the > EOG > channels even when I explicitly select them ignoring the 'MEG' > channels (I > get a plot with all channels MEG + EOG). > > I directly used rejectvisual_channel (used in line 263 > offt_rejectvisual) > function selecting the EOG channels but I'm getting again all > channels. > Somebody could tell me what I'm doing wrong? > > Thanks in advance, > > Diego > > > > PS: Code > > %epoching > cfg = []; > cfg.dataset = [direc d(rr,1).name]; > cfg.trialdef.eventtype = 'frontpanel trigger'; > cfg.trialdef.eventvalue = 4; > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 4; % in seconds > cfg.trialdef.epochmoving = 'inbackward'; > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > cfg.trialdef.jumps = 1; > cfg.trialfun = 'trialselec'; > > cfg = ft_definetrial(cfg); > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.lpfilter = 'yes'; > cfg.lpfreq = 250; > cfg.baselinewindow = [-1 0]; > cfg.keeptrials = 'yes'; > cfg.demean = 'yes'; > cfg.continuous = 'yes'; > > data = ft_preprocessing(cfg); > > %.............. > > > %visual data rejection > cfg = []; > cfg.channel = {'EEG057' 'EEG058'}; > cfg.method = 'channel'; > cfg.keepchannel = 'yes'; > data_c = ft_rejectvisual(cfg,data); > > > > -- > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > _______________________________________________ > 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 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From stan.vanpelt at fcdonders.ru.nl Mon May 16 21:40:11 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 May 2011 21:40:11 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> References: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <024701cc1401$122fb120$368f1360$@vanpelt@fcdonders.ru.nl> Hi Diego, Hm, sounds odd to me. Is your trial-definition output from ft_definetrial correct? So a cfg.trl that is not empty? Otherwise, you might try starting with an empty cfg again before calling ft_preprocessing? cfg=ft_definetrial(cfg); trials=cfg.trl; cfg=[]; cfg.trl=trials; cfg.dataset = [direc d(rr,1).name]; cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.continuous = 'yes'; etc.. data = ft_preprocessing(cfg); That should give you an output with a trial-structure, I'd say. Best, Stan -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano Soldevilla, D. (Diego) Sent: Monday, May 16, 2011 4:25 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] ft_rejectvisual channel selection Hi Stan, Thanks for your quickly answer. I get this error: Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording > In utilities/private/warning_once at 81 In utilities/private/fixtrialdef at 52 In ft_datatype_raw at 91 In ft_checkdata at 161 In ft_databrowser at 120 redrawing with viewmode butterfly ??? Improper index matrix reference. Error in ==> ft_databrowser>redraw_cb at 910 evtsample = [event(:).sample]; Error in ==> ft_databrowser at 419 redraw_cb(h); I don't know why my data have no trial definition when I'm sure that is epoched... Any ideas? Thanks in advance, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 4:16:16 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > You could try using ft_databrowser instead of ft_rejectvisual > (followed by > ft_rejectartifact), so: > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = {'EEG057','EEG058'}; > cfg = ft_databrowser(cfg,data); > > I think it should work like this. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:00 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] ft_rejectvisual channel selection > > Dear Fieldtrippers, > > I'm using ft_rejectvisual function to reject visually EOG artifacts > of > epoched trials. My problem consist that I'm not able to plot only the > EOG > channels even when I explicitly select them ignoring the 'MEG' > channels (I > get a plot with all channels MEG + EOG). > > I directly used rejectvisual_channel (used in line 263 > offt_rejectvisual) > function selecting the EOG channels but I'm getting again all > channels. > Somebody could tell me what I'm doing wrong? > > Thanks in advance, > > Diego > > > > PS: Code > > %epoching > cfg = []; > cfg.dataset = [direc d(rr,1).name]; > cfg.trialdef.eventtype = 'frontpanel trigger'; > cfg.trialdef.eventvalue = 4; > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 4; % in seconds > cfg.trialdef.epochmoving = 'inbackward'; > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > cfg.trialdef.jumps = 1; > cfg.trialfun = 'trialselec'; > > cfg = ft_definetrial(cfg); > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.lpfilter = 'yes'; > cfg.lpfreq = 250; > cfg.baselinewindow = [-1 0]; > cfg.keeptrials = 'yes'; > cfg.demean = 'yes'; > cfg.continuous = 'yes'; > > data = ft_preprocessing(cfg); > > %.............. > > > %visual data rejection > cfg = []; > cfg.channel = {'EEG057' 'EEG058'}; > cfg.method = 'channel'; > cfg.keepchannel = 'yes'; > data_c = ft_rejectvisual(cfg,data); > > > > -- > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > _______________________________________________ > 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 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.lozanosoldevilla at fcdonders.ru.nl Tue May 17 00:19:50 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Tue, 17 May 2011 00:19:50 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <940868980.135061.1305583605111.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> Hi Stan, You're right. It seems that my problem lies in the lack of trl because I previously resample my data and this last function do not creates a new trl with the updated begin and end samples. If I create a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) *data.fsample);, I get the same error but not with the original data (without resampling). Then I'll use data without resampling to check my artifacts. Thanks again, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 9:40:11 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > Hm, sounds odd to me. Is your trial-definition output from > ft_definetrial > correct? So a cfg.trl that is not empty? > > Otherwise, you might try starting with an empty cfg again before > calling > ft_preprocessing? > > cfg=ft_definetrial(cfg); > trials=cfg.trl; > > cfg=[]; > cfg.trl=trials; > cfg.dataset = [direc d(rr,1).name]; > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.continuous = 'yes'; > etc.. > data = ft_preprocessing(cfg); > > That should give you an output with a trial-structure, I'd say. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:25 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Stan, > > Thanks for your quickly answer. I get this error: > > Warning: the data does not contain a trial definition, assuming that > the > trials are consecutive segments of a continuous recording > > In utilities/private/warning_once at 81 > In utilities/private/fixtrialdef at 52 > In ft_datatype_raw at 91 > In ft_checkdata at 161 > In ft_databrowser at 120 > redrawing with viewmode butterfly > ??? Improper index matrix reference. > > Error in ==> ft_databrowser>redraw_cb at 910 > evtsample = [event(:).sample]; > > Error in ==> ft_databrowser at 419 > redraw_cb(h); > > I don't know why my data have no trial definition when I'm sure that > is > epoched... Any ideas? > > Thanks in advance, > > Diego > > > > ----- "Stan van Pelt" wrote: > > > From: "Stan van Pelt" > > To: "Email discussion list for the FieldTrip project" > > > Sent: Monday, 16 May, 2011 4:16:16 PM > > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > > > Hi Diego, > > > > You could try using ft_databrowser instead of ft_rejectvisual > > (followed by > > ft_rejectartifact), so: > > > > cfg = []; > > cfg.continuous = 'no'; > > cfg.channel = {'EEG057','EEG058'}; > > cfg = ft_databrowser(cfg,data); > > > > I think it should work like this. > > > > Best, > > Stan > > > > -----Original Message----- > > From: fieldtrip-bounces at donders.ru.nl > > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > > Soldevilla, > > D. (Diego) > > Sent: Monday, May 16, 2011 4:00 PM > > To: fieldtrip at donders.ru.nl > > Subject: [FieldTrip] ft_rejectvisual channel selection > > > > Dear Fieldtrippers, > > > > I'm using ft_rejectvisual function to reject visually EOG artifacts > > of > > epoched trials. My problem consist that I'm not able to plot only > the > > EOG > > channels even when I explicitly select them ignoring the 'MEG' > > channels (I > > get a plot with all channels MEG + EOG). > > > > I directly used rejectvisual_channel (used in line 263 > > offt_rejectvisual) > > function selecting the EOG channels but I'm getting again all > > channels. > > Somebody could tell me what I'm doing wrong? > > > > Thanks in advance, > > > > Diego > > > > > > > > PS: Code > > > > %epoching > > cfg = []; > > cfg.dataset = [direc d(rr,1).name]; > > cfg.trialdef.eventtype = 'frontpanel trigger'; > > cfg.trialdef.eventvalue = 4; > > cfg.trialdef.prestim = 1; % in seconds > > cfg.trialdef.poststim = 4; % in seconds > > cfg.trialdef.epochmoving = 'inbackward'; > > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > > cfg.trialdef.jumps = 1; > > cfg.trialfun = 'trialselec'; > > > > cfg = ft_definetrial(cfg); > > > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > > cfg.lpfilter = 'yes'; > > cfg.lpfreq = 250; > > cfg.baselinewindow = [-1 0]; > > cfg.keeptrials = 'yes'; > > cfg.demean = 'yes'; > > cfg.continuous = 'yes'; > > > > data = ft_preprocessing(cfg); > > > > %.............. > > > > > > %visual data rejection > > cfg = []; > > cfg.channel = {'EEG057' 'EEG058'}; > > cfg.method = 'channel'; > > cfg.keepchannel = 'yes'; > > data_c = ft_rejectvisual(cfg,data); > > > > > > > > -- > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Trigon, room 0.83 > > Kapittelweg 29 > > Radboud University Nijmegen > > NL-6500 HB Nijmegen > > The Netherlands > > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > > Tel: +31-(0)24-36-66274 > > Web: http://www.neuosc.com/ > > _______________________________________________ > > 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 > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > > > _______________________________________________ > 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 From younes_zerouali at hotmail.com Tue May 17 00:25:25 2011 From: younes_zerouali at hotmail.com (Younes Zerouali) Date: Mon, 16 May 2011 18:25:25 -0400 Subject: [FieldTrip] Segment anatomy from MRI (spm8) Message-ID: Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 17 08:18:39 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 17 May 2011 08:18:39 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: References: Message-ID: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit, skin_a = imerode(skin, s); brain_a = imdilate(brain, s); skull = (brain_a & skin_a); Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 17 08:42:22 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 17 May 2011 08:42:22 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> References: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> Message-ID: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote: > Hi Younes, > > this is actually not a problem with the function. The > "ft_volumesegment" will only return segmentations of the anatomical > mri with respect to three tissue types: grey matter, white matter, > and csf. You can use gray and white matter segmentations to > construct your brain compartement by typing e. g. "brain = > (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order > to get skull and skin compartements, you need your original > mri.anatomy which holds the image intensity on a black-to-white > scale. You can threshold the white values to segment the head from > the background, and this is then your skin compartement (e. g., > "skin = (mri.anatomy>300);" as shown in the tutorial). The skull > compartement is the oversection of the skin compartement and the > brain compartement after you blew up those compartements a bit, > skin_a = imerode(skin, s); > brain_a = imdilate(brain, s); > skull = (brain_a & skin_a); > Especially the construction of the skin is a lot of work, as you > need the wholes in the anatomical mri (eyes, ear, inhomogeneities) > by hand. > > Best regards and good luck, > Gregor > > > > > -- > Dr. rer. nat. Gregor Volberg > ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) > University of Regensburg > Institute for Experimental Psychology > 93040 Regensburg, Germany > Tel: +49 941 943 3862 > Fax: +49 941 943 3233 > http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html > > > >>> Younes Zerouali 5/17/2011 12:25 AM > >>> > Hi all, > > I'm trying to segment head anatomical surfaces (scalp, skull) using > the mri scan from patient Colin27 (MNI, Montreal) following the > steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel > ). > My problem is that the function "ft_volumesegment" doesn't return > all the variables that are mentionned in the tutorial. For example, > there is no field named "skull" or "scalp" in the argument returned > by this function. Anyone had this problem before? > > Best, > > > Younes > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 17 09:14:54 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 17 May 2011 09:14:54 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> References: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Message-ID: <4DD23C8E02000057000096DB@gwsmtp1.uni-regensburg.de> Dear Jan-Matthijs, I wasn't aware of this! Thanks a lot dear fieldtrippers, this is surely a helpful addition to ft_volumesegment. Best regards, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> jan-mathijs schoffelen 5/17/2011 8:42 AM >>> Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote: Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit, skin_a = imerode(skin, s); brain_a = imdilate(brain, s); skull = (brain_a & skin_a); Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue May 17 09:28:36 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 17 May 2011 09:28:36 +0200 Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> References: <940868980.135061.1305583605111.JavaMail.root@sculptor.zimbra.ru.nl> <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Hi Diego, Indeed, it is probably a good idea to check for artifacts before performing any resampling. The sample indices that are stored in trl (or sampleinfo) matrices, should always correspond to sample indices in the *original* dataset (on disk), and do not necessarily have any direct relation to sample indices in the data you have in memory. Therefore, if you resample the data, the samples in your data in memory do not directly correspond to samples in the dataset on disk anymore; so therefore trl or sampleinfo fields would not make sense, and might even lead to inconsistencies. This is the reason that ft_resampledata removes any such fields, if present, from your (in-memory) dataset. We are currently in the process of thinking hard about the trl and sampleinfo matrices, and might revise how these are handled in the future. In any case, it should become possible (already on our todo-list) to use the artifact detection functions on in-data memory without explicit sample indices. But, for now, your solution is the quickest one :) Best, Eelke 2011/5/17 Lozano Soldevilla, D. (Diego) : > Hi Stan, > > You're right. It seems that my problem lies in the lack of trl because I previously resample my data and this last function do not creates a new trl with the updated begin and end samples. If I create a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) *data.fsample);, I get the same error but not with the original data (without resampling). Then I'll use data without resampling to check my artifacts. > > Thanks again, > > Diego > > > > ----- "Stan van Pelt" wrote: > >> From: "Stan van Pelt" >> To: "Email discussion list for the FieldTrip project" >> Sent: Monday, 16 May, 2011 9:40:11 PM >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> >> Hi Diego, >> >> Hm, sounds odd to me. Is your trial-definition output from >> ft_definetrial >> correct? So a cfg.trl that is not empty? >> >> Otherwise, you might try starting with an empty cfg again before >> calling >> ft_preprocessing? >> >> cfg=ft_definetrial(cfg); >> trials=cfg.trl; >> >> cfg=[]; >> cfg.trl=trials; >> cfg.dataset                     = [direc d(rr,1).name]; >> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; >> cfg.continuous                  = 'yes'; >> etc.. >> data                            = ft_preprocessing(cfg); >> >> That should give you an output with a trial-structure, I'd say. >> >> Best, >> Stan >> >> -----Original Message----- >> From: fieldtrip-bounces at donders.ru.nl >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano >> Soldevilla, >> D. (Diego) >> Sent: Monday, May 16, 2011 4:25 PM >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> >> Hi Stan, >> >> Thanks for your quickly answer. I get this error: >> >> Warning: the data does not contain a trial definition, assuming that >> the >> trials are consecutive segments of a continuous recording >> > In utilities/private/warning_once at 81 >>   In utilities/private/fixtrialdef at 52 >>   In ft_datatype_raw at 91 >>   In ft_checkdata at 161 >>   In ft_databrowser at 120 >> redrawing with viewmode butterfly >> ??? Improper index matrix reference. >> >> Error in ==> ft_databrowser>redraw_cb at 910 >>   evtsample = [event(:).sample]; >> >> Error in ==> ft_databrowser at 419 >> redraw_cb(h); >> >> I don't know why my data have no trial definition when I'm sure that >> is >> epoched... Any ideas? >> >> Thanks in advance, >> >> Diego >> >> >> >> ----- "Stan van Pelt" wrote: >> >> > From: "Stan van Pelt" >> > To: "Email discussion list for the FieldTrip project" >> >> > Sent: Monday, 16 May, 2011 4:16:16 PM >> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> > >> > Hi Diego, >> > >> > You could try using ft_databrowser instead of ft_rejectvisual >> > (followed by >> > ft_rejectartifact), so: >> > >> > cfg            = []; >> > cfg.continuous = 'no'; >> > cfg.channel    = {'EEG057','EEG058'}; >> > cfg            = ft_databrowser(cfg,data); >> > >> > I think it should work like this. >> > >> > Best, >> > Stan >> > >> > -----Original Message----- >> > From: fieldtrip-bounces at donders.ru.nl >> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano >> > Soldevilla, >> > D. (Diego) >> > Sent: Monday, May 16, 2011 4:00 PM >> > To: fieldtrip at donders.ru.nl >> > Subject: [FieldTrip] ft_rejectvisual channel selection >> > >> > Dear Fieldtrippers, >> > >> > I'm using ft_rejectvisual function to reject visually EOG artifacts >> > of >> > epoched trials. My problem consist that I'm not able to plot only >> the >> > EOG >> > channels even when I explicitly select them ignoring the 'MEG' >> > channels (I >> > get a plot with all channels MEG + EOG). >> > >> > I directly used rejectvisual_channel (used in line 263 >> > offt_rejectvisual) >> > function selecting the EOG channels but I'm getting again all >> > channels. >> > Somebody could tell me what I'm doing wrong? >> > >> > Thanks in advance, >> > >> > Diego >> > >> > >> > >> > PS: Code >> > >> > %epoching >> > cfg = []; >> > cfg.dataset                     = [direc d(rr,1).name]; >> > cfg.trialdef.eventtype          = 'frontpanel trigger'; >> > cfg.trialdef.eventvalue         = 4; >> > cfg.trialdef.prestim            = 1; % in seconds >> > cfg.trialdef.poststim           = 4; % in seconds >> > cfg.trialdef.epochmoving        = 'inbackward'; >> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus >> > cfg.trialdef.jumps              = 1; >> > cfg.trialfun                    = 'trialselec'; >> > >> > cfg = ft_definetrial(cfg); >> > >> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; >> > cfg.lpfilter                    = 'yes'; >> > cfg.lpfreq                      = 250; >> > cfg.baselinewindow              = [-1 0]; >> > cfg.keeptrials                  = 'yes'; >> > cfg.demean                      = 'yes'; >> > cfg.continuous                  = 'yes'; >> > >> > data    = ft_preprocessing(cfg); >> > >> > %.............. >> > >> > >> > %visual data rejection >> > cfg             = []; >> > cfg.channel     = {'EEG057' 'EEG058'}; >> > cfg.method      = 'channel'; >> > cfg.keepchannel = 'yes'; >> > data_c          = ft_rejectvisual(cfg,data); >> > >> > >> > >> > -- >> > PhD Student >> > Donders Institute for Brain, Cognition and Behaviour >> > Centre for Cognitive Neuroimaging >> > Trigon, room 0.83 >> > Kapittelweg 29 >> > Radboud University Nijmegen >> > NL-6500 HB Nijmegen >> > The Netherlands >> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl >> > Tel:      +31-(0)24-36-66274 >> > Web:    http://www.neuosc.com/ >> > _______________________________________________ >> > 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 >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Trigon, room 0.83 >> Kapittelweg 29 >> Radboud University Nijmegen >> NL-6500 HB Nijmegen >> The Netherlands >> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl >> Tel:      +31-(0)24-36-66274 >> Web:    http://www.neuosc.com/ >> >> >> _______________________________________________ >> 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 > From d.lozanosoldevilla at fcdonders.ru.nl Tue May 17 09:37:09 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Tue, 17 May 2011 09:37:09 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <1942589717.137158.1305617671275.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <1909529539.137200.1305617829447.JavaMail.root@sculptor.zimbra.ru.nl> Thanks for your explanation Eelke ;). Now all makes sense. Diego ----- "Eelke Spaak" wrote: > From: "Eelke Spaak" > To: "Email discussion list for the FieldTrip project" > Sent: Tuesday, 17 May, 2011 9:28:36 AM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > Indeed, it is probably a good idea to check for artifacts before > performing any resampling. The sample indices that are stored in trl > (or sampleinfo) matrices, should always correspond to sample indices > in the *original* dataset (on disk), and do not necessarily have any > direct relation to sample indices in the data you have in memory. > Therefore, if you resample the data, the samples in your data in > memory do not directly correspond to samples in the dataset on disk > anymore; so therefore trl or sampleinfo fields would not make sense, > and might even lead to inconsistencies. This is the reason that > ft_resampledata removes any such fields, if present, from your > (in-memory) dataset. > > We are currently in the process of thinking hard about the trl and > sampleinfo matrices, and might revise how these are handled in the > future. In any case, it should become possible (already on our > todo-list) to use the artifact detection functions on in-data memory > without explicit sample indices. > > But, for now, your solution is the quickest one :) > > Best, > Eelke > > 2011/5/17 Lozano Soldevilla, D. (Diego) > : > > Hi Stan, > > > > You're right. It seems that my problem lies in the lack of trl > because I previously resample my data and this last function do not > creates a new trl with the updated begin and end samples. If I create > a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) > *data.fsample);, I get the same error but not with the original data > (without resampling). Then I'll use data without resampling to check > my artifacts. > > > > Thanks again, > > > > Diego > > > > > > > > ----- "Stan van Pelt" wrote: > > > >> From: "Stan van Pelt" > >> To: "Email discussion list for the FieldTrip project" > > >> Sent: Monday, 16 May, 2011 9:40:11 PM > >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > >> Hi Diego, > >> > >> Hm, sounds odd to me. Is your trial-definition output from > >> ft_definetrial > >> correct? So a cfg.trl that is not empty? > >> > >> Otherwise, you might try starting with an empty cfg again before > >> calling > >> ft_preprocessing? > >> > >> cfg=ft_definetrial(cfg); > >> trials=cfg.trl; > >> > >> cfg=[]; > >> cfg.trl=trials; > >> cfg.dataset                     = [direc d(rr,1).name]; > >> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; > >> cfg.continuous                  = 'yes'; > >> etc.. > >> data                            = ft_preprocessing(cfg); > >> > >> That should give you an output with a trial-structure, I'd say. > >> > >> Best, > >> Stan > >> > >> -----Original Message----- > >> From: fieldtrip-bounces at donders.ru.nl > >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > >> Soldevilla, > >> D. (Diego) > >> Sent: Monday, May 16, 2011 4:25 PM > >> To: Email discussion list for the FieldTrip project > >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > >> Hi Stan, > >> > >> Thanks for your quickly answer. I get this error: > >> > >> Warning: the data does not contain a trial definition, assuming > that > >> the > >> trials are consecutive segments of a continuous recording > >> > In utilities/private/warning_once at 81 > >>   In utilities/private/fixtrialdef at 52 > >>   In ft_datatype_raw at 91 > >>   In ft_checkdata at 161 > >>   In ft_databrowser at 120 > >> redrawing with viewmode butterfly > >> ??? Improper index matrix reference. > >> > >> Error in ==> ft_databrowser>redraw_cb at 910 > >>   evtsample = [event(:).sample]; > >> > >> Error in ==> ft_databrowser at 419 > >> redraw_cb(h); > >> > >> I don't know why my data have no trial definition when I'm sure > that > >> is > >> epoched... Any ideas? > >> > >> Thanks in advance, > >> > >> Diego > >> > >> > >> > >> ----- "Stan van Pelt" wrote: > >> > >> > From: "Stan van Pelt" > >> > To: "Email discussion list for the FieldTrip project" > >> > >> > Sent: Monday, 16 May, 2011 4:16:16 PM > >> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > > >> > Hi Diego, > >> > > >> > You could try using ft_databrowser instead of ft_rejectvisual > >> > (followed by > >> > ft_rejectartifact), so: > >> > > >> > cfg            = []; > >> > cfg.continuous = 'no'; > >> > cfg.channel    = {'EEG057','EEG058'}; > >> > cfg            = ft_databrowser(cfg,data); > >> > > >> > I think it should work like this. > >> > > >> > Best, > >> > Stan > >> > > >> > -----Original Message----- > >> > From: fieldtrip-bounces at donders.ru.nl > >> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > >> > Soldevilla, > >> > D. (Diego) > >> > Sent: Monday, May 16, 2011 4:00 PM > >> > To: fieldtrip at donders.ru.nl > >> > Subject: [FieldTrip] ft_rejectvisual channel selection > >> > > >> > Dear Fieldtrippers, > >> > > >> > I'm using ft_rejectvisual function to reject visually EOG > artifacts > >> > of > >> > epoched trials. My problem consist that I'm not able to plot > only > >> the > >> > EOG > >> > channels even when I explicitly select them ignoring the 'MEG' > >> > channels (I > >> > get a plot with all channels MEG + EOG). > >> > > >> > I directly used rejectvisual_channel (used in line 263 > >> > offt_rejectvisual) > >> > function selecting the EOG channels but I'm getting again all > >> > channels. > >> > Somebody could tell me what I'm doing wrong? > >> > > >> > Thanks in advance, > >> > > >> > Diego > >> > > >> > > >> > > >> > PS: Code > >> > > >> > %epoching > >> > cfg = []; > >> > cfg.dataset                     = [direc d(rr,1).name]; > >> > cfg.trialdef.eventtype          = 'frontpanel trigger'; > >> > cfg.trialdef.eventvalue         = 4; > >> > cfg.trialdef.prestim            = 1; % in seconds > >> > cfg.trialdef.poststim           = 4; % in seconds > >> > cfg.trialdef.epochmoving        = 'inbackward'; > >> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus > >> > cfg.trialdef.jumps              = 1; > >> > cfg.trialfun                    = 'trialselec'; > >> > > >> > cfg = ft_definetrial(cfg); > >> > > >> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; > >> > cfg.lpfilter                    = 'yes'; > >> > cfg.lpfreq                      = 250; > >> > cfg.baselinewindow              = [-1 0]; > >> > cfg.keeptrials                  = 'yes'; > >> > cfg.demean                      = 'yes'; > >> > cfg.continuous                  = 'yes'; > >> > > >> > data    = ft_preprocessing(cfg); > >> > > >> > %.............. > >> > > >> > > >> > %visual data rejection > >> > cfg             = []; > >> > cfg.channel     = {'EEG057' 'EEG058'}; > >> > cfg.method      = 'channel'; > >> > cfg.keepchannel = 'yes'; > >> > data_c          = ft_rejectvisual(cfg,data); > >> > > >> > > >> > > >> > -- > >> > PhD Student > >> > Donders Institute for Brain, Cognition and Behaviour > >> > Centre for Cognitive Neuroimaging > >> > Trigon, room 0.83 > >> > Kapittelweg 29 > >> > Radboud University Nijmegen > >> > NL-6500 HB Nijmegen > >> > The Netherlands > >> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > >> > Tel:      +31-(0)24-36-66274 > >> > Web:    http://www.neuosc.com/ > >> > _______________________________________________ > >> > 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 > >> Donders Institute for Brain, Cognition and Behaviour > >> Centre for Cognitive Neuroimaging > >> Trigon, room 0.83 > >> Kapittelweg 29 > >> Radboud University Nijmegen > >> NL-6500 HB Nijmegen > >> The Netherlands > >> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > >> Tel:      +31-(0)24-36-66274 > >> Web:    http://www.neuosc.com/ > >> > >> > >> _______________________________________________ > >> 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 -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From nuria.donamayor at neuro.uni-luebeck.de Tue May 17 10:03:50 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Tue, 17 May 2011 10:03:50 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, sorry it took me this long to answer. The variable format seems to be empty.... Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Freitag, 13. Mai 2011 16:43 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, Could you type dbstop if error on the command line, and evaluate what the variable 'format' is in your case? Thanks, Jan-Mathijs On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > Yes, it is exectly the same version. Better said, versions, because > I tried both 20110413 and 20110512.... > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com > ] > Gesendet: Freitag, 13. Mai 2011 13:39 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Dear Nuria > Is it exactly the same fieldtrip version? > I hope someone will solve this. > as temporary work around you can read the header on windows and then > move to linux > > yuval > > On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine > with a 64-bit Matlab version and I am getting an error I don't know > how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I > have no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to > the Linux machine), so I'm pretty clueless here... Can any of you > help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > > "Many were increasingly of the opinion that they'd all made a big > mistake in coming down from the trees in the first place. And some > said that even the trees had been a bad move, and that no one should > ever have left the oceans". Douglas Adams > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From amelie.serpollet at cea.fr Tue May 17 15:58:49 2011 From: amelie.serpollet at cea.fr (=?iso-8859-1?Q?SERPOLLET_Am=E9lie_228173?=) Date: Tue, 17 May 2011 15:58:49 +0200 Subject: [FieldTrip] questions about realtime buffer Message-ID: Dear Fieldtrip users, I'm implementing a realtime buffer in C++ pretty much like in "demo_combined" : my application creates a buffer server and an acquisition client. I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. If these modifications can be useful for other users and do not create other problems, I will share them. I encounter now a new problem : what if there are several acquisition clients ? I tried to create several couples "buffer-server + acquisition client" in different threads in my application, but it does not work at all, because of global variables (I suppose). It seems that one buffer server can not manage several acquisition clients, but I'm not sure of this point. Did anyone encounter this problem (or solve it) ? Or do anyone have an idea ? Best regards, Amelie Serpollet -------------- next part -------------- An HTML attachment was scrubbed... URL: From younes_zerouali at hotmail.com Tue May 17 16:11:36 2011 From: younes_zerouali at hotmail.com (Younes Zerouali) Date: Tue, 17 May 2011 10:11:36 -0400 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> References: , <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de>, <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Message-ID: Dear Gregor and Jan-Mathijs, Thank you both for prompt answers, I'll get to work and try that! Best, Younes From: jan.schoffelen at donders.ru.nl To: fieldtrip at donders.ru.nl Date: Tue, 17 May 2011 08:42:22 +0200 Subject: Re: [FieldTrip] Antw: Segment anatomy from MRI (spm8) Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote:Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit,skin_a = imerode(skin, s);brain_a = imdilate(brain, s);skull = (brain_a & skin_a);Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck,Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The NetherlandsJ.Schoffelen at donders.ru.nlTelephone: 0031-24-3614793 _______________________________________________ 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 jan.schoffelen at donders.ru.nl Tue May 17 16:24:21 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 17 May 2011 16:24:21 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> Message-ID: <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> Hi Nuria, Strange. Format should contain a number. What matlab version are you running on the Linux machine? Best, Jan-Mathijs On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > sorry it took me this long to answer. The variable format seems to > be empty.... > Nuria > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Freitag, 13. Mai 2011 16:43 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Could you type dbstop if error on the command line, and evaluate what > the variable 'format' is in your case? > > Thanks, > > Jan-Mathijs > > On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > >> Yes, it is exectly the same version. Better said, versions, because >> I tried both 20110413 and 20110512.... >> >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >> ] >> Gesendet: Freitag, 13. Mai 2011 13:39 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Dear Nuria >> Is it exactly the same fieldtrip version? >> I hope someone will solve this. >> as temporary work around you can read the header on windows and then >> move to linux >> >> yuval >> >> On 13 May 2011 11:42, Nuria Donamayor Alonso > > wrote: >> Dear fieltrip users, >> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >> with a 64-bit Matlab version and I am getting an error I don't know >> how to solve: >> >> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >> ??? SWITCH expression must be a scalar or string constant. >> >> Error in ==> read_4d_hdr at 60 >> switch format >> >> Error in ==> ft_read_header at 153 >> orig = read_4d_hdr(datafile); >> >> If I try to read the same data on my Windows PC with 32-bit Matlab I >> have no problem reading the header file (but I can't even finish the >> preprocessing before it runs out of memory, therefore the switch to >> the Linux machine), so I'm pretty clueless here... Can any of you >> help me? >> Thanks, >> Nuria >> >> >> >> Nuria Doñamayor Alonso, MSc >> Universitätsklinikum Schleswig-Holstein >> Campus Lübeck >> Klinik für Neurologie >> Ratzeburger Allee 160 >> 23538 Lübeck >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Y.Harpaz >> >> a link to the BIU MEG lab: >> http://faculty.biu.ac.il/~goldsa/index.html>> >> >> "Many were increasingly of the opinion that they'd all made a big >> mistake in coming down from the trees in the first place. And some >> said that even the trees had been a bad move, and that no one should >> ever have left the oceans". Douglas Adams >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From nuria.donamayor at neuro.uni-luebeck.de Tue May 17 16:49:17 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Tue, 17 May 2011 16:49:17 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, I'm using Matlab 7.11.0 (R2010b). Best, Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Dienstag, 17. Mai 2011 16:24 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, Strange. Format should contain a number. What matlab version are you running on the Linux machine? Best, Jan-Mathijs On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > sorry it took me this long to answer. The variable format seems to > be empty.... > Nuria > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Freitag, 13. Mai 2011 16:43 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Could you type dbstop if error on the command line, and evaluate what > the variable 'format' is in your case? > > Thanks, > > Jan-Mathijs > > On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > >> Yes, it is exectly the same version. Better said, versions, because >> I tried both 20110413 and 20110512.... >> >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >> ] >> Gesendet: Freitag, 13. Mai 2011 13:39 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Dear Nuria >> Is it exactly the same fieldtrip version? >> I hope someone will solve this. >> as temporary work around you can read the header on windows and then >> move to linux >> >> yuval >> >> On 13 May 2011 11:42, Nuria Donamayor Alonso > > wrote: >> Dear fieltrip users, >> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >> with a 64-bit Matlab version and I am getting an error I don't know >> how to solve: >> >> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >> ??? SWITCH expression must be a scalar or string constant. >> >> Error in ==> read_4d_hdr at 60 >> switch format >> >> Error in ==> ft_read_header at 153 >> orig = read_4d_hdr(datafile); >> >> If I try to read the same data on my Windows PC with 32-bit Matlab I >> have no problem reading the header file (but I can't even finish the >> preprocessing before it runs out of memory, therefore the switch to >> the Linux machine), so I'm pretty clueless here... Can any of you >> help me? >> Thanks, >> Nuria >> >> >> >> Nuria Doñamayor Alonso, MSc >> Universitätsklinikum Schleswig-Holstein >> Campus Lübeck >> Klinik für Neurologie >> Ratzeburger Allee 160 >> 23538 Lübeck >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Y.Harpaz >> >> a link to the BIU MEG lab: >> http://faculty.biu.ac.il/~goldsa/index.html>> >> >> "Many were increasingly of the opinion that they'd all made a big >> mistake in coming down from the trees in the first place. And some >> said that even the trees had been a bad move, and that no one should >> ever have left the oceans". Douglas Adams >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From batrod at gmail.com Tue May 17 20:50:43 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 17 May 2011 13:50:43 -0500 Subject: [FieldTrip] Problem with recent version of eeglab2fieldtrip Message-ID: Dear Fieldtrip users, Recently i experienced problems doing sone Time-freq analysis and i realized it's coming from the eeglab2fieldtrip function and more precisely one line that has been changed, apparently without being reported on the eeglab revision history and neither in fieldtrip revision history (but i may be wrong with this last one, i checked very quickly on google code) The problem occurs at the Line 47: data.label = { EEG.chanlocs(1:EEG.nbchan).labels }; % Eeglab version 9.0.2.3 data.label = { EEG.chanlocs(EEG.icachansind).labels }; % Eeglab verion 9.0.4.4 The old version works, whereas the new version will cause problem if you dont perform an ICA with eeglab, prior to the conversion. Hope this helps, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arno at cerco.ups-tlse.fr Wed May 18 00:08:36 2011 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Tue, 17 May 2011 15:08:36 -0700 Subject: [FieldTrip] Problem with recent version of eeglab2fieldtrip In-Reply-To: References: Message-ID: <07D46921-50BF-4C27-AA81-E4E96FD49698@cerco.ups-tlse.fr> Dear Rodolphe, I had changed that line because I could not fit dipoles for some ICA components (which is the main reason this function was originally designed for). The attached function should work for both components and channel data. Let me know if it does not. Best, Arno ps: the change was actually documented on the web (http://sccn.ucsd.edu/wiki/EEGLAB_revision_history_version_9) as "eeglab2fieldtrip.m, fix performing dipole fitting on subset of channels (SVN 9092 - Arno)" On May 17, 2011, at 11:50 AM, Rodolphe Nenert wrote: > Dear Fieldtrip users, > > Recently i experienced problems doing sone Time-freq analysis and i realized it's coming from the eeglab2fieldtrip function and more precisely one line that has been changed, apparently without being reported on the eeglab revision history and neither in fieldtrip revision history (but i may be wrong with this last one, i checked very quickly on google code) > > The problem occurs at the Line 47: > > data.label = { EEG.chanlocs(1:EEG.nbchan).labels }; % Eeglab version 9.0.2.3 > > data.label = { EEG.chanlocs(EEG.icachansind).labels }; % Eeglab verion 9.0.4.4 > > The old version works, whereas the new version will cause problem if you dont perform an ICA with eeglab, prior to the conversion. > > Hope this helps, > > Rodolphe. > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eeglab2fieldtrip.m Type: application/octet-stream Size: 5887 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed May 18 10:51:14 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 18 May 2011 10:51:14 +0200 Subject: [FieldTrip] Tutorial error Message-ID: Dear all, I am a very beginner with fieldtrip. I have tried to run the tutorial a couple of weeks ago, and it worked smoothly. Yesterday I have tried again, but surprisngly I got anerror message, as soon as I started the tutorial (the first step entitled: "reading and processing the interesting trials"): cfg = []; cfg.dataset = 'Subject01.ds'; cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for fully incongruent (FIC). cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 2; % in seconds cfg = ft_definetrial(cfg); ??? Attempt to reference field of non-structure array Error in ==> trialfun_general at 117 for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) This sounds really weird since it worked 2 weeks ago on the same machine and with the same version of Fieldtrip. Any advice would be very appreciated. Best wishes, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 18 11:02:29 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 18 May 2011 11:02:29 +0200 Subject: [FieldTrip] Tutorial error In-Reply-To: References: Message-ID: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> Dear Davide, I am not sure whether you are using the same fieldtrip version. There has been a glitch recently with the trialfun_general, but this should be fixed by now. Could you update to a superrecent version of fieldtrip and try again? Thanks, Jan-Mathijs PS: I cannot reproduce your error so I expect it to go away if you update. On May 18, 2011, at 10:51 AM, Davide Rivolta wrote: > Dear all, > > I am a very beginner with fieldtrip. > > I have tried to run the tutorial a couple of weeks ago, and it > worked smoothly. > > Yesterday I have tried again, but surprisngly I got anerror message, > as soon as I started the tutorial (the first step entitled: "reading > and processing the interesting trials"): > > > cfg = []; > cfg.dataset = 'Subject01.ds'; > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger > for fully incongruent (FIC). > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 2; % in seconds > > cfg = ft_definetrial(cfg); > > > ??? Attempt to reference field of non-structure array > > Error in ==> trialfun_general at 117 > for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) > > > > > This sounds really weird since it worked 2 weeks ago on the same > machine and with the same version of Fieldtrip. > > Any advice would be very appreciated. > > Best wishes, > > Davide > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Wed May 18 12:13:27 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 18 May 2011 12:13:27 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> Message-ID: <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> Hi Nuria, I cannot reproduce your problem on a linux machine we have here, running matlab 2010b (64-bit). Either there is something wrong with your dataset (does it happen as well for another dataset?), or there is something different with respect to the configuration of your Linux machine. Best, Jan-Mathijs On May 17, 2011, at 4:49 PM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > I'm using Matlab 7.11.0 (R2010b). > Best, > Nuria > > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Dienstag, 17. Mai 2011 16:24 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Strange. Format should contain a number. What matlab version are you > running on the Linux machine? > > Best, > > Jan-Mathijs > > > On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > >> Hi Jan-Mathijs, >> sorry it took me this long to answer. The variable format seems to >> be empty.... >> Nuria >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl >> ] >> Gesendet: Freitag, 13. Mai 2011 16:43 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Hi Nuria, >> >> Could you type dbstop if error on the command line, and evaluate what >> the variable 'format' is in your case? >> >> Thanks, >> >> Jan-Mathijs >> >> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: >> >>> Yes, it is exectly the same version. Better said, versions, because >>> I tried both 20110413 and 20110512.... >>> >>> ________________________________________ >>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >>> ] >>> Gesendet: Freitag, 13. Mai 2011 13:39 >>> An: Email discussion list for the FieldTrip project >>> Betreff: Re: [FieldTrip] problem reading 4d header >>> >>> Dear Nuria >>> Is it exactly the same fieldtrip version? >>> I hope someone will solve this. >>> as temporary work around you can read the header on windows and then >>> move to linux >>> >>> yuval >>> >>> On 13 May 2011 11:42, Nuria Donamayor Alonso >> > wrote: >>> Dear fieltrip users, >>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >>> with a 64-bit Matlab version and I am getting an error I don't know >>> how to solve: >>> >>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >>> ??? SWITCH expression must be a scalar or string constant. >>> >>> Error in ==> read_4d_hdr at 60 >>> switch format >>> >>> Error in ==> ft_read_header at 153 >>> orig = read_4d_hdr(datafile); >>> >>> If I try to read the same data on my Windows PC with 32-bit Matlab I >>> have no problem reading the header file (but I can't even finish the >>> preprocessing before it runs out of memory, therefore the switch to >>> the Linux machine), so I'm pretty clueless here... Can any of you >>> help me? >>> Thanks, >>> Nuria >>> >>> >>> >>> Nuria Doñamayor Alonso, MSc >>> Universitätsklinikum Schleswig-Holstein >>> Campus Lübeck >>> Klinik für Neurologie >>> Ratzeburger Allee 160 >>> 23538 Lübeck >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Y.Harpaz >>> >>> a link to the BIU MEG lab: >>> http://faculty.biu.ac.il/~goldsa/index.html>>> >>> >>> "Many were increasingly of the opinion that they'd all made a big >>> mistake in coming down from the trees in the first place. And some >>> said that even the trees had been a bad move, and that no one should >>> ever have left the oceans". Douglas Adams >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> >> _______________________________________________ >> 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 > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From drivolta81 at gmail.com Wed May 18 13:40:11 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 18 May 2011 13:40:11 +0200 Subject: [FieldTrip] Tutorial error In-Reply-To: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> References: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> Message-ID: Dear Jan-Mathijs This is the funny part. I run it (and worked) on the 201105053 version two weeks ago. Yesterday it did not work on the same version. So, I have downloaded the most recent version 20110516, but it is still not working. I do not really know what to do with it. Thanks for your kind help, Davide On Wed, May 18, 2011 at 11:02 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Davide, > > I am not sure whether you are using the same fieldtrip version. There has > been a glitch recently with the trialfun_general, but this should be fixed > by now. Could you update to a superrecent version of fieldtrip and try > again? > > Thanks, > > Jan-Mathijs > > PS: I cannot reproduce your error so I expect it to go away if you update. > > > On May 18, 2011, at 10:51 AM, Davide Rivolta wrote: > > Dear all, >> >> I am a very beginner with fieldtrip. >> >> I have tried to run the tutorial a couple of weeks ago, and it worked >> smoothly. >> >> Yesterday I have tried again, but surprisngly I got anerror message, as >> soon as I started the tutorial (the first step entitled: "reading and >> processing the interesting trials"): >> >> >> cfg = []; >> cfg.dataset = 'Subject01.ds'; >> cfg.trialdef.eventtype = 'backpanel trigger'; >> cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for >> fully incongruent (FIC). >> cfg.trialdef.prestim = 1; % in seconds >> cfg.trialdef.poststim = 2; % in seconds >> >> cfg = ft_definetrial(cfg); >> >> >> ??? Attempt to reference field of non-structure array >> >> Error in ==> trialfun_general at 117 >> for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) >> >> >> >> >> This sounds really weird since it worked 2 weeks ago on the same machine >> and with the same version of Fieldtrip. >> >> Any advice would be very appreciated. >> >> Best wishes, >> >> Davide >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuria.donamayor at neuro.uni-luebeck.de Wed May 18 15:00:33 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Wed, 18 May 2011 15:00:33 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de>, <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F903D@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, I get the same error message with all my datasets. Maybe it does have to do with my Linux machine... Any idea what I should look for to fix it? Thanks, Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Mittwoch, 18. Mai 2011 12:13 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, I cannot reproduce your problem on a linux machine we have here, running matlab 2010b (64-bit). Either there is something wrong with your dataset (does it happen as well for another dataset?), or there is something different with respect to the configuration of your Linux machine. Best, Jan-Mathijs On May 17, 2011, at 4:49 PM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > I'm using Matlab 7.11.0 (R2010b). > Best, > Nuria > > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Dienstag, 17. Mai 2011 16:24 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Strange. Format should contain a number. What matlab version are you > running on the Linux machine? > > Best, > > Jan-Mathijs > > > On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > >> Hi Jan-Mathijs, >> sorry it took me this long to answer. The variable format seems to >> be empty.... >> Nuria >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl >> ] >> Gesendet: Freitag, 13. Mai 2011 16:43 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Hi Nuria, >> >> Could you type dbstop if error on the command line, and evaluate what >> the variable 'format' is in your case? >> >> Thanks, >> >> Jan-Mathijs >> >> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: >> >>> Yes, it is exectly the same version. Better said, versions, because >>> I tried both 20110413 and 20110512.... >>> >>> ________________________________________ >>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >>> ] >>> Gesendet: Freitag, 13. Mai 2011 13:39 >>> An: Email discussion list for the FieldTrip project >>> Betreff: Re: [FieldTrip] problem reading 4d header >>> >>> Dear Nuria >>> Is it exactly the same fieldtrip version? >>> I hope someone will solve this. >>> as temporary work around you can read the header on windows and then >>> move to linux >>> >>> yuval >>> >>> On 13 May 2011 11:42, Nuria Donamayor Alonso >> > wrote: >>> Dear fieltrip users, >>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >>> with a 64-bit Matlab version and I am getting an error I don't know >>> how to solve: >>> >>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >>> ??? SWITCH expression must be a scalar or string constant. >>> >>> Error in ==> read_4d_hdr at 60 >>> switch format >>> >>> Error in ==> ft_read_header at 153 >>> orig = read_4d_hdr(datafile); >>> >>> If I try to read the same data on my Windows PC with 32-bit Matlab I >>> have no problem reading the header file (but I can't even finish the >>> preprocessing before it runs out of memory, therefore the switch to >>> the Linux machine), so I'm pretty clueless here... Can any of you >>> help me? >>> Thanks, >>> Nuria >>> >>> >>> >>> Nuria Doñamayor Alonso, MSc >>> Universitätsklinikum Schleswig-Holstein >>> Campus Lübeck >>> Klinik für Neurologie >>> Ratzeburger Allee 160 >>> 23538 Lübeck >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Y.Harpaz >>> >>> a link to the BIU MEG lab: >>> http://faculty.biu.ac.il/~goldsa/index.html>>> >>> >>> "Many were increasingly of the opinion that they'd all made a big >>> mistake in coming down from the trees in the first place. And some >>> said that even the trees had been a bad move, and that no one should >>> ever have left the oceans". Douglas Adams >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> >> _______________________________________________ >> 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 > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From michael.hanke at gmail.com Wed May 18 15:10:26 2011 From: michael.hanke at gmail.com (Michael Hanke) Date: Wed, 18 May 2011 09:10:26 -0400 Subject: [FieldTrip] Neuroscience software survey: What is popular, what has problems? Immediate results Message-ID: <20110518131026.GD19084@meiner> [Apologies for cross-posting] Dear neuroscience researchers and their IT staff We invite you to participate in a survey on software usage and computing environments in neuroscience research. It will take no more than five minutes to fill it out. Immediately after sending your answers you will get to see a summary of how other participants have responded before. This data will eventually be made available to software vendors and distributors to determine advantages and issue of popular computing environments in neuroscience research. Learn about what fellow neuroscientists are doing to address their computing demands -- take the survey! http://goo.gl/euIMc Thanks, -- PyMVPA/NeuroDebian Team: Yaroslav O. Halchenko & Michael Hanke Postdoctoral Fellows, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 From jdien07 at mac.com Fri May 20 04:30:59 2011 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 19 May 2011 22:30:59 -0400 Subject: [FieldTrip] problems using ft_freqanalysis Message-ID: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> Hi, I'm just starting to get up to speed on spectral analysis (I'm an ERPer). I'm using the following set-up: I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): cfg.method='mtmwelch'; cfg.output='pow'; [freq] = ft_freqanalysis(cfg, data); I got the error message: ------------------------- the input is raw data with 128 channels and 160 trials 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used taking every sample as time of interest the input is raw data with 128 channels and 160 trials ??? Error using ==> ft_freqanalysis at 216 you must specify a smoothing parameter with taper = dpss Error in ==> ft_freqanalysis_mtmwelch at 107 freq = ft_freqanalysis(cfgconvol, data); Error in ==> ft_freqanalysis at 271 [freq] = feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, data); ----------------------- Two things: 1) What would be an appropriate smoothing parameter? 2) Is this a bug? It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: cfg.foi=[1:1:30]; cfg.taper='hanning'; which resulted in: -------------------------- >> [freq] = ft_freqanalysis(cfg, data); the input is raw data with 128 channels and 160 trials 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used taking every sample as time of interest the input is raw data with 128 channels and 160 trials processing trials ??? Reference to non-existent field 't_ftimwin'. Error in ==> ft_freqanalysis at 454 [spectrum_mtmconvol,ntaper,foi,toi] = ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, 'timwin', cfg.t_ftimwin, 'taper', ... Error in ==> ft_freqanalysis_mtmwelch at 107 freq = ft_freqanalysis(cfgconvol, data); Error in ==> ft_freqanalysis at 271 [freq] = feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, data); -------------------- What am I doing wrong? I looked through the code but couldn't figure out what the problem was. I am very confused... fieldtrip-20110519 MATLAB Version 7.11.0.584 (R2010b) Operating System: Mac OS X Version: 10.6.7 Build: 10J869 >> cfg cfg = dataset: 'SLI_3011m_40m_POA.egis' method: 'mtmwelch' output: 'pow' taper: 'hanning' tapsmofrq: 4 foi: [1x30 double] >> data data = hdr: [1x1 struct] label: {128x1 cell} time: {1x160 cell} trial: {1x160 cell} fsample: 250 sampleinfo: [160x2 double] cfg: [1x1 struct] Thanks for any help you can give! Joe From jan.schoffelen at donders.ru.nl Fri May 20 07:36:03 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 20 May 2011 07:36:03 +0200 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> Message-ID: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Dear Joe, To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. Cheers, Jan-Mathijs On May 20, 2011, at 4:30 AM, Joseph Dien wrote: > Hi, > I'm just starting to get up to speed on spectral analysis (I'm an > ERPer). > I'm using the following set-up: > > I tried the following (for one second long trials with an Fs of > 250Hz and interest in frequencies below 30Hz): > > cfg.method='mtmwelch'; > cfg.output='pow'; > [freq] = ft_freqanalysis(cfg, data); > > I got the error message: > > ------------------------- > the input is raw data with 128 channels and 160 trials > 'mtmwelch' has not been implemented yet in the specest toolbox, the > old implementation is being used > taking every sample as time of interest > the input is raw data with 128 channels and 160 trials > ??? Error using ==> ft_freqanalysis at 216 > you must specify a smoothing parameter with taper = dpss > > Error in ==> ft_freqanalysis_mtmwelch at 107 > freq = ft_freqanalysis(cfgconvol, data); > > Error in ==> ft_freqanalysis at 271 > [freq] = > feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, > data); > > ----------------------- > Two things: > > 1) What would be an appropriate smoothing parameter? > > 2) Is this a bug? It defaulted to dpss as specified by the > documentation but it didn't provide a default smoothing parameter so > the default still resulted in a crash. > > Anyway, given the advice in the tutlrial to use a hanning window > rather than a multi-taper like dpss for frequencies below 30, I > tried the following: > > cfg.foi=[1:1:30]; > cfg.taper='hanning'; > > which resulted in: > > -------------------------- >>> [freq] = ft_freqanalysis(cfg, data); > the input is raw data with 128 channels and 160 trials > 'mtmwelch' has not been implemented yet in the specest toolbox, the > old implementation is being used > taking every sample as time of interest > the input is raw data with 128 channels and 160 trials > processing trials > ??? Reference to non-existent field 't_ftimwin'. > > Error in ==> ft_freqanalysis at 454 > [spectrum_mtmconvol,ntaper,foi,toi] = > ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, > 'timwin', cfg.t_ftimwin, 'taper', ... > > Error in ==> ft_freqanalysis_mtmwelch at 107 > freq = ft_freqanalysis(cfgconvol, data); > > Error in ==> ft_freqanalysis at 271 > [freq] = > feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, > data); > > > -------------------- > What am I doing wrong? I looked through the code but couldn't > figure out what the problem was. I am very confused... > > fieldtrip-20110519 > MATLAB Version 7.11.0.584 (R2010b) > Operating System: Mac OS X Version: 10.6.7 Build: 10J869 > > >>> cfg > > cfg = > > dataset: 'SLI_3011m_40m_POA.egis' > method: 'mtmwelch' > output: 'pow' > taper: 'hanning' > tapsmofrq: 4 > foi: [1x30 double] > >>> data > > data = > > hdr: [1x1 struct] > label: {128x1 cell} > time: {1x160 cell} > trial: {1x160 cell} > fsample: 250 > sampleinfo: [160x2 double] > cfg: [1x1 struct] > > > Thanks for any help you can give! > > Joe > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From Elena.Orekhova at neuro.gu.se Fri May 20 14:00:40 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 20 May 2011 12:00:40 +0000 Subject: [FieldTrip] ft_read_vol with Neuromag Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> Hi, I try to read volume from the Neuromag .fif file using vol = ft_read_vol(NEUROMAG_FIF_FILE_NAME, 'fileformat', 'neuromag_fif') I get the error: *********************** ??? Undefined variable "cfg" or class "cfg.gradfile". Error in ==> ft_read_vol at 77 fprintf('using Neuromag gradiometer definition from %s\n', cfg.gradfile); Any advice? Elena ________________________________ Elena V Orekhova, Ph.D. Inst. Neuroscience and Physiology University of Gothenburg S-413 45 Gothenburg, Sweden phone: +46 31 342 48 02 elena at neuro.gu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri May 20 16:54:16 2011 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 20 May 2011 10:54:16 -0400 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> Thanks for this helpful explanation! Can you provide me with guidance on what is involved in deciding the setting for the spectral smoothing parameter 'tapsmofrq' for dpss? Or where to look for information on this issue? Thanks again! Joe On May 20, 2011, at 1:36 AM, jan-mathijs schoffelen wrote: > Dear Joe, > > To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. > Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). > In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. > > Cheers, > > Jan-Mathijs > > > > On May 20, 2011, at 4:30 AM, Joseph Dien wrote: > >> Hi, >> I'm just starting to get up to speed on spectral analysis (I'm an ERPer). >> I'm using the following set-up: >> >> I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): >> >> cfg.method='mtmwelch'; >> cfg.output='pow'; >> [freq] = ft_freqanalysis(cfg, data); >> >> I got the error message: >> >> ------------------------- >> the input is raw data with 128 channels and 160 trials >> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >> taking every sample as time of interest >> the input is raw data with 128 channels and 160 trials >> ??? Error using ==> ft_freqanalysis at 216 >> you must specify a smoothing parameter with taper = dpss >> >> Error in ==> ft_freqanalysis_mtmwelch at 107 >> freq = ft_freqanalysis(cfgconvol, data); >> >> Error in ==> ft_freqanalysis at 271 >> [freq] = >> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >> data); >> >> ----------------------- >> Two things: >> >> 1) What would be an appropriate smoothing parameter? >> >> 2) Is this a bug? It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. >> >> Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: >> >> cfg.foi=[1:1:30]; >> cfg.taper='hanning'; >> >> which resulted in: >> >> -------------------------- >>>> [freq] = ft_freqanalysis(cfg, data); >> the input is raw data with 128 channels and 160 trials >> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >> taking every sample as time of interest >> the input is raw data with 128 channels and 160 trials >> processing trials >> ??? Reference to non-existent field 't_ftimwin'. >> >> Error in ==> ft_freqanalysis at 454 >> [spectrum_mtmconvol,ntaper,foi,toi] = >> ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, >> 'timwin', cfg.t_ftimwin, 'taper', ... >> >> Error in ==> ft_freqanalysis_mtmwelch at 107 >> freq = ft_freqanalysis(cfgconvol, data); >> >> Error in ==> ft_freqanalysis at 271 >> [freq] = >> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >> data); >> >> >> -------------------- >> What am I doing wrong? I looked through the code but couldn't figure out what the problem was. I am very confused... >> >> fieldtrip-20110519 >> MATLAB Version 7.11.0.584 (R2010b) >> Operating System: Mac OS X Version: 10.6.7 Build: 10J869 >> >> >>>> cfg >> >> cfg = >> >> dataset: 'SLI_3011m_40m_POA.egis' >> method: 'mtmwelch' >> output: 'pow' >> taper: 'hanning' >> tapsmofrq: 4 >> foi: [1x30 double] >> >>>> data >> >> data = >> >> hdr: [1x1 struct] >> label: {128x1 cell} >> time: {1x160 cell} >> trial: {1x160 cell} >> fsample: 250 >> sampleinfo: [160x2 double] >> cfg: [1x1 struct] >> >> >> Thanks for any help you can give! >> >> Joe >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From dgroppe at cogsci.ucsd.edu Fri May 20 17:38:50 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 20 May 2011 08:38:50 -0700 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> Message-ID: Hi Joe, David Kleinfeld and Partha Mitra have an excellent tutorial on multitaper spectral analysis that should help: http://www-physics.ucsd.edu/neurophysics/publications/CSHL_2009_SPECTRA_4.pdf -D On Fri, May 20, 2011 at 7:54 AM, Joseph Dien wrote: > Thanks for this helpful explanation!  Can you provide me with guidance on what is involved in deciding the setting for the spectral smoothing parameter 'tapsmofrq' for dpss?  Or where to look for information on this issue? > > Thanks again! > > Joe > > > On May 20, 2011, at 1:36 AM, jan-mathijs schoffelen wrote: > >> Dear Joe, >> >> To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. >> Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). >> In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. >> >> Cheers, >> >> Jan-Mathijs >> >> >> >> On May 20, 2011, at 4:30 AM, Joseph Dien wrote: >> >>> Hi, >>> I'm just starting to get up to speed on spectral analysis (I'm an ERPer). >>> I'm using the following set-up: >>> >>> I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): >>> >>> cfg.method='mtmwelch'; >>> cfg.output='pow'; >>> [freq] = ft_freqanalysis(cfg, data); >>> >>> I got the error message: >>> >>> ------------------------- >>> the input is raw data with 128 channels and 160 trials >>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >>> taking every sample as time of interest >>> the input is raw data with 128 channels and 160 trials >>> ??? Error using ==> ft_freqanalysis at 216 >>> you must specify a smoothing parameter with taper = dpss >>> >>> Error in ==> ft_freqanalysis_mtmwelch at 107 >>> freq = ft_freqanalysis(cfgconvol, data); >>> >>> Error in ==> ft_freqanalysis at 271 >>> [freq] = >>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >>> data); >>> >>> ----------------------- >>> Two things: >>> >>> 1) What would be an appropriate smoothing parameter? >>> >>> 2) Is this a bug?  It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. >>> >>> Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: >>> >>> cfg.foi=[1:1:30]; >>> cfg.taper='hanning'; >>> >>> which resulted in: >>> >>> -------------------------- >>>>> [freq] = ft_freqanalysis(cfg, data); >>> the input is raw data with 128 channels and 160 trials >>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >>> taking every sample as time of interest >>> the input is raw data with 128 channels and 160 trials >>> processing trials >>> ??? Reference to non-existent field 't_ftimwin'. >>> >>> Error in ==> ft_freqanalysis at 454 >>>     [spectrum_mtmconvol,ntaper,foi,toi] = >>>     ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, >>>     'timwin', cfg.t_ftimwin, 'taper', ... >>> >>> Error in ==> ft_freqanalysis_mtmwelch at 107 >>> freq = ft_freqanalysis(cfgconvol, data); >>> >>> Error in ==> ft_freqanalysis at 271 >>> [freq] = >>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >>> data); >>> >>> >>> -------------------- >>> What am I doing wrong?  I looked through the code but couldn't figure out what the problem was.  I am very confused... >>> >>> fieldtrip-20110519 >>> MATLAB Version 7.11.0.584 (R2010b) >>> Operating System: Mac OS X  Version: 10.6.7 Build: 10J869 >>> >>> >>>>> cfg >>> >>> cfg = >>> >>>   dataset: 'SLI_3011m_40m_POA.egis' >>>    method: 'mtmwelch' >>>    output: 'pow' >>>     taper: 'hanning' >>> tapsmofrq: 4 >>>       foi: [1x30 double] >>> >>>>> data >>> >>> data = >>> >>>        hdr: [1x1 struct] >>>      label: {128x1 cell} >>>       time: {1x160 cell} >>>      trial: {1x160 cell} >>>    fsample: 250 >>> sampleinfo: [160x2 double] >>>        cfg: [1x1 struct] >>> >>> >>> Thanks for any help you can give! >>> >>> Joe >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> _______________________________________________ >> 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 > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From Elena.Orekhova at neuro.gu.se Sat May 21 14:11:41 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Sat, 21 May 2011 12:11:41 +0000 Subject: [FieldTrip] rpa/nas/lpa coordinates Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> Hi I Just started to use Fieldtrip with my Neuromag MEG data and try to follow the example script ‘read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space’ The instruction suggests to take voxel coordinates of fiduscials from the Neuromag GUI for MRI-MEG Integration. I have already performed this step and saved the transformed mri in the /sets/XXX.fif file. Should I write any rpa/nas/lpa coordinates in this case? cfg.fiducial.rpa = [y x z]; cfg.fiducial.nas = [y x z]; cfg.fiducial.lpa = [y x z]; I have 2 4X4 transformations in the .fif file, not sure what they mean. mri.hdr.trans.trans 0.9913 0.1210 0.0518 -0.0032 -0.0948 0.9291 -0.3574 0.0254 -0.0914 0.3494 0.9325 -0.0519 0 0 0 1.0000 mri.hdr.voxel_trans.trans -0.0000 -0.0000 -0.0010 0.1058 -0.0005 0.0000 0.0000 0.1597 0 -0.0005 0.0001 0.1058 0 0 0 1.0000 I'll be most grateful for the help! Regards, Elena ________________________________ Elena V Orekhova, Ph.D. Inst. Neuroscience and Physiology University of Gothenburg S-413 45 Gothenburg, Sweden phone: +46 31 342 48 02 elena at neuro.gu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon May 23 09:33:34 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 23 May 2011 09:33:34 +0200 Subject: [FieldTrip] rpa/nas/lpa coordinates In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> Message-ID: Dear Elena > On 21 May 2011, at 14:11, Elena Orekhova wrote: > >> Hi >> I Just started to use Fieldtrip with my Neuromag MEG data and try >> to follow the example script >> ‘read_neuromag_mri_and_create_single- >> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space >> ’ I don't know all details of the Neuromag system, but recently we did add the http://fieldtrip.fcdonders.nl/getting_started/yokogawa documentation that explains reasonably general how coordinate system coregistration works. We also added a new function (FT_SENSORREALIGN) to ease the coregistration and we are working towards a more consistent representation of the corodinate systems in the relevant fieldtrip data structures. Although the details for your system are different (see http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined) , you might get a better overview of the steps that are involved by reading the yokogawa getting started. > The instruction suggests to take voxel coordinates of fiduscials > from the Neuromag > GUI for MRI-MEG Integration. I have already performed this step and > saved the > transformed mri in the /sets/XXX.fif file. I suggest you use the FT_DETERMINE_COORDSYS to perform a visual inspection of the coordinate systems of your anatomical MRI and of your sensor positions (data.grad, or you can use FT_READ_SENS to read them directly from the MEG fif file). Note that you have to use the function twice (on the mri and on the grad) and compare the figures yourself. > Should I write any rpa/nas/lpa coordinates in this case? > cfg.fiducial.rpa = [y x z]; > cfg.fiducial.nas = [y x z]; > cfg.fiducial.lpa = [y x z]; if you need them (see above), then these should be [x y z] and not [y x z]. > > I have 2 4X4 transformations in the .fif file, not sure what they > mean. Please read this page, which is a general introduction. > > mri.hdr.trans.trans > > 0.9913 0.1210 0.0518 -0.0032 > -0.0948 0.9291 -0.3574 0.0254 > -0.0914 0.3494 0.9325 -0.0519 > 0 0 0 1.0000 > mri.hdr.voxel_trans.trans > > -0.0000 -0.0000 -0.0010 0.1058 > -0.0005 0.0000 0.0000 0.1597 > 0 -0.0005 0.0001 0.1058 > 0 0 0 1.0000 the mri header is system specific, so I am not sure. But I guess that the first is the homogenous transformation matrix in head coordinates (linked to the fiducials) and the second is the homogenous transformation matrix in MRI coordinates. The first one appears to be in mm, the second one in meter. Please try mri.transform = mri.hdr.voxel_trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c mri.transform = mri.hdr.trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c The two figures will show you the origin, the direction of axes of the coordinate system and the scale. best regards, Robert From r.oostenveld at donders.ru.nl Mon May 23 09:41:17 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 23 May 2011 09:41:17 +0200 Subject: [FieldTrip] ft_read_vol with Neuromag In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> Message-ID: <4BFE3CE0-268F-4ACC-8863-5017DC5957AF@donders.ru.nl> Hi Elena Although some years ago FieldTrip was supporting volume conduction models from Neuromag using the meg-pd and the (closed source) meg-calc toolboxes from the company itself, I suspect that nobody has been using them the last few years. The mex files in meg-pd and meg-calc were often problematic to work with due to platform and library issues. The single-shell volume conduction model that is avaialble in Fieldtrip is currently the preferred volume model. Looking at the code, there is indeed a bug since cfg.gradfile is not defined. If you want to continue along the path of meg-pd and meg- calc, you could hardcode the filename and see how far you get. But I'd suspect that you don't have the required (commercial) mex files from meg-calc anyway. best regards Robert On 20 May 2011, at 14:00, Elena Orekhova wrote: > Hi, > I try to read volume from the Neuromag .fif file using > > vol = ft_read_vol(NEUROMAG_FIF_FILE_NAME, 'fileformat', > 'neuromag_fif') > > I get the error: > *********************** > ??? Undefined variable "cfg" or class "cfg.gradfile". > > Error in ==> ft_read_vol at 77 > fprintf('using Neuromag gradiometer definition from %s\n', > cfg.gradfile); > > Any advice? > > Elena > > Elena V Orekhova, Ph.D. > Inst. Neuroscience and Physiology > University of Gothenburg > S-413 45 Gothenburg, Sweden > phone: +46 31 342 48 02 > elena at neuro.gu.se > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Elena.Orekhova at neuro.gu.se Mon May 23 10:00:15 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 23 May 2011 08:00:15 +0000 Subject: [FieldTrip] segmentation problem with Neuromag Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC7CC3@exchccr1.neuro.gu.se> Dear Fieldtrip users and developers, I would like to start using Fieldtrip for the source analysis of the MEG data, but I have some problem with mri segmentation using Neuromag-306 .fif MRI file. I do: 1) import .fif, (Coordinate alignment was already done in Neuromag). mriname = 'NEUROMAGxxx.fif' [mri] = ft_read_mri(mriname) cfg = []; ft_sourceplot(cfg,mri); ***** attachment: mri.jpg ****** 2) do segmentation cfg = []; cfg.template = 'T1.nii'; %spm8 cfg.coordsys = 'neuromag'; cfg.write = 'no'; cfg.name = 'temp'; cfg.interactive = 'yes'; [segmentedmri] = ft_volumesegment(cfg, mri) 3) plot the original and segmented mri cfg = []; test.dim = [512 512 180]; test = segmentedmri; test.avg.pow = test.gray+test.white; test.anatomy = mri.anatomy; cfg.funparameter = 'avg.pow'; cfg.interactive = 'yes'; ft_sourceplot(cfg,test); ***** attachment : mri_segmented.jpg ****** Apparently, there is a displacement of the segmented mri image. It seems also that the segmented mri is bigger then the original mri. The similar (although not the same) picture is observed when I do coordinate alignment in the MNE and use the /sets/CORxxx.fif saved from the MNE sohtware. I have seen some discussions on this topic, but I have not found the solution. Should I swap x and y coordinates? How can I do it? I would be most grateful for help! Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mri.jpg Type: image/jpeg Size: 20047 bytes Desc: mri.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mri_segmented.jpg Type: image/jpeg Size: 59004 bytes Desc: mri_segmented.jpg URL: From odidodi at hotmail.com Mon May 23 10:44:31 2011 From: odidodi at hotmail.com (odelia nakar) Date: Mon, 23 May 2011 08:44:31 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Mon May 23 12:03:11 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 23 May 2011 10:03:11 +0000 Subject: [FieldTrip] rpa/nas/lpa coordinates In-Reply-To: References: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se>, Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC8D07@exchccr1.neuro.gu.se> Dear Robert, As you advised, I tried to use 'ft_determine_coordsys' to look at my non-segmented MRI, but got the error (see below). What can be the reason? /Elena >> >> mri mri = dim: [512 512 180] anatomy: [512x512x180 int16] hdr: [1x1 struct] transform: [4x4 double] unit: 'm' >> [dataout] = ft_determine_coordsys(mri) ??? Error using ==> surface Z must be a matrix, not a scalar or vector Error in ==> ft_plot_slice at 184 h = surface(Xh, Yh, Zh, V); Error in ==> ft_plot_ortho at 94 hx = ft_plot_slice(dat, varargin{:}); Error in ==> ft_determine_coordsys at 192 ft_plot_ortho(data.(funparam), 'transform', data.transform, 'resolution', 1, 'style', 'intersect'); >> ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Robert Oostenveld [r.oostenveld at donders.ru.nl] Sent: Monday, May 23, 2011 9:33 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] rpa/nas/lpa coordinates Dear Elena > On 21 May 2011, at 14:11, Elena Orekhova wrote: > >> Hi >> I Just started to use Fieldtrip with my Neuromag MEG data and try >> to follow the example script >> ‘read_neuromag_mri_and_create_single- >> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space >> ’ I don't know all details of the Neuromag system, but recently we did add the http://fieldtrip.fcdonders.nl/getting_started/yokogawa documentation that explains reasonably general how coordinate system coregistration works. We also added a new function (FT_SENSORREALIGN) to ease the coregistration and we are working towards a more consistent representation of the corodinate systems in the relevant fieldtrip data structures. Although the details for your system are different (see http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined) , you might get a better overview of the steps that are involved by reading the yokogawa getting started. > The instruction suggests to take voxel coordinates of fiduscials > from the Neuromag > GUI for MRI-MEG Integration. I have already performed this step and > saved the > transformed mri in the /sets/XXX.fif file. I suggest you use the FT_DETERMINE_COORDSYS to perform a visual inspection of the coordinate systems of your anatomical MRI and of your sensor positions (data.grad, or you can use FT_READ_SENS to read them directly from the MEG fif file). Note that you have to use the function twice (on the mri and on the grad) and compare the figures yourself. > Should I write any rpa/nas/lpa coordinates in this case? > cfg.fiducial.rpa = [y x z]; > cfg.fiducial.nas = [y x z]; > cfg.fiducial.lpa = [y x z]; if you need them (see above), then these should be [x y z] and not [y x z]. > > I have 2 4X4 transformations in the .fif file, not sure what they > mean. Please read this page, which is a general introduction. > > mri.hdr.trans.trans > > 0.9913 0.1210 0.0518 -0.0032 > -0.0948 0.9291 -0.3574 0.0254 > -0.0914 0.3494 0.9325 -0.0519 > 0 0 0 1.0000 > mri.hdr.voxel_trans.trans > > -0.0000 -0.0000 -0.0010 0.1058 > -0.0005 0.0000 0.0000 0.1597 > 0 -0.0005 0.0001 0.1058 > 0 0 0 1.0000 the mri header is system specific, so I am not sure. But I guess that the first is the homogenous transformation matrix in head coordinates (linked to the fiducials) and the second is the homogenous transformation matrix in MRI coordinates. The first one appears to be in mm, the second one in meter. Please try mri.transform = mri.hdr.voxel_trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c mri.transform = mri.hdr.trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c The two figures will show you the origin, the direction of axes of the coordinate system and the scale. best regards, Robert _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jinyinz at ece.cmu.edu Mon May 23 15:46:20 2011 From: jinyinz at ece.cmu.edu (jinyinz at ece.cmu.edu) Date: Mon, 23 May 2011 09:46:20 -0400 (EDT) Subject: [FieldTrip] the source space for MEG/EEG source localization Message-ID: <4412.128.2.133.95.1306158380.squirrel@webmail.ece.cmu.edu> Dear Fieldtrippers, I have a question about the source space selection for MEG/EEG source localization. Some source localization algorithms restrict the reconstruction to sources located on cortical surface. To implement such kind of algorithm, I used mne_setup_source_space to create a source space on cortical surface. By default mne_setup_source_space creates a decimated dipole grid on the white matter surface. Although this setting is widely used, some papers create a source space on the gray matter surface instead. Are there any specific reasons for selecting any of the two options? Thanks, Jinyin From dgroppe at cogsci.ucsd.edu Mon May 23 17:57:25 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Mon, 23 May 2011 08:57:25 -0700 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: > Hi all, > > I'm troubled by the fact that when I use ICA for blinks\eyes movements > removal, I remove the relevant components also from trials that do not > contain blinks\eyes movements. In order to avoid this bias we thought to > combine the data before ICA ("data" structure) with the data after ICA > ("dataica" structure), only in specific trials, as follows: > > datall=dataica; > datall.trial=data.trial; > datall.time=data.time; > blinks=[2 4 5 8 bla bla 156]; > for ind=1:length(blinks) >      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; > end > > To my first question: I just wanted to check that there is no problem with > that, or any reason not to use it. > > Another issue- I use motor learning task, and I'm trying to understand what > happens through the process, in terms of power-frequency changes through the > process. How would you recommend that I'd use the ft_freqanalysis function? > What method to use (or what do I need to consider when choosing the method > field)? > > > Thanks a lot, > Odelia. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From jdien07 at mac.com Tue May 24 03:07:57 2011 From: jdien07 at mac.com (Joseph Dien) Date: Mon, 23 May 2011 21:07:57 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote: > Hi Odelia, > When you use ICA (or any other spatial filter) to correct for EEG > artifacts, you're going to distort your data some by removing true EEG > activity in addition to the artifact (for an explanation, see: > http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). > So to minimize distortion, it would be better not to apply ICA > artifact correction to artifact-free data. However, if the frequency > of the artifact differs across experimental conditions, it could > confound your analysis. For example, I suspect people blink more > often to targets in an oddball experiment than standards. Thus if you > apply ICA only to blinky trials, you could find a difference between > the EEG response to standards and targets that simply reflects the > fact ICA removed more EEG activity in the target trials (i.e., it > wouldn't reflect a true difference in neural processing). > hope this helps, > -David > > On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: >> Hi all, >> >> I'm troubled by the fact that when I use ICA for blinks\eyes movements >> removal, I remove the relevant components also from trials that do not >> contain blinks\eyes movements. In order to avoid this bias we thought to >> combine the data before ICA ("data" structure) with the data after ICA >> ("dataica" structure), only in specific trials, as follows: >> >> datall=dataica; >> datall.trial=data.trial; >> datall.time=data.time; >> blinks=[2 4 5 8 bla bla 156]; >> for ind=1:length(blinks) >> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >> end >> >> To my first question: I just wanted to check that there is no problem with >> that, or any reason not to use it. >> >> Another issue- I use motor learning task, and I'm trying to understand what >> happens through the process, in terms of power-frequency changes through the >> process. How would you recommend that I'd use the ft_freqanalysis function? >> What method to use (or what do I need to consider when choosing the method >> field)? >> >> >> Thanks a lot, >> Odelia. >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From shackman at wisc.edu Tue May 24 04:00:34 2011 From: shackman at wisc.edu (Alexander J. Shackman) Date: Mon, 23 May 2011 21:00:34 -0500 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: And for a related perspective, see McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, *Neuroimage**, 54*, 4-9. http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: > I agree with David's reasoning. You may find the following article to be > of help as well in understanding the issues involved: > > Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of > simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping*, 28 > (8), 742-763. > > Cheers! > > Joe > > On May 23, 2011, at 11:57 AM, David Groppe wrote: > > Hi Odelia, > When you use ICA (or any other spatial filter) to correct for EEG > artifacts, you're going to distort your data some by removing true EEG > activity in addition to the artifact (for an explanation, see: > http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). > So to minimize distortion, it would be better not to apply ICA > artifact correction to artifact-free data. However, if the frequency > of the artifact differs across experimental conditions, it could > confound your analysis. For example, I suspect people blink more > often to targets in an oddball experiment than standards. Thus if you > apply ICA only to blinky trials, you could find a difference between > the EEG response to standards and targets that simply reflects the > fact ICA removed more EEG activity in the target trials (i.e., it > wouldn't reflect a true difference in neural processing). > hope this helps, > -David > > On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: > > Hi all, > > > I'm troubled by the fact that when I use ICA for blinks\eyes movements > > removal, I remove the relevant components also from trials that do not > > contain blinks\eyes movements. In order to avoid this bias we thought to > > combine the data before ICA ("data" structure) with the data after ICA > > ("dataica" structure), only in specific trials, as follows: > > > datall=dataica; > > datall.trial=data.trial; > > datall.time=data.time; > > blinks=[2 4 5 8 bla bla 156]; > > for ind=1:length(blinks) > > datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; > > end > > > To my first question: I just wanted to check that there is no problem with > > that, or any reason not to use it. > > > Another issue- I use motor learning task, and I'm trying to understand what > > happens through the process, in terms of power-frequency changes through > the > > process. How would you recommend that I'd use the ft_freqanalysis function? > > What method to use (or what do I need to consider when choosing the method > > field)? > > > > Thanks a lot, > > Odelia. > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://homepage.mac.com/jdien07/ > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Alexander J. Shackman, Ph.D. Wisconsin Psychiatric Institute & Clinics and Department of Psychology University of Wisconsin-Madison 1202 West Johnson Street Madison, Wisconsin 53706 Telephone: +1 (608) 358-5025 Fax: +1 (608) 265-2875 Email: shackman at wisc.edu http://psyphz.psych.wisc.edu/~shackman -------------- next part -------------- An HTML attachment was scrubbed... URL: From odidodi at hotmail.com Tue May 24 08:46:55 2011 From: odidodi at hotmail.com (odelia nakar) Date: Tue, 24 May 2011 06:46:55 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>, , , <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: Thank you all- Joe, Alexander and David, it is indeed very helpful and enlightening. I actually don't have any stimulus, but I wasn't aware of the hidden EMG. Have a good day (or night :))! Odelia. From: jdien07 at mac.com Date: Mon, 23 May 2011 21:07:57 -0400 To: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] ICA+frqanalysis questions I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote:Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph DienE-mail: jdien07 at mac.comPhone: 301-226-8848Fax: 301-226-8811http://homepage.mac.com/jdien07/ _______________________________________________ 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 stefan.debener at uni-oldenburg.de Tue May 24 09:11:16 2011 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Tue, 24 May 2011 09:11:16 +0200 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: <4DDB5A14.3090102@uni-oldenburg.de> Hi Odelia, I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... Best, Stefan Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: > And for a related perspective, see > > McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. > J. (2011). Electromyogenic artifacts and electroencephalographic > inferences revisited, */Neuroimage/*/, 54/, 4-9. > > http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf > > > > On Mon, May 23, 2011 at 8:07 PM, Joseph Dien > wrote: > > I agree with David's reasoning. You may find the following > article to be of help as well in understanding the issues involved: > > Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and > ICA of simulated ERPs: Promax versus Infomax rotations. /Human > Brain Mapping/, 28(8), 742-763. > > Cheers! > > Joe > > On May 23, 2011, at 11:57 AM, David Groppe wrote: > >> Hi Odelia, >> When you use ICA (or any other spatial filter) to correct for EEG >> artifacts, you're going to distort your data some by removing >> true EEG >> activity in addition to the artifact (for an explanation, see: >> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >> So to minimize distortion, it would be better not to apply ICA >> artifact correction to artifact-free data. However, if the frequency >> of the artifact differs across experimental conditions, it could >> confound your analysis. For example, I suspect people blink more >> often to targets in an oddball experiment than standards. Thus >> if you >> apply ICA only to blinky trials, you could find a difference between >> the EEG response to standards and targets that simply reflects the >> fact ICA removed more EEG activity in the target trials (i.e., it >> wouldn't reflect a true difference in neural processing). >> hope this helps, >> -David >> >> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >> > wrote: >>> Hi all, >>> >>> I'm troubled by the fact that when I use ICA for blinks\eyes >>> movements >>> removal, I remove the relevant components also from trials that >>> do not >>> contain blinks\eyes movements. In order to avoid this bias we >>> thought to >>> combine the data before ICA ("data" structure) with the data >>> after ICA >>> ("dataica" structure), only in specific trials, as follows: >>> >>> datall=dataica; >>> datall.trial=data.trial; >>> datall.time=data.time; >>> blinks=[2 4 5 8 bla bla 156]; >>> for ind=1:length(blinks) >>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>> end >>> >>> To my first question: I just wanted to check that there is no >>> problem with >>> that, or any reason not to use it. >>> >>> Another issue- I use motor learning task, and I'm trying to >>> understand what >>> happens through the process, in terms of power-frequency changes >>> through the >>> process. How would you recommend that I'd use the >>> ft_freqanalysis function? >>> What method to use (or what do I need to consider when choosing >>> the method >>> field)? >>> >>> >>> Thanks a lot, >>> Odelia. >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> David Groppe, Ph.D. >> Postdoctoral Researcher >> Kutaslab >> Dept. of Cognitive Science >> University of California, San Diego >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://homepage.mac.com/jdien07/ > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Alexander J. Shackman, Ph.D. > Wisconsin Psychiatric Institute & Clinics and > Department of Psychology > University of Wisconsin-Madison > 1202 West Johnson Street > Madison, Wisconsin 53706 > > Telephone: +1 (608) 358-5025 > Fax: +1 (608) 265-2875 > Email: shackman at wisc.edu > http://psyphz.psych.wisc.edu/~shackman > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Tue May 24 23:47:39 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Tue, 24 May 2011 14:47:39 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine Message-ID: Hi there, My lab is running MATLAB 7.8 on a Linux network and when we plot spectrograms using ft_multiplotTFR.m the computer we're using will often reboot. It appears to happen most often (if not exclusively), when we close the figure window produced by ft_multiplotTFR.m. The problem happens even if we create non-interactive figures (i.e., we set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., Java disabled). Has anyone else had this problem? Does anyone have an idea as to what a solution might be? Puzzlingly, we don't have this problem when running MATLAB on a Mac. much appreciated, -David -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From r.vandermeij at donders.ru.nl Wed May 25 00:23:58 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 24 May 2011 15:23:58 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: References: Message-ID: <4DDC2FFE.9000600@donders.ru.nl> Hi David, Depending on what you mean by crashing, it could be the opengl drivers. I've experienced similar issues with complex plotting functions. Try creating the figure-window (note, not the plot) using the zbuffer to circumvent it by figure('renderer','zbuffer') Hope it helps, Roemer On 24-May-11 14:47, David Groppe wrote: > Hi there, > My lab is running MATLAB 7.8 on a Linux network and when we plot > spectrograms using ft_multiplotTFR.m the computer we're using will > often reboot. It appears to happen most often (if not exclusively), > when we close the figure window produced by ft_multiplotTFR.m. The > problem happens even if we create non-interactive figures (i.e., we > set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., > Java disabled). Has anyone else had this problem? Does anyone have > an idea as to what a solution might be? Puzzlingly, we don't have > this problem when running MATLAB on a Mac. > much appreciated, > -David > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Radboud University Nijmegen P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Wed May 25 02:10:02 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Tue, 24 May 2011 17:10:02 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: <4DDC2FFE.9000600@donders.ru.nl> References: <4DDC2FFE.9000600@donders.ru.nl> Message-ID: Thanks very much for the response Roemer. By "crashing," I mean the screen suddenly goes blank and the machine reverts to the login screen. I've tried your suggestion and so far it looks like it's working! I'll let you know if the problem returns. greatly appreciated, -David On Tue, May 24, 2011 at 3:23 PM, Roemer van der Meij wrote: > Hi David, > > Depending on what you mean by crashing, it could be the opengl drivers. I've > experienced similar issues with complex plotting functions. Try creating the > figure-window (note, not the plot) using the zbuffer to circumvent it by > figure('renderer','zbuffer') > > Hope it helps, > Roemer > > > > On 24-May-11 14:47, David Groppe wrote: > > Hi there, > My lab is running MATLAB 7.8 on a Linux network and when we plot > spectrograms using ft_multiplotTFR.m the computer we're using will > often reboot. It appears to happen most often (if not exclusively), > when we close the figure window produced by ft_multiplotTFR.m. The > problem happens even if we create non-interactive figures (i.e., we > set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., > Java disabled). Has anyone else had this problem? Does anyone have > an idea as to what a solution might be? Puzzlingly, we don't have > this problem when running MATLAB on a Mac. > much appreciated, > -David > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > Radboud University Nijmegen > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From g.piantoni at nin.knaw.nl Wed May 25 08:59:20 2011 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Wed, 25 May 2011 08:59:20 +0200 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: References: <4DDC2FFE.9000600@donders.ru.nl> Message-ID: Hi David, I also had similar problems, such as crashing of the VNC window on a remote server. I agree with Roemer that it's probably due to buggy opengl drivers. More information at: http://www.mathworks.com/support/tech-notes/1200/1201.html#Section_4 Briefly, you can run as first command: >> opengl software to force matlab to use the (less buggy) software implementation of opengl. Then the trick "figure('renderer','zbuffer')" should not be necessary. Hope this helps. Gio -- Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.giovannipiantoni.com On Wed, May 25, 2011 at 02:10, David Groppe wrote: > Thanks very much for the response Roemer.  By "crashing," I mean the > screen suddenly goes blank and the machine reverts to the login > screen.  I've tried your suggestion and so far it looks like it's > working!  I'll let you know if the problem returns. >     greatly appreciated, >          -David > > On Tue, May 24, 2011 at 3:23 PM, Roemer van der Meij > wrote: >> Hi David, >> >> Depending on what you mean by crashing, it could be the opengl drivers. I've >> experienced similar issues with complex plotting functions. Try creating the >> figure-window (note, not the plot) using the zbuffer to circumvent it by >> figure('renderer','zbuffer') >> >> Hope it helps, >> Roemer >> >> >> >> On 24-May-11 14:47, David Groppe wrote: >> >> Hi there, >>    My lab is running MATLAB 7.8 on a Linux network and when we plot >> spectrograms using ft_multiplotTFR.m the computer we're using will >> often reboot.  It appears to happen most often (if not exclusively), >> when we close the figure window produced by ft_multiplotTFR.m.  The >> problem happens even if we create non-interactive figures (i.e., we >> set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., >> Java disabled).  Has anyone else had this problem?   Does anyone have >> an idea as to what a solution might be?  Puzzlingly, we don't have >> this problem when running MATLAB on a Mac. >>           much appreciated, >>                 -David >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> Radboud University Nijmegen >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From g.dimitriadis at donders.ru.nl Wed May 25 09:48:49 2011 From: g.dimitriadis at donders.ru.nl (George Dimitriadis) Date: Wed, 25 May 2011 09:48:49 +0200 Subject: [FieldTrip] (no subject) Message-ID: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> Hello guys, I just run an ft_freqanalysis using cfg.taper='dssp'. By mistake I took the cfg. tapsmofrq to be too small resulting in a single taper. This was fine, but when I run freqanalysis I got an error saying that the warning_once (ft_specest_mtmfft at 89) was not found. Apparently it was there to warn me about using only 1 tapper for smoothing with 'dssp'. I am just letting you know that for some reason the warning_once(char) function couldn't be found. Thanks George -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 25 10:10:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 25 May 2011 10:10:02 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> References: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> Message-ID: <6F47EF43-DE4D-4031-8BCC-F5C9D9AA13D3@donders.ru.nl> Hi George, Sorry about this. If you are running a local copy of fieldtrip, you can copy warning_once.m from fieldtrip/private into fieldtrip/specest/ private. It should work then. I'll fix it in the release version asap. Cheers, JM On May 25, 2011, at 9:48 AM, George Dimitriadis wrote: > Hello guys, > > I just run an ft_freqanalysis using cfg.taper=’dssp’. By mistake I > took the cfg. tapsmofrq to be too small resulting in a single taper. > This was fine, but when I run freqanalysis I got an error saying > that the warning_once (ft_specest_mtmfft at 89) was not found. > Apparently it was there to warn me about using only 1 tapper for > smoothing with ‘dssp’. I am just letting you know that for some > reason the warning_once(char) function couldn’t be found. > > Thanks > > George > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.N.Maijers at student.ru.nl Wed May 25 11:50:16 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Wed, 25 May 2011 11:50:16 +0200 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? Message-ID: <20110525115016.0fc02ea6@thuisrekenaar> Dear readers, I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit (Linux thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux). When I call "ft_timelockstatistics()" with "cfg.mva ={ft_mv_standardizer() ft_mv_svm()};" It fails: "selected 60 channels selected 351 time bins selected 1 frequency bins using "statistics_crossvalidate" for the statistical testing initializing random number generator with seed 1 validating 1 dataset(s) input 1 consists of 439 examples and 21060 features output 1 consists of 439 examples and 1 features validating using 5-fold cross-validation using 5 folds for 1 datasets dataset 1: validating fold 1 of 5 using 351 training samples and 88 test samples Compiling tprod for first use /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching for -lstdc++ /usr/bin/ld: cannot find -lstdc++ collect2: ld returned 1 exit status mex: link of ' "tprod.mexglx"' failed. ??? Error using ==> tprod at 132 unable to compile MEX version of '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', please make sure your MEX compiler is set up correctly (try 'mex -setup')." I have followed the instructions on https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX compiling but it was not successful. -> Before I singlehandedly bring my operating system configuration into disarray, I would like to learn from you the following. Do you know of ways to use a gcc to compile code written for a 32-bit architecture ona 64-bit machine? Or if necessary another compiler that works under Linux? -> If such a thing is certainly impossible, are there ways to avoid MEX compiling? Or could someone provide precompiled MEX files that would suit my configuration? [*] I have installed the Ubuntu package "ia32-libs" (version 20090808ubuntu9.1) [*] It seems that the only thing I need is 32-bit binaries for libstdc++. Perhaps I can introduce these in some creative way, but I would like to check with you all first. I hope you are willing to help me. As a novice to FieldTrip and even MATLAB, I have encountered many obstacles but I am determined to surmount them. Kind regards, Sander Maijers (BA Linguistics student) From S.N.Maijers at student.ru.nl Wed May 25 12:13:01 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Wed, 25 May 2011 12:13:01 +0200 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory Message-ID: <20110525121301.2f896b3e@thuisrekenaar> Dear readers, While all other functional subdirectories do get included after an "addpath" of the FieldTrip root directory, the "multivariate" subdirectories does not get included. It assume this is because of automatical detection that requirements of the FieldTrip multivariate module were not met. Yet while some parts of the multivariate module seem to rely on features exclusive to MATLAB 64-bit editions, others (like the ridge regression functionality) do not. >From my (tentative) investigation it appears that there is no standard way to add a path recursively from a startup.m file, even though that can be done with the graphical interface of MATLAB. What are your thoughts about this? Can anyone offer a method to automatically add FieldTrip including the multivariate module to the path upon startup of MATLAB that works in my situation? Kind regards, Sander Maijers P.S.: In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit Linux. From ekanal at cmu.edu Wed May 25 14:53:53 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Wed, 25 May 2011 08:53:53 -0400 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory In-Reply-To: <20110525121301.2f896b3e@thuisrekenaar> References: <20110525121301.2f896b3e@thuisrekenaar> Message-ID: <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> Hello Sander - Just so you know, there is a way to recursively add folders to a path, using the `genpath` command: addpath(genpath(path/to/folder)) However, as you said, it's probably just a better idea to add it to the `ft_defaults` file so it's added automatically, as you suggested. Elli On May 25, 2011, at 6:13 AM, Sander Maijers wrote: > Dear readers, > > While all other functional subdirectories do get included after an > "addpath" of the FieldTrip root directory, the "multivariate" > subdirectories does not get included. > > It assume this is because of automatical detection that requirements of > the FieldTrip multivariate module were not met. > > Yet while some parts of the multivariate module seem to rely on > features exclusive to MATLAB 64-bit editions, others (like the ridge > regression functionality) do not. > >> From my (tentative) investigation it appears that there is no standard > way to add a path recursively from a startup.m file, even though that > can be done with the graphical interface of MATLAB. > > What are your thoughts about this? > > Can anyone offer a method to automatically add FieldTrip including the > multivariate module to the path upon startup of MATLAB that works in > my situation? > > Kind regards, > Sander Maijers > > P.S.: > In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit > Linux. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From batrod at gmail.com Wed May 25 17:39:02 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Wed, 25 May 2011 10:39:02 -0500 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory In-Reply-To: <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> References: <20110525121301.2f896b3e@thuisrekenaar> <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> Message-ID: Hello Sander, Elli's suggestion is right. As you apparently want to do that on matlab startup and using Linux, you can add a matlab shortcut on your panel with the following instructions : matlab -r "yourinstructions" "yourinstructions" can be an addpath or wathever you want. I often use this initialization to avoid default path conflicts between spm, fieldtrip, eeglab, etc... Hope this helps, Rodolphe On Wed, May 25, 2011 at 7:53 AM, Kanal Eliezer wrote: > Hello Sander - > > Just so you know, there is a way to recursively add folders to a path, > using the `genpath` command: > > addpath(genpath(path/to/folder)) > > However, as you said, it's probably just a better idea to add it to the > `ft_defaults` file so it's added automatically, as you suggested. > > Elli > > > On May 25, 2011, at 6:13 AM, Sander Maijers wrote: > > > Dear readers, > > > > While all other functional subdirectories do get included after an > > "addpath" of the FieldTrip root directory, the "multivariate" > > subdirectories does not get included. > > > > It assume this is because of automatical detection that requirements of > > the FieldTrip multivariate module were not met. > > > > Yet while some parts of the multivariate module seem to rely on > > features exclusive to MATLAB 64-bit editions, others (like the ridge > > regression functionality) do not. > > > >> From my (tentative) investigation it appears that there is no standard > > way to add a path recursively from a startup.m file, even though that > > can be done with the graphical interface of MATLAB. > > > > What are your thoughts about this? > > > > Can anyone offer a method to automatically add FieldTrip including the > > multivariate module to the path upon startup of MATLAB that works in > > my situation? > > > > Kind regards, > > Sander Maijers > > > > P.S.: > > In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit > > Linux. > > > > _______________________________________________ > > 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 batrod at gmail.com Wed May 25 18:32:19 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Wed, 25 May 2011 11:32:19 -0500 Subject: [FieldTrip] Filtering and oscillations Message-ID: Dear Fieldtrippers, i have a theoretical question. Im interested into phase-lock analysis between sensors in alpha oscillations. Prior to do so, my data were bandpassed between 2 and 30 Hz. However, i heard that such a low-pass filter can alter informations usefull to phase-lock analysis. Any suggestions on that? Best regards, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jenwhitman at gmail.com Wed May 25 19:53:28 2011 From: jenwhitman at gmail.com (Jen Whitman) Date: Wed, 25 May 2011 10:53:28 -0700 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? In-Reply-To: <20110525115016.0fc02ea6@thuisrekenaar> References: <20110525115016.0fc02ea6@thuisrekenaar> Message-ID: As another ubuntu 64-bit user, I'd say your problem is with your matlab install rather than with fieldtrip. You may have inadvertently specified 32-bit instead of 64-bit when you installed matlab. If you type "computer" at the matlab prompt, it should say "GLNXA64". If not, I recommend redoing the matlab installation and making sure you specify your OS as 64-bit. If you still get error message about libstdc++.so, you may need to install that library using the 'synaptic package manger' (in your system menu under administration). A good resource for help if you have further difficulty may be linuxquestions.org. Best of luck! On Wed, May 25, 2011 at 2:50 AM, Sander Maijers wrote: > Dear readers, > > I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit (Linux > thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 > x86_64 GNU/Linux). > > When I call "ft_timelockstatistics()" with "cfg.mva ={ft_mv_standardizer() > ft_mv_svm()};" > > It fails: > > "selected 60 channels > selected 351 time bins > selected 1 frequency bins > using "statistics_crossvalidate" for the statistical testing > initializing random number generator with seed 1 > validating 1 dataset(s) > input 1 consists of 439 examples and 21060 features > output 1 consists of 439 examples and 1 features > validating using 5-fold cross-validation > using 5 folds for 1 datasets > dataset 1: validating fold 1 of 5 using 351 training samples and 88 test > samples Compiling tprod for first use > /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > searching for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching > for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > searching for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching > for -lstdc++ /usr/bin/ld: > cannot find -lstdc++ collect2: ld returned 1 exit status > > mex: link of ' "tprod.mexglx"' failed. > > ??? Error using ==> tprod at 132 unable to compile MEX version of > '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', > please make sure your MEX compiler is set up correctly (try 'mex -setup')." > > > I have followed the instructions on > https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX > compiling but it was not successful. > > -> Before I singlehandedly bring my operating system configuration into > disarray, I would like to learn from you the following. Do you know of ways > to use a gcc to compile code written for a 32-bit architecture ona 64-bit > machine? Or if necessary another compiler that works under Linux? > -> If such a thing is certainly impossible, are there ways to avoid MEX > compiling? Or could someone provide precompiled MEX files that would suit my > configuration? > > [*] I have installed the Ubuntu package "ia32-libs" (version > 20090808ubuntu9.1) > [*] It seems that the only thing I need is 32-bit binaries for libstdc++. > Perhaps I can introduce these in some creative way, but I would like to > check with you all first. > > I hope you are willing to help me. As a novice to FieldTrip and even > MATLAB, I have encountered many obstacles but I am determined to surmount > them. > > Kind regards, > Sander Maijers (BA Linguistics student) > _______________________________________________ > 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 S.N.Maijers at student.ru.nl Thu May 26 16:23:39 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Thu, 26 May 2011 16:23:39 +0200 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? In-Reply-To: References: <20110525115016.0fc02ea6@thuisrekenaar> Message-ID: <20110526162339.65dd030c@thuisrekenaar> Jen, thanks for your suggestion. That problem I had fixed before. I am among those who could not even get a 64-bit install if they wished so, because the Student edition of MATLAB is still 32-bit-only. This problem will occur later on, in case some MEX-compilation needs to be done, in my case with the multivariate module! I have succeeded in fixing the problem however. Those who are confronted with it as well, can read: http://fieldtrip.fcdonders.nl/faq/compile?&#fixing_mex-compilation_with_32-bit_variants_of_matlab_running_under_64-bit_linux . On Wed, 25 May 2011 10:53:28 -0700 Jen Whitman wrote: > As another ubuntu 64-bit user, I'd say your problem is with your > matlab install rather than with fieldtrip. You may have inadvertently > specified 32-bit instead of 64-bit when you installed matlab. If you > type "computer" at the matlab prompt, it should say "GLNXA64". If > not, I recommend redoing the matlab installation and making sure you > specify your OS as 64-bit. If you still get error message about > libstdc++.so, you may need to install that library using the > 'synaptic package manger' (in your system menu under administration). > A good resource for help if you have further difficulty may be > linuxquestions.org. > > Best of luck! > > On Wed, May 25, 2011 at 2:50 AM, Sander Maijers > wrote: > > > Dear readers, > > > > I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit > > (Linux thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 > > 18:42:20 UTC 2011 x86_64 GNU/Linux). > > > > When I call "ft_timelockstatistics()" with "cfg.mva > > ={ft_mv_standardizer() ft_mv_svm()};" > > > > It fails: > > > > "selected 60 channels > > selected 351 time bins > > selected 1 frequency bins > > using "statistics_crossvalidate" for the statistical testing > > initializing random number generator with seed 1 > > validating 1 dataset(s) > > input 1 consists of 439 examples and 21060 features > > output 1 consists of 439 examples and 1 features > > validating using 5-fold cross-validation > > using 5 folds for 1 datasets > > dataset 1: validating fold 1 of 5 using 351 training samples and 88 > > test samples Compiling tprod for first use > > /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when > > searching for -lstdc++ /usr/bin/ld: > > cannot find -lstdc++ collect2: ld returned 1 exit status > > > > mex: link of ' "tprod.mexglx"' failed. > > > > ??? Error using ==> tprod at 132 unable to compile MEX version of > > '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', > > please make sure your MEX compiler is set up correctly (try 'mex > > -setup')." > > > > > > I have followed the instructions on > > https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX > > compiling but it was not successful. > > > > -> Before I singlehandedly bring my operating system configuration > > into disarray, I would like to learn from you the following. Do you > > know of ways to use a gcc to compile code written for a 32-bit > > architecture ona 64-bit machine? Or if necessary another compiler > > that works under Linux? -> If such a thing is certainly impossible, > > are there ways to avoid MEX compiling? Or could someone provide > > precompiled MEX files that would suit my configuration? > > > > [*] I have installed the Ubuntu package "ia32-libs" (version > > 20090808ubuntu9.1) > > [*] It seems that the only thing I need is 32-bit binaries for > > libstdc++. Perhaps I can introduce these in some creative way, but > > I would like to check with you all first. > > > > I hope you are willing to help me. As a novice to FieldTrip and even > > MATLAB, I have encountered many obstacles but I am determined to > > surmount them. > > > > Kind regards, > > Sander Maijers (BA Linguistics student) > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > From dgroppe at cogsci.ucsd.edu Fri May 27 03:54:35 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Thu, 26 May 2011 18:54:35 -0700 Subject: [FieldTrip] duplicate spm directories Message-ID: Hi again, I'm running the March 28th version of Fieldtrip and am getting the following warning: Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20110328/private/warning_once at 75 In ft_defaults at 45 In ft_preprocessing at 179 Warning: one version of SPM is found here: /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm2/spm.m > In ft_defaults at 48 In ft_preprocessing at 179 Warning: one version of SPM is found here: /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm8/spm.m Can I simply remove the spm2 directory? thanks in advance, -D -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From jdien07 at mac.com Fri May 27 05:16:03 2011 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 26 May 2011 23:16:03 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <4DDB5A14.3090102@uni-oldenburg.de> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> Message-ID: <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Stefan, just to be clear, I don't think any of us were saying not to use ICA to correct blinks. David was just saying that there are potential concerns when one only applies the ICA to the blink trials rather than to all the trials. I myself use EEGlab's infomax implementation in the automatic eyeblink correction tool of my EP Toolkit (http://sourceforge.net/projects/erppcatoolkit/). Now that said, I should add a little more nuance to my response. One of the things I observed (or rather, that Tim Curran pointed out to me) is that when you apply ICA to remove eyeblink artifacts in this manner, it can actually substantially increase the noise level in the data, so for the trials without eyeblinks it can have a considerable cost. So in order to balance the cost/benefit ratio, what I did was to include a trial by trial criterion that the putative eyeblink factors would only be removed if doing so reduced the overall variance of the trial. This approach does still have some potential for causing the concerns that David raises but not as much as only applying the ICA to blink trials since it does end up getting applied to non-blink trials too. This does mean that one should be cautious about any apparent effects in the artifact corrected data that are centered around the eyes (that have a blink topography) but that goes without saying in any case. So anyway, I agree, it's not perfect but seems to be the best available option. Cheers! Joe On May 24, 2011, at 3:11 AM, Stefan Debener wrote: > Hi Odelia, > > I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... > > For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... > > Best, > Stefan > > > Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: >> >> And for a related perspective, see >> >> McMenamin, B. W., Shackman, A. J., Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, Neuroimage, 54, 4-9. >> >> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf >> >> >> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: >> I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: >> >> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. >> >> Cheers! >> >> Joe >> >> On May 23, 2011, at 11:57 AM, David Groppe wrote: >> >>> Hi Odelia, >>> When you use ICA (or any other spatial filter) to correct for EEG >>> artifacts, you're going to distort your data some by removing true EEG >>> activity in addition to the artifact (for an explanation, see: >>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >>> So to minimize distortion, it would be better not to apply ICA >>> artifact correction to artifact-free data. However, if the frequency >>> of the artifact differs across experimental conditions, it could >>> confound your analysis. For example, I suspect people blink more >>> often to targets in an oddball experiment than standards. Thus if you >>> apply ICA only to blinky trials, you could find a difference between >>> the EEG response to standards and targets that simply reflects the >>> fact ICA removed more EEG activity in the target trials (i.e., it >>> wouldn't reflect a true difference in neural processing). >>> hope this helps, >>> -David >>> >>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: >>>> Hi all, >>>> >>>> I'm troubled by the fact that when I use ICA for blinks\eyes movements >>>> removal, I remove the relevant components also from trials that do not >>>> contain blinks\eyes movements. In order to avoid this bias we thought to >>>> combine the data before ICA ("data" structure) with the data after ICA >>>> ("dataica" structure), only in specific trials, as follows: >>>> >>>> datall=dataica; >>>> datall.trial=data.trial; >>>> datall.time=data.time; >>>> blinks=[2 4 5 8 bla bla 156]; >>>> for ind=1:length(blinks) >>>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>>> end >>>> >>>> To my first question: I just wanted to check that there is no problem with >>>> that, or any reason not to use it. >>>> >>>> Another issue- I use motor learning task, and I'm trying to understand what >>>> happens through the process, in terms of power-frequency changes through the >>>> process. How would you recommend that I'd use the ft_freqanalysis function? >>>> What method to use (or what do I need to consider when choosing the method >>>> field)? >>>> >>>> >>>> Thanks a lot, >>>> Odelia. >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> David Groppe, Ph.D. >>> Postdoctoral Researcher >>> Kutaslab >>> Dept. of Cognitive Science >>> University of California, San Diego >>> http://www.cogsci.ucsd.edu/~dgroppe/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://homepage.mac.com/jdien07/ >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> Alexander J. Shackman, Ph.D. >> Wisconsin Psychiatric Institute & Clinics and >> Department of Psychology >> University of Wisconsin-Madison >> 1202 West Johnson Street >> Madison, Wisconsin 53706 >> >> Telephone: +1 (608) 358-5025 >> Fax: +1 (608) 265-2875 >> Email: shackman at wisc.edu >> http://psyphz.psych.wisc.edu/~shackman >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email: stefan.debener at uni-oldenburg.de > _______________________________________________ > 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 yuvharpaz at gmail.com Fri May 27 05:40:14 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 27 May 2011 06:40:14 +0300 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Message-ID: Dear discussion group Did anybody consider smoothing or filtering the component trace before rejecting it? it seems that the added noise to no-blink trials is in a frequency higher than that typical to blinks. what if we evaluate the component weight, creating a trace for the eyeblink component for every trial, then bandpass filter the blink trace , say 0.1-25Hz, and only then remove the component from the data? yuval On 27 May 2011 06:16, Joseph Dien wrote: > Stefan, just to be clear, I don't think any of us were saying not to use > ICA to correct blinks. David was just saying that there are potential > concerns when one only applies the ICA to the blink trials rather than to > all the trials. I myself use EEGlab's infomax implementation in the > automatic eyeblink correction tool of my EP Toolkit ( > http://sourceforge.net/projects/erppcatoolkit/). > > Now that said, I should add a little more nuance to my response. One of > the things I observed (or rather, that Tim Curran pointed out to me) is that > when you apply ICA to remove eyeblink artifacts in this manner, it can > actually substantially increase the noise level in the data, so for the > trials without eyeblinks it can have a considerable cost. So in order to > balance the cost/benefit ratio, what I did was to include a trial by trial > criterion that the putative eyeblink factors would only be removed if doing > so reduced the overall variance of the trial. This approach does still have > some potential for causing the concerns that David raises but not as much as > only applying the ICA to blink trials since it does end up getting applied > to non-blink trials too. This does mean that one should be cautious about > any apparent effects in the artifact corrected data that are centered around > the eyes (that have a blink topography) but that goes without saying in any > case. So anyway, I agree, it's not perfect but seems to be the best > available option. > > Cheers! > > Joe > > On May 24, 2011, at 3:11 AM, Stefan Debener wrote: > > Hi Odelia, > > I have a slightly different opinion here. It is certainly true that any > filter has the tendency to distort data (with distortion I mean that data > consists of a mixture of some wanted, true signal and some unwanted signal, > and that the removal of the unwanted part of the signal is neither complete > nor specific). In our lab we regularly use ICA for artefact removal (and > more), and the benefit/gain is clearly are much larger than the distortion. > In fact there are a number of examples out showing that currently only ICA > (or related tools) can recover the study of (a substantial fraction of the > wanted) EEG signal (but again, it is NOT a perfect tool at all), in > particular in cases where other means of SNR enhancement don't work well > (averaging, spectral analysis). I am happy to provide references if you are > interested... > > For the evaluation of outcome it would be reasonable to not evaluate the > ERP alone, as this could be misleading. Better evaluate the sensitivity and > specificity of an eye blink attentuation approach on the single trial (and > single subject) level, this will give you good insight. And it is worth > keeping in mind that the preprocessing of the data (among other issues, like > the quality of the recording and so on) largely determines the quality of > the output (for some introduction you may look up chapter 3.1 in Ullsperger > & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just > by a different preprocessing ICA output could vary between crap and > excellent unmixing. Thus a poor ICA eye blink attenuation would make me a > bit suspicious... > > Best, > Stefan > > > Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: > > And for a related perspective, see > > McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. > (2011). Electromyogenic artifacts and electroencephalographic inferences > revisited, *Neuroimage**, 54*, 4-9. > > http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf > > > On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: > >> I agree with David's reasoning. You may find the following article to >> be of help as well in understanding the issues involved: >> >> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of >> simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping*, >> 28(8), 742-763. >> >> Cheers! >> >> Joe >> >> On May 23, 2011, at 11:57 AM, David Groppe wrote: >> >> Hi Odelia, >> When you use ICA (or any other spatial filter) to correct for EEG >> artifacts, you're going to distort your data some by removing true EEG >> activity in addition to the artifact (for an explanation, see: >> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >> So to minimize distortion, it would be better not to apply ICA >> artifact correction to artifact-free data. However, if the frequency >> of the artifact differs across experimental conditions, it could >> confound your analysis. For example, I suspect people blink more >> often to targets in an oddball experiment than standards. Thus if you >> apply ICA only to blinky trials, you could find a difference between >> the EEG response to standards and targets that simply reflects the >> fact ICA removed more EEG activity in the target trials (i.e., it >> wouldn't reflect a true difference in neural processing). >> hope this helps, >> -David >> >> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >> wrote: >> >> Hi all, >> >> >> I'm troubled by the fact that when I use ICA for blinks\eyes movements >> >> removal, I remove the relevant components also from trials that do not >> >> contain blinks\eyes movements. In order to avoid this bias we thought to >> >> combine the data before ICA ("data" structure) with the data after ICA >> >> ("dataica" structure), only in specific trials, as follows: >> >> >> datall=dataica; >> >> datall.trial=data.trial; >> >> datall.time=data.time; >> >> blinks=[2 4 5 8 bla bla 156]; >> >> for ind=1:length(blinks) >> >> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >> >> end >> >> >> To my first question: I just wanted to check that there is no problem >> with >> >> that, or any reason not to use it. >> >> >> Another issue- I use motor learning task, and I'm trying to understand >> what >> >> happens through the process, in terms of power-frequency changes through >> the >> >> process. How would you recommend that I'd use the ft_freqanalysis >> function? >> >> What method to use (or what do I need to consider when choosing the method >> >> field)? >> >> >> >> Thanks a lot, >> >> Odelia. >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> >> -- >> David Groppe, Ph.D. >> Postdoctoral Researcher >> Kutaslab >> Dept. of Cognitive Science >> University of California, San Diego >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://homepage.mac.com/jdien07/ >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> > > > -- > Alexander J. Shackman, Ph.D. > Wisconsin Psychiatric Institute & Clinics and > Department of Psychology > University of Wisconsin-Madison > 1202 West Johnson Street > Madison, Wisconsin 53706 > > Telephone: +1 (608) 358-5025 > Fax: +1 (608) 265-2875 > Email: shackman at wisc.edu > http://psyphz.psych.wisc.edu/~shackman > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email: stefan.debener at uni-oldenburg.de > > _______________________________________________ > 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 > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahesh.casiraghi at gmail.com Fri May 27 06:32:01 2011 From: mahesh.casiraghi at gmail.com (Mahesh Casiraghi) Date: Fri, 27 May 2011 00:32:01 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Message-ID: Dear Yuval and discussion group, it seems to me that what you are proposing is getting close to what proposed by the hybrid approach of regica described here: *Manousos A. Klados, Christos Papadelis, Christoph Braun, Panagiotis D. Bamidis, REG-ICA: A hybrid methodology combining Blind Source Separation and regression techniques for the rejection of ocular artifacts, Biomedical Signal Processing and Control, In Press, Corrected Proof, Available online 16 March 2011, ISSN 1746-8094, DOI: 10.1016/j.bspc.2011.02.001.* They suggest to selectively run regression based AR only on those components which correlate with EOG signals. This makes sense to me and I have been trying to experiment that on some old data, although with no clear conclusions yet. It may be worth a try for Odelia: Anybody out there with some insights for this - or maybe a similar - approach? Cheers, Mahesh Mahesh M. Casiraghi PhD candidate - Cognitive Sciences Roberto Dell'Acqua Lab, University of Padova Pierre Jolicoeur Lab, Univesité de Montréal mahesh.casiraghi at umontreal.ca I have the conviction that when Physiology will be far enough advanced, the poet, the philosopher, and the physiologist will all understand each other. Claude Bernard On Thu, May 26, 2011 at 11:40 PM, Yuval Harpaz wrote: > Dear discussion group > Did anybody consider smoothing or filtering the component trace before > rejecting it? > it seems that the added noise to no-blink trials is in a frequency higher > than that typical to blinks. what if we evaluate the component weight, > creating a trace for the eyeblink component for every trial, then bandpass > filter the blink trace , say 0.1-25Hz, and only then remove the component > from the data? > yuval > > On 27 May 2011 06:16, Joseph Dien wrote: > >> Stefan, just to be clear, I don't think any of us were saying not to use >> ICA to correct blinks. David was just saying that there are potential >> concerns when one only applies the ICA to the blink trials rather than to >> all the trials. I myself use EEGlab's infomax implementation in the >> automatic eyeblink correction tool of my EP Toolkit ( >> http://sourceforge.net/projects/erppcatoolkit/). >> >> Now that said, I should add a little more nuance to my response. One of >> the things I observed (or rather, that Tim Curran pointed out to me) is that >> when you apply ICA to remove eyeblink artifacts in this manner, it can >> actually substantially increase the noise level in the data, so for the >> trials without eyeblinks it can have a considerable cost. So in order to >> balance the cost/benefit ratio, what I did was to include a trial by trial >> criterion that the putative eyeblink factors would only be removed if doing >> so reduced the overall variance of the trial. This approach does still have >> some potential for causing the concerns that David raises but not as much as >> only applying the ICA to blink trials since it does end up getting applied >> to non-blink trials too. This does mean that one should be cautious about >> any apparent effects in the artifact corrected data that are centered around >> the eyes (that have a blink topography) but that goes without saying in any >> case. So anyway, I agree, it's not perfect but seems to be the best >> available option. >> >> Cheers! >> >> Joe >> >> On May 24, 2011, at 3:11 AM, Stefan Debener wrote: >> >> Hi Odelia, >> >> I have a slightly different opinion here. It is certainly true that any >> filter has the tendency to distort data (with distortion I mean that data >> consists of a mixture of some wanted, true signal and some unwanted signal, >> and that the removal of the unwanted part of the signal is neither complete >> nor specific). In our lab we regularly use ICA for artefact removal (and >> more), and the benefit/gain is clearly are much larger than the distortion. >> In fact there are a number of examples out showing that currently only ICA >> (or related tools) can recover the study of (a substantial fraction of the >> wanted) EEG signal (but again, it is NOT a perfect tool at all), in >> particular in cases where other means of SNR enhancement don't work well >> (averaging, spectral analysis). I am happy to provide references if you are >> interested... >> >> For the evaluation of outcome it would be reasonable to not evaluate the >> ERP alone, as this could be misleading. Better evaluate the sensitivity and >> specificity of an eye blink attentuation approach on the single trial (and >> single subject) level, this will give you good insight. And it is worth >> keeping in mind that the preprocessing of the data (among other issues, like >> the quality of the recording and so on) largely determines the quality of >> the output (for some introduction you may look up chapter 3.1 in Ullsperger >> & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just >> by a different preprocessing ICA output could vary between crap and >> excellent unmixing. Thus a poor ICA eye blink attenuation would make me a >> bit suspicious... >> >> Best, >> Stefan >> >> >> Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: >> >> And for a related perspective, see >> >> McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. >> (2011). Electromyogenic artifacts and electroencephalographic inferences >> revisited, *Neuroimage**, 54*, 4-9. >> >> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf >> >> >> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: >> >>> I agree with David's reasoning. You may find the following article to >>> be of help as well in understanding the issues involved: >>> >>> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA >>> of simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping >>> *, 28(8), 742-763. >>> >>> Cheers! >>> >>> Joe >>> >>> On May 23, 2011, at 11:57 AM, David Groppe wrote: >>> >>> Hi Odelia, >>> When you use ICA (or any other spatial filter) to correct for EEG >>> artifacts, you're going to distort your data some by removing true EEG >>> activity in addition to the artifact (for an explanation, see: >>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >>> So to minimize distortion, it would be better not to apply ICA >>> artifact correction to artifact-free data. However, if the frequency >>> of the artifact differs across experimental conditions, it could >>> confound your analysis. For example, I suspect people blink more >>> often to targets in an oddball experiment than standards. Thus if you >>> apply ICA only to blinky trials, you could find a difference between >>> the EEG response to standards and targets that simply reflects the >>> fact ICA removed more EEG activity in the target trials (i.e., it >>> wouldn't reflect a true difference in neural processing). >>> hope this helps, >>> -David >>> >>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >>> wrote: >>> >>> Hi all, >>> >>> >>> I'm troubled by the fact that when I use ICA for blinks\eyes movements >>> >>> removal, I remove the relevant components also from trials that do not >>> >>> contain blinks\eyes movements. In order to avoid this bias we thought to >>> >>> combine the data before ICA ("data" structure) with the data after ICA >>> >>> ("dataica" structure), only in specific trials, as follows: >>> >>> >>> datall=dataica; >>> >>> datall.trial=data.trial; >>> >>> datall.time=data.time; >>> >>> blinks=[2 4 5 8 bla bla 156]; >>> >>> for ind=1:length(blinks) >>> >>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>> >>> end >>> >>> >>> To my first question: I just wanted to check that there is no problem >>> with >>> >>> that, or any reason not to use it. >>> >>> >>> Another issue- I use motor learning task, and I'm trying to understand >>> what >>> >>> happens through the process, in terms of power-frequency changes through >>> the >>> >>> process. How would you recommend that I'd use the ft_freqanalysis >>> function? >>> >>> What method to use (or what do I need to consider when choosing the >>> method >>> >>> field)? >>> >>> >>> >>> Thanks a lot, >>> >>> Odelia. >>> >>> >>> _______________________________________________ >>> >>> fieldtrip mailing list >>> >>> fieldtrip at donders.ru.nl >>> >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> >>> -- >>> David Groppe, Ph.D. >>> Postdoctoral Researcher >>> Kutaslab >>> Dept. of Cognitive Science >>> University of California, San Diego >>> http://www.cogsci.ucsd.edu/~dgroppe/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://homepage.mac.com/jdien07/ >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >> >> >> -- >> Alexander J. Shackman, Ph.D. >> Wisconsin Psychiatric Institute & Clinics and >> Department of Psychology >> University of Wisconsin-Madison >> 1202 West Johnson Street >> Madison, Wisconsin 53706 >> >> Telephone: +1 (608) 358-5025 >> Fax: +1 (608) 265-2875 >> Email: shackman at wisc.edu >> http://psyphz.psych.wisc.edu/~shackman >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Prof. Dr. Stefan Debener >> Neuropsychology Lab >> Department of Psychology >> University of Oldenburg >> D-26111 Oldenburg >> Germany >> >> Office: A7 0-038 >> Phone: +49-441-798-4271 >> Fax: +49-441-798-5522 >> Email: stefan.debener at uni-oldenburg.de >> >> _______________________________________________ >> 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 >> > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > *"Many were increasingly of the opinion that they'd all made a big mistake > in coming down from the trees in the first place. And some said that even > the trees had been a bad move, and that no one should ever have left the > oceans". Douglas Adams > * > > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri May 27 08:19:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 27 May 2011 08:19:02 +0200 Subject: [FieldTrip] duplicate spm directories In-Reply-To: References: Message-ID: <6BA914CC-EDD4-4D85-BC49-B790FD08447E@donders.ru.nl> Dear David, Yes, you can safely remove the spm2 directory. Unless you rely in your analysis pipeline on spm2-specific stuff. The only thing I can think of here would be to read in .mnc files. Cheers, Jan-Mathijs On May 27, 2011, at 3:54 AM, David Groppe wrote: > Hi again, > I'm running the March 28th version of Fieldtrip and am getting the > following warning: > > Warning: multiple versions of SPM on your path will confuse FieldTrip >> In fieldtrip-20110328/private/warning_once at 75 > In ft_defaults at 45 > In ft_preprocessing at 179 > Warning: one version of SPM is found here: > /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm2/spm.m >> In ft_defaults at 48 > In ft_preprocessing at 179 > Warning: one version of SPM is found here: > /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm8/spm.m > > > Can I simply remove the spm2 directory? > thanks in advance, > -D > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From akademonbrain at gmail.com Fri May 27 10:43:11 2011 From: akademonbrain at gmail.com (Aka Demon) Date: Fri, 27 May 2011 11:43:11 +0300 Subject: [FieldTrip] influences between the regions In-Reply-To: References: Message-ID: Dear experts After analyzing memory experiment EEG/MEG and source localization data, i figured out that there is little I can say about the interactions between the activated regions as I don’t have any information about the connection between the activated areas. So I was wondering if there are some useful works/tools that I can use to explorer the influences between the regions (such as information transfer from one region to the other). Thanks a lot Aka -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Fri May 27 14:26:28 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Fri, 27 May 2011 14:26:28 +0200 Subject: [FieldTrip] tutorial - ft_volumenormalise Message-ID: Dear Fieldtrippers, I am running the tutorial on how to localize oscillatory sources using beamformer techniques. It works smooth until I have to normalize the anatomical mri to the template. When, after I load the already-segmented subject file, I run ft_volumenormalise it says the following: ??? Attempted to access V.dim(4); index out of bounds because numel(V.dim)=3. Error in ==> spm_create_vol>create_vol at 94 swapped = spm_type(V.dim(4),'swapped'); Interestingly this is the same error I get when I try to run ft_volumesegment both using the tutorial and my anatomical MRIs. Has someone any idea? Am I doing something silly? Thank you so much, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Sat May 28 01:13:43 2011 From: rapela at ucsd.edu (=?iso-8859-1?Q?Joaqu=EDn_Rapela?=) Date: Fri, 27 May 2011 16:13:43 -0700 (PDT) Subject: [FieldTrip] lead field without with no MRI Message-ID: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> Dear all, I want to compute a lead field matrix but I have no MRI scan of my subjects. I would be happy with a concentric spheres model, or similar, adjusted to the electrodes locations (modified 10 20 system). I would be very grateful if somebody directs me to the appropriate functions in FieldTrip. My apologizes if this is a naive question. I am new to FieldTrip. Thanks in advance, Joaquin -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel/fax: (858) 822-7536 http://www-scf.usc.edu/~rapela ---------------------------------- There are men who struggle for a day and they are good. There are men who struggle for a year and they are better. There are men who struggle many years, and they are better still. But there are those who struggle all their lives: These are the indispensable ones. Bertolt Brecht From michael.wibral at web.de Sun May 29 09:26:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Sun, 29 May 2011 09:26:47 +0200 (CEST) Subject: [FieldTrip] influences between the regions Message-ID: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Sun May 29 21:38:50 2011 From: rapela at ucsd.edu (=?iso-8859-1?Q?Joaqu=EDn_Rapela?=) Date: Sun, 29 May 2011 12:38:50 -0700 (PDT) Subject: [FieldTrip] lead field with no MRI In-Reply-To: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> References: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> Message-ID: <46100.137.110.37.196.1306697930.squirrel@acs-webmail.ucsd.edu> Below I describe how to compute the leadfield matrix adjusted to a set of electrodes in an extended 10-20 system, without having an MRI image. Besides, I have a question: why in the help of the fieldtrip functions their output is not described? Cordially, Joaquin I had to dig into the EEGLAB Dipfit plugin to learn how to do this. I used the function ft_prepare_leadfield. It requires a head model and the channel locations. Since I have an extended 10-20 electrode system, I used a BEM head model that comes with Dipfit, and also uses an extended 10-20 system. This head model is in the plugins directory of dipfit2.2: hdmFile=/usr/local/eeglab/plugins/dipfit2.2/standard_BEM/standard_vol.mat and the channel locations for this head model are also in the dipfit2.2 directory: hmChanfile=/usr/local/eeglab/plugins/dipfit2.2/standard_BEM/elec/standard_1005.elc It turns out that the previous head model is not ready for ft_prepare_leadfield, and I had to use the function ft_prepare_vol_sens to prepare it. Also, I wanted to compute the leadfield matrix only for the channels in my data set, whose labels are in the variable dsChanlabels, so I passed dsChanlabels as the argument 'channel' of ft_prepare_vol_sens. Finally, I used the head model and sensors prepared by ft_prepare_vol_sens as input to ft_prepare_headmodel. I append the code that does the job. If you see any bug, please let me know. Warmly, Joaquin ### function grid = joacosPrepareLeadfield(dsChanlabels, hmChanfile, hdmFile) cfg = []; vol = ft_read_vol(hdmFile); sens = ft_read_sens(hmChanfile); [vol, sens] = ft_prepare_vol_sens(vol, sens, 'channel', dsChanlabels); cfg = []; cfg.elec = sens; cfg.vol = vol; cfg.grid.resolution = 20; data = []; grid = ft_prepare_leadfield(cfg, data); ### > Dear all, > > I want to compute a lead field matrix but I have no MRI scan of my > subjects. I would be happy with a concentric spheres model, or similar, > adjusted to the electrodes locations (modified 10 20 system). I would be > very grateful if somebody directs me to the appropriate functions in > FieldTrip. My apologizes if this is a naive question. I am new to > FieldTrip. > > Thanks in advance, Joaquin > > -- > Joaquin Rapela, PhD > Swartz Center for Computational Neuroscience > University of California San Diego > 9500 Gilman Drive, > San Diego, CA 92093-0559 > tel/fax: (858) 822-7536 > http://www-scf.usc.edu/~rapela > ---------------------------------- > > There are men who struggle for a day and they are good. > There are men who struggle for a year and they are better. > There are men who struggle many years, and they are better still. > But there are those who struggle all their lives: > These are the indispensable ones. > > Bertolt > Brecht > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel/fax: (858) 822-7536 http://www-scf.usc.edu/~rapela ---------------------------------- There are men who struggle for a day and they are good. There are men who struggle for a year and they are better. There are men who struggle many years, and they are better still. But there are those who struggle all their lives: These are the indispensable ones. Bertolt Brecht From Elena.Orekhova at neuro.gu.se Mon May 30 13:08:29 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 30 May 2011 11:08:29 +0000 Subject: [FieldTrip] SAM beamformeing on Neuromag data Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA679@exchccr1.neuro.gu.se> Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Mon May 30 14:08:08 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 30 May 2011 14:08:08 +0200 (CEST) Subject: [FieldTrip] SAM beamformeing on Neuromag data Message-ID: <1443619351.1500061.1306757288215.JavaMail.fmail@mwmweb072> An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Mon May 30 16:30:34 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 30 May 2011 14:30:34 +0000 Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA6D6@exchccr1.neuro.gu.se> Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From tobiasnavarroschroeder at googlemail.com Mon May 30 17:58:32 2011 From: tobiasnavarroschroeder at googlemail.com (Tobias Navarro Schroeder) Date: Mon, 30 May 2011 17:58:32 +0200 Subject: [FieldTrip] Beamforming on resting state data In-Reply-To: References: Message-ID: Hi Fieldtrippers, I performed DICS beamforming on resting-state data (i.e. no task, no baseline, eyes closed) of a clinical population and controls. According to the sensor data the patients have more gamma-band (60-90 Hz) activity over temporal areas (somewhat spread-out). Curiously, after beamforming and group comparisons with 'indepsamplesT' permutation statistics the difference map shows more gamma-band (60-90 Hz) activity for controls in the left, middle-temporal gyrus. Hence, the source-level results are opposite to the sensor-level results (although more spatially confined). This is *not* a problem of the design matrix, or confusing the groups. Question 1: Does anybody have experience with opposite results on source and sensor level? The individual raw beamforming results (interpolated on the subjects' MRIs) look suspicios as well. Due to the 'unit gain constraint' there should be an overestimation of power in the center of the head, but only a minority of subjects show that. Often I see temporal or parietal activity. Question 2: Would a lack of a blob in the center of the head in individual, raw, beamforming data indicate an erroneous source analysis? Thanks a lot for help and suggestions. Best, Tobias Navarro Schröder ps: The configurations for calculating the covariance and the beamforming is added below: 1) % Compute the covariance matrices cfg.output = 'powandcsd'; cfg.foi = 75; cfg.foilim = [75 75]; cfg.tapsmofrq = 15; % 75 +- 15 = 60 - 90 Hz cfg.pad = 'maxperlen'; % default cfg.method = 'wltconvol'; % wavelet analysis cfg.width = 5; % Width of the wavelet. Determines the temporal and spectral resolution of the analysis constant. 2) % Perform the actual beamforming % load grids of MRI volume fullnameGrid = [ CurSubject.mripath CurSubject.MRIModel]; cfg = load(fullnameGrid); cfg.vol = cfg.hdm; cfg.frequency = 75; cfg.method = 'dics'; cfg.keepfilter = 'yes'; % keep the beamformer filters (virtual electrodes) for later use cfg.keeptrial = 'no'; cfg.keepmom = 'yes'; % useful for connectivity calculations. Dipole moments.. cfg.projectmom = 'yes'; cfg.projectnoise = 'yes'; cfg.latency = 1; -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Mon May 30 17:58:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 30 May 2011 17:58:47 +0200 (CEST) Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> An HTML attachment was scrubbed... URL: From Tim.Bardouille at nrc-cnrc.gc.ca Mon May 30 18:23:22 2011 From: Tim.Bardouille at nrc-cnrc.gc.ca (Bardouille, Tim) Date: Mon, 30 May 2011 12:23:22 -0400 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: Hi Michael, Elena, If it becomes a sticking point, you could also run MaxFilter with the -nosss option. I don't have any experience with how this would affect the beamformer output, but it would at least resolve the rank issue. Tim. --------------------------------------------------------- Timothy Bardouille, PhD, Research Officer Laboratory for Clinical MEG NRC Institute for Biodiagnostics (Atlantic) Office: Halifax Infirmary 3900 - 1796 Summer Street Halifax, Nova Scotia B3H 3A7 Phone: 902-473-1865 Lab: 902-470-3936 Fax: 902-473-1851 --------------------------------------------------------- ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Michael Wibral [michael.wibral at web.de] Sent: May 30, 2011 12:58 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon May 30 21:27:13 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 30 May 2011 21:27:13 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> Hi Michael, Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? Best, Stephan El 30/05/2011, a las 17:58, Michael Wibral escribió: > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the > maxfilter papers the properties of the components removed by the > maxfilter do not require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a > tiny amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please > let me know!) > > > Michael > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 4:30:34 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since > MaxFilter reduces the rank of the covariance matrix by removing > noisy components, it may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de > ] > Sent: Monday, May 30, 2011 2:08 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the > different UNITS (not only scales) of gradiometers and magnetometers. > There was a problem with the sign of the leadfields but that should > have been fixed. > > There is one more fundamental problem however, that you should be > aware of (doesn't invalidate your source analysis but bears > potential for fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your > source signal back with unit gain. Added on top however is > neurophysiological crosstalk (minimized) and sensor noise of the > sensors with the largest weights in your Beamformer (not reducible). > So different sensor types willhave different (inverse) leadfield > strengths, theerfore also fiofefrent source noise levels. the > relative benefits of each sensor type changes from location to > location, so a location (and data) dependend weighting would in > principle be best. > I am not sure if and how this is implemented if FT (Bayesian > weighting would be optimal here..) > > What you could do as a first step is to beam separately and compare > the results. > > Michael > > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 1:08:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face > { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font- > family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal > { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: > Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font- > family: Courier; }span.HTMLPreformattedChar { font-family: > Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 > { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E > \671D "; }@font-face { font-family: "Cambria Math"; }@font-face > { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal > { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: > Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font- > family: Courier; }span.HTMLPreformattedChar { font-family: > Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 > { page: WordSection1; } > Dear All, > > I try to run beamformer analysis on the auditory MEG data (Neuromag) > and have basic questions. > > > 1.Magnetometers and gradiometers Neuromag sensors have different > scales. Does the Fieldtrip take care of this difference or should I > normalize the data? It yes, how to normalize? > > > 2. I would like to do SAM analysis of evoked field and look at the > time courses at ROIs (virtual channels). The only tutorial example > I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer) > . I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method > = 'sam'. > > > I would be most grateful for any example script of this type analysis! > > Regards, > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jstout211 at yahoo.com Mon May 30 23:28:16 2011 From: jstout211 at yahoo.com (Jeff Stout) Date: Mon, 30 May 2011 14:28:16 -0700 (PDT) Subject: [FieldTrip] MEGRealign channel Message-ID: <365289.7941.qm@web113516.mail.gq1.yahoo.com> Hi All, I am having trouble using the ft_megrealign command with a 4D Magnes 3600 system.  I am trying to use this command to interpolate bad channels that have been removed in preprocessing.  When I view the output of megrealign using ft_plot_sens, sensor 'A229' is badly misplaced (approximately 10 cm above the top of the sensor array), but all the other sensors appear appropriate.  In the dataset A229 has not been labelled as a bad channel, nor any of its neighboring channels. The location of A229 is significant in that it is the most inferior/anterior channel on the left side.  I am using the original grad file as a template input using ft_read_sens('c,rfDC') and scaling the MEG channels to cm.  I am not sure how helpful the code is - below is my input and some of the output.  I can provide an image if this would be helpful. temp = ft_read_sens(subjectdata.FA_dataset); temp.pnt = temp.pnt*100; temp.unit  = 'cm'; cfg = []; cfg.inwardshift = 1; cfg.vol=vol; cfg.template{1}= temp; cfg.channel={'MEG'}; con.grad.pnt = con.grad.pnt*100; con.grad.unit = 'cm'; con = ft_megrealign(cfg, con) computing surface normals mean distance towards template gradiometers is 0.00 cm creating dipole grid based on inward-shifted brain surface from volume conductor model Warning: the normals of the surface triangulation are inward oriented  > In fieldtrip-20110507/private/headsurface at 211   In ft_prepare_sourcemodel at 492   In ft_megrealign at 245 642 dipoles inside, 0 dipoles outside brain computing forward model for 642 dipoles pruning 122 from 246, i.e. removing the 122 smallest spatial components computing interpolation matrix #1 computing interpolation matrix #2 computing interpolation matrix #3 pruning 124 from 248, i.e. removing the 124 smallest spatial components realigning trial 1 original -> template             RV 14.42 % original             -> original RV 14.42 % original -> template -> original RV 14.44 % .................... Does anyone know why this would be occurring and how to fix it? Thanks, Jeff Stout -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 31 09:04:26 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 31 May 2011 09:04:26 +0200 Subject: [FieldTrip] MEGRealign channel In-Reply-To: <365289.7941.qm@web113516.mail.gq1.yahoo.com> References: <365289.7941.qm@web113516.mail.gq1.yahoo.com> Message-ID: <012FDE87-5002-4626-B821-D83AAC043C59@donders.ru.nl> Hi Jeff, Thanks for reporting this. We'll look into it as soon as possible. Best wishes, Jan-Mathijs On May 30, 2011, at 11:28 PM, Jeff Stout wrote: > > Hi All, > > I am having trouble using the ft_megrealign command with a 4D Magnes > 3600 system. I am trying to use this command to interpolate bad > channels that have been removed in preprocessing. When I view the > output of megrealign using ft_plot_sens, sensor 'A229' is badly > misplaced (approximately 10 cm above the top of the sensor array), > but all the other sensors appear appropriate. In the dataset A229 > has not been labelled as a bad channel, nor any of its neighboring > channels. The location of A229 is significant in that it is the most > inferior/anterior channel on the left side. I am using the original > grad file as a template input using ft_read_sens('c,rfDC') and > scaling the MEG channels to cm. I am not sure how helpful the code > is - below is my input and some of the output. I can provide an > image if this would be helpful. > > > temp = ft_read_sens(subjectdata.FA_dataset); > temp.pnt = temp.pnt*100; > temp.unit = 'cm'; > > cfg = []; > cfg.inwardshift = 1; > cfg.vol=vol; > cfg.template{1}= temp; > cfg.channel={'MEG'}; > con.grad.pnt = con.grad.pnt*100; > con.grad.unit = 'cm'; > con = ft_megrealign(cfg, con) > > computing surface normals > mean distance towards template gradiometers is 0.00 cm > creating dipole grid based on inward-shifted brain surface from > volume conductor model > Warning: the normals of the surface triangulation are inward oriented > > In fieldtrip-20110507/private/headsurface at 211 > In ft_prepare_sourcemodel at 492 > In ft_megrealign at 245 > 642 dipoles inside, 0 dipoles outside brain > computing forward model for 642 dipoles > pruning 122 from 246, i.e. removing the 122 smallest spatial > components > computing interpolation matrix #1 > computing interpolation matrix #2 > computing interpolation matrix #3 > pruning 124 from 248, i.e. removing the 124 smallest spatial > components > realigning trial 1 > original -> template RV 14.42 % > original -> original RV 14.42 % > original -> template -> original RV 14.44 % .................... > > > Does anyone know why this would be occurring and how to fix it? > > Thanks, > Jeff Stout > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Nina.Kahlbrock at uni-duesseldorf.de Tue May 31 09:23:51 2011 From: Nina.Kahlbrock at uni-duesseldorf.de (Nina Kahlbrock) Date: Tue, 31 May 2011 09:23:51 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> Message-ID: <001301cc1f63$b0faedc0$cd136386@VMED.UKD> Hi Stephan, you can find the discussion list at: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG Best, Nina _____ Von: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] Im Auftrag von Stephan Moratti Gesendet: Montag, 30. Mai 2011 21:27 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Michael, Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? Best, Stephan El 30/05/2011, a las 17:58, Michael Wibral escribió: Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael _____ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena _____ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael _____ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Tue May 31 11:42:21 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Tue, 31 May 2011 11:42:21 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <001301cc1f63$b0faedc0$cd136386@VMED.UKD> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> <001301cc1f63$b0faedc0$cd136386@VMED.UKD> Message-ID: Hallo Nina, Vielen Dank !!! Stephan El 31/05/2011, a las 09:23, Nina Kahlbrock escribió: > Hi Stephan, > > you can find the discussion list at: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG > > Best, > Nina > > Von: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] Im Auftrag von Stephan Moratti > Gesendet: Montag, 30. Mai 2011 21:27 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Hi Michael, > > Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? > > Best, > > Stephan > > El 30/05/2011, a las 17:58, Michael Wibral escribió: > > > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please let me know!) > > > Michael > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 4:30:34 PM > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] > Sent: Monday, May 30, 2011 2:08 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. > > There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. > I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) > > What you could do as a first step is to beam separately and compare the results. > > Michael > > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 1:08:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear All, > I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. > > 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? > > 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. > > > I would be most grateful for any example script of this type analysis! > > Regards, > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Department of Basic Psychology > Universidad Complutense de Madrid > > Centro de Tecnología Biomédica CBT, > Universidad Politécnica de Madrid, > > en la actualidad (currently at) en el > Centro de Magnetoencefalografía Dr. Perez Modrego, > Universidad Complutense de Madrid, > Faculdad de Medicina, > Pabellón 8, > Avda. Complutense, s/n, > 28040 Madrid, > Spain, > > email: smoratti at psi.ucm.es > Tel.: +34 91 394 2186 > Fax.: +34 91 394 2294 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Tue May 31 12:06:40 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Tue, 31 May 2011 10:06:40 +0000 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> Hi Michael, > If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. What lambda you would recommend? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 5:58 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuvharpaz at gmail.com Tue May 31 12:42:53 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Tue, 31 May 2011 13:42:53 +0300 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> Message-ID: Dear Elena and group it basically depends on how much co-variability there is. if you use a large frequency range and a large strech of time you need to correct little if any. if you use averaged data and say from 50 to 120ms from target onset you need more regularization. I used 5% even for relatively short time interval (but large freq. range) and found it reasonable. yuval On 31 May 2011 13:06, Elena Orekhova wrote: > Hi Michael, > > > > If you run into rank-deficiency issue with the covariance matrix a tiny > amount of regularization should fix this. > > What lambda you would recommend? > > Elena > > > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Michael Wibral [michael.wibral at web.de] > *Sent:* Monday, May 30, 2011 5:58 PM > > *To:* Email discussion list for the FieldTrip project > *Subject:* Re: [FieldTrip] SAM beamforming on Neuromag data > > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the maxfilter > papers the properties of the components removed by the maxfilter do not > require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a tiny > amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please let me > know!) > > > Michael > > ------------------------------ > *Von:* "Elena Orekhova" > *Gesendet:* May 30, 2011 4:30:34 PM > *An:* "Email discussion list for the FieldTrip project" < > fieldtrip at donders.ru.nl> > *Betreff:* Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since MaxFilter > reduces the rank of the covariance matrix by removing noisy components, it > may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Michael Wibral [michael.wibral at web.de] > *Sent:* Monday, May 30, 2011 2:08 PM > *To:* Email discussion list for the FieldTrip project > *Subject:* Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the > different UNITS (not only scales) of gradiometers and magnetometers. There > was a problem with the sign of the leadfields but that should have been > fixed. > > There is one more fundamental problem however, that you should be aware of > (doesn't invalidate your source analysis but bears potential for > fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your source > signal back with unit gain. Added on top however is neurophysiological > crosstalk (minimized) and sensor noise of the sensors with the largest > weights in your Beamformer (not reducible). So different sensor types > willhave different (inverse) leadfield strengths, theerfore also fiofefrent > source noise levels. the relative benefits of each sensor type changes from > location to location, so a location (and data) dependend weighting would in > principle be best. > I am not sure if and how this is implemented if FT (Bayesian weighting > would be optimal here..) > > What you could do as a first step is to beam separately and compare the > results. > > Michael > > > ------------------------------ > *Von:* "Elena Orekhova" > *Gesendet:* May 30, 2011 1:08:29 PM > *An:* "fieldtrip at donders.ru.nl" > *Betreff:* [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { > font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: > "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm > 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm > 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar > { font-family: Courier; }.MsoChpDefault { font-family: Cambria; > }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D > \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face > { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { > margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { > margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; > }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { > font-family: Cambria; }div.WordSection1 { page: WordSection1; } > > Dear All, > > I try to run beamformer analysis on the auditory MEG data (Neuromag) and > have basic questions. > > > > 1.Magnetometers and gradiometers Neuromag sensors have different scales. > Does the Fieldtrip take care of this difference or should I normalize the > data? It yes, how to normalize? > > > > 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. > > > > I would be most grateful for any example script of this type analysis! > > > > Regards, > > Elena > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- sent from my 4-year-old PC. poor fellow, only ipod classic, no mail there. Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Tue May 31 12:44:50 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 31 May 2011 12:44:50 +0200 (CEST) Subject: [FieldTrip] Beamforming on resting state data Message-ID: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> An HTML attachment was scrubbed... URL: From tobiasnavarroschroeder at googlemail.com Tue May 31 14:12:48 2011 From: tobiasnavarroschroeder at googlemail.com (Tobias Navarro Schroeder) Date: Tue, 31 May 2011 14:12:48 +0200 Subject: [FieldTrip] Beamforming on resting state data In-Reply-To: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> References: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> Message-ID: Hi Michael, thanks a lot for that suggestion. The gamma activity at the sensor level might indeed be of muscular origin and this would explain why it doesn't show up inside the head. Even after automatic & manual artifact rejection the patients were left with more gamma activity. To my 'untrained eye' the sensor topographies suggested that the activity would come from the brain. It didn't extend to the boundaries of the Topoplot, at least in the 60-90 Hz range. However, this was the case for other parts of the gamma-band. Greetings, Tobias On Tue, May 31, 2011 at 12:44 PM, Michael Wibral wrote: > Hi Tobias, > > it could be that the temporal activity at the sensor level is of muscular > origin. Given all runs well in beamforming you shouldn't see too much of > that insode the head - have you considered this possibility? > > Michael > > > > ------------------------------ > *Von:* "Tobias Navarro Schroeder" > *Gesendet:* May 30, 2011 5:58:32 PM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] Beamforming on resting state data > > > Hi Fieldtrippers, > > I performed DICS beamforming on resting-state data (i.e. no task, no > baseline, eyes closed) of a clinical population and controls. > According to the sensor data the patients have more gamma-band (60-90 > Hz) activity over temporal areas (somewhat spread-out). > Curiously, after beamforming and group comparisons with 'indepsamplesT' > permutation statistics the difference map shows more gamma-band (60-90 > Hz) activity for controls in the left, middle-temporal gyrus. > Hence, the source-level results are opposite to the sensor-level results > (although more spatially confined). This is *not* a problem of the design > matrix, or confusing the groups. > > Question 1: Does anybody have experience with opposite results on source > and sensor level? > > The individual raw beamforming results (interpolated on the subjects' MRIs) > look suspicios as well. Due to the 'unit gain constraint' there should be an > overestimation of power in the center of the head, but only a minority of > subjects show that. Often I see temporal or parietal activity. > > Question 2: > > Would a lack of a blob in the center of the head in individual, > raw, beamforming data indicate an erroneous source analysis? > > Thanks a lot for help and suggestions. > > Best, Tobias Navarro Schröder > > ps: The configurations for calculating the covariance and the beamforming > is added below: > > > > 1) % Compute the covariance matrices > > > > cfg.output = > 'powandcsd'; > > cfg.foi = 75; > > cfg.foilim = [75 75]; > > cfg.tapsmofrq = 15; % 75 +- 15 = 60 - 90 Hz > > cfg.pad = > 'maxperlen'; % default > > cfg.method = > 'wltconvol'; % wavelet analysis > > cfg.width = 5; > % Width of the wavelet. Determines the temporal and spectral resolution of > the analysis constant. > > > > 2) % Perform the actual beamforming > > % load grids of MRI volume > > fullnameGrid = [ CurSubject.mripath CurSubject.MRIModel]; > > cfg = load(fullnameGrid); > > cfg.vol = cfg.hdm; > > > > > > cfg.frequency = 75; > > cfg.method = > 'dics'; > > cfg.keepfilter = > 'yes'; % keep the beamformer filters (virtual electrodes) for later use > > cfg.keeptrial = > 'no'; > > cfg.keepmom = > 'yes'; % useful for connectivity calculations. Dipole moments.. > > cfg.projectmom = > 'yes'; > > cfg.projectnoise = > 'yes'; > > cfg.latency = 1; > > > _______________________________________________ > 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 michael.wibral at web.de Tue May 31 15:36:46 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 31 May 2011 15:36:46 +0200 (CEST) Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <1271334421.1768792.1306849006599.JavaMail.fmail@mwmweb074> An HTML attachment was scrubbed... URL: From valentin.umbach at hu-berlin.de Tue May 31 18:51:17 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Tue, 31 May 2011 18:51:17 +0200 Subject: [FieldTrip] Emotiv headset realtime capture Message-ID: Hi, I'm new to FieldTrip and I'm interested in using it to capture realtime data from the Emotiv headset using this interface: http://fieldtrip.fcdonders.nl/development/realtime/emotiv I'm not clear about how to make calls to this interface from within Matlab. Also, I would like to know if it's possible to access not just the raw EEG, but also the API output of the detection libraries (Affectiv Suite...). Any help is greatly appreciated! Best, Valentin -- Dipl.-Psych. Valentin J. Umbach Institut für Psychologie Humboldt-Universität zu Berlin Rudower Chaussee 18 12489 Berlin Tel. +49 30 2093 9438 E-Mail: valentin.umbach at hu-berlin.de From mcoskun at mail.uh.edu Tue May 31 23:09:13 2011 From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun) Date: Tue, 31 May 2011 16:09:13 -0500 Subject: [FieldTrip] Dipole Fitting Algorithm Message-ID: <726086fb76fc3.4de512a9@mail.uh.edu> Dear Fieldtrippers, I am having little trouble understanding the dipole fitting algorithm. Any comments will be greatly appreciated. 1) During dipole fitting, a model data (Vmodel) is created using the computed leadfield. How exactly this model data is computed? Is it simply the projection of the pinv'ed leadfield to the true data (Vdata)?  2) The error is computed between the model data and true data for the best dipole. Is this RMS error? 3) The last part of dipole fitting is a non-linear search. I really wonder what is the algorithm, what exactly non-linear search is doing? Thanks in advance Mehmet -------------- next part -------------- An HTML attachment was scrubbed... URL: From max.taubert at gmail.com Sun May 1 15:48:13 2011 From: max.taubert at gmail.com (Max T.) Date: Sun, 1 May 2011 15:48:13 +0200 Subject: [FieldTrip] Plotting Dipoles Message-ID: Dear all, I'd like to visualize the results of ft_dipolefitting, sadly I've got no individual MRIs. Is there any function like ft_sourceplot that can handle ft_dipolefitting-results, maybe using a template brain? Besides this, is there any function that can transform my Unit Sphere-coordinates into Talairach space? And is it possible to apply the 'adaptive spatial filter' if I dont want to use a Beamformer? Thanks in advance Max Taubert From m.severens at maartenskliniek.nl Mon May 2 13:57:17 2011 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 2 May 2011 13:57:17 +0200 Subject: [FieldTrip] adding lines in multiplot TFR Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> Dear fieldtrippers I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? Thanks in advance Best Marianne Severens Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3 6522 JV NIJMEGEN Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From jm.horschig at donders.ru.nl Mon May 2 14:10:11 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 02 May 2011 14:10:11 +0200 Subject: [FieldTrip] adding lines in multiplot TFR In-Reply-To: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl> Message-ID: <4DBE9F23.8070600@donders.ru.nl> Hi Marianne, Adding vertical lines to annotate, for example, events is not possible using ft_multiplot_XXX afaik. A similar feature is added in ft_databrowser, which however does only work for two-dimensional data (amplitude x time). One way around would be to filter your data in the desired frequency range and then use ft_databrowser. The function, however, still lacks some functionality and compatibility. Should you encounter any strange problems, feel free to contact me and we (the FT developer team) will try to improve the databrowser according to your experiences and wishes. Another, slightly less elegant way to answer your question is the following: Rutger from your group changed a fieldtrip method for his personal purposes. Unselfishly, he called the function rutgerplot_TFR. In this function, he added horizontal lines to annotate specific frequency bands. You can maybe ask him to re-write this hack to add vertical lines to annotate the events you are interested in. Hope this helps! Best, Jörn On 5/2/2011 1:57 PM, Severens, Marianne wrote: > Dear fieldtrippers > > I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. > I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? > > Thanks in advance > Best Marianne Severens > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3 > 6522 JV NIJMEGEN > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands From m.severens at maartenskliniek.nl Mon May 2 14:34:56 2011 From: m.severens at maartenskliniek.nl (Severens, Marianne) Date: Mon, 2 May 2011 14:34:56 +0200 Subject: [FieldTrip] adding lines in multiplot TFR In-Reply-To: <4DBE9F23.8070600@donders.ru.nl> References: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B6F@smkexch02.maartenskliniek.nl>, <4DBE9F23.8070600@donders.ru.nl> Message-ID: <70FC3ACFFB46314EBEAF9101EA45F50E06AE0F0B71@smkexch02.maartenskliniek.nl> Hi Jörn Thanks for your quick reply! The plots need to be TFR plots, with several frequency bins, so I think the databrowser is not really appropriate for this. I'll try to modify Rutger's solution to make the lines vertical! Best, Marianne ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Jörn M. Horschig [jm.horschig at donders.ru.nl] Sent: Monday, May 02, 2011 2:10 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] adding lines in multiplot TFR Hi Marianne, Adding vertical lines to annotate, for example, events is not possible using ft_multiplot_XXX afaik. A similar feature is added in ft_databrowser, which however does only work for two-dimensional data (amplitude x time). One way around would be to filter your data in the desired frequency range and then use ft_databrowser. The function, however, still lacks some functionality and compatibility. Should you encounter any strange problems, feel free to contact me and we (the FT developer team) will try to improve the databrowser according to your experiences and wishes. Another, slightly less elegant way to answer your question is the following: Rutger from your group changed a fieldtrip method for his personal purposes. Unselfishly, he called the function rutgerplot_TFR. In this function, he added horizontal lines to annotate specific frequency bands. You can maybe ask him to re-write this hack to add vertical lines to annotate the events you are interested in. Hope this helps! Best, Jörn On 5/2/2011 1:57 PM, Severens, Marianne wrote: > Dear fieldtrippers > > I have a question regarding the ft_multiplotTFR. Is it possible to add something to one (or more) of the subplots of the multiplot? My time axis of the TFR consists of several phases and I would like to add the transistion of one phase to the next in the plots with for example a vertical line. > I've tried to find the axes of the individual subplots, but these don't seem to exist. Has someone already tried something like this? > > Thanks in advance > Best Marianne Severens > > Disclaimer > Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. > > Sint Maartenskliniek > Hengstdal 3 > 6522 JV NIJMEGEN > Telefoon 024-3659 911 > Telefax 024-3659 204 > KvK nummer 41055111 > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Disclaimer Vrijgave van de informatie verzonden met dit e-mail bericht is geaccordeerd door de ontvanger en/of zijn behandelend arts. Verstrekking van deze informatie is conform het Privacy reglement van de Sint Maartenskliniek. De informatie is uitsluitend bestemd voor de geadresseerde. Gebruik van deze informatie door anderen dan de geadresseerde is, zonder voorafgaande schriftelijke toestemming van de rechthebbende , verboden. De Sint Maartenskliniek staat niet in voor de juiste en volledige overbrenging van de inhoud van een gezonden e-mail, noch voor de ontvangst daarvan. Sint Maartenskliniek Hengstdal 3 6522 JV NIJMEGEN Telefoon 024-3659 911 Telefax 024-3659 204 KvK nummer 41055111 From andrecravo at gmail.com Mon May 2 14:38:37 2011 From: andrecravo at gmail.com (Andre Cravo) Date: Mon, 2 May 2011 09:38:37 -0300 Subject: [FieldTrip] QuikCap 128 NSL layout In-Reply-To: References: Message-ID: Hello, I am collecting EEG data from a SynAmps RT 128 channels. I am using a QuikCap NSL, which although has 128 electrodes, does not follow standard 10-20 localisation. I'm trying to create a layout to visualise my data using the template fiducials of the cap. My script currently looks something like this: cfg =[]; cfg.elecfile='QuikCap_128_NSL.sfp' cfg.rotate=0; cfg.projection='polar' lay=ft_prepare_layout(cfg); ft_layoutplot(cfg) However, the electrodes seems to be shifted towards the back of the head. The layout I get can be seen in the FieldTrip_Layout figure attached. I have tried to realign the electrodes (using ft_electroderealign), but I get similar results. Has anyone ever had a similar problem? Please find attached the 'QuikCap_128_NSL.sfp' file with the fiducials and a .png figure of the electrode positions taken from NeuroScan's website. Thanks in advance for the help. Andre Cravo --- University of Sao Paulo-Brazil -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: QuikCap_128_NSL.sfp Type: application/octet-stream Size: 3888 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: neuroscan.png Type: image/png Size: 282038 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FieldTrip_Layout.png Type: image/png Size: 12814 bytes Desc: not available URL: From cmuehl at gmail.com Mon May 2 17:48:42 2011 From: cmuehl at gmail.com (Christian Muehl) Date: Mon, 2 May 2011 17:48:42 +0200 Subject: [FieldTrip] Call for Papers: Affective BCI Workshop, Memphis, USA Message-ID: ** Call for Papers ** 2nd Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2011 Apologies for multiple postings http://hmi.ewi.utwente.nl/abci2011 http://www.acii2011.org The second workshop on affective brain-computer interfaces will explore the advantages and limitations of using neurophysiological signals as a modality for the automatic recognition of affective and cognitive states, and the possibilities of using this information about the user state in innovative and adaptive applications. The goal is to bring researchers from the communities of brain computer interfacing, affective computing, neuroergonomics, affective and cognitive neuroscience together to present state-of-the-art progress and visions on the various overlaps between those disciplines. Recent research in brain-computer interfaces (BCI) shows that brain activity can be used as an active/voluntary, or passive/involuntary control modality in man-machine interaction. While active BCI paradigms have received a lot of attention in recent years, research on passive approaches to BCI still desperately needs concerted activity. However, it has been shown more than once that brain activations can carry information about the affective and cognitive state of a subject, and that the interaction between humans and machines can be aided by the recognition of those user states. To achieve robust passive BCIs, efforts from applied and basic sciences have to be combined. On the one hand, applied fields such as affective computing aim at the development of applications that adapt to changes in the user states and thereby enrich the interaction, leading to a more natural and effective usability. On the other hand, basic research in neuroscience advances our understanding of the neural processes associated with emotions. Furthermore, similar advancements are being made for more cognitive mental states, for example, attention, fatigue, and work load, which strongly interact with affective states. Topics of interest include, but are not limited to: * emotion elicitation and data collection for affective BCI * detection of affective and cognitive states with BCI and other modalities * adaptive interfaces and affective BCI Invited Talk: 'Brain Dynamics of Affective Engagement' by Scott Makeig, SCCN, University of California at San Diego, USA The workshop will be held in conjunction with the 4th International conference on Affective Computing and Intelligent Interaction (ACII2011) at the FedEx Institute of Technology at the University of Memphis, TN. Submission Instructions * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors (i.e., not submitted, in submission, or submitted to another conference or journal while in review). * Papers will be published in the proceedings of ACII 2011 by Springer. Papers should not exceed 10 pages and should be formatted according to the Springer LNCS formatting guidelines http://www.springer.com/computer/lncs?SGWID=0-164-6-793341-0. * Papers must be submitted as PDF through the EasyChair conference system, which can be accessed through the workshop web site and the ACII conference website. * For further information, contact abci at cs.utwente.nl Important Dates: 15th of June: Workshop papers due 1st of July: Notification of Acceptance 18th of July: Camera-ready papers due 9th of October: Workshop Programme Chairs: * Anton Nijholt, Universiteit Twente, The Netherlands * Brendan Allison, TU Graz, Austria * Stephen Dunne, Starlab Barcelona, Spain * Dirk Heylen, University of Twente, The Netherlands Local Organizer: * Christian Mühl, University of Twente, The Netherlands Programme Committee: * Egon L. van den Broek, University of Twente, The Netherlands * Touradj Ebrahimi, EPFL, Lausanne, Switzerland * Peter Desain, Radboud University Nijmegen, The Netherlands * Jan B.F. van Erp, TNO Human Factors, Soesterberg, The Netherlands * Stephen Fairclough, John Moores University, Liverpool, UK * Gary Garcia Molina, Philips Research, Eindhoven, The Netherlands * Audrey Girouard, Queen's University, Kingston, Canada * Jonghwa Kim, University of Augsburg, Germany * Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA * Robert Leeb, University of Lausanne, Switzerland * Scott Makeig, University of California at San Diego, USA * Femke Nijboer, University of Twente, The Netherlands * Ioannis Patras, Queen Mary University, London, UK * Thierry Pun, University of Geneva, Switzerland * Tanja Schultz, Karlsruhe Institute of Technology (KIT), Germany * Olga Sourina, NanYang Technological University, Singapore * Thomas J. Sullivan, NeuroSky, San Jose, USA * Thorsten Zander, Graz University of Technology, Austria From r.oostenveld at donders.ru.nl Tue May 3 10:20:05 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 3 May 2011 10:20:05 +0200 Subject: [FieldTrip] changed channel names for EGI data format from 'e' to 'E' Message-ID: <4522B5B9-579C-4AFF-A2CF-449420DAFFAF@donders.ru.nl> Dear fieldtrip users working on EGI data, The EGI system does not have well described channel names, but most software deals with it by prefixing the EGI channel names with an 'E', e.g. E1, E2 ... E256 It turned out that there were some inconsistent definitions whether it should be a lowercase 'e' or an uppercase 'E'. After consulting with some EGI experts (Joseph Dien, Catherine Poulsen, Ingrid Nieuwenhuis), I have just changed fieldtrip to use an uppercase 'E' consistently throughout the code. The EGI layouts (*.sfp files) also use this uppercase definition. The consequence is that string comparisons between channels like 'e1' and 'E1' might fail and that in the analysis (e.g. grandaveraging data with mixed case labels) the identical channels are not recognized/matched to each other. If you encounter problems like these, you should fix them by converting the channel labels for data that you have stored on disk in *.mat files to uppercase. That can be easily done with the "upper" function in MATLAB for example like this: data.label = upper(data.label); timelock.label = upper(timelock.label); freq.label = upper(freq.label); freq.labelcmb = upper(freq.labelcmb); Sorry for the inconvenience that this causes, hopefully in the future with the consistent definition of the channel labels we won't have problems like this any more. best regards, Robert From annajafarpour at gmail.com Tue May 3 19:40:20 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 18:40:20 +0100 Subject: [FieldTrip] tf online tutorial is missed Message-ID: Hello all, In the Fieldtrip online documentation, the tutorial about tf analysis is missed. Where else can I find a copy of the tutorial? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue May 3 19:55:44 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 3 May 2011 19:55:44 +0200 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Hello Anna, To be honest, I have no idea what happened, or why the time-frequency tutorial page was suddenly blank. However, I seem to have fixed the issue by clearing the page's contents, and re-adding it. I'll look into the issue further; but for now, your problem is solved. Best, Eelke 2011/5/3 Anna Jafarpour : > Hello all, > > In the Fieldtrip online documentation, the tutorial about tf analysis is > missed. Where else can I find a copy of the tutorial? > > Best, > Anna > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From annajafarpour at gmail.com Tue May 3 20:04:57 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 19:04:57 +0100 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Thank you :) On Tue, May 3, 2011 at 6:55 PM, Eelke Spaak wrote: > Hello Anna, > > To be honest, I have no idea what happened, or why the time-frequency > tutorial page was suddenly blank. However, I seem to have fixed the > issue by clearing the page's contents, and re-adding it. I'll look > into the issue further; but for now, your problem is solved. > > Best, > Eelke > > 2011/5/3 Anna Jafarpour : > > Hello all, > > > > In the Fieldtrip online documentation, the tutorial about tf analysis is > > missed. Where else can I find a copy of the tutorial? > > > > Best, > > Anna > > > > _______________________________________________ > > 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 annajafarpour at gmail.com Tue May 3 21:10:48 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Tue, 3 May 2011 20:10:48 +0100 Subject: [FieldTrip] trial selection Message-ID: Dear All, I am sorry if this is an FAQ; the online FAQ is not accessible. Is there any function for selecting trials according to the trialinfo? Or is there any function for copying specific trials (with its configuration) into a new variable? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.stolk at fcdonders.ru.nl Tue May 3 21:39:15 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Tue, 3 May 2011 21:39:15 +0200 (CEST) Subject: [FieldTrip] trial selection In-Reply-To: Message-ID: <1167814753.23605.1304451555946.JavaMail.root@sculptor.zimbra.ru.nl> Hi Anna, Have a look at the help of ft_redefinetrial. Possibly the configuration option cfg.trials is the one you're looking for. Yours, Arjen   ----- "Anna Jafarpour" schreef: > Van: "Anna Jafarpour" > Aan: "Email discussion list for the FieldTrip project" > Verzonden: Dinsdag 3 mei 2011 21:10:48 > Onderwerp: [FieldTrip] trial selection > > Dear All, > I am sorry if this is an FAQ; the online FAQ is not accessible. > Is there any function for selecting trials according to the trialinfo? Or is there any function for copying specific trials (with its configuration) into a new variable? > > Best, > Anna > > _______________________________________________ > 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 inbalots at gmail.com Wed May 4 14:25:30 2011 From: inbalots at gmail.com (Inbal Lots) Date: Wed, 4 May 2011 15:25:30 +0300 Subject: [FieldTrip] Question about trl Message-ID: Hello my name is Inbal and I wanted to ask about trl. Say I define trl myself, as following: trl = [1000 , 1600 , -100]; Lets assume that the sampling rate is 1000Hz trl defines, as far as I understand, the onset at sample #1000, the data start of the data to analyze , before onset, at sample #900 and the end of the data to analyze at sample # 1500. Is that so? Thanks Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at fcdonders.ru.nl Wed May 4 14:56:59 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Wed, 4 May 2011 14:56:59 +0200 (CEST) Subject: [FieldTrip] Question about trl In-Reply-To: <244f01cc0a5a$2d05a1e0$8710e5a0$@vanpelt@fcdonders.ru.nl> Message-ID: <915523278.28822.1304513819890.JavaMail.root@sculptor.zimbra.ru.nl> Hello Inbal, That is not quite correct. Say you define a trial as cfg.trl=[1000 1600 -100], then “-100” is the offset (in samples) of your time axis. So, for this trial, you will get a dataset of 600 samples (or also ms in your example case) length (=1600-1000), of which sample 101 will be defined as t=0s (-100 meaning that the 1 st sample of your trial is -100 samples from t=0). So, the third column in cfg.trl doesn’t affect which part of the data will de used to define the trial (samples 1000 to 1600 will always be read from your data), but only affects the position of t=0 on the time-axis of your trial (data.time). Best, Stan Stan van Pelt, PhD Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Kapittelweg 29, 6525 EN Nijmegen, Netherlands E-mail: stan.vanpelt at donders.ru.nl Website: www.ru.nl/donders/ Phone: (+31) (0)24 36 68495 Fax: (+31) (0)24 36 10989 > From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Inbal Lots > Sent: Wednesday, May 04, 2011 2:26 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] Question about trl Hello > my name is Inbal and I wanted to ask about trl. > Say I define trl myself, as following: > trl = [1000 , 1600 , -100]; > Lets assume that the sampling rate is 1000Hz > trl defines, as far as I understand, the onset at sample #1000, the data start of the data to analyze , before onset, at sample #900 and the end of the data to analyze at sample # 1500. Is that so? > > Thanks > Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From akiko at nyu.edu Wed May 4 15:17:49 2011 From: akiko at nyu.edu (Akiko Ikkai) Date: Wed, 04 May 2011 09:17:49 -0400 Subject: [FieldTrip] overlaying beamformer results to native/normalized space Message-ID: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> I sent a below message to the list last night, but it was bounced back. I'm trying from another email account. My apologies if this was duplicate... I'm trying to run beamformer analysis on my MEG data, using DICS, and having difficulty visualizing meaningful results. I was able to align MRI image to MEG sensors; after segmentation, ft_prepare_singleshell and ft_prepare_leadfield, plotting ft_data.grad and volume model confirms that they align reasonably. However, using data.grad, grid, and vol to run ft_sourceanalysis, and ft_sourceinterpolate with MRI (in ctf coordinate system and aligned to MEG sensors) somehow distorts the alignment, and the new volume model does not resemble the original. I'm assuming that, after ft_sourceinterpolate, if I segment source_interpolated.anatomy and run ft_prepare_singleshell and ft_prepare_leadfield, it should align with MEG sensors, just as the initial volume model aligned with MEG sensors... or am I making too much of an assumption here? Because of the misalignment, output data of ft_sourceinterpolate with "anatomy" and "avg.pow" does not agree with topoplot (run ft_freqanalysis on the same dataset). If anyone could explain why this alignment distortion might be happening during ft_sourceanalysis and/or ft_sourceinterpolate, I'd really appreciate it. Thanks in advance, Akiko -- Akiko Ikkai, Ph.D. Postdoctoral Fellow Department of Psychological and Brain Sciences Johns Hopkins University Ames Hall, 3400 N. Charles St. Baltimore, MD 21218 From ting.ac at gmail.com Wed May 4 15:56:57 2011 From: ting.ac at gmail.com (Allison Connolly) Date: Wed, 4 May 2011 08:56:57 -0500 Subject: [FieldTrip] error using spm_slice_vol Message-ID: Hi all, I am trying to segment an mri volume using. When I call ft_read_mri('filename'), I get an error that says: ??? Error using ==> spm_slice_vol at 28 spm_slice_vol.c not compiled - see spm_MAKE.sh Error in ==> spm_read_vols at 35 Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 p]),V(i).dim(1:2),0); Error in ==> ft_read_mri at 97 img = spm_read_vols(hdr); I tried installing the most up to date version of fieldtrip and I still get the same error. Can someone help me? -Allison -------------- next part -------------- An HTML attachment was scrubbed... URL: From annajafarpour at gmail.com Wed May 4 16:03:18 2011 From: annajafarpour at gmail.com (Anna Jafarpour) Date: Wed, 4 May 2011 15:03:18 +0100 Subject: [FieldTrip] Multivariate analysis of MEG data Message-ID: Hi, I am trying to run an SVM on a data (2 X 60 rpt 274 chan 1 freq 41 timep) using Fieltrip 20110420. But it gives an error and looks for ft_mv_standardizer. I cannot find this function anywhere (I set-pathed the multivariate folder as well). What is the problem? Best, Anna -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Wed May 4 22:24:40 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Wed, 4 May 2011 22:24:40 +0200 Subject: [FieldTrip] tf online tutorial is missed In-Reply-To: References: Message-ID: Dear wiki visitors, There were some issues on the fieldtrip wiki with pages suddenly displaying as empty. It turned out that it was due to a full hard-disk in our webserver. The problem has been resolved and now everything should work smoothly again. best regards, Robert On 3 May 2011, at 20:04, Anna Jafarpour wrote: > Thank you :) > > On Tue, May 3, 2011 at 6:55 PM, Eelke Spaak wrote: > Hello Anna, > > To be honest, I have no idea what happened, or why the time-frequency > tutorial page was suddenly blank. However, I seem to have fixed the > issue by clearing the page's contents, and re-adding it. I'll look > into the issue further; but for now, your problem is solved. > > Best, > Eelke > > 2011/5/3 Anna Jafarpour : > > Hello all, > > > > In the Fieldtrip online documentation, the tutorial about tf analysis is > > missed. Where else can I find a copy of the tutorial? > > > > Best, > > Anna > > > > _______________________________________________ > > 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ekanal at cmu.edu Thu May 5 00:05:54 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Wed, 4 May 2011 18:05:54 -0400 Subject: [FieldTrip] ft_channelselection fails with negation and regex matching Message-ID: <710C0AC3-5C40-4746-96FC-FBB2D5D1979F@cmu.edu> Hello fieldtrip - We have a Elekta Neuromag 306 scanner, and I'm trying to select only the gradiometers. The magnetometers are labeled 'MEGxxx1', where x can be any number, and the gradiometers are either 'MEGxxx2' or 'MEGxxx3'. However, using ft_channelselection results in the following error: ~~~~ >> ft_channelselection({'all','-STI*','-MEG*1'}, cfg.hdr.label) ??? Matrix index is out of range for deletion. Error in ==> ft_channelselection at 287 channel([ ~~~~ This error is somewhat complex, as I was able to determine that ft_channelselection recursively calls itself a number of times while running, and I was unable to figure out what is causing this problem. Any help would be appreciated. Thanks! Eliezer Kanal -------------------- Eliezer Kanal, Ph.D. Postdoctoral Fellow Center for the Neural Basis of Cognition Carnegie Mellon University 4400 Fifth Ave, Suite 110A Pittsburgh PA 15213 P: 412-268-4115 F: 412-268-5060 From a.stolk at fcdonders.ru.nl Thu May 5 09:54:53 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 5 May 2011 09:54:53 +0200 (CEST) Subject: [FieldTrip] ft_channelselection fails with negation and regex matching In-Reply-To: <710C0AC3-5C40-4746-96FC-FBB2D5D1979F@cmu.edu> Message-ID: <543079.33508.1304582093866.JavaMail.root@sculptor.zimbra.ru.nl> Hi Kanal, I've managed to replicate your bug with MEG data and we will try to sort this out. Yours, Arjen ----- "Kanal Eliezer" schreef: > Van: "Kanal Eliezer" > Aan: "Email FieldTrip project discussion list for the" > Verzonden: Donderdag 5 mei 2011 00:05:54 > Onderwerp: [FieldTrip] ft_channelselection fails with negation and regex matching > > Hello fieldtrip - > > We have a Elekta Neuromag 306 scanner, and I'm trying to select only > the gradiometers. The magnetometers are labeled 'MEGxxx1', where x can > be any number, and the gradiometers are either 'MEGxxx2' or 'MEGxxx3'. > However, using ft_channelselection results in the following error: > > ~~~~ > >> ft_channelselection({'all','-STI*','-MEG*1'}, cfg.hdr.label) > ??? Matrix index is out of range for deletion. > > Error in ==> ft_channelselection at 287 > channel([ > ~~~~ > > This error is somewhat complex, as I was able to determine that > ft_channelselection recursively calls itself a number of times while > running, and I was unable to figure out what is causing this problem. > Any help would be appreciated. Thanks! > > Eliezer Kanal > > > -------------------- > Eliezer Kanal, Ph.D. > Postdoctoral Fellow > Center for the Neural Basis of Cognition > Carnegie Mellon University > 4400 Fifth Ave, Suite 110A > Pittsburgh PA 15213 > P: 412-268-4115 > F: 412-268-5060 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From julian.keil at gmail.com Thu May 5 14:15:02 2011 From: julian.keil at gmail.com (Julian Keil) Date: Thu, 5 May 2011 14:15:02 +0200 Subject: [FieldTrip] cfg.maskparameter in ft_multiplotER Message-ID: <06AC35D0-BE3D-4B96-B67F-3E1B64DBAE22@gmail.com> Hi all, i have a question regarding the mask-option in ft_multiplotER (and singleplotER). After the montecarlo statistic with holm-correction, I get the following data structure: stats = prob: [145x679 double] mask: [145x679 double] stat: [145x679 double] ref: [145x679 double] dimord: 'chan_time' label: {145x1 cell} time: [1x679 double] cfg: [1x1 struct] I then use these options to plot the results: cfg=[]; cfg.interactive='yes'; cfg.layout='4D148.lay'; cfg.zparam='stat'; cfg.maskparameter='mask'; figure;ft_multiplotER(cfg,stats); Unfortunately, I get the error message: ??? Error using ==> ft_multiplotER at 528 data in cfg.maskparameter should be vector with one value per channel I am a bit confused, as this used to work fine with an older version of fieldtrip (fieldtrip-20110113). Can anyone explain to me how to handle the mask-option. I already tried to reduce the mask-matrix to a one-value-per channel vector, but this produces the error: ??? Attempt to reference field of non-structure array. Error in ==> ft_multiplotER at 527 if min(size(datmask)) ~= 1 || max(size(datmask)) ~= length(data.label) Maybe I missed some important changes in a recent fieldtrip-update.... Thanks a lot Julian Dipl. Psych. Julian Keil OBOB-Lab University of Konstanz Department of Psychology P.O. Box D25 78457 Konstanz Germany Tel: ++49 - (0)7531 - 88 42 50 Fax: ++49 - (0)7531 - 88 28 91 Email: julian.keil at uni-konstanz.de Homepage: http://www.uni-konstanz.de/obob -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Thu May 5 23:55:32 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Thu, 05 May 2011 14:55:32 -0700 Subject: [FieldTrip] fieldtrip2eeglab Message-ID: <4DC31CD4.6070508@berkeley.edu> Hi, Does a fieldtrip2eeglab script exist, to transform a Matlab structure generated by FieldTrip into a Matlab struct that EEGlab can swallow? I know the reverse does exist (eeglab2fieldtrip). I need to get some raw data (egi_mff dataformat, which is not implemented in EEGlab yet as far as I know) into EEGlab. Or if anyone has written some code that might do the trick, that would be very much appreciated as well! Thanks! Ingrid -- Ingrid Nieuwenhuis PhD Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 Tolman Hall, room 5305 From Maarten.van-Casteren at mrc-cbu.cam.ac.uk Fri May 6 14:10:13 2011 From: Maarten.van-Casteren at mrc-cbu.cam.ac.uk (Maarten van-Casteren) Date: Fri, 6 May 2011 12:10:13 +0000 Subject: [FieldTrip] Problem with user specified trial function Message-ID: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> Hi, I've just started to use Fieldtrip and I don't have much experience with Matlab, so I could just be making a stupid mistake, but I found some very strange behavious when I tried to specify my own trailfunction. I started from the example given on the tutorial pages of the wiki. I've indicated the line of interest with an additional '->'. This is what I used: for i=1:length(event) if strcmp(event(i).type, cfg.trialdef.eventtype) % it is a trigger, see whether it has the right value if ismember(event(i).value, cfg.trialdef.eventvalue) % add this to the trl definition begsample = event(i).sample - cfg.trialdef.prestim*hdr.Fs; endsample = event(i).sample + cfg.trialdef.poststim*hdr.Fs - 1; offset = -cfg.trialdef.prestim*hdr.Fs; trigger = event(i).value; % remember the trigger (=condition) for each trial -> trl(end+1, :) = [round([begsample endsample offset]) trigger]; end end end When I use it like this it will clip all sample and offset values at 0 - 65536, that is the limits of an unsigned integer. I had to change the actual line that appends the trial to this to make it work: trl(end+1, :) = [double(begsample) double(endsample) double(offset) double(trigger)]; All values are shown by the debugger as doubles anyway, so why this explicit conversion is needed is completely beyond me. Does anyone of you know what is going on? I already asked one of the local Matlab gurus, but he was even more amazed than me... Thanks, Maarten -------------- next part -------------- An HTML attachment was scrubbed... URL: From jm.horschig at donders.ru.nl Fri May 6 14:31:24 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Fri, 06 May 2011 14:31:24 +0200 Subject: [FieldTrip] Problem with user specified trial function In-Reply-To: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> References: <076BBBEE0241DF4FA4F09E43B8EB0176391359F1@WSR21.mrc-cbsu.local> Message-ID: <4DC3EA1C.4080606@donders.ru.nl> Hi Maarten, no idea what might go wrong there (for me your code snippet works fine). Anyway, you could try to first round cfg.trialdef.prestim*hdr.Fs (same for poststim) outside the loop and store them as local variables and then continue without having to round in every single iteration for every single trial-def, e.g.: trloff = round(-cfg.trialdef.prestim*hdr.Fs); trldur = round((cfg.trialdef.poststim+cfg.trialdef.prestim)*hdr.Fs) - 1; % that's from trialfun_general I bet this will make a difference, although it should of course not. Maybe someone else can confirm the error with your code snippet... Best, Jörn On 5/6/2011 2:10 PM, Maarten van-Casteren wrote: > > Hi, > > I've just started to use Fieldtrip and I don't > > have much experience with Matlab, so I could > > just be making a stupid mistake, but I found > > some very strange behavious when I tried to > > specify my own trailfunction. > > I started from the example given on the tutorial > > pages of the wiki. I've indicated the line of interest > > with an additional '->'. This is what I used: > > for i=1:length(event) > > if strcmp(event(i).type, cfg.trialdef.eventtype) > > % it is a trigger, see whether it has the right value > > if ismember(event(i).value, cfg.trialdef.eventvalue) > > % add this to the trl definition > > begsample = event(i).sample - cfg.trialdef.prestim*hdr.Fs; > > endsample = event(i).sample + cfg.trialdef.poststim*hdr.Fs - 1; > > offset = -cfg.trialdef.prestim*hdr.Fs; > > trigger = event(i).value; % remember the trigger > (=condition) for each trial > > -> trl(end+1, :) = [round([begsample endsample offset]) trigger]; > > end > > end > > end > > When I use it like this it will clip all sample and > > offset values at 0 -- 65536, that is the limits of an > > unsigned integer. I had to change the actual line > > that appends the trial to this to make it work: > > trl(end+1, :) = [double(begsample) double(endsample) double(offset) > double(trigger)]; > > All values are shown by the debugger as doubles > > anyway, so why this explicit conversion is needed > > is completely beyond me. > > Does anyone of you know what is going on? > > I already asked one of the local Matlab gurus, > > but he was even more amazed than me... > > Thanks, > > Maarten > > > _______________________________________________ > 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From fedeletommaso at yahoo.it Fri May 6 17:28:48 2011 From: fedeletommaso at yahoo.it (tommaso fedele) Date: Fri, 6 May 2011 16:28:48 +0100 (BST) Subject: [FieldTrip] FT_analysis of the average vs average(FT_analysis(single trials)) Message-ID: <686364.21106.qm@web28608.mail.ukl.yahoo.com> Hi all, I want to test if some component that I observe in the average of my ERP signal are phase locked to the stimulus. In oder to do so I compare 1. TFR_averaged_signal = ft_freqanalysis(cfg, averaged_signal) 2. TFR_singletrials_signal = ft_freqanalysis(cfg, singletrials_signal) with the first structure TFR_averaged_signal everything is fine, and I get my nice TF plot. with the second I should average through "trials". Is there a function for that? Or, is it correct to proceed plotting the average of TFR_singletrials_signal.powspctrm through the "trials-matrix dimension"? Thanks Tommaso -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon May 9 12:13:40 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 9 May 2011 12:13:40 +0200 Subject: [FieldTrip] fieldtrip2eeglab In-Reply-To: <4DC31CD4.6070508@berkeley.edu> References: <4DC31CD4.6070508@berkeley.edu> Message-ID: <45F6D404-F8C3-4339-AE25-25E52C8D2598@donders.ru.nl> Hi Ingrid, I searched my hard disk and found the attached file. Note that it is a very old file (last modified 2006) and I don't know whether the "EEG" structure is still like this, but it may help you get started. best, Robert On 5 May 2011, at 23:55, Ingrid Nieuwenhuis wrote: > Hi, > > Does a fieldtrip2eeglab script exist, to transform a Matlab > structure generated by FieldTrip into a Matlab struct that EEGlab > can swallow? I know the reverse does exist (eeglab2fieldtrip). I > need to get some raw data (egi_mff dataformat, which is not > implemented in EEGlab yet as far as I know) into EEGlab. Or if > anyone has written some code that might do the trick, that would be > very much appreciated as well! > > Thanks! > Ingrid -------------- next part -------------- A non-text attachment was scrubbed... Name: fieldtrip2eeglab.m Type: application/octet-stream Size: 1094 bytes Desc: not available URL: -------------- next part -------------- From jstout211 at yahoo.com Mon May 9 22:12:15 2011 From: jstout211 at yahoo.com (Jeff Stout) Date: Mon, 9 May 2011 13:12:15 -0700 (PDT) Subject: [FieldTrip] Leadfield calculations result in NaNs Message-ID: <102170.78349.qm@web113519.mail.gq1.yahoo.com> Hi,  I am having trouble generating leadfields for source analysis.  I am using data from a 4D magnetometer system (Magnes 3600), at St. Louis University. The data is averged time domain data.  The volume conductor is a single shell model generated from the headshape file(~4000 vert. and 8000 triangles).  I have vizualized the volume conductor, sensors, and "inside" grid and they appear to be in the correct locations relative to each other.  I have performed this analysis using the default source space for 4D ('m') and I have tried it scaling the headshape and sensors into cm to conform with the ctf source space.   Below is part of my code and the warning thrown by matlab.  After the calculation of the leadfields, it is apparent that they are all NaN's, so I am unable to generate source activations. cfg = [];cfg.headshape = shape;shape.pnt = shape.pnt*100;shape.unit  = 'cm';[vol,cfg] = ft_prepare_singleshell(cfg) cfg                 = [];cfg.grad            = avg.grad; cfg.grad.pnt = cfg.grad.pnt*100;cfg.grad.unit  = 'cm';cfg.vol             = vol;cfg.sourceunits = 'cm';cfg.coordsys   = 'ctf';cfg.reducerank      ='no';  cfg.channel         = {'MEG'};cfg.grid.resolution = 2[vol, sens] = ft_prepare_vol_sens(vol, cfg.grad)[grid] = ft_prepare_leadfield(cfg)    >> [grid] = ft_prepare_leadfield(cfg)using headmodel specified in the configurationusing gradiometers specified in the configurationcomputing surface normalsWarning: Matrix is singular, close to singular or badly scaled.   <<<<<<<<<<         Results may be inaccurate. RCOND = NaN. > In forward/private/meg_ini>getcoeffs at 111  In forward/private/meg_ini at 53  In ft_prepare_vol_sens at 275  In fieldtrip-20110507/private/prepare_headmodel at 114  In ft_prepare_leadfield at 150creating dipole grid based on automatic 3D grid with specified resolution3528 dipoles inside, 0 dipoles outside brainmaking tight grid3528 dipoles inside, 0 dipoles outside braincomputing leadfieldcomputing leadfield 1/3528computing leadfield 2/3528computing leadfield 3/3528computing leadfield 4/3528 ...... The leadfield data generated is a matrix of NaN's, which appear to be an issue when evaluating bas and gradbas in the get_coeffs subfunction  [bas,gradbas]=legs(x1,n1,order,scale). Does anyone know how to resolve this issue? Any help will be greatly appreciated. Thanks, Jeff Stout Open in Google Docs ViewerOpen link in new tabOpen link in new windowOpen link in new incognito windowDownload fileCopy link addressEdit PDF File on PDFescape.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From matthew at psych.columbia.edu Tue May 10 00:37:39 2011 From: matthew at psych.columbia.edu (Matthew Davidson) Date: Mon, 9 May 2011 18:37:39 -0400 Subject: [FieldTrip] Human neurophysiology analysis tech posting in San Diego Message-ID: Human Neurophysiology Analysis Technician – To assist a team of experienced neurophysiologists conduct language, memory, sleep and developmental studies in humans with MEG and intracranial recordings. MEG localization will use structural MRI constraints and functional MRI bias. Intracranial recordings include microelectrode arrays, unit-recordings, and laminar current source density analysis. The candidate must have high abstract intelligence in order to rapidly acquire different techniques, modify them as necessary, and recognize inconsistent results. Prior expertise with MatLab would be very useful, and some knowledge of neuroscience is expected. Collaborate with a large, talented and friendly group of scientists, programmers and technicians engaged in multimodal brain research. The position is available starting immediately, with the expectation that you would remain for at least 2 years, but it is subject to annual review and continuation of grant funding. Everyone is welcome to apply regardless of gender, ethnicity, or other irrelevancies. Please contact Eric Halgren, Ph.D., Multimodal Imaging Laboratory, University of California at San Diego,ehalgren at ucsd.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 10 08:36:51 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 10 May 2011 08:36:51 +0200 Subject: [FieldTrip] Leadfield calculations result in NaNs In-Reply-To: <102170.78349.qm@web113519.mail.gq1.yahoo.com> References: <102170.78349.qm@web113519.mail.gq1.yahoo.com> Message-ID: Dear Jeff, From what you describe I don't really know what's going wrong. Are you using the headsurface file generated with the polhemus? It could be that this causes the problem. For the singleshell model to work, you need a triangulated surface. The headsurface file contains only a point cloud. Matlab tries to create a triangulation from this point cloud, and I could imagine that this triangulation misbehaves here, leading some nans here and there (judging from your message this happens when the normals to the triangles are computed), which eventually cause nans all over the place. For the time being you could try to use a different volume conductor model (localspheres), or you may want to use a structural MRI for the singleshell creation (if available), to verify that the problem is caused by the headsurface file and not by fieldtrip. Best, Jan-Mathijs On May 9, 2011, at 10:12 PM, Jeff Stout wrote: > > Hi, > > I am having trouble generating leadfields for source analysis. I am > using data from a 4D magnetometer system (Magnes 3600), at St. Louis > University. > > The data is averged time domain data. The volume conductor is a > single shell model generated from the headshape file(~4000 vert. and > 8000 triangles). I have vizualized the volume conductor, sensors, > and "inside" grid and they appear to be in the correct locations > relative to each other. I have performed this analysis using the > default source space for 4D ('m') and I have tried it scaling the > headshape and sensors into cm to conform with the ctf source > space. Below is part of my code and the warning thrown by matlab. > After the calculation of the leadfields, it is apparent that they > are all NaN's, so I am unable to generate source activations. > > cfg = []; > cfg.headshape = shape; > shape.pnt = shape.pnt*100; > shape.unit = 'cm'; > [vol,cfg] = ft_prepare_singleshell(cfg) > > cfg = []; > cfg.grad = avg.grad; > cfg.grad.pnt = cfg.grad.pnt*100; > cfg.grad.unit = 'cm'; > cfg.vol = vol; > cfg.sourceunits = 'cm'; > cfg.coordsys = 'ctf'; > cfg.reducerank ='no'; > cfg.channel = {'MEG'}; > cfg.grid.resolution = 2 > [vol, sens] = ft_prepare_vol_sens(vol, cfg.grad) > [grid] = ft_prepare_leadfield(cfg) > > >> [grid] = ft_prepare_leadfield(cfg) > using headmodel specified in the configuration > using gradiometers specified in the configuration > computing surface normals > Warning: Matrix is singular, close to singular or badly scaled. > <<<<<<<<<< > Results may be inaccurate. RCOND = NaN. > > In forward/private/meg_ini>getcoeffs at 111 > In forward/private/meg_ini at 53 > In ft_prepare_vol_sens at 275 > In fieldtrip-20110507/private/prepare_headmodel at 114 > In ft_prepare_leadfield at 150 > creating dipole grid based on automatic 3D grid with specified > resolution > 3528 dipoles inside, 0 dipoles outside brain > making tight grid > 3528 dipoles inside, 0 dipoles outside brain > computing leadfield > computing leadfield 1/3528 > computing leadfield 2/3528 > computing leadfield 3/3528 > computing leadfield 4/3528 ...... > > > The leadfield data generated is a matrix of NaN's, which appear to > be an issue when evaluating bas and gradbas in the get_coeffs > subfunction [bas,gradbas]=legs(x1,n1,order,scale). > > Does anyone know how to resolve this issue? Any help will be greatly > appreciated. > > Thanks, > Jeff Stout > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan.debener at uni-oldenburg.de Tue May 10 09:04:47 2011 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Tue, 10 May 2011 09:04:47 +0200 Subject: [FieldTrip] Auditory BCI post-doc posting Message-ID: <4DC8E38F.5050902@uni-oldenburg.de> Dear all, We are seeking a scientist/post-doc who is interested in developing an auditiry brain computer interface. Please visit: http://www.hearingresearch.uni-oldenburg.de/52922.html (job offer #4), and feel free to contact me via email for further information. Thanks much, Stefan -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de From jan.schoffelen at donders.ru.nl Wed May 11 08:35:19 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 08:35:19 +0200 Subject: [FieldTrip] ft_freqstatistics Message-ID: <4EE8E6A8-5C67-45A6-A6CE-7D6FFA5C3D64@donders.ru.nl> Dear all, I just committed to the svn-repository a revamped version of ft_freqstatistics, the function which does channel-level statistics on frequency domain data. This was a necessary cleaning operation to keep the code up-to-date. Important for you to know is that nothing has changed in the handling of good old-fashioned (time-frequency) power. The new thing is that you don't need to hack your way into the function anymore in order to do group level statistics on connectivity data. Things should just run fine, but although I extensively tested the code (to my best knowledge) on plausible scenarios, please keep your eyes open. Best, Jan-Mathijs Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From ndavid at uke.de Wed May 11 10:45:32 2011 From: ndavid at uke.de (Nicole David) Date: Wed, 11 May 2011 10:45:32 +0200 Subject: [FieldTrip] Job Announcement (PhD Position) In-Reply-To: <03750F99-88BD-42D6-9133-8E4B4814E133@uke.de> References: <03750F99-88BD-42D6-9133-8E4B4814E133@uke.de> Message-ID: Dear FieldTrip list, I would like to announce an open PhD position with Prof. Andreas Engel at the Dept. of Neurophysiology and Pathophysiology, University Medical Center Hamburg-Eppendorf. For details, see below. Best, Nicole David ------------------------------- The Department of Neurophysiology and Pathophysiology at the University Medical Center Hamburg-Eppendorf (Director: Prof. Dr. Andreas K. Engel) invites applications for a PhD student position. The position is available with immediate start. The appointment will be for 3 years. The position is at the intersection of psychology, cognitive neuroscience and philosophy. More specifically, experiments investigating the sense of agency shall be carried out, using neuroscience techniques such as magnetoencephalography (MEG). The sense of agency refers to the monitoring of actions and the experience, or awareness, of such as self- or other-generated. Applicants should have experience in analyzing human EEG or MEG studies. Programming experience (Matlab) as well as fluent written and spoken English is considered mandatory. Applicants will be responsible for the management and implementation of research paradigms, data acquisition and analysis. Knowledge in theories of action and perception, multisensory processing, self-awareness and a basic understanding of information processing in the human brain would be preferred. The successful candidate will be member of the European collaborative project “Extending Sensorimotor Contingencies to Cognition – eSMCs” that has started in January 2011. The main objective of the project is to extend the Sensorimotor Contingency Theory as an action-based approach to perception and cognition, and to investigate its implications in studies of natural and artificial agents. More information on the project is to appear at http://eSMCs.eu. Information on the Dept. of Neurophysiology and Pathophysiology is available at http://www.uke.de/neurophysiologie and at http://www.40hz.de . Please send your application (including a CV) to Dr. Nicole David or Prof. Dr. Andreas K. Engel Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistrasse 52 20246 Hamburg Germany Submission of applications through email (ndavid at uke.de, ak.engel at uke.de) is encouraged. -- Pflichtangaben gemäß Gesetz über elektronische Handelsregister und Genossenschaftsregister sowie das Unternehmensregister (EHUG): Universitätsklinikum Hamburg-Eppendorf Körperschaft des öffentlichen Rechts Gerichtsstand: Hamburg Vorstandsmitglieder: Prof. Dr. Jörg F. Debatin (Vorsitzender) Dr. Alexander Kirstein Joachim Prölß Prof. Dr. Dr. Uwe Koch-Gromus -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 11 10:56:10 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 10:56:10 +0200 Subject: [FieldTrip] FT_analysis of the average vs average(FT_analysis(single trials)) In-Reply-To: <686364.21106.qm@web28608.mail.ukl.yahoo.com> References: <686364.21106.qm@web28608.mail.ukl.yahoo.com> Message-ID: Dear Tommaso, Yes, if you average across the trial-dimension you will obtain the TFR you're after. Best, JM On May 6, 2011, at 5:28 PM, tommaso fedele wrote: > Hi all, > I want to test if some component that I observe in the average of my > ERP signal are phase locked to the stimulus. > In oder to do so I compare > 1. TFR_averaged_signal = ft_freqanalysis(cfg, averaged_signal) > 2. TFR_singletrials_signal = ft_freqanalysis(cfg, > singletrials_signal) > > with the first structure TFR_averaged_signal everything is fine, and > I get my nice TF plot. > with the second I should average through "trials". Is there a > function for that? Or, is it correct to proceed plotting > the average of TFR_singletrials_signal.powspctrm through the > "trials-matrix dimension"? > > Thanks > Tommaso > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 11 10:59:06 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 10:59:06 +0200 Subject: [FieldTrip] error using spm_slice_vol In-Reply-To: References: Message-ID: Hi Allison, This looks like an SPM-related error to me, or it is operating system related. Can you check which spm-version you are using, in other words: is it the fieldtrip/external/spmXXX directory, or do you have spm somewhere else on your matlab-path? If it is the former, then it is a potential bug which needs fixing by us. Otherwise we cannot help it. What kind of operating system are you using? Best, Jan-Mathijs On May 4, 2011, at 3:56 PM, Allison Connolly wrote: > Hi all, > > I am trying to segment an mri volume using. When I call > ft_read_mri('filename'), I get an error that says: > > ??? Error using ==> spm_slice_vol at 28 > spm_slice_vol.c not compiled - see spm_MAKE.sh > > Error in ==> spm_read_vols at 35 > Y(:,:,p,i) = spm_slice_vol(V(i),spm_matrix([0 0 > p]),V(i).dim(1:2),0); > > Error in ==> ft_read_mri at 97 > img = spm_read_vols(hdr); > > I tried installing the most up to date version of fieldtrip and I > still get the same error. Can someone help me? > > -Allison > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Wed May 11 11:02:49 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 11 May 2011 11:02:49 +0200 Subject: [FieldTrip] overlaying beamformer results to native/normalized space In-Reply-To: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> References: <5990a22b3c17f9.4dc119bd@mail.nyu.edu> Message-ID: Dear Akiko, On May 4, 2011, at 3:17 PM, Akiko Ikkai wrote: > I sent a below message to the list last night, but it was bounced > back. I'm trying from another email account. My apologies if this > was duplicate... > > > > I'm trying to run beamformer analysis on my MEG data, using DICS, > and having difficulty visualizing meaningful results. > > I was able to align MRI image to MEG sensors; after segmentation, > ft_prepare_singleshell and ft_prepare_leadfield, plotting > ft_data.grad and volume model confirms that they align reasonably. > However, using data.grad, grid, and vol to run ft_sourceanalysis, > and ft_sourceinterpolate with MRI (in ctf coordinate system and > aligned to MEG sensors) somehow distorts the alignment, and the new > volume model does not resemble the original. So, the problem is that ft_sourceinterpolate does not behave as expected? > I'm assuming that, after ft_sourceinterpolate, if I segment > source_interpolated.anatomy and run ft_prepare_singleshell and > ft_prepare_leadfield, it should align with MEG sensors, just as the > initial volume model aligned with MEG sensors... or am I making too > much of an assumption here? Why would you want to do this? > Because of the misalignment, output data of ft_sourceinterpolate > with "anatomy" and "avg.pow" does not agree with topoplot (run > ft_freqanalysis on the same dataset). > If anyone could explain why this alignment distortion might be > happening during ft_sourceanalysis and/or ft_sourceinterpolate, I'd > really appreciate it. > I am afraid you need to be a bit more specific in order for us to understand what may be going wrong here. Best, Jan-Mathijs > Thanks in advance, Akiko > > -- > Akiko Ikkai, Ph.D. > Postdoctoral Fellow > Department of Psychological and Brain Sciences > Johns Hopkins University > Ames Hall, 3400 N. Charles St. > Baltimore, MD 21218 > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From ting.ac at gmail.com Wed May 11 19:30:14 2011 From: ting.ac at gmail.com (Allison Connolly) Date: Wed, 11 May 2011 12:30:14 -0500 Subject: [FieldTrip] channelcmb with removed channels Message-ID: I am trying to do beamforming on some MEG data. However, some of the sensors railed during the recordings, so I want to remove them from the analysis. I declare the channels I want to use during import with ft_preprocessing by saying: cfg.channel = {'MEG','-TRIGGER','-RESPONSE',... '-UACurrent','-MxA','-MyA','-MzA','-GxxA','-GyxA','-GyyA',... '-GzyA','-GzxA','-MxaA','-MyaA','-MzaA','-E1','-E2','-E3','-E4',... '-A40','-A57','-A76','-A77','-A79','-A81','-A88','-A89','-A96',... '-A100','-A102','-A103','-A108','-A112','-A113','-A114','-A116',... '-A120','-A121','-A123','-A124','-A125','-A126','-A127','-A128',... '-A129','-A130','-A131','-A124','-A139','-A140','-A141','-A142',... '-A144','-A145','-A146','-A147','-A148'}; Then I use ft_freqanalysis to calculate the cross spectral density and ft_prepare_leadfield to create the brain grid. When I try to run ft_sourceanalysis, I get this error: creating dipole grid based on user specified dipole positions 13718 dipoles inside, 144943 dipoles outside brain ??? In an assignment A(I) = B, a matrix A cannot be resized. Error in ==> prepare_freq_matrices at 115 Cf(find(crsspctrmindx)) = freq.crsspctrm(crsspctrmindx(find(crsspctrmindx)), fbin); Error in ==> ft_sourceanalysis at 461 [Cf, Cr, Pr, Ntrials, cfg] = prepare_freq_matrices(cfg, data); I think it is because I have removed channels. When I try to run ft_freqanalysis while specifying the channels in cfg.channel, i get this error: the input is raw data with 111 channels and 60 trials ??? Error using ==> ft_freqanalysis at 352 *channels in cfg.channelcmb not present in cfg.channel* * *I think I need to explicitly define cfg.channelcmb, but I don't know how to do this if I have removed channels. -Allison -------------- next part -------------- An HTML attachment was scrubbed... URL: From jpoll at ugr.es Thu May 12 14:10:46 2011 From: jpoll at ugr.es (JOAN PAUL POZUELOS LOPEZ) Date: Thu, 12 May 2011 14:10:46 +0200 Subject: [FieldTrip] Problems with the Buffer Message-ID: Hello everyone, Im new using the matlab for analyzing ERP´s. I have been using the FASTER program (Nolan, Whelan &Reilly, 2010, Journal of Neuroscience Methods) and i have encounter a problem with some files contained in the filedtrip toolbox. The problem its that when it is computing the ICA the process is not finished because theres an error that says: "error - invalid MEX_file 'c: Users\....\Matlab\external\fieldtrip-20110320\realtime\buffer\matlab\buffer.mexw32': could not find the specified module. When i check the folder containing the Buffer.mexw32 file, it is in the folder that the Filepath looks. Any suggestions on how to solve this problem?. Thank you very much for your help JOAN PAUL POZUELOS LOPEZ Departamento de Psicología Experimental y Fisiología del Comportamiento Universidad de Granada jpoll at ugr.es From nuria.donamayor at neuro.uni-luebeck.de Fri May 13 10:42:05 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Fri, 13 May 2011 10:42:05 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> Dear fieltrip users, I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a 64-bit Matlab version and I am getting an error I don't know how to solve: hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); ??? SWITCH expression must be a scalar or string constant. Error in ==> read_4d_hdr at 60 switch format Error in ==> ft_read_header at 153 orig = read_4d_hdr(datafile); If I try to read the same data on my Windows PC with 32-bit Matlab I have no problem reading the header file (but I can't even finish the preprocessing before it runs out of memory, therefore the switch to the Linux machine), so I'm pretty clueless here... Can any of you help me? Thanks, Nuria Nuria Doñamayor Alonso, MSc Universitätsklinikum Schleswig-Holstein Campus Lübeck Klinik für Neurologie Ratzeburger Allee 160 23538 Lübeck From paul_c at gmx.de Fri May 13 11:27:01 2011 From: paul_c at gmx.de (Paul Czienskowski) Date: Fri, 13 May 2011 11:27:01 +0200 Subject: [FieldTrip] Systematic electrode displacement Message-ID: <4DCCF965.4050408@gmx.de> Dear fieldtrippers, I've got an issue with electrode placement and I hope that someone has any idea how to tackle those issues. For research on my diploma thesis I am fitting simulated data with the realistic brain shape I used to simulate the data as well as a icbm model (BEM models). I used the electrode system for the icbm152 brain provided by Robert Oostenveld and did some manual correction to the realistic brains (which were normalised to icbm brain) with the ft_electroderealign function. I simulated the data in a position near the auditory cortex, since this is the location where we assume our real ERP. In my fitted data I encountered strange systematic errors (especially some kind of bias on the z-axis), as seen on the boxplot_coord_20110407.png file (note that it's both age groups: 1 for old and 2 for young, scale is meters). While investigating on the origin of this bias, I made a box plot of the distance of the electrodes in the icbm model and the electrodes in each of the realistic models (dist_electrodes.png). Obviously there already is an bias in the electrodes placement. First I assumed this was caused my the manual correction of the electrodes I performed. To check this out, I fitted the very data with the manually corrected electrodes on the icbm brain. Still I found that there was a bias, mainly on the z-axis and - what astonished me even more, there was still a bias in the electrodes. This is observable in the boxplot_20110512_electrode_locations_matched.png (sorry for the German captions), x-Axis is coordinate and y-axis is the deviation of the electrode's positions. Furthermore I simulated and fitted a position near the vertex (though still in the brain ;) ). There was not so much of a bias there, therefore I assume it's mainly the lateral and maybe posterior electrodes causing the bias, not that much the superior. Due to those results I assumed that it's got something to do with the automatic projection of the electrodes on the head surface. I had no time yet to compare those electrode positions manually (or better visually), but this is definitely on my agenda. I wondered, if anyone had an idea, how to improve this, for electrode deviations up to ~10 cm is way to much, asking me. I already checked if there maybe was any confusion in the order of the electrodes, but I just checked the labels and this does not support it. Thanks in advance and best regards, Paul Czienskowski -- Paul Czienskowski Björnsonstr. 25 12163 Berlin Tel.: (+49)(0)30/221609359 Handy: (+49)(0)1788378772 -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_coord_20110407.jpg Type: image/jpeg Size: 17510 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: dist_electrodes.png Type: image/png Size: 8323 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_20110512_electrode_locations_matched.png Type: image/png Size: 6945 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: boxplot_20110512_coordinates.png Type: image/png Size: 8841 bytes Desc: not available URL: From yuvharpaz at gmail.com Fri May 13 13:39:29 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 13 May 2011 14:39:29 +0300 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de> Message-ID: Dear Nuria Is it exactly the same fieldtrip version? I hope someone will solve this. as temporary work around you can read the header on windows and then move to linux yuval On 13 May 2011 11:42, Nuria Donamayor Alonso < nuria.donamayor at neuro.uni-luebeck.de> wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a > 64-bit Matlab version and I am getting an error I don't know how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I have > no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to the > Linux machine), so I'm pretty clueless here... Can any of you help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuria.donamayor at neuro.uni-luebeck.de Fri May 13 14:34:36 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Fri, 13 May 2011 14:34:36 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> Yes, it is exectly the same version. Better said, versions, because I tried both 20110413 and 20110512.... ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com] Gesendet: Freitag, 13. Mai 2011 13:39 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Dear Nuria Is it exactly the same fieldtrip version? I hope someone will solve this. as temporary work around you can read the header on windows and then move to linux yuval On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: Dear fieltrip users, I am using fieldtrip to analyze my 4D/BTI data on a Linux machine with a 64-bit Matlab version and I am getting an error I don't know how to solve: hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); ??? SWITCH expression must be a scalar or string constant. Error in ==> read_4d_hdr at 60 switch format Error in ==> ft_read_header at 153 orig = read_4d_hdr(datafile); If I try to read the same data on my Windows PC with 32-bit Matlab I have no problem reading the header file (but I can't even finish the preprocessing before it runs out of memory, therefore the switch to the Linux machine), so I'm pretty clueless here... Can any of you help me? Thanks, Nuria Nuria Doñamayor Alonso, MSc Universitätsklinikum Schleswig-Holstein Campus Lübeck Klinik für Neurologie Ratzeburger Allee 160 23538 Lübeck _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html "Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams From jan.schoffelen at donders.ru.nl Fri May 13 16:43:41 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 13 May 2011 16:43:41 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de> Message-ID: Hi Nuria, Could you type dbstop if error on the command line, and evaluate what the variable 'format' is in your case? Thanks, Jan-Mathijs On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > Yes, it is exectly the same version. Better said, versions, because > I tried both 20110413 and 20110512.... > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com > ] > Gesendet: Freitag, 13. Mai 2011 13:39 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Dear Nuria > Is it exactly the same fieldtrip version? > I hope someone will solve this. > as temporary work around you can read the header on windows and then > move to linux > > yuval > > On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine > with a 64-bit Matlab version and I am getting an error I don't know > how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I > have no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to > the Linux machine), so I'm pretty clueless here... Can any of you > help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > > "Many were increasingly of the opinion that they'd all made a big > mistake in coming down from the trees in the first place. And some > said that even the trees had been a bad move, and that no one should > ever have left the oceans". Douglas Adams > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From anokhina at psychiatry.wustl.edu Sat May 14 17:10:43 2011 From: anokhina at psychiatry.wustl.edu (Anokhin, Andrey) Date: Sat, 14 May 2011 10:10:43 -0500 Subject: [FieldTrip] job announcement Message-ID: <86712757862F3640B2F4BB5C14D8EDC4090EF4A245@wusmexmbx2.medpriv.wucon.wustl.edu> An HTML attachment was scrubbed... URL: From l.frei at psy.gla.ac.uk Sat May 14 22:37:45 2011 From: l.frei at psy.gla.ac.uk (Luisa Frei) Date: Sat, 14 May 2011 21:37:45 +0100 Subject: [FieldTrip] stats on planar gradient topographies Message-ID: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Hi there, I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. This the code I used: %%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.001; cfg.clusterstatistic = 'maxsize'; cfg.minnbchan = 4; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.005; cfg.numrandomization = 500; design = [ones(1,13) ones(1,13)+1]; cfg.design = design; cfg.ivar = 1; cfg.channel = {'MEG',sub(1).allbadchan{:}}; cfg.latency = [.15 .2]; [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? Thanks, Luisa Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change.  -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 2.png Type: application/applefile Size: 73 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Picture 2.png Type: image/png Size: 105588 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon May 16 14:32:07 2011 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 16 May 2011 14:32:07 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Message-ID: Hi Luisa, schnell from the top of my head: wie definierst du denn deine neighbors? Ich seh nirgendwo ein Feld cfg.neighbors.... Ich muss das bei unserem 4D-System immer angeben.... Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind falsch definierst, so könntest du zu deinen "random" Clustern kommen. Ich mache diese Neighbor-Struktur folgendermaßen: cfg=[]; cfg.neighbourdist=0.1; %cfg.grad=Comb_AV1_1{1}.grad; cfg.layout='4D148.lay'; cfg.channel={'all'}; %cfg.grad.pnt=cfg.grad.pnt*100; dummy=neighbourselection(cfg); Da bekomme ich auch immer einen Output, wie viele Channels so in der Umgebung sind (sollten in etwa 5 sein). Hoffe das hilft dir weiter Viele Grüße Julian Am 14.05.2011 um 22:37 schrieb Luisa Frei: > Hi there, > I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. > This the code I used: > > %%%%%%%%%%%%%%%%%%%%%%%%%%% > cfg = []; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.001; > cfg.clusterstatistic = 'maxsize'; > cfg.minnbchan = 4; > > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.005; > cfg.numrandomization = 500; > > design = [ones(1,13) ones(1,13)+1]; > > cfg.design = design; > cfg.ivar = 1; > > cfg.channel = {'MEG',sub(1).allbadchan{:}}; > cfg.latency = [.15 .2]; > > [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? > > Thanks, > Luisa > > Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change. > > _______________________________________________ > 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 jm.horschig at donders.ru.nl Mon May 16 14:52:24 2011 From: jm.horschig at donders.ru.nl (=?ISO-8859-1?Q?=22J=F6rn_M=2E_Horschig=22?=) Date: Mon, 16 May 2011 14:52:24 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> Message-ID: <4DD11E08.6050207@donders.ru.nl> Hi all, First of all, @julian: It would be nice if you wrote in English so that all people can understand what you are saying :) Second, I would like to mention ft_neighbourplot, which is a relative new function and plots sensors and its' neighbours in 2D or 3D, depending on whether you got 2D or 3D coordinates. Using that function, you can verify whether your neighbourselection looks meaningful and makes sense. Finally, we are currently working on changing/improving the neighbourselecion function. There will be different methods to choose from, and we (me) will create templates for the most common systems that can be used instead of relying on a particular mathematical selection method. We will announce this when it's done (probably soon). Maybe Julian is right and Luisa's problem is due to a 'wrong' neighbourselection. Given that cfg.minnbhchan is set to 4, this might be likely, because not all of the found clusters consist of 4 or more channels. What system are you using? Best, Jörn On 5/16/2011 2:32 PM, Julian Keil wrote: > Hi Luisa, > > schnell from the top of my head: wie definierst du denn deine neighbors? > Ich seh nirgendwo ein Feld cfg.neighbors.... > Ich muss das bei unserem 4D-System immer angeben.... > Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind > falsch definierst, so könntest du zu deinen "random" Clustern kommen. > > Ich mache diese Neighbor-Struktur folgendermaßen: > > cfg=[]; > cfg.neighbourdist=0.1; > %cfg.grad=Comb_AV1_1{1}.grad; > cfg.layout='4D148.lay'; > cfg.channel={'all'}; > %cfg.grad.pnt=cfg.grad.pnt*100; > dummy=neighbourselection(cfg); > > Da bekomme ich auch immer einen Output, wie viele Channels so in der > Umgebung sind (sollten in etwa 5 sein). > > Hoffe das hilft dir weiter > > Viele Grüße > > Julian > > Am 14.05.2011 um 22:37 schrieb Luisa Frei: > >> Hi there, >> I am trying to compute a simple cluster-based statistic in a between >> subjects design. I have followed the steps in the respective tutorial >> very closely. >> This the code I used: >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%% >> cfg = []; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'indepsamplesT'; >> >> cfg.correctm = 'cluster'; >> cfg.clusteralpha = 0.001; >> cfg.clusterstatistic = 'maxsize'; >> cfg.minnbchan = 4; >> >> cfg.tail = 0; >> cfg.clustertail = 0; >> cfg.alpha = 0.005; >> cfg.numrandomization = 500; >> >> design = [ones(1,13) ones(1,13)+1]; >> >> cfg.design = design; >> cfg.ivar = 1; >> >> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >> cfg.latency = [.15 .2]; >> >> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % >> individuals kept >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> My problem is, that I'm not sure which time resolution to use. I >> would like to use a small resolution of 10 ms, but this leads to a >> fairly random pattern of significant sensors (see attached figure, on >> the right). Of course, the more time points I include, the less >> significant sensors are left over. However, another problem is, that >> the ones that are left (figure, left), are not related to big >> differences in the activation pattern at all. How is it possible that >> my significant sensors end up being so randomly distributed? Also, >> ft_timelockstatistics only comes up with one positive and one >> negative cluster., but the sign. sensors are not always connected. >> Could anyone give some helpful input here? >> >> Thanks, >> Luisa >> >> Fyi: I have tried different thresholds and different numbers of >> neighbourhood channels, but there's not much of a change. >> _______________________________________________ >> 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 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 Kapitelweg 29 NL-6525 EN Nijmegen The Netherlands -------------- next part -------------- An HTML attachment was scrubbed... URL: From julian.keil at gmail.com Mon May 16 14:58:35 2011 From: julian.keil at gmail.com (Julian Keil) Date: Mon, 16 May 2011 14:58:35 +0200 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: <4DD11E08.6050207@donders.ru.nl> References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> <4DD11E08.6050207@donders.ru.nl> Message-ID: Hi all, sorry, I thought the answer would only go to Luisa. Apologies, Julian Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig: > Hi all, > > First of all, @julian: It would be nice if you wrote in English so that all people can understand what you are saying :) > > Second, I would like to mention ft_neighbourplot, which is a relative new function and plots sensors and its' neighbours in 2D or 3D, depending on whether you got 2D or 3D coordinates. Using that function, you can verify whether your neighbourselection looks meaningful and makes sense. > > Finally, we are currently working on changing/improving the neighbourselecion function. There will be different methods to choose from, and we (me) will create templates for the most common systems that can be used instead of relying on a particular mathematical selection method. We will announce this when it's done (probably soon). > > Maybe Julian is right and Luisa's problem is due to a 'wrong' neighbourselection. Given that cfg.minnbhchan is set to 4, this might be likely, because not all of the found clusters consist of 4 or more channels. What system are you using? > > Best, > Jörn > > > On 5/16/2011 2:32 PM, Julian Keil wrote: >> >> Hi Luisa, >> >> schnell from the top of my head: wie definierst du denn deine neighbors? >> Ich seh nirgendwo ein Feld cfg.neighbors.... >> Ich muss das bei unserem 4D-System immer angeben.... >> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen sind falsch definierst, so könntest du zu deinen "random" Clustern kommen. >> >> Ich mache diese Neighbor-Struktur folgendermaßen: >> >> cfg=[]; >> cfg.neighbourdist=0.1; >> %cfg.grad=Comb_AV1_1{1}.grad; >> cfg.layout='4D148.lay'; >> cfg.channel={'all'}; >> %cfg.grad.pnt=cfg.grad.pnt*100; >> dummy=neighbourselection(cfg); >> >> Da bekomme ich auch immer einen Output, wie viele Channels so in der Umgebung sind (sollten in etwa 5 sein). >> >> Hoffe das hilft dir weiter >> >> Viele Grüße >> >> Julian >> >> Am 14.05.2011 um 22:37 schrieb Luisa Frei: >> >>> Hi there, >>> I am trying to compute a simple cluster-based statistic in a between subjects design. I have followed the steps in the respective tutorial very closely. >>> This the code I used: >>> >>> %%%%%%%%%%%%%%%%%%%%%%%%%%% >>> cfg = []; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'indepsamplesT'; >>> >>> cfg.correctm = 'cluster'; >>> cfg.clusteralpha = 0.001; >>> cfg.clusterstatistic = 'maxsize'; >>> cfg.minnbchan = 4; >>> >>> cfg.tail = 0; >>> cfg.clustertail = 0; >>> cfg.alpha = 0.005; >>> cfg.numrandomization = 500; >>> >>> design = [ones(1,13) ones(1,13)+1]; >>> >>> cfg.design = design; >>> cfg.ivar = 1; >>> >>> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >>> cfg.latency = [.15 .2]; >>> >>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % individuals kept >>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>> >>> My problem is, that I'm not sure which time resolution to use. I would like to use a small resolution of 10 ms, but this leads to a fairly random pattern of significant sensors (see attached figure, on the right). Of course, the more time points I include, the less significant sensors are left over. However, another problem is, that the ones that are left (figure, left), are not related to big differences in the activation pattern at all. How is it possible that my significant sensors end up being so randomly distributed? Also, ft_timelockstatistics only comes up with one positive and one negative cluster., but the sign. sensors are not always connected. Could anyone give some helpful input here? >>> >>> Thanks, >>> Luisa >>> >>> Fyi: I have tried different thresholds and different numbers of neighbourhood channels, but there's not much of a change. >>> _______________________________________________ >>> 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 > > 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 > Kapitelweg 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 l.frei at psy.gla.ac.uk Mon May 16 15:10:27 2011 From: l.frei at psy.gla.ac.uk (Luisa Frei) Date: Mon, 16 May 2011 14:10:27 +0100 Subject: [FieldTrip] stats on planar gradient topographies In-Reply-To: References: <07267643-5DE9-427B-B1B3-3EAAF68D73CF@psy.gla.ac.uk> <4DD11E08.6050207@donders.ru.nl> Message-ID: <95704E05-6DEC-4B66-A9EA-381B9C88CA12@psy.gla.ac.uk> Thanks for all the answers, I'll try Julian's suggestion and let you know what happens. Luisa On 16 May 2011, at 13:58, Julian Keil wrote: > Hi all, > > sorry, I thought the answer would only go to Luisa. > > Apologies, > Julian > > Am 16.05.2011 um 14:52 schrieb Jörn M. Horschig: > >> Hi all, >> >> First of all, @julian: It would be nice if you wrote in English so >> that all people can understand what you are saying :) >> >> Second, I would like to mention ft_neighbourplot, which is a >> relative new function and plots sensors and its' neighbours in 2D >> or 3D, depending on whether you got 2D or 3D coordinates. Using >> that function, you can verify whether your neighbourselection >> looks meaningful and makes sense. >> >> Finally, we are currently working on changing/improving the >> neighbourselecion function. There will be different methods to >> choose from, and we (me) will create templates for the most common >> systems that can be used instead of relying on a particular >> mathematical selection method. We will announce this when it's >> done (probably soon). >> >> Maybe Julian is right and Luisa's problem is due to a 'wrong' >> neighbourselection. Given that cfg.minnbhchan is set to 4, this >> might be likely, because not all of the found clusters consist of >> 4 or more channels. What system are you using? >> >> Best, >> Jörn >> >> >> On 5/16/2011 2:32 PM, Julian Keil wrote: >>> >>> Hi Luisa, >>> >>> schnell from the top of my head: wie definierst du denn deine >>> neighbors? >>> Ich seh nirgendwo ein Feld cfg.neighbors.... >>> Ich muss das bei unserem 4D-System immer angeben.... >>> Es könnte sein, dass du die Struktur, welche Kanäle neben welchen >>> sind falsch definierst, so könntest du zu deinen "random" >>> Clustern kommen. >>> >>> Ich mache diese Neighbor-Struktur folgendermaßen: >>> >>> cfg=[]; >>> cfg.neighbourdist=0.1; >>> %cfg.grad=Comb_AV1_1{1}.grad; >>> cfg.layout='4D148.lay'; >>> cfg.channel={'all'}; >>> %cfg.grad.pnt=cfg.grad.pnt*100; >>> dummy=neighbourselection(cfg); >>> >>> Da bekomme ich auch immer einen Output, wie viele Channels so in >>> der Umgebung sind (sollten in etwa 5 sein). >>> >>> Hoffe das hilft dir weiter >>> >>> Viele Grüße >>> >>> Julian >>> >>> Am 14.05.2011 um 22:37 schrieb Luisa Frei: >>> >>>> Hi there, >>>> I am trying to compute a simple cluster-based statistic in a >>>> between subjects design. I have followed the steps in the >>>> respective tutorial very closely. >>>> This the code I used: >>>> >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> cfg = []; >>>> cfg.method = 'montecarlo'; >>>> cfg.statistic = 'indepsamplesT'; >>>> >>>> cfg.correctm = 'cluster'; >>>> cfg.clusteralpha = 0.001; >>>> cfg.clusterstatistic = 'maxsize'; >>>> cfg.minnbchan = 4; >>>> >>>> cfg.tail = 0; >>>> cfg.clustertail = 0; >>>> cfg.alpha = 0.005; >>>> cfg.numrandomization = 500; >>>> >>>> design = [ones(1,13) ones(1,13)+1]; >>>> >>>> cfg.design = design; >>>> cfg.ivar = 1; >>>> >>>> cfg.channel = {'MEG',sub(1).allbadchan{:}}; >>>> cfg.latency = [.15 .2]; >>>> >>>> [stat] = ft_timelockstatistics(cfg, grandavgG,grandavgE); % >>>> individuals kept >>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >>>> >>>> My problem is, that I'm not sure which time resolution to use. I >>>> would like to use a small resolution of 10 ms, but this leads to >>>> a fairly random pattern of significant sensors (see attached >>>> figure, on the right). Of course, the more time points I >>>> include, the less significant sensors are left over. However, >>>> another problem is, that the ones that are left (figure, left), >>>> are not related to big differences in the activation pattern at >>>> all. How is it possible that my significant sensors end up being >>>> so randomly distributed? Also, ft_timelockstatistics only comes >>>> up with one positive and one negative cluster., but the sign. >>>> sensors are not always connected. Could anyone give some helpful >>>> input here? >>>> >>>> Thanks, >>>> Luisa >>>> >>>> Fyi: I have tried different thresholds and different numbers of >>>> neighbourhood channels, but there's not much of a change. >>>> _______________________________________________ >>>> 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 >> >> 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 >> Kapitelweg 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.lozanosoldevilla at fcdonders.ru.nl Mon May 16 15:59:36 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 16 May 2011 15:59:36 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection Message-ID: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> Dear Fieldtrippers, I'm using ft_rejectvisual function to reject visually EOG artifacts of epoched trials. My problem consist that I'm not able to plot only the EOG channels even when I explicitly select them ignoring the 'MEG' channels (I get a plot with all channels MEG + EOG). I directly used rejectvisual_channel (used in line 263 offt_rejectvisual) function selecting the EOG channels but I'm getting again all channels. Somebody could tell me what I'm doing wrong? Thanks in advance, Diego PS: Code %epoching cfg = []; cfg.dataset = [direc d(rr,1).name]; cfg.trialdef.eventtype = 'frontpanel trigger'; cfg.trialdef.eventvalue = 4; cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 4; % in seconds cfg.trialdef.epochmoving = 'inbackward'; cfg.trialdef.pivoteventvalue = 2;% cue stimulus cfg.trialdef.jumps = 1; cfg.trialfun = 'trialselec'; cfg = ft_definetrial(cfg); cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.lpfilter = 'yes'; cfg.lpfreq = 250; cfg.baselinewindow = [-1 0]; cfg.keeptrials = 'yes'; cfg.demean = 'yes'; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); %.............. %visual data rejection cfg = []; cfg.channel = {'EEG057' 'EEG058'}; cfg.method = 'channel'; cfg.keepchannel = 'yes'; data_c = ft_rejectvisual(cfg,data); -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From stan.vanpelt at fcdonders.ru.nl Mon May 16 16:16:16 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 May 2011 16:16:16 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> References: <492082518.129940.1305554376843.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> Hi Diego, You could try using ft_databrowser instead of ft_rejectvisual (followed by ft_rejectartifact), so: cfg = []; cfg.continuous = 'no'; cfg.channel = {'EEG057','EEG058'}; cfg = ft_databrowser(cfg,data); I think it should work like this. Best, Stan -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano Soldevilla, D. (Diego) Sent: Monday, May 16, 2011 4:00 PM To: fieldtrip at donders.ru.nl Subject: [FieldTrip] ft_rejectvisual channel selection Dear Fieldtrippers, I'm using ft_rejectvisual function to reject visually EOG artifacts of epoched trials. My problem consist that I'm not able to plot only the EOG channels even when I explicitly select them ignoring the 'MEG' channels (I get a plot with all channels MEG + EOG). I directly used rejectvisual_channel (used in line 263 offt_rejectvisual) function selecting the EOG channels but I'm getting again all channels. Somebody could tell me what I'm doing wrong? Thanks in advance, Diego PS: Code %epoching cfg = []; cfg.dataset = [direc d(rr,1).name]; cfg.trialdef.eventtype = 'frontpanel trigger'; cfg.trialdef.eventvalue = 4; cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 4; % in seconds cfg.trialdef.epochmoving = 'inbackward'; cfg.trialdef.pivoteventvalue = 2;% cue stimulus cfg.trialdef.jumps = 1; cfg.trialfun = 'trialselec'; cfg = ft_definetrial(cfg); cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.lpfilter = 'yes'; cfg.lpfreq = 250; cfg.baselinewindow = [-1 0]; cfg.keeptrials = 'yes'; cfg.demean = 'yes'; cfg.continuous = 'yes'; data = ft_preprocessing(cfg); %.............. %visual data rejection cfg = []; cfg.channel = {'EEG057' 'EEG058'}; cfg.method = 'channel'; cfg.keepchannel = 'yes'; data_c = ft_rejectvisual(cfg,data); -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.lozanosoldevilla at fcdonders.ru.nl Mon May 16 16:24:38 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Mon, 16 May 2011 16:24:38 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> Message-ID: <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> Hi Stan, Thanks for your quickly answer. I get this error: Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording > In utilities/private/warning_once at 81 In utilities/private/fixtrialdef at 52 In ft_datatype_raw at 91 In ft_checkdata at 161 In ft_databrowser at 120 redrawing with viewmode butterfly ??? Improper index matrix reference. Error in ==> ft_databrowser>redraw_cb at 910 evtsample = [event(:).sample]; Error in ==> ft_databrowser at 419 redraw_cb(h); I don't know why my data have no trial definition when I'm sure that is epoched... Any ideas? Thanks in advance, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 4:16:16 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > You could try using ft_databrowser instead of ft_rejectvisual > (followed by > ft_rejectartifact), so: > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = {'EEG057','EEG058'}; > cfg = ft_databrowser(cfg,data); > > I think it should work like this. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:00 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] ft_rejectvisual channel selection > > Dear Fieldtrippers, > > I'm using ft_rejectvisual function to reject visually EOG artifacts > of > epoched trials. My problem consist that I'm not able to plot only the > EOG > channels even when I explicitly select them ignoring the 'MEG' > channels (I > get a plot with all channels MEG + EOG). > > I directly used rejectvisual_channel (used in line 263 > offt_rejectvisual) > function selecting the EOG channels but I'm getting again all > channels. > Somebody could tell me what I'm doing wrong? > > Thanks in advance, > > Diego > > > > PS: Code > > %epoching > cfg = []; > cfg.dataset = [direc d(rr,1).name]; > cfg.trialdef.eventtype = 'frontpanel trigger'; > cfg.trialdef.eventvalue = 4; > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 4; % in seconds > cfg.trialdef.epochmoving = 'inbackward'; > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > cfg.trialdef.jumps = 1; > cfg.trialfun = 'trialselec'; > > cfg = ft_definetrial(cfg); > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.lpfilter = 'yes'; > cfg.lpfreq = 250; > cfg.baselinewindow = [-1 0]; > cfg.keeptrials = 'yes'; > cfg.demean = 'yes'; > cfg.continuous = 'yes'; > > data = ft_preprocessing(cfg); > > %.............. > > > %visual data rejection > cfg = []; > cfg.channel = {'EEG057' 'EEG058'}; > cfg.method = 'channel'; > cfg.keepchannel = 'yes'; > data_c = ft_rejectvisual(cfg,data); > > > > -- > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > _______________________________________________ > 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 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From stan.vanpelt at fcdonders.ru.nl Mon May 16 21:40:11 2011 From: stan.vanpelt at fcdonders.ru.nl (Stan van Pelt) Date: Mon, 16 May 2011 21:40:11 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> References: <022901cc13d3$d13ec200$73bc4600$@vanpelt@fcdonders.ru.nl> <1082570781.130469.1305555878921.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <024701cc1401$122fb120$368f1360$@vanpelt@fcdonders.ru.nl> Hi Diego, Hm, sounds odd to me. Is your trial-definition output from ft_definetrial correct? So a cfg.trl that is not empty? Otherwise, you might try starting with an empty cfg again before calling ft_preprocessing? cfg=ft_definetrial(cfg); trials=cfg.trl; cfg=[]; cfg.trl=trials; cfg.dataset = [direc d(rr,1).name]; cfg.channel = {'MEG' 'EEG057' 'EEG058'}; cfg.continuous = 'yes'; etc.. data = ft_preprocessing(cfg); That should give you an output with a trial-structure, I'd say. Best, Stan -----Original Message----- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano Soldevilla, D. (Diego) Sent: Monday, May 16, 2011 4:25 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] ft_rejectvisual channel selection Hi Stan, Thanks for your quickly answer. I get this error: Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording > In utilities/private/warning_once at 81 In utilities/private/fixtrialdef at 52 In ft_datatype_raw at 91 In ft_checkdata at 161 In ft_databrowser at 120 redrawing with viewmode butterfly ??? Improper index matrix reference. Error in ==> ft_databrowser>redraw_cb at 910 evtsample = [event(:).sample]; Error in ==> ft_databrowser at 419 redraw_cb(h); I don't know why my data have no trial definition when I'm sure that is epoched... Any ideas? Thanks in advance, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 4:16:16 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > You could try using ft_databrowser instead of ft_rejectvisual > (followed by > ft_rejectartifact), so: > > cfg = []; > cfg.continuous = 'no'; > cfg.channel = {'EEG057','EEG058'}; > cfg = ft_databrowser(cfg,data); > > I think it should work like this. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:00 PM > To: fieldtrip at donders.ru.nl > Subject: [FieldTrip] ft_rejectvisual channel selection > > Dear Fieldtrippers, > > I'm using ft_rejectvisual function to reject visually EOG artifacts > of > epoched trials. My problem consist that I'm not able to plot only the > EOG > channels even when I explicitly select them ignoring the 'MEG' > channels (I > get a plot with all channels MEG + EOG). > > I directly used rejectvisual_channel (used in line 263 > offt_rejectvisual) > function selecting the EOG channels but I'm getting again all > channels. > Somebody could tell me what I'm doing wrong? > > Thanks in advance, > > Diego > > > > PS: Code > > %epoching > cfg = []; > cfg.dataset = [direc d(rr,1).name]; > cfg.trialdef.eventtype = 'frontpanel trigger'; > cfg.trialdef.eventvalue = 4; > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 4; % in seconds > cfg.trialdef.epochmoving = 'inbackward'; > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > cfg.trialdef.jumps = 1; > cfg.trialfun = 'trialselec'; > > cfg = ft_definetrial(cfg); > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.lpfilter = 'yes'; > cfg.lpfreq = 250; > cfg.baselinewindow = [-1 0]; > cfg.keeptrials = 'yes'; > cfg.demean = 'yes'; > cfg.continuous = 'yes'; > > data = ft_preprocessing(cfg); > > %.............. > > > %visual data rejection > cfg = []; > cfg.channel = {'EEG057' 'EEG058'}; > cfg.method = 'channel'; > cfg.keepchannel = 'yes'; > data_c = ft_rejectvisual(cfg,data); > > > > -- > PhD Student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > _______________________________________________ > 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 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From d.lozanosoldevilla at fcdonders.ru.nl Tue May 17 00:19:50 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Tue, 17 May 2011 00:19:50 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <940868980.135061.1305583605111.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> Hi Stan, You're right. It seems that my problem lies in the lack of trl because I previously resample my data and this last function do not creates a new trl with the updated begin and end samples. If I create a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) *data.fsample);, I get the same error but not with the original data (without resampling). Then I'll use data without resampling to check my artifacts. Thanks again, Diego ----- "Stan van Pelt" wrote: > From: "Stan van Pelt" > To: "Email discussion list for the FieldTrip project" > Sent: Monday, 16 May, 2011 9:40:11 PM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > Hm, sounds odd to me. Is your trial-definition output from > ft_definetrial > correct? So a cfg.trl that is not empty? > > Otherwise, you might try starting with an empty cfg again before > calling > ft_preprocessing? > > cfg=ft_definetrial(cfg); > trials=cfg.trl; > > cfg=[]; > cfg.trl=trials; > cfg.dataset = [direc d(rr,1).name]; > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > cfg.continuous = 'yes'; > etc.. > data = ft_preprocessing(cfg); > > That should give you an output with a trial-structure, I'd say. > > Best, > Stan > > -----Original Message----- > From: fieldtrip-bounces at donders.ru.nl > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > Soldevilla, > D. (Diego) > Sent: Monday, May 16, 2011 4:25 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Stan, > > Thanks for your quickly answer. I get this error: > > Warning: the data does not contain a trial definition, assuming that > the > trials are consecutive segments of a continuous recording > > In utilities/private/warning_once at 81 > In utilities/private/fixtrialdef at 52 > In ft_datatype_raw at 91 > In ft_checkdata at 161 > In ft_databrowser at 120 > redrawing with viewmode butterfly > ??? Improper index matrix reference. > > Error in ==> ft_databrowser>redraw_cb at 910 > evtsample = [event(:).sample]; > > Error in ==> ft_databrowser at 419 > redraw_cb(h); > > I don't know why my data have no trial definition when I'm sure that > is > epoched... Any ideas? > > Thanks in advance, > > Diego > > > > ----- "Stan van Pelt" wrote: > > > From: "Stan van Pelt" > > To: "Email discussion list for the FieldTrip project" > > > Sent: Monday, 16 May, 2011 4:16:16 PM > > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > > > Hi Diego, > > > > You could try using ft_databrowser instead of ft_rejectvisual > > (followed by > > ft_rejectartifact), so: > > > > cfg = []; > > cfg.continuous = 'no'; > > cfg.channel = {'EEG057','EEG058'}; > > cfg = ft_databrowser(cfg,data); > > > > I think it should work like this. > > > > Best, > > Stan > > > > -----Original Message----- > > From: fieldtrip-bounces at donders.ru.nl > > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > > Soldevilla, > > D. (Diego) > > Sent: Monday, May 16, 2011 4:00 PM > > To: fieldtrip at donders.ru.nl > > Subject: [FieldTrip] ft_rejectvisual channel selection > > > > Dear Fieldtrippers, > > > > I'm using ft_rejectvisual function to reject visually EOG artifacts > > of > > epoched trials. My problem consist that I'm not able to plot only > the > > EOG > > channels even when I explicitly select them ignoring the 'MEG' > > channels (I > > get a plot with all channels MEG + EOG). > > > > I directly used rejectvisual_channel (used in line 263 > > offt_rejectvisual) > > function selecting the EOG channels but I'm getting again all > > channels. > > Somebody could tell me what I'm doing wrong? > > > > Thanks in advance, > > > > Diego > > > > > > > > PS: Code > > > > %epoching > > cfg = []; > > cfg.dataset = [direc d(rr,1).name]; > > cfg.trialdef.eventtype = 'frontpanel trigger'; > > cfg.trialdef.eventvalue = 4; > > cfg.trialdef.prestim = 1; % in seconds > > cfg.trialdef.poststim = 4; % in seconds > > cfg.trialdef.epochmoving = 'inbackward'; > > cfg.trialdef.pivoteventvalue = 2;% cue stimulus > > cfg.trialdef.jumps = 1; > > cfg.trialfun = 'trialselec'; > > > > cfg = ft_definetrial(cfg); > > > > cfg.channel = {'MEG' 'EEG057' 'EEG058'}; > > cfg.lpfilter = 'yes'; > > cfg.lpfreq = 250; > > cfg.baselinewindow = [-1 0]; > > cfg.keeptrials = 'yes'; > > cfg.demean = 'yes'; > > cfg.continuous = 'yes'; > > > > data = ft_preprocessing(cfg); > > > > %.............. > > > > > > %visual data rejection > > cfg = []; > > cfg.channel = {'EEG057' 'EEG058'}; > > cfg.method = 'channel'; > > cfg.keepchannel = 'yes'; > > data_c = ft_rejectvisual(cfg,data); > > > > > > > > -- > > PhD Student > > Donders Institute for Brain, Cognition and Behaviour > > Centre for Cognitive Neuroimaging > > Trigon, room 0.83 > > Kapittelweg 29 > > Radboud University Nijmegen > > NL-6500 HB Nijmegen > > The Netherlands > > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > > Tel: +31-(0)24-36-66274 > > Web: http://www.neuosc.com/ > > _______________________________________________ > > 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 > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Trigon, room 0.83 > Kapittelweg 29 > Radboud University Nijmegen > NL-6500 HB Nijmegen > The Netherlands > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > Tel: +31-(0)24-36-66274 > Web: http://www.neuosc.com/ > > > _______________________________________________ > 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 From younes_zerouali at hotmail.com Tue May 17 00:25:25 2011 From: younes_zerouali at hotmail.com (Younes Zerouali) Date: Mon, 16 May 2011 18:25:25 -0400 Subject: [FieldTrip] Segment anatomy from MRI (spm8) Message-ID: Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 17 08:18:39 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 17 May 2011 08:18:39 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: References: Message-ID: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit, skin_a = imerode(skin, s); brain_a = imdilate(brain, s); skull = (brain_a & skin_a); Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 17 08:42:22 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 17 May 2011 08:42:22 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> References: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> Message-ID: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote: > Hi Younes, > > this is actually not a problem with the function. The > "ft_volumesegment" will only return segmentations of the anatomical > mri with respect to three tissue types: grey matter, white matter, > and csf. You can use gray and white matter segmentations to > construct your brain compartement by typing e. g. "brain = > (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order > to get skull and skin compartements, you need your original > mri.anatomy which holds the image intensity on a black-to-white > scale. You can threshold the white values to segment the head from > the background, and this is then your skin compartement (e. g., > "skin = (mri.anatomy>300);" as shown in the tutorial). The skull > compartement is the oversection of the skin compartement and the > brain compartement after you blew up those compartements a bit, > skin_a = imerode(skin, s); > brain_a = imdilate(brain, s); > skull = (brain_a & skin_a); > Especially the construction of the skin is a lot of work, as you > need the wholes in the anatomical mri (eyes, ear, inhomogeneities) > by hand. > > Best regards and good luck, > Gregor > > > > > -- > Dr. rer. nat. Gregor Volberg > ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) > University of Regensburg > Institute for Experimental Psychology > 93040 Regensburg, Germany > Tel: +49 941 943 3862 > Fax: +49 941 943 3233 > http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html > > > >>> Younes Zerouali 5/17/2011 12:25 AM > >>> > Hi all, > > I'm trying to segment head anatomical surfaces (scalp, skull) using > the mri scan from patient Colin27 (MNI, Montreal) following the > steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel > ). > My problem is that the function "ft_volumesegment" doesn't return > all the variables that are mentionned in the tutorial. For example, > there is no field named "skull" or "scalp" in the argument returned > by this function. Anyone had this problem before? > > Best, > > > Younes > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gregor.Volberg at psychologie.uni-regensburg.de Tue May 17 09:14:54 2011 From: Gregor.Volberg at psychologie.uni-regensburg.de (Gregor Volberg) Date: Tue, 17 May 2011 09:14:54 +0200 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> References: <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de> <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Message-ID: <4DD23C8E02000057000096DB@gwsmtp1.uni-regensburg.de> Dear Jan-Matthijs, I wasn't aware of this! Thanks a lot dear fieldtrippers, this is surely a helpful addition to ft_volumesegment. Best regards, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> jan-mathijs schoffelen 5/17/2011 8:42 AM >>> Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote: Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit, skin_a = imerode(skin, s); brain_a = imdilate(brain, s); skull = (brain_a & skin_a); Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck, Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at donders.ru.nl Tue May 17 09:28:36 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 17 May 2011 09:28:36 +0200 Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> References: <940868980.135061.1305583605111.JavaMail.root@sculptor.zimbra.ru.nl> <729723926.135100.1305584390797.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: Hi Diego, Indeed, it is probably a good idea to check for artifacts before performing any resampling. The sample indices that are stored in trl (or sampleinfo) matrices, should always correspond to sample indices in the *original* dataset (on disk), and do not necessarily have any direct relation to sample indices in the data you have in memory. Therefore, if you resample the data, the samples in your data in memory do not directly correspond to samples in the dataset on disk anymore; so therefore trl or sampleinfo fields would not make sense, and might even lead to inconsistencies. This is the reason that ft_resampledata removes any such fields, if present, from your (in-memory) dataset. We are currently in the process of thinking hard about the trl and sampleinfo matrices, and might revise how these are handled in the future. In any case, it should become possible (already on our todo-list) to use the artifact detection functions on in-data memory without explicit sample indices. But, for now, your solution is the quickest one :) Best, Eelke 2011/5/17 Lozano Soldevilla, D. (Diego) : > Hi Stan, > > You're right. It seems that my problem lies in the lack of trl because I previously resample my data and this last function do not creates a new trl with the updated begin and end samples. If I create a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) *data.fsample);, I get the same error but not with the original data (without resampling). Then I'll use data without resampling to check my artifacts. > > Thanks again, > > Diego > > > > ----- "Stan van Pelt" wrote: > >> From: "Stan van Pelt" >> To: "Email discussion list for the FieldTrip project" >> Sent: Monday, 16 May, 2011 9:40:11 PM >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> >> Hi Diego, >> >> Hm, sounds odd to me. Is your trial-definition output from >> ft_definetrial >> correct? So a cfg.trl that is not empty? >> >> Otherwise, you might try starting with an empty cfg again before >> calling >> ft_preprocessing? >> >> cfg=ft_definetrial(cfg); >> trials=cfg.trl; >> >> cfg=[]; >> cfg.trl=trials; >> cfg.dataset                     = [direc d(rr,1).name]; >> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; >> cfg.continuous                  = 'yes'; >> etc.. >> data                            = ft_preprocessing(cfg); >> >> That should give you an output with a trial-structure, I'd say. >> >> Best, >> Stan >> >> -----Original Message----- >> From: fieldtrip-bounces at donders.ru.nl >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano >> Soldevilla, >> D. (Diego) >> Sent: Monday, May 16, 2011 4:25 PM >> To: Email discussion list for the FieldTrip project >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> >> Hi Stan, >> >> Thanks for your quickly answer. I get this error: >> >> Warning: the data does not contain a trial definition, assuming that >> the >> trials are consecutive segments of a continuous recording >> > In utilities/private/warning_once at 81 >>   In utilities/private/fixtrialdef at 52 >>   In ft_datatype_raw at 91 >>   In ft_checkdata at 161 >>   In ft_databrowser at 120 >> redrawing with viewmode butterfly >> ??? Improper index matrix reference. >> >> Error in ==> ft_databrowser>redraw_cb at 910 >>   evtsample = [event(:).sample]; >> >> Error in ==> ft_databrowser at 419 >> redraw_cb(h); >> >> I don't know why my data have no trial definition when I'm sure that >> is >> epoched... Any ideas? >> >> Thanks in advance, >> >> Diego >> >> >> >> ----- "Stan van Pelt" wrote: >> >> > From: "Stan van Pelt" >> > To: "Email discussion list for the FieldTrip project" >> >> > Sent: Monday, 16 May, 2011 4:16:16 PM >> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection >> > >> > Hi Diego, >> > >> > You could try using ft_databrowser instead of ft_rejectvisual >> > (followed by >> > ft_rejectartifact), so: >> > >> > cfg            = []; >> > cfg.continuous = 'no'; >> > cfg.channel    = {'EEG057','EEG058'}; >> > cfg            = ft_databrowser(cfg,data); >> > >> > I think it should work like this. >> > >> > Best, >> > Stan >> > >> > -----Original Message----- >> > From: fieldtrip-bounces at donders.ru.nl >> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano >> > Soldevilla, >> > D. (Diego) >> > Sent: Monday, May 16, 2011 4:00 PM >> > To: fieldtrip at donders.ru.nl >> > Subject: [FieldTrip] ft_rejectvisual channel selection >> > >> > Dear Fieldtrippers, >> > >> > I'm using ft_rejectvisual function to reject visually EOG artifacts >> > of >> > epoched trials. My problem consist that I'm not able to plot only >> the >> > EOG >> > channels even when I explicitly select them ignoring the 'MEG' >> > channels (I >> > get a plot with all channels MEG + EOG). >> > >> > I directly used rejectvisual_channel (used in line 263 >> > offt_rejectvisual) >> > function selecting the EOG channels but I'm getting again all >> > channels. >> > Somebody could tell me what I'm doing wrong? >> > >> > Thanks in advance, >> > >> > Diego >> > >> > >> > >> > PS: Code >> > >> > %epoching >> > cfg = []; >> > cfg.dataset                     = [direc d(rr,1).name]; >> > cfg.trialdef.eventtype          = 'frontpanel trigger'; >> > cfg.trialdef.eventvalue         = 4; >> > cfg.trialdef.prestim            = 1; % in seconds >> > cfg.trialdef.poststim           = 4; % in seconds >> > cfg.trialdef.epochmoving        = 'inbackward'; >> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus >> > cfg.trialdef.jumps              = 1; >> > cfg.trialfun                    = 'trialselec'; >> > >> > cfg = ft_definetrial(cfg); >> > >> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; >> > cfg.lpfilter                    = 'yes'; >> > cfg.lpfreq                      = 250; >> > cfg.baselinewindow              = [-1 0]; >> > cfg.keeptrials                  = 'yes'; >> > cfg.demean                      = 'yes'; >> > cfg.continuous                  = 'yes'; >> > >> > data    = ft_preprocessing(cfg); >> > >> > %.............. >> > >> > >> > %visual data rejection >> > cfg             = []; >> > cfg.channel     = {'EEG057' 'EEG058'}; >> > cfg.method      = 'channel'; >> > cfg.keepchannel = 'yes'; >> > data_c          = ft_rejectvisual(cfg,data); >> > >> > >> > >> > -- >> > PhD Student >> > Donders Institute for Brain, Cognition and Behaviour >> > Centre for Cognitive Neuroimaging >> > Trigon, room 0.83 >> > Kapittelweg 29 >> > Radboud University Nijmegen >> > NL-6500 HB Nijmegen >> > The Netherlands >> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl >> > Tel:      +31-(0)24-36-66274 >> > Web:    http://www.neuosc.com/ >> > _______________________________________________ >> > 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 >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognitive Neuroimaging >> Trigon, room 0.83 >> Kapittelweg 29 >> Radboud University Nijmegen >> NL-6500 HB Nijmegen >> The Netherlands >> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl >> Tel:      +31-(0)24-36-66274 >> Web:    http://www.neuosc.com/ >> >> >> _______________________________________________ >> 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 > From d.lozanosoldevilla at fcdonders.ru.nl Tue May 17 09:37:09 2011 From: d.lozanosoldevilla at fcdonders.ru.nl (Lozano Soldevilla, D. (Diego)) Date: Tue, 17 May 2011 09:37:09 +0200 (CEST) Subject: [FieldTrip] ft_rejectvisual channel selection In-Reply-To: <1942589717.137158.1305617671275.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <1909529539.137200.1305617829447.JavaMail.root@sculptor.zimbra.ru.nl> Thanks for your explanation Eelke ;). Now all makes sense. Diego ----- "Eelke Spaak" wrote: > From: "Eelke Spaak" > To: "Email discussion list for the FieldTrip project" > Sent: Tuesday, 17 May, 2011 9:28:36 AM > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > > Hi Diego, > > Indeed, it is probably a good idea to check for artifacts before > performing any resampling. The sample indices that are stored in trl > (or sampleinfo) matrices, should always correspond to sample indices > in the *original* dataset (on disk), and do not necessarily have any > direct relation to sample indices in the data you have in memory. > Therefore, if you resample the data, the samples in your data in > memory do not directly correspond to samples in the dataset on disk > anymore; so therefore trl or sampleinfo fields would not make sense, > and might even lead to inconsistencies. This is the reason that > ft_resampledata removes any such fields, if present, from your > (in-memory) dataset. > > We are currently in the process of thinking hard about the trl and > sampleinfo matrices, and might revise how these are handled in the > future. In any case, it should become possible (already on our > todo-list) to use the artifact detection functions on in-data memory > without explicit sample indices. > > But, for now, your solution is the quickest one :) > > Best, > Eelke > > 2011/5/17 Lozano Soldevilla, D. (Diego) > : > > Hi Stan, > > > > You're right. It seems that my problem lies in the lack of trl > because I previously resample my data and this last function do not > creates a new trl with the updated begin and end samples. If I create > a new trl = round(data.cfg.previous.trl(:,1:3) * (1/data.cfg.origfs) > *data.fsample);, I get the same error but not with the original data > (without resampling). Then I'll use data without resampling to check > my artifacts. > > > > Thanks again, > > > > Diego > > > > > > > > ----- "Stan van Pelt" wrote: > > > >> From: "Stan van Pelt" > >> To: "Email discussion list for the FieldTrip project" > > >> Sent: Monday, 16 May, 2011 9:40:11 PM > >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > >> Hi Diego, > >> > >> Hm, sounds odd to me. Is your trial-definition output from > >> ft_definetrial > >> correct? So a cfg.trl that is not empty? > >> > >> Otherwise, you might try starting with an empty cfg again before > >> calling > >> ft_preprocessing? > >> > >> cfg=ft_definetrial(cfg); > >> trials=cfg.trl; > >> > >> cfg=[]; > >> cfg.trl=trials; > >> cfg.dataset                     = [direc d(rr,1).name]; > >> cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; > >> cfg.continuous                  = 'yes'; > >> etc.. > >> data                            = ft_preprocessing(cfg); > >> > >> That should give you an output with a trial-structure, I'd say. > >> > >> Best, > >> Stan > >> > >> -----Original Message----- > >> From: fieldtrip-bounces at donders.ru.nl > >> [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > >> Soldevilla, > >> D. (Diego) > >> Sent: Monday, May 16, 2011 4:25 PM > >> To: Email discussion list for the FieldTrip project > >> Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > >> Hi Stan, > >> > >> Thanks for your quickly answer. I get this error: > >> > >> Warning: the data does not contain a trial definition, assuming > that > >> the > >> trials are consecutive segments of a continuous recording > >> > In utilities/private/warning_once at 81 > >>   In utilities/private/fixtrialdef at 52 > >>   In ft_datatype_raw at 91 > >>   In ft_checkdata at 161 > >>   In ft_databrowser at 120 > >> redrawing with viewmode butterfly > >> ??? Improper index matrix reference. > >> > >> Error in ==> ft_databrowser>redraw_cb at 910 > >>   evtsample = [event(:).sample]; > >> > >> Error in ==> ft_databrowser at 419 > >> redraw_cb(h); > >> > >> I don't know why my data have no trial definition when I'm sure > that > >> is > >> epoched... Any ideas? > >> > >> Thanks in advance, > >> > >> Diego > >> > >> > >> > >> ----- "Stan van Pelt" wrote: > >> > >> > From: "Stan van Pelt" > >> > To: "Email discussion list for the FieldTrip project" > >> > >> > Sent: Monday, 16 May, 2011 4:16:16 PM > >> > Subject: Re: [FieldTrip] ft_rejectvisual channel selection > >> > > >> > Hi Diego, > >> > > >> > You could try using ft_databrowser instead of ft_rejectvisual > >> > (followed by > >> > ft_rejectartifact), so: > >> > > >> > cfg            = []; > >> > cfg.continuous = 'no'; > >> > cfg.channel    = {'EEG057','EEG058'}; > >> > cfg            = ft_databrowser(cfg,data); > >> > > >> > I think it should work like this. > >> > > >> > Best, > >> > Stan > >> > > >> > -----Original Message----- > >> > From: fieldtrip-bounces at donders.ru.nl > >> > [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Lozano > >> > Soldevilla, > >> > D. (Diego) > >> > Sent: Monday, May 16, 2011 4:00 PM > >> > To: fieldtrip at donders.ru.nl > >> > Subject: [FieldTrip] ft_rejectvisual channel selection > >> > > >> > Dear Fieldtrippers, > >> > > >> > I'm using ft_rejectvisual function to reject visually EOG > artifacts > >> > of > >> > epoched trials. My problem consist that I'm not able to plot > only > >> the > >> > EOG > >> > channels even when I explicitly select them ignoring the 'MEG' > >> > channels (I > >> > get a plot with all channels MEG + EOG). > >> > > >> > I directly used rejectvisual_channel (used in line 263 > >> > offt_rejectvisual) > >> > function selecting the EOG channels but I'm getting again all > >> > channels. > >> > Somebody could tell me what I'm doing wrong? > >> > > >> > Thanks in advance, > >> > > >> > Diego > >> > > >> > > >> > > >> > PS: Code > >> > > >> > %epoching > >> > cfg = []; > >> > cfg.dataset                     = [direc d(rr,1).name]; > >> > cfg.trialdef.eventtype          = 'frontpanel trigger'; > >> > cfg.trialdef.eventvalue         = 4; > >> > cfg.trialdef.prestim            = 1; % in seconds > >> > cfg.trialdef.poststim           = 4; % in seconds > >> > cfg.trialdef.epochmoving        = 'inbackward'; > >> > cfg.trialdef.pivoteventvalue    = 2;% cue stimulus > >> > cfg.trialdef.jumps              = 1; > >> > cfg.trialfun                    = 'trialselec'; > >> > > >> > cfg = ft_definetrial(cfg); > >> > > >> > cfg.channel                     = {'MEG' 'EEG057' 'EEG058'}; > >> > cfg.lpfilter                    = 'yes'; > >> > cfg.lpfreq                      = 250; > >> > cfg.baselinewindow              = [-1 0]; > >> > cfg.keeptrials                  = 'yes'; > >> > cfg.demean                      = 'yes'; > >> > cfg.continuous                  = 'yes'; > >> > > >> > data    = ft_preprocessing(cfg); > >> > > >> > %.............. > >> > > >> > > >> > %visual data rejection > >> > cfg             = []; > >> > cfg.channel     = {'EEG057' 'EEG058'}; > >> > cfg.method      = 'channel'; > >> > cfg.keepchannel = 'yes'; > >> > data_c          = ft_rejectvisual(cfg,data); > >> > > >> > > >> > > >> > -- > >> > PhD Student > >> > Donders Institute for Brain, Cognition and Behaviour > >> > Centre for Cognitive Neuroimaging > >> > Trigon, room 0.83 > >> > Kapittelweg 29 > >> > Radboud University Nijmegen > >> > NL-6500 HB Nijmegen > >> > The Netherlands > >> > E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > >> > Tel:      +31-(0)24-36-66274 > >> > Web:    http://www.neuosc.com/ > >> > _______________________________________________ > >> > 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 > >> Donders Institute for Brain, Cognition and Behaviour > >> Centre for Cognitive Neuroimaging > >> Trigon, room 0.83 > >> Kapittelweg 29 > >> Radboud University Nijmegen > >> NL-6500 HB Nijmegen > >> The Netherlands > >> E-Mail: d.lozanosoldevilla at fcdonders.ru.nl > >> Tel:      +31-(0)24-36-66274 > >> Web:    http://www.neuosc.com/ > >> > >> > >> _______________________________________________ > >> 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 -- PhD Student Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Trigon, room 0.83 Kapittelweg 29 Radboud University Nijmegen NL-6500 HB Nijmegen The Netherlands E-Mail: d.lozanosoldevilla at fcdonders.ru.nl Tel: +31-(0)24-36-66274 Web: http://www.neuosc.com/ From nuria.donamayor at neuro.uni-luebeck.de Tue May 17 10:03:50 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Tue, 17 May 2011 10:03:50 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, sorry it took me this long to answer. The variable format seems to be empty.... Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Freitag, 13. Mai 2011 16:43 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, Could you type dbstop if error on the command line, and evaluate what the variable 'format' is in your case? Thanks, Jan-Mathijs On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > Yes, it is exectly the same version. Better said, versions, because > I tried both 20110413 and 20110512.... > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com > ] > Gesendet: Freitag, 13. Mai 2011 13:39 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Dear Nuria > Is it exactly the same fieldtrip version? > I hope someone will solve this. > as temporary work around you can read the header on windows and then > move to linux > > yuval > > On 13 May 2011 11:42, Nuria Donamayor Alonso > wrote: > Dear fieltrip users, > I am using fieldtrip to analyze my 4D/BTI data on a Linux machine > with a 64-bit Matlab version and I am getting an error I don't know > how to solve: > > hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); > ??? SWITCH expression must be a scalar or string constant. > > Error in ==> read_4d_hdr at 60 > switch format > > Error in ==> ft_read_header at 153 > orig = read_4d_hdr(datafile); > > If I try to read the same data on my Windows PC with 32-bit Matlab I > have no problem reading the header file (but I can't even finish the > preprocessing before it runs out of memory, therefore the switch to > the Linux machine), so I'm pretty clueless here... Can any of you > help me? > Thanks, > Nuria > > > > Nuria Doñamayor Alonso, MSc > Universitätsklinikum Schleswig-Holstein > Campus Lübeck > Klinik für Neurologie > Ratzeburger Allee 160 > 23538 Lübeck > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > > "Many were increasingly of the opinion that they'd all made a big > mistake in coming down from the trees in the first place. And some > said that even the trees had been a bad move, and that no one should > ever have left the oceans". Douglas Adams > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From amelie.serpollet at cea.fr Tue May 17 15:58:49 2011 From: amelie.serpollet at cea.fr (=?iso-8859-1?Q?SERPOLLET_Am=E9lie_228173?=) Date: Tue, 17 May 2011 15:58:49 +0200 Subject: [FieldTrip] questions about realtime buffer Message-ID: Dear Fieldtrip users, I'm implementing a realtime buffer in C++ pretty much like in "demo_combined" : my application creates a buffer server and an acquisition client. I encountered a first problem when trying to close the buffer server cleanly, but with some small changes in tcpsocket.c and tcpserver.c, I think I solved the problem. If these modifications can be useful for other users and do not create other problems, I will share them. I encounter now a new problem : what if there are several acquisition clients ? I tried to create several couples "buffer-server + acquisition client" in different threads in my application, but it does not work at all, because of global variables (I suppose). It seems that one buffer server can not manage several acquisition clients, but I'm not sure of this point. Did anyone encounter this problem (or solve it) ? Or do anyone have an idea ? Best regards, Amelie Serpollet -------------- next part -------------- An HTML attachment was scrubbed... URL: From younes_zerouali at hotmail.com Tue May 17 16:11:36 2011 From: younes_zerouali at hotmail.com (Younes Zerouali) Date: Tue, 17 May 2011 10:11:36 -0400 Subject: [FieldTrip] Antw: Segment anatomy from MRI (spm8) In-Reply-To: <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> References: , <4DD22F5F02000057000096B7@gwsmtp1.uni-regensburg.de>, <8CFF865E-294F-46A9-AF69-89C0C26283D0@donders.ru.nl> Message-ID: Dear Gregor and Jan-Mathijs, Thank you both for prompt answers, I'll get to work and try that! Best, Younes From: jan.schoffelen at donders.ru.nl To: fieldtrip at donders.ru.nl Date: Tue, 17 May 2011 08:42:22 +0200 Subject: Re: [FieldTrip] Antw: Segment anatomy from MRI (spm8) Dear Gregor and Younes, We recently added functionaity to ft_volumesegment to actually compute the brainmask or scalp surface. Gregor is right in that until a few weeks ago, ft_volumesegment only returned the probabilistic maps for the grey whit and csf compartments. Nowadays, given the appropriate cfg, it can do much more (see the documentation on the wiki for the cfg-settings). For this of course you need an up-to-date version of FieldTrip! Best wishes, Jan-Mathijs On May 17, 2011, at 8:18 AM, Gregor Volberg wrote:Hi Younes, this is actually not a problem with the function. The "ft_volumesegment" will only return segmentations of the anatomical mri with respect to three tissue types: grey matter, white matter, and csf. You can use gray and white matter segmentations to construct your brain compartement by typing e. g. "brain = (seg.gray>0.5 | seg.white>0.5);" as given in the tutorial. In order to get skull and skin compartements, you need your original mri.anatomy which holds the image intensity on a black-to-white scale. You can threshold the white values to segment the head from the background, and this is then your skin compartement (e. g., "skin = (mri.anatomy>300);" as shown in the tutorial). The skull compartement is the oversection of the skin compartement and the brain compartement after you blew up those compartements a bit,skin_a = imerode(skin, s);brain_a = imdilate(brain, s);skull = (brain_a & skin_a);Especially the construction of the skin is a lot of work, as you need the wholes in the anatomical mri (eyes, ear, inhomogeneities) by hand. Best regards and good luck,Gregor -- Dr. rer. nat. Gregor Volberg ( mailto:gregor.volberg at psychologie.uni-regensburg.de ) University of Regensburg Institute for Experimental Psychology 93040 Regensburg, Germany Tel: +49 941 943 3862 Fax: +49 941 943 3233 http://www.psychologie.uni-regensburg.de/Greenlee/team/volberg/volberg.html >>> Younes Zerouali 5/17/2011 12:25 AM >>> Hi all, I'm trying to segment head anatomical surfaces (scalp, skull) using the mri scan from patient Colin27 (MNI, Montreal) following the steps described in the tutorial (http://fieldtrip.fcdonders.nl/tutorial/headmodel). My problem is that the function "ft_volumesegment" doesn't return all the variables that are mentionned in the tutorial. For example, there is no field named "skull" or "scalp" in the argument returned by this function. Anyone had this problem before? Best, Younes _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The NetherlandsJ.Schoffelen at donders.ru.nlTelephone: 0031-24-3614793 _______________________________________________ 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 jan.schoffelen at donders.ru.nl Tue May 17 16:24:21 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 17 May 2011 16:24:21 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de> Message-ID: <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> Hi Nuria, Strange. Format should contain a number. What matlab version are you running on the Linux machine? Best, Jan-Mathijs On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > sorry it took me this long to answer. The variable format seems to > be empty.... > Nuria > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Freitag, 13. Mai 2011 16:43 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Could you type dbstop if error on the command line, and evaluate what > the variable 'format' is in your case? > > Thanks, > > Jan-Mathijs > > On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > >> Yes, it is exectly the same version. Better said, versions, because >> I tried both 20110413 and 20110512.... >> >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >> ] >> Gesendet: Freitag, 13. Mai 2011 13:39 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Dear Nuria >> Is it exactly the same fieldtrip version? >> I hope someone will solve this. >> as temporary work around you can read the header on windows and then >> move to linux >> >> yuval >> >> On 13 May 2011 11:42, Nuria Donamayor Alonso > > wrote: >> Dear fieltrip users, >> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >> with a 64-bit Matlab version and I am getting an error I don't know >> how to solve: >> >> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >> ??? SWITCH expression must be a scalar or string constant. >> >> Error in ==> read_4d_hdr at 60 >> switch format >> >> Error in ==> ft_read_header at 153 >> orig = read_4d_hdr(datafile); >> >> If I try to read the same data on my Windows PC with 32-bit Matlab I >> have no problem reading the header file (but I can't even finish the >> preprocessing before it runs out of memory, therefore the switch to >> the Linux machine), so I'm pretty clueless here... Can any of you >> help me? >> Thanks, >> Nuria >> >> >> >> Nuria Doñamayor Alonso, MSc >> Universitätsklinikum Schleswig-Holstein >> Campus Lübeck >> Klinik für Neurologie >> Ratzeburger Allee 160 >> 23538 Lübeck >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Y.Harpaz >> >> a link to the BIU MEG lab: >> http://faculty.biu.ac.il/~goldsa/index.html>> >> >> "Many were increasingly of the opinion that they'd all made a big >> mistake in coming down from the trees in the first place. And some >> said that even the trees had been a bad move, and that no one should >> ever have left the oceans". Douglas Adams >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From nuria.donamayor at neuro.uni-luebeck.de Tue May 17 16:49:17 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Tue, 17 May 2011 16:49:17 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, I'm using Matlab 7.11.0 (R2010b). Best, Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Dienstag, 17. Mai 2011 16:24 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, Strange. Format should contain a number. What matlab version are you running on the Linux machine? Best, Jan-Mathijs On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > sorry it took me this long to answer. The variable format seems to > be empty.... > Nuria > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Freitag, 13. Mai 2011 16:43 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Could you type dbstop if error on the command line, and evaluate what > the variable 'format' is in your case? > > Thanks, > > Jan-Mathijs > > On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: > >> Yes, it is exectly the same version. Better said, versions, because >> I tried both 20110413 and 20110512.... >> >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >> ] >> Gesendet: Freitag, 13. Mai 2011 13:39 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Dear Nuria >> Is it exactly the same fieldtrip version? >> I hope someone will solve this. >> as temporary work around you can read the header on windows and then >> move to linux >> >> yuval >> >> On 13 May 2011 11:42, Nuria Donamayor Alonso > > wrote: >> Dear fieltrip users, >> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >> with a 64-bit Matlab version and I am getting an error I don't know >> how to solve: >> >> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >> ??? SWITCH expression must be a scalar or string constant. >> >> Error in ==> read_4d_hdr at 60 >> switch format >> >> Error in ==> ft_read_header at 153 >> orig = read_4d_hdr(datafile); >> >> If I try to read the same data on my Windows PC with 32-bit Matlab I >> have no problem reading the header file (but I can't even finish the >> preprocessing before it runs out of memory, therefore the switch to >> the Linux machine), so I'm pretty clueless here... Can any of you >> help me? >> Thanks, >> Nuria >> >> >> >> Nuria Doñamayor Alonso, MSc >> Universitätsklinikum Schleswig-Holstein >> Campus Lübeck >> Klinik für Neurologie >> Ratzeburger Allee 160 >> 23538 Lübeck >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Y.Harpaz >> >> a link to the BIU MEG lab: >> http://faculty.biu.ac.il/~goldsa/index.html>> >> >> "Many were increasingly of the opinion that they'd all made a big >> mistake in coming down from the trees in the first place. And some >> said that even the trees had been a bad move, and that no one should >> ever have left the oceans". Douglas Adams >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From batrod at gmail.com Tue May 17 20:50:43 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 17 May 2011 13:50:43 -0500 Subject: [FieldTrip] Problem with recent version of eeglab2fieldtrip Message-ID: Dear Fieldtrip users, Recently i experienced problems doing sone Time-freq analysis and i realized it's coming from the eeglab2fieldtrip function and more precisely one line that has been changed, apparently without being reported on the eeglab revision history and neither in fieldtrip revision history (but i may be wrong with this last one, i checked very quickly on google code) The problem occurs at the Line 47: data.label = { EEG.chanlocs(1:EEG.nbchan).labels }; % Eeglab version 9.0.2.3 data.label = { EEG.chanlocs(EEG.icachansind).labels }; % Eeglab verion 9.0.4.4 The old version works, whereas the new version will cause problem if you dont perform an ICA with eeglab, prior to the conversion. Hope this helps, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From arno at cerco.ups-tlse.fr Wed May 18 00:08:36 2011 From: arno at cerco.ups-tlse.fr (Arnaud Delorme) Date: Tue, 17 May 2011 15:08:36 -0700 Subject: [FieldTrip] Problem with recent version of eeglab2fieldtrip In-Reply-To: References: Message-ID: <07D46921-50BF-4C27-AA81-E4E96FD49698@cerco.ups-tlse.fr> Dear Rodolphe, I had changed that line because I could not fit dipoles for some ICA components (which is the main reason this function was originally designed for). The attached function should work for both components and channel data. Let me know if it does not. Best, Arno ps: the change was actually documented on the web (http://sccn.ucsd.edu/wiki/EEGLAB_revision_history_version_9) as "eeglab2fieldtrip.m, fix performing dipole fitting on subset of channels (SVN 9092 - Arno)" On May 17, 2011, at 11:50 AM, Rodolphe Nenert wrote: > Dear Fieldtrip users, > > Recently i experienced problems doing sone Time-freq analysis and i realized it's coming from the eeglab2fieldtrip function and more precisely one line that has been changed, apparently without being reported on the eeglab revision history and neither in fieldtrip revision history (but i may be wrong with this last one, i checked very quickly on google code) > > The problem occurs at the Line 47: > > data.label = { EEG.chanlocs(1:EEG.nbchan).labels }; % Eeglab version 9.0.2.3 > > data.label = { EEG.chanlocs(EEG.icachansind).labels }; % Eeglab verion 9.0.4.4 > > The old version works, whereas the new version will cause problem if you dont perform an ICA with eeglab, prior to the conversion. > > Hope this helps, > > Rodolphe. > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eeglab2fieldtrip.m Type: application/octet-stream Size: 5887 bytes Desc: not available URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Wed May 18 10:51:14 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 18 May 2011 10:51:14 +0200 Subject: [FieldTrip] Tutorial error Message-ID: Dear all, I am a very beginner with fieldtrip. I have tried to run the tutorial a couple of weeks ago, and it worked smoothly. Yesterday I have tried again, but surprisngly I got anerror message, as soon as I started the tutorial (the first step entitled: "reading and processing the interesting trials"): cfg = []; cfg.dataset = 'Subject01.ds'; cfg.trialdef.eventtype = 'backpanel trigger'; cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for fully incongruent (FIC). cfg.trialdef.prestim = 1; % in seconds cfg.trialdef.poststim = 2; % in seconds cfg = ft_definetrial(cfg); ??? Attempt to reference field of non-structure array Error in ==> trialfun_general at 117 for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) This sounds really weird since it worked 2 weeks ago on the same machine and with the same version of Fieldtrip. Any advice would be very appreciated. Best wishes, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 18 11:02:29 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 18 May 2011 11:02:29 +0200 Subject: [FieldTrip] Tutorial error In-Reply-To: References: Message-ID: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> Dear Davide, I am not sure whether you are using the same fieldtrip version. There has been a glitch recently with the trialfun_general, but this should be fixed by now. Could you update to a superrecent version of fieldtrip and try again? Thanks, Jan-Mathijs PS: I cannot reproduce your error so I expect it to go away if you update. On May 18, 2011, at 10:51 AM, Davide Rivolta wrote: > Dear all, > > I am a very beginner with fieldtrip. > > I have tried to run the tutorial a couple of weeks ago, and it > worked smoothly. > > Yesterday I have tried again, but surprisngly I got anerror message, > as soon as I started the tutorial (the first step entitled: "reading > and processing the interesting trials"): > > > cfg = []; > cfg.dataset = 'Subject01.ds'; > cfg.trialdef.eventtype = 'backpanel trigger'; > cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger > for fully incongruent (FIC). > cfg.trialdef.prestim = 1; % in seconds > cfg.trialdef.poststim = 2; % in seconds > > cfg = ft_definetrial(cfg); > > > ??? Attempt to reference field of non-structure array > > Error in ==> trialfun_general at 117 > for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) > > > > > This sounds really weird since it worked 2 weeks ago on the same > machine and with the same version of Fieldtrip. > > Any advice would be very appreciated. > > Best wishes, > > Davide > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From jan.schoffelen at donders.ru.nl Wed May 18 12:13:27 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 18 May 2011 12:13:27 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de> Message-ID: <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> Hi Nuria, I cannot reproduce your problem on a linux machine we have here, running matlab 2010b (64-bit). Either there is something wrong with your dataset (does it happen as well for another dataset?), or there is something different with respect to the configuration of your Linux machine. Best, Jan-Mathijs On May 17, 2011, at 4:49 PM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > I'm using Matlab 7.11.0 (R2010b). > Best, > Nuria > > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Dienstag, 17. Mai 2011 16:24 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Strange. Format should contain a number. What matlab version are you > running on the Linux machine? > > Best, > > Jan-Mathijs > > > On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > >> Hi Jan-Mathijs, >> sorry it took me this long to answer. The variable format seems to >> be empty.... >> Nuria >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl >> ] >> Gesendet: Freitag, 13. Mai 2011 16:43 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Hi Nuria, >> >> Could you type dbstop if error on the command line, and evaluate what >> the variable 'format' is in your case? >> >> Thanks, >> >> Jan-Mathijs >> >> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: >> >>> Yes, it is exectly the same version. Better said, versions, because >>> I tried both 20110413 and 20110512.... >>> >>> ________________________________________ >>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >>> ] >>> Gesendet: Freitag, 13. Mai 2011 13:39 >>> An: Email discussion list for the FieldTrip project >>> Betreff: Re: [FieldTrip] problem reading 4d header >>> >>> Dear Nuria >>> Is it exactly the same fieldtrip version? >>> I hope someone will solve this. >>> as temporary work around you can read the header on windows and then >>> move to linux >>> >>> yuval >>> >>> On 13 May 2011 11:42, Nuria Donamayor Alonso >> > wrote: >>> Dear fieltrip users, >>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >>> with a 64-bit Matlab version and I am getting an error I don't know >>> how to solve: >>> >>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >>> ??? SWITCH expression must be a scalar or string constant. >>> >>> Error in ==> read_4d_hdr at 60 >>> switch format >>> >>> Error in ==> ft_read_header at 153 >>> orig = read_4d_hdr(datafile); >>> >>> If I try to read the same data on my Windows PC with 32-bit Matlab I >>> have no problem reading the header file (but I can't even finish the >>> preprocessing before it runs out of memory, therefore the switch to >>> the Linux machine), so I'm pretty clueless here... Can any of you >>> help me? >>> Thanks, >>> Nuria >>> >>> >>> >>> Nuria Doñamayor Alonso, MSc >>> Universitätsklinikum Schleswig-Holstein >>> Campus Lübeck >>> Klinik für Neurologie >>> Ratzeburger Allee 160 >>> 23538 Lübeck >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Y.Harpaz >>> >>> a link to the BIU MEG lab: >>> http://faculty.biu.ac.il/~goldsa/index.html>>> >>> >>> "Many were increasingly of the opinion that they'd all made a big >>> mistake in coming down from the trees in the first place. And some >>> said that even the trees had been a bad move, and that no one should >>> ever have left the oceans". Douglas Adams >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> >> _______________________________________________ >> 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 > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From drivolta81 at gmail.com Wed May 18 13:40:11 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Wed, 18 May 2011 13:40:11 +0200 Subject: [FieldTrip] Tutorial error In-Reply-To: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> References: <746130EC-C81A-4276-8C83-ADB61811B2A3@donders.ru.nl> Message-ID: Dear Jan-Mathijs This is the funny part. I run it (and worked) on the 201105053 version two weeks ago. Yesterday it did not work on the same version. So, I have downloaded the most recent version 20110516, but it is still not working. I do not really know what to do with it. Thanks for your kind help, Davide On Wed, May 18, 2011 at 11:02 AM, jan-mathijs schoffelen < jan.schoffelen at donders.ru.nl> wrote: > Dear Davide, > > I am not sure whether you are using the same fieldtrip version. There has > been a glitch recently with the trialfun_general, but this should be fixed > by now. Could you update to a superrecent version of fieldtrip and try > again? > > Thanks, > > Jan-Mathijs > > PS: I cannot reproduce your error so I expect it to go away if you update. > > > On May 18, 2011, at 10:51 AM, Davide Rivolta wrote: > > Dear all, >> >> I am a very beginner with fieldtrip. >> >> I have tried to run the tutorial a couple of weeks ago, and it worked >> smoothly. >> >> Yesterday I have tried again, but surprisngly I got anerror message, as >> soon as I started the tutorial (the first step entitled: "reading and >> processing the interesting trials"): >> >> >> cfg = []; >> cfg.dataset = 'Subject01.ds'; >> cfg.trialdef.eventtype = 'backpanel trigger'; >> cfg.trialdef.eventvalue = 3; % the value of the stimulus trigger for >> fully incongruent (FIC). >> cfg.trialdef.prestim = 1; % in seconds >> cfg.trialdef.poststim = 2; % in seconds >> >> cfg = ft_definetrial(cfg); >> >> >> ??? Attempt to reference field of non-structure array >> >> Error in ==> trialfun_general at 117 >> for i=find(strcmp(cfg.trialdef.eventtype, {event.type})) >> >> >> >> >> This sounds really weird since it worked 2 weeks ago on the same machine >> and with the same version of Fieldtrip. >> >> Any advice would be very appreciated. >> >> Best wishes, >> >> Davide >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Davide Rivolta, PhD -------------- next part -------------- An HTML attachment was scrubbed... URL: From nuria.donamayor at neuro.uni-luebeck.de Wed May 18 15:00:33 2011 From: nuria.donamayor at neuro.uni-luebeck.de (Nuria Donamayor Alonso) Date: Wed, 18 May 2011 15:00:33 +0200 Subject: [FieldTrip] problem reading 4d header In-Reply-To: <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> References: <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509522@solaris.neuro.uni-luebeck.de> <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509523@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B82509524@solaris.neuro.uni-luebeck.de>, <810A8E06C75EB447A8CEB73DBFD7BB0E4B8250952A@solaris.neuro.uni-luebeck.de>, <5D378D09-8B7D-4744-95DD-219C29BF2A4B@donders.ru.nl> <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F9036@solaris.neuro.uni-luebeck.de>, <0CBFB37A-FE20-436C-A5DA-FB7901EA2E80@donders.ru.nl> Message-ID: <810A8E06C75EB447A8CEB73DBFD7BB0E4B888F903D@solaris.neuro.uni-luebeck.de> Hi Jan-Mathijs, I get the same error message with all my datasets. Maybe it does have to do with my Linux machine... Any idea what I should look for to fix it? Thanks, Nuria ________________________________________ Von: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl] Gesendet: Mittwoch, 18. Mai 2011 12:13 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] problem reading 4d header Hi Nuria, I cannot reproduce your problem on a linux machine we have here, running matlab 2010b (64-bit). Either there is something wrong with your dataset (does it happen as well for another dataset?), or there is something different with respect to the configuration of your Linux machine. Best, Jan-Mathijs On May 17, 2011, at 4:49 PM, Nuria Donamayor Alonso wrote: > Hi Jan-Mathijs, > I'm using Matlab 7.11.0 (R2010b). > Best, > Nuria > > > ________________________________________ > Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl > ] > Gesendet: Dienstag, 17. Mai 2011 16:24 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] problem reading 4d header > > Hi Nuria, > > Strange. Format should contain a number. What matlab version are you > running on the Linux machine? > > Best, > > Jan-Mathijs > > > On May 17, 2011, at 10:03 AM, Nuria Donamayor Alonso wrote: > >> Hi Jan-Mathijs, >> sorry it took me this long to answer. The variable format seems to >> be empty.... >> Nuria >> ________________________________________ >> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >> bounces at donders.ru.nl] im Auftrag von jan-mathijs schoffelen [jan.schoffelen at donders.ru.nl >> ] >> Gesendet: Freitag, 13. Mai 2011 16:43 >> An: Email discussion list for the FieldTrip project >> Betreff: Re: [FieldTrip] problem reading 4d header >> >> Hi Nuria, >> >> Could you type dbstop if error on the command line, and evaluate what >> the variable 'format' is in your case? >> >> Thanks, >> >> Jan-Mathijs >> >> On May 13, 2011, at 2:34 PM, Nuria Donamayor Alonso wrote: >> >>> Yes, it is exectly the same version. Better said, versions, because >>> I tried both 20110413 and 20110512.... >>> >>> ________________________________________ >>> Von: fieldtrip-bounces at donders.ru.nl [fieldtrip- >>> bounces at donders.ru.nl] im Auftrag von Yuval Harpaz [yuvharpaz at gmail.com >>> ] >>> Gesendet: Freitag, 13. Mai 2011 13:39 >>> An: Email discussion list for the FieldTrip project >>> Betreff: Re: [FieldTrip] problem reading 4d header >>> >>> Dear Nuria >>> Is it exactly the same fieldtrip version? >>> I hope someone will solve this. >>> as temporary work around you can read the header on windows and then >>> move to linux >>> >>> yuval >>> >>> On 13 May 2011 11:42, Nuria Donamayor Alonso >> > wrote: >>> Dear fieltrip users, >>> I am using fieldtrip to analyze my 4D/BTI data on a Linux machine >>> with a 64-bit Matlab version and I am getting an error I don't know >>> how to solve: >>> >>> hdr = ft_read_header(['/data/ld1/home/bx95/c,rfDC']); >>> ??? SWITCH expression must be a scalar or string constant. >>> >>> Error in ==> read_4d_hdr at 60 >>> switch format >>> >>> Error in ==> ft_read_header at 153 >>> orig = read_4d_hdr(datafile); >>> >>> If I try to read the same data on my Windows PC with 32-bit Matlab I >>> have no problem reading the header file (but I can't even finish the >>> preprocessing before it runs out of memory, therefore the switch to >>> the Linux machine), so I'm pretty clueless here... Can any of you >>> help me? >>> Thanks, >>> Nuria >>> >>> >>> >>> Nuria Doñamayor Alonso, MSc >>> Universitätsklinikum Schleswig-Holstein >>> Campus Lübeck >>> Klinik für Neurologie >>> Ratzeburger Allee 160 >>> 23538 Lübeck >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> -- >>> Y.Harpaz >>> >>> a link to the BIU MEG lab: >>> http://faculty.biu.ac.il/~goldsa/index.html>>> >>> >>> "Many were increasingly of the opinion that they'd all made a big >>> mistake in coming down from the trees in the first place. And some >>> said that even the trees had been a bad move, and that no one should >>> ever have left the oceans". Douglas Adams >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> >> _______________________________________________ >> 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 > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > > _______________________________________________ > 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 Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From michael.hanke at gmail.com Wed May 18 15:10:26 2011 From: michael.hanke at gmail.com (Michael Hanke) Date: Wed, 18 May 2011 09:10:26 -0400 Subject: [FieldTrip] Neuroscience software survey: What is popular, what has problems? Immediate results Message-ID: <20110518131026.GD19084@meiner> [Apologies for cross-posting] Dear neuroscience researchers and their IT staff We invite you to participate in a survey on software usage and computing environments in neuroscience research. It will take no more than five minutes to fill it out. Immediately after sending your answers you will get to see a summary of how other participants have responded before. This data will eventually be made available to software vendors and distributors to determine advantages and issue of popular computing environments in neuroscience research. Learn about what fellow neuroscientists are doing to address their computing demands -- take the survey! http://goo.gl/euIMc Thanks, -- PyMVPA/NeuroDebian Team: Yaroslav O. Halchenko & Michael Hanke Postdoctoral Fellows, Department of Psychological and Brain Sciences Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 From jdien07 at mac.com Fri May 20 04:30:59 2011 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 19 May 2011 22:30:59 -0400 Subject: [FieldTrip] problems using ft_freqanalysis Message-ID: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> Hi, I'm just starting to get up to speed on spectral analysis (I'm an ERPer). I'm using the following set-up: I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): cfg.method='mtmwelch'; cfg.output='pow'; [freq] = ft_freqanalysis(cfg, data); I got the error message: ------------------------- the input is raw data with 128 channels and 160 trials 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used taking every sample as time of interest the input is raw data with 128 channels and 160 trials ??? Error using ==> ft_freqanalysis at 216 you must specify a smoothing parameter with taper = dpss Error in ==> ft_freqanalysis_mtmwelch at 107 freq = ft_freqanalysis(cfgconvol, data); Error in ==> ft_freqanalysis at 271 [freq] = feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, data); ----------------------- Two things: 1) What would be an appropriate smoothing parameter? 2) Is this a bug? It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: cfg.foi=[1:1:30]; cfg.taper='hanning'; which resulted in: -------------------------- >> [freq] = ft_freqanalysis(cfg, data); the input is raw data with 128 channels and 160 trials 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used taking every sample as time of interest the input is raw data with 128 channels and 160 trials processing trials ??? Reference to non-existent field 't_ftimwin'. Error in ==> ft_freqanalysis at 454 [spectrum_mtmconvol,ntaper,foi,toi] = ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, 'timwin', cfg.t_ftimwin, 'taper', ... Error in ==> ft_freqanalysis_mtmwelch at 107 freq = ft_freqanalysis(cfgconvol, data); Error in ==> ft_freqanalysis at 271 [freq] = feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, data); -------------------- What am I doing wrong? I looked through the code but couldn't figure out what the problem was. I am very confused... fieldtrip-20110519 MATLAB Version 7.11.0.584 (R2010b) Operating System: Mac OS X Version: 10.6.7 Build: 10J869 >> cfg cfg = dataset: 'SLI_3011m_40m_POA.egis' method: 'mtmwelch' output: 'pow' taper: 'hanning' tapsmofrq: 4 foi: [1x30 double] >> data data = hdr: [1x1 struct] label: {128x1 cell} time: {1x160 cell} trial: {1x160 cell} fsample: 250 sampleinfo: [160x2 double] cfg: [1x1 struct] Thanks for any help you can give! Joe From jan.schoffelen at donders.ru.nl Fri May 20 07:36:03 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 20 May 2011 07:36:03 +0200 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> Message-ID: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Dear Joe, To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. Cheers, Jan-Mathijs On May 20, 2011, at 4:30 AM, Joseph Dien wrote: > Hi, > I'm just starting to get up to speed on spectral analysis (I'm an > ERPer). > I'm using the following set-up: > > I tried the following (for one second long trials with an Fs of > 250Hz and interest in frequencies below 30Hz): > > cfg.method='mtmwelch'; > cfg.output='pow'; > [freq] = ft_freqanalysis(cfg, data); > > I got the error message: > > ------------------------- > the input is raw data with 128 channels and 160 trials > 'mtmwelch' has not been implemented yet in the specest toolbox, the > old implementation is being used > taking every sample as time of interest > the input is raw data with 128 channels and 160 trials > ??? Error using ==> ft_freqanalysis at 216 > you must specify a smoothing parameter with taper = dpss > > Error in ==> ft_freqanalysis_mtmwelch at 107 > freq = ft_freqanalysis(cfgconvol, data); > > Error in ==> ft_freqanalysis at 271 > [freq] = > feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, > data); > > ----------------------- > Two things: > > 1) What would be an appropriate smoothing parameter? > > 2) Is this a bug? It defaulted to dpss as specified by the > documentation but it didn't provide a default smoothing parameter so > the default still resulted in a crash. > > Anyway, given the advice in the tutlrial to use a hanning window > rather than a multi-taper like dpss for frequencies below 30, I > tried the following: > > cfg.foi=[1:1:30]; > cfg.taper='hanning'; > > which resulted in: > > -------------------------- >>> [freq] = ft_freqanalysis(cfg, data); > the input is raw data with 128 channels and 160 trials > 'mtmwelch' has not been implemented yet in the specest toolbox, the > old implementation is being used > taking every sample as time of interest > the input is raw data with 128 channels and 160 trials > processing trials > ??? Reference to non-existent field 't_ftimwin'. > > Error in ==> ft_freqanalysis at 454 > [spectrum_mtmconvol,ntaper,foi,toi] = > ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, > 'timwin', cfg.t_ftimwin, 'taper', ... > > Error in ==> ft_freqanalysis_mtmwelch at 107 > freq = ft_freqanalysis(cfgconvol, data); > > Error in ==> ft_freqanalysis at 271 > [freq] = > feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, > data); > > > -------------------- > What am I doing wrong? I looked through the code but couldn't > figure out what the problem was. I am very confused... > > fieldtrip-20110519 > MATLAB Version 7.11.0.584 (R2010b) > Operating System: Mac OS X Version: 10.6.7 Build: 10J869 > > >>> cfg > > cfg = > > dataset: 'SLI_3011m_40m_POA.egis' > method: 'mtmwelch' > output: 'pow' > taper: 'hanning' > tapsmofrq: 4 > foi: [1x30 double] > >>> data > > data = > > hdr: [1x1 struct] > label: {128x1 cell} > time: {1x160 cell} > trial: {1x160 cell} > fsample: 250 > sampleinfo: [160x2 double] > cfg: [1x1 struct] > > > Thanks for any help you can give! > > Joe > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From Elena.Orekhova at neuro.gu.se Fri May 20 14:00:40 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Fri, 20 May 2011 12:00:40 +0000 Subject: [FieldTrip] ft_read_vol with Neuromag Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> Hi, I try to read volume from the Neuromag .fif file using vol = ft_read_vol(NEUROMAG_FIF_FILE_NAME, 'fileformat', 'neuromag_fif') I get the error: *********************** ??? Undefined variable "cfg" or class "cfg.gradfile". Error in ==> ft_read_vol at 77 fprintf('using Neuromag gradiometer definition from %s\n', cfg.gradfile); Any advice? Elena ________________________________ Elena V Orekhova, Ph.D. Inst. Neuroscience and Physiology University of Gothenburg S-413 45 Gothenburg, Sweden phone: +46 31 342 48 02 elena at neuro.gu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From jdien07 at mac.com Fri May 20 16:54:16 2011 From: jdien07 at mac.com (Joseph Dien) Date: Fri, 20 May 2011 10:54:16 -0400 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> Thanks for this helpful explanation! Can you provide me with guidance on what is involved in deciding the setting for the spectral smoothing parameter 'tapsmofrq' for dpss? Or where to look for information on this issue? Thanks again! Joe On May 20, 2011, at 1:36 AM, jan-mathijs schoffelen wrote: > Dear Joe, > > To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. > Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). > In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. > > Cheers, > > Jan-Mathijs > > > > On May 20, 2011, at 4:30 AM, Joseph Dien wrote: > >> Hi, >> I'm just starting to get up to speed on spectral analysis (I'm an ERPer). >> I'm using the following set-up: >> >> I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): >> >> cfg.method='mtmwelch'; >> cfg.output='pow'; >> [freq] = ft_freqanalysis(cfg, data); >> >> I got the error message: >> >> ------------------------- >> the input is raw data with 128 channels and 160 trials >> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >> taking every sample as time of interest >> the input is raw data with 128 channels and 160 trials >> ??? Error using ==> ft_freqanalysis at 216 >> you must specify a smoothing parameter with taper = dpss >> >> Error in ==> ft_freqanalysis_mtmwelch at 107 >> freq = ft_freqanalysis(cfgconvol, data); >> >> Error in ==> ft_freqanalysis at 271 >> [freq] = >> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >> data); >> >> ----------------------- >> Two things: >> >> 1) What would be an appropriate smoothing parameter? >> >> 2) Is this a bug? It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. >> >> Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: >> >> cfg.foi=[1:1:30]; >> cfg.taper='hanning'; >> >> which resulted in: >> >> -------------------------- >>>> [freq] = ft_freqanalysis(cfg, data); >> the input is raw data with 128 channels and 160 trials >> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >> taking every sample as time of interest >> the input is raw data with 128 channels and 160 trials >> processing trials >> ??? Reference to non-existent field 't_ftimwin'. >> >> Error in ==> ft_freqanalysis at 454 >> [spectrum_mtmconvol,ntaper,foi,toi] = >> ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, >> 'timwin', cfg.t_ftimwin, 'taper', ... >> >> Error in ==> ft_freqanalysis_mtmwelch at 107 >> freq = ft_freqanalysis(cfgconvol, data); >> >> Error in ==> ft_freqanalysis at 271 >> [freq] = >> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >> data); >> >> >> -------------------- >> What am I doing wrong? I looked through the code but couldn't figure out what the problem was. I am very confused... >> >> fieldtrip-20110519 >> MATLAB Version 7.11.0.584 (R2010b) >> Operating System: Mac OS X Version: 10.6.7 Build: 10J869 >> >> >>>> cfg >> >> cfg = >> >> dataset: 'SLI_3011m_40m_POA.egis' >> method: 'mtmwelch' >> output: 'pow' >> taper: 'hanning' >> tapsmofrq: 4 >> foi: [1x30 double] >> >>>> data >> >> data = >> >> hdr: [1x1 struct] >> label: {128x1 cell} >> time: {1x160 cell} >> trial: {1x160 cell} >> fsample: 250 >> sampleinfo: [160x2 double] >> cfg: [1x1 struct] >> >> >> Thanks for any help you can give! >> >> Joe >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > Dr. J.M. (Jan-Mathijs) Schoffelen > Donders Institute for Brain, Cognition and Behaviour, > Centre for Cognitive Neuroimaging, > Radboud University Nijmegen, The Netherlands > J.Schoffelen at donders.ru.nl > Telephone: 0031-24-3614793 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From dgroppe at cogsci.ucsd.edu Fri May 20 17:38:50 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 20 May 2011 08:38:50 -0700 Subject: [FieldTrip] problems using ft_freqanalysis In-Reply-To: <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <08A9B8BE-658D-4503-94D3-74D2CB0692DF@mac.com> Message-ID: Hi Joe, David Kleinfeld and Partha Mitra have an excellent tutorial on multitaper spectral analysis that should help: http://www-physics.ucsd.edu/neurophysics/publications/CSHL_2009_SPECTRA_4.pdf -D On Fri, May 20, 2011 at 7:54 AM, Joseph Dien wrote: > Thanks for this helpful explanation!  Can you provide me with guidance on what is involved in deciding the setting for the spectral smoothing parameter 'tapsmofrq' for dpss?  Or where to look for information on this issue? > > Thanks again! > > Joe > > > On May 20, 2011, at 1:36 AM, jan-mathijs schoffelen wrote: > >> Dear Joe, >> >> To begin with, since you are still 'tabula rasa' in the field of frequency analysis, I'd like you to forget about the 'mtmwelch' method ;o). I believe that at some point this method was implemented to 'just have it in the package'. As far as I am aware, it is hardly ever used and not actively maintained. >> Essentially, Welch's method cuts the data into overlapping segments, computes a power spectrum, and averages across the segments again. The way it is implemented in Fieldtrip, is that one needs to specify the length of the timewindow in which to cut the data. This is the cfg.t_ftimwin. (as a side note: for the underlying computations fieldtrip relies on the method 'mtmconvol', which allows for a frequency specific segment length, which in this context does not really make sense, but is handy to emulate a wavelet analysis). >> In your case however, I would advice to use cfg.method = 'mtmfft', because at this stage you are not interested in the temporal dimension of your spectrum. This method requires a slightly different cfg (in terms of fields and their content) with respect to mtmwelch/mtmconvol, but I hope that you can find your way around in the documentation to get it up and running. As to the 'tapsmofrq' in this case, if you have sufficiently long trials, you can still use some smoothing for the estimation of the low frequencies. The advice to use hanning for the lower frequencies specifically pertains to time-frequency estimation. >> >> Cheers, >> >> Jan-Mathijs >> >> >> >> On May 20, 2011, at 4:30 AM, Joseph Dien wrote: >> >>> Hi, >>> I'm just starting to get up to speed on spectral analysis (I'm an ERPer). >>> I'm using the following set-up: >>> >>> I tried the following (for one second long trials with an Fs of 250Hz and interest in frequencies below 30Hz): >>> >>> cfg.method='mtmwelch'; >>> cfg.output='pow'; >>> [freq] = ft_freqanalysis(cfg, data); >>> >>> I got the error message: >>> >>> ------------------------- >>> the input is raw data with 128 channels and 160 trials >>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >>> taking every sample as time of interest >>> the input is raw data with 128 channels and 160 trials >>> ??? Error using ==> ft_freqanalysis at 216 >>> you must specify a smoothing parameter with taper = dpss >>> >>> Error in ==> ft_freqanalysis_mtmwelch at 107 >>> freq = ft_freqanalysis(cfgconvol, data); >>> >>> Error in ==> ft_freqanalysis at 271 >>> [freq] = >>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >>> data); >>> >>> ----------------------- >>> Two things: >>> >>> 1) What would be an appropriate smoothing parameter? >>> >>> 2) Is this a bug?  It defaulted to dpss as specified by the documentation but it didn't provide a default smoothing parameter so the default still resulted in a crash. >>> >>> Anyway, given the advice in the tutlrial to use a hanning window rather than a multi-taper like dpss for frequencies below 30, I tried the following: >>> >>> cfg.foi=[1:1:30]; >>> cfg.taper='hanning'; >>> >>> which resulted in: >>> >>> -------------------------- >>>>> [freq] = ft_freqanalysis(cfg, data); >>> the input is raw data with 128 channels and 160 trials >>> 'mtmwelch' has not been implemented yet in the specest toolbox, the old implementation is being used >>> taking every sample as time of interest >>> the input is raw data with 128 channels and 160 trials >>> processing trials >>> ??? Reference to non-existent field 't_ftimwin'. >>> >>> Error in ==> ft_freqanalysis at 454 >>>     [spectrum_mtmconvol,ntaper,foi,toi] = >>>     ft_specest_mtmconvol(dat, time, 'timeoi', cfg.toi, >>>     'timwin', cfg.t_ftimwin, 'taper', ... >>> >>> Error in ==> ft_freqanalysis_mtmwelch at 107 >>> freq = ft_freqanalysis(cfgconvol, data); >>> >>> Error in ==> ft_freqanalysis at 271 >>> [freq] = >>> feval(sprintf('ft_freqanalysis_%s',lower(cfg.method)), cfg, >>> data); >>> >>> >>> -------------------- >>> What am I doing wrong?  I looked through the code but couldn't figure out what the problem was.  I am very confused... >>> >>> fieldtrip-20110519 >>> MATLAB Version 7.11.0.584 (R2010b) >>> Operating System: Mac OS X  Version: 10.6.7 Build: 10J869 >>> >>> >>>>> cfg >>> >>> cfg = >>> >>>   dataset: 'SLI_3011m_40m_POA.egis' >>>    method: 'mtmwelch' >>>    output: 'pow' >>>     taper: 'hanning' >>> tapsmofrq: 4 >>>       foi: [1x30 double] >>> >>>>> data >>> >>> data = >>> >>>        hdr: [1x1 struct] >>>      label: {128x1 cell} >>>       time: {1x160 cell} >>>      trial: {1x160 cell} >>>    fsample: 250 >>> sampleinfo: [160x2 double] >>>        cfg: [1x1 struct] >>> >>> >>> Thanks for any help you can give! >>> >>> Joe >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> Dr. J.M. (Jan-Mathijs) Schoffelen >> Donders Institute for Brain, Cognition and Behaviour, >> Centre for Cognitive Neuroimaging, >> Radboud University Nijmegen, The Netherlands >> J.Schoffelen at donders.ru.nl >> Telephone: 0031-24-3614793 >> >> _______________________________________________ >> 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 > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From Elena.Orekhova at neuro.gu.se Sat May 21 14:11:41 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Sat, 21 May 2011 12:11:41 +0000 Subject: [FieldTrip] rpa/nas/lpa coordinates Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> Hi I Just started to use Fieldtrip with my Neuromag MEG data and try to follow the example script ‘read_neuromag_mri_and_create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space’ The instruction suggests to take voxel coordinates of fiduscials from the Neuromag GUI for MRI-MEG Integration. I have already performed this step and saved the transformed mri in the /sets/XXX.fif file. Should I write any rpa/nas/lpa coordinates in this case? cfg.fiducial.rpa = [y x z]; cfg.fiducial.nas = [y x z]; cfg.fiducial.lpa = [y x z]; I have 2 4X4 transformations in the .fif file, not sure what they mean. mri.hdr.trans.trans 0.9913 0.1210 0.0518 -0.0032 -0.0948 0.9291 -0.3574 0.0254 -0.0914 0.3494 0.9325 -0.0519 0 0 0 1.0000 mri.hdr.voxel_trans.trans -0.0000 -0.0000 -0.0010 0.1058 -0.0005 0.0000 0.0000 0.1597 0 -0.0005 0.0001 0.1058 0 0 0 1.0000 I'll be most grateful for the help! Regards, Elena ________________________________ Elena V Orekhova, Ph.D. Inst. Neuroscience and Physiology University of Gothenburg S-413 45 Gothenburg, Sweden phone: +46 31 342 48 02 elena at neuro.gu.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon May 23 09:33:34 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 23 May 2011 09:33:34 +0200 Subject: [FieldTrip] rpa/nas/lpa coordinates In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se> Message-ID: Dear Elena > On 21 May 2011, at 14:11, Elena Orekhova wrote: > >> Hi >> I Just started to use Fieldtrip with my Neuromag MEG data and try >> to follow the example script >> ‘read_neuromag_mri_and_create_single- >> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space >> ’ I don't know all details of the Neuromag system, but recently we did add the http://fieldtrip.fcdonders.nl/getting_started/yokogawa documentation that explains reasonably general how coordinate system coregistration works. We also added a new function (FT_SENSORREALIGN) to ease the coregistration and we are working towards a more consistent representation of the corodinate systems in the relevant fieldtrip data structures. Although the details for your system are different (see http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined) , you might get a better overview of the steps that are involved by reading the yokogawa getting started. > The instruction suggests to take voxel coordinates of fiduscials > from the Neuromag > GUI for MRI-MEG Integration. I have already performed this step and > saved the > transformed mri in the /sets/XXX.fif file. I suggest you use the FT_DETERMINE_COORDSYS to perform a visual inspection of the coordinate systems of your anatomical MRI and of your sensor positions (data.grad, or you can use FT_READ_SENS to read them directly from the MEG fif file). Note that you have to use the function twice (on the mri and on the grad) and compare the figures yourself. > Should I write any rpa/nas/lpa coordinates in this case? > cfg.fiducial.rpa = [y x z]; > cfg.fiducial.nas = [y x z]; > cfg.fiducial.lpa = [y x z]; if you need them (see above), then these should be [x y z] and not [y x z]. > > I have 2 4X4 transformations in the .fif file, not sure what they > mean. Please read this page, which is a general introduction. > > mri.hdr.trans.trans > > 0.9913 0.1210 0.0518 -0.0032 > -0.0948 0.9291 -0.3574 0.0254 > -0.0914 0.3494 0.9325 -0.0519 > 0 0 0 1.0000 > mri.hdr.voxel_trans.trans > > -0.0000 -0.0000 -0.0010 0.1058 > -0.0005 0.0000 0.0000 0.1597 > 0 -0.0005 0.0001 0.1058 > 0 0 0 1.0000 the mri header is system specific, so I am not sure. But I guess that the first is the homogenous transformation matrix in head coordinates (linked to the fiducials) and the second is the homogenous transformation matrix in MRI coordinates. The first one appears to be in mm, the second one in meter. Please try mri.transform = mri.hdr.voxel_trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c mri.transform = mri.hdr.trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c The two figures will show you the origin, the direction of axes of the coordinate system and the scale. best regards, Robert From r.oostenveld at donders.ru.nl Mon May 23 09:41:17 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 23 May 2011 09:41:17 +0200 Subject: [FieldTrip] ft_read_vol with Neuromag In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> References: <32CC77C0C8A7AD4B9410934642608E1F03EBDF0C@exchccr1.neuro.gu.se> Message-ID: <4BFE3CE0-268F-4ACC-8863-5017DC5957AF@donders.ru.nl> Hi Elena Although some years ago FieldTrip was supporting volume conduction models from Neuromag using the meg-pd and the (closed source) meg-calc toolboxes from the company itself, I suspect that nobody has been using them the last few years. The mex files in meg-pd and meg-calc were often problematic to work with due to platform and library issues. The single-shell volume conduction model that is avaialble in Fieldtrip is currently the preferred volume model. Looking at the code, there is indeed a bug since cfg.gradfile is not defined. If you want to continue along the path of meg-pd and meg- calc, you could hardcode the filename and see how far you get. But I'd suspect that you don't have the required (commercial) mex files from meg-calc anyway. best regards Robert On 20 May 2011, at 14:00, Elena Orekhova wrote: > Hi, > I try to read volume from the Neuromag .fif file using > > vol = ft_read_vol(NEUROMAG_FIF_FILE_NAME, 'fileformat', > 'neuromag_fif') > > I get the error: > *********************** > ??? Undefined variable "cfg" or class "cfg.gradfile". > > Error in ==> ft_read_vol at 77 > fprintf('using Neuromag gradiometer definition from %s\n', > cfg.gradfile); > > Any advice? > > Elena > > Elena V Orekhova, Ph.D. > Inst. Neuroscience and Physiology > University of Gothenburg > S-413 45 Gothenburg, Sweden > phone: +46 31 342 48 02 > elena at neuro.gu.se > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From Elena.Orekhova at neuro.gu.se Mon May 23 10:00:15 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 23 May 2011 08:00:15 +0000 Subject: [FieldTrip] segmentation problem with Neuromag Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC7CC3@exchccr1.neuro.gu.se> Dear Fieldtrip users and developers, I would like to start using Fieldtrip for the source analysis of the MEG data, but I have some problem with mri segmentation using Neuromag-306 .fif MRI file. I do: 1) import .fif, (Coordinate alignment was already done in Neuromag). mriname = 'NEUROMAGxxx.fif' [mri] = ft_read_mri(mriname) cfg = []; ft_sourceplot(cfg,mri); ***** attachment: mri.jpg ****** 2) do segmentation cfg = []; cfg.template = 'T1.nii'; %spm8 cfg.coordsys = 'neuromag'; cfg.write = 'no'; cfg.name = 'temp'; cfg.interactive = 'yes'; [segmentedmri] = ft_volumesegment(cfg, mri) 3) plot the original and segmented mri cfg = []; test.dim = [512 512 180]; test = segmentedmri; test.avg.pow = test.gray+test.white; test.anatomy = mri.anatomy; cfg.funparameter = 'avg.pow'; cfg.interactive = 'yes'; ft_sourceplot(cfg,test); ***** attachment : mri_segmented.jpg ****** Apparently, there is a displacement of the segmented mri image. It seems also that the segmented mri is bigger then the original mri. The similar (although not the same) picture is observed when I do coordinate alignment in the MNE and use the /sets/CORxxx.fif saved from the MNE sohtware. I have seen some discussions on this topic, but I have not found the solution. Should I swap x and y coordinates? How can I do it? I would be most grateful for help! Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mri.jpg Type: image/jpeg Size: 20047 bytes Desc: mri.jpg URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: mri_segmented.jpg Type: image/jpeg Size: 59004 bytes Desc: mri_segmented.jpg URL: From odidodi at hotmail.com Mon May 23 10:44:31 2011 From: odidodi at hotmail.com (odelia nakar) Date: Mon, 23 May 2011 08:44:31 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Mon May 23 12:03:11 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 23 May 2011 10:03:11 +0000 Subject: [FieldTrip] rpa/nas/lpa coordinates In-Reply-To: References: <32CC77C0C8A7AD4B9410934642608E1F03EC3C2B@exchccr1.neuro.gu.se>, Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03EC8D07@exchccr1.neuro.gu.se> Dear Robert, As you advised, I tried to use 'ft_determine_coordsys' to look at my non-segmented MRI, but got the error (see below). What can be the reason? /Elena >> >> mri mri = dim: [512 512 180] anatomy: [512x512x180 int16] hdr: [1x1 struct] transform: [4x4 double] unit: 'm' >> [dataout] = ft_determine_coordsys(mri) ??? Error using ==> surface Z must be a matrix, not a scalar or vector Error in ==> ft_plot_slice at 184 h = surface(Xh, Yh, Zh, V); Error in ==> ft_plot_ortho at 94 hx = ft_plot_slice(dat, varargin{:}); Error in ==> ft_determine_coordsys at 192 ft_plot_ortho(data.(funparam), 'transform', data.transform, 'resolution', 1, 'style', 'intersect'); >> ________________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Robert Oostenveld [r.oostenveld at donders.ru.nl] Sent: Monday, May 23, 2011 9:33 AM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] rpa/nas/lpa coordinates Dear Elena > On 21 May 2011, at 14:11, Elena Orekhova wrote: > >> Hi >> I Just started to use Fieldtrip with my Neuromag MEG data and try >> to follow the example script >> ‘read_neuromag_mri_and_create_single- >> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space >> ’ I don't know all details of the Neuromag system, but recently we did add the http://fieldtrip.fcdonders.nl/getting_started/yokogawa documentation that explains reasonably general how coordinate system coregistration works. We also added a new function (FT_SENSORREALIGN) to ease the coregistration and we are working towards a more consistent representation of the corodinate systems in the relevant fieldtrip data structures. Although the details for your system are different (see http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined) , you might get a better overview of the steps that are involved by reading the yokogawa getting started. > The instruction suggests to take voxel coordinates of fiduscials > from the Neuromag > GUI for MRI-MEG Integration. I have already performed this step and > saved the > transformed mri in the /sets/XXX.fif file. I suggest you use the FT_DETERMINE_COORDSYS to perform a visual inspection of the coordinate systems of your anatomical MRI and of your sensor positions (data.grad, or you can use FT_READ_SENS to read them directly from the MEG fif file). Note that you have to use the function twice (on the mri and on the grad) and compare the figures yourself. > Should I write any rpa/nas/lpa coordinates in this case? > cfg.fiducial.rpa = [y x z]; > cfg.fiducial.nas = [y x z]; > cfg.fiducial.lpa = [y x z]; if you need them (see above), then these should be [x y z] and not [y x z]. > > I have 2 4X4 transformations in the .fif file, not sure what they > mean. Please read this page, which is a general introduction. > > mri.hdr.trans.trans > > 0.9913 0.1210 0.0518 -0.0032 > -0.0948 0.9291 -0.3574 0.0254 > -0.0914 0.3494 0.9325 -0.0519 > 0 0 0 1.0000 > mri.hdr.voxel_trans.trans > > -0.0000 -0.0000 -0.0010 0.1058 > -0.0005 0.0000 0.0000 0.1597 > 0 -0.0005 0.0001 0.1058 > 0 0 0 1.0000 the mri header is system specific, so I am not sure. But I guess that the first is the homogenous transformation matrix in head coordinates (linked to the fiducials) and the second is the homogenous transformation matrix in MRI coordinates. The first one appears to be in mm, the second one in meter. Please try mri.transform = mri.hdr.voxel_trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c mri.transform = mri.hdr.trans.trans; figure ft_determine_coordsys(mri) % press ctrl-c The two figures will show you the origin, the direction of axes of the coordinate system and the scale. best regards, Robert _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jinyinz at ece.cmu.edu Mon May 23 15:46:20 2011 From: jinyinz at ece.cmu.edu (jinyinz at ece.cmu.edu) Date: Mon, 23 May 2011 09:46:20 -0400 (EDT) Subject: [FieldTrip] the source space for MEG/EEG source localization Message-ID: <4412.128.2.133.95.1306158380.squirrel@webmail.ece.cmu.edu> Dear Fieldtrippers, I have a question about the source space selection for MEG/EEG source localization. Some source localization algorithms restrict the reconstruction to sources located on cortical surface. To implement such kind of algorithm, I used mne_setup_source_space to create a source space on cortical surface. By default mne_setup_source_space creates a decimated dipole grid on the white matter surface. Although this setting is widely used, some papers create a source space on the gray matter surface instead. Are there any specific reasons for selecting any of the two options? Thanks, Jinyin From dgroppe at cogsci.ucsd.edu Mon May 23 17:57:25 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Mon, 23 May 2011 08:57:25 -0700 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: > Hi all, > > I'm troubled by the fact that when I use ICA for blinks\eyes movements > removal, I remove the relevant components also from trials that do not > contain blinks\eyes movements. In order to avoid this bias we thought to > combine the data before ICA ("data" structure) with the data after ICA > ("dataica" structure), only in specific trials, as follows: > > datall=dataica; > datall.trial=data.trial; > datall.time=data.time; > blinks=[2 4 5 8 bla bla 156]; > for ind=1:length(blinks) >      datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; > end > > To my first question: I just wanted to check that there is no problem with > that, or any reason not to use it. > > Another issue- I use motor learning task, and I'm trying to understand what > happens through the process, in terms of power-frequency changes through the > process. How would you recommend that I'd use the ft_freqanalysis function? > What method to use (or what do I need to consider when choosing the method > field)? > > > Thanks a lot, > Odelia. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From jdien07 at mac.com Tue May 24 03:07:57 2011 From: jdien07 at mac.com (Joseph Dien) Date: Mon, 23 May 2011 21:07:57 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> Message-ID: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote: > Hi Odelia, > When you use ICA (or any other spatial filter) to correct for EEG > artifacts, you're going to distort your data some by removing true EEG > activity in addition to the artifact (for an explanation, see: > http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). > So to minimize distortion, it would be better not to apply ICA > artifact correction to artifact-free data. However, if the frequency > of the artifact differs across experimental conditions, it could > confound your analysis. For example, I suspect people blink more > often to targets in an oddball experiment than standards. Thus if you > apply ICA only to blinky trials, you could find a difference between > the EEG response to standards and targets that simply reflects the > fact ICA removed more EEG activity in the target trials (i.e., it > wouldn't reflect a true difference in neural processing). > hope this helps, > -David > > On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: >> Hi all, >> >> I'm troubled by the fact that when I use ICA for blinks\eyes movements >> removal, I remove the relevant components also from trials that do not >> contain blinks\eyes movements. In order to avoid this bias we thought to >> combine the data before ICA ("data" structure) with the data after ICA >> ("dataica" structure), only in specific trials, as follows: >> >> datall=dataica; >> datall.trial=data.trial; >> datall.time=data.time; >> blinks=[2 4 5 8 bla bla 156]; >> for ind=1:length(blinks) >> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >> end >> >> To my first question: I just wanted to check that there is no problem with >> that, or any reason not to use it. >> >> Another issue- I use motor learning task, and I'm trying to understand what >> happens through the process, in terms of power-frequency changes through the >> process. How would you recommend that I'd use the ft_freqanalysis function? >> What method to use (or what do I need to consider when choosing the method >> field)? >> >> >> Thanks a lot, >> Odelia. >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph Dien E-mail: jdien07 at mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://homepage.mac.com/jdien07/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From shackman at wisc.edu Tue May 24 04:00:34 2011 From: shackman at wisc.edu (Alexander J. Shackman) Date: Mon, 23 May 2011 21:00:34 -0500 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: And for a related perspective, see McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, *Neuroimage**, 54*, 4-9. http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: > I agree with David's reasoning. You may find the following article to be > of help as well in understanding the issues involved: > > Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of > simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping*, 28 > (8), 742-763. > > Cheers! > > Joe > > On May 23, 2011, at 11:57 AM, David Groppe wrote: > > Hi Odelia, > When you use ICA (or any other spatial filter) to correct for EEG > artifacts, you're going to distort your data some by removing true EEG > activity in addition to the artifact (for an explanation, see: > http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). > So to minimize distortion, it would be better not to apply ICA > artifact correction to artifact-free data. However, if the frequency > of the artifact differs across experimental conditions, it could > confound your analysis. For example, I suspect people blink more > often to targets in an oddball experiment than standards. Thus if you > apply ICA only to blinky trials, you could find a difference between > the EEG response to standards and targets that simply reflects the > fact ICA removed more EEG activity in the target trials (i.e., it > wouldn't reflect a true difference in neural processing). > hope this helps, > -David > > On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: > > Hi all, > > > I'm troubled by the fact that when I use ICA for blinks\eyes movements > > removal, I remove the relevant components also from trials that do not > > contain blinks\eyes movements. In order to avoid this bias we thought to > > combine the data before ICA ("data" structure) with the data after ICA > > ("dataica" structure), only in specific trials, as follows: > > > datall=dataica; > > datall.trial=data.trial; > > datall.time=data.time; > > blinks=[2 4 5 8 bla bla 156]; > > for ind=1:length(blinks) > > datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; > > end > > > To my first question: I just wanted to check that there is no problem with > > that, or any reason not to use it. > > > Another issue- I use motor learning task, and I'm trying to understand what > > happens through the process, in terms of power-frequency changes through > the > > process. How would you recommend that I'd use the ft_freqanalysis function? > > What method to use (or what do I need to consider when choosing the method > > field)? > > > > Thanks a lot, > > Odelia. > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -------------------------------------------------------------------------------- > > Joseph Dien > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://homepage.mac.com/jdien07/ > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Alexander J. Shackman, Ph.D. Wisconsin Psychiatric Institute & Clinics and Department of Psychology University of Wisconsin-Madison 1202 West Johnson Street Madison, Wisconsin 53706 Telephone: +1 (608) 358-5025 Fax: +1 (608) 265-2875 Email: shackman at wisc.edu http://psyphz.psych.wisc.edu/~shackman -------------- next part -------------- An HTML attachment was scrubbed... URL: From odidodi at hotmail.com Tue May 24 08:46:55 2011 From: odidodi at hotmail.com (odelia nakar) Date: Tue, 24 May 2011 06:46:55 +0000 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com>, <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl>, , , <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: Thank you all- Joe, Alexander and David, it is indeed very helpful and enlightening. I actually don't have any stimulus, but I wasn't aware of the hidden EMG. Have a good day (or night :))! Odelia. From: jdien07 at mac.com Date: Mon, 23 May 2011 21:07:57 -0400 To: fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] ICA+frqanalysis questions I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. Cheers! Joe On May 23, 2011, at 11:57 AM, David Groppe wrote:Hi Odelia, When you use ICA (or any other spatial filter) to correct for EEG artifacts, you're going to distort your data some by removing true EEG activity in addition to the artifact (for an explanation, see: http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). So to minimize distortion, it would be better not to apply ICA artifact correction to artifact-free data. However, if the frequency of the artifact differs across experimental conditions, it could confound your analysis. For example, I suspect people blink more often to targets in an oddball experiment than standards. Thus if you apply ICA only to blinky trials, you could find a difference between the EEG response to standards and targets that simply reflects the fact ICA removed more EEG activity in the target trials (i.e., it wouldn't reflect a true difference in neural processing). hope this helps, -David On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: Hi all, I'm troubled by the fact that when I use ICA for blinks\eyes movements removal, I remove the relevant components also from trials that do not contain blinks\eyes movements. In order to avoid this bias we thought to combine the data before ICA ("data" structure) with the data after ICA ("dataica" structure), only in specific trials, as follows: datall=dataica; datall.trial=data.trial; datall.time=data.time; blinks=[2 4 5 8 bla bla 156]; for ind=1:length(blinks) datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; end To my first question: I just wanted to check that there is no problem with that, or any reason not to use it. Another issue- I use motor learning task, and I'm trying to understand what happens through the process, in terms of power-frequency changes through the process. How would you recommend that I'd use the ft_freqanalysis function? What method to use (or what do I need to consider when choosing the method field)? Thanks a lot, Odelia. _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------------------------------------------------------------------------- Joseph DienE-mail: jdien07 at mac.comPhone: 301-226-8848Fax: 301-226-8811http://homepage.mac.com/jdien07/ _______________________________________________ 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 stefan.debener at uni-oldenburg.de Tue May 24 09:11:16 2011 From: stefan.debener at uni-oldenburg.de (Stefan Debener) Date: Tue, 24 May 2011 09:11:16 +0200 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> Message-ID: <4DDB5A14.3090102@uni-oldenburg.de> Hi Odelia, I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... Best, Stefan Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: > And for a related perspective, see > > McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. > J. (2011). Electromyogenic artifacts and electroencephalographic > inferences revisited, */Neuroimage/*/, 54/, 4-9. > > http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf > > > > On Mon, May 23, 2011 at 8:07 PM, Joseph Dien > wrote: > > I agree with David's reasoning. You may find the following > article to be of help as well in understanding the issues involved: > > Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and > ICA of simulated ERPs: Promax versus Infomax rotations. /Human > Brain Mapping/, 28(8), 742-763. > > Cheers! > > Joe > > On May 23, 2011, at 11:57 AM, David Groppe wrote: > >> Hi Odelia, >> When you use ICA (or any other spatial filter) to correct for EEG >> artifacts, you're going to distort your data some by removing >> true EEG >> activity in addition to the artifact (for an explanation, see: >> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >> So to minimize distortion, it would be better not to apply ICA >> artifact correction to artifact-free data. However, if the frequency >> of the artifact differs across experimental conditions, it could >> confound your analysis. For example, I suspect people blink more >> often to targets in an oddball experiment than standards. Thus >> if you >> apply ICA only to blinky trials, you could find a difference between >> the EEG response to standards and targets that simply reflects the >> fact ICA removed more EEG activity in the target trials (i.e., it >> wouldn't reflect a true difference in neural processing). >> hope this helps, >> -David >> >> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >> > wrote: >>> Hi all, >>> >>> I'm troubled by the fact that when I use ICA for blinks\eyes >>> movements >>> removal, I remove the relevant components also from trials that >>> do not >>> contain blinks\eyes movements. In order to avoid this bias we >>> thought to >>> combine the data before ICA ("data" structure) with the data >>> after ICA >>> ("dataica" structure), only in specific trials, as follows: >>> >>> datall=dataica; >>> datall.trial=data.trial; >>> datall.time=data.time; >>> blinks=[2 4 5 8 bla bla 156]; >>> for ind=1:length(blinks) >>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>> end >>> >>> To my first question: I just wanted to check that there is no >>> problem with >>> that, or any reason not to use it. >>> >>> Another issue- I use motor learning task, and I'm trying to >>> understand what >>> happens through the process, in terms of power-frequency changes >>> through the >>> process. How would you recommend that I'd use the >>> ft_freqanalysis function? >>> What method to use (or what do I need to consider when choosing >>> the method >>> field)? >>> >>> >>> Thanks a lot, >>> Odelia. >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> David Groppe, Ph.D. >> Postdoctoral Researcher >> Kutaslab >> Dept. of Cognitive Science >> University of California, San Diego >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -------------------------------------------------------------------------------- > > Joseph Dien > E-mail: jdien07 at mac.com > Phone: 301-226-8848 > Fax: 301-226-8811 > http://homepage.mac.com/jdien07/ > > > > > > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > -- > Alexander J. Shackman, Ph.D. > Wisconsin Psychiatric Institute & Clinics and > Department of Psychology > University of Wisconsin-Madison > 1202 West Johnson Street > Madison, Wisconsin 53706 > > Telephone: +1 (608) 358-5025 > Fax: +1 (608) 265-2875 > Email: shackman at wisc.edu > http://psyphz.psych.wisc.edu/~shackman > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Prof. Dr. Stefan Debener Neuropsychology Lab Department of Psychology University of Oldenburg D-26111 Oldenburg Germany Office: A7 0-038 Phone: +49-441-798-4271 Fax: +49-441-798-5522 Email: stefan.debener at uni-oldenburg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Tue May 24 23:47:39 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Tue, 24 May 2011 14:47:39 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine Message-ID: Hi there, My lab is running MATLAB 7.8 on a Linux network and when we plot spectrograms using ft_multiplotTFR.m the computer we're using will often reboot. It appears to happen most often (if not exclusively), when we close the figure window produced by ft_multiplotTFR.m. The problem happens even if we create non-interactive figures (i.e., we set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., Java disabled). Has anyone else had this problem? Does anyone have an idea as to what a solution might be? Puzzlingly, we don't have this problem when running MATLAB on a Mac. much appreciated, -David -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From r.vandermeij at donders.ru.nl Wed May 25 00:23:58 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 24 May 2011 15:23:58 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: References: Message-ID: <4DDC2FFE.9000600@donders.ru.nl> Hi David, Depending on what you mean by crashing, it could be the opengl drivers. I've experienced similar issues with complex plotting functions. Try creating the figure-window (note, not the plot) using the zbuffer to circumvent it by figure('renderer','zbuffer') Hope it helps, Roemer On 24-May-11 14:47, David Groppe wrote: > Hi there, > My lab is running MATLAB 7.8 on a Linux network and when we plot > spectrograms using ft_multiplotTFR.m the computer we're using will > often reboot. It appears to happen most often (if not exclusively), > when we close the figure window produced by ft_multiplotTFR.m. The > problem happens even if we create non-interactive figures (i.e., we > set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., > Java disabled). Has anyone else had this problem? Does anyone have > an idea as to what a solution might be? Puzzlingly, we don't have > this problem when running MATLAB on a Mac. > much appreciated, > -David > -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition Radboud University Nijmegen P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Wed May 25 02:10:02 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Tue, 24 May 2011 17:10:02 -0700 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: <4DDC2FFE.9000600@donders.ru.nl> References: <4DDC2FFE.9000600@donders.ru.nl> Message-ID: Thanks very much for the response Roemer. By "crashing," I mean the screen suddenly goes blank and the machine reverts to the login screen. I've tried your suggestion and so far it looks like it's working! I'll let you know if the problem returns. greatly appreciated, -David On Tue, May 24, 2011 at 3:23 PM, Roemer van der Meij wrote: > Hi David, > > Depending on what you mean by crashing, it could be the opengl drivers. I've > experienced similar issues with complex plotting functions. Try creating the > figure-window (note, not the plot) using the zbuffer to circumvent it by > figure('renderer','zbuffer') > > Hope it helps, > Roemer > > > > On 24-May-11 14:47, David Groppe wrote: > > Hi there, > My lab is running MATLAB 7.8 on a Linux network and when we plot > spectrograms using ft_multiplotTFR.m the computer we're using will > often reboot. It appears to happen most often (if not exclusively), > when we close the figure window produced by ft_multiplotTFR.m. The > problem happens even if we create non-interactive figures (i.e., we > set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., > Java disabled). Has anyone else had this problem? Does anyone have > an idea as to what a solution might be? Puzzlingly, we don't have > this problem when running MATLAB on a Mac. > much appreciated, > -David > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > Radboud University Nijmegen > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From g.piantoni at nin.knaw.nl Wed May 25 08:59:20 2011 From: g.piantoni at nin.knaw.nl (Gio Piantoni) Date: Wed, 25 May 2011 08:59:20 +0200 Subject: [FieldTrip] ft_multiplotTFR.m crashing Linux machine In-Reply-To: References: <4DDC2FFE.9000600@donders.ru.nl> Message-ID: Hi David, I also had similar problems, such as crashing of the VNC window on a remote server. I agree with Roemer that it's probably due to buggy opengl drivers. More information at: http://www.mathworks.com/support/tech-notes/1200/1201.html#Section_4 Briefly, you can run as first command: >> opengl software to force matlab to use the (less buggy) software implementation of opengl. Then the trick "figure('renderer','zbuffer')" should not be necessary. Hope this helps. Gio -- Giovanni Piantoni, Ph.D. student Dept. Sleep & Cognition Netherlands Institute for Neuroscience Meibergdreef 47 1105 BA Amsterdam (NL) +31 (0)20 5665492 g.piantoni at nin.knaw.nl www.giovannipiantoni.com On Wed, May 25, 2011 at 02:10, David Groppe wrote: > Thanks very much for the response Roemer.  By "crashing," I mean the > screen suddenly goes blank and the machine reverts to the login > screen.  I've tried your suggestion and so far it looks like it's > working!  I'll let you know if the problem returns. >     greatly appreciated, >          -David > > On Tue, May 24, 2011 at 3:23 PM, Roemer van der Meij > wrote: >> Hi David, >> >> Depending on what you mean by crashing, it could be the opengl drivers. I've >> experienced similar issues with complex plotting functions. Try creating the >> figure-window (note, not the plot) using the zbuffer to circumvent it by >> figure('renderer','zbuffer') >> >> Hope it helps, >> Roemer >> >> >> >> On 24-May-11 14:47, David Groppe wrote: >> >> Hi there, >>    My lab is running MATLAB 7.8 on a Linux network and when we plot >> spectrograms using ft_multiplotTFR.m the computer we're using will >> often reboot.  It appears to happen most often (if not exclusively), >> when we close the figure window produced by ft_multiplotTFR.m.  The >> problem happens even if we create non-interactive figures (i.e., we >> set cfg.interactive to 'no') or run MATLAB in the -nojvm mode (i.e., >> Java disabled).  Has anyone else had this problem?   Does anyone have >> an idea as to what a solution might be?  Puzzlingly, we don't have >> this problem when running MATLAB on a Mac. >>           much appreciated, >>                 -David >> >> >> -- >> Roemer van der Meij M.Sc. >> PhD student >> Donders Institute for Brain, Cognition and Behaviour >> Centre for Cognition >> Radboud University Nijmegen >> P.O. Box 9104 >> 6500 HE Nijmegen >> The Netherlands >> Tel: +31(0)24 3655932 >> E-mail: r.vandermeij at donders.ru.nl >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > From g.dimitriadis at donders.ru.nl Wed May 25 09:48:49 2011 From: g.dimitriadis at donders.ru.nl (George Dimitriadis) Date: Wed, 25 May 2011 09:48:49 +0200 Subject: [FieldTrip] (no subject) Message-ID: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> Hello guys, I just run an ft_freqanalysis using cfg.taper='dssp'. By mistake I took the cfg. tapsmofrq to be too small resulting in a single taper. This was fine, but when I run freqanalysis I got an error saying that the warning_once (ft_specest_mtmfft at 89) was not found. Apparently it was there to warn me about using only 1 tapper for smoothing with 'dssp'. I am just letting you know that for some reason the warning_once(char) function couldn't be found. Thanks George -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed May 25 10:10:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 25 May 2011 10:10:02 +0200 Subject: [FieldTrip] (no subject) In-Reply-To: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> References: <039701cc1ab0$32773060$97659120$@dimitriadis@donders.ru.nl> Message-ID: <6F47EF43-DE4D-4031-8BCC-F5C9D9AA13D3@donders.ru.nl> Hi George, Sorry about this. If you are running a local copy of fieldtrip, you can copy warning_once.m from fieldtrip/private into fieldtrip/specest/ private. It should work then. I'll fix it in the release version asap. Cheers, JM On May 25, 2011, at 9:48 AM, George Dimitriadis wrote: > Hello guys, > > I just run an ft_freqanalysis using cfg.taper=’dssp’. By mistake I > took the cfg. tapsmofrq to be too small resulting in a single taper. > This was fine, but when I run freqanalysis I got an error saying > that the warning_once (ft_specest_mtmfft at 89) was not found. > Apparently it was there to warn me about using only 1 tapper for > smoothing with ‘dssp’. I am just letting you know that for some > reason the warning_once(char) function couldn’t be found. > > Thanks > > George > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From S.N.Maijers at student.ru.nl Wed May 25 11:50:16 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Wed, 25 May 2011 11:50:16 +0200 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? Message-ID: <20110525115016.0fc02ea6@thuisrekenaar> Dear readers, I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit (Linux thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 x86_64 GNU/Linux). When I call "ft_timelockstatistics()" with "cfg.mva ={ft_mv_standardizer() ft_mv_svm()};" It fails: "selected 60 channels selected 351 time bins selected 1 frequency bins using "statistics_crossvalidate" for the statistical testing initializing random number generator with seed 1 validating 1 dataset(s) input 1 consists of 439 examples and 21060 features output 1 consists of 439 examples and 1 features validating using 5-fold cross-validation using 5 folds for 1 datasets dataset 1: validating fold 1 of 5 using 351 training samples and 88 test samples Compiling tprod for first use /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when searching for -lstdc++ /usr/bin/ld: skipping incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching for -lstdc++ /usr/bin/ld: cannot find -lstdc++ collect2: ld returned 1 exit status mex: link of ' "tprod.mexglx"' failed. ??? Error using ==> tprod at 132 unable to compile MEX version of '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', please make sure your MEX compiler is set up correctly (try 'mex -setup')." I have followed the instructions on https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX compiling but it was not successful. -> Before I singlehandedly bring my operating system configuration into disarray, I would like to learn from you the following. Do you know of ways to use a gcc to compile code written for a 32-bit architecture ona 64-bit machine? Or if necessary another compiler that works under Linux? -> If such a thing is certainly impossible, are there ways to avoid MEX compiling? Or could someone provide precompiled MEX files that would suit my configuration? [*] I have installed the Ubuntu package "ia32-libs" (version 20090808ubuntu9.1) [*] It seems that the only thing I need is 32-bit binaries for libstdc++. Perhaps I can introduce these in some creative way, but I would like to check with you all first. I hope you are willing to help me. As a novice to FieldTrip and even MATLAB, I have encountered many obstacles but I am determined to surmount them. Kind regards, Sander Maijers (BA Linguistics student) From S.N.Maijers at student.ru.nl Wed May 25 12:13:01 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Wed, 25 May 2011 12:13:01 +0200 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory Message-ID: <20110525121301.2f896b3e@thuisrekenaar> Dear readers, While all other functional subdirectories do get included after an "addpath" of the FieldTrip root directory, the "multivariate" subdirectories does not get included. It assume this is because of automatical detection that requirements of the FieldTrip multivariate module were not met. Yet while some parts of the multivariate module seem to rely on features exclusive to MATLAB 64-bit editions, others (like the ridge regression functionality) do not. >From my (tentative) investigation it appears that there is no standard way to add a path recursively from a startup.m file, even though that can be done with the graphical interface of MATLAB. What are your thoughts about this? Can anyone offer a method to automatically add FieldTrip including the multivariate module to the path upon startup of MATLAB that works in my situation? Kind regards, Sander Maijers P.S.: In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit Linux. From ekanal at cmu.edu Wed May 25 14:53:53 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Wed, 25 May 2011 08:53:53 -0400 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory In-Reply-To: <20110525121301.2f896b3e@thuisrekenaar> References: <20110525121301.2f896b3e@thuisrekenaar> Message-ID: <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> Hello Sander - Just so you know, there is a way to recursively add folders to a path, using the `genpath` command: addpath(genpath(path/to/folder)) However, as you said, it's probably just a better idea to add it to the `ft_defaults` file so it's added automatically, as you suggested. Elli On May 25, 2011, at 6:13 AM, Sander Maijers wrote: > Dear readers, > > While all other functional subdirectories do get included after an > "addpath" of the FieldTrip root directory, the "multivariate" > subdirectories does not get included. > > It assume this is because of automatical detection that requirements of > the FieldTrip multivariate module were not met. > > Yet while some parts of the multivariate module seem to rely on > features exclusive to MATLAB 64-bit editions, others (like the ridge > regression functionality) do not. > >> From my (tentative) investigation it appears that there is no standard > way to add a path recursively from a startup.m file, even though that > can be done with the graphical interface of MATLAB. > > What are your thoughts about this? > > Can anyone offer a method to automatically add FieldTrip including the > multivariate module to the path upon startup of MATLAB that works in > my situation? > > Kind regards, > Sander Maijers > > P.S.: > In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit > Linux. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From batrod at gmail.com Wed May 25 17:39:02 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Wed, 25 May 2011 10:39:02 -0500 Subject: [FieldTrip] [multivariate] "multivariate" subdirectory not included upon "addpath" of FieldTrip root directory In-Reply-To: <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> References: <20110525121301.2f896b3e@thuisrekenaar> <31810FB1-D384-4B77-8BCA-E2369C8A4F4C@cmu.edu> Message-ID: Hello Sander, Elli's suggestion is right. As you apparently want to do that on matlab startup and using Linux, you can add a matlab shortcut on your panel with the following instructions : matlab -r "yourinstructions" "yourinstructions" can be an addpath or wathever you want. I often use this initialization to avoid default path conflicts between spm, fieldtrip, eeglab, etc... Hope this helps, Rodolphe On Wed, May 25, 2011 at 7:53 AM, Kanal Eliezer wrote: > Hello Sander - > > Just so you know, there is a way to recursively add folders to a path, > using the `genpath` command: > > addpath(genpath(path/to/folder)) > > However, as you said, it's probably just a better idea to add it to the > `ft_defaults` file so it's added automatically, as you suggested. > > Elli > > > On May 25, 2011, at 6:13 AM, Sander Maijers wrote: > > > Dear readers, > > > > While all other functional subdirectories do get included after an > > "addpath" of the FieldTrip root directory, the "multivariate" > > subdirectories does not get included. > > > > It assume this is because of automatical detection that requirements of > > the FieldTrip multivariate module were not met. > > > > Yet while some parts of the multivariate module seem to rely on > > features exclusive to MATLAB 64-bit editions, others (like the ridge > > regression functionality) do not. > > > >> From my (tentative) investigation it appears that there is no standard > > way to add a path recursively from a startup.m file, even though that > > can be done with the graphical interface of MATLAB. > > > > What are your thoughts about this? > > > > Can anyone offer a method to automatically add FieldTrip including the > > multivariate module to the path upon startup of MATLAB that works in > > my situation? > > > > Kind regards, > > Sander Maijers > > > > P.S.: > > In case it would be relevant: I use MATLAB R2011a 32-bit under 64-bit > > Linux. > > > > _______________________________________________ > > 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 batrod at gmail.com Wed May 25 18:32:19 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Wed, 25 May 2011 11:32:19 -0500 Subject: [FieldTrip] Filtering and oscillations Message-ID: Dear Fieldtrippers, i have a theoretical question. Im interested into phase-lock analysis between sensors in alpha oscillations. Prior to do so, my data were bandpassed between 2 and 30 Hz. However, i heard that such a low-pass filter can alter informations usefull to phase-lock analysis. Any suggestions on that? Best regards, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jenwhitman at gmail.com Wed May 25 19:53:28 2011 From: jenwhitman at gmail.com (Jen Whitman) Date: Wed, 25 May 2011 10:53:28 -0700 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? In-Reply-To: <20110525115016.0fc02ea6@thuisrekenaar> References: <20110525115016.0fc02ea6@thuisrekenaar> Message-ID: As another ubuntu 64-bit user, I'd say your problem is with your matlab install rather than with fieldtrip. You may have inadvertently specified 32-bit instead of 64-bit when you installed matlab. If you type "computer" at the matlab prompt, it should say "GLNXA64". If not, I recommend redoing the matlab installation and making sure you specify your OS as 64-bit. If you still get error message about libstdc++.so, you may need to install that library using the 'synaptic package manger' (in your system menu under administration). A good resource for help if you have further difficulty may be linuxquestions.org. Best of luck! On Wed, May 25, 2011 at 2:50 AM, Sander Maijers wrote: > Dear readers, > > I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit (Linux > thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 18:42:20 UTC 2011 > x86_64 GNU/Linux). > > When I call "ft_timelockstatistics()" with "cfg.mva ={ft_mv_standardizer() > ft_mv_svm()};" > > It fails: > > "selected 60 channels > selected 351 time bins > selected 1 frequency bins > using "statistics_crossvalidate" for the statistical testing > initializing random number generator with seed 1 > validating 1 dataset(s) > input 1 consists of 439 examples and 21060 features > output 1 consists of 439 examples and 1 features > validating using 5-fold cross-validation > using 5 folds for 1 datasets > dataset 1: validating fold 1 of 5 using 351 training samples and 88 test > samples Compiling tprod for first use > /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > searching for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching > for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > searching for -lstdc++ /usr/bin/ld: skipping > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when searching > for -lstdc++ /usr/bin/ld: > cannot find -lstdc++ collect2: ld returned 1 exit status > > mex: link of ' "tprod.mexglx"' failed. > > ??? Error using ==> tprod at 132 unable to compile MEX version of > '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', > please make sure your MEX compiler is set up correctly (try 'mex -setup')." > > > I have followed the instructions on > https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX > compiling but it was not successful. > > -> Before I singlehandedly bring my operating system configuration into > disarray, I would like to learn from you the following. Do you know of ways > to use a gcc to compile code written for a 32-bit architecture ona 64-bit > machine? Or if necessary another compiler that works under Linux? > -> If such a thing is certainly impossible, are there ways to avoid MEX > compiling? Or could someone provide precompiled MEX files that would suit my > configuration? > > [*] I have installed the Ubuntu package "ia32-libs" (version > 20090808ubuntu9.1) > [*] It seems that the only thing I need is 32-bit binaries for libstdc++. > Perhaps I can introduce these in some creative way, but I would like to > check with you all first. > > I hope you are willing to help me. As a novice to FieldTrip and even > MATLAB, I have encountered many obstacles but I am determined to surmount > them. > > Kind regards, > Sander Maijers (BA Linguistics student) > _______________________________________________ > 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 S.N.Maijers at student.ru.nl Thu May 26 16:23:39 2011 From: S.N.Maijers at student.ru.nl (Sander Maijers) Date: Thu, 26 May 2011 16:23:39 +0200 Subject: [FieldTrip] [multivariate] MEX compiling for 32-bit MATLAB under 64-bit Linux: who helps? In-Reply-To: References: <20110525115016.0fc02ea6@thuisrekenaar> Message-ID: <20110526162339.65dd030c@thuisrekenaar> Jen, thanks for your suggestion. That problem I had fixed before. I am among those who could not even get a 64-bit install if they wished so, because the Student edition of MATLAB is still 32-bit-only. This problem will occur later on, in case some MEX-compilation needs to be done, in my case with the multivariate module! I have succeeded in fixing the problem however. Those who are confronted with it as well, can read: http://fieldtrip.fcdonders.nl/faq/compile?&#fixing_mex-compilation_with_32-bit_variants_of_matlab_running_under_64-bit_linux . On Wed, 25 May 2011 10:53:28 -0700 Jen Whitman wrote: > As another ubuntu 64-bit user, I'd say your problem is with your > matlab install rather than with fieldtrip. You may have inadvertently > specified 32-bit instead of 64-bit when you installed matlab. If you > type "computer" at the matlab prompt, it should say "GLNXA64". If > not, I recommend redoing the matlab installation and making sure you > specify your OS as 64-bit. If you still get error message about > libstdc++.so, you may need to install that library using the > 'synaptic package manger' (in your system menu under administration). > A good resource for help if you have further difficulty may be > linuxquestions.org. > > Best of luck! > > On Wed, May 25, 2011 at 2:50 AM, Sander Maijers > wrote: > > > Dear readers, > > > > I am running MATLAB R2011a 32-bit under Ubuntu Linux 10.10 64-bit > > (Linux thuisrekenaar 2.6.35-28-generic #50-Ubuntu SMP Fri Mar 18 > > 18:42:20 UTC 2011 x86_64 GNU/Linux). > > > > When I call "ft_timelockstatistics()" with "cfg.mva > > ={ft_mv_standardizer() ft_mv_svm()};" > > > > It fails: > > > > "selected 60 channels > > selected 351 time bins > > selected 1 frequency bins > > using "statistics_crossvalidate" for the statistical testing > > initializing random number generator with seed 1 > > validating 1 dataset(s) > > input 1 consists of 439 examples and 21060 features > > output 1 consists of 439 examples and 1 features > > validating using 5-fold cross-validation > > using 5 folds for 1 datasets > > dataset 1: validating fold 1 of 5 using 351 training samples and 88 > > test samples Compiling tprod for first use > > /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.so when > > searching for -lstdc++ /usr/bin/ld: skipping > > incompatible /usr/lib/gcc/x86_64-linux-gnu/4.3.5/libstdc++.a when > > searching for -lstdc++ /usr/bin/ld: > > cannot find -lstdc++ collect2: ld returned 1 exit status > > > > mex: link of ' "tprod.mexglx"' failed. > > > > ??? Error using ==> tprod at 132 unable to compile MEX version of > > '/mnt/data1/0/9/data/software/UNIX/scientific/FieldTrip/bin/fieldtrip-read-only/multivariate/external/farquhar/tprod/tprod', > > please make sure your MEX compiler is set up correctly (try 'mex > > -setup')." > > > > > > I have followed the instructions on > > https://help.ubuntu.com/community/MATLAB#MEX functions to enable MEX > > compiling but it was not successful. > > > > -> Before I singlehandedly bring my operating system configuration > > into disarray, I would like to learn from you the following. Do you > > know of ways to use a gcc to compile code written for a 32-bit > > architecture ona 64-bit machine? Or if necessary another compiler > > that works under Linux? -> If such a thing is certainly impossible, > > are there ways to avoid MEX compiling? Or could someone provide > > precompiled MEX files that would suit my configuration? > > > > [*] I have installed the Ubuntu package "ia32-libs" (version > > 20090808ubuntu9.1) > > [*] It seems that the only thing I need is 32-bit binaries for > > libstdc++. Perhaps I can introduce these in some creative way, but > > I would like to check with you all first. > > > > I hope you are willing to help me. As a novice to FieldTrip and even > > MATLAB, I have encountered many obstacles but I am determined to > > surmount them. > > > > Kind regards, > > Sander Maijers (BA Linguistics student) > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > From dgroppe at cogsci.ucsd.edu Fri May 27 03:54:35 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Thu, 26 May 2011 18:54:35 -0700 Subject: [FieldTrip] duplicate spm directories Message-ID: Hi again, I'm running the March 28th version of Fieldtrip and am getting the following warning: Warning: multiple versions of SPM on your path will confuse FieldTrip > In fieldtrip-20110328/private/warning_once at 75 In ft_defaults at 45 In ft_preprocessing at 179 Warning: one version of SPM is found here: /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm2/spm.m > In ft_defaults at 48 In ft_preprocessing at 179 Warning: one version of SPM is found here: /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm8/spm.m Can I simply remove the spm2 directory? thanks in advance, -D -- David Groppe, Ph.D. Postdoctoral Researcher Kutaslab Dept. of Cognitive Science University of California, San Diego http://www.cogsci.ucsd.edu/~dgroppe/ From jdien07 at mac.com Fri May 27 05:16:03 2011 From: jdien07 at mac.com (Joseph Dien) Date: Thu, 26 May 2011 23:16:03 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <4DDB5A14.3090102@uni-oldenburg.de> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> Message-ID: <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Stefan, just to be clear, I don't think any of us were saying not to use ICA to correct blinks. David was just saying that there are potential concerns when one only applies the ICA to the blink trials rather than to all the trials. I myself use EEGlab's infomax implementation in the automatic eyeblink correction tool of my EP Toolkit (http://sourceforge.net/projects/erppcatoolkit/). Now that said, I should add a little more nuance to my response. One of the things I observed (or rather, that Tim Curran pointed out to me) is that when you apply ICA to remove eyeblink artifacts in this manner, it can actually substantially increase the noise level in the data, so for the trials without eyeblinks it can have a considerable cost. So in order to balance the cost/benefit ratio, what I did was to include a trial by trial criterion that the putative eyeblink factors would only be removed if doing so reduced the overall variance of the trial. This approach does still have some potential for causing the concerns that David raises but not as much as only applying the ICA to blink trials since it does end up getting applied to non-blink trials too. This does mean that one should be cautious about any apparent effects in the artifact corrected data that are centered around the eyes (that have a blink topography) but that goes without saying in any case. So anyway, I agree, it's not perfect but seems to be the best available option. Cheers! Joe On May 24, 2011, at 3:11 AM, Stefan Debener wrote: > Hi Odelia, > > I have a slightly different opinion here. It is certainly true that any filter has the tendency to distort data (with distortion I mean that data consists of a mixture of some wanted, true signal and some unwanted signal, and that the removal of the unwanted part of the signal is neither complete nor specific). In our lab we regularly use ICA for artefact removal (and more), and the benefit/gain is clearly are much larger than the distortion. In fact there are a number of examples out showing that currently only ICA (or related tools) can recover the study of (a substantial fraction of the wanted) EEG signal (but again, it is NOT a perfect tool at all), in particular in cases where other means of SNR enhancement don't work well (averaging, spectral analysis). I am happy to provide references if you are interested... > > For the evaluation of outcome it would be reasonable to not evaluate the ERP alone, as this could be misleading. Better evaluate the sensitivity and specificity of an eye blink attentuation approach on the single trial (and single subject) level, this will give you good insight. And it is worth keeping in mind that the preprocessing of the data (among other issues, like the quality of the recording and so on) largely determines the quality of the output (for some introduction you may look up chapter 3.1 in Ullsperger & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just by a different preprocessing ICA output could vary between crap and excellent unmixing. Thus a poor ICA eye blink attenuation would make me a bit suspicious... > > Best, > Stefan > > > Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: >> >> And for a related perspective, see >> >> McMenamin, B. W., Shackman, A. J., Greischar, L. L. & Davidson, R. J. (2011). Electromyogenic artifacts and electroencephalographic inferences revisited, Neuroimage, 54, 4-9. >> >> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf >> >> >> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: >> I agree with David's reasoning. You may find the following article to be of help as well in understanding the issues involved: >> >> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of simulated ERPs: Promax versus Infomax rotations. Human Brain Mapping, 28(8), 742-763. >> >> Cheers! >> >> Joe >> >> On May 23, 2011, at 11:57 AM, David Groppe wrote: >> >>> Hi Odelia, >>> When you use ICA (or any other spatial filter) to correct for EEG >>> artifacts, you're going to distort your data some by removing true EEG >>> activity in addition to the artifact (for an explanation, see: >>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >>> So to minimize distortion, it would be better not to apply ICA >>> artifact correction to artifact-free data. However, if the frequency >>> of the artifact differs across experimental conditions, it could >>> confound your analysis. For example, I suspect people blink more >>> often to targets in an oddball experiment than standards. Thus if you >>> apply ICA only to blinky trials, you could find a difference between >>> the EEG response to standards and targets that simply reflects the >>> fact ICA removed more EEG activity in the target trials (i.e., it >>> wouldn't reflect a true difference in neural processing). >>> hope this helps, >>> -David >>> >>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar wrote: >>>> Hi all, >>>> >>>> I'm troubled by the fact that when I use ICA for blinks\eyes movements >>>> removal, I remove the relevant components also from trials that do not >>>> contain blinks\eyes movements. In order to avoid this bias we thought to >>>> combine the data before ICA ("data" structure) with the data after ICA >>>> ("dataica" structure), only in specific trials, as follows: >>>> >>>> datall=dataica; >>>> datall.trial=data.trial; >>>> datall.time=data.time; >>>> blinks=[2 4 5 8 bla bla 156]; >>>> for ind=1:length(blinks) >>>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>>> end >>>> >>>> To my first question: I just wanted to check that there is no problem with >>>> that, or any reason not to use it. >>>> >>>> Another issue- I use motor learning task, and I'm trying to understand what >>>> happens through the process, in terms of power-frequency changes through the >>>> process. How would you recommend that I'd use the ft_freqanalysis function? >>>> What method to use (or what do I need to consider when choosing the method >>>> field)? >>>> >>>> >>>> Thanks a lot, >>>> Odelia. >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> David Groppe, Ph.D. >>> Postdoctoral Researcher >>> Kutaslab >>> Dept. of Cognitive Science >>> University of California, San Diego >>> http://www.cogsci.ucsd.edu/~dgroppe/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://homepage.mac.com/jdien07/ >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -- >> Alexander J. Shackman, Ph.D. >> Wisconsin Psychiatric Institute & Clinics and >> Department of Psychology >> University of Wisconsin-Madison >> 1202 West Johnson Street >> Madison, Wisconsin 53706 >> >> Telephone: +1 (608) 358-5025 >> Fax: +1 (608) 265-2875 >> Email: shackman at wisc.edu >> http://psyphz.psych.wisc.edu/~shackman >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email: stefan.debener at uni-oldenburg.de > _______________________________________________ > 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 yuvharpaz at gmail.com Fri May 27 05:40:14 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Fri, 27 May 2011 06:40:14 +0300 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Message-ID: Dear discussion group Did anybody consider smoothing or filtering the component trace before rejecting it? it seems that the added noise to no-blink trials is in a frequency higher than that typical to blinks. what if we evaluate the component weight, creating a trace for the eyeblink component for every trial, then bandpass filter the blink trace , say 0.1-25Hz, and only then remove the component from the data? yuval On 27 May 2011 06:16, Joseph Dien wrote: > Stefan, just to be clear, I don't think any of us were saying not to use > ICA to correct blinks. David was just saying that there are potential > concerns when one only applies the ICA to the blink trials rather than to > all the trials. I myself use EEGlab's infomax implementation in the > automatic eyeblink correction tool of my EP Toolkit ( > http://sourceforge.net/projects/erppcatoolkit/). > > Now that said, I should add a little more nuance to my response. One of > the things I observed (or rather, that Tim Curran pointed out to me) is that > when you apply ICA to remove eyeblink artifacts in this manner, it can > actually substantially increase the noise level in the data, so for the > trials without eyeblinks it can have a considerable cost. So in order to > balance the cost/benefit ratio, what I did was to include a trial by trial > criterion that the putative eyeblink factors would only be removed if doing > so reduced the overall variance of the trial. This approach does still have > some potential for causing the concerns that David raises but not as much as > only applying the ICA to blink trials since it does end up getting applied > to non-blink trials too. This does mean that one should be cautious about > any apparent effects in the artifact corrected data that are centered around > the eyes (that have a blink topography) but that goes without saying in any > case. So anyway, I agree, it's not perfect but seems to be the best > available option. > > Cheers! > > Joe > > On May 24, 2011, at 3:11 AM, Stefan Debener wrote: > > Hi Odelia, > > I have a slightly different opinion here. It is certainly true that any > filter has the tendency to distort data (with distortion I mean that data > consists of a mixture of some wanted, true signal and some unwanted signal, > and that the removal of the unwanted part of the signal is neither complete > nor specific). In our lab we regularly use ICA for artefact removal (and > more), and the benefit/gain is clearly are much larger than the distortion. > In fact there are a number of examples out showing that currently only ICA > (or related tools) can recover the study of (a substantial fraction of the > wanted) EEG signal (but again, it is NOT a perfect tool at all), in > particular in cases where other means of SNR enhancement don't work well > (averaging, spectral analysis). I am happy to provide references if you are > interested... > > For the evaluation of outcome it would be reasonable to not evaluate the > ERP alone, as this could be misleading. Better evaluate the sensitivity and > specificity of an eye blink attentuation approach on the single trial (and > single subject) level, this will give you good insight. And it is worth > keeping in mind that the preprocessing of the data (among other issues, like > the quality of the recording and so on) largely determines the quality of > the output (for some introduction you may look up chapter 3.1 in Ullsperger > & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just > by a different preprocessing ICA output could vary between crap and > excellent unmixing. Thus a poor ICA eye blink attenuation would make me a > bit suspicious... > > Best, > Stefan > > > Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: > > And for a related perspective, see > > McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. > (2011). Electromyogenic artifacts and electroencephalographic inferences > revisited, *Neuroimage**, 54*, 4-9. > > http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf > > > On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: > >> I agree with David's reasoning. You may find the following article to >> be of help as well in understanding the issues involved: >> >> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA of >> simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping*, >> 28(8), 742-763. >> >> Cheers! >> >> Joe >> >> On May 23, 2011, at 11:57 AM, David Groppe wrote: >> >> Hi Odelia, >> When you use ICA (or any other spatial filter) to correct for EEG >> artifacts, you're going to distort your data some by removing true EEG >> activity in addition to the artifact (for an explanation, see: >> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >> So to minimize distortion, it would be better not to apply ICA >> artifact correction to artifact-free data. However, if the frequency >> of the artifact differs across experimental conditions, it could >> confound your analysis. For example, I suspect people blink more >> often to targets in an oddball experiment than standards. Thus if you >> apply ICA only to blinky trials, you could find a difference between >> the EEG response to standards and targets that simply reflects the >> fact ICA removed more EEG activity in the target trials (i.e., it >> wouldn't reflect a true difference in neural processing). >> hope this helps, >> -David >> >> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >> wrote: >> >> Hi all, >> >> >> I'm troubled by the fact that when I use ICA for blinks\eyes movements >> >> removal, I remove the relevant components also from trials that do not >> >> contain blinks\eyes movements. In order to avoid this bias we thought to >> >> combine the data before ICA ("data" structure) with the data after ICA >> >> ("dataica" structure), only in specific trials, as follows: >> >> >> datall=dataica; >> >> datall.trial=data.trial; >> >> datall.time=data.time; >> >> blinks=[2 4 5 8 bla bla 156]; >> >> for ind=1:length(blinks) >> >> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >> >> end >> >> >> To my first question: I just wanted to check that there is no problem >> with >> >> that, or any reason not to use it. >> >> >> Another issue- I use motor learning task, and I'm trying to understand >> what >> >> happens through the process, in terms of power-frequency changes through >> the >> >> process. How would you recommend that I'd use the ft_freqanalysis >> function? >> >> What method to use (or what do I need to consider when choosing the method >> >> field)? >> >> >> >> Thanks a lot, >> >> Odelia. >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> >> -- >> David Groppe, Ph.D. >> Postdoctoral Researcher >> Kutaslab >> Dept. of Cognitive Science >> University of California, San Diego >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien >> E-mail: jdien07 at mac.com >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://homepage.mac.com/jdien07/ >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> > > > -- > Alexander J. Shackman, Ph.D. > Wisconsin Psychiatric Institute & Clinics and > Department of Psychology > University of Wisconsin-Madison > 1202 West Johnson Street > Madison, Wisconsin 53706 > > Telephone: +1 (608) 358-5025 > Fax: +1 (608) 265-2875 > Email: shackman at wisc.edu > http://psyphz.psych.wisc.edu/~shackman > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > Prof. Dr. Stefan Debener > Neuropsychology Lab > Department of Psychology > University of Oldenburg > D-26111 Oldenburg > Germany > > Office: A7 0-038 > Phone: +49-441-798-4271 > Fax: +49-441-798-5522 > Email: stefan.debener at uni-oldenburg.de > > _______________________________________________ > 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 > -- Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahesh.casiraghi at gmail.com Fri May 27 06:32:01 2011 From: mahesh.casiraghi at gmail.com (Mahesh Casiraghi) Date: Fri, 27 May 2011 00:32:01 -0400 Subject: [FieldTrip] ICA+frqanalysis questions In-Reply-To: References: <48E7CEFF-DD7B-41AD-9B37-EDE35849E305@mac.com> <543865F0-2B31-49D6-8CE7-D7CB24849F17@donders.ru.nl> <09D31350-934E-44DA-AC0B-22CBFA1CFEAD@mac.com> <4DDB5A14.3090102@uni-oldenburg.de> <34CEBDBD-7738-403D-A563-4A6FDBD83C04@mac.com> Message-ID: Dear Yuval and discussion group, it seems to me that what you are proposing is getting close to what proposed by the hybrid approach of regica described here: *Manousos A. Klados, Christos Papadelis, Christoph Braun, Panagiotis D. Bamidis, REG-ICA: A hybrid methodology combining Blind Source Separation and regression techniques for the rejection of ocular artifacts, Biomedical Signal Processing and Control, In Press, Corrected Proof, Available online 16 March 2011, ISSN 1746-8094, DOI: 10.1016/j.bspc.2011.02.001.* They suggest to selectively run regression based AR only on those components which correlate with EOG signals. This makes sense to me and I have been trying to experiment that on some old data, although with no clear conclusions yet. It may be worth a try for Odelia: Anybody out there with some insights for this - or maybe a similar - approach? Cheers, Mahesh Mahesh M. Casiraghi PhD candidate - Cognitive Sciences Roberto Dell'Acqua Lab, University of Padova Pierre Jolicoeur Lab, Univesité de Montréal mahesh.casiraghi at umontreal.ca I have the conviction that when Physiology will be far enough advanced, the poet, the philosopher, and the physiologist will all understand each other. Claude Bernard On Thu, May 26, 2011 at 11:40 PM, Yuval Harpaz wrote: > Dear discussion group > Did anybody consider smoothing or filtering the component trace before > rejecting it? > it seems that the added noise to no-blink trials is in a frequency higher > than that typical to blinks. what if we evaluate the component weight, > creating a trace for the eyeblink component for every trial, then bandpass > filter the blink trace , say 0.1-25Hz, and only then remove the component > from the data? > yuval > > On 27 May 2011 06:16, Joseph Dien wrote: > >> Stefan, just to be clear, I don't think any of us were saying not to use >> ICA to correct blinks. David was just saying that there are potential >> concerns when one only applies the ICA to the blink trials rather than to >> all the trials. I myself use EEGlab's infomax implementation in the >> automatic eyeblink correction tool of my EP Toolkit ( >> http://sourceforge.net/projects/erppcatoolkit/). >> >> Now that said, I should add a little more nuance to my response. One of >> the things I observed (or rather, that Tim Curran pointed out to me) is that >> when you apply ICA to remove eyeblink artifacts in this manner, it can >> actually substantially increase the noise level in the data, so for the >> trials without eyeblinks it can have a considerable cost. So in order to >> balance the cost/benefit ratio, what I did was to include a trial by trial >> criterion that the putative eyeblink factors would only be removed if doing >> so reduced the overall variance of the trial. This approach does still have >> some potential for causing the concerns that David raises but not as much as >> only applying the ICA to blink trials since it does end up getting applied >> to non-blink trials too. This does mean that one should be cautious about >> any apparent effects in the artifact corrected data that are centered around >> the eyes (that have a blink topography) but that goes without saying in any >> case. So anyway, I agree, it's not perfect but seems to be the best >> available option. >> >> Cheers! >> >> Joe >> >> On May 24, 2011, at 3:11 AM, Stefan Debener wrote: >> >> Hi Odelia, >> >> I have a slightly different opinion here. It is certainly true that any >> filter has the tendency to distort data (with distortion I mean that data >> consists of a mixture of some wanted, true signal and some unwanted signal, >> and that the removal of the unwanted part of the signal is neither complete >> nor specific). In our lab we regularly use ICA for artefact removal (and >> more), and the benefit/gain is clearly are much larger than the distortion. >> In fact there are a number of examples out showing that currently only ICA >> (or related tools) can recover the study of (a substantial fraction of the >> wanted) EEG signal (but again, it is NOT a perfect tool at all), in >> particular in cases where other means of SNR enhancement don't work well >> (averaging, spectral analysis). I am happy to provide references if you are >> interested... >> >> For the evaluation of outcome it would be reasonable to not evaluate the >> ERP alone, as this could be misleading. Better evaluate the sensitivity and >> specificity of an eye blink attentuation approach on the single trial (and >> single subject) level, this will give you good insight. And it is worth >> keeping in mind that the preprocessing of the data (among other issues, like >> the quality of the recording and so on) largely determines the quality of >> the output (for some introduction you may look up chapter 3.1 in Ullsperger >> & Debener, 2010, Simultaneous EEG and FMRI, Oxford University Press). Just >> by a different preprocessing ICA output could vary between crap and >> excellent unmixing. Thus a poor ICA eye blink attenuation would make me a >> bit suspicious... >> >> Best, >> Stefan >> >> >> Am 5/24/11 4:00 AM, schrieb Alexander J. Shackman: >> >> And for a related perspective, see >> >> McMenamin, B. W., *Shackman, A. J.*, Greischar, L. L. & Davidson, R. J. >> (2011). Electromyogenic artifacts and electroencephalographic inferences >> revisited, *Neuroimage**, 54*, 4-9. >> >> http://psyphz.psych.wisc.edu/~shackman/mcmenamin_shackman_ni2011.pdf >> >> >> On Mon, May 23, 2011 at 8:07 PM, Joseph Dien wrote: >> >>> I agree with David's reasoning. You may find the following article to >>> be of help as well in understanding the issues involved: >>> >>> Dien, J., Khoe, W., & Mangun, G. R. (2007). Evaluation of PCA and ICA >>> of simulated ERPs: Promax versus Infomax rotations. *Human Brain Mapping >>> *, 28(8), 742-763. >>> >>> Cheers! >>> >>> Joe >>> >>> On May 23, 2011, at 11:57 AM, David Groppe wrote: >>> >>> Hi Odelia, >>> When you use ICA (or any other spatial filter) to correct for EEG >>> artifacts, you're going to distort your data some by removing true EEG >>> activity in addition to the artifact (for an explanation, see: >>> http://www.cogsci.ucsd.edu/%7Edgroppe/PUBLICATIONS/GroppeCSO2008.pdf). >>> So to minimize distortion, it would be better not to apply ICA >>> artifact correction to artifact-free data. However, if the frequency >>> of the artifact differs across experimental conditions, it could >>> confound your analysis. For example, I suspect people blink more >>> often to targets in an oddball experiment than standards. Thus if you >>> apply ICA only to blinky trials, you could find a difference between >>> the EEG response to standards and targets that simply reflects the >>> fact ICA removed more EEG activity in the target trials (i.e., it >>> wouldn't reflect a true difference in neural processing). >>> hope this helps, >>> -David >>> >>> On Mon, May 23, 2011 at 1:44 AM, odelia nakar >>> wrote: >>> >>> Hi all, >>> >>> >>> I'm troubled by the fact that when I use ICA for blinks\eyes movements >>> >>> removal, I remove the relevant components also from trials that do not >>> >>> contain blinks\eyes movements. In order to avoid this bias we thought to >>> >>> combine the data before ICA ("data" structure) with the data after ICA >>> >>> ("dataica" structure), only in specific trials, as follows: >>> >>> >>> datall=dataica; >>> >>> datall.trial=data.trial; >>> >>> datall.time=data.time; >>> >>> blinks=[2 4 5 8 bla bla 156]; >>> >>> for ind=1:length(blinks) >>> >>> datall.trial{1,blinks(ind)}=dataica.trial{1,blinks(ind)}; >>> >>> end >>> >>> >>> To my first question: I just wanted to check that there is no problem >>> with >>> >>> that, or any reason not to use it. >>> >>> >>> Another issue- I use motor learning task, and I'm trying to understand >>> what >>> >>> happens through the process, in terms of power-frequency changes through >>> the >>> >>> process. How would you recommend that I'd use the ft_freqanalysis >>> function? >>> >>> What method to use (or what do I need to consider when choosing the >>> method >>> >>> field)? >>> >>> >>> >>> Thanks a lot, >>> >>> Odelia. >>> >>> >>> _______________________________________________ >>> >>> fieldtrip mailing list >>> >>> fieldtrip at donders.ru.nl >>> >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> >>> -- >>> David Groppe, Ph.D. >>> Postdoctoral Researcher >>> Kutaslab >>> Dept. of Cognitive Science >>> University of California, San Diego >>> http://www.cogsci.ucsd.edu/~dgroppe/ >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> >>> -------------------------------------------------------------------------------- >>> >>> Joseph Dien >>> E-mail: jdien07 at mac.com >>> Phone: 301-226-8848 >>> Fax: 301-226-8811 >>> http://homepage.mac.com/jdien07/ >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >> >> >> -- >> Alexander J. Shackman, Ph.D. >> Wisconsin Psychiatric Institute & Clinics and >> Department of Psychology >> University of Wisconsin-Madison >> 1202 West Johnson Street >> Madison, Wisconsin 53706 >> >> Telephone: +1 (608) 358-5025 >> Fax: +1 (608) 265-2875 >> Email: shackman at wisc.edu >> http://psyphz.psych.wisc.edu/~shackman >> >> >> _______________________________________________ >> fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> -- >> Prof. Dr. Stefan Debener >> Neuropsychology Lab >> Department of Psychology >> University of Oldenburg >> D-26111 Oldenburg >> Germany >> >> Office: A7 0-038 >> Phone: +49-441-798-4271 >> Fax: +49-441-798-5522 >> Email: stefan.debener at uni-oldenburg.de >> >> _______________________________________________ >> 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 >> > > > > -- > Y.Harpaz > > a link to the BIU MEG lab: > http://faculty.biu.ac.il/~goldsa/index.html > > *"Many were increasingly of the opinion that they'd all made a big mistake > in coming down from the trees in the first place. And some said that even > the trees had been a bad move, and that no one should ever have left the > oceans". Douglas Adams > * > > > _______________________________________________ > 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 jan.schoffelen at donders.ru.nl Fri May 27 08:19:02 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 27 May 2011 08:19:02 +0200 Subject: [FieldTrip] duplicate spm directories In-Reply-To: References: Message-ID: <6BA914CC-EDD4-4D85-BC49-B790FD08447E@donders.ru.nl> Dear David, Yes, you can safely remove the spm2 directory. Unless you rely in your analysis pipeline on spm2-specific stuff. The only thing I can think of here would be to read in .mnc files. Cheers, Jan-Mathijs On May 27, 2011, at 3:54 AM, David Groppe wrote: > Hi again, > I'm running the March 28th version of Fieldtrip and am getting the > following warning: > > Warning: multiple versions of SPM on your path will confuse FieldTrip >> In fieldtrip-20110328/private/warning_once at 75 > In ft_defaults at 45 > In ft_preprocessing at 179 > Warning: one version of SPM is found here: > /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm2/spm.m >> In ft_defaults at 48 > In ft_preprocessing at 179 > Warning: one version of SPM is found here: > /Users/dgroppe/Documents/MATLAB/fieldtrip-20110328/external/spm8/spm.m > > > Can I simply remove the spm2 directory? > thanks in advance, > -D > > -- > David Groppe, Ph.D. > Postdoctoral Researcher > Kutaslab > Dept. of Cognitive Science > University of California, San Diego > http://www.cogsci.ucsd.edu/~dgroppe/ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 From akademonbrain at gmail.com Fri May 27 10:43:11 2011 From: akademonbrain at gmail.com (Aka Demon) Date: Fri, 27 May 2011 11:43:11 +0300 Subject: [FieldTrip] influences between the regions In-Reply-To: References: Message-ID: Dear experts After analyzing memory experiment EEG/MEG and source localization data, i figured out that there is little I can say about the interactions between the activated regions as I don’t have any information about the connection between the activated areas. So I was wondering if there are some useful works/tools that I can use to explorer the influences between the regions (such as information transfer from one region to the other). Thanks a lot Aka -------------- next part -------------- An HTML attachment was scrubbed... URL: From drivolta81 at gmail.com Fri May 27 14:26:28 2011 From: drivolta81 at gmail.com (Davide Rivolta) Date: Fri, 27 May 2011 14:26:28 +0200 Subject: [FieldTrip] tutorial - ft_volumenormalise Message-ID: Dear Fieldtrippers, I am running the tutorial on how to localize oscillatory sources using beamformer techniques. It works smooth until I have to normalize the anatomical mri to the template. When, after I load the already-segmented subject file, I run ft_volumenormalise it says the following: ??? Attempted to access V.dim(4); index out of bounds because numel(V.dim)=3. Error in ==> spm_create_vol>create_vol at 94 swapped = spm_type(V.dim(4),'swapped'); Interestingly this is the same error I get when I try to run ft_volumesegment both using the tutorial and my anatomical MRIs. Has someone any idea? Am I doing something silly? Thank you so much, Davide -------------- next part -------------- An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Sat May 28 01:13:43 2011 From: rapela at ucsd.edu (=?iso-8859-1?Q?Joaqu=EDn_Rapela?=) Date: Fri, 27 May 2011 16:13:43 -0700 (PDT) Subject: [FieldTrip] lead field without with no MRI Message-ID: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> Dear all, I want to compute a lead field matrix but I have no MRI scan of my subjects. I would be happy with a concentric spheres model, or similar, adjusted to the electrodes locations (modified 10 20 system). I would be very grateful if somebody directs me to the appropriate functions in FieldTrip. My apologizes if this is a naive question. I am new to FieldTrip. Thanks in advance, Joaquin -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel/fax: (858) 822-7536 http://www-scf.usc.edu/~rapela ---------------------------------- There are men who struggle for a day and they are good. There are men who struggle for a year and they are better. There are men who struggle many years, and they are better still. But there are those who struggle all their lives: These are the indispensable ones. Bertolt Brecht From michael.wibral at web.de Sun May 29 09:26:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Sun, 29 May 2011 09:26:47 +0200 (CEST) Subject: [FieldTrip] influences between the regions Message-ID: <1324085935.896862.1306654007541.JavaMail.fmail@mwmweb084> An HTML attachment was scrubbed... URL: From rapela at ucsd.edu Sun May 29 21:38:50 2011 From: rapela at ucsd.edu (=?iso-8859-1?Q?Joaqu=EDn_Rapela?=) Date: Sun, 29 May 2011 12:38:50 -0700 (PDT) Subject: [FieldTrip] lead field with no MRI In-Reply-To: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> References: <60859.137.110.244.8.1306538023.squirrel@acs-webmail.ucsd.edu> Message-ID: <46100.137.110.37.196.1306697930.squirrel@acs-webmail.ucsd.edu> Below I describe how to compute the leadfield matrix adjusted to a set of electrodes in an extended 10-20 system, without having an MRI image. Besides, I have a question: why in the help of the fieldtrip functions their output is not described? Cordially, Joaquin I had to dig into the EEGLAB Dipfit plugin to learn how to do this. I used the function ft_prepare_leadfield. It requires a head model and the channel locations. Since I have an extended 10-20 electrode system, I used a BEM head model that comes with Dipfit, and also uses an extended 10-20 system. This head model is in the plugins directory of dipfit2.2: hdmFile=/usr/local/eeglab/plugins/dipfit2.2/standard_BEM/standard_vol.mat and the channel locations for this head model are also in the dipfit2.2 directory: hmChanfile=/usr/local/eeglab/plugins/dipfit2.2/standard_BEM/elec/standard_1005.elc It turns out that the previous head model is not ready for ft_prepare_leadfield, and I had to use the function ft_prepare_vol_sens to prepare it. Also, I wanted to compute the leadfield matrix only for the channels in my data set, whose labels are in the variable dsChanlabels, so I passed dsChanlabels as the argument 'channel' of ft_prepare_vol_sens. Finally, I used the head model and sensors prepared by ft_prepare_vol_sens as input to ft_prepare_headmodel. I append the code that does the job. If you see any bug, please let me know. Warmly, Joaquin ### function grid = joacosPrepareLeadfield(dsChanlabels, hmChanfile, hdmFile) cfg = []; vol = ft_read_vol(hdmFile); sens = ft_read_sens(hmChanfile); [vol, sens] = ft_prepare_vol_sens(vol, sens, 'channel', dsChanlabels); cfg = []; cfg.elec = sens; cfg.vol = vol; cfg.grid.resolution = 20; data = []; grid = ft_prepare_leadfield(cfg, data); ### > Dear all, > > I want to compute a lead field matrix but I have no MRI scan of my > subjects. I would be happy with a concentric spheres model, or similar, > adjusted to the electrodes locations (modified 10 20 system). I would be > very grateful if somebody directs me to the appropriate functions in > FieldTrip. My apologizes if this is a naive question. I am new to > FieldTrip. > > Thanks in advance, Joaquin > > -- > Joaquin Rapela, PhD > Swartz Center for Computational Neuroscience > University of California San Diego > 9500 Gilman Drive, > San Diego, CA 92093-0559 > tel/fax: (858) 822-7536 > http://www-scf.usc.edu/~rapela > ---------------------------------- > > There are men who struggle for a day and they are good. > There are men who struggle for a year and they are better. > There are men who struggle many years, and they are better still. > But there are those who struggle all their lives: > These are the indispensable ones. > > Bertolt > Brecht > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Joaquin Rapela, PhD Swartz Center for Computational Neuroscience University of California San Diego 9500 Gilman Drive, San Diego, CA 92093-0559 tel/fax: (858) 822-7536 http://www-scf.usc.edu/~rapela ---------------------------------- There are men who struggle for a day and they are good. There are men who struggle for a year and they are better. There are men who struggle many years, and they are better still. But there are those who struggle all their lives: These are the indispensable ones. Bertolt Brecht From Elena.Orekhova at neuro.gu.se Mon May 30 13:08:29 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 30 May 2011 11:08:29 +0000 Subject: [FieldTrip] SAM beamformeing on Neuromag data Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA679@exchccr1.neuro.gu.se> Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Mon May 30 14:08:08 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 30 May 2011 14:08:08 +0200 (CEST) Subject: [FieldTrip] SAM beamformeing on Neuromag data Message-ID: <1443619351.1500061.1306757288215.JavaMail.fmail@mwmweb072> An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Mon May 30 16:30:34 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Mon, 30 May 2011 14:30:34 +0000 Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA6D6@exchccr1.neuro.gu.se> Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From tobiasnavarroschroeder at googlemail.com Mon May 30 17:58:32 2011 From: tobiasnavarroschroeder at googlemail.com (Tobias Navarro Schroeder) Date: Mon, 30 May 2011 17:58:32 +0200 Subject: [FieldTrip] Beamforming on resting state data In-Reply-To: References: Message-ID: Hi Fieldtrippers, I performed DICS beamforming on resting-state data (i.e. no task, no baseline, eyes closed) of a clinical population and controls. According to the sensor data the patients have more gamma-band (60-90 Hz) activity over temporal areas (somewhat spread-out). Curiously, after beamforming and group comparisons with 'indepsamplesT' permutation statistics the difference map shows more gamma-band (60-90 Hz) activity for controls in the left, middle-temporal gyrus. Hence, the source-level results are opposite to the sensor-level results (although more spatially confined). This is *not* a problem of the design matrix, or confusing the groups. Question 1: Does anybody have experience with opposite results on source and sensor level? The individual raw beamforming results (interpolated on the subjects' MRIs) look suspicios as well. Due to the 'unit gain constraint' there should be an overestimation of power in the center of the head, but only a minority of subjects show that. Often I see temporal or parietal activity. Question 2: Would a lack of a blob in the center of the head in individual, raw, beamforming data indicate an erroneous source analysis? Thanks a lot for help and suggestions. Best, Tobias Navarro Schröder ps: The configurations for calculating the covariance and the beamforming is added below: 1) % Compute the covariance matrices cfg.output = 'powandcsd'; cfg.foi = 75; cfg.foilim = [75 75]; cfg.tapsmofrq = 15; % 75 +- 15 = 60 - 90 Hz cfg.pad = 'maxperlen'; % default cfg.method = 'wltconvol'; % wavelet analysis cfg.width = 5; % Width of the wavelet. Determines the temporal and spectral resolution of the analysis constant. 2) % Perform the actual beamforming % load grids of MRI volume fullnameGrid = [ CurSubject.mripath CurSubject.MRIModel]; cfg = load(fullnameGrid); cfg.vol = cfg.hdm; cfg.frequency = 75; cfg.method = 'dics'; cfg.keepfilter = 'yes'; % keep the beamformer filters (virtual electrodes) for later use cfg.keeptrial = 'no'; cfg.keepmom = 'yes'; % useful for connectivity calculations. Dipole moments.. cfg.projectmom = 'yes'; cfg.projectnoise = 'yes'; cfg.latency = 1; -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Mon May 30 17:58:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 30 May 2011 17:58:47 +0200 (CEST) Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> An HTML attachment was scrubbed... URL: From Tim.Bardouille at nrc-cnrc.gc.ca Mon May 30 18:23:22 2011 From: Tim.Bardouille at nrc-cnrc.gc.ca (Bardouille, Tim) Date: Mon, 30 May 2011 12:23:22 -0400 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: Hi Michael, Elena, If it becomes a sticking point, you could also run MaxFilter with the -nosss option. I don't have any experience with how this would affect the beamformer output, but it would at least resolve the rank issue. Tim. --------------------------------------------------------- Timothy Bardouille, PhD, Research Officer Laboratory for Clinical MEG NRC Institute for Biodiagnostics (Atlantic) Office: Halifax Infirmary 3900 - 1796 Summer Street Halifax, Nova Scotia B3H 3A7 Phone: 902-473-1865 Lab: 902-470-3936 Fax: 902-473-1851 --------------------------------------------------------- ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] On Behalf Of Michael Wibral [michael.wibral at web.de] Sent: May 30, 2011 12:58 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Mon May 30 21:27:13 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Mon, 30 May 2011 21:27:13 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> Hi Michael, Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? Best, Stephan El 30/05/2011, a las 17:58, Michael Wibral escribió: > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the > maxfilter papers the properties of the components removed by the > maxfilter do not require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a > tiny amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please > let me know!) > > > Michael > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 4:30:34 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since > MaxFilter reduces the rank of the covariance matrix by removing > noisy components, it may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip- > bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de > ] > Sent: Monday, May 30, 2011 2:08 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the > different UNITS (not only scales) of gradiometers and magnetometers. > There was a problem with the sign of the leadfields but that should > have been fixed. > > There is one more fundamental problem however, that you should be > aware of (doesn't invalidate your source analysis but bears > potential for fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your > source signal back with unit gain. Added on top however is > neurophysiological crosstalk (minimized) and sensor noise of the > sensors with the largest weights in your Beamformer (not reducible). > So different sensor types willhave different (inverse) leadfield > strengths, theerfore also fiofefrent source noise levels. the > relative benefits of each sensor type changes from location to > location, so a location (and data) dependend weighting would in > principle be best. > I am not sure if and how this is implemented if FT (Bayesian > weighting would be optimal here..) > > What you could do as a first step is to beam separately and compare > the results. > > Michael > > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 1:08:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face > { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font- > family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal > { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: > Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font- > family: Courier; }span.HTMLPreformattedChar { font-family: > Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 > { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E > \671D "; }@font-face { font-family: "Cambria Math"; }@font-face > { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal > { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: > Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font- > family: Courier; }span.HTMLPreformattedChar { font-family: > Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 > { page: WordSection1; } > Dear All, > > I try to run beamformer analysis on the auditory MEG data (Neuromag) > and have basic questions. > > > 1.Magnetometers and gradiometers Neuromag sensors have different > scales. Does the Fieldtrip take care of this difference or should I > normalize the data? It yes, how to normalize? > > > 2. I would like to do SAM analysis of evoked field and look at the > time courses at ROIs (virtual channels). The only tutorial example > I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer) > . I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method > = 'sam'. > > > I would be most grateful for any example script of this type analysis! > > Regards, > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From jstout211 at yahoo.com Mon May 30 23:28:16 2011 From: jstout211 at yahoo.com (Jeff Stout) Date: Mon, 30 May 2011 14:28:16 -0700 (PDT) Subject: [FieldTrip] MEGRealign channel Message-ID: <365289.7941.qm@web113516.mail.gq1.yahoo.com> Hi All, I am having trouble using the ft_megrealign command with a 4D Magnes 3600 system.  I am trying to use this command to interpolate bad channels that have been removed in preprocessing.  When I view the output of megrealign using ft_plot_sens, sensor 'A229' is badly misplaced (approximately 10 cm above the top of the sensor array), but all the other sensors appear appropriate.  In the dataset A229 has not been labelled as a bad channel, nor any of its neighboring channels. The location of A229 is significant in that it is the most inferior/anterior channel on the left side.  I am using the original grad file as a template input using ft_read_sens('c,rfDC') and scaling the MEG channels to cm.  I am not sure how helpful the code is - below is my input and some of the output.  I can provide an image if this would be helpful. temp = ft_read_sens(subjectdata.FA_dataset); temp.pnt = temp.pnt*100; temp.unit  = 'cm'; cfg = []; cfg.inwardshift = 1; cfg.vol=vol; cfg.template{1}= temp; cfg.channel={'MEG'}; con.grad.pnt = con.grad.pnt*100; con.grad.unit = 'cm'; con = ft_megrealign(cfg, con) computing surface normals mean distance towards template gradiometers is 0.00 cm creating dipole grid based on inward-shifted brain surface from volume conductor model Warning: the normals of the surface triangulation are inward oriented  > In fieldtrip-20110507/private/headsurface at 211   In ft_prepare_sourcemodel at 492   In ft_megrealign at 245 642 dipoles inside, 0 dipoles outside brain computing forward model for 642 dipoles pruning 122 from 246, i.e. removing the 122 smallest spatial components computing interpolation matrix #1 computing interpolation matrix #2 computing interpolation matrix #3 pruning 124 from 248, i.e. removing the 124 smallest spatial components realigning trial 1 original -> template             RV 14.42 % original             -> original RV 14.42 % original -> template -> original RV 14.44 % .................... Does anyone know why this would be occurring and how to fix it? Thanks, Jeff Stout -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue May 31 09:04:26 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 31 May 2011 09:04:26 +0200 Subject: [FieldTrip] MEGRealign channel In-Reply-To: <365289.7941.qm@web113516.mail.gq1.yahoo.com> References: <365289.7941.qm@web113516.mail.gq1.yahoo.com> Message-ID: <012FDE87-5002-4626-B821-D83AAC043C59@donders.ru.nl> Hi Jeff, Thanks for reporting this. We'll look into it as soon as possible. Best wishes, Jan-Mathijs On May 30, 2011, at 11:28 PM, Jeff Stout wrote: > > Hi All, > > I am having trouble using the ft_megrealign command with a 4D Magnes > 3600 system. I am trying to use this command to interpolate bad > channels that have been removed in preprocessing. When I view the > output of megrealign using ft_plot_sens, sensor 'A229' is badly > misplaced (approximately 10 cm above the top of the sensor array), > but all the other sensors appear appropriate. In the dataset A229 > has not been labelled as a bad channel, nor any of its neighboring > channels. The location of A229 is significant in that it is the most > inferior/anterior channel on the left side. I am using the original > grad file as a template input using ft_read_sens('c,rfDC') and > scaling the MEG channels to cm. I am not sure how helpful the code > is - below is my input and some of the output. I can provide an > image if this would be helpful. > > > temp = ft_read_sens(subjectdata.FA_dataset); > temp.pnt = temp.pnt*100; > temp.unit = 'cm'; > > cfg = []; > cfg.inwardshift = 1; > cfg.vol=vol; > cfg.template{1}= temp; > cfg.channel={'MEG'}; > con.grad.pnt = con.grad.pnt*100; > con.grad.unit = 'cm'; > con = ft_megrealign(cfg, con) > > computing surface normals > mean distance towards template gradiometers is 0.00 cm > creating dipole grid based on inward-shifted brain surface from > volume conductor model > Warning: the normals of the surface triangulation are inward oriented > > In fieldtrip-20110507/private/headsurface at 211 > In ft_prepare_sourcemodel at 492 > In ft_megrealign at 245 > 642 dipoles inside, 0 dipoles outside brain > computing forward model for 642 dipoles > pruning 122 from 246, i.e. removing the 122 smallest spatial > components > computing interpolation matrix #1 > computing interpolation matrix #2 > computing interpolation matrix #3 > pruning 124 from 248, i.e. removing the 124 smallest spatial > components > realigning trial 1 > original -> template RV 14.42 % > original -> original RV 14.42 % > original -> template -> original RV 14.44 % .................... > > > Does anyone know why this would be occurring and how to fix it? > > Thanks, > Jeff Stout > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip Dr. J.M. (Jan-Mathijs) Schoffelen Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging, Radboud University Nijmegen, The Netherlands J.Schoffelen at donders.ru.nl Telephone: 0031-24-3614793 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Nina.Kahlbrock at uni-duesseldorf.de Tue May 31 09:23:51 2011 From: Nina.Kahlbrock at uni-duesseldorf.de (Nina Kahlbrock) Date: Tue, 31 May 2011 09:23:51 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> Message-ID: <001301cc1f63$b0faedc0$cd136386@VMED.UKD> Hi Stephan, you can find the discussion list at: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG Best, Nina _____ Von: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] Im Auftrag von Stephan Moratti Gesendet: Montag, 30. Mai 2011 21:27 An: Email discussion list for the FieldTrip project Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Michael, Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? Best, Stephan El 30/05/2011, a las 17:58, Michael Wibral escribió: Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael _____ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena _____ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael _____ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From smoratti at psi.ucm.es Tue May 31 11:42:21 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Tue, 31 May 2011 11:42:21 +0200 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <001301cc1f63$b0faedc0$cd136386@VMED.UKD> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <985E1472-0208-46C2-BB6D-0D6A185888FB@psi.ucm.es> <001301cc1f63$b0faedc0$cd136386@VMED.UKD> Message-ID: Hallo Nina, Vielen Dank !!! Stephan El 31/05/2011, a las 09:23, Nina Kahlbrock escribió: > Hi Stephan, > > you can find the discussion list at: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=NEUROMEG > > Best, > Nina > > Von: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] Im Auftrag von Stephan Moratti > Gesendet: Montag, 30. Mai 2011 21:27 > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Hi Michael, > > Thanks for your comments! We have just started with a Neuromag system in Madrid and we ran into the same questions. Thanks for posting your comments. Could you tell me where I can find the Neuromag discussion list, please? > > Best, > > Stephan > > El 30/05/2011, a las 17:58, Michael Wibral escribió: > > > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please let me know!) > > > Michael > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 4:30:34 PM > An: "Email discussion list for the FieldTrip project" > Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] > Sent: Monday, May 30, 2011 2:08 PM > To: Email discussion list for the FieldTrip project > Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. > > There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. > I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) > > What you could do as a first step is to beam separately and compare the results. > > Michael > > > Von: "Elena Orekhova" > Gesendet: May 30, 2011 1:08:29 PM > An: "fieldtrip at donders.ru.nl" > Betreff: [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } > Dear All, > I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. > > 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? > > 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. > > > I would be most grateful for any example script of this type analysis! > > Regards, > Elena > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > ________________________________________________________ > Stephan Moratti, PhD > > see also: http://web.me.com/smoratti/ > > Department of Basic Psychology > Universidad Complutense de Madrid > > Centro de Tecnología Biomédica CBT, > Universidad Politécnica de Madrid, > > en la actualidad (currently at) en el > Centro de Magnetoencefalografía Dr. Perez Modrego, > Universidad Complutense de Madrid, > Faculdad de Medicina, > Pabellón 8, > Avda. Complutense, s/n, > 28040 Madrid, > Spain, > > email: smoratti at psi.ucm.es > Tel.: +34 91 394 2186 > Fax.: +34 91 394 2294 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip ________________________________________________________ Stephan Moratti, PhD see also: http://web.me.com/smoratti/ Department of Basic Psychology Universidad Complutense de Madrid Centro de Tecnología Biomédica CBT, Universidad Politécnica de Madrid, en la actualidad (currently at) en el Centro de Magnetoencefalografía Dr. Perez Modrego, Universidad Complutense de Madrid, Faculdad de Medicina, Pabellón 8, Avda. Complutense, s/n, 28040 Madrid, Spain, email: smoratti at psi.ucm.es Tel.: +34 91 394 2186 Fax.: +34 91 394 2294 -------------- next part -------------- An HTML attachment was scrubbed... URL: From Elena.Orekhova at neuro.gu.se Tue May 31 12:06:40 2011 From: Elena.Orekhova at neuro.gu.se (Elena Orekhova) Date: Tue, 31 May 2011 10:06:40 +0000 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> Message-ID: <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> Hi Michael, > If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. What lambda you would recommend? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 5:58 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamforming on Neuromag data Hi Elena, as far as I can see from the neuromeg discussion list and the maxfilter papers the properties of the components removed by the maxfilter do not require a leadfield update. If you run into rank-deficiency issue with the covariance matrix a tiny amount of regularization should fix this. (Note: If someone who reads this is of a different opinion, please let me know!) Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 4:30:34 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] SAM beamforming on Neuromag data Thank you for this. I have more concerns. I applied MaxFilter to the data. Since MaxFilter reduces the rank of the covariance matrix by removing noisy components, it may influence the beamformer results. Is it safe to do beamforming with MaxFiltered data? Elena ________________________________ From: fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] on behalf of Michael Wibral [michael.wibral at web.de] Sent: Monday, May 30, 2011 2:08 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] SAM beamformeing on Neuromag data Hi Elena, as far as I know, the leadfield computation should be aware of the different UNITS (not only scales) of gradiometers and magnetometers. There was a problem with the sign of the leadfields but that should have been fixed. There is one more fundamental problem however, that you should be aware of (doesn't invalidate your source analysis but bears potential for fine-tuning), which is the projection of noise: In beamforming the unit gain constraint guarantees that you get your source signal back with unit gain. Added on top however is neurophysiological crosstalk (minimized) and sensor noise of the sensors with the largest weights in your Beamformer (not reducible). So different sensor types willhave different (inverse) leadfield strengths, theerfore also fiofefrent source noise levels. the relative benefits of each sensor type changes from location to location, so a location (and data) dependend weighting would in principle be best. I am not sure if and how this is implemented if FT (Bayesian weighting would be optimal here..) What you could do as a first step is to beam separately and compare the results. Michael ________________________________ Von: "Elena Orekhova" Gesendet: May 30, 2011 1:08:29 PM An: "fieldtrip at donders.ru.nl" Betreff: [FieldTrip] SAM beamformeing on Neuromag data @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { font-family: Cambria; }div.WordSection1 { page: WordSection1; } Dear All, I try to run beamformer analysis on the auditory MEG data (Neuromag) and have basic questions. 1.Magnetometers and gradiometers Neuromag sensors have different scales. Does the Fieldtrip take care of this difference or should I normalize the data? It yes, how to normalize? 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. I would be most grateful for any example script of this type analysis! Regards, Elena -------------- next part -------------- An HTML attachment was scrubbed... URL: From yuvharpaz at gmail.com Tue May 31 12:42:53 2011 From: yuvharpaz at gmail.com (Yuval Harpaz) Date: Tue, 31 May 2011 13:42:53 +0300 Subject: [FieldTrip] SAM beamforming on Neuromag data In-Reply-To: <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> References: <602108165.1563605.1306771127429.JavaMail.fmail@mwmweb072> <32CC77C0C8A7AD4B9410934642608E1F03ECA7E7@exchccr1.neuro.gu.se> Message-ID: Dear Elena and group it basically depends on how much co-variability there is. if you use a large frequency range and a large strech of time you need to correct little if any. if you use averaged data and say from 50 to 120ms from target onset you need more regularization. I used 5% even for relatively short time interval (but large freq. range) and found it reasonable. yuval On 31 May 2011 13:06, Elena Orekhova wrote: > Hi Michael, > > > > If you run into rank-deficiency issue with the covariance matrix a tiny > amount of regularization should fix this. > > What lambda you would recommend? > > Elena > > > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Michael Wibral [michael.wibral at web.de] > *Sent:* Monday, May 30, 2011 5:58 PM > > *To:* Email discussion list for the FieldTrip project > *Subject:* Re: [FieldTrip] SAM beamforming on Neuromag data > > > Hi Elena, > > as far as I can see from the neuromeg discussion list and the maxfilter > papers the properties of the components removed by the maxfilter do not > require a leadfield update. > If you run into rank-deficiency issue with the covariance matrix a tiny > amount of regularization should fix this. > (Note: If someone who reads this is of a different opinion, please let me > know!) > > > Michael > > ------------------------------ > *Von:* "Elena Orekhova" > *Gesendet:* May 30, 2011 4:30:34 PM > *An:* "Email discussion list for the FieldTrip project" < > fieldtrip at donders.ru.nl> > *Betreff:* Re: [FieldTrip] SAM beamforming on Neuromag data > > Thank you for this. > > I have more concerns. I applied MaxFilter to the data. Since MaxFilter > reduces the rank of the covariance matrix by removing noisy components, it > may influence the beamformer results. > Is it safe to do beamforming with MaxFiltered data? > > Elena > > ------------------------------ > *From:* fieldtrip-bounces at donders.ru.nl [fieldtrip-bounces at donders.ru.nl] > on behalf of Michael Wibral [michael.wibral at web.de] > *Sent:* Monday, May 30, 2011 2:08 PM > *To:* Email discussion list for the FieldTrip project > *Subject:* Re: [FieldTrip] SAM beamformeing on Neuromag data > > > Hi Elena, > > as far as I know, the leadfield computation should be aware of the > different UNITS (not only scales) of gradiometers and magnetometers. There > was a problem with the sign of the leadfields but that should have been > fixed. > > There is one more fundamental problem however, that you should be aware of > (doesn't invalidate your source analysis but bears potential for > fine-tuning), which is the projection of noise: > In beamforming the unit gain constraint guarantees that you get your source > signal back with unit gain. Added on top however is neurophysiological > crosstalk (minimized) and sensor noise of the sensors with the largest > weights in your Beamformer (not reducible). So different sensor types > willhave different (inverse) leadfield strengths, theerfore also fiofefrent > source noise levels. the relative benefits of each sensor type changes from > location to location, so a location (and data) dependend weighting would in > principle be best. > I am not sure if and how this is implemented if FT (Bayesian weighting > would be optimal here..) > > What you could do as a first step is to beam separately and compare the > results. > > Michael > > > ------------------------------ > *Von:* "Elena Orekhova" > *Gesendet:* May 30, 2011 1:08:29 PM > *An:* "fieldtrip at donders.ru.nl" > *Betreff:* [FieldTrip] SAM beamformeing on Neuromag data > > @font-face { font-family: "\FF2D \FF33 \660E \671D "; }@font-face { > font-family: "\FF2D \FF33 \660E \671D "; }@font-face { font-family: > "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0cm 0cm > 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { margin: 0cm 0cm > 0.0001pt; font-size: 10pt; font-family: Courier; }span.HTMLPreformattedChar > { font-family: Courier; }.MsoChpDefault { font-family: Cambria; > }div.WordSection1 { page: WordSection1; }@font-face { font-family: "\FF2D > \FF33 \660E \671D "; }@font-face { font-family: "Cambria Math"; }@font-face > { font-family: "Cambria"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { > margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: Cambria; }pre { > margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: Courier; > }span.HTMLPreformattedChar { font-family: Courier; }.MsoChpDefault { > font-family: Cambria; }div.WordSection1 { page: WordSection1; } > > Dear All, > > I try to run beamformer analysis on the auditory MEG data (Neuromag) and > have basic questions. > > > > 1.Magnetometers and gradiometers Neuromag sensors have different scales. > Does the Fieldtrip take care of this difference or should I normalize the > data? It yes, how to normalize? > > > > 2. I would like to do SAM analysis of evoked field and look at the time courses at ROIs (virtual channels). The only tutorial example I have found was for the lcmv-beamformer > (cfg.method = 'lcmv'; http://fieldtrip.fcdonders.nl/example/lcmv-beamformer). I am not sure > which parameters should I specify in ft_sourceanalysis if cfg.method = 'sam'. > > > > I would be most grateful for any example script of this type analysis! > > > > Regards, > > Elena > > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- sent from my 4-year-old PC. poor fellow, only ipod classic, no mail there. Y.Harpaz a link to the BIU MEG lab: http://faculty.biu.ac.il/~goldsa/index.html *"Many were increasingly of the opinion that they'd all made a big mistake in coming down from the trees in the first place. And some said that even the trees had been a bad move, and that no one should ever have left the oceans". Douglas Adams * -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.wibral at web.de Tue May 31 12:44:50 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 31 May 2011 12:44:50 +0200 (CEST) Subject: [FieldTrip] Beamforming on resting state data Message-ID: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> An HTML attachment was scrubbed... URL: From tobiasnavarroschroeder at googlemail.com Tue May 31 14:12:48 2011 From: tobiasnavarroschroeder at googlemail.com (Tobias Navarro Schroeder) Date: Tue, 31 May 2011 14:12:48 +0200 Subject: [FieldTrip] Beamforming on resting state data In-Reply-To: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> References: <2026821476.1720343.1306838690403.JavaMail.fmail@mwmweb074> Message-ID: Hi Michael, thanks a lot for that suggestion. The gamma activity at the sensor level might indeed be of muscular origin and this would explain why it doesn't show up inside the head. Even after automatic & manual artifact rejection the patients were left with more gamma activity. To my 'untrained eye' the sensor topographies suggested that the activity would come from the brain. It didn't extend to the boundaries of the Topoplot, at least in the 60-90 Hz range. However, this was the case for other parts of the gamma-band. Greetings, Tobias On Tue, May 31, 2011 at 12:44 PM, Michael Wibral wrote: > Hi Tobias, > > it could be that the temporal activity at the sensor level is of muscular > origin. Given all runs well in beamforming you shouldn't see too much of > that insode the head - have you considered this possibility? > > Michael > > > > ------------------------------ > *Von:* "Tobias Navarro Schroeder" > *Gesendet:* May 30, 2011 5:58:32 PM > *An:* fieldtrip at donders.ru.nl > *Betreff:* [FieldTrip] Beamforming on resting state data > > > Hi Fieldtrippers, > > I performed DICS beamforming on resting-state data (i.e. no task, no > baseline, eyes closed) of a clinical population and controls. > According to the sensor data the patients have more gamma-band (60-90 > Hz) activity over temporal areas (somewhat spread-out). > Curiously, after beamforming and group comparisons with 'indepsamplesT' > permutation statistics the difference map shows more gamma-band (60-90 > Hz) activity for controls in the left, middle-temporal gyrus. > Hence, the source-level results are opposite to the sensor-level results > (although more spatially confined). This is *not* a problem of the design > matrix, or confusing the groups. > > Question 1: Does anybody have experience with opposite results on source > and sensor level? > > The individual raw beamforming results (interpolated on the subjects' MRIs) > look suspicios as well. Due to the 'unit gain constraint' there should be an > overestimation of power in the center of the head, but only a minority of > subjects show that. Often I see temporal or parietal activity. > > Question 2: > > Would a lack of a blob in the center of the head in individual, > raw, beamforming data indicate an erroneous source analysis? > > Thanks a lot for help and suggestions. > > Best, Tobias Navarro Schröder > > ps: The configurations for calculating the covariance and the beamforming > is added below: > > > > 1) % Compute the covariance matrices > > > > cfg.output = > 'powandcsd'; > > cfg.foi = 75; > > cfg.foilim = [75 75]; > > cfg.tapsmofrq = 15; % 75 +- 15 = 60 - 90 Hz > > cfg.pad = > 'maxperlen'; % default > > cfg.method = > 'wltconvol'; % wavelet analysis > > cfg.width = 5; > % Width of the wavelet. Determines the temporal and spectral resolution of > the analysis constant. > > > > 2) % Perform the actual beamforming > > % load grids of MRI volume > > fullnameGrid = [ CurSubject.mripath CurSubject.MRIModel]; > > cfg = load(fullnameGrid); > > cfg.vol = cfg.hdm; > > > > > > cfg.frequency = 75; > > cfg.method = > 'dics'; > > cfg.keepfilter = > 'yes'; % keep the beamformer filters (virtual electrodes) for later use > > cfg.keeptrial = > 'no'; > > cfg.keepmom = > 'yes'; % useful for connectivity calculations. Dipole moments.. > > cfg.projectmom = > 'yes'; > > cfg.projectnoise = > 'yes'; > > cfg.latency = 1; > > > _______________________________________________ > 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 michael.wibral at web.de Tue May 31 15:36:46 2011 From: michael.wibral at web.de (Michael Wibral) Date: Tue, 31 May 2011 15:36:46 +0200 (CEST) Subject: [FieldTrip] SAM beamforming on Neuromag data Message-ID: <1271334421.1768792.1306849006599.JavaMail.fmail@mwmweb074> An HTML attachment was scrubbed... URL: From valentin.umbach at hu-berlin.de Tue May 31 18:51:17 2011 From: valentin.umbach at hu-berlin.de (Valentin J. Umbach) Date: Tue, 31 May 2011 18:51:17 +0200 Subject: [FieldTrip] Emotiv headset realtime capture Message-ID: Hi, I'm new to FieldTrip and I'm interested in using it to capture realtime data from the Emotiv headset using this interface: http://fieldtrip.fcdonders.nl/development/realtime/emotiv I'm not clear about how to make calls to this interface from within Matlab. Also, I would like to know if it's possible to access not just the raw EEG, but also the API output of the detection libraries (Affectiv Suite...). Any help is greatly appreciated! Best, Valentin -- Dipl.-Psych. Valentin J. Umbach Institut für Psychologie Humboldt-Universität zu Berlin Rudower Chaussee 18 12489 Berlin Tel. +49 30 2093 9438 E-Mail: valentin.umbach at hu-berlin.de From mcoskun at mail.uh.edu Tue May 31 23:09:13 2011 From: mcoskun at mail.uh.edu (Mehmet-Akif Coskun) Date: Tue, 31 May 2011 16:09:13 -0500 Subject: [FieldTrip] Dipole Fitting Algorithm Message-ID: <726086fb76fc3.4de512a9@mail.uh.edu> Dear Fieldtrippers, I am having little trouble understanding the dipole fitting algorithm. Any comments will be greatly appreciated. 1) During dipole fitting, a model data (Vmodel) is created using the computed leadfield. How exactly this model data is computed? Is it simply the projection of the pinv'ed leadfield to the true data (Vdata)?  2) The error is computed between the model data and true data for the best dipole. Is this RMS error? 3) The last part of dipole fitting is a non-linear search. I really wonder what is the algorithm, what exactly non-linear search is doing? Thanks in advance Mehmet -------------- next part -------------- An HTML attachment was scrubbed... URL: