From sherrykhan78 at gmail.com Mon Jan 3 17:17:45 2011 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 3 Jan 2011 11:17:45 -0500 Subject: [FieldTrip] Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School Message-ID: Postdoctoral Fellowship: Multimodal Neuroimaging *Description:* A postdoctoral position pursuing multimodal imaging is available with the TRANSCEND Research Program (www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org) which is affiliated with the Massachusetts General Hospital, Harvard and MIT. There is a second location at a clinical site, the MGH-affiliated Lurie Family Center for Autism, where we have a 128 lead EGI EEG in a shielded room as well as a photogrammetry machine and autonomic monitoring equipment, and will shortly have a near-infrared tissue spectrometer (NIRS) machine. The program’s emphasis is on pathophysiologically oriented brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL), on co-registering EEG and MEG with MRI, and on studying neurovascular coupling with EEG and NIRS. This position will involve analysis of existing multimodal imaging data and collection of new data. It will involve working closely with a multidisciplinary team and with children, and will also involve some research oriented analysis of data collected for clinical purposes. The age range of our subjects is primarily from early infancy to mid-adolescence, with some additional studies including young adults. An ample opportunity will also be provided to the candidate to self-explore and lead research. *Requirements:* Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Candidates without this training and experience need not apply. Prior experience in MRI analysis and EEG signal processing is required. Salary will be consistent with Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees and will range between $45,000 to $55,000 depending upon qualifications and experience. Compensation also includes full staff benefits, including health insurance, and vacation time. *Contact:* Interested applicants may send a CV and statement of interest addressing background and specific pertinence of the candidate’s interest to Dr. Martha R. Herbert at mherbert1 at partners.organd cc transcend at partners.org . Applications will be considered until the position is filled. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jan 6 09:43:47 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 6 Jan 2011 09:43:47 +0100 Subject: [FieldTrip] code change potentially relevant for MEG people Message-ID: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> Dear all, Happy new year to all of you! I just made a change to the code which may be relevant to some. This change will be present in tonight's release version, and will be immediate for the in-house users at the Donders Centre. If you are not doing MEG research you can stop here. If you never use FieldTrip to compute leadfields for MEG data you can stop here. If you never use the 'singleshell' method for your MEG leadfield computation, or if you don't know what that means, you can stop here. There appeared to be a huge difference in magnitude of MEG-leadfields computed with FieldTrip using different algorithms. Particularly, there was a big discrepancy between the 'singleshell' method on the one hand, and the localspheres/singlesphere method on the other hand. It turned out to be the case that there was a scaling factor in the singleshell method, which (assuming the geometrical units were in cm) would yield a magnetic field/gradient in ft or ft/cm. At the moment FieldTrip does not everywhere explicitly impose particular physical units on the data and therefore also should not make particular assumptions. To make the three methods of leadfield computation more equivalent we changed the implicit unit-assuming code. What does this all mean to you? Probably not an awful lot. Yet, you need to be aware that by scaling the leadfields, the magnitude of the inverse solution will probably also change (unless you use norm- normalized leadfields). It is not correct to compare analysis results using old-scale leadfields with analysis results using new-scale leadfields, if the respective analysis results have not been normalized in a meaningful way. In other words, comparing raw power is not correct, comparing neural activity indices, relative changes, t- statistics etc. is probably alright. Sorry for the inconvenience, Best wishes 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 a.stolk at fcdonders.ru.nl Thu Jan 6 11:06:49 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 6 Jan 2011 11:06:49 +0100 (CET) Subject: [FieldTrip] code change potentially relevant for MEG people In-Reply-To: <524787489.95342.1294308215741.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <225327747.95381.1294308409346.JavaMail.root@sculptor.zimbra.ru.nl> Hey JM, Ik plot groepsgemiddelde aboslute powers (zie plotje) waarbij de voxel van interesse gekozen wordt aan de hand van significant verschillen. Dus blobs die gevonden zijn na indep T-testen op de subject level en dep T-test op groepslevel. De prepare-single-shell algoritme is dezelfde voor elke conditie in elke proefpersoon. Ik struikel over deze zin 'comparing raw power is not correct'. Je bedoelt 'comparing raw powers computed with separate (old and new implementation) is not correct'? Ciao! ----- "jan-mathijs schoffelen" schreef: > Van: "jan-mathijs schoffelen" > Aan: "FieldTrip List" > Verzonden: Donderdag 6 januari 2011 09:43:47 > Onderwerp: [FieldTrip] code change potentially relevant for MEG people > > Dear all, > > Happy new year to all of you! I just made a change to the code which > > may be relevant to some. This change will be present in tonight's > release version, and will be immediate for the in-house users at the > > Donders Centre. > > If you are not doing MEG research you can stop here. > If you never use FieldTrip to compute leadfields for MEG data you can > > stop here. > If you never use the 'singleshell' method for your MEG leadfield > computation, or if you don't know what that means, you can stop here. > > There appeared to be a huge difference in magnitude of MEG-leadfields > > computed with FieldTrip using different algorithms. Particularly, > there was a big discrepancy between the 'singleshell' method on the > one hand, and the localspheres/singlesphere method on the other hand. > > It turned out to be the case that there was a scaling factor in the > singleshell method, which (assuming the geometrical units were in cm) > > would yield a magnetic field/gradient in ft or ft/cm. At the moment > FieldTrip does not everywhere explicitly impose particular physical > units on the data and therefore also should not make particular > assumptions. To make the three methods of leadfield computation more > > equivalent we changed the implicit unit-assuming code. > > What does this all mean to you? Probably not an awful lot. Yet, you > need to be aware that by scaling the leadfields, the magnitude of the > > inverse solution will probably also change (unless you use norm- > normalized leadfields). It is not correct to compare analysis results > > using old-scale leadfields with analysis results using new-scale > leadfields, if the respective analysis results have not been > normalized in a meaningful way. In other words, comparing raw power is > > not correct, comparing neural activity indices, relative changes, t- > statistics etc. is probably alright. > > Sorry for the inconvenience, > > Best wishes > > 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 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- A non-text attachment was scrubbed... Name: tessie2_half_light_bottom.pdf Type: application/pdf Size: 8613 bytes Desc: not available URL: From smoratti at psi.ucm.es Thu Jan 6 12:10:15 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 06 Jan 2011 12:10:15 +0100 Subject: [FieldTrip] code change potentially relevant for MEG people In-Reply-To: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> References: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> Message-ID: <24BDB4F2-6935-4334-BF09-C543377EFD1D@psi.ucm.es> Hi Jan-Mathijs, Happy new year! Thanks for the update! I think the MEG community appreciates a lot the Fieldtrip work you all do! Best, Stephan El 06/01/2011, a las 9:43, jan-mathijs schoffelen escribió: > Dear all, > > Happy new year to all of you! I just made a change to the code which > may be relevant to some. This change will be present in tonight's > release version, and will be immediate for the in-house users at the > Donders Centre. > > If you are not doing MEG research you can stop here. > If you never use FieldTrip to compute leadfields for MEG data you > can stop here. > If you never use the 'singleshell' method for your MEG leadfield > computation, or if you don't know what that means, you can stop here. > > There appeared to be a huge difference in magnitude of MEG- > leadfields computed with FieldTrip using different algorithms. > Particularly, there was a big discrepancy between the 'singleshell' > method on the one hand, and the localspheres/singlesphere method on > the other hand. It turned out to be the case that there was a > scaling factor in the singleshell method, which (assuming the > geometrical units were in cm) would yield a magnetic field/gradient > in ft or ft/cm. At the moment FieldTrip does not everywhere > explicitly impose particular physical units on the data and > therefore also should not make particular assumptions. To make the > three methods of leadfield computation more equivalent we changed > the implicit unit-assuming code. > > What does this all mean to you? Probably not an awful lot. Yet, you > need to be aware that by scaling the leadfields, the magnitude of > the inverse solution will probably also change (unless you use norm- > normalized leadfields). It is not correct to compare analysis > results using old-scale leadfields with analysis results using new- > scale leadfields, if the respective analysis results have not been > normalized in a meaningful way. In other words, comparing raw power > is not correct, comparing neural activity indices, relative changes, > t-statistics etc. is probably alright. > > Sorry for the inconvenience, > > Best wishes > > 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 > > _______________________________________________ > 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 r.vandermeij at donders.ru.nl Thu Jan 6 14:10:04 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 06 Jan 2011 14:10:04 +0100 Subject: [FieldTrip] new implementation of wltconvol (renamed to wavelet): specest Message-ID: <4D25BF2C.8030805@donders.ru.nl> Hello everybody! As of today, we have switched to a new implementation for the 'wltconvol' method for frequency analysis, and it has also been renamed to 'wavelet'. For a while now we have been rewriting the low-level code in a different format, one that is more flexible to adapt in the future and that allows for the low-level algorithms to be downloaded in a separate module: /specest/. The changes will be on our ftp-server by tonight. The switch to the new implementation brings about several changes. With respect to the changes are observable to the end-user, there are several FAQs created at our wiki. For the end-user observable changes for 'wavelet' (formerly 'wltconvol'), please have a look /here/ , and for a bigger description with respect to your output.freq please go /here/ . Because of these changes, we strongly advise to either use the new or the old implementation for your entire analysis project. The old implementation is still available by using 'wltconvol_old' as cfg.method (however, this code no longer being updated). You can call also call the function: ft_freqanalysis_old, which is the old interface-function. If you are interested, you can track the progress of the /specest /module by going /here/ . As soon as the other low-level functions are ready and implemented, another e-mail will be sent to the mailing-list. If anything is unclear, or if there are any bugs that have slipped through our fingers, please send an e-mail to the mailing-list and/or report a bug in our /Bugzilla bug tracking system /. Kind regards, Roemer van der Meij -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From shhirano at npsych.med.kyushu-u.ac.jp Sun Jan 9 03:03:52 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Sun, 9 Jan 2011 11:03:52 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: Dear Dr Eric Maris and members of Fieldtrip mailing list At first, I'm sorry for my poor English. I'm a post-doc research fellow of Department of Neuropsychiatry, Kyushu University, Fukuoka, Japan. I'm studying about auditory abnormalities in mental disorders, for example, schizophrenia, bipolar disorder, using MEG. I'm very impressed and interested in Dr Eric Maris and Dr Robert Oostenveld paper, "Nonparametrical statistical testing of EEG and MEG data, on Journal of Neuroscience Methods, 2007". I'd like to apply their stastical methods to our data, but there are some points that I can't understand in their paper. Those are about cluster-based statistics. In the right column in page 180 in their paper, they wrote 5 steps of statistics methods. At 5th step, they take the largest of the cluster- level statistics, then how do they test this largest of the cluster- level statistics? I thought that, after 5th step, I should make the permutation distribution of cluster-level statistics of selected cluster, and I should test the given cluster-level statistics with this permutation distribution. Is this right? Any answer will help me. Best regards, Shogo Hirano, M.D., Ph.D. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From r.vandermeij at donders.ru.nl Sun Jan 9 12:49:05 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Sun, 09 Jan 2011 12:49:05 +0100 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper In-Reply-To: References: Message-ID: <4D29A0B1.1020208@donders.ru.nl> Hi Shogo, After computing your cluster-level statistics you indeed take the largest one, and this will be compared to the permutation distribution. However, this distribution is constructed by doing the following e.g. 500 times: 1) randomly swapping the units of observation (UO) between conditions (in case of a between UO design) 2) computing your cluster-level-statistic for this random combination of UOs 3) taking the largest of these (largest of /all clusters/ in this random permutation, not a /'selected' cluster/) This will result in 500 'largest cluster-level-statistics'. If your original statistic is bigger/smaller than a certain percentage, say 95% when testing single-sided to an alpha of 0.05, then you reject the null-hypothesis of interchangeability of your conditions. Whether it should be bigger or smaller depends on your direction of testing. Hope this helps, Best, Roemer On 9-1-2011 3:03, ?? ?? wrote: > Dear Dr Eric Maris and members of Fieldtrip mailing list > > At first, I'm sorry for my poor English. > I'm a post-doc research fellow of Department of Neuropsychiatry, > Kyushu University, Fukuoka, Japan. > I'm studying about auditory abnormalities in mental disorders, for > example, schizophrenia, bipolar disorder, using MEG. > I'm very impressed and interested in Dr Eric Maris and Dr Robert > Oostenveld paper, "Nonparametrical statistical testing of EEG and MEG > data, on Journal of Neuroscience Methods, 2007". > I'd like to apply their stastical methods to our data, but there are > some points that I can't understand in their paper. > Those are about cluster-based statistics. > In the right column in page 180 in their paper, they wrote 5 steps of > statistics methods. At 5th step, they take the largest of the > cluster-level statistics, then how do they test this largest of the > cluster-level statistics? > I thought that, after 5th step, I should make the permutation > distribution of cluster-level statistics of selected cluster, and I > should test the given cluster-level statistics with this permutation > distribution. Is this right? > Any answer will help me. > > Best regards, > > Shogo Hirano, M.D., Ph.D. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Mon Jan 10 21:58:41 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 10 Jan 2011 12:58:41 -0800 Subject: [FieldTrip] reading EDF+ annotation channel with FieldTrip Message-ID: <4D2B7301.2060900@berkeley.edu> Hi I would like to read in EDF+ data with FieldTrip, including triggers that are coded in the annotation channel. FieldTrip has recently been updated to be able to read EDF+ data (Thanks Robert!). Before, FieldTrip could only read EDF data (so then it could not read events which are coded on the annotation channel). However, in the EDF+ data that I have (which is generate by Net Station software, EGI company), the events on the annotation channel are not read in correctly. I asked EGI support for the definition they use to write the events to the annotation channel in the EDF+ format as is produced by Net Station, and I got this answer from one of their technicians: - Each annotation channel contains a time keeping TAL for each EDF+ block, which is +blockTime[20][20][0] Then, it contains each event for the block, in this format. +startTime[21]duration[20]name[20][0] All times are in seconds. The values in [ ] are the numbers that are written into the binary file, and are described in the EDF+ specification. My knowledge on reading in data and the EDF+ format is not sufficient to understand this. I would like to update read_edf (in private of fileio) to also be able to read in the EGI version of EDF+ data. Does anyone know how to do this? Any help would be greatly appreciated. And while I'm at it, are there any other EGI users on the list that are or will be using the new MFF data format? I would like to use this new data format in FieldTrip, but so far FieldTrip can't read it in yet. Did anyone already write some code to read this format in that we could include into FieldTrip? Also, I've just created a "getting started with EGI data " page on the FieldTrip wiki. I'll document my experiences there. Everyone else with relevant info is (as allways) invited to help fill it. Thanks a lot, All the best, Ingrid -- Ingrid Nieuwenhuis PhD Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From recasensmarc at gmail.com Tue Jan 11 19:33:53 2011 From: recasensmarc at gmail.com (Marc Recasens) Date: Tue, 11 Jan 2011 19:33:53 +0100 Subject: [FieldTrip] Define a ROI in sourcestatistics Message-ID: <4D2CA291.4020003@gmail.com> Hi all. I've been trying to define a region of interest (ROI) in order to restrict my analyses to a particular region on the temporal lobe during sourcestatistics. I have two grandaverage sources like: pos: [33480x3 double] dim: [31 36 30] avg: [1x1 struct] var: [1x1 struct] dimord: 'voxel' trial: [1x13 struct] inside: [12773x1 double] outside: [20707x1 double] df: [33480x1 double] cfg: [1x1 struct] And I apply ft_sourcestatistics with the following configuration: cfg =[]; cfg.dim = GA_dev_source.dim; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'bonferoni'; cfg.numrandomization = 1000; cfg.alpha = 0.05; cfg.tail = 0; nsubj = length(GA_dev_source.trial); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; cfg.ivar = 2; stat = ft_sourcestatistics(cfg, GA_dev_source, GA_stad_source) However it's not very straightforward to me to apply a ROI restriction to this analysis. I downloaded the files from http://fmri.wfubmc.edu (TD_lobe.img, TD_lobe.mat, TD_lobe_Border.mat, TD_lobe_List.mat) which I am suposed to use for the ROI. I tried to add this to the previous configuration: cfg.atlas = '.../TD_lobe.img'; (the template brain containing the different lobes) cfg.inputcoord = 'mni'; cfg.roi = ROI(12).Nom_C; The names of the roi i want to extract ('Temporal Lobe') But then... stat_roi = prob: [31x36x30 double] <---- All zeros. mask: [31x36x30 logical] stat: [31x36x30 double] ref: [31x36x30 double] dim: [31 36 30] inside: [0x1 double] <---- which means there's nothing inside the volume outside: [33480x1 double] pos: [33480x3 double] cfg: [1x1 struct] Amb I defining the ROI incorrectly??? Is it because the dimensions of the atlas and the source are not equal? Could anyone give a good example of how to do it? Any suggestion will be appreciated. Thanks in advance. -- Marc Recasens Tel.: +34 639 24 15 98 -------------- next part -------------- An HTML attachment was scrubbed... URL: From shhirano at npsych.med.kyushu-u.ac.jp Wed Jan 12 10:51:19 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Wed, 12 Jan 2011 18:51:19 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> Dear Dr Roemer van der Meij I really appreciate your kind answer! Your answer enable me understand the statistics after Dr Maris's 5 steps. However, there are still two points I'd like to understand. First, after Dr Maris's 5 steps, I should get the largest claster statistics from the clasters derived from observed data (hereinafter I call these clasters as "observed clasters"). Then, I should enter your 3 steps. In your 2nd step, I should compute cluster-level-statistics from random permutation data. Here, I have an question. When I define clusters from random permutation data, which should I define where clusters are the same place (e.g. time, sensor and so on) as "observed clasters" or should I define newly where clusters are from random permutation data regardless of the places of "observed clasters"? I think the latter is right, this is OK? Second, If I have interests in the cluster that has the second or third... non first largest cluster-level-statistics from the experimental hypothesis, how should I test these clusters? Thank you very much for your kindness! Any answer help me. Best regards, Shogo -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From jan.schoffelen at donders.ru.nl Wed Jan 12 14:48:40 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 12 Jan 2011 14:48:40 +0100 Subject: [FieldTrip] change to ft_volumesegment Message-ID: <82650747-4258-47F4-844E-FB6FE6D69E1C@donders.ru.nl> Dear all, I just want to let you know that I incorporated a change in ft_volumesegment. Sometimes the segmented volumes came with a flipped orientation with respect to the original anatomy, necessitating some manual flipping in order to stay consistent with the mri's transformation matrix. I made some changes to ft_volumesegment so that this manual flipping should not be necessary anymore (at least on the anatomical MRIs I tested the code with). Explicitly checking the alignment is of course still allowed and recommended. Best wishes, 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 stephen.whitmarsh at gmail.com Wed Jan 12 14:58:49 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 12 Jan 2011 14:58:49 +0100 Subject: [FieldTrip] Improved Fieldtrip Wiki! Message-ID: Dear FieldTrippers, First of all, a happy new year! As we hope you agree, we have tried to improve the FieldTrip Wiki on several points: · Better overview through some simple changes to the organization of the menubar · Cleaning up the appearance of the Wiki through the style sheet, and some other aesthetic considerations · Helping FieldTrip newbies by adding an elaborate walkthrough · Adding the ability to upload and display .SVG images, for now much used in the walkthrough · Adding the ability to use editorial notes – take a look online to see what we mean by that. · In general creating a kinder, home-y atmosphere. · Ofcourse, like always, we are the community and if you have any suggestions of comments about the content or appearance of the website, feel free to post them in the email discussion list. · Coming soon: Download pages as formatted PDF with one press of a button, and much, much more! Thanks and credits go to Eelke Spaak for applying his Jedi webskills to the FieldTrip Wiki! Regards, S -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Thu Jan 13 16:09:11 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Thu, 13 Jan 2011 16:09:11 +0100 Subject: [FieldTrip] fieldtrip question - help needed Message-ID: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> Hello can anybody spend some more words on the chapter "Fixing a missing sensor"? I'm trying to use it with a AtB (like ITAB-Chieti) device...but I cannot understand how to use it. I've several troubles when I've to declare the layout, since I don't have a layout file, but I construct that starting from grad... Do you have any hint for me? Sara Rombetto ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From inbalots at gmail.com Thu Jan 13 18:14:45 2011 From: inbalots at gmail.com (Inbal Lots) Date: Thu, 13 Jan 2011 19:14:45 +0200 Subject: [FieldTrip] Question about wavelet analysis Message-ID: Hello I have several questions: 1. Just wanted to make sure: When I use [res] = ft_freqanalysis(cfg,data) with data that have several trials - and I define cfg.keeptrials = 'yes'; I get an analysis for each trial in [res]. Then I use ft_multiplotTFR(cfg,res) with cfg.trials = 'all'; The result is an average on the wavelet result of all trials? (and not a wavelet on the averaged signal of all trials) 2. Is there a way for me to see the wavelet analysis result of each trial and to browse easily between them? rather than calling ft_multiplotTFR(cfg,res) each time with cfg.trials = i ; where i is the desired trial number? 3. How can I use other mother wavelet? (and not just Morlet wavelets) 4. How can I control the colormap min and max values so that they will be similar in all figures? (like doing imagesc(pic,clim))? Thank you very much Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Jan 13 18:19:16 2011 From: g.piantoni at nin.knaw.nl (Giovanni Piantoni) Date: Thu, 13 Jan 2011 18:19:16 +0100 Subject: [FieldTrip] peer Message-ID: Dear FieldTrip/peer developers, I was trying the peer module out on two computer (both 64bit Linux, one Ubuntu and one Red-Hat). Thanks for the effort in developing the module! The module works great, following the information on the wiki page. On both computers, I'm able to call peermaster and peerslave, getting the correct peerinfo and peerlist. When I try on Ubuntu, it works flawlessly (but it only has two cores, so no much gain there). However, when I try on Red Hat (which has many more cores), peermaster sends the job to the peerslave and the job is executed (f.e., with peercellfun(@mkdir, {'test'}) it creates a folder called test), but the peerslave is not able to tell the peermaster that the job has completed. See below for details: In the peermaster matlab command line: >> peermaster peer: init peerinit: user at computername, id = 3682858105 peer: spawning announce thread peer: spawning discover thread peer: spawning expire thread peer: spawning tcpserver thread >> peerinfo hostid = 3682858105 hostname = computername user = user group = unknown socket = port = 1701 status = master memavail = 4294967295 bytes timavail = 86400 seconds allowuser = {} allowgroup = {} allowhost = {} tcpserver thread is running udsserver thread is NOT running announce thread is running discover thread is running expire thread is running there are 0 jobs in this peer's buffer >> peerlist there are 3 peers running in total (1 hosts, 1 users) there are 1 peers running on 1 hosts as master there are 2 peers running on 1 hosts as idle slave with 8.0 GB memory available there are 0 peers running on 0 hosts as busy slave with 0 bytes and 0 seconds required there are 0 peers running on 0 hosts as zombie idle slave at user at computername:1702, memavail = 4.0 GB, timavail = 1.0 days idle slave at user at computername:1703, memavail = 4.0 GB, timavail = 1.0 days master at user at computername:1701 >> peercellfun(@pause, {1 2}) Then, if I look at one of the two peerslave computers, I see: executing job 25 from user at computername (jobid=2068920377, memreq=1073741824, timreq=3600) executing job took 2.002441 seconds and 0 bytes Warning: failed to return job results to the master And if I "dbstop if caught error", I see in the peerslave: Error using ==> peer failed to locate specified peer Where the error occurs at: peer('put', joblist.hostid, argout, options, 'jobid', joblist.jobid); however: >> joblist.hostid ans = 3682858105 which is the correct hostid for the peermaster. Do you have any idea where the problem might lie? How can I debug this? If it's not easy to solve, how can I run each job once (bc the peermaster keeps on sending request if it doesn't know that the first job was completed)? Thanks a lot! 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.nin.knaw.nl/research_groups/van_someren_group/ From jan.schoffelen at donders.ru.nl Fri Jan 14 09:39:39 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 09:39:39 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> Message-ID: <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> Cara Sara, I am not sure whether I totally understand your question. Are you referring to the example script 'fixing a missing sensor'? When I look at it on our (renewed) wiki (still brings tears to my eyes), I don't see any mention of a layout. I agree with you that the example however can be made a bit more clear. This is my take on it, starting from the back of the pipeline: The 'fixing' algorithm replaces a 'dead' channel with the average signal recorded at its neighbours. In the current implementation, the description of the sensors and the data (=the grad-structure and the data.trial) which go into ft_channelrepair need to contain a full description of the sensor-array, including the faulty one. In other words, if your sensor array has 10 sensors, one of which you want to have repaired, the input to ft_channelrepair needs a data-structure containing data from the spatial location of those 10 sensors (this is in data.grad, and needed to determine which channels are the neighbours). For consistency, the time course of the faulty channel also needs to be there. The actual time courses of the faulty channel will not be used, and these can take any value. Depending on the hardware and recording protocol, a faulty channel is either present or not in the data. In the example script, the faulty channel was not even recorded, and this is the reason for the first part of the script: the creation of a dummy channel, initialized with 0's in order to make ft_channelrepair work. If, however, your dataset actually contains data on the faulty channel (which may look very noisy), you can skip the first part of the script, and directly go to the second part. Best wishes, Jan-Mathijs On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: > Hello > can anybody spend some more words on the chapter "Fixing a missing > sensor"? > I'm trying to use it with a AtB (like ITAB-Chieti) device...but I > cannot understand how to use it. I've several troubles when I've to > declare the layout, since I don't have a layout file, but I construct > that starting from grad... > Do you have any hint for me? > > Sara Rombetto > > > ------------------------------------------- > * Dott.ssa Sara Rombetto * > * Istituto di Cibernetica "E. Caianiello" * > * Via Campi Flegrei, 34 * > * 80078 Pozzuoli (NA) * > * Italy * > * tel +390818675054 * > * fax +390818675326 * > ------------------------------------------- > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > 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 Fri Jan 14 09:48:13 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 09:48:13 +0100 Subject: [FieldTrip] Question about wavelet analysis In-Reply-To: References: Message-ID: <0CECFFCC-6802-42DE-81C3-B8FD25E5F1F2@donders.ru.nl> Dear Inbal, > 1. Just wanted to make sure: > When I use [res] = ft_freqanalysis(cfg,data) with data that have > several trials - and I define cfg.keeptrials = 'yes'; > I get an analysis for each trial in [res]. Then I use > ft_multiplotTFR(cfg,res) with cfg.trials = 'all'; > The result is an average on the wavelet result of all trials? (and > not a wavelet on the averaged signal of all trials) > Yes, ft_multiplotTFR computes an average spectrogram over observations/ trials > 2. Is there a way for me to see the wavelet analysis result of each > trial and to browse easily between them? > rather than calling ft_multiplotTFR(cfg,res) each time with > cfg.trials = i ; where i is the desired trial number? > At the moment, no. I never really thought of looking at single trial multiplots but I can imagine the need for this functionality. Your workaround indeed works, but may be a bit tedioius. > 3. How can I use other mother wavelet? (and not just Morlet wavelets) > What kind of wavelet would you like to use? If the wavelet consists of a tapered cosine/sine wave in which the Gaussian taper will be replaced by something else, you could use cfg.method = 'mtmconvol'. This is an efficient implementation of a wavelet-like analysis, where there is some freedom to define your own taper. At present this relies on matlab's window-function (or on the slepian sequences; different story), so the different tapers are limited to those available in matlab. However, it is relatively straightforward to tap into the code here, and provide your own taper. A dangerous, but possible option is to temporarily overload the matlab window-function with your own, spitting out the requested taper. > 4. How can I control the colormap min and max values so that they > will be similar in all figures? (like doing imagesc(pic,clim))? > I guess cfg.zlim should do the trick. Best, JM > Thank you very much > > Inbal > _______________________________________________ > 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 jungky at korea.ac.kr Fri Jan 14 09:58:38 2011 From: jungky at korea.ac.kr (Jung, Ki-Young) Date: Fri, 14 Jan 2011 00:58:38 -0800 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: Message-ID: Dear all, I'd like to do statistical comparison using cluster based permuation between two groups on ERP data. But I am receiving following error messages ??? Undefined function or method 'bwlabeln' for input arguments of type 'double'. Error in ==> findcluster at 89  [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :),  nfreq, ntime), 4); Error in ==> clusterstat at 194     posclusobs = findcluster(reshape(postailobs,     [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); Error in ==> statistics_montecarlo at 321  [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285   [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 125 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); My configuration for ft_freqstatistics are cfg = []; cfg.channel          = 'all'; cfg.latency          = 'all'; cfg.frequency        = [30 50]; cfg.method           = 'montecarlo'; cfg.statistic        = 'indepsamplesT'; cfg.correctm         = 'cluster'; cfg.clusteralpha     = 0.025; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan        = 2; cfg.tail             = 0; cfg.clustertail      = 0; cfg.alpha            = 0.025; cfg.numrandomization = 500; cfg.neighbours       = [ ]; design = [ones(1, 16), ones(1, 16)*2]; cfg.design           = design; cfg.ivar             = 1; [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); Data structure of con_grand_avg are con_grand_avg =       label: {27x1 cell}        freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50]        time: [1x21 double]      dimord: 'subj_chan_freq_time'   powspctrm: [4-D double]         cfg: [1x1 struct] Any comment helps me. Best regards, Ki-Young Jung From julian.keil at gmail.com Fri Jan 14 10:04:19 2011 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 14 Jan 2011 10:04:19 +0100 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: Message-ID: <5CAF6334-C41B-429B-8575-E3CAAA20EB37@gmail.com> Hi, did you check with 'which bwlabeln' if you have the respcetive function? It's part of the image processing toolbox for matlab. Good Luck. Julian Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > Dear all, > > I'd like to do statistical comparison using cluster based permuation > between two groups on ERP data. > But I am receiving following error messages > ??? Undefined function or method 'bwlabeln' for input arguments of > type 'double'. > > Error in ==> findcluster at 89 > [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), > nfreq, ntime), 4); > > Error in ==> clusterstat at 194 > posclusobs = findcluster(reshape(postailobs, > [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); > > Error in ==> statistics_montecarlo at 321 > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_freqstatistics at 125 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > My configuration for ft_freqstatistics are > cfg = []; > cfg.channel = 'all'; > cfg.latency = 'all'; > cfg.frequency = [30 50]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.025; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg.neighbours = [ ]; > design = [ones(1, 16), ones(1, 16)*2]; > cfg.design = design; > cfg.ivar = 1; > [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); > > > Data structure of con_grand_avg are > > con_grand_avg = > label: {27x1 cell} > freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50] > time: [1x21 double] > dimord: 'subj_chan_freq_time' > powspctrm: [4-D double] > cfg: [1x1 struct] > > > Any comment helps me. > > > Best regards, > > Ki-Young Jung > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.rombetto at cib.na.cnr.it Fri Jan 14 11:03:18 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Fri, 14 Jan 2011 11:03:18 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> Message-ID: <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> Hello yes I'm referring to the example script 'fixing a missing sensor'. Even if you consider the structure grad, you also load LABEL275.mat and GRAD275.mat, that is the layout in someway. What I do is to process my data: I define trials and preprocess them. Then I use ft_rejectvisual to remove artifacts and noisy channels. After this my data are ok, but I have some missing channels. In order to solve the inverse problem, I'm using a software that needs all the channels....and this is the reason why I'm trying to "fix the missing sensor". Sara > Cara Sara, > > I am not sure whether I totally understand your question. Are you > referring to the example script 'fixing a missing sensor'? > When I look at it on our (renewed) wiki (still brings tears to my > eyes), I don't see any mention of a layout. > > I agree with you that the example however can be made a bit more clear. > This is my take on it, starting from the back of the pipeline: > > The 'fixing' algorithm replaces a 'dead' channel with the average > signal recorded at its neighbours. In the current implementation, the > description of the sensors and the data (=the grad-structure and the > data.trial) which go into ft_channelrepair need to contain a full > description of the sensor-array, including the faulty one. In other > words, if your sensor array has 10 sensors, one of which you want to > have repaired, the input to ft_channelrepair needs a data-structure > containing data from the spatial location of those 10 sensors (this is > in data.grad, and needed to determine which channels are the > neighbours). For consistency, the time course of the faulty channel > also needs to be there. The actual time courses of the faulty channel > will not be used, and these can take any value. Depending on the > hardware and recording protocol, a faulty channel is either present or > not in the data. In the example script, the faulty channel was not even > recorded, and this is the reason for the first part of the script: the > creation of a dummy channel, initialized with 0's in order to make > ft_channelrepair work. If, however, your dataset actually contains data > on the faulty channel (which may look very noisy), you can skip the > first part of the script, and directly go to the second part. > > Best wishes, > > Jan-Mathijs > > > On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: > >> Hello >> can anybody spend some more words on the chapter "Fixing a missing sensor"? >> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >> cannot understand how to use it. I've several troubles when I've to >> declare the layout, since I don't have a layout file, but I construct >> that starting from grad... >> Do you have any hint for me? >> >> Sara Rombetto >> >> >> ------------------------------------------- >> * Dott.ssa Sara Rombetto * >> * Istituto di Cibernetica "E. Caianiello" * >> * Via Campi Flegrei, 34 * >> * 80078 Pozzuoli (NA) * >> * Italy * >> * tel +390818675054 * >> * fax +390818675326 * >> ------------------------------------------- >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> _______________________________________________ >> 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 ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From jan.schoffelen at donders.ru.nl Fri Jan 14 11:30:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 11:30:45 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> Message-ID: <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> Cara Sara, OK. Indeed, if you have run ft_rejectvisual and removed some channels, these are missing from your actual data. The original data.grad should however still contain the labels of all channels, and you can use grad.label as 'LABEL275', provided the order of the remaining channels did not change. Alternatively, you could define cfg.keepchannel = 'nan', before calling ft_rejectvisual. The noisy channels will then still be 'present' in your data (but set to NaN). I believe that this would take away the need to do the first part of the script. Best JM PS: please note that it is not optimal to do source reconstruction after replacing noisy channels with an average of their neighbours. At least you need to take this into account in the creation of the leadfields. On Jan 14, 2011, at 11:03 AM, s.rombetto at cib.na.cnr.it wrote: > Hello > yes I'm referring to the example script 'fixing a missing sensor'. > Even if you consider the structure grad, you also load LABEL275.mat > and GRAD275.mat, that is the layout in someway. > > What I do is to process my data: I define trials and preprocess > them. Then I use ft_rejectvisual to remove artifacts and noisy > channels. > After this my data are ok, but I have some missing channels. > In order to solve the inverse problem, I'm using a software that > needs all the channels....and this is the reason why I'm trying to > "fix the missing sensor". > > Sara > >> Cara Sara, >> >> I am not sure whether I totally understand your question. Are you >> referring to the example script 'fixing a missing sensor'? >> When I look at it on our (renewed) wiki (still brings tears to my >> eyes), I don't see any mention of a layout. >> >> I agree with you that the example however can be made a bit more >> clear. >> This is my take on it, starting from the back of the pipeline: >> >> The 'fixing' algorithm replaces a 'dead' channel with the average >> signal recorded at its neighbours. In the current implementation, the >> description of the sensors and the data (=the grad-structure and the >> data.trial) which go into ft_channelrepair need to contain a full >> description of the sensor-array, including the faulty one. In other >> words, if your sensor array has 10 sensors, one of which you want to >> have repaired, the input to ft_channelrepair needs a data-structure >> containing data from the spatial location of those 10 sensors (this >> is >> in data.grad, and needed to determine which channels are the >> neighbours). For consistency, the time course of the faulty channel >> also needs to be there. The actual time courses of the faulty channel >> will not be used, and these can take any value. Depending on the >> hardware and recording protocol, a faulty channel is either present >> or >> not in the data. In the example script, the faulty channel was not >> even >> recorded, and this is the reason for the first part of the script: >> the >> creation of a dummy channel, initialized with 0's in order to make >> ft_channelrepair work. If, however, your dataset actually contains >> data >> on the faulty channel (which may look very noisy), you can skip the >> first part of the script, and directly go to the second part. >> >> Best wishes, >> >> Jan-Mathijs >> >> >> On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: >> >>> Hello >>> can anybody spend some more words on the chapter "Fixing a missing >>> sensor"? >>> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >>> cannot understand how to use it. I've several troubles when I've to >>> declare the layout, since I don't have a layout file, but I >>> construct >>> that starting from grad... >>> Do you have any hint for me? >>> >>> Sara Rombetto >>> >>> >>> ------------------------------------------- >>> * Dott.ssa Sara Rombetto * >>> * Istituto di Cibernetica "E. Caianiello" * >>> * Via Campi Flegrei, 34 * >>> * 80078 Pozzuoli (NA) * >>> * Italy * >>> * tel +390818675054 * >>> * fax +390818675326 * >>> ------------------------------------------- >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> >>> _______________________________________________ >>> 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 > > > > ------------------------------------------- > * Dott.ssa Sara Rombetto * > * Istituto di Cibernetica "E. Caianiello" * > * Via Campi Flegrei, 34 * > * 80078 Pozzuoli (NA) * > * Italy * > * tel +390818675054 * > * fax +390818675326 * > ------------------------------------------- > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > _______________________________________________ > 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 s.rombetto at cib.na.cnr.it Fri Jan 14 11:40:09 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Fri, 14 Jan 2011 11:40:09 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> Message-ID: <20110114114009.bkaw65hmaog880g4@arco.cib.na.cnr.it> thanks that's right. But we also fabricate squids, so the broken channels can change. So I was looking for a temporary solution. best regards Sara > Cara Sara, > > OK. Indeed, if you have run ft_rejectvisual and removed some channels, > these are missing from your actual data. The original data.grad should > however still contain the labels of all channels, and you can use > grad.label as 'LABEL275', provided the order of the remaining channels > did not change. Alternatively, you could define cfg.keepchannel = > 'nan', before calling ft_rejectvisual. The noisy channels will then > still be 'present' in your data (but set to NaN). I believe that this > would take away the need to do the first part of the script. > > Best > > JM > > PS: please note that it is not optimal to do source reconstruction > after replacing noisy channels with an average of their neighbours. At > least you need to take this into account in the creation of the > leadfields. > > > On Jan 14, 2011, at 11:03 AM, s.rombetto at cib.na.cnr.it wrote: > >> Hello >> yes I'm referring to the example script 'fixing a missing sensor'. >> Even if you consider the structure grad, you also load LABEL275.mat >> and GRAD275.mat, that is the layout in someway. >> >> What I do is to process my data: I define trials and preprocess >> them. Then I use ft_rejectvisual to remove artifacts and noisy >> channels. >> After this my data are ok, but I have some missing channels. >> In order to solve the inverse problem, I'm using a software that >> needs all the channels....and this is the reason why I'm trying to >> "fix the missing sensor". >> >> Sara >> >>> Cara Sara, >>> >>> I am not sure whether I totally understand your question. Are you >>> referring to the example script 'fixing a missing sensor'? >>> When I look at it on our (renewed) wiki (still brings tears to my >>> eyes), I don't see any mention of a layout. >>> >>> I agree with you that the example however can be made a bit more clear. >>> This is my take on it, starting from the back of the pipeline: >>> >>> The 'fixing' algorithm replaces a 'dead' channel with the average >>> signal recorded at its neighbours. In the current implementation, the >>> description of the sensors and the data (=the grad-structure and the >>> data.trial) which go into ft_channelrepair need to contain a full >>> description of the sensor-array, including the faulty one. In other >>> words, if your sensor array has 10 sensors, one of which you want to >>> have repaired, the input to ft_channelrepair needs a data-structure >>> containing data from the spatial location of those 10 sensors (this is >>> in data.grad, and needed to determine which channels are the >>> neighbours). For consistency, the time course of the faulty channel >>> also needs to be there. The actual time courses of the faulty channel >>> will not be used, and these can take any value. Depending on the >>> hardware and recording protocol, a faulty channel is either present or >>> not in the data. In the example script, the faulty channel was not even >>> recorded, and this is the reason for the first part of the script: the >>> creation of a dummy channel, initialized with 0's in order to make >>> ft_channelrepair work. If, however, your dataset actually contains data >>> on the faulty channel (which may look very noisy), you can skip the >>> first part of the script, and directly go to the second part. >>> >>> Best wishes, >>> >>> Jan-Mathijs >>> >>> >>> On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: >>> >>>> Hello >>>> can anybody spend some more words on the chapter "Fixing a >>>> missing sensor"? >>>> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >>>> cannot understand how to use it. I've several troubles when I've to >>>> declare the layout, since I don't have a layout file, but I construct >>>> that starting from grad... >>>> Do you have any hint for me? >>>> >>>> Sara Rombetto >>>> >>>> >>>> ------------------------------------------- >>>> * Dott.ssa Sara Rombetto * >>>> * Istituto di Cibernetica "E. Caianiello" * >>>> * Via Campi Flegrei, 34 * >>>> * 80078 Pozzuoli (NA) * >>>> * Italy * >>>> * tel +390818675054 * >>>> * fax +390818675326 * >>>> ------------------------------------------- >>>> >>>> ---------------------------------------------------------------- >>>> This message was sent using IMP, the Internet Messaging Program. >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> >> >> ------------------------------------------- >> * Dott.ssa Sara Rombetto * >> * Istituto di Cibernetica "E. Caianiello" * >> * Via Campi Flegrei, 34 * >> * 80078 Pozzuoli (NA) * >> * Italy * >> * tel +390818675054 * >> * fax +390818675326 * >> ------------------------------------------- >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> _______________________________________________ >> 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 ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From julian.keil at gmail.com Fri Jan 14 12:51:14 2011 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 14 Jan 2011 12:51:14 +0100 Subject: [FieldTrip] grid - bug in ft_prepare_leadfield Message-ID: <78914DC7-8F9C-41C6-9FA1-853ABFA19B5C@gmail.com> Hi, there might be a bug in the latest release of ft_prepare leadfield (version 20110113): In line 172: [sourcegrid, tmpcfg] ... but later on, the code only refers to "grid" not "sourcegrid". Changing "sourcegrid" to "grid" solves the problem. By the way, I get a conflict with the graph2d-toolbox, as this toolbox has a function called grid.m Greetings 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 jungky at korea.ac.kr Fri Jan 14 18:58:23 2011 From: jungky at korea.ac.kr (Jung, Ki-Young) Date: Fri, 14 Jan 2011 09:58:23 -0800 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: <1294996134883354.0.mail@mail> References: <1294996134883354.0.mail@mail> Message-ID: Thanks! But I have still trouble with this message. ??? Error using ==> statistics_montecarlo Too many input arguments. Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 125 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Best regards, KY On Fri, Jan 14, 2011 at 1:04 AM, Julian Keil wrote: > Hi, > > did you check with 'which bwlabeln' if you have the respcetive function? > It's part of the image processing toolbox for matlab. > > Good Luck. > > Julian > > Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > >> Dear all, >> >> I'd like to do statistical comparison using cluster based permuation >> between two groups on ERP data. >> But I am receiving following error messages >> ??? Undefined function or method 'bwlabeln' for input arguments of >> type 'double'. >> >> Error in ==> findcluster at 89 >>  [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), >>  nfreq, ntime), 4); >> >> Error in ==> clusterstat at 194 >>     posclusobs = findcluster(reshape(postailobs, >>     [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); >> >> Error in ==> statistics_montecarlo at 321 >>  [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >> >> Error in ==> statistics_wrapper at 285 >>   [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); >> >> Error in ==> ft_freqstatistics at 125 >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); >> >> My configuration for ft_freqstatistics are >> cfg = []; >> cfg.channel          = 'all'; >> cfg.latency          = 'all'; >> cfg.frequency        = [30 50]; >> cfg.method           = 'montecarlo'; >> cfg.statistic        = 'indepsamplesT'; >> cfg.correctm         = 'cluster'; >> cfg.clusteralpha     = 0.025; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan        = 2; >> cfg.tail             = 0; >> cfg.clustertail      = 0; >> cfg.alpha            = 0.025; >> cfg.numrandomization = 500; >> cfg.neighbours       = [ ]; >> design = [ones(1, 16), ones(1, 16)*2]; >> cfg.design           = design; >> cfg.ivar             = 1; >> [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); >> >> >> Data structure of con_grand_avg are >> >> con_grand_avg = >>       label: {27x1 cell} >>        freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50] >>        time: [1x21 double] >>      dimord: 'subj_chan_freq_time' >>   powspctrm: [4-D double] >>         cfg: [1x1 struct] >> >> >> Any comment helps me. >> >> >> Best regards, >> >> Ki-Young Jung >> >> _______________________________________________ >> 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 batrod at gmail.com Fri Jan 14 22:29:41 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Fri, 14 Jan 2011 15:29:41 -0600 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: <1294996134883354.0.mail@mail> Message-ID: I may be wrong but as far as i remember, the cluster analysis can only be done on one value of frequency, average or not. There is no cfg.avgoverfreq option n your script. But again i might be wrong. Rodolphe On Fri, Jan 14, 2011 at 11:58 AM, Jung, Ki-Young wrote: > Thanks! But I have still trouble with this message. > > ??? Error using ==> statistics_montecarlo > Too many input arguments. > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_freqstatistics at 125 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Best regards, > > KY > > On Fri, Jan 14, 2011 at 1:04 AM, Julian Keil > wrote: > > Hi, > > > > did you check with 'which bwlabeln' if you have the respcetive function? > > It's part of the image processing toolbox for matlab. > > > > Good Luck. > > > > Julian > > > > Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > > > >> Dear all, > >> > >> I'd like to do statistical comparison using cluster based permuation > >> between two groups on ERP data. > >> But I am receiving following error messages > >> ??? Undefined function or method 'bwlabeln' for input arguments of > >> type 'double'. > >> > >> Error in ==> findcluster at 89 > >> [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, > :, :), > >> nfreq, ntime), 4); > >> > >> Error in ==> clusterstat at 194 > >> posclusobs = findcluster(reshape(postailobs, > >> [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); > >> > >> Error in ==> statistics_montecarlo at 321 > >> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > >> > >> Error in ==> statistics_wrapper at 285 > >> [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > >> > >> Error in ==> ft_freqstatistics at 125 > >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > >> > >> My configuration for ft_freqstatistics are > >> cfg = []; > >> cfg.channel = 'all'; > >> cfg.latency = 'all'; > >> cfg.frequency = [30 50]; > >> cfg.method = 'montecarlo'; > >> cfg.statistic = 'indepsamplesT'; > >> cfg.correctm = 'cluster'; > >> cfg.clusteralpha = 0.025; > >> cfg.clusterstatistic = 'maxsum'; > >> cfg.minnbchan = 2; > >> cfg.tail = 0; > >> cfg.clustertail = 0; > >> cfg.alpha = 0.025; > >> cfg.numrandomization = 500; > >> cfg.neighbours = [ ]; > >> design = [ones(1, 16), ones(1, 16)*2]; > >> cfg.design = design; > >> cfg.ivar = 1; > >> [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); > >> > >> > >> Data structure of con_grand_avg are > >> > >> con_grand_avg = > >> label: {27x1 cell} > >> freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 > 49 50] > >> time: [1x21 double] > >> dimord: 'subj_chan_freq_time' > >> powspctrm: [4-D double] > >> cfg: [1x1 struct] > >> > >> > >> Any comment helps me. > >> > >> > >> Best regards, > >> > >> Ki-Young Jung > >> > >> _______________________________________________ > >> 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 dgroppe at cogsci.ucsd.edu Fri Jan 14 22:36:13 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 14 Jan 2011 13:36:13 -0800 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout Message-ID: Hi Fieldtripians, I'm trying to export some EEGLAB data to Fieldtrip and am having trouble plotting the data topographically. I constructed a layout file for my 31 electrodes (see attached) and tried to plot the topography of my data using ft_topoplotER.m. This produced the attached figures all_chans.jpg and just_scalp_chans.jpg. The topography should look like that in the attached image, eeglab_topo.jpg. As you can see, the electrodes are shrunk too far into the head and can be off center. Trying to change the channel layout file to fix this has little effect because ft_prepare_layout.m automatically normalizes the electrode coordinates to fill a unit circle. Given the topoplots in the fieldtrip tutorial, there's obviously a way around this problem but save for editing the ft_prepare_layout.m, I don't know what to do. thanks in advance for your help, -David -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ -------------- next part -------------- A non-text attachment was scrubbed... Name: eeglab_topo.jpg Type: image/jpeg Size: 92401 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: all_chans.jpg Type: image/jpeg Size: 92441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: just_scalp_chans.jpg Type: image/jpeg Size: 82349 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 31chan.lay Type: application/octet-stream Size: 1067 bytes Desc: not available URL: From batrod at gmail.com Fri Jan 14 22:52:48 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Fri, 14 Jan 2011 15:52:48 -0600 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout In-Reply-To: References: Message-ID: David, i had the same issue with my own layout. The position of my electrodes was not fitting the head, even if the proportion were right, like in your first image. I solved this problem by multiplying the position with different numbers until i found the perfect one. This is the part of code that does this: lay = ft_prepare_layout(cfg); lay.pos(:,1) = 1.5*lay.pos(:,1); Replace 1.5 by something that works for you. Hope this helps, Rodolphe. On Fri, Jan 14, 2011 at 3:36 PM, David Groppe wrote: > Hi Fieldtripians, > I'm trying to export some EEGLAB data to Fieldtrip and am having > trouble plotting the data topographically. I constructed a layout file > for my 31 electrodes (see attached) and tried to plot the topography > of my data using ft_topoplotER.m. This produced the attached figures > all_chans.jpg and just_scalp_chans.jpg. The topography should look > like that in the attached image, eeglab_topo.jpg. As you can see, the > electrodes are shrunk too far into the head and can be off center. > Trying to change the channel layout file to fix this has little effect > because ft_prepare_layout.m automatically normalizes the electrode > coordinates to fill a unit circle. Given the topoplots in the > fieldtrip tutorial, there's obviously a way around this problem but > save for editing the ft_prepare_layout.m, I don't know what to do. > thanks in advance for your help, > -David > > -- > David Groppe, Ph.D. > dgroppe at cogsci.ucsd.edu > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > 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 karl.doron at gmail.com Sat Jan 15 18:05:46 2011 From: karl.doron at gmail.com (Karl Doron) Date: Sat, 15 Jan 2011 09:05:46 -0800 Subject: [FieldTrip] singleplotTFR error Message-ID: Hello, Has anyone else reported a problem with ft_singleplotTFR and output of the new specest module? multiplotTFR works, but 'interactive' method fails. It looks like the error occurs when trying to mask NaNs % masking only possible for evenly spaced axis if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) warning('(one of the) axis are not evenly spaced -> nans cannot be masked out -> cfg.masknans is set to ''no'';') cfg.masknans = 'no'; end Thank you, karl doron UCSB -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Sat Jan 15 18:49:09 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Sat, 15 Jan 2011 09:49:09 -0800 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout In-Reply-To: References: Message-ID: Thanks for the email Rodolphe. It's good to know I'm not the only one who has had this problem. I was hoping for a solution that didn't involve editing the code, since that makes it a pain to update our version of fieldtrip when a new version is released. It looks like that might be the only way though. cheers, -David On Fri, Jan 14, 2011 at 1:52 PM, Rodolphe Nenert wrote: > David, > i had the same issue with my own layout. The position of my electrodes was > not fitting the head, even if the proportion were right, like in your first > image. > I solved this problem by multiplying the position with different numbers > until i found the perfect one. > This is the part of code that does this: > lay = ft_prepare_layout(cfg); > lay.pos(:,1) = 1.5*lay.pos(:,1); > Replace 1.5 by something that works for you. > Hope this helps, > Rodolphe. > > On Fri, Jan 14, 2011 at 3:36 PM, David Groppe > wrote: >> >> Hi Fieldtripians, >>   I'm trying to export some EEGLAB data to Fieldtrip and am having >> trouble plotting the data topographically. I constructed a layout file >> for my 31 electrodes (see attached) and tried to plot the topography >> of my data using ft_topoplotER.m.  This produced the attached figures >> all_chans.jpg and just_scalp_chans.jpg.  The topography should look >> like that in the attached image, eeglab_topo.jpg.  As you can see, the >> electrodes are shrunk too far into the head and can be off center. >> Trying to change the channel layout file to fix this has little effect >> because ft_prepare_layout.m automatically normalizes the electrode >> coordinates to fill a unit circle.  Given the topoplots in the >> fieldtrip tutorial, there's obviously a way around this problem but >> save for editing the ft_prepare_layout.m, I don't know what to do. >>     thanks in advance for your help, >>            -David >> >> -- >> David Groppe, Ph.D. >> dgroppe at cogsci.ucsd.edu >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> _______________________________________________ >> 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. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From dgroppe at cogsci.ucsd.edu Sat Jan 15 23:43:29 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Sat, 15 Jan 2011 14:43:29 -0800 Subject: [FieldTrip] logic behind normalizing tapers Message-ID: Hi again Fieldtrippers, I noticed that when estimating power spectra ft_specest_mtmfft.m scales tapers such that their sum squared value is 1 before applying them to the data. For example: %lines 106-108 of ft_specest_mtmfft.m case 'hanning' tap = hanning(ndatsample)'; tap = tap./norm(tap, 'fro'); I realize this simply scales the power spectrum, but what's the rationale for this? Other EEG analysis software and tutorials I've read don't do this. much thanks, -David -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From TAVABIK at email.chop.edu Sun Jan 16 07:58:50 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Sun, 16 Jan 2011 01:58:50 -0500 Subject: [FieldTrip] MEG Artifact removal Message-ID: Greetings - Would someone please comment on the following procedure: (1) dummy=ft_rejectvisual(cfg,raw-data) where cfg.method='trial', cfg.channel='MEG' (2) dummy2=ft_rejectvisual(cfg,dummy) where cfg.method='channel', cfg.channel='MEG' (3) save artifact-rejected-data dummy2 Is this what is actually recommended by the visual artifact rejection tutorial, if not, then is it correct to assume that the final data structure (artifact-rejected-data) is the 'clean' data? Also, are there any automatic artifact rejection options available for trial (CTF) MEG data? Thanks in advance. -K. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- From r.vandermeij at donders.ru.nl Sun Jan 16 11:20:11 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Sun, 16 Jan 2011 11:20:11 +0100 Subject: [FieldTrip] singleplotTFR error In-Reply-To: References: Message-ID: <4D32C65B.5020304@donders.ru.nl> Hi Karl, Could you give some more information on the errors? Could you also post your cfg's? That will help in finding and fixing the bug. What FieldTrip version are you using? Best, Roemer On 15-1-2011 18:05, Karl Doron wrote: > Hello, > > Has anyone else reported a problem with ft_singleplotTFR and output of > the new specest module? > > multiplotTFR works, but 'interactive' method fails. > > It looks like the error occurs when trying to mask NaNs > > % masking only possible for evenly spaced axis > > if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) > > warning('(one of the) axis are not evenly spaced -> nans cannot be > masked out -> cfg.masknans is set to ''no'';') > > cfg.masknans = 'no'; > > end > > > > Thank you, > karl doron > UCSB > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From karl.doron at gmail.com Mon Jan 17 02:51:13 2011 From: karl.doron at gmail.com (Karl Doron) Date: Sun, 16 Jan 2011 17:51:13 -0800 Subject: [FieldTrip] singleplotTFR error In-Reply-To: <4D32C65B.5020304@donders.ru.nl> References: <4D32C65B.5020304@donders.ru.nl> Message-ID: Hello Roemer, Here's the cfg's and output from calls to ft_freqanalysis with method='wavelet' and the subsequent call to ft_singleplotTFR and the resulting error. The imagesc command will however plot the data at that channel imagesc(squeeze(wvpow.powspctrm(strmatch('A177',label),:,:))) Thanks for any help! cfg = []; cfg.output = 'pow'; cfg.channel = 'MEG'; cfg.method = 'wavelet'; cfg.foi = 10:2:30; cfg.toi = 0.0:0.05:2.75; wvpow = ft_freqanalysis(cfg, data_spctrm); wvpow = label: {246x1 cell} dimord: 'chan_freq_time' freq: [1x11 double] time: [1x56 double] powspctrm: [246x11x56 double] grad: [1x1 struct] cfg: [1x1 struct] %Singleplot results cfg = []; cfg.channel = 'A177'; cfg.grad = grad; cfg.xlim = [0.6 2.5]; cfg.ylim = [10 20]; figure; ft_singleplotTFR(cfg, wvpow) Warning: (one of the) axis are not evenly spaced -> nans cannot be masked out -> cfg.masknans is set to 'no'; > In ft_singleplotTFR at 296 ??? Attempted to access c(6,1); index out of bounds because size(c)=[5,37]. Error in ==> uimage at 124 ce(j,i) = c(indi(end), indj(end)); Error in ==> uimagesc at 46 hh = uimage(varargin{:},'CDataMapping','scaled'); Error in ==> ft_plot_matrix at 192 h = uimagesc(hdat, vdat, cdat, clim); Error in ==> ft_singleplotTFR at 327 ft_plot_matrix(data.(cfg.xparam)(xidc),data.(cfg.yparam)(yidc), TFR, 'clim',[zmin,zmax],'tag','cip') On Sun, Jan 16, 2011 at 2:20 AM, Roemer van der Meij < r.vandermeij at donders.ru.nl> wrote: > Hi Karl, > > Could you give some more information on the errors? Could you also post > your cfg's? That will help in finding and fixing the bug. What FieldTrip > version are you using? > > Best, > Roemer > > > > On 15-1-2011 18:05, Karl Doron wrote: > > Hello, > > Has anyone else reported a problem with ft_singleplotTFR and output of > the new specest module? > > multiplotTFR works, but 'interactive' method fails. > > It looks like the error occurs when trying to mask NaNs > > % masking only possible for evenly spaced axis > > if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) > > warning('(one of the) axis are not evenly spaced -> nans cannot be > masked out -> cfg.masknans is set to ''no'';') > > cfg.masknans = 'no'; > > end > > > Thank you, > karl doron > UCSB > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > 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 mcregar at upo.es Mon Jan 17 15:42:43 2011 From: mcregar at upo.es (Maite Crespo Garcia) Date: Mon, 17 Jan 2011 15:42:43 +0100 Subject: [FieldTrip] Noise projection for coherence estimates... Message-ID: <4374c5456d2776bd.4d346373@upo.es> Hello all, I would like to know if beamformer coherence estimates should be normalized dividing them by an equivalent noise projection as for power estimates. My experiment has a baseline. Would it be correct to divide coherence during active state by baseline coherence? What would be the better approach? Thank you very much in advance. Best regards, Maité -------------- next part -------------- An HTML attachment was scrubbed... URL: From sangita.dandekar at gmail.com Mon Jan 17 17:44:52 2011 From: sangita.dandekar at gmail.com (Sangita Dandekar) Date: Mon, 17 Jan 2011 11:44:52 -0500 Subject: [FieldTrip] searchable email discussion archive? Message-ID: The new fieldtrip page looks good. I was just wondering whether there is a method in place to search the discussion list email archives using keywords? The page at: http://mailman.science.ru.nl/pipermail/fieldtrip/ is sortable by field but I haven't been able to figure out how to do a keyword search. The old webpage's searchable email archive was extremely useful. Are there plans to create the same sort searchable archive for the new page? Thanks in advance for any help, Sangi -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Mon Jan 17 18:08:11 2011 From: matt.mollison at gmail.com (Matt Mollison) Date: Mon, 17 Jan 2011 10:08:11 -0700 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: References: Message-ID: Sangi, I agree that the search functionality at the old site was quite useful. One method that I've used for searching the new archives is to go to google.comand include "site: http://mailman.science.ru.nl/pipermail/fieldtrip/" with the terms that you wish to search for. Hope that helps. Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Mon, Jan 17, 2011 at 9:44 AM, Sangita Dandekar < sangita.dandekar at gmail.com> wrote: > The new fieldtrip page looks good. I was just wondering whether there is a > method in place to search the discussion list email archives using keywords? > > The page at: > http://mailman.science.ru.nl/pipermail/fieldtrip/ > > is sortable by field but I haven't been able to figure out how to do a > keyword search. The old webpage's searchable email archive was extremely > useful. Are there > plans to create the same sort searchable archive for the new page? > > Thanks in advance for any help, > Sangi > > _______________________________________________ > 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 mcregar at upo.es Mon Jan 17 18:13:18 2011 From: mcregar at upo.es (Maite Crespo Garcia) Date: Mon, 17 Jan 2011 18:13:18 +0100 Subject: [FieldTrip] Noise projection for coherence estimates... In-Reply-To: <4374c5456d2776bd.4d346373@upo.es> References: <4374c5456d2776bd.4d346373@upo.es> Message-ID: <45d37fe857bb6844.4d3486be@upo.es> I realized after writing the previous post that the coherence estimate is a ratio itself. Likely, using projected noise has no sense. But I'm still not sure about the right approach (compare to baseline and then between conditions?). Any suggestion? Thanks, Maité ----- Mensaje original ----- De: Maite Crespo Garcia Fecha: Lunes, 17 de Enero de 2011, 4:25 pm Asunto: [FieldTrip] Noise projection for coherence estimates... A: fieldtrip at donders.ru.nl > Hello all, > > I would like to know if beamformer coherence estimates should be normalized dividing them by an equivalent noise projection as for power estimates. My experiment has a baseline. Would it be correct to divide coherence during active state by baseline coherence? What would be the better approach? > > Thank you very much in advance. > > Best regards, > Maité > _______________________________________________ > 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.oosthoek at donders.ru.nl Tue Jan 18 09:18:46 2011 From: s.oosthoek at donders.ru.nl (Simon Oosthoek) Date: Tue, 18 Jan 2011 09:18:46 +0100 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: References: Message-ID: <4D354CE6.8000009@donders.ru.nl> Matt Mollison wrote: > Sangi, > > I agree that the search functionality at the old site was quite > useful. One method that I've used for searching the new archives is to > go to google.com and include > "site:http://mailman.science.ru.nl/pipermail/fieldtrip/" with the > terms that you wish to search for. > I think this is the best method to use, because I doubt the search functionality can easily be included on the mailman site. Perhaps I can fabricate a search box using google on the wiki for the mailinglist... Cheers Simon From stephen.whitmarsh at gmail.com Tue Jan 18 10:37:55 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 18 Jan 2011 10:37:55 +0100 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: <-6003509403171258621@unknownmsgid> References: <-6003509403171258621@unknownmsgid> Message-ID: Dear All, We will be giving a weekend FieldTrip workshop at the City College New York soon (February 5th – 6th) and still have a couple of last-minute spaces left for those in the NYC region interested in joining. Please see attachment for details. Sincerely, Stephen Whitmarsh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FieldTrip Weekend Workshop NYC.pdf Type: application/pdf Size: 86868 bytes Desc: not available URL: From eelke.spaak at donders.ru.nl Tue Jan 18 10:39:12 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 18 Jan 2011 10:39:12 +0100 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: <4D354CE6.8000009@donders.ru.nl> References: <4D354CE6.8000009@donders.ru.nl> Message-ID: Hello everyone, I've just added a Google Custom search box to the Discussion list page on the wiki (http://fieldtrip.fcdonders.nl/discussion_list). (Note that we are having a bit of trouble with some of our fileservers at the moment, and therefore the wiki might be offline every now and then. We hope to have these problems fixed shortly.) Best, Eelke 2011/1/18 Simon Oosthoek : > Matt Mollison wrote: >> >> Sangi, >> >> I agree that the search functionality at the old site was quite useful. >> One method that I've used for searching the new archives is to go to >> google.com and include >> "site:http://mailman.science.ru.nl/pipermail/fieldtrip/" with the terms that >> you wish to search for. >> > I think this is the best method to use, because I doubt the search > functionality can easily be included on the mailman site. > Perhaps I can fabricate a search box using google on the wiki for the > mailinglist... > > Cheers > > Simon > From venug001 at crimson.ua.edu Tue Jan 18 14:39:36 2011 From: venug001 at crimson.ua.edu (Gopakumar Venugopalan) Date: Tue, 18 Jan 2011 04:39:36 -0900 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, and just finished my post doc last week. I wonder what options might be open to me. Thanks in advance. Warm regards gopa On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear All, > > > > We will be giving a weekend FieldTrip workshop at the City College New York > soon (February 5th – 6th) and still have a couple of last-minute spaces > left for those in the NYC region interested in joining. Please see > attachment for details. > > > > Sincerely, > > Stephen Whitmarsh > > > _______________________________________________ > 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 venug001 at crimson.ua.edu Tue Jan 18 14:40:48 2011 From: venug001 at crimson.ua.edu (Gopakumar Venugopalan) Date: Tue, 18 Jan 2011 04:40:48 -0900 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: I responded to the fieldtrip listserv by mistake, would you please delete it and NOT include it in your digest or forward. Warm regards gopa On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan < venug001 at crimson.ua.edu> wrote: > Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, > and just finished my post doc last week. I wonder what options might be open > to me. Thanks in advance. > Warm regards > gopa > > On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < > stephen.whitmarsh at gmail.com> wrote: > >> Dear All, >> >> >> >> We will be giving a weekend FieldTrip workshop at the City College New >> York soon (February 5th – 6th) and still have a couple of last-minute >> spaces left for those in the NYC region interested in joining. Please see >> attachment for details. >> >> >> >> Sincerely, >> >> Stephen Whitmarsh >> >> >> _______________________________________________ >> 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 Tue Jan 18 18:43:11 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 18 Jan 2011 11:43:11 -0600 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Dear Fieldtrip users, i just received the info about the NY workshop taking place on 5th and 6th february. Unfortunately, its too late for me to make it. As i'd like to participate to such workshop/formation, is there a webpage or a place where i can find such informations about future events? Rodolphe On Tue, Jan 18, 2011 at 7:40 AM, Gopakumar Venugopalan < venug001 at crimson.ua.edu> wrote: > I responded to the fieldtrip listserv by mistake, would you please delete > it and NOT include it in your digest or forward. > Warm regards > gopa > > On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan < > venug001 at crimson.ua.edu> wrote: > >> Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, >> and just finished my post doc last week. I wonder what options might be open >> to me. Thanks in advance. >> Warm regards >> gopa >> >> On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> >>> Dear All, >>> >>> >>> >>> We will be giving a weekend FieldTrip workshop at the City College New >>> York soon (February 5th – 6th) and still have a couple of last-minute >>> spaces left for those in the NYC region interested in joining. Please see >>> attachment for details. >>> >>> >>> >>> Sincerely, >>> >>> Stephen Whitmarsh >>> >>> >>> _______________________________________________ >>> 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 m.chait at ucl.ac.uk Wed Jan 19 11:48:37 2011 From: m.chait at ucl.ac.uk (Maria Chait) Date: Wed, 19 Jan 2011 10:48:37 -0000 Subject: [FieldTrip] RA position at the UCL Ear Institute - MEG & auditory change detection Message-ID: <079f01cbb7c6$6d996c50$48cc44f0$@chait@ucl.ac.uk> Dear Colleagues, I am writing to point your attention to a research assistant job opening at the UCL Ear Institute and would be grateful if you could distribute the advert to relevant students in your department. Please note that it is possible to undertake a UCL PhD degree within the context of this research work. Research Assistant - Ref: 1174144 Closing Date: 17/02/2011 Apply on: www.ucl.ac.uk/hr/jobs A research assistant position (salary £27,796 - £29,318 per annum Inclusive of London allowance) is available to work on a Wellcome Trust funded project that will use MEG functional brain imaging to investigate the neural systems that support auditory change detection in the human brain. You will be supervised by Dr Maria Chait (UCL Ear Institute) and Prof. Tim Griffiths (Newcastle University). The post holder will be based at UCL Ear Institute, and report to Dr Maria Chait. MEG scanning will be carried out at UCL’s Wellcome Trust Centre for Neuroimaging. Initial funding for this post is available for 36 months. There is the possibility (if UCL eligibility criteria are satisfied) to undertake a UCL PhD degree within the context of this research work. Your main duties and responsibilities will be: 1. Design and execute MEG brain imaging experiments. 2. Develop MatLab software for running the experiments and for data analysis 3. Train subjects in preparation for relevant experiments. 4. Record and analyze imaging data. 5. Assist in the preparation of manuscripts. The UCL Ear Institute provides state-of-the-art research facilities across a wide range of disciplines and is one of the foremost centres for hearing, speech and language-related research within Europe. The Wellcome Trust Centre for Neuroimaging is a leading centre for brain imaging, bringing together clinicians and scientists who study higher cognitive function using neuroimaging techniques. Key Requirements Applicants should hold a 1St class, or upper 2nd (or equivalent) bachelor’s degree (masters degree an advantage) in an engineering or scientific subject and have substantial experience in digital signal processing and computer programming. Previous experience with functional brain imaging and/or acoustics is desirable. Further Details You should apply for this post (Ref #: 1174144) through UCL's online recruitment website, www.ucl.ac.uk/hr/jobs, where you can download a job description and person specification. If you have any queries please contact Dr. Maria Chait (email m.chait at ucl.ac.uk) Maria Chait PhD m.chait at ucl.ac.uk Research Fellow UCL Ear Institute 332 Gray's Inn Road London WC1X 8EE -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jan 20 10:51:48 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 20 Jan 2011 10:51:48 +0100 Subject: [FieldTrip] FieldtripR? In-Reply-To: References: Message-ID: <87C19057-05F3-4A69-85A4-0B932BA8FC6A@donders.ru.nl> Dear Mike, [CCed to the fieldtrip email discussion list]] On 19 Jan 2011, at 23:39, Mike Lawrence wrote: > I just came across your Fieldtrip software and it looks very > impressive. However, I'm not a MATLAB user; I feel that scientific > software needs to be both free and open source for the purposes of > replication and extension, so I use R instead (well, I also use R > because it's the lingua franca of statistics, so it provides access to > cutting edge routines). I therefore thought I'd request that the > Fieldtrip team work to port the Fieldtrip code to R. There is > currently a paucity of EEG analysis packages for R and a port of > Fieldtrip would make a great contribution. Thanks for your constructive suggestion. The FieldTrip software is open source, but indeed requires commercial software (MATLAB) to run. Most people run it on Windows or Apple OSX, even further commercial dependencies for those users. Requests for porting FieldTrip to free languages (other than Matlab) come up regularly, e.g. to make a compiled C/C++ version, an Octave version, a Python version or an R version. Regretfully, we are not able to honor these requests. FieldTrip is developped for, and by scientists that are mostly funded by national and international scientific projects. Those projects require our contributors to focus on their scientific results, and FieldTrip can be considered as just spinoff. For people that want to use FieldTrip without Matlab, pragmatically I would first suggest to look into Octave: large parts (but not all parts) of our code will execute properly in Octave with no or little changes. An alternative that requires MATLAB for development, but does not require MATLAB for running it, would be to use the MATLAB compiler to compile it into a stand-alone version that can be distributed free of charge. Contributions in either the direction of Octave or a compiled version, or contributions in porting it to another language, are most certainly welcome and would receive our support. If you feel that we should receive funding from our national or from international research funding agency to do the work that is required in porting it to a free platform, please consider contacting http://www.nwo.nl and similar agencies to make a plea for this. best regards, Robert PS please also see my "coffee machine" email at http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003339.html , which is part of a similar thread. --- FieldTrip project leader Senior Researcher and MEG physicist at the Donders Centre for Cognitive Neuroimaging From michael.wibral at web.de Thu Jan 20 10:51:59 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 20 Jan 2011 10:51:59 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection Message-ID: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> Deal Fieldtrip users, there is something else I do not understand in the tutorial: if you read in the data in trials (as it is done) how can you do padding later as it is suggested. I tried to run the example code on teh website reading in the data such that it contains trials. If I then try to search for muscle artifacts I get the 'subscript indices must be positive or logical ... values', indicating that the code tries to access data that aren't there. If I set the padding to zero (instead of 0.1) it works. So I am wondering wether somehow one should actually run these things on continuous data (contrary to what is indicated in the tutorial)? Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From michael.wibral at web.de Thu Jan 20 10:52:17 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 20 Jan 2011 10:52:17 +0100 (CET) Subject: [FieldTrip] error in the artifact rejection tutorial? Message-ID: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> Dear fieldtrip community, there seems to be a slight inconsistency in the tutorial section on artifact removal (which I otherwise like a lot because it calrifies a lot of the 'black-boxiness' of these particular fieldtrip functions (thanks a lot). The part I am referring to is in the jump removal section. It starts with the lines: % jump cfg = []; if isfield(cfg, 'padding') && cfg.padding~=0 padding = cfg.padding; else padding = 0; end I wonder whther these lines should go somewhere else as after clearing cfg the code will alwazs end up in the second part if the if condition, as there can be no 'padding' field. Didn't want to change this my self, as I might misunderstand something. Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Thu Jan 20 15:06:33 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 20 Jan 2011 15:06:33 +0100 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: <5E34E57B-F699-4267-858B-D903CE79F61C@donders.ru.nl> Dear Rodolphe We will host a toolkit course on "Advanced MEG and EEG analysis" at the Donders in Nijmegen. Please have a look at http://www.ru.nl/donders/agenda-events/courses/toolkits-2011/ . Note that it only contains the preliminary program (simply copied from last year) and that the final programm will look slightly different. The registation has just openend this week, and a formal annoucement will follow. Please do note that it tends to be oversubscribed: we select the participants on their motivation and background and not on who registers first. best regards, Robert On 18 Jan 2011, at 18:43, Rodolphe Nenert wrote: > Dear Fieldtrip users, > > i just received the info about the NY workshop taking place on 5th > and 6th february. Unfortunately, its too late for me to make it. As > i'd like to participate to such workshop/formation, is there a > webpage or a place where i can find such informations about future > events? > > Rodolphe From jan.schoffelen at donders.ru.nl Fri Jan 21 09:52:23 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 21 Jan 2011 09:52:23 +0100 Subject: [FieldTrip] error in the artifact rejection tutorial? In-Reply-To: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> References: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> Message-ID: Dear Michael, Please feel free to delete this particular line (and/or edit any other line) from the wiki. Declaring cfg empty before the conditional statements indeed does not makes sense. Best wishes, JM On Jan 20, 2011, at 10:52 AM, Michael Wibral wrote: > Dear fieldtrip community, > > there seems to be a slight inconsistency in the tutorial section on > artifact removal (which I otherwise like a lot because it calrifies > a lot of the 'black-boxiness' of these particular fieldtrip > functions (thanks a lot). > The part I am referring to is in the jump removal section. > > It starts with the lines: > > > % jump > cfg = []; > if isfield(cfg, 'padding') && cfg.padding~=0 > padding = cfg.padding; > else > padding = 0; > end > > > I wonder whther these lines should go somewhere else as after > clearing cfg the code will alwazs end up in the second part if the > if condition, as there can be no 'padding' field. > Didn't want to change this my self, as I might misunderstand > something. > > Michael > Wibral.vcf>_______________________________________________ > 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 Fri Jan 21 09:55:48 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 21 Jan 2011 09:55:48 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> Message-ID: Dear Michael, Yes, I agree with you here as well. In principle the ft_artifact_zvalue supports data as a second input argument, but in such case the different types of padding in the cfg do not make sense. I would indeed remove the second input arguments in the example code snippets. Could I ask you to take care of that? Thanks, JM On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: > Deal Fieldtrip users, > > there is something else I do not understand in the tutorial: if you > read in the data in trials (as it is done) how can you do padding > later as it is suggested. I tried to run the example code on teh > website reading in the data such that it contains trials. If I then > try to search for muscle artifacts I get the 'subscript indices must > be positive or logical ... values', indicating that the code tries > to access data that aren't there. If I set the padding to zero > (instead of 0.1) it works. So I am wondering wether somehow one > should actually run these things on continuous data (contrary to > what is indicated in the tutorial)? > > Michael > Wibral.vcf>_______________________________________________ > 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 karch at mpib-berlin.mpg.de Fri Jan 21 16:49:20 2011 From: karch at mpib-berlin.mpg.de (Karch, Julian) Date: Fri, 21 Jan 2011 16:49:20 +0100 Subject: [FieldTrip] WG: References: <82EE999347EBF142A8D78EF16FB83D8D01C82524@MPIBMAIL01.mpib-berlin.mpg.de> Message-ID: <82EE999347EBF142A8D78EF16FB83D8D01C82525@MPIBMAIL01.mpib-berlin.mpg.de> Hello, i just tried to go through the Multivariates Tutorial (http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis) unluckly when i typed "stat = ft_timelockstatistics(cfg,tleft,tright);" matlab aborted with the exit code: ??? Error using ==> tprod at 119 unable to compile MEX version of 'E:/julian/matlab/fieldtrip/multivariate/external/farquhar/tprod/tprod', please make sure your MEX compiler is set up correctly (try 'mex -setup'). I'm using MATLAB 7.10.0 64 Bit on Windows 7. I definitively have a working mex compiler as compiling the example yprime.c is working perfectly. I also tried to compile the files manually by typing mex('ddtprod.c','dstprod.c','sdtprod.c','sstprod.c','tprod_util.c','tprod_mex.c','mxInfo.c');. This resulted in the following output: ddtprod.c e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier C:\PROGRA~1\MATLAB\R2010A\BIN\MEX.PL: Error: Compile of 'ddtprod.c' failed. Any suggestions? Julian Karch Research Assistant Max Planck Institute for Human Development Department Lifespan Psychology Lentzeallee 94 14195 Berlin Tel.: 030 / 82406-294 Email: karch at mpib-berlin.mpg.de Internet: www.mpib-berlin.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Fri Jan 21 20:07:17 2011 From: frank.ye.mei at gmail.com (Frank (Ye) Mei) Date: Fri, 21 Jan 2011 14:07:17 -0500 Subject: [FieldTrip] problem downloading fieldtrip Message-ID: <4D39D965.20601@gmail.com> I cann't download the fieldtrip toolbox. I didn't get the email with download instructions. Thank you for your download request, an email with download instructions has been sent to ............ If you object to giving your real email address, please consider using a service like http://www.spamgourmet.com, http://www.mailinator.com or http://10minutemail.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From todavidkim at gmail.com Fri Jan 21 20:21:27 2011 From: todavidkim at gmail.com (David Kim) Date: Fri, 21 Jan 2011 11:21:27 -0800 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: <4D39D965.20601@gmail.com> References: <4D39D965.20601@gmail.com> Message-ID: Hi Frank, While you are awaiting the official response from fieldtrip folks you might try this: http://code.google.com/p/fieldtrip/source/checkout If you have a working understanding of of how to use svn, I found this to be a great way to install and update fieldtrip software. On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: > I cann't download the fieldtrip toolbox. I didn't get the email with > download instructions. > > Thank you for your download request, an email with download instructions > has been sent to ............ > > If you object to giving your real email address, please consider using a > service like http://www.spamgourmet.com, http://www.mailinator.com or > http://10minutemail.com. > > > _______________________________________________ > 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 dgroppe at cogsci.ucsd.edu Sat Jan 22 08:29:00 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 21 Jan 2011 23:29:00 -0800 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Speaking of workshops, Fieldtrip users might be interested in some of the talks from the 12th EEGLAB workshop that took place a couple of months ago. Videos of the talks were just posted online: http://thesciencenetwork.org/programs/12th-eeglab-workshop Talk slides and supportive material are available on the EEGLAB wiki as well: http://sccn.ucsd.edu/wiki/Twelfth_EEGLAB_Workshop Although the talks obviously don't cover the logistics of using Fieldtrip, some of the methods implemented by Fieldtrip (e.g., time-frequency analysis, independent components analysis) are and might be of use to those of you just getting started with these techniques. Moreover, there are some neat talks on future directions in EEG technology (e.g., dry electrodes and EEG recording from moving participants). cheers, -David On Tue, Jan 18, 2011 at 9:43 AM, Rodolphe Nenert wrote: > Dear Fieldtrip users, > i just received the info about the NY workshop taking place on 5th and 6th > february. Unfortunately, its too late for me to make it. As i'd like to > participate to such workshop/formation, is there a webpage or a place where > i can find such informations about future events? > Rodolphe > > On Tue, Jan 18, 2011 at 7:40 AM, Gopakumar Venugopalan > wrote: >> >> I responded to the fieldtrip listserv by mistake, would you please delete >> it and NOT include it in your digest or forward. >> Warm regards >> gopa >> >> On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan >> wrote: >>> >>> Dear Stepben Whitmarsh, I would be interested, don't live in the NYC >>> area, and just finished my post doc last week. I wonder what options might >>> be open to me. Thanks in advance. >>> Warm regards >>> gopa >>> >>> On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh >>> wrote: >>>> >>>> Dear All, >>>> >>>> >>>> >>>> We will be giving a weekend FieldTrip workshop at the City College New >>>> York soon (February 5th – 6th) and still have a couple of last-minute spaces >>>> left for those in the NYC region interested in joining. Please see >>>> attachment for details. >>>> >>>> >>>> >>>> Sincerely, >>>> >>>> Stephen Whitmarsh >>>> >>>> _______________________________________________ >>>> 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 > -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From kassayag at gmail.com Sat Jan 22 08:45:07 2011 From: kassayag at gmail.com (karen assayag) Date: Sat, 22 Jan 2011 09:45:07 +0200 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: References: <4D39D965.20601@gmail.com> Message-ID: is the download good for mac ? On Fri, Jan 21, 2011 at 9:21 PM, David Kim wrote: > Hi Frank, > > While you are awaiting the official response from fieldtrip folks you might > try this: > > http://code.google.com/p/fieldtrip/source/checkout > > If you have a working understanding of of how to use svn, > I found this to be a great way to install and update fieldtrip software. > > On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: > >> I cann't download the fieldtrip toolbox. I didn't get the email with >> download instructions. >> >> Thank you for your download request, an email with download instructions >> has been sent to ............ >> >> If you object to giving your real email address, please consider using a >> service like http://www.spamgourmet.com, http://www.mailinator.com or >> http://10minutemail.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 > -- Karen -------------- next part -------------- An HTML attachment was scrubbed... URL: From todavidkim at gmail.com Sat Jan 22 08:54:42 2011 From: todavidkim at gmail.com (David Kim) Date: Fri, 21 Jan 2011 23:54:42 -0800 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: References: <4D39D965.20601@gmail.com> Message-ID: Hi Karen, Again, you might want to hear the official response from the fieldtrip folks, but I've successfully used svn on several OS platforms without an issue (WinXP, Win7, CentOs, Ubuntu). So I'm assuming it works across platforms. I just did a search on my CentOs machine, and it looks like the svn version includes all the mexmac files. I would give it a try. On Fri, Jan 21, 2011 at 11:45 PM, karen assayag wrote: > is the download good for mac ? > > > On Fri, Jan 21, 2011 at 9:21 PM, David Kim wrote: > >> Hi Frank, >> >> While you are awaiting the official response from fieldtrip folks you >> might try this: >> >> http://code.google.com/p/fieldtrip/source/checkout >> >> If you have a working understanding of of how to use svn, >> I found this to be a great way to install and update fieldtrip software. >> >> On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: >> >>> I cann't download the fieldtrip toolbox. I didn't get the email with >>> download instructions. >>> >>> Thank you for your download request, an email with download instructions >>> has been sent to ............ >>> >>> If you object to giving your real email address, please consider using a >>> service like http://www.spamgourmet.com, http://www.mailinator.com or >>> http://10minutemail.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 >> > > > > -- > Karen > > > > _______________________________________________ > 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 Marcel.Bastiaansen at mpi.nl Mon Jan 24 11:44:07 2011 From: Marcel.Bastiaansen at mpi.nl (Bastiaansen, Marcel) Date: Mon, 24 Jan 2011 11:44:07 +0100 Subject: [FieldTrip] question on beamformers Message-ID: <4D3D57F7.8090504@mpi.nl> Dear all, I have the following conceptual issue with using beamforming: I have data from 2 conditions, A and B. Both contain a prestimulus interval and a poststimulus interval. When plotting the TF representations of power, using a *relative* baseline (poststimulus interval / prestimulus interval), a strong difference emerges between the conditions in the beta frequency range. Especially if I plot the *difference between the conditions*, the beta effect is long-lasting, narrow-band and topographically focused. Ideal for beamforming, I'd say. In setting up the beamformer analysis, I am faced with the following issue: the effect is most clearly present in the *relative* power changes, so I would want to compute spatial filters for both the pre and the post time intervals. My hunch would be to compute common spatial filters for both pre intervals (preA and preB), and common filters for both post intervals (postA and postB). Then, (after projecting the trials through the filters), compute the relative power again (pre/post for each condition). Does this approach make sense? Next question is then, at which point in the analysis pipeline should one do the condition subtraction? (I'd want to do that because at the TFR level the effect comes out most clearly in the condition difference) Best, Marcel -- dr. Marcel C.M. Bastiaansen. Max Planck Institute for Psycholinguistics Visiting Adress: Wundtlaan 1, 6525 XD Nijmegen, the Netherlands Mailing adress: P.O. Box 310, 6500 AH Nijmegen, the Netherlands phone: +31 24 3521 347 fax: +31 24 3521 213 mail: marcel.bastiaansen at mpi.nl http://www.mpi.nl/people/bastiaansen-marcel and Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Visiting address: Kapittelweg 29, 6525 EN Nijmegen, the Netherlands Mailing address: PO Box 9101, 6500 HB Nijmegen, the Netherlands phone: + 31 24 3610 882 fax: + 31 24 3610 989 mail: marcel.bastiaansen at fcdonders.ru.nl web: http://www.ru.nl/neuroimaging/staff/neurocognition_of/marcel_bastiaansen/ -- From michael.wibral at web.de Mon Jan 24 11:48:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 11:48:47 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056>, Message-ID: <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> Hi Jan-Mathijs, I am a bit unsure how to proceed: (1) sketch the artifact correction way like this ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> ft_preprocessing OR (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. I think I should go for option (1) as this seems to be the standard use on continuous data. Sometime in the futrure one should then add a tutorial for those that have data in trials to start with. Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 21, 2011 9:55:48 AM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Dear Michael, > >Yes, I agree with you here as well. In principle the >ft_artifact_zvalue supports data as a second input argument, but in >such case the different types of padding in the cfg do not make sense. >I would indeed remove the second input arguments in the example code >snippets. Could I ask you to take care of that? > >Thanks, > >JM > > >On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: > >> Deal Fieldtrip users, >> >> there is something else I do not understand in the tutorial: if you >> read in the data in trials (as it is done) how can you do padding >> later as it is suggested. I tried to run the example code on teh >> website reading in the data such that it contains trials. If I then >> try to search for muscle artifacts I get the 'subscript indices must >> be positive or logical ... values', indicating that the code tries >> to access data that aren't there. If I set the padding to zero >> (instead of 0.1) it works. So I am wondering wether somehow one >> should actually run these things on continuous data (contrary to >> what is indicated in the tutorial)? >> >> Michael >> > Wibral.vcf>_______________________________________________ >> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Mon Jan 24 12:12:57 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 24 Jan 2011 12:12:57 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> Message-ID: <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> Dear Michael, I agree. The tutorial should be 'de'-confused by sketching option 1, and another one should be describing option 2, or the original should be clearly making the distinction. Best, JM On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: > Hi Jan-Mathijs, > > I am a bit unsure how to proceed: > > (1) sketch the artifact correction way like this > ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> > ft_preprocessing > OR > (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> > artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. > > I think I should go for option (1) as this seems to be the standard > use on continuous data. Sometime in the futrure one should then add > a tutorial for those that have data in trials to start with. > > Michael > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 21, 2011 9:55:48 AM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Dear Michael, >> >> Yes, I agree with you here as well. In principle the >> ft_artifact_zvalue supports data as a second input argument, but in >> such case the different types of padding in the cfg do not make >> sense. >> I would indeed remove the second input arguments in the example code >> snippets. Could I ask you to take care of that? >> >> Thanks, >> >> JM >> >> >> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >> >>> Deal Fieldtrip users, >>> >>> there is something else I do not understand in the tutorial: if you >>> read in the data in trials (as it is done) how can you do padding >>> later as it is suggested. I tried to run the example code on teh >>> website reading in the data such that it contains trials. If I then >>> try to search for muscle artifacts I get the 'subscript indices must >>> be positive or logical ... values', indicating that the code tries >>> to access data that aren't there. If I set the padding to zero >>> (instead of 0.1) it works. So I am wondering wether somehow one >>> should actually run these things on continuous data (contrary to >>> what is indicated in the tutorial)? >>> >>> Michael >>> >> Wibral.vcf>_______________________________________________ >>> 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 stephen.whitmarsh at gmail.com Mon Jan 24 12:18:47 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 24 Jan 2011 12:18:47 +0100 Subject: [FieldTrip] question on beamformers In-Reply-To: <4D3D57F7.8090504@mpi.nl> References: <4D3D57F7.8090504@mpi.nl> Message-ID: Dear Marcel, My two cents are the following: I would recommend to compute common filter over ALL conditions, pre AND post. This will make sure you use as much information as possible to calculate your cross-spectral density matrix and subsequent filter. I assume you assume that the location/orientation of the sources do not change before and after stimulus. Also, in the case that you are looking for a post-stimulus beta DECREASE it will help you to accurately determine post-stimulus activity based on a filter calculated from of a period where there is most (beta) signal. Then, for your contrast project your conditions, pre and post *separately* and do your relative contrast then: e.g. projected post-stimulus activity A / projected pre-stimulus activity A, and same for B. Then compare relative A - or / by B. Bottom line, do your common filter on everything, project and compare everything separately after that. Hope that helps, Stephen On 24 January 2011 11:44, Bastiaansen, Marcel wrote: > Dear all, > > I have the following conceptual issue with using beamforming: > > I have data from 2 conditions, A and B. Both contain a prestimulus interval > and a poststimulus interval. > > When plotting the TF representations of power, using a *relative* baseline > (poststimulus interval / prestimulus interval), a strong difference emerges > between the conditions in the beta frequency range. Especially if I plot the > *difference between the conditions*, the beta effect is long-lasting, > narrow-band and topographically focused. Ideal for beamforming, I'd say. > > In setting up the beamformer analysis, I am faced with the following issue: > the effect is most clearly present in the *relative* power changes, so I > would want to compute spatial filters for both the pre and the post time > intervals. My hunch would be to compute common spatial filters for both pre > intervals (preA and preB), and common filters for both post intervals (postA > and postB). Then, (after projecting the trials through the filters), compute > the relative power again (pre/post for each condition). Does this approach > make sense? > > Next question is then, at which point in the analysis pipeline should one > do the condition subtraction? (I'd want to do that because at the TFR level > the effect comes out most clearly in the condition difference) > > > Best, > Marcel > > > > -- > dr. Marcel C.M. Bastiaansen. > > Max Planck Institute for Psycholinguistics > Visiting Adress: Wundtlaan 1, 6525 XD Nijmegen, the Netherlands > Mailing adress: P.O. Box 310, 6500 AH Nijmegen, the Netherlands > phone: +31 24 3521 347 > fax: +31 24 3521 213 > mail: marcel.bastiaansen at mpi.nl > http://www.mpi.nl/people/bastiaansen-marcel > > and > > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Visiting address: Kapittelweg 29, 6525 EN Nijmegen, the Netherlands > Mailing address: PO Box 9101, 6500 HB Nijmegen, the Netherlands > phone: + 31 24 3610 882 > fax: + 31 24 3610 989 > mail: marcel.bastiaansen at fcdonders.ru.nl > web: > http://www.ru.nl/neuroimaging/staff/neurocognition_of/marcel_bastiaansen/ > -- > _______________________________________________ > 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 Mon Jan 24 13:51:38 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 13:51:38 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054>, <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> Message-ID: <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> Hi Jan mathijs, I tried to get option1 running, stumbled over the following little obstacle however: I tried to keep one cfg throughout the steps ft_definetrial; ft_artifact_zvalue, ft_rejectartifcat (with option complete and some tracking of where artfecats were found), ft_preprocessing (cutting out the clean trials from the cont. data). IMHO this used to be the way most people did this kind of procesing a while ago. However, I can't get ft_artifact_zvalue to run with different settings one after another for jump/musvle/EOG. FT claims after the first run of ft_artifact_zvalue that the z-value thing has been performed and refuse to detect other artifacts with new settings. >From here I only see two alternative: specifying a really lengthy cfg every time a new (also struggling with the cfg.dataset versus cfg.datafile issue) and do the bookkeeping of cfg.trl and related things myself or manually removing the cfg.artdef.zvalue.artifct field to get the z-value based detection to run again. This seems a bit odd to me. Any suggestions? Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 12:12:57 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Dear Michael, > >I agree. The tutorial should be 'de'-confused by sketching option 1, >and another one should be describing option 2, or the original should >be clearly making the distinction. > >Best, > >JM > > >On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: > >> Hi Jan-Mathijs, >> >> I am a bit unsure how to proceed: >> >> (1) sketch the artifact correction way like this >> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >> ft_preprocessing >> OR >> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. >> >> I think I should go for option (1) as this seems to be the standard >> use on continuous data. Sometime in the futrure one should then add >> a tutorial for those that have data in trials to start with. >> >> Michael >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 21, 2011 9:55:48 AM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> Yes, I agree with you here as well. In principle the >>> ft_artifact_zvalue supports data as a second input argument, but in >>> such case the different types of padding in the cfg do not make >>> sense. >>> I would indeed remove the second input arguments in the example code >>> snippets. Could I ask you to take care of that? >>> >>> Thanks, >>> >>> JM >>> >>> >>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>> >>>> Deal Fieldtrip users, >>>> >>>> there is something else I do not understand in the tutorial: if you >>>> read in the data in trials (as it is done) how can you do padding >>>> later as it is suggested. I tried to run the example code on teh >>>> website reading in the data such that it contains trials. If I then >>>> try to search for muscle artifacts I get the 'subscript indices must >>>> be positive or logical ... values', indicating that the code tries >>>> to access data that aren't there. If I set the padding to zero >>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>> should actually run these things on continuous data (contrary to >>>> what is indicated in the tutorial)? >>>> >>>> Michael >>>> >>> Wibral.vcf>_______________________________________________ >>>> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Mon Jan 24 16:41:09 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 24 Jan 2011 16:41:09 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> Message-ID: Hmmm, apparently this approach needs to be ironed out a bit (also from our side). For now, I'd say that it should work if you keep per type of artifact the artifact field in the output configuration, and just concatenate these prior to calling ft_rejectartifact. I will moreover CC this e-mail to the people involved in creating the first version of the renewed tutorial, and will bring up the issue in this week's FieldTrip developers meeting. Best, JM On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > Hi Jan mathijs, > > I tried to get option1 running, stumbled over the following little > obstacle however: > > I tried to keep one cfg throughout the steps ft_definetrial; > ft_artifact_zvalue, ft_rejectartifcat (with option complete and some > tracking of where artfecats were found), ft_preprocessing (cutting > out the clean trials from the cont. data). IMHO this used to be the > way most people did this kind of procesing a while ago. > > However, I can't get ft_artifact_zvalue to run with different > settings one after another for jump/musvle/EOG. FT claims after the > first run of ft_artifact_zvalue that the z-value thing has been > performed and refuse to detect other artifacts with new settings. > >> From here I only see two alternative: specifying a really lengthy >> cfg every time a new (also struggling with the cfg.dataset versus >> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >> things myself or manually removing the cfg.artdef.zvalue.artifct >> field to get the z-value based detection to run again. This seems a >> bit odd to me. > > Any suggestions? > > Michael > > > > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 24, 2011 12:12:57 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Dear Michael, >> >> I agree. The tutorial should be 'de'-confused by sketching option 1, >> and another one should be describing option 2, or the original should >> be clearly making the distinction. >> >> Best, >> >> JM >> >> >> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >> >>> Hi Jan-Mathijs, >>> >>> I am a bit unsure how to proceed: >>> >>> (1) sketch the artifact correction way like this >>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>> ft_preprocessing >>> OR >>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>> ft_preprocessing. >>> >>> I think I should go for option (1) as this seems to be the standard >>> use on continuous data. Sometime in the futrure one should then add >>> a tutorial for those that have data in trials to start with. >>> >>> Michael >>> >>> -----Ursprüngliche Nachricht----- >>> Von: "jan-mathijs schoffelen" >>> Gesendet: Jan 21, 2011 9:55:48 AM >>> An: "Email discussion list for the FieldTrip project" >>> >>> Betreff: Re: [FieldTrip] more on artfifact rejection >>> >>>> Dear Michael, >>>> >>>> Yes, I agree with you here as well. In principle the >>>> ft_artifact_zvalue supports data as a second input argument, but in >>>> such case the different types of padding in the cfg do not make >>>> sense. >>>> I would indeed remove the second input arguments in the example >>>> code >>>> snippets. Could I ask you to take care of that? >>>> >>>> Thanks, >>>> >>>> JM >>>> >>>> >>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>> >>>>> Deal Fieldtrip users, >>>>> >>>>> there is something else I do not understand in the tutorial: if >>>>> you >>>>> read in the data in trials (as it is done) how can you do padding >>>>> later as it is suggested. I tried to run the example code on teh >>>>> website reading in the data such that it contains trials. If I >>>>> then >>>>> try to search for muscle artifacts I get the 'subscript indices >>>>> must >>>>> be positive or logical ... values', indicating that the code tries >>>>> to access data that aren't there. If I set the padding to zero >>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>> should actually run these things on continuous data (contrary to >>>>> what is indicated in the tutorial)? >>>>> >>>>> Michael >>>>> >>>> Wibral.vcf>_______________________________________________ >>>>> 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 Patricia.Wollstadt at gmx.de Mon Jan 24 17:47:26 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Mon, 24 Jan 2011 17:47:26 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction Message-ID: <20110124164726.247880@gmx.net> Dear Fieldtrip-users, I'm currently trying to calculate freqstatistics for four experimental groups, using the following options: groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) length(subjects{4})]; design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; % 1 to N subjects design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group membership cfg=[]; cfg.design=design; cfg.uvar = 1; cfg.ivar = 2; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesF'; cfg.correctm = 'fdr'; cfg.numrandomization = 180000; cfg.alpha = 0.01/7; cfg.tail = 1; cfg.design = design; cfg.channels = myChannels; cfg.avgovertime = 'yes'; cfg.avgoverfreq = 'yes'; cfg.frequency = [1 3]; stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); With these settings, the coputation itself runs fine, but the resulting 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists of only ones). This would mean, that I found significant effects for all channels. Is this possible or rather due to an error somewhere in my script? Is it likely, that these are 'real' zeroes or rather very small values, close to zero? Any hints and suggestions are very welcome, thank you in advance, Kind regards Patricia Wollstadt -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl From michael.wibral at web.de Mon Jan 24 18:27:08 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 18:27:08 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054>, Message-ID: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Hi Jan-Mathijs, this is basically what we do at the moment, i.e. fooling artifcat_zvalue by removing the one field it complains about amnd using rejetartefact only at the very last. See the attched code - I really do not want to post this code on the tutorial website as I am not fully sure what I am doing :-). Michael %% CODE ft_defaults; Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/DATASETS/'; Design={ 'DMG13_NewMooney_20110120_0', [2 3], 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; } for ss=1:size(Design,1) % over subjects for cc=1:length(Design{ss,4}) % over conditions for ff=1:length(Design{ss,2}) % over .ds datasets/runs FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), '.ds') FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) % core data reading cfg=[]; cfg.dataset=FullFileName; cfg.headerformat = 'ctf_ds'; % for you to check whether still necessary ctf.dataformat = 'ctf_ds'; cfg.cond=Design{ss,4}(cc) cfg.continuous='yes'; cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? cfg.trialfun=Design{ss,3}; cfg=ft_definetrial(cfg); cfg.trl(end,:)=[]; trl=cfg.trl; % keep track of the trials padding=0.75 % 750 ms %%%%%%%%% artifact rejection section %%% jump % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 35; cfg.artfctdef.zvalue.trlpadding = 0.5*padding; cfg.artfctdef.zvalue.artpadding = 0.5*padding; cfg.artfctdef.zvalue.fltpadding = 0; % algorithmic parameters cfg.artfctdef.zvalue.medianfilter = 'yes'; cfg.artfctdef.zvalue.medianfiltord = 9; % in samples cfg.artfctdef.zvalue.absdiff = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'jump'; [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); % cfg.artfctdef.jump.artifact = artifact_jump; % cfg = ft_rejectartifact(cfg); %%% muscle cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % remove field from structure otherwise this won't run ?? % cutoff and padding  cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 15; cfg.artfctdef.zvalue.trlpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; cfg.artfctdef.zvalue.artpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfreq = [110 140]; cfg.artfctdef.zvalue.bpfiltord = 6; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.boxcar = 0.2; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'muscle'; [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); %%% EOG cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % cutoff and padding cfg.artfctdef.zvalue.channel = 'MRT41'; cfg.artfctdef.zvalue.cutoff = 10; cfg.artfctdef.zvalue.trlpadding = 0.5; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 3; cfg.artfctdef.zvalue.hilbert = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'EOG'; [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); cfg.trl=trl; cfg.artfctdef.reject = 'complete'; % this rejects complete trials, use 'partial' if you want to do partial artifact rejection % collect all the info about the artifacts that were found cfg.artfctdef.eog.artifact =artifact_EOG; cfg.artfctdef.jump.artifact = artifact_jump; cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); Data_no_artifacts=ft_preprocessing(cfg); % some additional filtering for DC removal and detrending cfg=[]; cfg.detrend='yes' cfg.hpfilt='yes' cfg.hpfreq=1; TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); clear Data_no_artifacts;  end ... ... end end -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 4:41:09 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Hmmm, apparently this approach needs to be ironed out a bit (also from >our side). For now, I'd say that it should work if you keep per type >of artifact the artifact field in the output configuration, and just >concatenate these prior to calling ft_rejectartifact. I will moreover >CC this e-mail to the people involved in creating the first version of >the renewed tutorial, and will bring up the issue in this week's >FieldTrip developers meeting. > >Best, > >JM > >On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > >> Hi Jan mathijs, >> >> I tried to get option1 running, stumbled over the following little >> obstacle however: >> >> I tried to keep one cfg throughout the steps ft_definetrial; >> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >> tracking of where artfecats were found), ft_preprocessing (cutting >> out the clean trials from the cont. data). IMHO this used to be the >> way most people did this kind of procesing a while ago. >> >> However, I can't get ft_artifact_zvalue to run with different >> settings one after another for jump/musvle/EOG. FT claims after the >> first run of ft_artifact_zvalue that the z-value thing has been >> performed and refuse to detect other artifacts with new settings. >> >>> From here I only see two alternative: specifying a really lengthy >>> cfg every time a new (also struggling with the cfg.dataset versus >>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>> things myself or manually removing the cfg.artdef.zvalue.artifct >>> field to get the z-value based detection to run again. This seems a >>> bit odd to me. >> >> Any suggestions? >> >> Michael >> >> >> >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 24, 2011 12:12:57 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> I agree. The tutorial should be 'de'-confused by sketching option 1, >>> and another one should be describing option 2, or the original should >>> be clearly making the distinction. >>> >>> Best, >>> >>> JM >>> >>> >>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>> >>>> Hi Jan-Mathijs, >>>> >>>> I am a bit unsure how to proceed: >>>> >>>> (1) sketch the artifact correction way like this >>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>> ft_preprocessing >>>> OR >>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>> ft_preprocessing. >>>> >>>> I think I should go for option (1) as this seems to be the standard >>>> use on continuous data. Sometime in the futrure one should then add >>>> a tutorial for those that have data in trials to start with. >>>> >>>> Michael >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: "jan-mathijs schoffelen" >>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>> An: "Email discussion list for the FieldTrip project" >>>> >>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>> >>>>> Dear Michael, >>>>> >>>>> Yes, I agree with you here as well. In principle the >>>>> ft_artifact_zvalue supports data as a second input argument, but in >>>>> such case the different types of padding in the cfg do not make >>>>> sense. >>>>> I would indeed remove the second input arguments in the example >>>>> code >>>>> snippets. Could I ask you to take care of that? >>>>> >>>>> Thanks, >>>>> >>>>> JM >>>>> >>>>> >>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>> >>>>>> Deal Fieldtrip users, >>>>>> >>>>>> there is something else I do not understand in the tutorial: if >>>>>> you >>>>>> read in the data in trials (as it is done) how can you do padding >>>>>> later as it is suggested. I tried to run the example code on teh >>>>>> website reading in the data such that it contains trials. If I >>>>>> then >>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>> must >>>>>> be positive or logical ... values', indicating that the code tries >>>>>> to access data that aren't there. If I set the padding to zero >>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>> should actually run these things on continuous data (contrary to >>>>>> what is indicated in the tutorial)? >>>>>> >>>>>> Michael >>>>>> >>>>> Wibral.vcf>_______________________________________________ >>>>>> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From batrod at gmail.com Mon Jan 24 18:39:31 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Mon, 24 Jan 2011 11:39:31 -0600 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110124164726.247880@gmx.net> References: <20110124164726.247880@gmx.net> Message-ID: Dear Patricia, Your alpha seems a little bit low, why taking 0.01/7= 0.0014 ? I may be wrong but i guess that a fdr correction on a such value of alpha will be very hard with your data. Rodolphe N., PhD. On Mon, Jan 24, 2011 at 10:47 AM, Patricia Wollstadt < Patricia.Wollstadt at gmx.de> wrote: > Dear Fieldtrip-users, > > I'm currently trying to calculate freqstatistics for four experimental > groups, using the following options: > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > length(subjects{4})]; > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > % 1 to N subjects > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group > membership > > > cfg=[]; > cfg.design=design; > cfg.uvar = 1; > cfg.ivar = 2; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; > cfg.correctm = 'fdr'; > cfg.numrandomization = 180000; > cfg.alpha = 0.01/7; > cfg.tail = 1; > cfg.design = design; > cfg.channels = myChannels; > cfg.avgovertime = 'yes'; > cfg.avgoverfreq = 'yes'; > cfg.frequency = [1 3]; > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); > > With these settings, the coputation itself runs fine, but the resulting > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists > of only ones). This would mean, that I found significant effects for all > channels. Is this possible or rather due to an error somewhere in my script? > Is it likely, that these are 'real' zeroes or rather very small values, > close to zero? > Any hints and suggestions are very welcome, thank you in advance, > > Kind regards > > Patricia Wollstadt > > > -- > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > _______________________________________________ > 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 Patricia.Wollstadt at gmx.de Mon Jan 24 19:25:15 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Mon, 24 Jan 2011 19:25:15 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: References: <20110124164726.247880@gmx.net> Message-ID: <20110124182515.12260@gmx.net> Hi Rodolphe, usually I compute this statistic for seven individual frequency bands (I left this part of the script out to keep the example-code short), so I did an additional correction of my alpha niveau. Regards, Patricia -------- Original-Nachricht -------- > Datum: Mon, 24 Jan 2011 11:39:31 -0600 > Von: Rodolphe Nenert > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction > Dear Patricia, > > Your alpha seems a little bit low, why taking 0.01/7= 0.0014 ? > I may be wrong but i guess that a fdr correction on a such value of alpha > will be very hard with your data. > > Rodolphe N., PhD. > > On Mon, Jan 24, 2011 at 10:47 AM, Patricia Wollstadt < > Patricia.Wollstadt at gmx.de> wrote: > > > Dear Fieldtrip-users, > > > > I'm currently trying to calculate freqstatistics for four experimental > > groups, using the following options: > > > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > > length(subjects{4})]; > > > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > > % 1 to N subjects > > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group > > membership > > > > > > cfg=[]; > > cfg.design=design; > > cfg.uvar = 1; > > cfg.ivar = 2; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'indepsamplesF'; > > cfg.correctm = 'fdr'; > > cfg.numrandomization = 180000; > > cfg.alpha = 0.01/7; > > cfg.tail = 1; > > cfg.design = design; > > cfg.channels = myChannels; > > cfg.avgovertime = 'yes'; > > cfg.avgoverfreq = 'yes'; > > cfg.frequency = [1 3]; > > > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, > group4avg); > > > > With these settings, the coputation itself runs fine, but the resulting > > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix > consists > > of only ones). This would mean, that I found significant effects for all > > channels. Is this possible or rather due to an error somewhere in my > script? > > Is it likely, that these are 'real' zeroes or rather very small values, > > close to zero? > > Any hints and suggestions are very welcome, thank you in advance, > > > > Kind regards > > > > Patricia Wollstadt > > > > > > -- > > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail From ekanal at cmu.edu Mon Jan 24 21:26:09 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Mon, 24 Jan 2011 15:26:09 -0500 Subject: [FieldTrip] questions about averaging/clustering tutorial Message-ID: <4233AF54-D71B-423D-A509-F225C92049C1@cmu.edu> Hello Fieldtrippers - Two unrelated questions about the averaging and clustering tutorials: 1) By the end of the averaging routine, there were only ~75 useful trials per condition left, which seems to be quite small to me. I understand that different studies will require different numbers of trials, but I was wondering whether you could go into a little detail as to why you chose to complete the study with (seemingly) so few trials. 2) In the cluster tutorial, you specify "cfg.clusteralpha = 0.05" and "cfg.clustertail = 0". If the tail is double-sided, wouldn't you want to use a cluster alpha of 0.025? Thanks - Elli Kanal From r.vandermeij at donders.ru.nl Tue Jan 25 17:40:02 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 25 Jan 2011 17:40:02 +0100 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper In-Reply-To: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> References: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> Message-ID: <4D3EFCE2.2010209@donders.ru.nl> Hi Shogo, Haven't earned that title yet ;). My apologies for my late reply. > In your 2nd step, I should compute cluster-level-statistics from > random permutation data. > Here, I have an question. > When I define clusters from random permutation data, which should I > define where clusters are the same place (e.g. time, sensor and so on) > as "observed clasters" or should I define newly where clusters are > from random permutation data regardless of the places of "observed > clasters"? The idea is that for every random permutation of data, you calculate your statistics and cluster over them. Then, select the largest of these, whether it occurs at different time-points than your observed clusters or not. The null-hypothesis that your are trying to refute is not of the form "this cluster is significant is bigger than zero", but of the form "the data is interchangeable between conditions". Therefore, you gather 'largest-clusters' from 1000 random combinations of data. If your biggest cluster is bigger than 95% of the biggest clusters (alpha = 0.05, single-sided test), than the data is /not /interchangeable, and thus significantly different between conditions. This is exemplified by /all /clusters that surpass the test based on the /same /permutation-distribution of 'biggest-clusters'. Your data is different between conditions, and all peaks in the mountain-range are representing this (if they surpass the cluster-level test) (my favorite analogy). > I think the latter is right, this is OK? Yes. > > Second, If I have interests in the cluster that has the second or > third... non first largest cluster-level-statistics from the > experimental hypothesis, how should I test these clusters? All clusters are tested against the permutation-distribution of 'biggest-clusters'. Any of the smaller observed-clusters that are still bigger than 95% of your distribution-of-biggest-clusters (alpha = 0.05, single-sided), are part of /*all* /the clusters that /*together *show that the data differs between conditions/. Best, Roemer -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From Patricia.Wollstadt at gmx.de Tue Jan 25 18:08:38 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Tue, 25 Jan 2011 18:08:38 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110124164726.247880@gmx.net> References: <20110124164726.247880@gmx.net> Message-ID: <20110125170838.254600@gmx.net> Dear all, I'm still trying to identify the underlying reason for the issue described below. I ran the analysis in debug mode (I'm using Matlab2008b and the Fieldtrip-release from the 16th of January 2011) and found that the matrix 'resample', that is generated in 'statistics_montecarlo', line 187: resample = resampledesign(cfg, design); doesn't contain actual permutations of my initial design, but rather sorted rowvectors from 1 to 80 (no of subjects). So (since there is no permutation of the units of observation) the 'randstat' that is subsequently calculated for each row of the resample-matrix is always the same. Is this maybe due to my design and my units of observations respectively? I am looking at age-dependent variations in resting-state data, so my UO are 80 subjects, divided into four age groups. The commandline-output of the 'resampledesign'-function is as follows: total number of measurements = 80 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 80 levels number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Is this correct? Shouldn't this read 'repeated measurement in variable 2 over 4 levels' with the number of subjects per group as repeated measurements within a condition? Still I am pretty sure about my design matrix, which contains the indices 1 to 80 (for all subjects) in the first row (this is my cfg.uvar) with the corresponding age groups (1 to 4) in the second row (cfg.ivar, see my previous email below). I use an 'indepsamplesF'-statistic, since I am comparing between four groups of different subjects (averaged over trials). I hope, I got the settings and my design right. Any suggestions, whether this is a problem due to wrong configurations in my script are very welcome. Right now I work around this issue by replacing line 279 in 'statistics_montecarlo': tmpdesign = design(:,resample(i,:)); with: tmpdesign = design(:,randperm(size(design,2))); creating permutations of my design 'by hand'. Is this acceptable or is there anything I'm maybe missing. Thank you very much, kind regards, Patricia -------- Original-Nachricht -------- > Datum: Mon, 24 Jan 2011 17:47:26 +0100 > Von: "Patricia Wollstadt" > An: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] ft_freqstatistics and FDR-correction > Dear Fieldtrip-users, > > I'm currently trying to calculate freqstatistics for four experimental > groups, using the following options: > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > length(subjects{4})]; > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > % 1 to N subjects > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group membership > > > cfg=[]; > cfg.design=design; > cfg.uvar = 1; > cfg.ivar = 2; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; > cfg.correctm = 'fdr'; > cfg.numrandomization = 180000; > cfg.alpha = 0.01/7; > cfg.tail = 1; > cfg.design = design; > cfg.channels = myChannels; > cfg.avgovertime = 'yes'; > cfg.avgoverfreq = 'yes'; > cfg.frequency = [1 3]; > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); > > With these settings, the coputation itself runs fine, but the resulting > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists of > only ones). This would mean, that I found significant effects for all > channels. Is this possible or rather due to an error somewhere in my script? Is > it likely, that these are 'real' zeroes or rather very small values, close > to zero? > Any hints and suggestions are very welcome, thank you in advance, > > Kind regards > > Patricia Wollstadt > > > -- > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de From r.vandermeij at donders.ru.nl Tue Jan 25 17:53:53 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 25 Jan 2011 17:53:53 +0100 Subject: [FieldTrip] singleplotTFR error In-Reply-To: References: <4D32C65B.5020304@donders.ru.nl> Message-ID: <4D3F0021.2060701@donders.ru.nl> Hi Karl, Sorry for my late reply. We are looking for a proper fix for this issue, it occurs in several situations. Any axes that are not monotonously increasing causes a crash in uimagesc, because it cannot determine how to plot the data (if I recall correctly, uimagesc plots multiple copies of the same data when axes are not evenly spaced). For the moment, you can try to hack the frequency axis to conform to the monotonously increasing part/(in most cases a simple round() would do it)/. Or, you can hack it by changing it to a linear index, and then add the axis-labels by hand afterwards /(by using set(gca,'ytick', [index vector], 'yticklabel', string-array of num2str(freq-axis))/. Best, Roemer On 17-01-11 2:51, Karl Doron wrote: > Hello Roemer, > > Here's the cfg's and output from calls to ft_freqanalysis with > method='wavelet' and the subsequent call to ft_singleplotTFR and the > resulting error. The imagesc command will however plot the data at > that > channel imagesc(squeeze(wvpow.powspctrm(strmatch('A177',label),:,:))) > Thanks for any help! > > cfg = []; > > cfg.output = 'pow'; > > cfg.channel = 'MEG'; > > cfg.method = 'wavelet'; > > cfg.foi = 10:2:30; > > cfg.toi = 0.0:0.05:2.75; > > wvpow = ft_freqanalysis(cfg, data_spctrm); > > wvpow = > > label: {246x1 cell} > > dimord: 'chan_freq_time' > > freq: [1x11 double] > > time: [1x56 double] > > powspctrm: [246x11x56 double] > > grad: [1x1 struct] > > cfg: [1x1 struct] > > %Singleplot results > > cfg = []; > > cfg.channel = 'A177'; > > cfg.grad = grad; > > cfg.xlim = [0.6 2.5]; > > cfg.ylim = [10 20]; > > figure; > > ft_singleplotTFR(cfg, wvpow) > > Warning: (one of the) axis are not evenly spaced -> nans cannot > > be maskedout->cfg.masknansissetto'no'; > > > In ft_singleplotTFR at 296 > > ??? Attempted toaccessc(6,1); index outofboundsbecause > > size(c)=[5,37]. > > Error in==>uimageat124 > > ce(j,i) = c(indi(end), indj(end)); > > Error in==>uimagescat46 > > hh = uimage(varargin{:},'CDataMapping','scaled'); > > Error in==>ft_plot_matrixat192 > > h = uimagesc(hdat, vdat, cdat, clim); > > Error in==>ft_singleplotTFRat327 > > ft_plot_matrix(data.(cfg.xparam)(xidc),data.(cfg.yparam)(yidc), > > TFR, 'clim',[zmin,zmax],'tag','cip') > > > > On Sun, Jan 16, 2011 at 2:20 AM, Roemer van der Meij > > wrote: > > Hi Karl, > > Could you give some more information on the errors? Could you also > post your cfg's? That will help in finding and fixing the bug. > What FieldTrip version are you using? > > Best, > Roemer > > > > On 15-1-2011 18:05, Karl Doron wrote: >> Hello, >> >> Has anyone else reported a problem with ft_singleplotTFR and >> output of the new specest module? >> >> multiplotTFR works, but 'interactive' method fails. >> >> It looks like the error occurs when trying to mask NaNs >> >> % masking only possible for evenly spaced axis >> >> if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) >> >> warning('(one of the) axis are not evenly spaced -> nans cannot >> be masked out -> cfg.masknans is set to ''no'';') >> >> cfg.masknans = 'no'; >> >> end >> >> >> >> Thank you, >> karl doron >> UCSB >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > 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 -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 25 20:57:03 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 25 Jan 2011 20:57:03 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110125170838.254600@gmx.net> References: <20110124164726.247880@gmx.net> <20110125170838.254600@gmx.net> Message-ID: <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> Hi Patricia, I don't really understand what is going on, but could you try to specify your design only in a single row (design = design(2,:) in your case), specify cfg.ivar = 1; and cfg=rmfield(cfg,'uvar'), and see how it runs? As such the uvar row is not relevant in an independent samples design. Best, Jan-Mathijs On Jan 25, 2011, at 6:08 PM, Patricia Wollstadt wrote: > Dear all, > > I'm still trying to identify the underlying reason for the issue > described below. I ran the analysis in debug mode (I'm using > Matlab2008b and the Fieldtrip-release from the 16th of January 2011) > and found that the matrix 'resample', that is generated in > 'statistics_montecarlo', line 187: > > resample = resampledesign(cfg, design); > > doesn't contain actual permutations of my initial design, but rather > sorted rowvectors from 1 to 80 (no of subjects). So (since there is > no permutation of the units of observation) the 'randstat' that is > subsequently calculated for each row of the resample-matrix is > always the same. > Is this maybe due to my design and my units of observations > respectively? I am looking at age-dependent variations in resting- > state data, so my UO are 80 subjects, divided into four age groups. > The commandline-output of the 'resampledesign'-function is as follows: > > total number of measurements = 80 > total number of variables = 2 > number of independent variables = 1 > number of unit variables = 1 > number of within-cell variables = 0 > number of control variables = 0 > using a permutation resampling approach > repeated measurement in variable 1 over 80 levels > number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 > 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > 1 1 > > > Is this correct? Shouldn't this read 'repeated measurement in > variable 2 over 4 levels' with the number of subjects per group as > repeated measurements within a condition? Still I am pretty sure > about my design matrix, which contains the indices 1 to 80 (for all > subjects) in the first row (this is my cfg.uvar) with the > corresponding age groups (1 to 4) in the second row (cfg.ivar, see > my previous email below). I use an 'indepsamplesF'-statistic, since > I am comparing between four groups of different subjects (averaged > over trials). > > I hope, I got the settings and my design right. Any suggestions, > whether this is a problem due to wrong configurations in my script > are very welcome. > > Right now I work around this issue by replacing line 279 in > 'statistics_montecarlo': > > tmpdesign = design(:,resample(i,:)); > > with: > > tmpdesign = design(:,randperm(size(design,2))); > > creating permutations of my design 'by hand'. Is this acceptable or > is there anything I'm maybe missing. > > Thank you very much, kind regards, > > Patricia > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 24 Jan 2011 17:47:26 +0100 >> Von: "Patricia Wollstadt" >> An: fieldtrip at donders.ru.nl >> Betreff: [FieldTrip] ft_freqstatistics and FDR-correction > >> Dear Fieldtrip-users, >> >> I'm currently trying to calculate freqstatistics for four >> experimental >> groups, using the following options: >> >> groupSize=[length(subjects{1}) length(subjects{2}) >> length(subjects{3}) >> length(subjects{4})]; >> >> design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; >> % 1 to N subjects >> design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) >> 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> >> group membership >> >> >> cfg=[]; >> cfg.design=design; >> cfg.uvar = 1; >> cfg.ivar = 2; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'indepsamplesF'; >> cfg.correctm = 'fdr'; >> cfg.numrandomization = 180000; >> cfg.alpha = 0.01/7; >> cfg.tail = 1; >> cfg.design = design; >> cfg.channels = myChannels; >> cfg.avgovertime = 'yes'; >> cfg.avgoverfreq = 'yes'; >> cfg.frequency = [1 3]; >> >> stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, >> group4avg); >> >> With these settings, the coputation itself runs fine, but the >> resulting >> 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix >> consists of >> only ones). This would mean, that I found significant effects for all >> channels. Is this possible or rather due to an error somewhere in >> my script? Is >> it likely, that these are 'real' zeroes or rather very small >> values, close >> to zero? >> Any hints and suggestions are very welcome, thank you in advance, >> >> Kind regards >> >> Patricia Wollstadt >> >> >> -- >> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit >> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > _______________________________________________ > 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 batrod at gmail.com Tue Jan 25 21:02:02 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 25 Jan 2011 14:02:02 -0600 Subject: [FieldTrip] Error in correlation analysis with ft_freqstatistics Message-ID: Dear Fieldtrip Users, im actually trying to do a correlation analysis between frequency power and behavioral results. The problem is when i change the design matrix containing the classical independent variables to behavioral scores, as indicate in the walktrough section of the fieldtrip website : cfg.design = [ .1 .2 .4 .3 etc...]; cfg.ivar = 1; Then, Matlab gives me the following errors: ??? Error using ==> statfun_indepsamplesF at 55 Invalid specification of the independent variable in the design array. Error in ==> statistics_montecarlo at 241 [statobs, cfg] = statfun(cfg, dat, design); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 127 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Does anyone have an example of a script for such analysis that works? Thanks, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 25 21:16:38 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 25 Jan 2011 21:16:38 +0100 Subject: [FieldTrip] Error in correlation analysis with ft_freqstatistics In-Reply-To: References: Message-ID: <196CB43E-E377-449F-ABB4-BA02DED6BF0A@donders.ru.nl> Dear Rodolphe, The trick here is not to specify cfg.statistic = 'indepsamplesF'; You need to specify cfg.statistic = 'yourownfunction', and create an m- file 'statfun_yourownfunction.m' that computes a correlation. That could look like function s = statfun_yourownfunction(cfg, dat, design) % mean subtract mdat = mean(dat,2); dat = dat - mdat(:,ones(1,size(dat,2))); mdesign = mean(design); design = design - mean(design); % covariance covdat = dat*design'; % variance vdat = sum(dat.^2,2); vdes = sum(design.^2); % correlation s.stat = covdat./sqrt(vdat.*vdes); This is just typed down in half a minute so don't take it for granted. Best, Jan-Mathijs On Jan 25, 2011, at 9:02 PM, Rodolphe Nenert wrote: > Dear Fieldtrip Users, > > im actually trying to do a correlation analysis between frequency > power and behavioral results. > The problem is when i change the design matrix containing the > classical independent variables to behavioral scores, as indicate in > the walktrough section of the fieldtrip website : > > cfg.design = [ .1 .2 .4 .3 etc...]; > cfg.ivar = 1; > > Then, Matlab gives me the following errors: > > ??? Error using ==> statfun_indepsamplesF at 55 > Invalid specification of the independent variable in the design array. > > Error in ==> statistics_montecarlo at 241 > [statobs, cfg] = statfun(cfg, dat, design); > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, > 'issource',issource); > > Error in ==> ft_freqstatistics at 127 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Does anyone have an example of a script for such analysis that works? > > Thanks, > > Rodolphe. > _______________________________________________ > 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 shhirano at npsych.med.kyushu-u.ac.jp Wed Jan 26 00:45:28 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Wed, 26 Jan 2011 08:45:28 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: <10E711DB-D7B4-4E82-AEEB-310C773BBD60@npsych.med.kyushu-u.ac.jp> Dear Roemer I really appreciate your very clear-cut answer. I'm going to test my data. Thank you very much for your kindness! Best regards, Shogo -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From michael.wibral at web.de Wed Jan 26 10:08:51 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 26 Jan 2011 10:08:51 +0100 (CET) Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> References: <20110124164726.247880@gmx.net> <20110125170838.254600@gmx.net>, <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> Message-ID: <1367146600.2032784.1296032931966.JavaMail.fmail@mwmweb056> Hi Patricia, I also would have thought your design to be correct. Maybe the unneccessary specification of the uvar screws thinsg up?? However, you really do not have any repeated measures in your design - here the output of FT is correct. I interpret it in the following way: You specified cfg.uvar - indicating to FT the possibility that this might be a repeated measures design. FT identified the units of observation as being 80 (correct), and then checked how many repeated measures you ran in each UO and found just 1 - which is also correct. I agree that naming the units of observation (UO) as 'levels' of the UO variable is a bit odd, should rather be 'units of observation'. The concept of repeated measures is also very often misunderstood: in repated measures you do not actually repeat anything, rather you perform different measurements (treatments) WITHIN a unit of observation - so a repated measures design is a within UO design. Your subjects just have one age, so there are no different treatments (levels of the indep variable) per subjects and, hence, no 'repeated measures'. Hope this clarifies terminology for further discussion. Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 25, 2011 8:57:03 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction >Hi Patricia, > >I don't really understand what is going on, but could you try to >specify your design only in a single row (design = design(2,:) in your >case), specify cfg.ivar = 1; and cfg=rmfield(cfg,'uvar'), and see how >it runs? As such the uvar row is not relevant in an independent >samples design. > >Best, > >Jan-Mathijs > > > >On Jan 25, 2011, at 6:08 PM, Patricia Wollstadt wrote: > >> Dear all, >> >> I'm still trying to identify the underlying reason for the issue >> described below. I ran the analysis in debug mode (I'm using >> Matlab2008b and the Fieldtrip-release from the 16th of January 2011) >> and found that the matrix 'resample', that is generated in >> 'statistics_montecarlo', line 187: >> >> resample = resampledesign(cfg, design); >> >> doesn't contain actual permutations of my initial design, but rather >> sorted rowvectors from 1 to 80 (no of subjects). So (since there is >> no permutation of the units of observation) the 'randstat' that is >> subsequently calculated for each row of the resample-matrix is >> always the same. >> Is this maybe due to my design and my units of observations >> respectively? I am looking at age-dependent variations in resting- >> state data, so my UO are 80 subjects, divided into four age groups. >> The commandline-output of the 'resampledesign'-function is as follows: >> >> total number of measurements = 80 >> total number of variables = 2 >> number of independent variables = 1 >> number of unit variables = 1 >> number of within-cell variables = 0 >> number of control variables = 0 >> using a permutation resampling approach >> repeated measurement in variable 1 over 80 levels >> number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 >> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >> 1 1 >> >> >> Is this correct? Shouldn't this read 'repeated measurement in >> variable 2 over 4 levels' with the number of subjects per group as >> repeated measurements within a condition? Still I am pretty sure >> about my design matrix, which contains the indices 1 to 80 (for all >> subjects) in the first row (this is my cfg.uvar) with the >> corresponding age groups (1 to 4) in the second row (cfg.ivar, see >> my previous email below). I use an 'indepsamplesF'-statistic, since >> I am comparing between four groups of different subjects (averaged >> over trials). >> >> I hope, I got the settings and my design right. Any suggestions, >> whether this is a problem due to wrong configurations in my script >> are very welcome. >> >> Right now I work around this issue by replacing line 279 in >> 'statistics_montecarlo': >> >> tmpdesign = design(:,resample(i,:)); >> >> with: >> >> tmpdesign = design(:,randperm(size(design,2))); >> >> creating permutations of my design 'by hand'. Is this acceptable or >> is there anything I'm maybe missing. >> >> Thank you very much, kind regards, >> >> Patricia >> >> >> >> >> -------- Original-Nachricht -------- >>> Datum: Mon, 24 Jan 2011 17:47:26 +0100 >>> Von: "Patricia Wollstadt" >>> An: fieldtrip at donders.ru.nl >>> Betreff: [FieldTrip] ft_freqstatistics and FDR-correction >> >>> Dear Fieldtrip-users, >>> >>> I'm currently trying to calculate freqstatistics for four >>> experimental >>> groups, using the following options: >>> >>> groupSize=[length(subjects{1}) length(subjects{2}) >>> length(subjects{3}) >>> length(subjects{4})]; >>> >>> design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; >>> % 1 to N subjects >>> design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) >>> 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> >>> group membership >>> >>> >>> cfg=[]; >>> cfg.design=design; >>> cfg.uvar = 1; >>> cfg.ivar = 2; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'indepsamplesF'; >>> cfg.correctm = 'fdr'; >>> cfg.numrandomization = 180000; >>> cfg.alpha = 0.01/7; >>> cfg.tail = 1; >>> cfg.design = design; >>> cfg.channels = myChannels; >>> cfg.avgovertime = 'yes'; >>> cfg.avgoverfreq = 'yes'; >>> cfg.frequency = [1 3]; >>> >>> stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, >>> group4avg); >>> >>> With these settings, the coputation itself runs fine, but the >>> resulting >>> 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix >>> consists of >>> only ones). This would mean, that I found significant effects for all >>> channels. Is this possible or rather due to an error somewhere in >>> my script? Is >>> it likely, that these are 'real' zeroes or rather very small >>> values, close >>> to zero? >>> Any hints and suggestions are very welcome, thank you in advance, >>> >>> Kind regards >>> >>> Patricia Wollstadt >>> >>> >>> -- >>> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit >>> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir >> belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de >> _______________________________________________ >> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Wed Jan 26 11:45:23 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 26 Jan 2011 11:45:23 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: <9B00A155-4D0A-493D-A617-2F9E90439E35@donders.ru.nl> Dear Michael and the rest of the world, I updated the documentation page on artifact rejection with a more explicit statement that specifying the padding only works with data on disk (and removed the second input arguments in the code examples). I'll discuss the other issue with the rest soon. Best JM On Jan 24, 2011, at 6:27 PM, Michael Wibral wrote: > Hi Jan-Mathijs, > > this is basically what we do at the moment, i.e. fooling > artifcat_zvalue by removing the one field it complains about amnd > using rejetartefact only at the very last. > See the attched code - I really do not want to post this code on the > tutorial website as I am not fully sure what I am doing :-). > > Michael > > %% CODE > ft_defaults; > Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/ > DATASETS/'; > Design={ > 'DMG13_NewMooney_20110120_0', [2 3], > 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; > } > > > for ss=1:size(Design,1) % over subjects > for cc=1:length(Design{ss,4}) % over conditions > for ff=1:length(Design{ss,2}) % over .ds datasets/runs > > FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), > '.ds') > FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) > % core data reading > cfg=[]; > cfg.dataset=FullFileName; > cfg.headerformat = 'ctf_ds'; % for you to check whether still > necessary > ctf.dataformat = 'ctf_ds'; > cfg.cond=Design{ss,4}(cc) > cfg.continuous='yes'; > > cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '- > MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? > cfg.trialfun=Design{ss,3}; > cfg=ft_definetrial(cfg); > cfg.trl(end,:)=[]; > trl=cfg.trl; % keep track of the trials > > padding=0.75 % 750 ms > > > %%%%%%%%% artifact rejection section > %%% jump > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MEG'; > cfg.artfctdef.zvalue.cutoff = 35; > cfg.artfctdef.zvalue.trlpadding = 0.5*padding; > cfg.artfctdef.zvalue.artpadding = 0.5*padding; > cfg.artfctdef.zvalue.fltpadding = 0; > > % algorithmic parameters > cfg.artfctdef.zvalue.medianfilter = 'yes'; > cfg.artfctdef.zvalue.medianfiltord = 9; % in samples > cfg.artfctdef.zvalue.absdiff = 'yes'; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'jump'; > [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); > % cfg.artfctdef.jump.artifact = artifact_jump; > % cfg = ft_rejectartifact(cfg); > > %%% muscle > cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % > remove field from structure otherwise this won't run ?? > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MEG'; > cfg.artfctdef.zvalue.cutoff = 15; > cfg.artfctdef.zvalue.trlpadding = 0.1; > cfg.artfctdef.zvalue.fltpadding = 0.1; > cfg.artfctdef.zvalue.artpadding = 0.1; > > % algorithmic parameters > cfg.artfctdef.zvalue.bpfilter = 'yes'; > cfg.artfctdef.zvalue.bpfreq = [110 140]; > cfg.artfctdef.zvalue.bpfiltord = 6; > cfg.artfctdef.zvalue.bpfilttype = 'but'; > cfg.artfctdef.zvalue.hilbert = 'yes'; > cfg.artfctdef.zvalue.boxcar = 0.2; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'muscle'; > [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); > cfg.artfctdef.muscle.artifact = artifact_muscle; > cfg = ft_rejectartifact(cfg); > > %%% EOG > > > cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MRT41'; > cfg.artfctdef.zvalue.cutoff = 10; > cfg.artfctdef.zvalue.trlpadding = 0.5; > cfg.artfctdef.zvalue.artpadding = 0.1; > cfg.artfctdef.zvalue.fltpadding = 0.1; > % algorithmic parameters > cfg.artfctdef.zvalue.bpfilter = 'yes'; > cfg.artfctdef.zvalue.bpfilttype = 'but'; > cfg.artfctdef.zvalue.bpfreq = [1 15]; > cfg.artfctdef.zvalue.bpfiltord = 3; > cfg.artfctdef.zvalue.hilbert = 'yes'; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'EOG'; > [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); > > cfg.trl=trl; > cfg.artfctdef.reject = 'complete'; % this rejects complete trials, > use 'partial' if you want to do partial artifact rejection > % collect all the info about the artifacts that were found > cfg.artfctdef.eog.artifact =artifact_EOG; > cfg.artfctdef.jump.artifact = artifact_jump; > cfg.artfctdef.muscle.artifact = artifact_muscle; > cfg = ft_rejectartifact(cfg); > > Data_no_artifacts=ft_preprocessing(cfg); > > % some additional filtering for DC removal and detrending > cfg=[]; > cfg.detrend='yes' > cfg.hpfilt='yes' > cfg.hpfreq=1; > TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); > clear Data_no_artifacts; > > end > ... > ... > end > end > > > > > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 24, 2011 4:41:09 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Hmmm, apparently this approach needs to be ironed out a bit (also >> from >> our side). For now, I'd say that it should work if you keep per type >> of artifact the artifact field in the output configuration, and just >> concatenate these prior to calling ft_rejectartifact. I will moreover >> CC this e-mail to the people involved in creating the first version >> of >> the renewed tutorial, and will bring up the issue in this week's >> FieldTrip developers meeting. >> >> Best, >> >> JM >> >> On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: >> >>> Hi Jan mathijs, >>> >>> I tried to get option1 running, stumbled over the following little >>> obstacle however: >>> >>> I tried to keep one cfg throughout the steps ft_definetrial; >>> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >>> tracking of where artfecats were found), ft_preprocessing (cutting >>> out the clean trials from the cont. data). IMHO this used to be the >>> way most people did this kind of procesing a while ago. >>> >>> However, I can't get ft_artifact_zvalue to run with different >>> settings one after another for jump/musvle/EOG. FT claims after the >>> first run of ft_artifact_zvalue that the z-value thing has been >>> performed and refuse to detect other artifacts with new settings. >>> >>>> From here I only see two alternative: specifying a really lengthy >>>> cfg every time a new (also struggling with the cfg.dataset versus >>>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>>> things myself or manually removing the cfg.artdef.zvalue.artifct >>>> field to get the z-value based detection to run again. This seems a >>>> bit odd to me. >>> >>> Any suggestions? >>> >>> Michael >>> >>> >>> >>> >>> -----Ursprüngliche Nachricht----- >>> Von: "jan-mathijs schoffelen" >>> Gesendet: Jan 24, 2011 12:12:57 PM >>> An: "Email discussion list for the FieldTrip project" >>> >>> Betreff: Re: [FieldTrip] more on artfifact rejection >>> >>>> Dear Michael, >>>> >>>> I agree. The tutorial should be 'de'-confused by sketching option >>>> 1, >>>> and another one should be describing option 2, or the original >>>> should >>>> be clearly making the distinction. >>>> >>>> Best, >>>> >>>> JM >>>> >>>> >>>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>>> >>>>> Hi Jan-Mathijs, >>>>> >>>>> I am a bit unsure how to proceed: >>>>> >>>>> (1) sketch the artifact correction way like this >>>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>>> ft_preprocessing >>>>> OR >>>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>>> ft_preprocessing. >>>>> >>>>> I think I should go for option (1) as this seems to be the >>>>> standard >>>>> use on continuous data. Sometime in the futrure one should then >>>>> add >>>>> a tutorial for those that have data in trials to start with. >>>>> >>>>> Michael >>>>> >>>>> -----Ursprüngliche Nachricht----- >>>>> Von: "jan-mathijs schoffelen" >>>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>>> An: "Email discussion list for the FieldTrip project" >>>>> >>>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>>> >>>>>> Dear Michael, >>>>>> >>>>>> Yes, I agree with you here as well. In principle the >>>>>> ft_artifact_zvalue supports data as a second input argument, >>>>>> but in >>>>>> such case the different types of padding in the cfg do not make >>>>>> sense. >>>>>> I would indeed remove the second input arguments in the example >>>>>> code >>>>>> snippets. Could I ask you to take care of that? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> JM >>>>>> >>>>>> >>>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>>> >>>>>>> Deal Fieldtrip users, >>>>>>> >>>>>>> there is something else I do not understand in the tutorial: if >>>>>>> you >>>>>>> read in the data in trials (as it is done) how can you do >>>>>>> padding >>>>>>> later as it is suggested. I tried to run the example code on teh >>>>>>> website reading in the data such that it contains trials. If I >>>>>>> then >>>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>>> must >>>>>>> be positive or logical ... values', indicating that the code >>>>>>> tries >>>>>>> to access data that aren't there. If I set the padding to zero >>>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>>> should actually run these things on continuous data (contrary to >>>>>>> what is indicated in the tutorial)? >>>>>>> >>>>>>> Michael >>>>>>> >>>>>> Wibral.vcf>_______________________________________________ >>>>>>> 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 >>>>> >>>> Wibral.vcf>_______________________________________________ >>>>> 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 tom_campbell75 at hotmail.com Thu Jan 27 00:26:27 2011 From: tom_campbell75 at hotmail.com (Tom Campbell) Date: Wed, 26 Jan 2011 23:26:27 +0000 Subject: [FieldTrip] depsamplesF Message-ID: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. -------------- next part -------------- An HTML attachment was scrubbed... URL: From olga at graphicmind.info Thu Jan 27 04:16:51 2011 From: olga at graphicmind.info (Olga Sysoeva) Date: Thu, 27 Jan 2011 06:16:51 +0300 Subject: [FieldTrip] depsamplesF In-Reply-To: References: Message-ID: <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: > Dear Eric Maris, Robert Oostenveld and colleagues, > > I write with some queries with reference to your previous > correspondence on the Fieldtrip listserv and would very much > appreciate if you could please answer them. > > I am trying to use Fieldtrip to analyse timelocked ERP data from > what is a 16(participant: [1:16]) X2(Background: congruent, > incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to > runing well treating this as a 16(participant: [1:16]) X4(Visual > stimulus: animal-congruent background, animal-incongruent > background, vehicle-congruent, vehicle-incongruent )design with 4 > conditions, though I haven't looked at the results of the tests yet. > If I then run cluster analyses of differences of theoretical > interest via depsamplest, please how would I bonferroni correct? I > am interested in what clusters exist in the background and stimulus > main effects and their background X stimulus interaction. Please is > this possible in fieldtrip to use depsamplesF to work with a > Participant X "2-way" design? > > Best regards, > > Tom Campbell. > > > > > _______________________________________________ > 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 tom_campbell75 at hotmail.com Thu Jan 27 06:02:29 2011 From: tom_campbell75 at hotmail.com (Tom Campbell) Date: Thu, 27 Jan 2011 05:02:29 +0000 Subject: [FieldTrip] depsamplesF In-Reply-To: <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> References: , <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Message-ID: Thank you very much for this helpful advice Olga. That would have also been my impression until I found this discussion between Maya Zuckerman and Eric Maris: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003335.html http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html , which I may have misunderstood. I can see from the list that people are interested in using depsampleF to investigate interactions between two independent variables (e.g., background: I,II x stimulus: a,b) in experiments with multiple participants. I can also see a several people have had problems with this. Given for datasets I_a, I_b, II_a, II_b I'd like to do something like: cfg.design =????; ... cfg.statistic ='depsamplesF'; ... [stat] = ft_timelockstatistics(cfg, I_a, I_b, II_a, II_b); to find the tests of of main effect clusters for each factor and interaction clusters. How to specify up cfg.design could be one of the problems, as could be what other cfg parameters need to be specified. I may be barking up completely the wrong tree. Assuming the interaction is significant, there are 4 differences that would be of theoretical interest: I_a vs I_b, II_a vs II_b,I_a vs II_a,I_b vs II_b). For instance, a "classical" interaction might exhibit the abolition of significance of an effect ab seen at I at level II of that factor. So, if I understand the Zuckerman-Maris dialogue, if I used the permutation test to test such I_a vd II_b differences as in the tutorial: cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; ... [I_avsb_stat] = ft_timelockstatistics(cfg, I_a, I_b); [II_avsb_stat] = ft_timelockstatistics(cfg, II_a, II_b); [IvsII_a_stat] = ft_timelockstatistics(cfg, I_a, II_a); [IvsII_b_stat] = ft_timelockstatistics(cfg, I_a, II_b); ,I may have to either do some bonferonni correction: -at the cluster level (cluster.alpha) -or at the level at which each t-test can be included in a cluster (cfg.alpha). Please would you verify which, if at all? If I am testing 4 such differences with 4 permutation tests then if the bonferroni correction is to be at the cluster level, please should the correction depend upon the number of clusters as well as the number of such differences tested? Please, I look forward to any clarifications. With best regards, Tom Campbell. From: olga at graphicmind.info To: tom_campbell75 at hotmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] depsamplesF Date: Thu, 27 Jan 2011 06:16:51 +0300 Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. _______________________________________________ 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 lumatobu2 at hotmail.com Fri Jan 28 04:52:09 2011 From: lumatobu2 at hotmail.com (Ludwing Torres) Date: Thu, 27 Jan 2011 22:52:09 -0500 Subject: [FieldTrip] help with inverse computing Message-ID: Hello, I have the next script that computes the forward model of the brain activity: clear all close all clc % load electrodes positions elec = []; load electrodes1020 % array of electrode positions i_elec=[4 6 18 19 21 23 25 27 28 31 33 35 37 40 41 43 45 47 49 50 53 55 57 59 62 63 65 67 69 71 72 84 86]; % load concentric spheres or bem load standard_vol.mat % vol.cond = [1 1/80 1]; % load spheric_vol_162.mat %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.vol = vol; % cfg.elec = elec; cfg.elec.pnt = elec.pnt(i_elec,1:3); cfg.elec.label = elec.label(i_elec); fs=250; ns=250; cfg.fsample = fs; time = (1:ns)/fs; signal1 = 1*sin(2*time*6*pi); signal2 = 1*cos(2*time*12*pi); signal3 = 1*cos(2*time*8*pi); % head model [vols, sens, cfg] = prepare_headmodel(cfg, []); dipin=[]; [x,y,z]=meshgrid(linspace(-40,40,4), linspace(-40,40,4), linspace(0,30,3) ); dipin.pos=[x(:) y(:) z(:)]; mom_t=zeros(3*length(dipin.pos),ns); x_orig=mom_t; n_orig=mom_t; n_orig(20,:)=signal1; n_orig(80,:)=signal2; n_orig(40,:)=signal3; a11=1.2; b11=0.05; M11=3*length(dipin.pos); A = a11*diag(ones(M11,1)) + b11*(diag(ones(M11-1,1),1) + diag(ones(M11-1,1),-1)); b12=0; b13=0; c11=-0.9; for b=1:ns, if b==1, x_orig(:,b)=n_orig(:,b); end if b==2, x_orig(:,b)=A*x_orig(:,b-1)+b12*x_orig(:,b-1).^2-b13*x_orig(:,b-1).^3+n_orig(:,b); end if b>2, x_orig(:,b)=A*x_orig(:,b-1)+b12*x_orig(:,b-1).^2+b13*x_orig(:,b-1).^3+c11*x_orig(:,b-2)+n_orig(:,b); end end C=compute_leadfield(dipin.pos, sens, vols); dat=C*x_orig; now I have to compute the inverse model, that is, I have to obtain the x_orig data, knowing only the data stored in dat and C. For that, I made the next script (After runing the previous) In which I use different functions of FieldTrip to recover the x data: [vol1,sens1]=prepare_vol_sens(vol, sens); inside=inside_vol(dipin.pos,vol1); %After that I get 48 dipoles inside and 0 outside dipin.outside=[]; dipin.inside=1:48; %Inverse computing using MNE dipout=minimumnormestimate(dipin,sens1,vol1,dat); % I store the dipole moments obtained as a matrix Xres=[]; for ii=1:48 Xres=[Xres;dipout.mom{ii}]; end % I compute a relative error between the original x and the obtained x to compare error1=norm(Xres-x_orig,'fro')/norm(x_orig,'fro') %Using Residual variance [dipout2] = residualvariance(dipin, sens1, vol1, dat); Xres2=[]; for ii=1:48 Xres2=[Xres2;dipout2.mom{ii}]; end error2=norm(Xres2-x_orig,'fro')/norm(x_orig,'fro') %Using dipole fitting [dipout4] = dipole_fit(dipin, sens1, vol1, dat) error4=norm(dipout4.mom-x_orig,'fro')/norm(x_orig,'fro') The error obtained using residual variance is very different to the error of the two other methods. Besides, I get a very big error (92%) with the other two methods. I don't know if I'm doing something wrong, please If anyone could help me, I could pay you. Thanks C=compute_leadfield(dipin.pos, sens, vols); dat=C*x_orig; -------------- next part -------------- An HTML attachment was scrubbed... URL: From TAVABIK at email.chop.edu Fri Jan 28 06:06:41 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 28 Jan 2011 00:06:41 -0500 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054>, , <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: Greetings - this has been an informative discussion. My question remains is , what is the consensus on an approach for automatic artifact rejection with trial (CTF) data? E.g., could one use the artifact rejection section of Michael's code without any padding? I have not found any tutorials or suggestions on how to use the artifact rejection tools on trial data...have I missed something. -Kambiz ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ 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, January 24, 2011 12:27 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] more on artfifact rejection Hi Jan-Mathijs, this is basically what we do at the moment, i.e. fooling artifcat_zvalue by removing the one field it complains about amnd using rejetartefact only at the very last. See the attched code - I really do not want to post this code on the tutorial website as I am not fully sure what I am doing :-). Michael %% CODE ft_defaults; Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/DATASETS/'; Design={ 'DMG13_NewMooney_20110120_0', [2 3], 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; } for ss=1:size(Design,1) % over subjects for cc=1:length(Design{ss,4}) % over conditions for ff=1:length(Design{ss,2}) % over .ds datasets/runs FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), '.ds') FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) % core data reading cfg=[]; cfg.dataset=FullFileName; cfg.headerformat = 'ctf_ds'; % for you to check whether still necessary ctf.dataformat = 'ctf_ds'; cfg.cond=Design{ss,4}(cc) cfg.continuous='yes'; cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? cfg.trialfun=Design{ss,3}; cfg=ft_definetrial(cfg); cfg.trl(end,:)=[]; trl=cfg.trl; % keep track of the trials padding=0.75 % 750 ms %%%%%%%%% artifact rejection section %%% jump % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 35; cfg.artfctdef.zvalue.trlpadding = 0.5*padding; cfg.artfctdef.zvalue.artpadding = 0.5*padding; cfg.artfctdef.zvalue.fltpadding = 0; % algorithmic parameters cfg.artfctdef.zvalue.medianfilter = 'yes'; cfg.artfctdef.zvalue.medianfiltord = 9; % in samples cfg.artfctdef.zvalue.absdiff = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'jump'; [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); % cfg.artfctdef.jump.artifact = artifact_jump; % cfg = ft_rejectartifact(cfg); %%% muscle cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % remove field from structure otherwise this won't run ?? % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 15; cfg.artfctdef.zvalue.trlpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; cfg.artfctdef.zvalue.artpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfreq = [110 140]; cfg.artfctdef.zvalue.bpfiltord = 6; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.boxcar = 0.2; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'muscle'; [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); %%% EOG cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % cutoff and padding cfg.artfctdef.zvalue.channel = 'MRT41'; cfg.artfctdef.zvalue.cutoff = 10; cfg.artfctdef.zvalue.trlpadding = 0.5; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 3; cfg.artfctdef.zvalue.hilbert = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'EOG'; [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); cfg.trl=trl; cfg.artfctdef.reject = 'complete'; % this rejects complete trials, use 'partial' if you want to do partial artifact rejection % collect all the info about the artifacts that were found cfg.artfctdef.eog.artifact =artifact_EOG; cfg.artfctdef.jump.artifact = artifact_jump; cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); Data_no_artifacts=ft_preprocessing(cfg); % some additional filtering for DC removal and detrending cfg=[]; cfg.detrend='yes' cfg.hpfilt='yes' cfg.hpfreq=1; TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); clear Data_no_artifacts; end ... ... end end -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 4:41:09 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Hmmm, apparently this approach needs to be ironed out a bit (also from >our side). For now, I'd say that it should work if you keep per type >of artifact the artifact field in the output configuration, and just >concatenate these prior to calling ft_rejectartifact. I will moreover >CC this e-mail to the people involved in creating the first version of >the renewed tutorial, and will bring up the issue in this week's >FieldTrip developers meeting. > >Best, > >JM > >On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > >> Hi Jan mathijs, >> >> I tried to get option1 running, stumbled over the following little >> obstacle however: >> >> I tried to keep one cfg throughout the steps ft_definetrial; >> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >> tracking of where artfecats were found), ft_preprocessing (cutting >> out the clean trials from the cont. data). IMHO this used to be the >> way most people did this kind of procesing a while ago. >> >> However, I can't get ft_artifact_zvalue to run with different >> settings one after another for jump/musvle/EOG. FT claims after the >> first run of ft_artifact_zvalue that the z-value thing has been >> performed and refuse to detect other artifacts with new settings. >> >>> From here I only see two alternative: specifying a really lengthy >>> cfg every time a new (also struggling with the cfg.dataset versus >>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>> things myself or manually removing the cfg.artdef.zvalue.artifct >>> field to get the z-value based detection to run again. This seems a >>> bit odd to me. >> >> Any suggestions? >> >> Michael >> >> >> >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 24, 2011 12:12:57 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> I agree. The tutorial should be 'de'-confused by sketching option 1, >>> and another one should be describing option 2, or the original should >>> be clearly making the distinction. >>> >>> Best, >>> >>> JM >>> >>> >>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>> >>>> Hi Jan-Mathijs, >>>> >>>> I am a bit unsure how to proceed: >>>> >>>> (1) sketch the artifact correction way like this >>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>> ft_preprocessing >>>> OR >>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>> ft_preprocessing. >>>> >>>> I think I should go for option (1) as this seems to be the standard >>>> use on continuous data. Sometime in the futrure one should then add >>>> a tutorial for those that have data in trials to start with. >>>> >>>> Michael >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: "jan-mathijs schoffelen" >>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>> An: "Email discussion list for the FieldTrip project" >>>> >>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>> >>>>> Dear Michael, >>>>> >>>>> Yes, I agree with you here as well. In principle the >>>>> ft_artifact_zvalue supports data as a second input argument, but in >>>>> such case the different types of padding in the cfg do not make >>>>> sense. >>>>> I would indeed remove the second input arguments in the example >>>>> code >>>>> snippets. Could I ask you to take care of that? >>>>> >>>>> Thanks, >>>>> >>>>> JM >>>>> >>>>> >>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>> >>>>>> Deal Fieldtrip users, >>>>>> >>>>>> there is something else I do not understand in the tutorial: if >>>>>> you >>>>>> read in the data in trials (as it is done) how can you do padding >>>>>> later as it is suggested. I tried to run the example code on teh >>>>>> website reading in the data such that it contains trials. If I >>>>>> then >>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>> must >>>>>> be positive or logical ... values', indicating that the code tries >>>>>> to access data that aren't there. If I set the padding to zero >>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>> should actually run these things on continuous data (contrary to >>>>>> what is indicated in the tutorial)? >>>>>> >>>>>> Michael >>>>>> >>>>> Wibral.vcf>_______________________________________________ >>>>>> 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 e.maris at donders.ru.nl Fri Jan 28 10:43:42 2011 From: e.maris at donders.ru.nl (Eric Maris) Date: Fri, 28 Jan 2011 10:43:42 +0100 Subject: [FieldTrip] depsamplesF In-Reply-To: References: , <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Message-ID: <001001cbbecf$dc470260$94d50720$@maris@donders.ru.nl> Hi Tom, To test main and interaction effects in your 2x2 within subjects design, you have to perform 3 tests, each using the statfun desamplesT. Say you have the output of ft_timelockanalysis for all four conditions: tlout_Ia, tlout_Ib, tlout_IIa, tlout_IIb. Your then proceed as follows: 1. Main effect of I versus II: calculate the mean of tlout_Ia.avg and tlout_Ib.avg and put this is a a new struct variable tlout_I, which has the same fields as tlout_Ia and tlout_Ib. Do the same with tlout_IIa.avg and tlout_IIb.avg and make a new struct variable tlout_II. Then run ft_timelockstatistics with input arguments tlout_I and tlout_II. With this analysis you will test the main effect of I-versus-II. 2. In the same way, you now test the main effect of a versus b. In your calculations, the roles of (I,II) and (a,b) are now reversed. 3. Interaction of I-vs-II and a-vs-b. Calculate the differences (tlout_Ia.avg-tlout_Ib.avg) and (tlout_IIa.avg-tlout_IIb.avg), put them in output structures and statistically compare them using ft_timelockstatistics. With this analysis, you test the interaction of I-vs-II and a-vs-b. There is no need for Bonferroni correction or an adjustment of cfg.clusteralpha (which does not affect the false alarm rate anyhow) and cfg.alpha. Best, Eric Mari Thank you very much for this helpful advice Olga. That would have also been my impression until I found this discussion between Maya Zuckerman and Eric Maris: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003335.html http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html , which I may have misunderstood. I can see from the list that people are interested in using depsampleF to investigate interactions between two independent variables (e.g., background: I,II x stimulus: a,b) in experiments with multiple participants. I can also see a several people have had problems with this. Given for datasets I_a, I_b, II_a, II_b I'd like to do something like: cfg.design =????; ... cfg.statistic ='depsamplesF'; ... [stat] = ft_timelockstatistics(cfg, I_a, I_b, II_a, II_b); to find the tests of of main effect clusters for each factor and interaction clusters. How to specify up cfg.design could be one of the problems, as could be what other cfg parameters need to be specified. I may be barking up completely the wrong tree. Assuming the interaction is significant, there are 4 differences that would be of theoretical interest: I_a vs I_b, II_a vs II_b,I_a vs II_a,I_b vs II_b). For instance, a "classical" interaction might exhibit the abolition of significance of an effect ab seen at I at level II of that factor. So, if I understand the Zuckerman-Maris dialogue, if I used the permutation test to test such I_a vd II_b differences as in the tutorial: cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; ... [I_avsb_stat] = ft_timelockstatistics(cfg, I_a, I_b); [II_avsb_stat] = ft_timelockstatistics(cfg, II_a, II_b); [IvsII_a_stat] = ft_timelockstatistics(cfg, I_a, II_a); [IvsII_b_stat] = ft_timelockstatistics(cfg, I_a, II_b); ,I may have to either do some bonferonni correction: -at the cluster level (cluster.alpha) -or at the level at which each t-test can be included in a cluster (cfg.alpha). Please would you verify which, if at all? If I am testing 4 such differences with 4 permutation tests then if the bonferroni correction is to be at the cluster level, please should the correction depend upon the number of clusters as well as the number of such differences tested? Please, I look forward to any clarifications. With best regards, Tom Campbell. _____ From: olga at graphicmind.info To: tom_campbell75 at hotmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] depsamplesF Date: Thu, 27 Jan 2011 06:16:51 +0300 Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. _______________________________________________ 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 hanneke.meeren at uvt.nl Fri Jan 28 13:03:34 2011 From: hanneke.meeren at uvt.nl (Meeren.H.K.M. ) Date: Fri, 28 Jan 2011 13:03:34 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha Message-ID: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> Dear Fieldtrippers, I am relatively new to fieldtrip, and just starting to make some serious use of the cluster-based permutation routines, and I would just like to (double)check something before I continu. I use ft_timelockstatistics with the following configuration structure: cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; etc. >From my understanding of the tutorial the "cfg.clusteralpha" stands for the alpha-value used for the initial test-statistic (in my case a paired t-test) for thresholding the data, and that the "cfg.alpha" field contains the alpha-value for the second step, i.e. selecting clusters after the permutation tests. However, the naming of the parameters seems rather contraintuitive to me. I would have expected it to be the other way around, i.e "cfg.clusteralpha" for my clusters (second step), and not the initial t-test. Could anyone confirm (or deny) the way it is written in the tutorial? Thanks a lot, Hanneke Meeren ---------------------------------- Hanneke K.M. Meeren, PhD. Researcher and Lecturer Medical Psychology and Cognitive Neuroscience Tilburg University P.O. Box 90153 5000 LE Tilburg The Netherlands email: hanneke.meeren at uvt.nl From r.oostenveld at donders.ru.nl Fri Jan 28 13:43:06 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 28 Jan 2011 13:43:06 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> Dear Kambiz Although other people's preferences might differ, I would suggest that you use visual inspection to detect your artifacts. For trial-based data you cannot apply filter padding. The consequence is that the automatic artifact detection routine implemented in fieldtrip is likely to suffer from false alarms at the edges of your trials, and reduced sensitivity away from the edges. Visual detection of artifacts can be done using ft_rejectvisual (check out the three options it has), and using ft_databrowser. best regards, Robert On 28 Jan 2011, at 6:06, Tavabi, Kambiz wrote: > Greetings - this has been an informative discussion. My question remains is , what is the consensus on an approach for automatic artifact rejection with trial (CTF) data? E.g., could one use the artifact rejection section of Michael's code without any padding? I have not found any tutorials or suggestions on how to use the artifact rejection tools on trial data...have I missed something. > -Kambiz From e.maris at donders.ru.nl Fri Jan 28 14:05:07 2011 From: e.maris at donders.ru.nl (Eric Maris) Date: Fri, 28 Jan 2011 14:05:07 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha In-Reply-To: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> Message-ID: <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> Hi Hanneke, > I am relatively new to fieldtrip, and just starting to make some > serious use of the cluster-based permutation routines, and I would just > like to (double)check something before I continu. > > I use ft_timelockstatistics with the following configuration structure: > cfg.parameter = 'individual'; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > etc. > > >From my understanding of the tutorial the "cfg.clusteralpha" stands > for the alpha-value used for the initial test-statistic (in my case a > paired t-test) for thresholding the data, This is correct. and that the "cfg.alpha" > field contains the alpha-value for the second step, i.e. selecting > clusters after the permutation tests. This is not correct. Actually, cfg.alpha is superfluous. In the output, every cluster has a p-value assigned to it, and if there is one or more cluster with a p-value less than your critical alpha-level (mostly 0.05 for a one-sided and 0.025 for a two-sided test), then you have found a significant difference. Best, Eric > > However, the naming of the parameters seems rather contraintuitive to > me. I would have expected it to be the other way around, i.e > "cfg.clusteralpha" for my clusters (second step), and not the initial > t-test. > > Could anyone confirm (or deny) the way it is written in the tutorial? > > Thanks a lot, > > Hanneke Meeren > > ---------------------------------- > Hanneke K.M. Meeren, PhD. > Researcher and Lecturer > Medical Psychology and Cognitive Neuroscience > Tilburg University > P.O. Box 90153 > 5000 LE Tilburg > The Netherlands > email: hanneke.meeren at uvt.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.vandermeij at donders.ru.nl Fri Jan 28 14:32:56 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Fri, 28 Jan 2011 14:32:56 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha In-Reply-To: <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> Message-ID: <4D42C588.4080709@donders.ru.nl> > This is not correct. Actually, cfg.alpha is superfluous. In the output, > every cluster has a p-value assigned to it, and if there is one or more > cluster with a p-value less than your critical alpha-level (mostly 0.05 for > a one-sided and 0.025 for a two-sided test), then you have found a > significant difference. > It does affect the output.mask field, which can be used for plotting. This will have a 0 for a time-frequency-channel triplet if its p-value is above cfg.alpha, and a 1 when it is below it. Other than that, it is superfluous. Best, Roemer -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Jan 28 17:58:35 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 28 Jan 2011 17:58:35 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> Message-ID: Dear Kambiz, Please note there is a short description of the use of ft_databrowser in the walkthrough: http://fieldtrip.fcdonders.nl/walkthrough#visual_data_inspection As well as some documentation on visual artifact rejection http://fieldtrip.fcdonders.nl/tutorial/visual_artifact_rejection Best, Stephen On 28 January 2011 13:43, Robert Oostenveld wrote: > Dear Kambiz > > Although other people's preferences might differ, I would suggest that you > use visual inspection to detect your artifacts. For trial-based data you > cannot apply filter padding. The consequence is that the automatic artifact > detection routine implemented in fieldtrip is likely to suffer from false > alarms at the edges of your trials, and reduced sensitivity away from the > edges. > > Visual detection of artifacts can be done using ft_rejectvisual (check out > the three options it has), and using ft_databrowser. > > best regards, > Robert > > > On 28 Jan 2011, at 6:06, Tavabi, Kambiz wrote: > > > Greetings - this has been an informative discussion. My question remains > is , what is the consensus on an approach for automatic artifact rejection > with trial (CTF) data? E.g., could one use the artifact rejection section of > Michael's code without any padding? I have not found any tutorials or > suggestions on how to use the artifact rejection tools on trial data...have > I missed something. > > -Kambiz > > > _______________________________________________ > 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 hanneke.meeren at uvt.nl Mon Jan 31 10:41:51 2011 From: hanneke.meeren at uvt.nl (H.K.M. Meeren) Date: Mon, 31 Jan 2011 10:41:51 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <4D42C588.4080709@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> Message-ID: <000f01cbc12b$163b4a50$42b1def0$@meeren@uvt.nl> Dear Developers, I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. Could someone quickly send me a download link? Thanks a lot! Hanneke ----------------------------- Hanneke K.M. Meeren, Ph.D. Lecturer and Researcher Cognitive Neuroscience University of Tilburg Room P 614 P.O.Box 90153 5000 LE Tilburg The Netherlands Phone: +31 (0)13 466 3005 Fax: +31 (0)13 466 2067 email: hanneke.meeren at uvt.nl ----------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jan 31 15:31:07 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 31 Jan 2011 15:31:07 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$%maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> Message-ID: <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> Hi Hanneke I hope you (and potential others searching for it) have found it by now, if not, please go to http://fieldtrip.fcdonders.nl/download.php There are some problems with the new wiki layout rendering on older versions of MS Internet Explorer which we try to fix a.s.a.p. best regards, Robert On 31 Jan 2011, at 10:41, H.K.M. Meeren wrote: > Dear Developers, > > I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. > Could someone quickly send me a download link? > &n bsp;Thanks a lot! > > Hanneke > ----------------------------- > Hanneke K.M. Meeren, Ph.D. > Lecturer and Researcher > Cognitive Neuroscience > University of Tilburg > Room P 614 > P.O.Box 90153 > 5000 LE Tilburg > The Netherlands > Phone: +31 (0)13 466 3005 > Fax: +31 (0)13 466 2067 > email: hanneke.meeren at uvt.nl > ----------------------------- > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From hanneke.meeren at uvt.nl Mon Jan 31 16:29:19 2011 From: hanneke.meeren at uvt.nl (H.K.M. Meeren) Date: Mon, 31 Jan 2011 16:29:19 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$%maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> Message-ID: <001a01cbc15b$a1049d50$e30dd7f0$@meeren@uvt.nl> Hi Robert and others, Yes, the problem has been solved, thanks a lot. I have already downloaded by now. Stephen Whitmarsh sent me the exact same link earlier. Apparantly I replied to him personally, and not the whole discussion forum... Best regards, Hanneke --------------------------- Hanneke K.M. Meeren, Ph.D. University of Tilburg Room P 614 Tel: +31 (0)13 466 3005 --------------------------- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Robert Oostenveld Sent: maandag 31 januari 2011 15:31 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website Importance: High Hi Hanneke I hope you (and potential others searching for it) have found it by now, if not, please go to http://fieldtrip.fcdonders.nl/download.php There are some problems with the new wiki layout rendering on older versions of MS Internet Explorer which we try to fix a.s.a.p. best regards, Robert On 31 Jan 2011, at 10:41, H.K.M. Meeren wrote: Dear Developers, I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. Could someone quickly send me a download link? &n bsp;Thanks a lot! Hanneke ----------------------------- Hanneke K.M. Meeren, Ph.D. Lecturer and Researcher Cognitive Neuroscience University of Tilburg Room P 614 P.O.Box 90153 5000 LE Tilburg The Netherlands Phone: +31 (0)13 466 3005 Fax: +31 (0)13 466 2067 email: hanneke.meeren at uvt.nl ----------------------------- _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sherrykhan78 at gmail.com Mon Jan 3 17:17:45 2011 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 3 Jan 2011 11:17:45 -0500 Subject: [FieldTrip] Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School Message-ID: Postdoctoral Fellowship: Multimodal Neuroimaging *Description:* A postdoctoral position pursuing multimodal imaging is available with the TRANSCEND Research Program (www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org) which is affiliated with the Massachusetts General Hospital, Harvard and MIT. There is a second location at a clinical site, the MGH-affiliated Lurie Family Center for Autism, where we have a 128 lead EGI EEG in a shielded room as well as a photogrammetry machine and autonomic monitoring equipment, and will shortly have a near-infrared tissue spectrometer (NIRS) machine. The program’s emphasis is on pathophysiologically oriented brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL), on co-registering EEG and MEG with MRI, and on studying neurovascular coupling with EEG and NIRS. This position will involve analysis of existing multimodal imaging data and collection of new data. It will involve working closely with a multidisciplinary team and with children, and will also involve some research oriented analysis of data collected for clinical purposes. The age range of our subjects is primarily from early infancy to mid-adolescence, with some additional studies including young adults. An ample opportunity will also be provided to the candidate to self-explore and lead research. *Requirements:* Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Candidates without this training and experience need not apply. Prior experience in MRI analysis and EEG signal processing is required. Salary will be consistent with Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees and will range between $45,000 to $55,000 depending upon qualifications and experience. Compensation also includes full staff benefits, including health insurance, and vacation time. *Contact:* Interested applicants may send a CV and statement of interest addressing background and specific pertinence of the candidate’s interest to Dr. Martha R. Herbert at mherbert1 at partners.organd cc transcend at partners.org . Applications will be considered until the position is filled. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jan 6 09:43:47 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 6 Jan 2011 09:43:47 +0100 Subject: [FieldTrip] code change potentially relevant for MEG people Message-ID: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> Dear all, Happy new year to all of you! I just made a change to the code which may be relevant to some. This change will be present in tonight's release version, and will be immediate for the in-house users at the Donders Centre. If you are not doing MEG research you can stop here. If you never use FieldTrip to compute leadfields for MEG data you can stop here. If you never use the 'singleshell' method for your MEG leadfield computation, or if you don't know what that means, you can stop here. There appeared to be a huge difference in magnitude of MEG-leadfields computed with FieldTrip using different algorithms. Particularly, there was a big discrepancy between the 'singleshell' method on the one hand, and the localspheres/singlesphere method on the other hand. It turned out to be the case that there was a scaling factor in the singleshell method, which (assuming the geometrical units were in cm) would yield a magnetic field/gradient in ft or ft/cm. At the moment FieldTrip does not everywhere explicitly impose particular physical units on the data and therefore also should not make particular assumptions. To make the three methods of leadfield computation more equivalent we changed the implicit unit-assuming code. What does this all mean to you? Probably not an awful lot. Yet, you need to be aware that by scaling the leadfields, the magnitude of the inverse solution will probably also change (unless you use norm- normalized leadfields). It is not correct to compare analysis results using old-scale leadfields with analysis results using new-scale leadfields, if the respective analysis results have not been normalized in a meaningful way. In other words, comparing raw power is not correct, comparing neural activity indices, relative changes, t- statistics etc. is probably alright. Sorry for the inconvenience, Best wishes 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 a.stolk at fcdonders.ru.nl Thu Jan 6 11:06:49 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 6 Jan 2011 11:06:49 +0100 (CET) Subject: [FieldTrip] code change potentially relevant for MEG people In-Reply-To: <524787489.95342.1294308215741.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <225327747.95381.1294308409346.JavaMail.root@sculptor.zimbra.ru.nl> Hey JM, Ik plot groepsgemiddelde aboslute powers (zie plotje) waarbij de voxel van interesse gekozen wordt aan de hand van significant verschillen. Dus blobs die gevonden zijn na indep T-testen op de subject level en dep T-test op groepslevel. De prepare-single-shell algoritme is dezelfde voor elke conditie in elke proefpersoon. Ik struikel over deze zin 'comparing raw power is not correct'. Je bedoelt 'comparing raw powers computed with separate (old and new implementation) is not correct'? Ciao! ----- "jan-mathijs schoffelen" schreef: > Van: "jan-mathijs schoffelen" > Aan: "FieldTrip List" > Verzonden: Donderdag 6 januari 2011 09:43:47 > Onderwerp: [FieldTrip] code change potentially relevant for MEG people > > Dear all, > > Happy new year to all of you! I just made a change to the code which > > may be relevant to some. This change will be present in tonight's > release version, and will be immediate for the in-house users at the > > Donders Centre. > > If you are not doing MEG research you can stop here. > If you never use FieldTrip to compute leadfields for MEG data you can > > stop here. > If you never use the 'singleshell' method for your MEG leadfield > computation, or if you don't know what that means, you can stop here. > > There appeared to be a huge difference in magnitude of MEG-leadfields > > computed with FieldTrip using different algorithms. Particularly, > there was a big discrepancy between the 'singleshell' method on the > one hand, and the localspheres/singlesphere method on the other hand. > > It turned out to be the case that there was a scaling factor in the > singleshell method, which (assuming the geometrical units were in cm) > > would yield a magnetic field/gradient in ft or ft/cm. At the moment > FieldTrip does not everywhere explicitly impose particular physical > units on the data and therefore also should not make particular > assumptions. To make the three methods of leadfield computation more > > equivalent we changed the implicit unit-assuming code. > > What does this all mean to you? Probably not an awful lot. Yet, you > need to be aware that by scaling the leadfields, the magnitude of the > > inverse solution will probably also change (unless you use norm- > normalized leadfields). It is not correct to compare analysis results > > using old-scale leadfields with analysis results using new-scale > leadfields, if the respective analysis results have not been > normalized in a meaningful way. In other words, comparing raw power is > > not correct, comparing neural activity indices, relative changes, t- > statistics etc. is probably alright. > > Sorry for the inconvenience, > > Best wishes > > 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 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- A non-text attachment was scrubbed... Name: tessie2_half_light_bottom.pdf Type: application/pdf Size: 8613 bytes Desc: not available URL: From smoratti at psi.ucm.es Thu Jan 6 12:10:15 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 06 Jan 2011 12:10:15 +0100 Subject: [FieldTrip] code change potentially relevant for MEG people In-Reply-To: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> References: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> Message-ID: <24BDB4F2-6935-4334-BF09-C543377EFD1D@psi.ucm.es> Hi Jan-Mathijs, Happy new year! Thanks for the update! I think the MEG community appreciates a lot the Fieldtrip work you all do! Best, Stephan El 06/01/2011, a las 9:43, jan-mathijs schoffelen escribió: > Dear all, > > Happy new year to all of you! I just made a change to the code which > may be relevant to some. This change will be present in tonight's > release version, and will be immediate for the in-house users at the > Donders Centre. > > If you are not doing MEG research you can stop here. > If you never use FieldTrip to compute leadfields for MEG data you > can stop here. > If you never use the 'singleshell' method for your MEG leadfield > computation, or if you don't know what that means, you can stop here. > > There appeared to be a huge difference in magnitude of MEG- > leadfields computed with FieldTrip using different algorithms. > Particularly, there was a big discrepancy between the 'singleshell' > method on the one hand, and the localspheres/singlesphere method on > the other hand. It turned out to be the case that there was a > scaling factor in the singleshell method, which (assuming the > geometrical units were in cm) would yield a magnetic field/gradient > in ft or ft/cm. At the moment FieldTrip does not everywhere > explicitly impose particular physical units on the data and > therefore also should not make particular assumptions. To make the > three methods of leadfield computation more equivalent we changed > the implicit unit-assuming code. > > What does this all mean to you? Probably not an awful lot. Yet, you > need to be aware that by scaling the leadfields, the magnitude of > the inverse solution will probably also change (unless you use norm- > normalized leadfields). It is not correct to compare analysis > results using old-scale leadfields with analysis results using new- > scale leadfields, if the respective analysis results have not been > normalized in a meaningful way. In other words, comparing raw power > is not correct, comparing neural activity indices, relative changes, > t-statistics etc. is probably alright. > > Sorry for the inconvenience, > > Best wishes > > 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 > > _______________________________________________ > 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 r.vandermeij at donders.ru.nl Thu Jan 6 14:10:04 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 06 Jan 2011 14:10:04 +0100 Subject: [FieldTrip] new implementation of wltconvol (renamed to wavelet): specest Message-ID: <4D25BF2C.8030805@donders.ru.nl> Hello everybody! As of today, we have switched to a new implementation for the 'wltconvol' method for frequency analysis, and it has also been renamed to 'wavelet'. For a while now we have been rewriting the low-level code in a different format, one that is more flexible to adapt in the future and that allows for the low-level algorithms to be downloaded in a separate module: /specest/. The changes will be on our ftp-server by tonight. The switch to the new implementation brings about several changes. With respect to the changes are observable to the end-user, there are several FAQs created at our wiki. For the end-user observable changes for 'wavelet' (formerly 'wltconvol'), please have a look /here/ , and for a bigger description with respect to your output.freq please go /here/ . Because of these changes, we strongly advise to either use the new or the old implementation for your entire analysis project. The old implementation is still available by using 'wltconvol_old' as cfg.method (however, this code no longer being updated). You can call also call the function: ft_freqanalysis_old, which is the old interface-function. If you are interested, you can track the progress of the /specest /module by going /here/ . As soon as the other low-level functions are ready and implemented, another e-mail will be sent to the mailing-list. If anything is unclear, or if there are any bugs that have slipped through our fingers, please send an e-mail to the mailing-list and/or report a bug in our /Bugzilla bug tracking system /. Kind regards, Roemer van der Meij -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From shhirano at npsych.med.kyushu-u.ac.jp Sun Jan 9 03:03:52 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Sun, 9 Jan 2011 11:03:52 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: Dear Dr Eric Maris and members of Fieldtrip mailing list At first, I'm sorry for my poor English. I'm a post-doc research fellow of Department of Neuropsychiatry, Kyushu University, Fukuoka, Japan. I'm studying about auditory abnormalities in mental disorders, for example, schizophrenia, bipolar disorder, using MEG. I'm very impressed and interested in Dr Eric Maris and Dr Robert Oostenveld paper, "Nonparametrical statistical testing of EEG and MEG data, on Journal of Neuroscience Methods, 2007". I'd like to apply their stastical methods to our data, but there are some points that I can't understand in their paper. Those are about cluster-based statistics. In the right column in page 180 in their paper, they wrote 5 steps of statistics methods. At 5th step, they take the largest of the cluster- level statistics, then how do they test this largest of the cluster- level statistics? I thought that, after 5th step, I should make the permutation distribution of cluster-level statistics of selected cluster, and I should test the given cluster-level statistics with this permutation distribution. Is this right? Any answer will help me. Best regards, Shogo Hirano, M.D., Ph.D. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From r.vandermeij at donders.ru.nl Sun Jan 9 12:49:05 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Sun, 09 Jan 2011 12:49:05 +0100 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper In-Reply-To: References: Message-ID: <4D29A0B1.1020208@donders.ru.nl> Hi Shogo, After computing your cluster-level statistics you indeed take the largest one, and this will be compared to the permutation distribution. However, this distribution is constructed by doing the following e.g. 500 times: 1) randomly swapping the units of observation (UO) between conditions (in case of a between UO design) 2) computing your cluster-level-statistic for this random combination of UOs 3) taking the largest of these (largest of /all clusters/ in this random permutation, not a /'selected' cluster/) This will result in 500 'largest cluster-level-statistics'. If your original statistic is bigger/smaller than a certain percentage, say 95% when testing single-sided to an alpha of 0.05, then you reject the null-hypothesis of interchangeability of your conditions. Whether it should be bigger or smaller depends on your direction of testing. Hope this helps, Best, Roemer On 9-1-2011 3:03, ?? ?? wrote: > Dear Dr Eric Maris and members of Fieldtrip mailing list > > At first, I'm sorry for my poor English. > I'm a post-doc research fellow of Department of Neuropsychiatry, > Kyushu University, Fukuoka, Japan. > I'm studying about auditory abnormalities in mental disorders, for > example, schizophrenia, bipolar disorder, using MEG. > I'm very impressed and interested in Dr Eric Maris and Dr Robert > Oostenveld paper, "Nonparametrical statistical testing of EEG and MEG > data, on Journal of Neuroscience Methods, 2007". > I'd like to apply their stastical methods to our data, but there are > some points that I can't understand in their paper. > Those are about cluster-based statistics. > In the right column in page 180 in their paper, they wrote 5 steps of > statistics methods. At 5th step, they take the largest of the > cluster-level statistics, then how do they test this largest of the > cluster-level statistics? > I thought that, after 5th step, I should make the permutation > distribution of cluster-level statistics of selected cluster, and I > should test the given cluster-level statistics with this permutation > distribution. Is this right? > Any answer will help me. > > Best regards, > > Shogo Hirano, M.D., Ph.D. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Mon Jan 10 21:58:41 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 10 Jan 2011 12:58:41 -0800 Subject: [FieldTrip] reading EDF+ annotation channel with FieldTrip Message-ID: <4D2B7301.2060900@berkeley.edu> Hi I would like to read in EDF+ data with FieldTrip, including triggers that are coded in the annotation channel. FieldTrip has recently been updated to be able to read EDF+ data (Thanks Robert!). Before, FieldTrip could only read EDF data (so then it could not read events which are coded on the annotation channel). However, in the EDF+ data that I have (which is generate by Net Station software, EGI company), the events on the annotation channel are not read in correctly. I asked EGI support for the definition they use to write the events to the annotation channel in the EDF+ format as is produced by Net Station, and I got this answer from one of their technicians: - Each annotation channel contains a time keeping TAL for each EDF+ block, which is +blockTime[20][20][0] Then, it contains each event for the block, in this format. +startTime[21]duration[20]name[20][0] All times are in seconds. The values in [ ] are the numbers that are written into the binary file, and are described in the EDF+ specification. My knowledge on reading in data and the EDF+ format is not sufficient to understand this. I would like to update read_edf (in private of fileio) to also be able to read in the EGI version of EDF+ data. Does anyone know how to do this? Any help would be greatly appreciated. And while I'm at it, are there any other EGI users on the list that are or will be using the new MFF data format? I would like to use this new data format in FieldTrip, but so far FieldTrip can't read it in yet. Did anyone already write some code to read this format in that we could include into FieldTrip? Also, I've just created a "getting started with EGI data " page on the FieldTrip wiki. I'll document my experiences there. Everyone else with relevant info is (as allways) invited to help fill it. Thanks a lot, All the best, Ingrid -- Ingrid Nieuwenhuis PhD Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From recasensmarc at gmail.com Tue Jan 11 19:33:53 2011 From: recasensmarc at gmail.com (Marc Recasens) Date: Tue, 11 Jan 2011 19:33:53 +0100 Subject: [FieldTrip] Define a ROI in sourcestatistics Message-ID: <4D2CA291.4020003@gmail.com> Hi all. I've been trying to define a region of interest (ROI) in order to restrict my analyses to a particular region on the temporal lobe during sourcestatistics. I have two grandaverage sources like: pos: [33480x3 double] dim: [31 36 30] avg: [1x1 struct] var: [1x1 struct] dimord: 'voxel' trial: [1x13 struct] inside: [12773x1 double] outside: [20707x1 double] df: [33480x1 double] cfg: [1x1 struct] And I apply ft_sourcestatistics with the following configuration: cfg =[]; cfg.dim = GA_dev_source.dim; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'bonferoni'; cfg.numrandomization = 1000; cfg.alpha = 0.05; cfg.tail = 0; nsubj = length(GA_dev_source.trial); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; cfg.ivar = 2; stat = ft_sourcestatistics(cfg, GA_dev_source, GA_stad_source) However it's not very straightforward to me to apply a ROI restriction to this analysis. I downloaded the files from http://fmri.wfubmc.edu (TD_lobe.img, TD_lobe.mat, TD_lobe_Border.mat, TD_lobe_List.mat) which I am suposed to use for the ROI. I tried to add this to the previous configuration: cfg.atlas = '.../TD_lobe.img'; (the template brain containing the different lobes) cfg.inputcoord = 'mni'; cfg.roi = ROI(12).Nom_C; The names of the roi i want to extract ('Temporal Lobe') But then... stat_roi = prob: [31x36x30 double] <---- All zeros. mask: [31x36x30 logical] stat: [31x36x30 double] ref: [31x36x30 double] dim: [31 36 30] inside: [0x1 double] <---- which means there's nothing inside the volume outside: [33480x1 double] pos: [33480x3 double] cfg: [1x1 struct] Amb I defining the ROI incorrectly??? Is it because the dimensions of the atlas and the source are not equal? Could anyone give a good example of how to do it? Any suggestion will be appreciated. Thanks in advance. -- Marc Recasens Tel.: +34 639 24 15 98 -------------- next part -------------- An HTML attachment was scrubbed... URL: From shhirano at npsych.med.kyushu-u.ac.jp Wed Jan 12 10:51:19 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Wed, 12 Jan 2011 18:51:19 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> Dear Dr Roemer van der Meij I really appreciate your kind answer! Your answer enable me understand the statistics after Dr Maris's 5 steps. However, there are still two points I'd like to understand. First, after Dr Maris's 5 steps, I should get the largest claster statistics from the clasters derived from observed data (hereinafter I call these clasters as "observed clasters"). Then, I should enter your 3 steps. In your 2nd step, I should compute cluster-level-statistics from random permutation data. Here, I have an question. When I define clusters from random permutation data, which should I define where clusters are the same place (e.g. time, sensor and so on) as "observed clasters" or should I define newly where clusters are from random permutation data regardless of the places of "observed clasters"? I think the latter is right, this is OK? Second, If I have interests in the cluster that has the second or third... non first largest cluster-level-statistics from the experimental hypothesis, how should I test these clusters? Thank you very much for your kindness! Any answer help me. Best regards, Shogo -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From jan.schoffelen at donders.ru.nl Wed Jan 12 14:48:40 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 12 Jan 2011 14:48:40 +0100 Subject: [FieldTrip] change to ft_volumesegment Message-ID: <82650747-4258-47F4-844E-FB6FE6D69E1C@donders.ru.nl> Dear all, I just want to let you know that I incorporated a change in ft_volumesegment. Sometimes the segmented volumes came with a flipped orientation with respect to the original anatomy, necessitating some manual flipping in order to stay consistent with the mri's transformation matrix. I made some changes to ft_volumesegment so that this manual flipping should not be necessary anymore (at least on the anatomical MRIs I tested the code with). Explicitly checking the alignment is of course still allowed and recommended. Best wishes, 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 stephen.whitmarsh at gmail.com Wed Jan 12 14:58:49 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 12 Jan 2011 14:58:49 +0100 Subject: [FieldTrip] Improved Fieldtrip Wiki! Message-ID: Dear FieldTrippers, First of all, a happy new year! As we hope you agree, we have tried to improve the FieldTrip Wiki on several points: · Better overview through some simple changes to the organization of the menubar · Cleaning up the appearance of the Wiki through the style sheet, and some other aesthetic considerations · Helping FieldTrip newbies by adding an elaborate walkthrough · Adding the ability to upload and display .SVG images, for now much used in the walkthrough · Adding the ability to use editorial notes – take a look online to see what we mean by that. · In general creating a kinder, home-y atmosphere. · Ofcourse, like always, we are the community and if you have any suggestions of comments about the content or appearance of the website, feel free to post them in the email discussion list. · Coming soon: Download pages as formatted PDF with one press of a button, and much, much more! Thanks and credits go to Eelke Spaak for applying his Jedi webskills to the FieldTrip Wiki! Regards, S -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Thu Jan 13 16:09:11 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Thu, 13 Jan 2011 16:09:11 +0100 Subject: [FieldTrip] fieldtrip question - help needed Message-ID: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> Hello can anybody spend some more words on the chapter "Fixing a missing sensor"? I'm trying to use it with a AtB (like ITAB-Chieti) device...but I cannot understand how to use it. I've several troubles when I've to declare the layout, since I don't have a layout file, but I construct that starting from grad... Do you have any hint for me? Sara Rombetto ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From inbalots at gmail.com Thu Jan 13 18:14:45 2011 From: inbalots at gmail.com (Inbal Lots) Date: Thu, 13 Jan 2011 19:14:45 +0200 Subject: [FieldTrip] Question about wavelet analysis Message-ID: Hello I have several questions: 1. Just wanted to make sure: When I use [res] = ft_freqanalysis(cfg,data) with data that have several trials - and I define cfg.keeptrials = 'yes'; I get an analysis for each trial in [res]. Then I use ft_multiplotTFR(cfg,res) with cfg.trials = 'all'; The result is an average on the wavelet result of all trials? (and not a wavelet on the averaged signal of all trials) 2. Is there a way for me to see the wavelet analysis result of each trial and to browse easily between them? rather than calling ft_multiplotTFR(cfg,res) each time with cfg.trials = i ; where i is the desired trial number? 3. How can I use other mother wavelet? (and not just Morlet wavelets) 4. How can I control the colormap min and max values so that they will be similar in all figures? (like doing imagesc(pic,clim))? Thank you very much Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Jan 13 18:19:16 2011 From: g.piantoni at nin.knaw.nl (Giovanni Piantoni) Date: Thu, 13 Jan 2011 18:19:16 +0100 Subject: [FieldTrip] peer Message-ID: Dear FieldTrip/peer developers, I was trying the peer module out on two computer (both 64bit Linux, one Ubuntu and one Red-Hat). Thanks for the effort in developing the module! The module works great, following the information on the wiki page. On both computers, I'm able to call peermaster and peerslave, getting the correct peerinfo and peerlist. When I try on Ubuntu, it works flawlessly (but it only has two cores, so no much gain there). However, when I try on Red Hat (which has many more cores), peermaster sends the job to the peerslave and the job is executed (f.e., with peercellfun(@mkdir, {'test'}) it creates a folder called test), but the peerslave is not able to tell the peermaster that the job has completed. See below for details: In the peermaster matlab command line: >> peermaster peer: init peerinit: user at computername, id = 3682858105 peer: spawning announce thread peer: spawning discover thread peer: spawning expire thread peer: spawning tcpserver thread >> peerinfo hostid = 3682858105 hostname = computername user = user group = unknown socket = port = 1701 status = master memavail = 4294967295 bytes timavail = 86400 seconds allowuser = {} allowgroup = {} allowhost = {} tcpserver thread is running udsserver thread is NOT running announce thread is running discover thread is running expire thread is running there are 0 jobs in this peer's buffer >> peerlist there are 3 peers running in total (1 hosts, 1 users) there are 1 peers running on 1 hosts as master there are 2 peers running on 1 hosts as idle slave with 8.0 GB memory available there are 0 peers running on 0 hosts as busy slave with 0 bytes and 0 seconds required there are 0 peers running on 0 hosts as zombie idle slave at user at computername:1702, memavail = 4.0 GB, timavail = 1.0 days idle slave at user at computername:1703, memavail = 4.0 GB, timavail = 1.0 days master at user at computername:1701 >> peercellfun(@pause, {1 2}) Then, if I look at one of the two peerslave computers, I see: executing job 25 from user at computername (jobid=2068920377, memreq=1073741824, timreq=3600) executing job took 2.002441 seconds and 0 bytes Warning: failed to return job results to the master And if I "dbstop if caught error", I see in the peerslave: Error using ==> peer failed to locate specified peer Where the error occurs at: peer('put', joblist.hostid, argout, options, 'jobid', joblist.jobid); however: >> joblist.hostid ans = 3682858105 which is the correct hostid for the peermaster. Do you have any idea where the problem might lie? How can I debug this? If it's not easy to solve, how can I run each job once (bc the peermaster keeps on sending request if it doesn't know that the first job was completed)? Thanks a lot! 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.nin.knaw.nl/research_groups/van_someren_group/ From jan.schoffelen at donders.ru.nl Fri Jan 14 09:39:39 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 09:39:39 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> Message-ID: <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> Cara Sara, I am not sure whether I totally understand your question. Are you referring to the example script 'fixing a missing sensor'? When I look at it on our (renewed) wiki (still brings tears to my eyes), I don't see any mention of a layout. I agree with you that the example however can be made a bit more clear. This is my take on it, starting from the back of the pipeline: The 'fixing' algorithm replaces a 'dead' channel with the average signal recorded at its neighbours. In the current implementation, the description of the sensors and the data (=the grad-structure and the data.trial) which go into ft_channelrepair need to contain a full description of the sensor-array, including the faulty one. In other words, if your sensor array has 10 sensors, one of which you want to have repaired, the input to ft_channelrepair needs a data-structure containing data from the spatial location of those 10 sensors (this is in data.grad, and needed to determine which channels are the neighbours). For consistency, the time course of the faulty channel also needs to be there. The actual time courses of the faulty channel will not be used, and these can take any value. Depending on the hardware and recording protocol, a faulty channel is either present or not in the data. In the example script, the faulty channel was not even recorded, and this is the reason for the first part of the script: the creation of a dummy channel, initialized with 0's in order to make ft_channelrepair work. If, however, your dataset actually contains data on the faulty channel (which may look very noisy), you can skip the first part of the script, and directly go to the second part. Best wishes, Jan-Mathijs On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: > Hello > can anybody spend some more words on the chapter "Fixing a missing > sensor"? > I'm trying to use it with a AtB (like ITAB-Chieti) device...but I > cannot understand how to use it. I've several troubles when I've to > declare the layout, since I don't have a layout file, but I construct > that starting from grad... > Do you have any hint for me? > > Sara Rombetto > > > ------------------------------------------- > * Dott.ssa Sara Rombetto * > * Istituto di Cibernetica "E. Caianiello" * > * Via Campi Flegrei, 34 * > * 80078 Pozzuoli (NA) * > * Italy * > * tel +390818675054 * > * fax +390818675326 * > ------------------------------------------- > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > 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 Fri Jan 14 09:48:13 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 09:48:13 +0100 Subject: [FieldTrip] Question about wavelet analysis In-Reply-To: References: Message-ID: <0CECFFCC-6802-42DE-81C3-B8FD25E5F1F2@donders.ru.nl> Dear Inbal, > 1. Just wanted to make sure: > When I use [res] = ft_freqanalysis(cfg,data) with data that have > several trials - and I define cfg.keeptrials = 'yes'; > I get an analysis for each trial in [res]. Then I use > ft_multiplotTFR(cfg,res) with cfg.trials = 'all'; > The result is an average on the wavelet result of all trials? (and > not a wavelet on the averaged signal of all trials) > Yes, ft_multiplotTFR computes an average spectrogram over observations/ trials > 2. Is there a way for me to see the wavelet analysis result of each > trial and to browse easily between them? > rather than calling ft_multiplotTFR(cfg,res) each time with > cfg.trials = i ; where i is the desired trial number? > At the moment, no. I never really thought of looking at single trial multiplots but I can imagine the need for this functionality. Your workaround indeed works, but may be a bit tedioius. > 3. How can I use other mother wavelet? (and not just Morlet wavelets) > What kind of wavelet would you like to use? If the wavelet consists of a tapered cosine/sine wave in which the Gaussian taper will be replaced by something else, you could use cfg.method = 'mtmconvol'. This is an efficient implementation of a wavelet-like analysis, where there is some freedom to define your own taper. At present this relies on matlab's window-function (or on the slepian sequences; different story), so the different tapers are limited to those available in matlab. However, it is relatively straightforward to tap into the code here, and provide your own taper. A dangerous, but possible option is to temporarily overload the matlab window-function with your own, spitting out the requested taper. > 4. How can I control the colormap min and max values so that they > will be similar in all figures? (like doing imagesc(pic,clim))? > I guess cfg.zlim should do the trick. Best, JM > Thank you very much > > Inbal > _______________________________________________ > 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 jungky at korea.ac.kr Fri Jan 14 09:58:38 2011 From: jungky at korea.ac.kr (Jung, Ki-Young) Date: Fri, 14 Jan 2011 00:58:38 -0800 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: Message-ID: Dear all, I'd like to do statistical comparison using cluster based permuation between two groups on ERP data. But I am receiving following error messages ??? Undefined function or method 'bwlabeln' for input arguments of type 'double'. Error in ==> findcluster at 89  [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :),  nfreq, ntime), 4); Error in ==> clusterstat at 194     posclusobs = findcluster(reshape(postailobs,     [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); Error in ==> statistics_montecarlo at 321  [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285   [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 125 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); My configuration for ft_freqstatistics are cfg = []; cfg.channel          = 'all'; cfg.latency          = 'all'; cfg.frequency        = [30 50]; cfg.method           = 'montecarlo'; cfg.statistic        = 'indepsamplesT'; cfg.correctm         = 'cluster'; cfg.clusteralpha     = 0.025; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan        = 2; cfg.tail             = 0; cfg.clustertail      = 0; cfg.alpha            = 0.025; cfg.numrandomization = 500; cfg.neighbours       = [ ]; design = [ones(1, 16), ones(1, 16)*2]; cfg.design           = design; cfg.ivar             = 1; [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); Data structure of con_grand_avg are con_grand_avg =       label: {27x1 cell}        freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50]        time: [1x21 double]      dimord: 'subj_chan_freq_time'   powspctrm: [4-D double]         cfg: [1x1 struct] Any comment helps me. Best regards, Ki-Young Jung From julian.keil at gmail.com Fri Jan 14 10:04:19 2011 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 14 Jan 2011 10:04:19 +0100 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: Message-ID: <5CAF6334-C41B-429B-8575-E3CAAA20EB37@gmail.com> Hi, did you check with 'which bwlabeln' if you have the respcetive function? It's part of the image processing toolbox for matlab. Good Luck. Julian Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > Dear all, > > I'd like to do statistical comparison using cluster based permuation > between two groups on ERP data. > But I am receiving following error messages > ??? Undefined function or method 'bwlabeln' for input arguments of > type 'double'. > > Error in ==> findcluster at 89 > [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), > nfreq, ntime), 4); > > Error in ==> clusterstat at 194 > posclusobs = findcluster(reshape(postailobs, > [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); > > Error in ==> statistics_montecarlo at 321 > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_freqstatistics at 125 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > My configuration for ft_freqstatistics are > cfg = []; > cfg.channel = 'all'; > cfg.latency = 'all'; > cfg.frequency = [30 50]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.025; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg.neighbours = [ ]; > design = [ones(1, 16), ones(1, 16)*2]; > cfg.design = design; > cfg.ivar = 1; > [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); > > > Data structure of con_grand_avg are > > con_grand_avg = > label: {27x1 cell} > freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50] > time: [1x21 double] > dimord: 'subj_chan_freq_time' > powspctrm: [4-D double] > cfg: [1x1 struct] > > > Any comment helps me. > > > Best regards, > > Ki-Young Jung > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.rombetto at cib.na.cnr.it Fri Jan 14 11:03:18 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Fri, 14 Jan 2011 11:03:18 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> Message-ID: <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> Hello yes I'm referring to the example script 'fixing a missing sensor'. Even if you consider the structure grad, you also load LABEL275.mat and GRAD275.mat, that is the layout in someway. What I do is to process my data: I define trials and preprocess them. Then I use ft_rejectvisual to remove artifacts and noisy channels. After this my data are ok, but I have some missing channels. In order to solve the inverse problem, I'm using a software that needs all the channels....and this is the reason why I'm trying to "fix the missing sensor". Sara > Cara Sara, > > I am not sure whether I totally understand your question. Are you > referring to the example script 'fixing a missing sensor'? > When I look at it on our (renewed) wiki (still brings tears to my > eyes), I don't see any mention of a layout. > > I agree with you that the example however can be made a bit more clear. > This is my take on it, starting from the back of the pipeline: > > The 'fixing' algorithm replaces a 'dead' channel with the average > signal recorded at its neighbours. In the current implementation, the > description of the sensors and the data (=the grad-structure and the > data.trial) which go into ft_channelrepair need to contain a full > description of the sensor-array, including the faulty one. In other > words, if your sensor array has 10 sensors, one of which you want to > have repaired, the input to ft_channelrepair needs a data-structure > containing data from the spatial location of those 10 sensors (this is > in data.grad, and needed to determine which channels are the > neighbours). For consistency, the time course of the faulty channel > also needs to be there. The actual time courses of the faulty channel > will not be used, and these can take any value. Depending on the > hardware and recording protocol, a faulty channel is either present or > not in the data. In the example script, the faulty channel was not even > recorded, and this is the reason for the first part of the script: the > creation of a dummy channel, initialized with 0's in order to make > ft_channelrepair work. If, however, your dataset actually contains data > on the faulty channel (which may look very noisy), you can skip the > first part of the script, and directly go to the second part. > > Best wishes, > > Jan-Mathijs > > > On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: > >> Hello >> can anybody spend some more words on the chapter "Fixing a missing sensor"? >> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >> cannot understand how to use it. I've several troubles when I've to >> declare the layout, since I don't have a layout file, but I construct >> that starting from grad... >> Do you have any hint for me? >> >> Sara Rombetto >> >> >> ------------------------------------------- >> * Dott.ssa Sara Rombetto * >> * Istituto di Cibernetica "E. Caianiello" * >> * Via Campi Flegrei, 34 * >> * 80078 Pozzuoli (NA) * >> * Italy * >> * tel +390818675054 * >> * fax +390818675326 * >> ------------------------------------------- >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> _______________________________________________ >> 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 ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From jan.schoffelen at donders.ru.nl Fri Jan 14 11:30:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 11:30:45 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> Message-ID: <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> Cara Sara, OK. Indeed, if you have run ft_rejectvisual and removed some channels, these are missing from your actual data. The original data.grad should however still contain the labels of all channels, and you can use grad.label as 'LABEL275', provided the order of the remaining channels did not change. Alternatively, you could define cfg.keepchannel = 'nan', before calling ft_rejectvisual. The noisy channels will then still be 'present' in your data (but set to NaN). I believe that this would take away the need to do the first part of the script. Best JM PS: please note that it is not optimal to do source reconstruction after replacing noisy channels with an average of their neighbours. At least you need to take this into account in the creation of the leadfields. On Jan 14, 2011, at 11:03 AM, s.rombetto at cib.na.cnr.it wrote: > Hello > yes I'm referring to the example script 'fixing a missing sensor'. > Even if you consider the structure grad, you also load LABEL275.mat > and GRAD275.mat, that is the layout in someway. > > What I do is to process my data: I define trials and preprocess > them. Then I use ft_rejectvisual to remove artifacts and noisy > channels. > After this my data are ok, but I have some missing channels. > In order to solve the inverse problem, I'm using a software that > needs all the channels....and this is the reason why I'm trying to > "fix the missing sensor". > > Sara > >> Cara Sara, >> >> I am not sure whether I totally understand your question. Are you >> referring to the example script 'fixing a missing sensor'? >> When I look at it on our (renewed) wiki (still brings tears to my >> eyes), I don't see any mention of a layout. >> >> I agree with you that the example however can be made a bit more >> clear. >> This is my take on it, starting from the back of the pipeline: >> >> The 'fixing' algorithm replaces a 'dead' channel with the average >> signal recorded at its neighbours. In the current implementation, the >> description of the sensors and the data (=the grad-structure and the >> data.trial) which go into ft_channelrepair need to contain a full >> description of the sensor-array, including the faulty one. In other >> words, if your sensor array has 10 sensors, one of which you want to >> have repaired, the input to ft_channelrepair needs a data-structure >> containing data from the spatial location of those 10 sensors (this >> is >> in data.grad, and needed to determine which channels are the >> neighbours). For consistency, the time course of the faulty channel >> also needs to be there. The actual time courses of the faulty channel >> will not be used, and these can take any value. Depending on the >> hardware and recording protocol, a faulty channel is either present >> or >> not in the data. In the example script, the faulty channel was not >> even >> recorded, and this is the reason for the first part of the script: >> the >> creation of a dummy channel, initialized with 0's in order to make >> ft_channelrepair work. If, however, your dataset actually contains >> data >> on the faulty channel (which may look very noisy), you can skip the >> first part of the script, and directly go to the second part. >> >> Best wishes, >> >> Jan-Mathijs >> >> >> On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: >> >>> Hello >>> can anybody spend some more words on the chapter "Fixing a missing >>> sensor"? >>> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >>> cannot understand how to use it. I've several troubles when I've to >>> declare the layout, since I don't have a layout file, but I >>> construct >>> that starting from grad... >>> Do you have any hint for me? >>> >>> Sara Rombetto >>> >>> >>> ------------------------------------------- >>> * Dott.ssa Sara Rombetto * >>> * Istituto di Cibernetica "E. Caianiello" * >>> * Via Campi Flegrei, 34 * >>> * 80078 Pozzuoli (NA) * >>> * Italy * >>> * tel +390818675054 * >>> * fax +390818675326 * >>> ------------------------------------------- >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> >>> _______________________________________________ >>> 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 > > > > ------------------------------------------- > * Dott.ssa Sara Rombetto * > * Istituto di Cibernetica "E. Caianiello" * > * Via Campi Flegrei, 34 * > * 80078 Pozzuoli (NA) * > * Italy * > * tel +390818675054 * > * fax +390818675326 * > ------------------------------------------- > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > _______________________________________________ > 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 s.rombetto at cib.na.cnr.it Fri Jan 14 11:40:09 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Fri, 14 Jan 2011 11:40:09 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> Message-ID: <20110114114009.bkaw65hmaog880g4@arco.cib.na.cnr.it> thanks that's right. But we also fabricate squids, so the broken channels can change. So I was looking for a temporary solution. best regards Sara > Cara Sara, > > OK. Indeed, if you have run ft_rejectvisual and removed some channels, > these are missing from your actual data. The original data.grad should > however still contain the labels of all channels, and you can use > grad.label as 'LABEL275', provided the order of the remaining channels > did not change. Alternatively, you could define cfg.keepchannel = > 'nan', before calling ft_rejectvisual. The noisy channels will then > still be 'present' in your data (but set to NaN). I believe that this > would take away the need to do the first part of the script. > > Best > > JM > > PS: please note that it is not optimal to do source reconstruction > after replacing noisy channels with an average of their neighbours. At > least you need to take this into account in the creation of the > leadfields. > > > On Jan 14, 2011, at 11:03 AM, s.rombetto at cib.na.cnr.it wrote: > >> Hello >> yes I'm referring to the example script 'fixing a missing sensor'. >> Even if you consider the structure grad, you also load LABEL275.mat >> and GRAD275.mat, that is the layout in someway. >> >> What I do is to process my data: I define trials and preprocess >> them. Then I use ft_rejectvisual to remove artifacts and noisy >> channels. >> After this my data are ok, but I have some missing channels. >> In order to solve the inverse problem, I'm using a software that >> needs all the channels....and this is the reason why I'm trying to >> "fix the missing sensor". >> >> Sara >> >>> Cara Sara, >>> >>> I am not sure whether I totally understand your question. Are you >>> referring to the example script 'fixing a missing sensor'? >>> When I look at it on our (renewed) wiki (still brings tears to my >>> eyes), I don't see any mention of a layout. >>> >>> I agree with you that the example however can be made a bit more clear. >>> This is my take on it, starting from the back of the pipeline: >>> >>> The 'fixing' algorithm replaces a 'dead' channel with the average >>> signal recorded at its neighbours. In the current implementation, the >>> description of the sensors and the data (=the grad-structure and the >>> data.trial) which go into ft_channelrepair need to contain a full >>> description of the sensor-array, including the faulty one. In other >>> words, if your sensor array has 10 sensors, one of which you want to >>> have repaired, the input to ft_channelrepair needs a data-structure >>> containing data from the spatial location of those 10 sensors (this is >>> in data.grad, and needed to determine which channels are the >>> neighbours). For consistency, the time course of the faulty channel >>> also needs to be there. The actual time courses of the faulty channel >>> will not be used, and these can take any value. Depending on the >>> hardware and recording protocol, a faulty channel is either present or >>> not in the data. In the example script, the faulty channel was not even >>> recorded, and this is the reason for the first part of the script: the >>> creation of a dummy channel, initialized with 0's in order to make >>> ft_channelrepair work. If, however, your dataset actually contains data >>> on the faulty channel (which may look very noisy), you can skip the >>> first part of the script, and directly go to the second part. >>> >>> Best wishes, >>> >>> Jan-Mathijs >>> >>> >>> On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: >>> >>>> Hello >>>> can anybody spend some more words on the chapter "Fixing a >>>> missing sensor"? >>>> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >>>> cannot understand how to use it. I've several troubles when I've to >>>> declare the layout, since I don't have a layout file, but I construct >>>> that starting from grad... >>>> Do you have any hint for me? >>>> >>>> Sara Rombetto >>>> >>>> >>>> ------------------------------------------- >>>> * Dott.ssa Sara Rombetto * >>>> * Istituto di Cibernetica "E. Caianiello" * >>>> * Via Campi Flegrei, 34 * >>>> * 80078 Pozzuoli (NA) * >>>> * Italy * >>>> * tel +390818675054 * >>>> * fax +390818675326 * >>>> ------------------------------------------- >>>> >>>> ---------------------------------------------------------------- >>>> This message was sent using IMP, the Internet Messaging Program. >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> >> >> ------------------------------------------- >> * Dott.ssa Sara Rombetto * >> * Istituto di Cibernetica "E. Caianiello" * >> * Via Campi Flegrei, 34 * >> * 80078 Pozzuoli (NA) * >> * Italy * >> * tel +390818675054 * >> * fax +390818675326 * >> ------------------------------------------- >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> _______________________________________________ >> 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 ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From julian.keil at gmail.com Fri Jan 14 12:51:14 2011 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 14 Jan 2011 12:51:14 +0100 Subject: [FieldTrip] grid - bug in ft_prepare_leadfield Message-ID: <78914DC7-8F9C-41C6-9FA1-853ABFA19B5C@gmail.com> Hi, there might be a bug in the latest release of ft_prepare leadfield (version 20110113): In line 172: [sourcegrid, tmpcfg] ... but later on, the code only refers to "grid" not "sourcegrid". Changing "sourcegrid" to "grid" solves the problem. By the way, I get a conflict with the graph2d-toolbox, as this toolbox has a function called grid.m Greetings 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 jungky at korea.ac.kr Fri Jan 14 18:58:23 2011 From: jungky at korea.ac.kr (Jung, Ki-Young) Date: Fri, 14 Jan 2011 09:58:23 -0800 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: <1294996134883354.0.mail@mail> References: <1294996134883354.0.mail@mail> Message-ID: Thanks! But I have still trouble with this message. ??? Error using ==> statistics_montecarlo Too many input arguments. Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 125 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Best regards, KY On Fri, Jan 14, 2011 at 1:04 AM, Julian Keil wrote: > Hi, > > did you check with 'which bwlabeln' if you have the respcetive function? > It's part of the image processing toolbox for matlab. > > Good Luck. > > Julian > > Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > >> Dear all, >> >> I'd like to do statistical comparison using cluster based permuation >> between two groups on ERP data. >> But I am receiving following error messages >> ??? Undefined function or method 'bwlabeln' for input arguments of >> type 'double'. >> >> Error in ==> findcluster at 89 >>  [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), >>  nfreq, ntime), 4); >> >> Error in ==> clusterstat at 194 >>     posclusobs = findcluster(reshape(postailobs, >>     [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); >> >> Error in ==> statistics_montecarlo at 321 >>  [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >> >> Error in ==> statistics_wrapper at 285 >>   [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); >> >> Error in ==> ft_freqstatistics at 125 >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); >> >> My configuration for ft_freqstatistics are >> cfg = []; >> cfg.channel          = 'all'; >> cfg.latency          = 'all'; >> cfg.frequency        = [30 50]; >> cfg.method           = 'montecarlo'; >> cfg.statistic        = 'indepsamplesT'; >> cfg.correctm         = 'cluster'; >> cfg.clusteralpha     = 0.025; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan        = 2; >> cfg.tail             = 0; >> cfg.clustertail      = 0; >> cfg.alpha            = 0.025; >> cfg.numrandomization = 500; >> cfg.neighbours       = [ ]; >> design = [ones(1, 16), ones(1, 16)*2]; >> cfg.design           = design; >> cfg.ivar             = 1; >> [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); >> >> >> Data structure of con_grand_avg are >> >> con_grand_avg = >>       label: {27x1 cell} >>        freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50] >>        time: [1x21 double] >>      dimord: 'subj_chan_freq_time' >>   powspctrm: [4-D double] >>         cfg: [1x1 struct] >> >> >> Any comment helps me. >> >> >> Best regards, >> >> Ki-Young Jung >> >> _______________________________________________ >> 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 batrod at gmail.com Fri Jan 14 22:29:41 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Fri, 14 Jan 2011 15:29:41 -0600 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: <1294996134883354.0.mail@mail> Message-ID: I may be wrong but as far as i remember, the cluster analysis can only be done on one value of frequency, average or not. There is no cfg.avgoverfreq option n your script. But again i might be wrong. Rodolphe On Fri, Jan 14, 2011 at 11:58 AM, Jung, Ki-Young wrote: > Thanks! But I have still trouble with this message. > > ??? Error using ==> statistics_montecarlo > Too many input arguments. > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_freqstatistics at 125 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Best regards, > > KY > > On Fri, Jan 14, 2011 at 1:04 AM, Julian Keil > wrote: > > Hi, > > > > did you check with 'which bwlabeln' if you have the respcetive function? > > It's part of the image processing toolbox for matlab. > > > > Good Luck. > > > > Julian > > > > Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > > > >> Dear all, > >> > >> I'd like to do statistical comparison using cluster based permuation > >> between two groups on ERP data. > >> But I am receiving following error messages > >> ??? Undefined function or method 'bwlabeln' for input arguments of > >> type 'double'. > >> > >> Error in ==> findcluster at 89 > >> [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, > :, :), > >> nfreq, ntime), 4); > >> > >> Error in ==> clusterstat at 194 > >> posclusobs = findcluster(reshape(postailobs, > >> [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); > >> > >> Error in ==> statistics_montecarlo at 321 > >> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > >> > >> Error in ==> statistics_wrapper at 285 > >> [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > >> > >> Error in ==> ft_freqstatistics at 125 > >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > >> > >> My configuration for ft_freqstatistics are > >> cfg = []; > >> cfg.channel = 'all'; > >> cfg.latency = 'all'; > >> cfg.frequency = [30 50]; > >> cfg.method = 'montecarlo'; > >> cfg.statistic = 'indepsamplesT'; > >> cfg.correctm = 'cluster'; > >> cfg.clusteralpha = 0.025; > >> cfg.clusterstatistic = 'maxsum'; > >> cfg.minnbchan = 2; > >> cfg.tail = 0; > >> cfg.clustertail = 0; > >> cfg.alpha = 0.025; > >> cfg.numrandomization = 500; > >> cfg.neighbours = [ ]; > >> design = [ones(1, 16), ones(1, 16)*2]; > >> cfg.design = design; > >> cfg.ivar = 1; > >> [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); > >> > >> > >> Data structure of con_grand_avg are > >> > >> con_grand_avg = > >> label: {27x1 cell} > >> freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 > 49 50] > >> time: [1x21 double] > >> dimord: 'subj_chan_freq_time' > >> powspctrm: [4-D double] > >> cfg: [1x1 struct] > >> > >> > >> Any comment helps me. > >> > >> > >> Best regards, > >> > >> Ki-Young Jung > >> > >> _______________________________________________ > >> 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 dgroppe at cogsci.ucsd.edu Fri Jan 14 22:36:13 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 14 Jan 2011 13:36:13 -0800 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout Message-ID: Hi Fieldtripians, I'm trying to export some EEGLAB data to Fieldtrip and am having trouble plotting the data topographically. I constructed a layout file for my 31 electrodes (see attached) and tried to plot the topography of my data using ft_topoplotER.m. This produced the attached figures all_chans.jpg and just_scalp_chans.jpg. The topography should look like that in the attached image, eeglab_topo.jpg. As you can see, the electrodes are shrunk too far into the head and can be off center. Trying to change the channel layout file to fix this has little effect because ft_prepare_layout.m automatically normalizes the electrode coordinates to fill a unit circle. Given the topoplots in the fieldtrip tutorial, there's obviously a way around this problem but save for editing the ft_prepare_layout.m, I don't know what to do. thanks in advance for your help, -David -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ -------------- next part -------------- A non-text attachment was scrubbed... Name: eeglab_topo.jpg Type: image/jpeg Size: 92401 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: all_chans.jpg Type: image/jpeg Size: 92441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: just_scalp_chans.jpg Type: image/jpeg Size: 82349 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 31chan.lay Type: application/octet-stream Size: 1067 bytes Desc: not available URL: From batrod at gmail.com Fri Jan 14 22:52:48 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Fri, 14 Jan 2011 15:52:48 -0600 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout In-Reply-To: References: Message-ID: David, i had the same issue with my own layout. The position of my electrodes was not fitting the head, even if the proportion were right, like in your first image. I solved this problem by multiplying the position with different numbers until i found the perfect one. This is the part of code that does this: lay = ft_prepare_layout(cfg); lay.pos(:,1) = 1.5*lay.pos(:,1); Replace 1.5 by something that works for you. Hope this helps, Rodolphe. On Fri, Jan 14, 2011 at 3:36 PM, David Groppe wrote: > Hi Fieldtripians, > I'm trying to export some EEGLAB data to Fieldtrip and am having > trouble plotting the data topographically. I constructed a layout file > for my 31 electrodes (see attached) and tried to plot the topography > of my data using ft_topoplotER.m. This produced the attached figures > all_chans.jpg and just_scalp_chans.jpg. The topography should look > like that in the attached image, eeglab_topo.jpg. As you can see, the > electrodes are shrunk too far into the head and can be off center. > Trying to change the channel layout file to fix this has little effect > because ft_prepare_layout.m automatically normalizes the electrode > coordinates to fill a unit circle. Given the topoplots in the > fieldtrip tutorial, there's obviously a way around this problem but > save for editing the ft_prepare_layout.m, I don't know what to do. > thanks in advance for your help, > -David > > -- > David Groppe, Ph.D. > dgroppe at cogsci.ucsd.edu > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > 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 karl.doron at gmail.com Sat Jan 15 18:05:46 2011 From: karl.doron at gmail.com (Karl Doron) Date: Sat, 15 Jan 2011 09:05:46 -0800 Subject: [FieldTrip] singleplotTFR error Message-ID: Hello, Has anyone else reported a problem with ft_singleplotTFR and output of the new specest module? multiplotTFR works, but 'interactive' method fails. It looks like the error occurs when trying to mask NaNs % masking only possible for evenly spaced axis if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) warning('(one of the) axis are not evenly spaced -> nans cannot be masked out -> cfg.masknans is set to ''no'';') cfg.masknans = 'no'; end Thank you, karl doron UCSB -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Sat Jan 15 18:49:09 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Sat, 15 Jan 2011 09:49:09 -0800 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout In-Reply-To: References: Message-ID: Thanks for the email Rodolphe. It's good to know I'm not the only one who has had this problem. I was hoping for a solution that didn't involve editing the code, since that makes it a pain to update our version of fieldtrip when a new version is released. It looks like that might be the only way though. cheers, -David On Fri, Jan 14, 2011 at 1:52 PM, Rodolphe Nenert wrote: > David, > i had the same issue with my own layout. The position of my electrodes was > not fitting the head, even if the proportion were right, like in your first > image. > I solved this problem by multiplying the position with different numbers > until i found the perfect one. > This is the part of code that does this: > lay = ft_prepare_layout(cfg); > lay.pos(:,1) = 1.5*lay.pos(:,1); > Replace 1.5 by something that works for you. > Hope this helps, > Rodolphe. > > On Fri, Jan 14, 2011 at 3:36 PM, David Groppe > wrote: >> >> Hi Fieldtripians, >>   I'm trying to export some EEGLAB data to Fieldtrip and am having >> trouble plotting the data topographically. I constructed a layout file >> for my 31 electrodes (see attached) and tried to plot the topography >> of my data using ft_topoplotER.m.  This produced the attached figures >> all_chans.jpg and just_scalp_chans.jpg.  The topography should look >> like that in the attached image, eeglab_topo.jpg.  As you can see, the >> electrodes are shrunk too far into the head and can be off center. >> Trying to change the channel layout file to fix this has little effect >> because ft_prepare_layout.m automatically normalizes the electrode >> coordinates to fill a unit circle.  Given the topoplots in the >> fieldtrip tutorial, there's obviously a way around this problem but >> save for editing the ft_prepare_layout.m, I don't know what to do. >>     thanks in advance for your help, >>            -David >> >> -- >> David Groppe, Ph.D. >> dgroppe at cogsci.ucsd.edu >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> _______________________________________________ >> 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. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From dgroppe at cogsci.ucsd.edu Sat Jan 15 23:43:29 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Sat, 15 Jan 2011 14:43:29 -0800 Subject: [FieldTrip] logic behind normalizing tapers Message-ID: Hi again Fieldtrippers, I noticed that when estimating power spectra ft_specest_mtmfft.m scales tapers such that their sum squared value is 1 before applying them to the data. For example: %lines 106-108 of ft_specest_mtmfft.m case 'hanning' tap = hanning(ndatsample)'; tap = tap./norm(tap, 'fro'); I realize this simply scales the power spectrum, but what's the rationale for this? Other EEG analysis software and tutorials I've read don't do this. much thanks, -David -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From TAVABIK at email.chop.edu Sun Jan 16 07:58:50 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Sun, 16 Jan 2011 01:58:50 -0500 Subject: [FieldTrip] MEG Artifact removal Message-ID: Greetings - Would someone please comment on the following procedure: (1) dummy=ft_rejectvisual(cfg,raw-data) where cfg.method='trial', cfg.channel='MEG' (2) dummy2=ft_rejectvisual(cfg,dummy) where cfg.method='channel', cfg.channel='MEG' (3) save artifact-rejected-data dummy2 Is this what is actually recommended by the visual artifact rejection tutorial, if not, then is it correct to assume that the final data structure (artifact-rejected-data) is the 'clean' data? Also, are there any automatic artifact rejection options available for trial (CTF) MEG data? Thanks in advance. -K. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- From r.vandermeij at donders.ru.nl Sun Jan 16 11:20:11 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Sun, 16 Jan 2011 11:20:11 +0100 Subject: [FieldTrip] singleplotTFR error In-Reply-To: References: Message-ID: <4D32C65B.5020304@donders.ru.nl> Hi Karl, Could you give some more information on the errors? Could you also post your cfg's? That will help in finding and fixing the bug. What FieldTrip version are you using? Best, Roemer On 15-1-2011 18:05, Karl Doron wrote: > Hello, > > Has anyone else reported a problem with ft_singleplotTFR and output of > the new specest module? > > multiplotTFR works, but 'interactive' method fails. > > It looks like the error occurs when trying to mask NaNs > > % masking only possible for evenly spaced axis > > if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) > > warning('(one of the) axis are not evenly spaced -> nans cannot be > masked out -> cfg.masknans is set to ''no'';') > > cfg.masknans = 'no'; > > end > > > > Thank you, > karl doron > UCSB > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From karl.doron at gmail.com Mon Jan 17 02:51:13 2011 From: karl.doron at gmail.com (Karl Doron) Date: Sun, 16 Jan 2011 17:51:13 -0800 Subject: [FieldTrip] singleplotTFR error In-Reply-To: <4D32C65B.5020304@donders.ru.nl> References: <4D32C65B.5020304@donders.ru.nl> Message-ID: Hello Roemer, Here's the cfg's and output from calls to ft_freqanalysis with method='wavelet' and the subsequent call to ft_singleplotTFR and the resulting error. The imagesc command will however plot the data at that channel imagesc(squeeze(wvpow.powspctrm(strmatch('A177',label),:,:))) Thanks for any help! cfg = []; cfg.output = 'pow'; cfg.channel = 'MEG'; cfg.method = 'wavelet'; cfg.foi = 10:2:30; cfg.toi = 0.0:0.05:2.75; wvpow = ft_freqanalysis(cfg, data_spctrm); wvpow = label: {246x1 cell} dimord: 'chan_freq_time' freq: [1x11 double] time: [1x56 double] powspctrm: [246x11x56 double] grad: [1x1 struct] cfg: [1x1 struct] %Singleplot results cfg = []; cfg.channel = 'A177'; cfg.grad = grad; cfg.xlim = [0.6 2.5]; cfg.ylim = [10 20]; figure; ft_singleplotTFR(cfg, wvpow) Warning: (one of the) axis are not evenly spaced -> nans cannot be masked out -> cfg.masknans is set to 'no'; > In ft_singleplotTFR at 296 ??? Attempted to access c(6,1); index out of bounds because size(c)=[5,37]. Error in ==> uimage at 124 ce(j,i) = c(indi(end), indj(end)); Error in ==> uimagesc at 46 hh = uimage(varargin{:},'CDataMapping','scaled'); Error in ==> ft_plot_matrix at 192 h = uimagesc(hdat, vdat, cdat, clim); Error in ==> ft_singleplotTFR at 327 ft_plot_matrix(data.(cfg.xparam)(xidc),data.(cfg.yparam)(yidc), TFR, 'clim',[zmin,zmax],'tag','cip') On Sun, Jan 16, 2011 at 2:20 AM, Roemer van der Meij < r.vandermeij at donders.ru.nl> wrote: > Hi Karl, > > Could you give some more information on the errors? Could you also post > your cfg's? That will help in finding and fixing the bug. What FieldTrip > version are you using? > > Best, > Roemer > > > > On 15-1-2011 18:05, Karl Doron wrote: > > Hello, > > Has anyone else reported a problem with ft_singleplotTFR and output of > the new specest module? > > multiplotTFR works, but 'interactive' method fails. > > It looks like the error occurs when trying to mask NaNs > > % masking only possible for evenly spaced axis > > if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) > > warning('(one of the) axis are not evenly spaced -> nans cannot be > masked out -> cfg.masknans is set to ''no'';') > > cfg.masknans = 'no'; > > end > > > Thank you, > karl doron > UCSB > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > 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 mcregar at upo.es Mon Jan 17 15:42:43 2011 From: mcregar at upo.es (Maite Crespo Garcia) Date: Mon, 17 Jan 2011 15:42:43 +0100 Subject: [FieldTrip] Noise projection for coherence estimates... Message-ID: <4374c5456d2776bd.4d346373@upo.es> Hello all, I would like to know if beamformer coherence estimates should be normalized dividing them by an equivalent noise projection as for power estimates. My experiment has a baseline. Would it be correct to divide coherence during active state by baseline coherence? What would be the better approach? Thank you very much in advance. Best regards, Maité -------------- next part -------------- An HTML attachment was scrubbed... URL: From sangita.dandekar at gmail.com Mon Jan 17 17:44:52 2011 From: sangita.dandekar at gmail.com (Sangita Dandekar) Date: Mon, 17 Jan 2011 11:44:52 -0500 Subject: [FieldTrip] searchable email discussion archive? Message-ID: The new fieldtrip page looks good. I was just wondering whether there is a method in place to search the discussion list email archives using keywords? The page at: http://mailman.science.ru.nl/pipermail/fieldtrip/ is sortable by field but I haven't been able to figure out how to do a keyword search. The old webpage's searchable email archive was extremely useful. Are there plans to create the same sort searchable archive for the new page? Thanks in advance for any help, Sangi -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Mon Jan 17 18:08:11 2011 From: matt.mollison at gmail.com (Matt Mollison) Date: Mon, 17 Jan 2011 10:08:11 -0700 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: References: Message-ID: Sangi, I agree that the search functionality at the old site was quite useful. One method that I've used for searching the new archives is to go to google.comand include "site: http://mailman.science.ru.nl/pipermail/fieldtrip/" with the terms that you wish to search for. Hope that helps. Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Mon, Jan 17, 2011 at 9:44 AM, Sangita Dandekar < sangita.dandekar at gmail.com> wrote: > The new fieldtrip page looks good. I was just wondering whether there is a > method in place to search the discussion list email archives using keywords? > > The page at: > http://mailman.science.ru.nl/pipermail/fieldtrip/ > > is sortable by field but I haven't been able to figure out how to do a > keyword search. The old webpage's searchable email archive was extremely > useful. Are there > plans to create the same sort searchable archive for the new page? > > Thanks in advance for any help, > Sangi > > _______________________________________________ > 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 mcregar at upo.es Mon Jan 17 18:13:18 2011 From: mcregar at upo.es (Maite Crespo Garcia) Date: Mon, 17 Jan 2011 18:13:18 +0100 Subject: [FieldTrip] Noise projection for coherence estimates... In-Reply-To: <4374c5456d2776bd.4d346373@upo.es> References: <4374c5456d2776bd.4d346373@upo.es> Message-ID: <45d37fe857bb6844.4d3486be@upo.es> I realized after writing the previous post that the coherence estimate is a ratio itself. Likely, using projected noise has no sense. But I'm still not sure about the right approach (compare to baseline and then between conditions?). Any suggestion? Thanks, Maité ----- Mensaje original ----- De: Maite Crespo Garcia Fecha: Lunes, 17 de Enero de 2011, 4:25 pm Asunto: [FieldTrip] Noise projection for coherence estimates... A: fieldtrip at donders.ru.nl > Hello all, > > I would like to know if beamformer coherence estimates should be normalized dividing them by an equivalent noise projection as for power estimates. My experiment has a baseline. Would it be correct to divide coherence during active state by baseline coherence? What would be the better approach? > > Thank you very much in advance. > > Best regards, > Maité > _______________________________________________ > 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.oosthoek at donders.ru.nl Tue Jan 18 09:18:46 2011 From: s.oosthoek at donders.ru.nl (Simon Oosthoek) Date: Tue, 18 Jan 2011 09:18:46 +0100 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: References: Message-ID: <4D354CE6.8000009@donders.ru.nl> Matt Mollison wrote: > Sangi, > > I agree that the search functionality at the old site was quite > useful. One method that I've used for searching the new archives is to > go to google.com and include > "site:http://mailman.science.ru.nl/pipermail/fieldtrip/" with the > terms that you wish to search for. > I think this is the best method to use, because I doubt the search functionality can easily be included on the mailman site. Perhaps I can fabricate a search box using google on the wiki for the mailinglist... Cheers Simon From stephen.whitmarsh at gmail.com Tue Jan 18 10:37:55 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 18 Jan 2011 10:37:55 +0100 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: <-6003509403171258621@unknownmsgid> References: <-6003509403171258621@unknownmsgid> Message-ID: Dear All, We will be giving a weekend FieldTrip workshop at the City College New York soon (February 5th – 6th) and still have a couple of last-minute spaces left for those in the NYC region interested in joining. Please see attachment for details. Sincerely, Stephen Whitmarsh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FieldTrip Weekend Workshop NYC.pdf Type: application/pdf Size: 86868 bytes Desc: not available URL: From eelke.spaak at donders.ru.nl Tue Jan 18 10:39:12 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 18 Jan 2011 10:39:12 +0100 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: <4D354CE6.8000009@donders.ru.nl> References: <4D354CE6.8000009@donders.ru.nl> Message-ID: Hello everyone, I've just added a Google Custom search box to the Discussion list page on the wiki (http://fieldtrip.fcdonders.nl/discussion_list). (Note that we are having a bit of trouble with some of our fileservers at the moment, and therefore the wiki might be offline every now and then. We hope to have these problems fixed shortly.) Best, Eelke 2011/1/18 Simon Oosthoek : > Matt Mollison wrote: >> >> Sangi, >> >> I agree that the search functionality at the old site was quite useful. >> One method that I've used for searching the new archives is to go to >> google.com and include >> "site:http://mailman.science.ru.nl/pipermail/fieldtrip/" with the terms that >> you wish to search for. >> > I think this is the best method to use, because I doubt the search > functionality can easily be included on the mailman site. > Perhaps I can fabricate a search box using google on the wiki for the > mailinglist... > > Cheers > > Simon > From venug001 at crimson.ua.edu Tue Jan 18 14:39:36 2011 From: venug001 at crimson.ua.edu (Gopakumar Venugopalan) Date: Tue, 18 Jan 2011 04:39:36 -0900 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, and just finished my post doc last week. I wonder what options might be open to me. Thanks in advance. Warm regards gopa On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear All, > > > > We will be giving a weekend FieldTrip workshop at the City College New York > soon (February 5th – 6th) and still have a couple of last-minute spaces > left for those in the NYC region interested in joining. Please see > attachment for details. > > > > Sincerely, > > Stephen Whitmarsh > > > _______________________________________________ > 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 venug001 at crimson.ua.edu Tue Jan 18 14:40:48 2011 From: venug001 at crimson.ua.edu (Gopakumar Venugopalan) Date: Tue, 18 Jan 2011 04:40:48 -0900 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: I responded to the fieldtrip listserv by mistake, would you please delete it and NOT include it in your digest or forward. Warm regards gopa On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan < venug001 at crimson.ua.edu> wrote: > Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, > and just finished my post doc last week. I wonder what options might be open > to me. Thanks in advance. > Warm regards > gopa > > On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < > stephen.whitmarsh at gmail.com> wrote: > >> Dear All, >> >> >> >> We will be giving a weekend FieldTrip workshop at the City College New >> York soon (February 5th – 6th) and still have a couple of last-minute >> spaces left for those in the NYC region interested in joining. Please see >> attachment for details. >> >> >> >> Sincerely, >> >> Stephen Whitmarsh >> >> >> _______________________________________________ >> 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 Tue Jan 18 18:43:11 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 18 Jan 2011 11:43:11 -0600 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Dear Fieldtrip users, i just received the info about the NY workshop taking place on 5th and 6th february. Unfortunately, its too late for me to make it. As i'd like to participate to such workshop/formation, is there a webpage or a place where i can find such informations about future events? Rodolphe On Tue, Jan 18, 2011 at 7:40 AM, Gopakumar Venugopalan < venug001 at crimson.ua.edu> wrote: > I responded to the fieldtrip listserv by mistake, would you please delete > it and NOT include it in your digest or forward. > Warm regards > gopa > > On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan < > venug001 at crimson.ua.edu> wrote: > >> Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, >> and just finished my post doc last week. I wonder what options might be open >> to me. Thanks in advance. >> Warm regards >> gopa >> >> On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> >>> Dear All, >>> >>> >>> >>> We will be giving a weekend FieldTrip workshop at the City College New >>> York soon (February 5th – 6th) and still have a couple of last-minute >>> spaces left for those in the NYC region interested in joining. Please see >>> attachment for details. >>> >>> >>> >>> Sincerely, >>> >>> Stephen Whitmarsh >>> >>> >>> _______________________________________________ >>> 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 m.chait at ucl.ac.uk Wed Jan 19 11:48:37 2011 From: m.chait at ucl.ac.uk (Maria Chait) Date: Wed, 19 Jan 2011 10:48:37 -0000 Subject: [FieldTrip] RA position at the UCL Ear Institute - MEG & auditory change detection Message-ID: <079f01cbb7c6$6d996c50$48cc44f0$@chait@ucl.ac.uk> Dear Colleagues, I am writing to point your attention to a research assistant job opening at the UCL Ear Institute and would be grateful if you could distribute the advert to relevant students in your department. Please note that it is possible to undertake a UCL PhD degree within the context of this research work. Research Assistant - Ref: 1174144 Closing Date: 17/02/2011 Apply on: www.ucl.ac.uk/hr/jobs A research assistant position (salary £27,796 - £29,318 per annum Inclusive of London allowance) is available to work on a Wellcome Trust funded project that will use MEG functional brain imaging to investigate the neural systems that support auditory change detection in the human brain. You will be supervised by Dr Maria Chait (UCL Ear Institute) and Prof. Tim Griffiths (Newcastle University). The post holder will be based at UCL Ear Institute, and report to Dr Maria Chait. MEG scanning will be carried out at UCL’s Wellcome Trust Centre for Neuroimaging. Initial funding for this post is available for 36 months. There is the possibility (if UCL eligibility criteria are satisfied) to undertake a UCL PhD degree within the context of this research work. Your main duties and responsibilities will be: 1. Design and execute MEG brain imaging experiments. 2. Develop MatLab software for running the experiments and for data analysis 3. Train subjects in preparation for relevant experiments. 4. Record and analyze imaging data. 5. Assist in the preparation of manuscripts. The UCL Ear Institute provides state-of-the-art research facilities across a wide range of disciplines and is one of the foremost centres for hearing, speech and language-related research within Europe. The Wellcome Trust Centre for Neuroimaging is a leading centre for brain imaging, bringing together clinicians and scientists who study higher cognitive function using neuroimaging techniques. Key Requirements Applicants should hold a 1St class, or upper 2nd (or equivalent) bachelor’s degree (masters degree an advantage) in an engineering or scientific subject and have substantial experience in digital signal processing and computer programming. Previous experience with functional brain imaging and/or acoustics is desirable. Further Details You should apply for this post (Ref #: 1174144) through UCL's online recruitment website, www.ucl.ac.uk/hr/jobs, where you can download a job description and person specification. If you have any queries please contact Dr. Maria Chait (email m.chait at ucl.ac.uk) Maria Chait PhD m.chait at ucl.ac.uk Research Fellow UCL Ear Institute 332 Gray's Inn Road London WC1X 8EE -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jan 20 10:51:48 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 20 Jan 2011 10:51:48 +0100 Subject: [FieldTrip] FieldtripR? In-Reply-To: References: Message-ID: <87C19057-05F3-4A69-85A4-0B932BA8FC6A@donders.ru.nl> Dear Mike, [CCed to the fieldtrip email discussion list]] On 19 Jan 2011, at 23:39, Mike Lawrence wrote: > I just came across your Fieldtrip software and it looks very > impressive. However, I'm not a MATLAB user; I feel that scientific > software needs to be both free and open source for the purposes of > replication and extension, so I use R instead (well, I also use R > because it's the lingua franca of statistics, so it provides access to > cutting edge routines). I therefore thought I'd request that the > Fieldtrip team work to port the Fieldtrip code to R. There is > currently a paucity of EEG analysis packages for R and a port of > Fieldtrip would make a great contribution. Thanks for your constructive suggestion. The FieldTrip software is open source, but indeed requires commercial software (MATLAB) to run. Most people run it on Windows or Apple OSX, even further commercial dependencies for those users. Requests for porting FieldTrip to free languages (other than Matlab) come up regularly, e.g. to make a compiled C/C++ version, an Octave version, a Python version or an R version. Regretfully, we are not able to honor these requests. FieldTrip is developped for, and by scientists that are mostly funded by national and international scientific projects. Those projects require our contributors to focus on their scientific results, and FieldTrip can be considered as just spinoff. For people that want to use FieldTrip without Matlab, pragmatically I would first suggest to look into Octave: large parts (but not all parts) of our code will execute properly in Octave with no or little changes. An alternative that requires MATLAB for development, but does not require MATLAB for running it, would be to use the MATLAB compiler to compile it into a stand-alone version that can be distributed free of charge. Contributions in either the direction of Octave or a compiled version, or contributions in porting it to another language, are most certainly welcome and would receive our support. If you feel that we should receive funding from our national or from international research funding agency to do the work that is required in porting it to a free platform, please consider contacting http://www.nwo.nl and similar agencies to make a plea for this. best regards, Robert PS please also see my "coffee machine" email at http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003339.html , which is part of a similar thread. --- FieldTrip project leader Senior Researcher and MEG physicist at the Donders Centre for Cognitive Neuroimaging From michael.wibral at web.de Thu Jan 20 10:51:59 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 20 Jan 2011 10:51:59 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection Message-ID: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> Deal Fieldtrip users, there is something else I do not understand in the tutorial: if you read in the data in trials (as it is done) how can you do padding later as it is suggested. I tried to run the example code on teh website reading in the data such that it contains trials. If I then try to search for muscle artifacts I get the 'subscript indices must be positive or logical ... values', indicating that the code tries to access data that aren't there. If I set the padding to zero (instead of 0.1) it works. So I am wondering wether somehow one should actually run these things on continuous data (contrary to what is indicated in the tutorial)? Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From michael.wibral at web.de Thu Jan 20 10:52:17 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 20 Jan 2011 10:52:17 +0100 (CET) Subject: [FieldTrip] error in the artifact rejection tutorial? Message-ID: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> Dear fieldtrip community, there seems to be a slight inconsistency in the tutorial section on artifact removal (which I otherwise like a lot because it calrifies a lot of the 'black-boxiness' of these particular fieldtrip functions (thanks a lot). The part I am referring to is in the jump removal section. It starts with the lines: % jump cfg = []; if isfield(cfg, 'padding') && cfg.padding~=0 padding = cfg.padding; else padding = 0; end I wonder whther these lines should go somewhere else as after clearing cfg the code will alwazs end up in the second part if the if condition, as there can be no 'padding' field. Didn't want to change this my self, as I might misunderstand something. Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Thu Jan 20 15:06:33 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 20 Jan 2011 15:06:33 +0100 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: <5E34E57B-F699-4267-858B-D903CE79F61C@donders.ru.nl> Dear Rodolphe We will host a toolkit course on "Advanced MEG and EEG analysis" at the Donders in Nijmegen. Please have a look at http://www.ru.nl/donders/agenda-events/courses/toolkits-2011/ . Note that it only contains the preliminary program (simply copied from last year) and that the final programm will look slightly different. The registation has just openend this week, and a formal annoucement will follow. Please do note that it tends to be oversubscribed: we select the participants on their motivation and background and not on who registers first. best regards, Robert On 18 Jan 2011, at 18:43, Rodolphe Nenert wrote: > Dear Fieldtrip users, > > i just received the info about the NY workshop taking place on 5th > and 6th february. Unfortunately, its too late for me to make it. As > i'd like to participate to such workshop/formation, is there a > webpage or a place where i can find such informations about future > events? > > Rodolphe From jan.schoffelen at donders.ru.nl Fri Jan 21 09:52:23 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 21 Jan 2011 09:52:23 +0100 Subject: [FieldTrip] error in the artifact rejection tutorial? In-Reply-To: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> References: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> Message-ID: Dear Michael, Please feel free to delete this particular line (and/or edit any other line) from the wiki. Declaring cfg empty before the conditional statements indeed does not makes sense. Best wishes, JM On Jan 20, 2011, at 10:52 AM, Michael Wibral wrote: > Dear fieldtrip community, > > there seems to be a slight inconsistency in the tutorial section on > artifact removal (which I otherwise like a lot because it calrifies > a lot of the 'black-boxiness' of these particular fieldtrip > functions (thanks a lot). > The part I am referring to is in the jump removal section. > > It starts with the lines: > > > % jump > cfg = []; > if isfield(cfg, 'padding') && cfg.padding~=0 > padding = cfg.padding; > else > padding = 0; > end > > > I wonder whther these lines should go somewhere else as after > clearing cfg the code will alwazs end up in the second part if the > if condition, as there can be no 'padding' field. > Didn't want to change this my self, as I might misunderstand > something. > > Michael > Wibral.vcf>_______________________________________________ > 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 Fri Jan 21 09:55:48 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 21 Jan 2011 09:55:48 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> Message-ID: Dear Michael, Yes, I agree with you here as well. In principle the ft_artifact_zvalue supports data as a second input argument, but in such case the different types of padding in the cfg do not make sense. I would indeed remove the second input arguments in the example code snippets. Could I ask you to take care of that? Thanks, JM On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: > Deal Fieldtrip users, > > there is something else I do not understand in the tutorial: if you > read in the data in trials (as it is done) how can you do padding > later as it is suggested. I tried to run the example code on teh > website reading in the data such that it contains trials. If I then > try to search for muscle artifacts I get the 'subscript indices must > be positive or logical ... values', indicating that the code tries > to access data that aren't there. If I set the padding to zero > (instead of 0.1) it works. So I am wondering wether somehow one > should actually run these things on continuous data (contrary to > what is indicated in the tutorial)? > > Michael > Wibral.vcf>_______________________________________________ > 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 karch at mpib-berlin.mpg.de Fri Jan 21 16:49:20 2011 From: karch at mpib-berlin.mpg.de (Karch, Julian) Date: Fri, 21 Jan 2011 16:49:20 +0100 Subject: [FieldTrip] WG: References: <82EE999347EBF142A8D78EF16FB83D8D01C82524@MPIBMAIL01.mpib-berlin.mpg.de> Message-ID: <82EE999347EBF142A8D78EF16FB83D8D01C82525@MPIBMAIL01.mpib-berlin.mpg.de> Hello, i just tried to go through the Multivariates Tutorial (http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis) unluckly when i typed "stat = ft_timelockstatistics(cfg,tleft,tright);" matlab aborted with the exit code: ??? Error using ==> tprod at 119 unable to compile MEX version of 'E:/julian/matlab/fieldtrip/multivariate/external/farquhar/tprod/tprod', please make sure your MEX compiler is set up correctly (try 'mex -setup'). I'm using MATLAB 7.10.0 64 Bit on Windows 7. I definitively have a working mex compiler as compiling the example yprime.c is working perfectly. I also tried to compile the files manually by typing mex('ddtprod.c','dstprod.c','sdtprod.c','sstprod.c','tprod_util.c','tprod_mex.c','mxInfo.c');. This resulted in the following output: ddtprod.c e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier C:\PROGRA~1\MATLAB\R2010A\BIN\MEX.PL: Error: Compile of 'ddtprod.c' failed. Any suggestions? Julian Karch Research Assistant Max Planck Institute for Human Development Department Lifespan Psychology Lentzeallee 94 14195 Berlin Tel.: 030 / 82406-294 Email: karch at mpib-berlin.mpg.de Internet: www.mpib-berlin.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Fri Jan 21 20:07:17 2011 From: frank.ye.mei at gmail.com (Frank (Ye) Mei) Date: Fri, 21 Jan 2011 14:07:17 -0500 Subject: [FieldTrip] problem downloading fieldtrip Message-ID: <4D39D965.20601@gmail.com> I cann't download the fieldtrip toolbox. I didn't get the email with download instructions. Thank you for your download request, an email with download instructions has been sent to ............ If you object to giving your real email address, please consider using a service like http://www.spamgourmet.com, http://www.mailinator.com or http://10minutemail.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From todavidkim at gmail.com Fri Jan 21 20:21:27 2011 From: todavidkim at gmail.com (David Kim) Date: Fri, 21 Jan 2011 11:21:27 -0800 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: <4D39D965.20601@gmail.com> References: <4D39D965.20601@gmail.com> Message-ID: Hi Frank, While you are awaiting the official response from fieldtrip folks you might try this: http://code.google.com/p/fieldtrip/source/checkout If you have a working understanding of of how to use svn, I found this to be a great way to install and update fieldtrip software. On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: > I cann't download the fieldtrip toolbox. I didn't get the email with > download instructions. > > Thank you for your download request, an email with download instructions > has been sent to ............ > > If you object to giving your real email address, please consider using a > service like http://www.spamgourmet.com, http://www.mailinator.com or > http://10minutemail.com. > > > _______________________________________________ > 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 dgroppe at cogsci.ucsd.edu Sat Jan 22 08:29:00 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 21 Jan 2011 23:29:00 -0800 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Speaking of workshops, Fieldtrip users might be interested in some of the talks from the 12th EEGLAB workshop that took place a couple of months ago. Videos of the talks were just posted online: http://thesciencenetwork.org/programs/12th-eeglab-workshop Talk slides and supportive material are available on the EEGLAB wiki as well: http://sccn.ucsd.edu/wiki/Twelfth_EEGLAB_Workshop Although the talks obviously don't cover the logistics of using Fieldtrip, some of the methods implemented by Fieldtrip (e.g., time-frequency analysis, independent components analysis) are and might be of use to those of you just getting started with these techniques. Moreover, there are some neat talks on future directions in EEG technology (e.g., dry electrodes and EEG recording from moving participants). cheers, -David On Tue, Jan 18, 2011 at 9:43 AM, Rodolphe Nenert wrote: > Dear Fieldtrip users, > i just received the info about the NY workshop taking place on 5th and 6th > february. Unfortunately, its too late for me to make it. As i'd like to > participate to such workshop/formation, is there a webpage or a place where > i can find such informations about future events? > Rodolphe > > On Tue, Jan 18, 2011 at 7:40 AM, Gopakumar Venugopalan > wrote: >> >> I responded to the fieldtrip listserv by mistake, would you please delete >> it and NOT include it in your digest or forward. >> Warm regards >> gopa >> >> On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan >> wrote: >>> >>> Dear Stepben Whitmarsh, I would be interested, don't live in the NYC >>> area, and just finished my post doc last week. I wonder what options might >>> be open to me. Thanks in advance. >>> Warm regards >>> gopa >>> >>> On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh >>> wrote: >>>> >>>> Dear All, >>>> >>>> >>>> >>>> We will be giving a weekend FieldTrip workshop at the City College New >>>> York soon (February 5th – 6th) and still have a couple of last-minute spaces >>>> left for those in the NYC region interested in joining. Please see >>>> attachment for details. >>>> >>>> >>>> >>>> Sincerely, >>>> >>>> Stephen Whitmarsh >>>> >>>> _______________________________________________ >>>> 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 > -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From kassayag at gmail.com Sat Jan 22 08:45:07 2011 From: kassayag at gmail.com (karen assayag) Date: Sat, 22 Jan 2011 09:45:07 +0200 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: References: <4D39D965.20601@gmail.com> Message-ID: is the download good for mac ? On Fri, Jan 21, 2011 at 9:21 PM, David Kim wrote: > Hi Frank, > > While you are awaiting the official response from fieldtrip folks you might > try this: > > http://code.google.com/p/fieldtrip/source/checkout > > If you have a working understanding of of how to use svn, > I found this to be a great way to install and update fieldtrip software. > > On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: > >> I cann't download the fieldtrip toolbox. I didn't get the email with >> download instructions. >> >> Thank you for your download request, an email with download instructions >> has been sent to ............ >> >> If you object to giving your real email address, please consider using a >> service like http://www.spamgourmet.com, http://www.mailinator.com or >> http://10minutemail.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 > -- Karen -------------- next part -------------- An HTML attachment was scrubbed... URL: From todavidkim at gmail.com Sat Jan 22 08:54:42 2011 From: todavidkim at gmail.com (David Kim) Date: Fri, 21 Jan 2011 23:54:42 -0800 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: References: <4D39D965.20601@gmail.com> Message-ID: Hi Karen, Again, you might want to hear the official response from the fieldtrip folks, but I've successfully used svn on several OS platforms without an issue (WinXP, Win7, CentOs, Ubuntu). So I'm assuming it works across platforms. I just did a search on my CentOs machine, and it looks like the svn version includes all the mexmac files. I would give it a try. On Fri, Jan 21, 2011 at 11:45 PM, karen assayag wrote: > is the download good for mac ? > > > On Fri, Jan 21, 2011 at 9:21 PM, David Kim wrote: > >> Hi Frank, >> >> While you are awaiting the official response from fieldtrip folks you >> might try this: >> >> http://code.google.com/p/fieldtrip/source/checkout >> >> If you have a working understanding of of how to use svn, >> I found this to be a great way to install and update fieldtrip software. >> >> On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: >> >>> I cann't download the fieldtrip toolbox. I didn't get the email with >>> download instructions. >>> >>> Thank you for your download request, an email with download instructions >>> has been sent to ............ >>> >>> If you object to giving your real email address, please consider using a >>> service like http://www.spamgourmet.com, http://www.mailinator.com or >>> http://10minutemail.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 >> > > > > -- > Karen > > > > _______________________________________________ > 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 Marcel.Bastiaansen at mpi.nl Mon Jan 24 11:44:07 2011 From: Marcel.Bastiaansen at mpi.nl (Bastiaansen, Marcel) Date: Mon, 24 Jan 2011 11:44:07 +0100 Subject: [FieldTrip] question on beamformers Message-ID: <4D3D57F7.8090504@mpi.nl> Dear all, I have the following conceptual issue with using beamforming: I have data from 2 conditions, A and B. Both contain a prestimulus interval and a poststimulus interval. When plotting the TF representations of power, using a *relative* baseline (poststimulus interval / prestimulus interval), a strong difference emerges between the conditions in the beta frequency range. Especially if I plot the *difference between the conditions*, the beta effect is long-lasting, narrow-band and topographically focused. Ideal for beamforming, I'd say. In setting up the beamformer analysis, I am faced with the following issue: the effect is most clearly present in the *relative* power changes, so I would want to compute spatial filters for both the pre and the post time intervals. My hunch would be to compute common spatial filters for both pre intervals (preA and preB), and common filters for both post intervals (postA and postB). Then, (after projecting the trials through the filters), compute the relative power again (pre/post for each condition). Does this approach make sense? Next question is then, at which point in the analysis pipeline should one do the condition subtraction? (I'd want to do that because at the TFR level the effect comes out most clearly in the condition difference) Best, Marcel -- dr. Marcel C.M. Bastiaansen. Max Planck Institute for Psycholinguistics Visiting Adress: Wundtlaan 1, 6525 XD Nijmegen, the Netherlands Mailing adress: P.O. Box 310, 6500 AH Nijmegen, the Netherlands phone: +31 24 3521 347 fax: +31 24 3521 213 mail: marcel.bastiaansen at mpi.nl http://www.mpi.nl/people/bastiaansen-marcel and Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Visiting address: Kapittelweg 29, 6525 EN Nijmegen, the Netherlands Mailing address: PO Box 9101, 6500 HB Nijmegen, the Netherlands phone: + 31 24 3610 882 fax: + 31 24 3610 989 mail: marcel.bastiaansen at fcdonders.ru.nl web: http://www.ru.nl/neuroimaging/staff/neurocognition_of/marcel_bastiaansen/ -- From michael.wibral at web.de Mon Jan 24 11:48:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 11:48:47 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056>, Message-ID: <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> Hi Jan-Mathijs, I am a bit unsure how to proceed: (1) sketch the artifact correction way like this ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> ft_preprocessing OR (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. I think I should go for option (1) as this seems to be the standard use on continuous data. Sometime in the futrure one should then add a tutorial for those that have data in trials to start with. Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 21, 2011 9:55:48 AM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Dear Michael, > >Yes, I agree with you here as well. In principle the >ft_artifact_zvalue supports data as a second input argument, but in >such case the different types of padding in the cfg do not make sense. >I would indeed remove the second input arguments in the example code >snippets. Could I ask you to take care of that? > >Thanks, > >JM > > >On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: > >> Deal Fieldtrip users, >> >> there is something else I do not understand in the tutorial: if you >> read in the data in trials (as it is done) how can you do padding >> later as it is suggested. I tried to run the example code on teh >> website reading in the data such that it contains trials. If I then >> try to search for muscle artifacts I get the 'subscript indices must >> be positive or logical ... values', indicating that the code tries >> to access data that aren't there. If I set the padding to zero >> (instead of 0.1) it works. So I am wondering wether somehow one >> should actually run these things on continuous data (contrary to >> what is indicated in the tutorial)? >> >> Michael >> > Wibral.vcf>_______________________________________________ >> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Mon Jan 24 12:12:57 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 24 Jan 2011 12:12:57 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> Message-ID: <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> Dear Michael, I agree. The tutorial should be 'de'-confused by sketching option 1, and another one should be describing option 2, or the original should be clearly making the distinction. Best, JM On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: > Hi Jan-Mathijs, > > I am a bit unsure how to proceed: > > (1) sketch the artifact correction way like this > ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> > ft_preprocessing > OR > (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> > artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. > > I think I should go for option (1) as this seems to be the standard > use on continuous data. Sometime in the futrure one should then add > a tutorial for those that have data in trials to start with. > > Michael > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 21, 2011 9:55:48 AM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Dear Michael, >> >> Yes, I agree with you here as well. In principle the >> ft_artifact_zvalue supports data as a second input argument, but in >> such case the different types of padding in the cfg do not make >> sense. >> I would indeed remove the second input arguments in the example code >> snippets. Could I ask you to take care of that? >> >> Thanks, >> >> JM >> >> >> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >> >>> Deal Fieldtrip users, >>> >>> there is something else I do not understand in the tutorial: if you >>> read in the data in trials (as it is done) how can you do padding >>> later as it is suggested. I tried to run the example code on teh >>> website reading in the data such that it contains trials. If I then >>> try to search for muscle artifacts I get the 'subscript indices must >>> be positive or logical ... values', indicating that the code tries >>> to access data that aren't there. If I set the padding to zero >>> (instead of 0.1) it works. So I am wondering wether somehow one >>> should actually run these things on continuous data (contrary to >>> what is indicated in the tutorial)? >>> >>> Michael >>> >> Wibral.vcf>_______________________________________________ >>> 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 stephen.whitmarsh at gmail.com Mon Jan 24 12:18:47 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 24 Jan 2011 12:18:47 +0100 Subject: [FieldTrip] question on beamformers In-Reply-To: <4D3D57F7.8090504@mpi.nl> References: <4D3D57F7.8090504@mpi.nl> Message-ID: Dear Marcel, My two cents are the following: I would recommend to compute common filter over ALL conditions, pre AND post. This will make sure you use as much information as possible to calculate your cross-spectral density matrix and subsequent filter. I assume you assume that the location/orientation of the sources do not change before and after stimulus. Also, in the case that you are looking for a post-stimulus beta DECREASE it will help you to accurately determine post-stimulus activity based on a filter calculated from of a period where there is most (beta) signal. Then, for your contrast project your conditions, pre and post *separately* and do your relative contrast then: e.g. projected post-stimulus activity A / projected pre-stimulus activity A, and same for B. Then compare relative A - or / by B. Bottom line, do your common filter on everything, project and compare everything separately after that. Hope that helps, Stephen On 24 January 2011 11:44, Bastiaansen, Marcel wrote: > Dear all, > > I have the following conceptual issue with using beamforming: > > I have data from 2 conditions, A and B. Both contain a prestimulus interval > and a poststimulus interval. > > When plotting the TF representations of power, using a *relative* baseline > (poststimulus interval / prestimulus interval), a strong difference emerges > between the conditions in the beta frequency range. Especially if I plot the > *difference between the conditions*, the beta effect is long-lasting, > narrow-band and topographically focused. Ideal for beamforming, I'd say. > > In setting up the beamformer analysis, I am faced with the following issue: > the effect is most clearly present in the *relative* power changes, so I > would want to compute spatial filters for both the pre and the post time > intervals. My hunch would be to compute common spatial filters for both pre > intervals (preA and preB), and common filters for both post intervals (postA > and postB). Then, (after projecting the trials through the filters), compute > the relative power again (pre/post for each condition). Does this approach > make sense? > > Next question is then, at which point in the analysis pipeline should one > do the condition subtraction? (I'd want to do that because at the TFR level > the effect comes out most clearly in the condition difference) > > > Best, > Marcel > > > > -- > dr. Marcel C.M. Bastiaansen. > > Max Planck Institute for Psycholinguistics > Visiting Adress: Wundtlaan 1, 6525 XD Nijmegen, the Netherlands > Mailing adress: P.O. Box 310, 6500 AH Nijmegen, the Netherlands > phone: +31 24 3521 347 > fax: +31 24 3521 213 > mail: marcel.bastiaansen at mpi.nl > http://www.mpi.nl/people/bastiaansen-marcel > > and > > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Visiting address: Kapittelweg 29, 6525 EN Nijmegen, the Netherlands > Mailing address: PO Box 9101, 6500 HB Nijmegen, the Netherlands > phone: + 31 24 3610 882 > fax: + 31 24 3610 989 > mail: marcel.bastiaansen at fcdonders.ru.nl > web: > http://www.ru.nl/neuroimaging/staff/neurocognition_of/marcel_bastiaansen/ > -- > _______________________________________________ > 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 Mon Jan 24 13:51:38 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 13:51:38 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054>, <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> Message-ID: <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> Hi Jan mathijs, I tried to get option1 running, stumbled over the following little obstacle however: I tried to keep one cfg throughout the steps ft_definetrial; ft_artifact_zvalue, ft_rejectartifcat (with option complete and some tracking of where artfecats were found), ft_preprocessing (cutting out the clean trials from the cont. data). IMHO this used to be the way most people did this kind of procesing a while ago. However, I can't get ft_artifact_zvalue to run with different settings one after another for jump/musvle/EOG. FT claims after the first run of ft_artifact_zvalue that the z-value thing has been performed and refuse to detect other artifacts with new settings. >From here I only see two alternative: specifying a really lengthy cfg every time a new (also struggling with the cfg.dataset versus cfg.datafile issue) and do the bookkeeping of cfg.trl and related things myself or manually removing the cfg.artdef.zvalue.artifct field to get the z-value based detection to run again. This seems a bit odd to me. Any suggestions? Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 12:12:57 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Dear Michael, > >I agree. The tutorial should be 'de'-confused by sketching option 1, >and another one should be describing option 2, or the original should >be clearly making the distinction. > >Best, > >JM > > >On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: > >> Hi Jan-Mathijs, >> >> I am a bit unsure how to proceed: >> >> (1) sketch the artifact correction way like this >> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >> ft_preprocessing >> OR >> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. >> >> I think I should go for option (1) as this seems to be the standard >> use on continuous data. Sometime in the futrure one should then add >> a tutorial for those that have data in trials to start with. >> >> Michael >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 21, 2011 9:55:48 AM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> Yes, I agree with you here as well. In principle the >>> ft_artifact_zvalue supports data as a second input argument, but in >>> such case the different types of padding in the cfg do not make >>> sense. >>> I would indeed remove the second input arguments in the example code >>> snippets. Could I ask you to take care of that? >>> >>> Thanks, >>> >>> JM >>> >>> >>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>> >>>> Deal Fieldtrip users, >>>> >>>> there is something else I do not understand in the tutorial: if you >>>> read in the data in trials (as it is done) how can you do padding >>>> later as it is suggested. I tried to run the example code on teh >>>> website reading in the data such that it contains trials. If I then >>>> try to search for muscle artifacts I get the 'subscript indices must >>>> be positive or logical ... values', indicating that the code tries >>>> to access data that aren't there. If I set the padding to zero >>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>> should actually run these things on continuous data (contrary to >>>> what is indicated in the tutorial)? >>>> >>>> Michael >>>> >>> Wibral.vcf>_______________________________________________ >>>> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Mon Jan 24 16:41:09 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 24 Jan 2011 16:41:09 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> Message-ID: Hmmm, apparently this approach needs to be ironed out a bit (also from our side). For now, I'd say that it should work if you keep per type of artifact the artifact field in the output configuration, and just concatenate these prior to calling ft_rejectartifact. I will moreover CC this e-mail to the people involved in creating the first version of the renewed tutorial, and will bring up the issue in this week's FieldTrip developers meeting. Best, JM On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > Hi Jan mathijs, > > I tried to get option1 running, stumbled over the following little > obstacle however: > > I tried to keep one cfg throughout the steps ft_definetrial; > ft_artifact_zvalue, ft_rejectartifcat (with option complete and some > tracking of where artfecats were found), ft_preprocessing (cutting > out the clean trials from the cont. data). IMHO this used to be the > way most people did this kind of procesing a while ago. > > However, I can't get ft_artifact_zvalue to run with different > settings one after another for jump/musvle/EOG. FT claims after the > first run of ft_artifact_zvalue that the z-value thing has been > performed and refuse to detect other artifacts with new settings. > >> From here I only see two alternative: specifying a really lengthy >> cfg every time a new (also struggling with the cfg.dataset versus >> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >> things myself or manually removing the cfg.artdef.zvalue.artifct >> field to get the z-value based detection to run again. This seems a >> bit odd to me. > > Any suggestions? > > Michael > > > > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 24, 2011 12:12:57 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Dear Michael, >> >> I agree. The tutorial should be 'de'-confused by sketching option 1, >> and another one should be describing option 2, or the original should >> be clearly making the distinction. >> >> Best, >> >> JM >> >> >> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >> >>> Hi Jan-Mathijs, >>> >>> I am a bit unsure how to proceed: >>> >>> (1) sketch the artifact correction way like this >>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>> ft_preprocessing >>> OR >>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>> ft_preprocessing. >>> >>> I think I should go for option (1) as this seems to be the standard >>> use on continuous data. Sometime in the futrure one should then add >>> a tutorial for those that have data in trials to start with. >>> >>> Michael >>> >>> -----Ursprüngliche Nachricht----- >>> Von: "jan-mathijs schoffelen" >>> Gesendet: Jan 21, 2011 9:55:48 AM >>> An: "Email discussion list for the FieldTrip project" >>> >>> Betreff: Re: [FieldTrip] more on artfifact rejection >>> >>>> Dear Michael, >>>> >>>> Yes, I agree with you here as well. In principle the >>>> ft_artifact_zvalue supports data as a second input argument, but in >>>> such case the different types of padding in the cfg do not make >>>> sense. >>>> I would indeed remove the second input arguments in the example >>>> code >>>> snippets. Could I ask you to take care of that? >>>> >>>> Thanks, >>>> >>>> JM >>>> >>>> >>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>> >>>>> Deal Fieldtrip users, >>>>> >>>>> there is something else I do not understand in the tutorial: if >>>>> you >>>>> read in the data in trials (as it is done) how can you do padding >>>>> later as it is suggested. I tried to run the example code on teh >>>>> website reading in the data such that it contains trials. If I >>>>> then >>>>> try to search for muscle artifacts I get the 'subscript indices >>>>> must >>>>> be positive or logical ... values', indicating that the code tries >>>>> to access data that aren't there. If I set the padding to zero >>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>> should actually run these things on continuous data (contrary to >>>>> what is indicated in the tutorial)? >>>>> >>>>> Michael >>>>> >>>> Wibral.vcf>_______________________________________________ >>>>> 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 Patricia.Wollstadt at gmx.de Mon Jan 24 17:47:26 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Mon, 24 Jan 2011 17:47:26 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction Message-ID: <20110124164726.247880@gmx.net> Dear Fieldtrip-users, I'm currently trying to calculate freqstatistics for four experimental groups, using the following options: groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) length(subjects{4})]; design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; % 1 to N subjects design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group membership cfg=[]; cfg.design=design; cfg.uvar = 1; cfg.ivar = 2; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesF'; cfg.correctm = 'fdr'; cfg.numrandomization = 180000; cfg.alpha = 0.01/7; cfg.tail = 1; cfg.design = design; cfg.channels = myChannels; cfg.avgovertime = 'yes'; cfg.avgoverfreq = 'yes'; cfg.frequency = [1 3]; stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); With these settings, the coputation itself runs fine, but the resulting 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists of only ones). This would mean, that I found significant effects for all channels. Is this possible or rather due to an error somewhere in my script? Is it likely, that these are 'real' zeroes or rather very small values, close to zero? Any hints and suggestions are very welcome, thank you in advance, Kind regards Patricia Wollstadt -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl From michael.wibral at web.de Mon Jan 24 18:27:08 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 18:27:08 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054>, Message-ID: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Hi Jan-Mathijs, this is basically what we do at the moment, i.e. fooling artifcat_zvalue by removing the one field it complains about amnd using rejetartefact only at the very last. See the attched code - I really do not want to post this code on the tutorial website as I am not fully sure what I am doing :-). Michael %% CODE ft_defaults; Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/DATASETS/'; Design={ 'DMG13_NewMooney_20110120_0', [2 3], 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; } for ss=1:size(Design,1) % over subjects for cc=1:length(Design{ss,4}) % over conditions for ff=1:length(Design{ss,2}) % over .ds datasets/runs FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), '.ds') FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) % core data reading cfg=[]; cfg.dataset=FullFileName; cfg.headerformat = 'ctf_ds'; % for you to check whether still necessary ctf.dataformat = 'ctf_ds'; cfg.cond=Design{ss,4}(cc) cfg.continuous='yes'; cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? cfg.trialfun=Design{ss,3}; cfg=ft_definetrial(cfg); cfg.trl(end,:)=[]; trl=cfg.trl; % keep track of the trials padding=0.75 % 750 ms %%%%%%%%% artifact rejection section %%% jump % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 35; cfg.artfctdef.zvalue.trlpadding = 0.5*padding; cfg.artfctdef.zvalue.artpadding = 0.5*padding; cfg.artfctdef.zvalue.fltpadding = 0; % algorithmic parameters cfg.artfctdef.zvalue.medianfilter = 'yes'; cfg.artfctdef.zvalue.medianfiltord = 9; % in samples cfg.artfctdef.zvalue.absdiff = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'jump'; [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); % cfg.artfctdef.jump.artifact = artifact_jump; % cfg = ft_rejectartifact(cfg); %%% muscle cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % remove field from structure otherwise this won't run ?? % cutoff and padding  cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 15; cfg.artfctdef.zvalue.trlpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; cfg.artfctdef.zvalue.artpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfreq = [110 140]; cfg.artfctdef.zvalue.bpfiltord = 6; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.boxcar = 0.2; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'muscle'; [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); %%% EOG cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % cutoff and padding cfg.artfctdef.zvalue.channel = 'MRT41'; cfg.artfctdef.zvalue.cutoff = 10; cfg.artfctdef.zvalue.trlpadding = 0.5; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 3; cfg.artfctdef.zvalue.hilbert = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'EOG'; [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); cfg.trl=trl; cfg.artfctdef.reject = 'complete'; % this rejects complete trials, use 'partial' if you want to do partial artifact rejection % collect all the info about the artifacts that were found cfg.artfctdef.eog.artifact =artifact_EOG; cfg.artfctdef.jump.artifact = artifact_jump; cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); Data_no_artifacts=ft_preprocessing(cfg); % some additional filtering for DC removal and detrending cfg=[]; cfg.detrend='yes' cfg.hpfilt='yes' cfg.hpfreq=1; TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); clear Data_no_artifacts;  end ... ... end end -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 4:41:09 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Hmmm, apparently this approach needs to be ironed out a bit (also from >our side). For now, I'd say that it should work if you keep per type >of artifact the artifact field in the output configuration, and just >concatenate these prior to calling ft_rejectartifact. I will moreover >CC this e-mail to the people involved in creating the first version of >the renewed tutorial, and will bring up the issue in this week's >FieldTrip developers meeting. > >Best, > >JM > >On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > >> Hi Jan mathijs, >> >> I tried to get option1 running, stumbled over the following little >> obstacle however: >> >> I tried to keep one cfg throughout the steps ft_definetrial; >> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >> tracking of where artfecats were found), ft_preprocessing (cutting >> out the clean trials from the cont. data). IMHO this used to be the >> way most people did this kind of procesing a while ago. >> >> However, I can't get ft_artifact_zvalue to run with different >> settings one after another for jump/musvle/EOG. FT claims after the >> first run of ft_artifact_zvalue that the z-value thing has been >> performed and refuse to detect other artifacts with new settings. >> >>> From here I only see two alternative: specifying a really lengthy >>> cfg every time a new (also struggling with the cfg.dataset versus >>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>> things myself or manually removing the cfg.artdef.zvalue.artifct >>> field to get the z-value based detection to run again. This seems a >>> bit odd to me. >> >> Any suggestions? >> >> Michael >> >> >> >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 24, 2011 12:12:57 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> I agree. The tutorial should be 'de'-confused by sketching option 1, >>> and another one should be describing option 2, or the original should >>> be clearly making the distinction. >>> >>> Best, >>> >>> JM >>> >>> >>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>> >>>> Hi Jan-Mathijs, >>>> >>>> I am a bit unsure how to proceed: >>>> >>>> (1) sketch the artifact correction way like this >>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>> ft_preprocessing >>>> OR >>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>> ft_preprocessing. >>>> >>>> I think I should go for option (1) as this seems to be the standard >>>> use on continuous data. Sometime in the futrure one should then add >>>> a tutorial for those that have data in trials to start with. >>>> >>>> Michael >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: "jan-mathijs schoffelen" >>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>> An: "Email discussion list for the FieldTrip project" >>>> >>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>> >>>>> Dear Michael, >>>>> >>>>> Yes, I agree with you here as well. In principle the >>>>> ft_artifact_zvalue supports data as a second input argument, but in >>>>> such case the different types of padding in the cfg do not make >>>>> sense. >>>>> I would indeed remove the second input arguments in the example >>>>> code >>>>> snippets. Could I ask you to take care of that? >>>>> >>>>> Thanks, >>>>> >>>>> JM >>>>> >>>>> >>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>> >>>>>> Deal Fieldtrip users, >>>>>> >>>>>> there is something else I do not understand in the tutorial: if >>>>>> you >>>>>> read in the data in trials (as it is done) how can you do padding >>>>>> later as it is suggested. I tried to run the example code on teh >>>>>> website reading in the data such that it contains trials. If I >>>>>> then >>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>> must >>>>>> be positive or logical ... values', indicating that the code tries >>>>>> to access data that aren't there. If I set the padding to zero >>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>> should actually run these things on continuous data (contrary to >>>>>> what is indicated in the tutorial)? >>>>>> >>>>>> Michael >>>>>> >>>>> Wibral.vcf>_______________________________________________ >>>>>> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From batrod at gmail.com Mon Jan 24 18:39:31 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Mon, 24 Jan 2011 11:39:31 -0600 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110124164726.247880@gmx.net> References: <20110124164726.247880@gmx.net> Message-ID: Dear Patricia, Your alpha seems a little bit low, why taking 0.01/7= 0.0014 ? I may be wrong but i guess that a fdr correction on a such value of alpha will be very hard with your data. Rodolphe N., PhD. On Mon, Jan 24, 2011 at 10:47 AM, Patricia Wollstadt < Patricia.Wollstadt at gmx.de> wrote: > Dear Fieldtrip-users, > > I'm currently trying to calculate freqstatistics for four experimental > groups, using the following options: > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > length(subjects{4})]; > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > % 1 to N subjects > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group > membership > > > cfg=[]; > cfg.design=design; > cfg.uvar = 1; > cfg.ivar = 2; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; > cfg.correctm = 'fdr'; > cfg.numrandomization = 180000; > cfg.alpha = 0.01/7; > cfg.tail = 1; > cfg.design = design; > cfg.channels = myChannels; > cfg.avgovertime = 'yes'; > cfg.avgoverfreq = 'yes'; > cfg.frequency = [1 3]; > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); > > With these settings, the coputation itself runs fine, but the resulting > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists > of only ones). This would mean, that I found significant effects for all > channels. Is this possible or rather due to an error somewhere in my script? > Is it likely, that these are 'real' zeroes or rather very small values, > close to zero? > Any hints and suggestions are very welcome, thank you in advance, > > Kind regards > > Patricia Wollstadt > > > -- > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > _______________________________________________ > 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 Patricia.Wollstadt at gmx.de Mon Jan 24 19:25:15 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Mon, 24 Jan 2011 19:25:15 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: References: <20110124164726.247880@gmx.net> Message-ID: <20110124182515.12260@gmx.net> Hi Rodolphe, usually I compute this statistic for seven individual frequency bands (I left this part of the script out to keep the example-code short), so I did an additional correction of my alpha niveau. Regards, Patricia -------- Original-Nachricht -------- > Datum: Mon, 24 Jan 2011 11:39:31 -0600 > Von: Rodolphe Nenert > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction > Dear Patricia, > > Your alpha seems a little bit low, why taking 0.01/7= 0.0014 ? > I may be wrong but i guess that a fdr correction on a such value of alpha > will be very hard with your data. > > Rodolphe N., PhD. > > On Mon, Jan 24, 2011 at 10:47 AM, Patricia Wollstadt < > Patricia.Wollstadt at gmx.de> wrote: > > > Dear Fieldtrip-users, > > > > I'm currently trying to calculate freqstatistics for four experimental > > groups, using the following options: > > > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > > length(subjects{4})]; > > > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > > % 1 to N subjects > > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group > > membership > > > > > > cfg=[]; > > cfg.design=design; > > cfg.uvar = 1; > > cfg.ivar = 2; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'indepsamplesF'; > > cfg.correctm = 'fdr'; > > cfg.numrandomization = 180000; > > cfg.alpha = 0.01/7; > > cfg.tail = 1; > > cfg.design = design; > > cfg.channels = myChannels; > > cfg.avgovertime = 'yes'; > > cfg.avgoverfreq = 'yes'; > > cfg.frequency = [1 3]; > > > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, > group4avg); > > > > With these settings, the coputation itself runs fine, but the resulting > > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix > consists > > of only ones). This would mean, that I found significant effects for all > > channels. Is this possible or rather due to an error somewhere in my > script? > > Is it likely, that these are 'real' zeroes or rather very small values, > > close to zero? > > Any hints and suggestions are very welcome, thank you in advance, > > > > Kind regards > > > > Patricia Wollstadt > > > > > > -- > > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail From ekanal at cmu.edu Mon Jan 24 21:26:09 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Mon, 24 Jan 2011 15:26:09 -0500 Subject: [FieldTrip] questions about averaging/clustering tutorial Message-ID: <4233AF54-D71B-423D-A509-F225C92049C1@cmu.edu> Hello Fieldtrippers - Two unrelated questions about the averaging and clustering tutorials: 1) By the end of the averaging routine, there were only ~75 useful trials per condition left, which seems to be quite small to me. I understand that different studies will require different numbers of trials, but I was wondering whether you could go into a little detail as to why you chose to complete the study with (seemingly) so few trials. 2) In the cluster tutorial, you specify "cfg.clusteralpha = 0.05" and "cfg.clustertail = 0". If the tail is double-sided, wouldn't you want to use a cluster alpha of 0.025? Thanks - Elli Kanal From r.vandermeij at donders.ru.nl Tue Jan 25 17:40:02 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 25 Jan 2011 17:40:02 +0100 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper In-Reply-To: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> References: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> Message-ID: <4D3EFCE2.2010209@donders.ru.nl> Hi Shogo, Haven't earned that title yet ;). My apologies for my late reply. > In your 2nd step, I should compute cluster-level-statistics from > random permutation data. > Here, I have an question. > When I define clusters from random permutation data, which should I > define where clusters are the same place (e.g. time, sensor and so on) > as "observed clasters" or should I define newly where clusters are > from random permutation data regardless of the places of "observed > clasters"? The idea is that for every random permutation of data, you calculate your statistics and cluster over them. Then, select the largest of these, whether it occurs at different time-points than your observed clusters or not. The null-hypothesis that your are trying to refute is not of the form "this cluster is significant is bigger than zero", but of the form "the data is interchangeable between conditions". Therefore, you gather 'largest-clusters' from 1000 random combinations of data. If your biggest cluster is bigger than 95% of the biggest clusters (alpha = 0.05, single-sided test), than the data is /not /interchangeable, and thus significantly different between conditions. This is exemplified by /all /clusters that surpass the test based on the /same /permutation-distribution of 'biggest-clusters'. Your data is different between conditions, and all peaks in the mountain-range are representing this (if they surpass the cluster-level test) (my favorite analogy). > I think the latter is right, this is OK? Yes. > > Second, If I have interests in the cluster that has the second or > third... non first largest cluster-level-statistics from the > experimental hypothesis, how should I test these clusters? All clusters are tested against the permutation-distribution of 'biggest-clusters'. Any of the smaller observed-clusters that are still bigger than 95% of your distribution-of-biggest-clusters (alpha = 0.05, single-sided), are part of /*all* /the clusters that /*together *show that the data differs between conditions/. Best, Roemer -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From Patricia.Wollstadt at gmx.de Tue Jan 25 18:08:38 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Tue, 25 Jan 2011 18:08:38 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110124164726.247880@gmx.net> References: <20110124164726.247880@gmx.net> Message-ID: <20110125170838.254600@gmx.net> Dear all, I'm still trying to identify the underlying reason for the issue described below. I ran the analysis in debug mode (I'm using Matlab2008b and the Fieldtrip-release from the 16th of January 2011) and found that the matrix 'resample', that is generated in 'statistics_montecarlo', line 187: resample = resampledesign(cfg, design); doesn't contain actual permutations of my initial design, but rather sorted rowvectors from 1 to 80 (no of subjects). So (since there is no permutation of the units of observation) the 'randstat' that is subsequently calculated for each row of the resample-matrix is always the same. Is this maybe due to my design and my units of observations respectively? I am looking at age-dependent variations in resting-state data, so my UO are 80 subjects, divided into four age groups. The commandline-output of the 'resampledesign'-function is as follows: total number of measurements = 80 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 80 levels number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Is this correct? Shouldn't this read 'repeated measurement in variable 2 over 4 levels' with the number of subjects per group as repeated measurements within a condition? Still I am pretty sure about my design matrix, which contains the indices 1 to 80 (for all subjects) in the first row (this is my cfg.uvar) with the corresponding age groups (1 to 4) in the second row (cfg.ivar, see my previous email below). I use an 'indepsamplesF'-statistic, since I am comparing between four groups of different subjects (averaged over trials). I hope, I got the settings and my design right. Any suggestions, whether this is a problem due to wrong configurations in my script are very welcome. Right now I work around this issue by replacing line 279 in 'statistics_montecarlo': tmpdesign = design(:,resample(i,:)); with: tmpdesign = design(:,randperm(size(design,2))); creating permutations of my design 'by hand'. Is this acceptable or is there anything I'm maybe missing. Thank you very much, kind regards, Patricia -------- Original-Nachricht -------- > Datum: Mon, 24 Jan 2011 17:47:26 +0100 > Von: "Patricia Wollstadt" > An: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] ft_freqstatistics and FDR-correction > Dear Fieldtrip-users, > > I'm currently trying to calculate freqstatistics for four experimental > groups, using the following options: > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > length(subjects{4})]; > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > % 1 to N subjects > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group membership > > > cfg=[]; > cfg.design=design; > cfg.uvar = 1; > cfg.ivar = 2; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; > cfg.correctm = 'fdr'; > cfg.numrandomization = 180000; > cfg.alpha = 0.01/7; > cfg.tail = 1; > cfg.design = design; > cfg.channels = myChannels; > cfg.avgovertime = 'yes'; > cfg.avgoverfreq = 'yes'; > cfg.frequency = [1 3]; > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); > > With these settings, the coputation itself runs fine, but the resulting > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists of > only ones). This would mean, that I found significant effects for all > channels. Is this possible or rather due to an error somewhere in my script? Is > it likely, that these are 'real' zeroes or rather very small values, close > to zero? > Any hints and suggestions are very welcome, thank you in advance, > > Kind regards > > Patricia Wollstadt > > > -- > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de From r.vandermeij at donders.ru.nl Tue Jan 25 17:53:53 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 25 Jan 2011 17:53:53 +0100 Subject: [FieldTrip] singleplotTFR error In-Reply-To: References: <4D32C65B.5020304@donders.ru.nl> Message-ID: <4D3F0021.2060701@donders.ru.nl> Hi Karl, Sorry for my late reply. We are looking for a proper fix for this issue, it occurs in several situations. Any axes that are not monotonously increasing causes a crash in uimagesc, because it cannot determine how to plot the data (if I recall correctly, uimagesc plots multiple copies of the same data when axes are not evenly spaced). For the moment, you can try to hack the frequency axis to conform to the monotonously increasing part/(in most cases a simple round() would do it)/. Or, you can hack it by changing it to a linear index, and then add the axis-labels by hand afterwards /(by using set(gca,'ytick', [index vector], 'yticklabel', string-array of num2str(freq-axis))/. Best, Roemer On 17-01-11 2:51, Karl Doron wrote: > Hello Roemer, > > Here's the cfg's and output from calls to ft_freqanalysis with > method='wavelet' and the subsequent call to ft_singleplotTFR and the > resulting error. The imagesc command will however plot the data at > that > channel imagesc(squeeze(wvpow.powspctrm(strmatch('A177',label),:,:))) > Thanks for any help! > > cfg = []; > > cfg.output = 'pow'; > > cfg.channel = 'MEG'; > > cfg.method = 'wavelet'; > > cfg.foi = 10:2:30; > > cfg.toi = 0.0:0.05:2.75; > > wvpow = ft_freqanalysis(cfg, data_spctrm); > > wvpow = > > label: {246x1 cell} > > dimord: 'chan_freq_time' > > freq: [1x11 double] > > time: [1x56 double] > > powspctrm: [246x11x56 double] > > grad: [1x1 struct] > > cfg: [1x1 struct] > > %Singleplot results > > cfg = []; > > cfg.channel = 'A177'; > > cfg.grad = grad; > > cfg.xlim = [0.6 2.5]; > > cfg.ylim = [10 20]; > > figure; > > ft_singleplotTFR(cfg, wvpow) > > Warning: (one of the) axis are not evenly spaced -> nans cannot > > be maskedout->cfg.masknansissetto'no'; > > > In ft_singleplotTFR at 296 > > ??? Attempted toaccessc(6,1); index outofboundsbecause > > size(c)=[5,37]. > > Error in==>uimageat124 > > ce(j,i) = c(indi(end), indj(end)); > > Error in==>uimagescat46 > > hh = uimage(varargin{:},'CDataMapping','scaled'); > > Error in==>ft_plot_matrixat192 > > h = uimagesc(hdat, vdat, cdat, clim); > > Error in==>ft_singleplotTFRat327 > > ft_plot_matrix(data.(cfg.xparam)(xidc),data.(cfg.yparam)(yidc), > > TFR, 'clim',[zmin,zmax],'tag','cip') > > > > On Sun, Jan 16, 2011 at 2:20 AM, Roemer van der Meij > > wrote: > > Hi Karl, > > Could you give some more information on the errors? Could you also > post your cfg's? That will help in finding and fixing the bug. > What FieldTrip version are you using? > > Best, > Roemer > > > > On 15-1-2011 18:05, Karl Doron wrote: >> Hello, >> >> Has anyone else reported a problem with ft_singleplotTFR and >> output of the new specest module? >> >> multiplotTFR works, but 'interactive' method fails. >> >> It looks like the error occurs when trying to mask NaNs >> >> % masking only possible for evenly spaced axis >> >> if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) >> >> warning('(one of the) axis are not evenly spaced -> nans cannot >> be masked out -> cfg.masknans is set to ''no'';') >> >> cfg.masknans = 'no'; >> >> end >> >> >> >> Thank you, >> karl doron >> UCSB >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > 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 -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 25 20:57:03 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 25 Jan 2011 20:57:03 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110125170838.254600@gmx.net> References: <20110124164726.247880@gmx.net> <20110125170838.254600@gmx.net> Message-ID: <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> Hi Patricia, I don't really understand what is going on, but could you try to specify your design only in a single row (design = design(2,:) in your case), specify cfg.ivar = 1; and cfg=rmfield(cfg,'uvar'), and see how it runs? As such the uvar row is not relevant in an independent samples design. Best, Jan-Mathijs On Jan 25, 2011, at 6:08 PM, Patricia Wollstadt wrote: > Dear all, > > I'm still trying to identify the underlying reason for the issue > described below. I ran the analysis in debug mode (I'm using > Matlab2008b and the Fieldtrip-release from the 16th of January 2011) > and found that the matrix 'resample', that is generated in > 'statistics_montecarlo', line 187: > > resample = resampledesign(cfg, design); > > doesn't contain actual permutations of my initial design, but rather > sorted rowvectors from 1 to 80 (no of subjects). So (since there is > no permutation of the units of observation) the 'randstat' that is > subsequently calculated for each row of the resample-matrix is > always the same. > Is this maybe due to my design and my units of observations > respectively? I am looking at age-dependent variations in resting- > state data, so my UO are 80 subjects, divided into four age groups. > The commandline-output of the 'resampledesign'-function is as follows: > > total number of measurements = 80 > total number of variables = 2 > number of independent variables = 1 > number of unit variables = 1 > number of within-cell variables = 0 > number of control variables = 0 > using a permutation resampling approach > repeated measurement in variable 1 over 80 levels > number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 > 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > 1 1 > > > Is this correct? Shouldn't this read 'repeated measurement in > variable 2 over 4 levels' with the number of subjects per group as > repeated measurements within a condition? Still I am pretty sure > about my design matrix, which contains the indices 1 to 80 (for all > subjects) in the first row (this is my cfg.uvar) with the > corresponding age groups (1 to 4) in the second row (cfg.ivar, see > my previous email below). I use an 'indepsamplesF'-statistic, since > I am comparing between four groups of different subjects (averaged > over trials). > > I hope, I got the settings and my design right. Any suggestions, > whether this is a problem due to wrong configurations in my script > are very welcome. > > Right now I work around this issue by replacing line 279 in > 'statistics_montecarlo': > > tmpdesign = design(:,resample(i,:)); > > with: > > tmpdesign = design(:,randperm(size(design,2))); > > creating permutations of my design 'by hand'. Is this acceptable or > is there anything I'm maybe missing. > > Thank you very much, kind regards, > > Patricia > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 24 Jan 2011 17:47:26 +0100 >> Von: "Patricia Wollstadt" >> An: fieldtrip at donders.ru.nl >> Betreff: [FieldTrip] ft_freqstatistics and FDR-correction > >> Dear Fieldtrip-users, >> >> I'm currently trying to calculate freqstatistics for four >> experimental >> groups, using the following options: >> >> groupSize=[length(subjects{1}) length(subjects{2}) >> length(subjects{3}) >> length(subjects{4})]; >> >> design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; >> % 1 to N subjects >> design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) >> 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> >> group membership >> >> >> cfg=[]; >> cfg.design=design; >> cfg.uvar = 1; >> cfg.ivar = 2; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'indepsamplesF'; >> cfg.correctm = 'fdr'; >> cfg.numrandomization = 180000; >> cfg.alpha = 0.01/7; >> cfg.tail = 1; >> cfg.design = design; >> cfg.channels = myChannels; >> cfg.avgovertime = 'yes'; >> cfg.avgoverfreq = 'yes'; >> cfg.frequency = [1 3]; >> >> stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, >> group4avg); >> >> With these settings, the coputation itself runs fine, but the >> resulting >> 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix >> consists of >> only ones). This would mean, that I found significant effects for all >> channels. Is this possible or rather due to an error somewhere in >> my script? Is >> it likely, that these are 'real' zeroes or rather very small >> values, close >> to zero? >> Any hints and suggestions are very welcome, thank you in advance, >> >> Kind regards >> >> Patricia Wollstadt >> >> >> -- >> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit >> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > _______________________________________________ > 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 batrod at gmail.com Tue Jan 25 21:02:02 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 25 Jan 2011 14:02:02 -0600 Subject: [FieldTrip] Error in correlation analysis with ft_freqstatistics Message-ID: Dear Fieldtrip Users, im actually trying to do a correlation analysis between frequency power and behavioral results. The problem is when i change the design matrix containing the classical independent variables to behavioral scores, as indicate in the walktrough section of the fieldtrip website : cfg.design = [ .1 .2 .4 .3 etc...]; cfg.ivar = 1; Then, Matlab gives me the following errors: ??? Error using ==> statfun_indepsamplesF at 55 Invalid specification of the independent variable in the design array. Error in ==> statistics_montecarlo at 241 [statobs, cfg] = statfun(cfg, dat, design); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 127 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Does anyone have an example of a script for such analysis that works? Thanks, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 25 21:16:38 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 25 Jan 2011 21:16:38 +0100 Subject: [FieldTrip] Error in correlation analysis with ft_freqstatistics In-Reply-To: References: Message-ID: <196CB43E-E377-449F-ABB4-BA02DED6BF0A@donders.ru.nl> Dear Rodolphe, The trick here is not to specify cfg.statistic = 'indepsamplesF'; You need to specify cfg.statistic = 'yourownfunction', and create an m- file 'statfun_yourownfunction.m' that computes a correlation. That could look like function s = statfun_yourownfunction(cfg, dat, design) % mean subtract mdat = mean(dat,2); dat = dat - mdat(:,ones(1,size(dat,2))); mdesign = mean(design); design = design - mean(design); % covariance covdat = dat*design'; % variance vdat = sum(dat.^2,2); vdes = sum(design.^2); % correlation s.stat = covdat./sqrt(vdat.*vdes); This is just typed down in half a minute so don't take it for granted. Best, Jan-Mathijs On Jan 25, 2011, at 9:02 PM, Rodolphe Nenert wrote: > Dear Fieldtrip Users, > > im actually trying to do a correlation analysis between frequency > power and behavioral results. > The problem is when i change the design matrix containing the > classical independent variables to behavioral scores, as indicate in > the walktrough section of the fieldtrip website : > > cfg.design = [ .1 .2 .4 .3 etc...]; > cfg.ivar = 1; > > Then, Matlab gives me the following errors: > > ??? Error using ==> statfun_indepsamplesF at 55 > Invalid specification of the independent variable in the design array. > > Error in ==> statistics_montecarlo at 241 > [statobs, cfg] = statfun(cfg, dat, design); > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, > 'issource',issource); > > Error in ==> ft_freqstatistics at 127 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Does anyone have an example of a script for such analysis that works? > > Thanks, > > Rodolphe. > _______________________________________________ > 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 shhirano at npsych.med.kyushu-u.ac.jp Wed Jan 26 00:45:28 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Wed, 26 Jan 2011 08:45:28 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: <10E711DB-D7B4-4E82-AEEB-310C773BBD60@npsych.med.kyushu-u.ac.jp> Dear Roemer I really appreciate your very clear-cut answer. I'm going to test my data. Thank you very much for your kindness! Best regards, Shogo -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From michael.wibral at web.de Wed Jan 26 10:08:51 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 26 Jan 2011 10:08:51 +0100 (CET) Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> References: <20110124164726.247880@gmx.net> <20110125170838.254600@gmx.net>, <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> Message-ID: <1367146600.2032784.1296032931966.JavaMail.fmail@mwmweb056> Hi Patricia, I also would have thought your design to be correct. Maybe the unneccessary specification of the uvar screws thinsg up?? However, you really do not have any repeated measures in your design - here the output of FT is correct. I interpret it in the following way: You specified cfg.uvar - indicating to FT the possibility that this might be a repeated measures design. FT identified the units of observation as being 80 (correct), and then checked how many repeated measures you ran in each UO and found just 1 - which is also correct. I agree that naming the units of observation (UO) as 'levels' of the UO variable is a bit odd, should rather be 'units of observation'. The concept of repeated measures is also very often misunderstood: in repated measures you do not actually repeat anything, rather you perform different measurements (treatments) WITHIN a unit of observation - so a repated measures design is a within UO design. Your subjects just have one age, so there are no different treatments (levels of the indep variable) per subjects and, hence, no 'repeated measures'. Hope this clarifies terminology for further discussion. Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 25, 2011 8:57:03 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction >Hi Patricia, > >I don't really understand what is going on, but could you try to >specify your design only in a single row (design = design(2,:) in your >case), specify cfg.ivar = 1; and cfg=rmfield(cfg,'uvar'), and see how >it runs? As such the uvar row is not relevant in an independent >samples design. > >Best, > >Jan-Mathijs > > > >On Jan 25, 2011, at 6:08 PM, Patricia Wollstadt wrote: > >> Dear all, >> >> I'm still trying to identify the underlying reason for the issue >> described below. I ran the analysis in debug mode (I'm using >> Matlab2008b and the Fieldtrip-release from the 16th of January 2011) >> and found that the matrix 'resample', that is generated in >> 'statistics_montecarlo', line 187: >> >> resample = resampledesign(cfg, design); >> >> doesn't contain actual permutations of my initial design, but rather >> sorted rowvectors from 1 to 80 (no of subjects). So (since there is >> no permutation of the units of observation) the 'randstat' that is >> subsequently calculated for each row of the resample-matrix is >> always the same. >> Is this maybe due to my design and my units of observations >> respectively? I am looking at age-dependent variations in resting- >> state data, so my UO are 80 subjects, divided into four age groups. >> The commandline-output of the 'resampledesign'-function is as follows: >> >> total number of measurements = 80 >> total number of variables = 2 >> number of independent variables = 1 >> number of unit variables = 1 >> number of within-cell variables = 0 >> number of control variables = 0 >> using a permutation resampling approach >> repeated measurement in variable 1 over 80 levels >> number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 >> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >> 1 1 >> >> >> Is this correct? Shouldn't this read 'repeated measurement in >> variable 2 over 4 levels' with the number of subjects per group as >> repeated measurements within a condition? Still I am pretty sure >> about my design matrix, which contains the indices 1 to 80 (for all >> subjects) in the first row (this is my cfg.uvar) with the >> corresponding age groups (1 to 4) in the second row (cfg.ivar, see >> my previous email below). I use an 'indepsamplesF'-statistic, since >> I am comparing between four groups of different subjects (averaged >> over trials). >> >> I hope, I got the settings and my design right. Any suggestions, >> whether this is a problem due to wrong configurations in my script >> are very welcome. >> >> Right now I work around this issue by replacing line 279 in >> 'statistics_montecarlo': >> >> tmpdesign = design(:,resample(i,:)); >> >> with: >> >> tmpdesign = design(:,randperm(size(design,2))); >> >> creating permutations of my design 'by hand'. Is this acceptable or >> is there anything I'm maybe missing. >> >> Thank you very much, kind regards, >> >> Patricia >> >> >> >> >> -------- Original-Nachricht -------- >>> Datum: Mon, 24 Jan 2011 17:47:26 +0100 >>> Von: "Patricia Wollstadt" >>> An: fieldtrip at donders.ru.nl >>> Betreff: [FieldTrip] ft_freqstatistics and FDR-correction >> >>> Dear Fieldtrip-users, >>> >>> I'm currently trying to calculate freqstatistics for four >>> experimental >>> groups, using the following options: >>> >>> groupSize=[length(subjects{1}) length(subjects{2}) >>> length(subjects{3}) >>> length(subjects{4})]; >>> >>> design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; >>> % 1 to N subjects >>> design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) >>> 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> >>> group membership >>> >>> >>> cfg=[]; >>> cfg.design=design; >>> cfg.uvar = 1; >>> cfg.ivar = 2; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'indepsamplesF'; >>> cfg.correctm = 'fdr'; >>> cfg.numrandomization = 180000; >>> cfg.alpha = 0.01/7; >>> cfg.tail = 1; >>> cfg.design = design; >>> cfg.channels = myChannels; >>> cfg.avgovertime = 'yes'; >>> cfg.avgoverfreq = 'yes'; >>> cfg.frequency = [1 3]; >>> >>> stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, >>> group4avg); >>> >>> With these settings, the coputation itself runs fine, but the >>> resulting >>> 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix >>> consists of >>> only ones). This would mean, that I found significant effects for all >>> channels. Is this possible or rather due to an error somewhere in >>> my script? Is >>> it likely, that these are 'real' zeroes or rather very small >>> values, close >>> to zero? >>> Any hints and suggestions are very welcome, thank you in advance, >>> >>> Kind regards >>> >>> Patricia Wollstadt >>> >>> >>> -- >>> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit >>> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir >> belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de >> _______________________________________________ >> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Wed Jan 26 11:45:23 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 26 Jan 2011 11:45:23 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: <9B00A155-4D0A-493D-A617-2F9E90439E35@donders.ru.nl> Dear Michael and the rest of the world, I updated the documentation page on artifact rejection with a more explicit statement that specifying the padding only works with data on disk (and removed the second input arguments in the code examples). I'll discuss the other issue with the rest soon. Best JM On Jan 24, 2011, at 6:27 PM, Michael Wibral wrote: > Hi Jan-Mathijs, > > this is basically what we do at the moment, i.e. fooling > artifcat_zvalue by removing the one field it complains about amnd > using rejetartefact only at the very last. > See the attched code - I really do not want to post this code on the > tutorial website as I am not fully sure what I am doing :-). > > Michael > > %% CODE > ft_defaults; > Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/ > DATASETS/'; > Design={ > 'DMG13_NewMooney_20110120_0', [2 3], > 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; > } > > > for ss=1:size(Design,1) % over subjects > for cc=1:length(Design{ss,4}) % over conditions > for ff=1:length(Design{ss,2}) % over .ds datasets/runs > > FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), > '.ds') > FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) > % core data reading > cfg=[]; > cfg.dataset=FullFileName; > cfg.headerformat = 'ctf_ds'; % for you to check whether still > necessary > ctf.dataformat = 'ctf_ds'; > cfg.cond=Design{ss,4}(cc) > cfg.continuous='yes'; > > cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '- > MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? > cfg.trialfun=Design{ss,3}; > cfg=ft_definetrial(cfg); > cfg.trl(end,:)=[]; > trl=cfg.trl; % keep track of the trials > > padding=0.75 % 750 ms > > > %%%%%%%%% artifact rejection section > %%% jump > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MEG'; > cfg.artfctdef.zvalue.cutoff = 35; > cfg.artfctdef.zvalue.trlpadding = 0.5*padding; > cfg.artfctdef.zvalue.artpadding = 0.5*padding; > cfg.artfctdef.zvalue.fltpadding = 0; > > % algorithmic parameters > cfg.artfctdef.zvalue.medianfilter = 'yes'; > cfg.artfctdef.zvalue.medianfiltord = 9; % in samples > cfg.artfctdef.zvalue.absdiff = 'yes'; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'jump'; > [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); > % cfg.artfctdef.jump.artifact = artifact_jump; > % cfg = ft_rejectartifact(cfg); > > %%% muscle > cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % > remove field from structure otherwise this won't run ?? > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MEG'; > cfg.artfctdef.zvalue.cutoff = 15; > cfg.artfctdef.zvalue.trlpadding = 0.1; > cfg.artfctdef.zvalue.fltpadding = 0.1; > cfg.artfctdef.zvalue.artpadding = 0.1; > > % algorithmic parameters > cfg.artfctdef.zvalue.bpfilter = 'yes'; > cfg.artfctdef.zvalue.bpfreq = [110 140]; > cfg.artfctdef.zvalue.bpfiltord = 6; > cfg.artfctdef.zvalue.bpfilttype = 'but'; > cfg.artfctdef.zvalue.hilbert = 'yes'; > cfg.artfctdef.zvalue.boxcar = 0.2; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'muscle'; > [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); > cfg.artfctdef.muscle.artifact = artifact_muscle; > cfg = ft_rejectartifact(cfg); > > %%% EOG > > > cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MRT41'; > cfg.artfctdef.zvalue.cutoff = 10; > cfg.artfctdef.zvalue.trlpadding = 0.5; > cfg.artfctdef.zvalue.artpadding = 0.1; > cfg.artfctdef.zvalue.fltpadding = 0.1; > % algorithmic parameters > cfg.artfctdef.zvalue.bpfilter = 'yes'; > cfg.artfctdef.zvalue.bpfilttype = 'but'; > cfg.artfctdef.zvalue.bpfreq = [1 15]; > cfg.artfctdef.zvalue.bpfiltord = 3; > cfg.artfctdef.zvalue.hilbert = 'yes'; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'EOG'; > [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); > > cfg.trl=trl; > cfg.artfctdef.reject = 'complete'; % this rejects complete trials, > use 'partial' if you want to do partial artifact rejection > % collect all the info about the artifacts that were found > cfg.artfctdef.eog.artifact =artifact_EOG; > cfg.artfctdef.jump.artifact = artifact_jump; > cfg.artfctdef.muscle.artifact = artifact_muscle; > cfg = ft_rejectartifact(cfg); > > Data_no_artifacts=ft_preprocessing(cfg); > > % some additional filtering for DC removal and detrending > cfg=[]; > cfg.detrend='yes' > cfg.hpfilt='yes' > cfg.hpfreq=1; > TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); > clear Data_no_artifacts; > > end > ... > ... > end > end > > > > > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 24, 2011 4:41:09 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Hmmm, apparently this approach needs to be ironed out a bit (also >> from >> our side). For now, I'd say that it should work if you keep per type >> of artifact the artifact field in the output configuration, and just >> concatenate these prior to calling ft_rejectartifact. I will moreover >> CC this e-mail to the people involved in creating the first version >> of >> the renewed tutorial, and will bring up the issue in this week's >> FieldTrip developers meeting. >> >> Best, >> >> JM >> >> On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: >> >>> Hi Jan mathijs, >>> >>> I tried to get option1 running, stumbled over the following little >>> obstacle however: >>> >>> I tried to keep one cfg throughout the steps ft_definetrial; >>> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >>> tracking of where artfecats were found), ft_preprocessing (cutting >>> out the clean trials from the cont. data). IMHO this used to be the >>> way most people did this kind of procesing a while ago. >>> >>> However, I can't get ft_artifact_zvalue to run with different >>> settings one after another for jump/musvle/EOG. FT claims after the >>> first run of ft_artifact_zvalue that the z-value thing has been >>> performed and refuse to detect other artifacts with new settings. >>> >>>> From here I only see two alternative: specifying a really lengthy >>>> cfg every time a new (also struggling with the cfg.dataset versus >>>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>>> things myself or manually removing the cfg.artdef.zvalue.artifct >>>> field to get the z-value based detection to run again. This seems a >>>> bit odd to me. >>> >>> Any suggestions? >>> >>> Michael >>> >>> >>> >>> >>> -----Ursprüngliche Nachricht----- >>> Von: "jan-mathijs schoffelen" >>> Gesendet: Jan 24, 2011 12:12:57 PM >>> An: "Email discussion list for the FieldTrip project" >>> >>> Betreff: Re: [FieldTrip] more on artfifact rejection >>> >>>> Dear Michael, >>>> >>>> I agree. The tutorial should be 'de'-confused by sketching option >>>> 1, >>>> and another one should be describing option 2, or the original >>>> should >>>> be clearly making the distinction. >>>> >>>> Best, >>>> >>>> JM >>>> >>>> >>>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>>> >>>>> Hi Jan-Mathijs, >>>>> >>>>> I am a bit unsure how to proceed: >>>>> >>>>> (1) sketch the artifact correction way like this >>>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>>> ft_preprocessing >>>>> OR >>>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>>> ft_preprocessing. >>>>> >>>>> I think I should go for option (1) as this seems to be the >>>>> standard >>>>> use on continuous data. Sometime in the futrure one should then >>>>> add >>>>> a tutorial for those that have data in trials to start with. >>>>> >>>>> Michael >>>>> >>>>> -----Ursprüngliche Nachricht----- >>>>> Von: "jan-mathijs schoffelen" >>>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>>> An: "Email discussion list for the FieldTrip project" >>>>> >>>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>>> >>>>>> Dear Michael, >>>>>> >>>>>> Yes, I agree with you here as well. In principle the >>>>>> ft_artifact_zvalue supports data as a second input argument, >>>>>> but in >>>>>> such case the different types of padding in the cfg do not make >>>>>> sense. >>>>>> I would indeed remove the second input arguments in the example >>>>>> code >>>>>> snippets. Could I ask you to take care of that? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> JM >>>>>> >>>>>> >>>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>>> >>>>>>> Deal Fieldtrip users, >>>>>>> >>>>>>> there is something else I do not understand in the tutorial: if >>>>>>> you >>>>>>> read in the data in trials (as it is done) how can you do >>>>>>> padding >>>>>>> later as it is suggested. I tried to run the example code on teh >>>>>>> website reading in the data such that it contains trials. If I >>>>>>> then >>>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>>> must >>>>>>> be positive or logical ... values', indicating that the code >>>>>>> tries >>>>>>> to access data that aren't there. If I set the padding to zero >>>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>>> should actually run these things on continuous data (contrary to >>>>>>> what is indicated in the tutorial)? >>>>>>> >>>>>>> Michael >>>>>>> >>>>>> Wibral.vcf>_______________________________________________ >>>>>>> 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 >>>>> >>>> Wibral.vcf>_______________________________________________ >>>>> 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 tom_campbell75 at hotmail.com Thu Jan 27 00:26:27 2011 From: tom_campbell75 at hotmail.com (Tom Campbell) Date: Wed, 26 Jan 2011 23:26:27 +0000 Subject: [FieldTrip] depsamplesF Message-ID: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. -------------- next part -------------- An HTML attachment was scrubbed... URL: From olga at graphicmind.info Thu Jan 27 04:16:51 2011 From: olga at graphicmind.info (Olga Sysoeva) Date: Thu, 27 Jan 2011 06:16:51 +0300 Subject: [FieldTrip] depsamplesF In-Reply-To: References: Message-ID: <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: > Dear Eric Maris, Robert Oostenveld and colleagues, > > I write with some queries with reference to your previous > correspondence on the Fieldtrip listserv and would very much > appreciate if you could please answer them. > > I am trying to use Fieldtrip to analyse timelocked ERP data from > what is a 16(participant: [1:16]) X2(Background: congruent, > incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to > runing well treating this as a 16(participant: [1:16]) X4(Visual > stimulus: animal-congruent background, animal-incongruent > background, vehicle-congruent, vehicle-incongruent )design with 4 > conditions, though I haven't looked at the results of the tests yet. > If I then run cluster analyses of differences of theoretical > interest via depsamplest, please how would I bonferroni correct? I > am interested in what clusters exist in the background and stimulus > main effects and their background X stimulus interaction. Please is > this possible in fieldtrip to use depsamplesF to work with a > Participant X "2-way" design? > > Best regards, > > Tom Campbell. > > > > > _______________________________________________ > 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 tom_campbell75 at hotmail.com Thu Jan 27 06:02:29 2011 From: tom_campbell75 at hotmail.com (Tom Campbell) Date: Thu, 27 Jan 2011 05:02:29 +0000 Subject: [FieldTrip] depsamplesF In-Reply-To: <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> References: , <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Message-ID: Thank you very much for this helpful advice Olga. That would have also been my impression until I found this discussion between Maya Zuckerman and Eric Maris: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003335.html http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html , which I may have misunderstood. I can see from the list that people are interested in using depsampleF to investigate interactions between two independent variables (e.g., background: I,II x stimulus: a,b) in experiments with multiple participants. I can also see a several people have had problems with this. Given for datasets I_a, I_b, II_a, II_b I'd like to do something like: cfg.design =????; ... cfg.statistic ='depsamplesF'; ... [stat] = ft_timelockstatistics(cfg, I_a, I_b, II_a, II_b); to find the tests of of main effect clusters for each factor and interaction clusters. How to specify up cfg.design could be one of the problems, as could be what other cfg parameters need to be specified. I may be barking up completely the wrong tree. Assuming the interaction is significant, there are 4 differences that would be of theoretical interest: I_a vs I_b, II_a vs II_b,I_a vs II_a,I_b vs II_b). For instance, a "classical" interaction might exhibit the abolition of significance of an effect ab seen at I at level II of that factor. So, if I understand the Zuckerman-Maris dialogue, if I used the permutation test to test such I_a vd II_b differences as in the tutorial: cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; ... [I_avsb_stat] = ft_timelockstatistics(cfg, I_a, I_b); [II_avsb_stat] = ft_timelockstatistics(cfg, II_a, II_b); [IvsII_a_stat] = ft_timelockstatistics(cfg, I_a, II_a); [IvsII_b_stat] = ft_timelockstatistics(cfg, I_a, II_b); ,I may have to either do some bonferonni correction: -at the cluster level (cluster.alpha) -or at the level at which each t-test can be included in a cluster (cfg.alpha). Please would you verify which, if at all? If I am testing 4 such differences with 4 permutation tests then if the bonferroni correction is to be at the cluster level, please should the correction depend upon the number of clusters as well as the number of such differences tested? Please, I look forward to any clarifications. With best regards, Tom Campbell. From: olga at graphicmind.info To: tom_campbell75 at hotmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] depsamplesF Date: Thu, 27 Jan 2011 06:16:51 +0300 Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. _______________________________________________ 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 lumatobu2 at hotmail.com Fri Jan 28 04:52:09 2011 From: lumatobu2 at hotmail.com (Ludwing Torres) Date: Thu, 27 Jan 2011 22:52:09 -0500 Subject: [FieldTrip] help with inverse computing Message-ID: Hello, I have the next script that computes the forward model of the brain activity: clear all close all clc % load electrodes positions elec = []; load electrodes1020 % array of electrode positions i_elec=[4 6 18 19 21 23 25 27 28 31 33 35 37 40 41 43 45 47 49 50 53 55 57 59 62 63 65 67 69 71 72 84 86]; % load concentric spheres or bem load standard_vol.mat % vol.cond = [1 1/80 1]; % load spheric_vol_162.mat %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.vol = vol; % cfg.elec = elec; cfg.elec.pnt = elec.pnt(i_elec,1:3); cfg.elec.label = elec.label(i_elec); fs=250; ns=250; cfg.fsample = fs; time = (1:ns)/fs; signal1 = 1*sin(2*time*6*pi); signal2 = 1*cos(2*time*12*pi); signal3 = 1*cos(2*time*8*pi); % head model [vols, sens, cfg] = prepare_headmodel(cfg, []); dipin=[]; [x,y,z]=meshgrid(linspace(-40,40,4), linspace(-40,40,4), linspace(0,30,3) ); dipin.pos=[x(:) y(:) z(:)]; mom_t=zeros(3*length(dipin.pos),ns); x_orig=mom_t; n_orig=mom_t; n_orig(20,:)=signal1; n_orig(80,:)=signal2; n_orig(40,:)=signal3; a11=1.2; b11=0.05; M11=3*length(dipin.pos); A = a11*diag(ones(M11,1)) + b11*(diag(ones(M11-1,1),1) + diag(ones(M11-1,1),-1)); b12=0; b13=0; c11=-0.9; for b=1:ns, if b==1, x_orig(:,b)=n_orig(:,b); end if b==2, x_orig(:,b)=A*x_orig(:,b-1)+b12*x_orig(:,b-1).^2-b13*x_orig(:,b-1).^3+n_orig(:,b); end if b>2, x_orig(:,b)=A*x_orig(:,b-1)+b12*x_orig(:,b-1).^2+b13*x_orig(:,b-1).^3+c11*x_orig(:,b-2)+n_orig(:,b); end end C=compute_leadfield(dipin.pos, sens, vols); dat=C*x_orig; now I have to compute the inverse model, that is, I have to obtain the x_orig data, knowing only the data stored in dat and C. For that, I made the next script (After runing the previous) In which I use different functions of FieldTrip to recover the x data: [vol1,sens1]=prepare_vol_sens(vol, sens); inside=inside_vol(dipin.pos,vol1); %After that I get 48 dipoles inside and 0 outside dipin.outside=[]; dipin.inside=1:48; %Inverse computing using MNE dipout=minimumnormestimate(dipin,sens1,vol1,dat); % I store the dipole moments obtained as a matrix Xres=[]; for ii=1:48 Xres=[Xres;dipout.mom{ii}]; end % I compute a relative error between the original x and the obtained x to compare error1=norm(Xres-x_orig,'fro')/norm(x_orig,'fro') %Using Residual variance [dipout2] = residualvariance(dipin, sens1, vol1, dat); Xres2=[]; for ii=1:48 Xres2=[Xres2;dipout2.mom{ii}]; end error2=norm(Xres2-x_orig,'fro')/norm(x_orig,'fro') %Using dipole fitting [dipout4] = dipole_fit(dipin, sens1, vol1, dat) error4=norm(dipout4.mom-x_orig,'fro')/norm(x_orig,'fro') The error obtained using residual variance is very different to the error of the two other methods. Besides, I get a very big error (92%) with the other two methods. I don't know if I'm doing something wrong, please If anyone could help me, I could pay you. Thanks C=compute_leadfield(dipin.pos, sens, vols); dat=C*x_orig; -------------- next part -------------- An HTML attachment was scrubbed... URL: From TAVABIK at email.chop.edu Fri Jan 28 06:06:41 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 28 Jan 2011 00:06:41 -0500 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054>, , <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: Greetings - this has been an informative discussion. My question remains is , what is the consensus on an approach for automatic artifact rejection with trial (CTF) data? E.g., could one use the artifact rejection section of Michael's code without any padding? I have not found any tutorials or suggestions on how to use the artifact rejection tools on trial data...have I missed something. -Kambiz ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ 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, January 24, 2011 12:27 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] more on artfifact rejection Hi Jan-Mathijs, this is basically what we do at the moment, i.e. fooling artifcat_zvalue by removing the one field it complains about amnd using rejetartefact only at the very last. See the attched code - I really do not want to post this code on the tutorial website as I am not fully sure what I am doing :-). Michael %% CODE ft_defaults; Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/DATASETS/'; Design={ 'DMG13_NewMooney_20110120_0', [2 3], 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; } for ss=1:size(Design,1) % over subjects for cc=1:length(Design{ss,4}) % over conditions for ff=1:length(Design{ss,2}) % over .ds datasets/runs FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), '.ds') FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) % core data reading cfg=[]; cfg.dataset=FullFileName; cfg.headerformat = 'ctf_ds'; % for you to check whether still necessary ctf.dataformat = 'ctf_ds'; cfg.cond=Design{ss,4}(cc) cfg.continuous='yes'; cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? cfg.trialfun=Design{ss,3}; cfg=ft_definetrial(cfg); cfg.trl(end,:)=[]; trl=cfg.trl; % keep track of the trials padding=0.75 % 750 ms %%%%%%%%% artifact rejection section %%% jump % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 35; cfg.artfctdef.zvalue.trlpadding = 0.5*padding; cfg.artfctdef.zvalue.artpadding = 0.5*padding; cfg.artfctdef.zvalue.fltpadding = 0; % algorithmic parameters cfg.artfctdef.zvalue.medianfilter = 'yes'; cfg.artfctdef.zvalue.medianfiltord = 9; % in samples cfg.artfctdef.zvalue.absdiff = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'jump'; [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); % cfg.artfctdef.jump.artifact = artifact_jump; % cfg = ft_rejectartifact(cfg); %%% muscle cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % remove field from structure otherwise this won't run ?? % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 15; cfg.artfctdef.zvalue.trlpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; cfg.artfctdef.zvalue.artpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfreq = [110 140]; cfg.artfctdef.zvalue.bpfiltord = 6; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.boxcar = 0.2; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'muscle'; [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); %%% EOG cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % cutoff and padding cfg.artfctdef.zvalue.channel = 'MRT41'; cfg.artfctdef.zvalue.cutoff = 10; cfg.artfctdef.zvalue.trlpadding = 0.5; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 3; cfg.artfctdef.zvalue.hilbert = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'EOG'; [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); cfg.trl=trl; cfg.artfctdef.reject = 'complete'; % this rejects complete trials, use 'partial' if you want to do partial artifact rejection % collect all the info about the artifacts that were found cfg.artfctdef.eog.artifact =artifact_EOG; cfg.artfctdef.jump.artifact = artifact_jump; cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); Data_no_artifacts=ft_preprocessing(cfg); % some additional filtering for DC removal and detrending cfg=[]; cfg.detrend='yes' cfg.hpfilt='yes' cfg.hpfreq=1; TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); clear Data_no_artifacts; end ... ... end end -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 4:41:09 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Hmmm, apparently this approach needs to be ironed out a bit (also from >our side). For now, I'd say that it should work if you keep per type >of artifact the artifact field in the output configuration, and just >concatenate these prior to calling ft_rejectartifact. I will moreover >CC this e-mail to the people involved in creating the first version of >the renewed tutorial, and will bring up the issue in this week's >FieldTrip developers meeting. > >Best, > >JM > >On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > >> Hi Jan mathijs, >> >> I tried to get option1 running, stumbled over the following little >> obstacle however: >> >> I tried to keep one cfg throughout the steps ft_definetrial; >> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >> tracking of where artfecats were found), ft_preprocessing (cutting >> out the clean trials from the cont. data). IMHO this used to be the >> way most people did this kind of procesing a while ago. >> >> However, I can't get ft_artifact_zvalue to run with different >> settings one after another for jump/musvle/EOG. FT claims after the >> first run of ft_artifact_zvalue that the z-value thing has been >> performed and refuse to detect other artifacts with new settings. >> >>> From here I only see two alternative: specifying a really lengthy >>> cfg every time a new (also struggling with the cfg.dataset versus >>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>> things myself or manually removing the cfg.artdef.zvalue.artifct >>> field to get the z-value based detection to run again. This seems a >>> bit odd to me. >> >> Any suggestions? >> >> Michael >> >> >> >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 24, 2011 12:12:57 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> I agree. The tutorial should be 'de'-confused by sketching option 1, >>> and another one should be describing option 2, or the original should >>> be clearly making the distinction. >>> >>> Best, >>> >>> JM >>> >>> >>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>> >>>> Hi Jan-Mathijs, >>>> >>>> I am a bit unsure how to proceed: >>>> >>>> (1) sketch the artifact correction way like this >>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>> ft_preprocessing >>>> OR >>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>> ft_preprocessing. >>>> >>>> I think I should go for option (1) as this seems to be the standard >>>> use on continuous data. Sometime in the futrure one should then add >>>> a tutorial for those that have data in trials to start with. >>>> >>>> Michael >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: "jan-mathijs schoffelen" >>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>> An: "Email discussion list for the FieldTrip project" >>>> >>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>> >>>>> Dear Michael, >>>>> >>>>> Yes, I agree with you here as well. In principle the >>>>> ft_artifact_zvalue supports data as a second input argument, but in >>>>> such case the different types of padding in the cfg do not make >>>>> sense. >>>>> I would indeed remove the second input arguments in the example >>>>> code >>>>> snippets. Could I ask you to take care of that? >>>>> >>>>> Thanks, >>>>> >>>>> JM >>>>> >>>>> >>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>> >>>>>> Deal Fieldtrip users, >>>>>> >>>>>> there is something else I do not understand in the tutorial: if >>>>>> you >>>>>> read in the data in trials (as it is done) how can you do padding >>>>>> later as it is suggested. I tried to run the example code on teh >>>>>> website reading in the data such that it contains trials. If I >>>>>> then >>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>> must >>>>>> be positive or logical ... values', indicating that the code tries >>>>>> to access data that aren't there. If I set the padding to zero >>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>> should actually run these things on continuous data (contrary to >>>>>> what is indicated in the tutorial)? >>>>>> >>>>>> Michael >>>>>> >>>>> Wibral.vcf>_______________________________________________ >>>>>> 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 e.maris at donders.ru.nl Fri Jan 28 10:43:42 2011 From: e.maris at donders.ru.nl (Eric Maris) Date: Fri, 28 Jan 2011 10:43:42 +0100 Subject: [FieldTrip] depsamplesF In-Reply-To: References: , <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Message-ID: <001001cbbecf$dc470260$94d50720$@maris@donders.ru.nl> Hi Tom, To test main and interaction effects in your 2x2 within subjects design, you have to perform 3 tests, each using the statfun desamplesT. Say you have the output of ft_timelockanalysis for all four conditions: tlout_Ia, tlout_Ib, tlout_IIa, tlout_IIb. Your then proceed as follows: 1. Main effect of I versus II: calculate the mean of tlout_Ia.avg and tlout_Ib.avg and put this is a a new struct variable tlout_I, which has the same fields as tlout_Ia and tlout_Ib. Do the same with tlout_IIa.avg and tlout_IIb.avg and make a new struct variable tlout_II. Then run ft_timelockstatistics with input arguments tlout_I and tlout_II. With this analysis you will test the main effect of I-versus-II. 2. In the same way, you now test the main effect of a versus b. In your calculations, the roles of (I,II) and (a,b) are now reversed. 3. Interaction of I-vs-II and a-vs-b. Calculate the differences (tlout_Ia.avg-tlout_Ib.avg) and (tlout_IIa.avg-tlout_IIb.avg), put them in output structures and statistically compare them using ft_timelockstatistics. With this analysis, you test the interaction of I-vs-II and a-vs-b. There is no need for Bonferroni correction or an adjustment of cfg.clusteralpha (which does not affect the false alarm rate anyhow) and cfg.alpha. Best, Eric Mari Thank you very much for this helpful advice Olga. That would have also been my impression until I found this discussion between Maya Zuckerman and Eric Maris: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003335.html http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html , which I may have misunderstood. I can see from the list that people are interested in using depsampleF to investigate interactions between two independent variables (e.g., background: I,II x stimulus: a,b) in experiments with multiple participants. I can also see a several people have had problems with this. Given for datasets I_a, I_b, II_a, II_b I'd like to do something like: cfg.design =????; ... cfg.statistic ='depsamplesF'; ... [stat] = ft_timelockstatistics(cfg, I_a, I_b, II_a, II_b); to find the tests of of main effect clusters for each factor and interaction clusters. How to specify up cfg.design could be one of the problems, as could be what other cfg parameters need to be specified. I may be barking up completely the wrong tree. Assuming the interaction is significant, there are 4 differences that would be of theoretical interest: I_a vs I_b, II_a vs II_b,I_a vs II_a,I_b vs II_b). For instance, a "classical" interaction might exhibit the abolition of significance of an effect ab seen at I at level II of that factor. So, if I understand the Zuckerman-Maris dialogue, if I used the permutation test to test such I_a vd II_b differences as in the tutorial: cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; ... [I_avsb_stat] = ft_timelockstatistics(cfg, I_a, I_b); [II_avsb_stat] = ft_timelockstatistics(cfg, II_a, II_b); [IvsII_a_stat] = ft_timelockstatistics(cfg, I_a, II_a); [IvsII_b_stat] = ft_timelockstatistics(cfg, I_a, II_b); ,I may have to either do some bonferonni correction: -at the cluster level (cluster.alpha) -or at the level at which each t-test can be included in a cluster (cfg.alpha). Please would you verify which, if at all? If I am testing 4 such differences with 4 permutation tests then if the bonferroni correction is to be at the cluster level, please should the correction depend upon the number of clusters as well as the number of such differences tested? Please, I look forward to any clarifications. With best regards, Tom Campbell. _____ From: olga at graphicmind.info To: tom_campbell75 at hotmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] depsamplesF Date: Thu, 27 Jan 2011 06:16:51 +0300 Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. _______________________________________________ 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 hanneke.meeren at uvt.nl Fri Jan 28 13:03:34 2011 From: hanneke.meeren at uvt.nl (Meeren.H.K.M. ) Date: Fri, 28 Jan 2011 13:03:34 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha Message-ID: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> Dear Fieldtrippers, I am relatively new to fieldtrip, and just starting to make some serious use of the cluster-based permutation routines, and I would just like to (double)check something before I continu. I use ft_timelockstatistics with the following configuration structure: cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; etc. >From my understanding of the tutorial the "cfg.clusteralpha" stands for the alpha-value used for the initial test-statistic (in my case a paired t-test) for thresholding the data, and that the "cfg.alpha" field contains the alpha-value for the second step, i.e. selecting clusters after the permutation tests. However, the naming of the parameters seems rather contraintuitive to me. I would have expected it to be the other way around, i.e "cfg.clusteralpha" for my clusters (second step), and not the initial t-test. Could anyone confirm (or deny) the way it is written in the tutorial? Thanks a lot, Hanneke Meeren ---------------------------------- Hanneke K.M. Meeren, PhD. Researcher and Lecturer Medical Psychology and Cognitive Neuroscience Tilburg University P.O. Box 90153 5000 LE Tilburg The Netherlands email: hanneke.meeren at uvt.nl From r.oostenveld at donders.ru.nl Fri Jan 28 13:43:06 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 28 Jan 2011 13:43:06 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> Dear Kambiz Although other people's preferences might differ, I would suggest that you use visual inspection to detect your artifacts. For trial-based data you cannot apply filter padding. The consequence is that the automatic artifact detection routine implemented in fieldtrip is likely to suffer from false alarms at the edges of your trials, and reduced sensitivity away from the edges. Visual detection of artifacts can be done using ft_rejectvisual (check out the three options it has), and using ft_databrowser. best regards, Robert On 28 Jan 2011, at 6:06, Tavabi, Kambiz wrote: > Greetings - this has been an informative discussion. My question remains is , what is the consensus on an approach for automatic artifact rejection with trial (CTF) data? E.g., could one use the artifact rejection section of Michael's code without any padding? I have not found any tutorials or suggestions on how to use the artifact rejection tools on trial data...have I missed something. > -Kambiz From e.maris at donders.ru.nl Fri Jan 28 14:05:07 2011 From: e.maris at donders.ru.nl (Eric Maris) Date: Fri, 28 Jan 2011 14:05:07 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha In-Reply-To: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> Message-ID: <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> Hi Hanneke, > I am relatively new to fieldtrip, and just starting to make some > serious use of the cluster-based permutation routines, and I would just > like to (double)check something before I continu. > > I use ft_timelockstatistics with the following configuration structure: > cfg.parameter = 'individual'; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > etc. > > >From my understanding of the tutorial the "cfg.clusteralpha" stands > for the alpha-value used for the initial test-statistic (in my case a > paired t-test) for thresholding the data, This is correct. and that the "cfg.alpha" > field contains the alpha-value for the second step, i.e. selecting > clusters after the permutation tests. This is not correct. Actually, cfg.alpha is superfluous. In the output, every cluster has a p-value assigned to it, and if there is one or more cluster with a p-value less than your critical alpha-level (mostly 0.05 for a one-sided and 0.025 for a two-sided test), then you have found a significant difference. Best, Eric > > However, the naming of the parameters seems rather contraintuitive to > me. I would have expected it to be the other way around, i.e > "cfg.clusteralpha" for my clusters (second step), and not the initial > t-test. > > Could anyone confirm (or deny) the way it is written in the tutorial? > > Thanks a lot, > > Hanneke Meeren > > ---------------------------------- > Hanneke K.M. Meeren, PhD. > Researcher and Lecturer > Medical Psychology and Cognitive Neuroscience > Tilburg University > P.O. Box 90153 > 5000 LE Tilburg > The Netherlands > email: hanneke.meeren at uvt.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.vandermeij at donders.ru.nl Fri Jan 28 14:32:56 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Fri, 28 Jan 2011 14:32:56 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha In-Reply-To: <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> Message-ID: <4D42C588.4080709@donders.ru.nl> > This is not correct. Actually, cfg.alpha is superfluous. In the output, > every cluster has a p-value assigned to it, and if there is one or more > cluster with a p-value less than your critical alpha-level (mostly 0.05 for > a one-sided and 0.025 for a two-sided test), then you have found a > significant difference. > It does affect the output.mask field, which can be used for plotting. This will have a 0 for a time-frequency-channel triplet if its p-value is above cfg.alpha, and a 1 when it is below it. Other than that, it is superfluous. Best, Roemer -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Jan 28 17:58:35 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 28 Jan 2011 17:58:35 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> Message-ID: Dear Kambiz, Please note there is a short description of the use of ft_databrowser in the walkthrough: http://fieldtrip.fcdonders.nl/walkthrough#visual_data_inspection As well as some documentation on visual artifact rejection http://fieldtrip.fcdonders.nl/tutorial/visual_artifact_rejection Best, Stephen On 28 January 2011 13:43, Robert Oostenveld wrote: > Dear Kambiz > > Although other people's preferences might differ, I would suggest that you > use visual inspection to detect your artifacts. For trial-based data you > cannot apply filter padding. The consequence is that the automatic artifact > detection routine implemented in fieldtrip is likely to suffer from false > alarms at the edges of your trials, and reduced sensitivity away from the > edges. > > Visual detection of artifacts can be done using ft_rejectvisual (check out > the three options it has), and using ft_databrowser. > > best regards, > Robert > > > On 28 Jan 2011, at 6:06, Tavabi, Kambiz wrote: > > > Greetings - this has been an informative discussion. My question remains > is , what is the consensus on an approach for automatic artifact rejection > with trial (CTF) data? E.g., could one use the artifact rejection section of > Michael's code without any padding? I have not found any tutorials or > suggestions on how to use the artifact rejection tools on trial data...have > I missed something. > > -Kambiz > > > _______________________________________________ > 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 hanneke.meeren at uvt.nl Mon Jan 31 10:41:51 2011 From: hanneke.meeren at uvt.nl (H.K.M. Meeren) Date: Mon, 31 Jan 2011 10:41:51 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <4D42C588.4080709@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> Message-ID: <000f01cbc12b$163b4a50$42b1def0$@meeren@uvt.nl> Dear Developers, I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. Could someone quickly send me a download link? Thanks a lot! Hanneke ----------------------------- Hanneke K.M. Meeren, Ph.D. Lecturer and Researcher Cognitive Neuroscience University of Tilburg Room P 614 P.O.Box 90153 5000 LE Tilburg The Netherlands Phone: +31 (0)13 466 3005 Fax: +31 (0)13 466 2067 email: hanneke.meeren at uvt.nl ----------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jan 31 15:31:07 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 31 Jan 2011 15:31:07 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$%maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> Message-ID: <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> Hi Hanneke I hope you (and potential others searching for it) have found it by now, if not, please go to http://fieldtrip.fcdonders.nl/download.php There are some problems with the new wiki layout rendering on older versions of MS Internet Explorer which we try to fix a.s.a.p. best regards, Robert On 31 Jan 2011, at 10:41, H.K.M. Meeren wrote: > Dear Developers, > > I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. > Could someone quickly send me a download link? > &n bsp;Thanks a lot! > > Hanneke > ----------------------------- > Hanneke K.M. Meeren, Ph.D. > Lecturer and Researcher > Cognitive Neuroscience > University of Tilburg > Room P 614 > P.O.Box 90153 > 5000 LE Tilburg > The Netherlands > Phone: +31 (0)13 466 3005 > Fax: +31 (0)13 466 2067 > email: hanneke.meeren at uvt.nl > ----------------------------- > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From hanneke.meeren at uvt.nl Mon Jan 31 16:29:19 2011 From: hanneke.meeren at uvt.nl (H.K.M. Meeren) Date: Mon, 31 Jan 2011 16:29:19 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$%maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> Message-ID: <001a01cbc15b$a1049d50$e30dd7f0$@meeren@uvt.nl> Hi Robert and others, Yes, the problem has been solved, thanks a lot. I have already downloaded by now. Stephen Whitmarsh sent me the exact same link earlier. Apparantly I replied to him personally, and not the whole discussion forum... Best regards, Hanneke --------------------------- Hanneke K.M. Meeren, Ph.D. University of Tilburg Room P 614 Tel: +31 (0)13 466 3005 --------------------------- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Robert Oostenveld Sent: maandag 31 januari 2011 15:31 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website Importance: High Hi Hanneke I hope you (and potential others searching for it) have found it by now, if not, please go to http://fieldtrip.fcdonders.nl/download.php There are some problems with the new wiki layout rendering on older versions of MS Internet Explorer which we try to fix a.s.a.p. best regards, Robert On 31 Jan 2011, at 10:41, H.K.M. Meeren wrote: Dear Developers, I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. Could someone quickly send me a download link? &n bsp;Thanks a lot! Hanneke ----------------------------- Hanneke K.M. Meeren, Ph.D. Lecturer and Researcher Cognitive Neuroscience University of Tilburg Room P 614 P.O.Box 90153 5000 LE Tilburg The Netherlands Phone: +31 (0)13 466 3005 Fax: +31 (0)13 466 2067 email: hanneke.meeren at uvt.nl ----------------------------- _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From sherrykhan78 at gmail.com Mon Jan 3 17:17:45 2011 From: sherrykhan78 at gmail.com (Sheraz Khan) Date: Mon, 3 Jan 2011 11:17:45 -0500 Subject: [FieldTrip] Postdoctoral Fellowship: Multimodal Neuroimaging -MGH/Harvard Medical School Message-ID: Postdoctoral Fellowship: Multimodal Neuroimaging *Description:* A postdoctoral position pursuing multimodal imaging is available with the TRANSCEND Research Program (www.transcendresearch.org) at the Martinos Center for Biomedical Imaging in Charlestown, MA (www.martinos.org) which is affiliated with the Massachusetts General Hospital, Harvard and MIT. There is a second location at a clinical site, the MGH-affiliated Lurie Family Center for Autism, where we have a 128 lead EGI EEG in a shielded room as well as a photogrammetry machine and autonomic monitoring equipment, and will shortly have a near-infrared tissue spectrometer (NIRS) machine. The program’s emphasis is on pathophysiologically oriented brain research and application of advanced imaging acquisition and analysis techniques to neurological and sensory aspects of autism spectrum disorders. Emphasis will be on MRI (DTI, spectroscopy, morphometry, ASL), on co-registering EEG and MEG with MRI, and on studying neurovascular coupling with EEG and NIRS. This position will involve analysis of existing multimodal imaging data and collection of new data. It will involve working closely with a multidisciplinary team and with children, and will also involve some research oriented analysis of data collected for clinical purposes. The age range of our subjects is primarily from early infancy to mid-adolescence, with some additional studies including young adults. An ample opportunity will also be provided to the candidate to self-explore and lead research. *Requirements:* Candidates must have PhD in neuroscience, physics, biomedical engineering, electrical engineering, computer science or other related fields. Candidates without this training and experience need not apply. Prior experience in MRI analysis and EEG signal processing is required. Salary will be consistent with Massachusetts General Hospital, Harvard Medical School policies for Postdoctoral trainees and will range between $45,000 to $55,000 depending upon qualifications and experience. Compensation also includes full staff benefits, including health insurance, and vacation time. *Contact:* Interested applicants may send a CV and statement of interest addressing background and specific pertinence of the candidate’s interest to Dr. Martha R. Herbert at mherbert1 at partners.organd cc transcend at partners.org . Applications will be considered until the position is filled. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Thu Jan 6 09:43:47 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Thu, 6 Jan 2011 09:43:47 +0100 Subject: [FieldTrip] code change potentially relevant for MEG people Message-ID: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> Dear all, Happy new year to all of you! I just made a change to the code which may be relevant to some. This change will be present in tonight's release version, and will be immediate for the in-house users at the Donders Centre. If you are not doing MEG research you can stop here. If you never use FieldTrip to compute leadfields for MEG data you can stop here. If you never use the 'singleshell' method for your MEG leadfield computation, or if you don't know what that means, you can stop here. There appeared to be a huge difference in magnitude of MEG-leadfields computed with FieldTrip using different algorithms. Particularly, there was a big discrepancy between the 'singleshell' method on the one hand, and the localspheres/singlesphere method on the other hand. It turned out to be the case that there was a scaling factor in the singleshell method, which (assuming the geometrical units were in cm) would yield a magnetic field/gradient in ft or ft/cm. At the moment FieldTrip does not everywhere explicitly impose particular physical units on the data and therefore also should not make particular assumptions. To make the three methods of leadfield computation more equivalent we changed the implicit unit-assuming code. What does this all mean to you? Probably not an awful lot. Yet, you need to be aware that by scaling the leadfields, the magnitude of the inverse solution will probably also change (unless you use norm- normalized leadfields). It is not correct to compare analysis results using old-scale leadfields with analysis results using new-scale leadfields, if the respective analysis results have not been normalized in a meaningful way. In other words, comparing raw power is not correct, comparing neural activity indices, relative changes, t- statistics etc. is probably alright. Sorry for the inconvenience, Best wishes 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 a.stolk at fcdonders.ru.nl Thu Jan 6 11:06:49 2011 From: a.stolk at fcdonders.ru.nl (Stolk, A.) Date: Thu, 6 Jan 2011 11:06:49 +0100 (CET) Subject: [FieldTrip] code change potentially relevant for MEG people In-Reply-To: <524787489.95342.1294308215741.JavaMail.root@sculptor.zimbra.ru.nl> Message-ID: <225327747.95381.1294308409346.JavaMail.root@sculptor.zimbra.ru.nl> Hey JM, Ik plot groepsgemiddelde aboslute powers (zie plotje) waarbij de voxel van interesse gekozen wordt aan de hand van significant verschillen. Dus blobs die gevonden zijn na indep T-testen op de subject level en dep T-test op groepslevel. De prepare-single-shell algoritme is dezelfde voor elke conditie in elke proefpersoon. Ik struikel over deze zin 'comparing raw power is not correct'. Je bedoelt 'comparing raw powers computed with separate (old and new implementation) is not correct'? Ciao! ----- "jan-mathijs schoffelen" schreef: > Van: "jan-mathijs schoffelen" > Aan: "FieldTrip List" > Verzonden: Donderdag 6 januari 2011 09:43:47 > Onderwerp: [FieldTrip] code change potentially relevant for MEG people > > Dear all, > > Happy new year to all of you! I just made a change to the code which > > may be relevant to some. This change will be present in tonight's > release version, and will be immediate for the in-house users at the > > Donders Centre. > > If you are not doing MEG research you can stop here. > If you never use FieldTrip to compute leadfields for MEG data you can > > stop here. > If you never use the 'singleshell' method for your MEG leadfield > computation, or if you don't know what that means, you can stop here. > > There appeared to be a huge difference in magnitude of MEG-leadfields > > computed with FieldTrip using different algorithms. Particularly, > there was a big discrepancy between the 'singleshell' method on the > one hand, and the localspheres/singlesphere method on the other hand. > > It turned out to be the case that there was a scaling factor in the > singleshell method, which (assuming the geometrical units were in cm) > > would yield a magnetic field/gradient in ft or ft/cm. At the moment > FieldTrip does not everywhere explicitly impose particular physical > units on the data and therefore also should not make particular > assumptions. To make the three methods of leadfield computation more > > equivalent we changed the implicit unit-assuming code. > > What does this all mean to you? Probably not an awful lot. Yet, you > need to be aware that by scaling the leadfields, the magnitude of the > > inverse solution will probably also change (unless you use norm- > normalized leadfields). It is not correct to compare analysis results > > using old-scale leadfields with analysis results using new-scale > leadfields, if the respective analysis results have not been > normalized in a meaningful way. In other words, comparing raw power is > > not correct, comparing neural activity indices, relative changes, t- > statistics etc. is probably alright. > > Sorry for the inconvenience, > > Best wishes > > 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 > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- A non-text attachment was scrubbed... Name: tessie2_half_light_bottom.pdf Type: application/pdf Size: 8613 bytes Desc: not available URL: From smoratti at psi.ucm.es Thu Jan 6 12:10:15 2011 From: smoratti at psi.ucm.es (Stephan Moratti) Date: Thu, 06 Jan 2011 12:10:15 +0100 Subject: [FieldTrip] code change potentially relevant for MEG people In-Reply-To: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> References: <0B436C13-9491-4A98-881B-8D790AE99DF6@donders.ru.nl> Message-ID: <24BDB4F2-6935-4334-BF09-C543377EFD1D@psi.ucm.es> Hi Jan-Mathijs, Happy new year! Thanks for the update! I think the MEG community appreciates a lot the Fieldtrip work you all do! Best, Stephan El 06/01/2011, a las 9:43, jan-mathijs schoffelen escribió: > Dear all, > > Happy new year to all of you! I just made a change to the code which > may be relevant to some. This change will be present in tonight's > release version, and will be immediate for the in-house users at the > Donders Centre. > > If you are not doing MEG research you can stop here. > If you never use FieldTrip to compute leadfields for MEG data you > can stop here. > If you never use the 'singleshell' method for your MEG leadfield > computation, or if you don't know what that means, you can stop here. > > There appeared to be a huge difference in magnitude of MEG- > leadfields computed with FieldTrip using different algorithms. > Particularly, there was a big discrepancy between the 'singleshell' > method on the one hand, and the localspheres/singlesphere method on > the other hand. It turned out to be the case that there was a > scaling factor in the singleshell method, which (assuming the > geometrical units were in cm) would yield a magnetic field/gradient > in ft or ft/cm. At the moment FieldTrip does not everywhere > explicitly impose particular physical units on the data and > therefore also should not make particular assumptions. To make the > three methods of leadfield computation more equivalent we changed > the implicit unit-assuming code. > > What does this all mean to you? Probably not an awful lot. Yet, you > need to be aware that by scaling the leadfields, the magnitude of > the inverse solution will probably also change (unless you use norm- > normalized leadfields). It is not correct to compare analysis > results using old-scale leadfields with analysis results using new- > scale leadfields, if the respective analysis results have not been > normalized in a meaningful way. In other words, comparing raw power > is not correct, comparing neural activity indices, relative changes, > t-statistics etc. is probably alright. > > Sorry for the inconvenience, > > Best wishes > > 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 > > _______________________________________________ > 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 r.vandermeij at donders.ru.nl Thu Jan 6 14:10:04 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Thu, 06 Jan 2011 14:10:04 +0100 Subject: [FieldTrip] new implementation of wltconvol (renamed to wavelet): specest Message-ID: <4D25BF2C.8030805@donders.ru.nl> Hello everybody! As of today, we have switched to a new implementation for the 'wltconvol' method for frequency analysis, and it has also been renamed to 'wavelet'. For a while now we have been rewriting the low-level code in a different format, one that is more flexible to adapt in the future and that allows for the low-level algorithms to be downloaded in a separate module: /specest/. The changes will be on our ftp-server by tonight. The switch to the new implementation brings about several changes. With respect to the changes are observable to the end-user, there are several FAQs created at our wiki. For the end-user observable changes for 'wavelet' (formerly 'wltconvol'), please have a look /here/ , and for a bigger description with respect to your output.freq please go /here/ . Because of these changes, we strongly advise to either use the new or the old implementation for your entire analysis project. The old implementation is still available by using 'wltconvol_old' as cfg.method (however, this code no longer being updated). You can call also call the function: ft_freqanalysis_old, which is the old interface-function. If you are interested, you can track the progress of the /specest /module by going /here/ . As soon as the other low-level functions are ready and implemented, another e-mail will be sent to the mailing-list. If anything is unclear, or if there are any bugs that have slipped through our fingers, please send an e-mail to the mailing-list and/or report a bug in our /Bugzilla bug tracking system /. Kind regards, Roemer van der Meij -- Roemer van der Meij MSc PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From shhirano at npsych.med.kyushu-u.ac.jp Sun Jan 9 03:03:52 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Sun, 9 Jan 2011 11:03:52 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: Dear Dr Eric Maris and members of Fieldtrip mailing list At first, I'm sorry for my poor English. I'm a post-doc research fellow of Department of Neuropsychiatry, Kyushu University, Fukuoka, Japan. I'm studying about auditory abnormalities in mental disorders, for example, schizophrenia, bipolar disorder, using MEG. I'm very impressed and interested in Dr Eric Maris and Dr Robert Oostenveld paper, "Nonparametrical statistical testing of EEG and MEG data, on Journal of Neuroscience Methods, 2007". I'd like to apply their stastical methods to our data, but there are some points that I can't understand in their paper. Those are about cluster-based statistics. In the right column in page 180 in their paper, they wrote 5 steps of statistics methods. At 5th step, they take the largest of the cluster- level statistics, then how do they test this largest of the cluster- level statistics? I thought that, after 5th step, I should make the permutation distribution of cluster-level statistics of selected cluster, and I should test the given cluster-level statistics with this permutation distribution. Is this right? Any answer will help me. Best regards, Shogo Hirano, M.D., Ph.D. -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From r.vandermeij at donders.ru.nl Sun Jan 9 12:49:05 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Sun, 09 Jan 2011 12:49:05 +0100 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper In-Reply-To: References: Message-ID: <4D29A0B1.1020208@donders.ru.nl> Hi Shogo, After computing your cluster-level statistics you indeed take the largest one, and this will be compared to the permutation distribution. However, this distribution is constructed by doing the following e.g. 500 times: 1) randomly swapping the units of observation (UO) between conditions (in case of a between UO design) 2) computing your cluster-level-statistic for this random combination of UOs 3) taking the largest of these (largest of /all clusters/ in this random permutation, not a /'selected' cluster/) This will result in 500 'largest cluster-level-statistics'. If your original statistic is bigger/smaller than a certain percentage, say 95% when testing single-sided to an alpha of 0.05, then you reject the null-hypothesis of interchangeability of your conditions. Whether it should be bigger or smaller depends on your direction of testing. Hope this helps, Best, Roemer On 9-1-2011 3:03, ?? ?? wrote: > Dear Dr Eric Maris and members of Fieldtrip mailing list > > At first, I'm sorry for my poor English. > I'm a post-doc research fellow of Department of Neuropsychiatry, > Kyushu University, Fukuoka, Japan. > I'm studying about auditory abnormalities in mental disorders, for > example, schizophrenia, bipolar disorder, using MEG. > I'm very impressed and interested in Dr Eric Maris and Dr Robert > Oostenveld paper, "Nonparametrical statistical testing of EEG and MEG > data, on Journal of Neuroscience Methods, 2007". > I'd like to apply their stastical methods to our data, but there are > some points that I can't understand in their paper. > Those are about cluster-based statistics. > In the right column in page 180 in their paper, they wrote 5 steps of > statistics methods. At 5th step, they take the largest of the > cluster-level statistics, then how do they test this largest of the > cluster-level statistics? > I thought that, after 5th step, I should make the permutation > distribution of cluster-level statistics of selected cluster, and I > should test the given cluster-level statistics with this permutation > distribution. Is this right? > Any answer will help me. > > Best regards, > > Shogo Hirano, M.D., Ph.D. > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From inieuwenhuis at berkeley.edu Mon Jan 10 21:58:41 2011 From: inieuwenhuis at berkeley.edu (Ingrid Nieuwenhuis) Date: Mon, 10 Jan 2011 12:58:41 -0800 Subject: [FieldTrip] reading EDF+ annotation channel with FieldTrip Message-ID: <4D2B7301.2060900@berkeley.edu> Hi I would like to read in EDF+ data with FieldTrip, including triggers that are coded in the annotation channel. FieldTrip has recently been updated to be able to read EDF+ data (Thanks Robert!). Before, FieldTrip could only read EDF data (so then it could not read events which are coded on the annotation channel). However, in the EDF+ data that I have (which is generate by Net Station software, EGI company), the events on the annotation channel are not read in correctly. I asked EGI support for the definition they use to write the events to the annotation channel in the EDF+ format as is produced by Net Station, and I got this answer from one of their technicians: - Each annotation channel contains a time keeping TAL for each EDF+ block, which is +blockTime[20][20][0] Then, it contains each event for the block, in this format. +startTime[21]duration[20]name[20][0] All times are in seconds. The values in [ ] are the numbers that are written into the binary file, and are described in the EDF+ specification. My knowledge on reading in data and the EDF+ format is not sufficient to understand this. I would like to update read_edf (in private of fileio) to also be able to read in the EGI version of EDF+ data. Does anyone know how to do this? Any help would be greatly appreciated. And while I'm at it, are there any other EGI users on the list that are or will be using the new MFF data format? I would like to use this new data format in FieldTrip, but so far FieldTrip can't read it in yet. Did anyone already write some code to read this format in that we could include into FieldTrip? Also, I've just created a "getting started with EGI data " page on the FieldTrip wiki. I'll document my experiences there. Everyone else with relevant info is (as allways) invited to help fill it. Thanks a lot, All the best, Ingrid -- Ingrid Nieuwenhuis PhD Sleep and Neuroimaging Laboratory Department of Psychology University of California, Berkeley California 94720-1650 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An HTML attachment was scrubbed... URL: From recasensmarc at gmail.com Tue Jan 11 19:33:53 2011 From: recasensmarc at gmail.com (Marc Recasens) Date: Tue, 11 Jan 2011 19:33:53 +0100 Subject: [FieldTrip] Define a ROI in sourcestatistics Message-ID: <4D2CA291.4020003@gmail.com> Hi all. I've been trying to define a region of interest (ROI) in order to restrict my analyses to a particular region on the temporal lobe during sourcestatistics. I have two grandaverage sources like: pos: [33480x3 double] dim: [31 36 30] avg: [1x1 struct] var: [1x1 struct] dimord: 'voxel' trial: [1x13 struct] inside: [12773x1 double] outside: [20707x1 double] df: [33480x1 double] cfg: [1x1 struct] And I apply ft_sourcestatistics with the following configuration: cfg =[]; cfg.dim = GA_dev_source.dim; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.parameter = 'pow'; cfg.correctm = 'bonferoni'; cfg.numrandomization = 1000; cfg.alpha = 0.05; cfg.tail = 0; nsubj = length(GA_dev_source.trial); cfg.design(1,:) = [1:nsubj 1:nsubj]; cfg.design(2,:) = [ones(1,nsubj) ones(1,nsubj)*2]; cfg.uvar = 1; cfg.ivar = 2; stat = ft_sourcestatistics(cfg, GA_dev_source, GA_stad_source) However it's not very straightforward to me to apply a ROI restriction to this analysis. I downloaded the files from http://fmri.wfubmc.edu (TD_lobe.img, TD_lobe.mat, TD_lobe_Border.mat, TD_lobe_List.mat) which I am suposed to use for the ROI. I tried to add this to the previous configuration: cfg.atlas = '.../TD_lobe.img'; (the template brain containing the different lobes) cfg.inputcoord = 'mni'; cfg.roi = ROI(12).Nom_C; The names of the roi i want to extract ('Temporal Lobe') But then... stat_roi = prob: [31x36x30 double] <---- All zeros. mask: [31x36x30 logical] stat: [31x36x30 double] ref: [31x36x30 double] dim: [31 36 30] inside: [0x1 double] <---- which means there's nothing inside the volume outside: [33480x1 double] pos: [33480x3 double] cfg: [1x1 struct] Amb I defining the ROI incorrectly??? Is it because the dimensions of the atlas and the source are not equal? Could anyone give a good example of how to do it? Any suggestion will be appreciated. Thanks in advance. -- Marc Recasens Tel.: +34 639 24 15 98 -------------- next part -------------- An HTML attachment was scrubbed... URL: From shhirano at npsych.med.kyushu-u.ac.jp Wed Jan 12 10:51:19 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Wed, 12 Jan 2011 18:51:19 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> Dear Dr Roemer van der Meij I really appreciate your kind answer! Your answer enable me understand the statistics after Dr Maris's 5 steps. However, there are still two points I'd like to understand. First, after Dr Maris's 5 steps, I should get the largest claster statistics from the clasters derived from observed data (hereinafter I call these clasters as "observed clasters"). Then, I should enter your 3 steps. In your 2nd step, I should compute cluster-level-statistics from random permutation data. Here, I have an question. When I define clusters from random permutation data, which should I define where clusters are the same place (e.g. time, sensor and so on) as "observed clasters" or should I define newly where clusters are from random permutation data regardless of the places of "observed clasters"? I think the latter is right, this is OK? Second, If I have interests in the cluster that has the second or third... non first largest cluster-level-statistics from the experimental hypothesis, how should I test these clusters? Thank you very much for your kindness! Any answer help me. Best regards, Shogo -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From jan.schoffelen at donders.ru.nl Wed Jan 12 14:48:40 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 12 Jan 2011 14:48:40 +0100 Subject: [FieldTrip] change to ft_volumesegment Message-ID: <82650747-4258-47F4-844E-FB6FE6D69E1C@donders.ru.nl> Dear all, I just want to let you know that I incorporated a change in ft_volumesegment. Sometimes the segmented volumes came with a flipped orientation with respect to the original anatomy, necessitating some manual flipping in order to stay consistent with the mri's transformation matrix. I made some changes to ft_volumesegment so that this manual flipping should not be necessary anymore (at least on the anatomical MRIs I tested the code with). Explicitly checking the alignment is of course still allowed and recommended. Best wishes, 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 stephen.whitmarsh at gmail.com Wed Jan 12 14:58:49 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Wed, 12 Jan 2011 14:58:49 +0100 Subject: [FieldTrip] Improved Fieldtrip Wiki! Message-ID: Dear FieldTrippers, First of all, a happy new year! As we hope you agree, we have tried to improve the FieldTrip Wiki on several points: · Better overview through some simple changes to the organization of the menubar · Cleaning up the appearance of the Wiki through the style sheet, and some other aesthetic considerations · Helping FieldTrip newbies by adding an elaborate walkthrough · Adding the ability to upload and display .SVG images, for now much used in the walkthrough · Adding the ability to use editorial notes – take a look online to see what we mean by that. · In general creating a kinder, home-y atmosphere. · Ofcourse, like always, we are the community and if you have any suggestions of comments about the content or appearance of the website, feel free to post them in the email discussion list. · Coming soon: Download pages as formatted PDF with one press of a button, and much, much more! Thanks and credits go to Eelke Spaak for applying his Jedi webskills to the FieldTrip Wiki! Regards, S -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.rombetto at cib.na.cnr.it Thu Jan 13 16:09:11 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Thu, 13 Jan 2011 16:09:11 +0100 Subject: [FieldTrip] fieldtrip question - help needed Message-ID: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> Hello can anybody spend some more words on the chapter "Fixing a missing sensor"? I'm trying to use it with a AtB (like ITAB-Chieti) device...but I cannot understand how to use it. I've several troubles when I've to declare the layout, since I don't have a layout file, but I construct that starting from grad... Do you have any hint for me? Sara Rombetto ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From inbalots at gmail.com Thu Jan 13 18:14:45 2011 From: inbalots at gmail.com (Inbal Lots) Date: Thu, 13 Jan 2011 19:14:45 +0200 Subject: [FieldTrip] Question about wavelet analysis Message-ID: Hello I have several questions: 1. Just wanted to make sure: When I use [res] = ft_freqanalysis(cfg,data) with data that have several trials - and I define cfg.keeptrials = 'yes'; I get an analysis for each trial in [res]. Then I use ft_multiplotTFR(cfg,res) with cfg.trials = 'all'; The result is an average on the wavelet result of all trials? (and not a wavelet on the averaged signal of all trials) 2. Is there a way for me to see the wavelet analysis result of each trial and to browse easily between them? rather than calling ft_multiplotTFR(cfg,res) each time with cfg.trials = i ; where i is the desired trial number? 3. How can I use other mother wavelet? (and not just Morlet wavelets) 4. How can I control the colormap min and max values so that they will be similar in all figures? (like doing imagesc(pic,clim))? Thank you very much Inbal -------------- next part -------------- An HTML attachment was scrubbed... URL: From g.piantoni at nin.knaw.nl Thu Jan 13 18:19:16 2011 From: g.piantoni at nin.knaw.nl (Giovanni Piantoni) Date: Thu, 13 Jan 2011 18:19:16 +0100 Subject: [FieldTrip] peer Message-ID: Dear FieldTrip/peer developers, I was trying the peer module out on two computer (both 64bit Linux, one Ubuntu and one Red-Hat). Thanks for the effort in developing the module! The module works great, following the information on the wiki page. On both computers, I'm able to call peermaster and peerslave, getting the correct peerinfo and peerlist. When I try on Ubuntu, it works flawlessly (but it only has two cores, so no much gain there). However, when I try on Red Hat (which has many more cores), peermaster sends the job to the peerslave and the job is executed (f.e., with peercellfun(@mkdir, {'test'}) it creates a folder called test), but the peerslave is not able to tell the peermaster that the job has completed. See below for details: In the peermaster matlab command line: >> peermaster peer: init peerinit: user at computername, id = 3682858105 peer: spawning announce thread peer: spawning discover thread peer: spawning expire thread peer: spawning tcpserver thread >> peerinfo hostid = 3682858105 hostname = computername user = user group = unknown socket = port = 1701 status = master memavail = 4294967295 bytes timavail = 86400 seconds allowuser = {} allowgroup = {} allowhost = {} tcpserver thread is running udsserver thread is NOT running announce thread is running discover thread is running expire thread is running there are 0 jobs in this peer's buffer >> peerlist there are 3 peers running in total (1 hosts, 1 users) there are 1 peers running on 1 hosts as master there are 2 peers running on 1 hosts as idle slave with 8.0 GB memory available there are 0 peers running on 0 hosts as busy slave with 0 bytes and 0 seconds required there are 0 peers running on 0 hosts as zombie idle slave at user at computername:1702, memavail = 4.0 GB, timavail = 1.0 days idle slave at user at computername:1703, memavail = 4.0 GB, timavail = 1.0 days master at user at computername:1701 >> peercellfun(@pause, {1 2}) Then, if I look at one of the two peerslave computers, I see: executing job 25 from user at computername (jobid=2068920377, memreq=1073741824, timreq=3600) executing job took 2.002441 seconds and 0 bytes Warning: failed to return job results to the master And if I "dbstop if caught error", I see in the peerslave: Error using ==> peer failed to locate specified peer Where the error occurs at: peer('put', joblist.hostid, argout, options, 'jobid', joblist.jobid); however: >> joblist.hostid ans = 3682858105 which is the correct hostid for the peermaster. Do you have any idea where the problem might lie? How can I debug this? If it's not easy to solve, how can I run each job once (bc the peermaster keeps on sending request if it doesn't know that the first job was completed)? Thanks a lot! 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.nin.knaw.nl/research_groups/van_someren_group/ From jan.schoffelen at donders.ru.nl Fri Jan 14 09:39:39 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 09:39:39 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> Message-ID: <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> Cara Sara, I am not sure whether I totally understand your question. Are you referring to the example script 'fixing a missing sensor'? When I look at it on our (renewed) wiki (still brings tears to my eyes), I don't see any mention of a layout. I agree with you that the example however can be made a bit more clear. This is my take on it, starting from the back of the pipeline: The 'fixing' algorithm replaces a 'dead' channel with the average signal recorded at its neighbours. In the current implementation, the description of the sensors and the data (=the grad-structure and the data.trial) which go into ft_channelrepair need to contain a full description of the sensor-array, including the faulty one. In other words, if your sensor array has 10 sensors, one of which you want to have repaired, the input to ft_channelrepair needs a data-structure containing data from the spatial location of those 10 sensors (this is in data.grad, and needed to determine which channels are the neighbours). For consistency, the time course of the faulty channel also needs to be there. The actual time courses of the faulty channel will not be used, and these can take any value. Depending on the hardware and recording protocol, a faulty channel is either present or not in the data. In the example script, the faulty channel was not even recorded, and this is the reason for the first part of the script: the creation of a dummy channel, initialized with 0's in order to make ft_channelrepair work. If, however, your dataset actually contains data on the faulty channel (which may look very noisy), you can skip the first part of the script, and directly go to the second part. Best wishes, Jan-Mathijs On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: > Hello > can anybody spend some more words on the chapter "Fixing a missing > sensor"? > I'm trying to use it with a AtB (like ITAB-Chieti) device...but I > cannot understand how to use it. I've several troubles when I've to > declare the layout, since I don't have a layout file, but I construct > that starting from grad... > Do you have any hint for me? > > Sara Rombetto > > > ------------------------------------------- > * Dott.ssa Sara Rombetto * > * Istituto di Cibernetica "E. Caianiello" * > * Via Campi Flegrei, 34 * > * 80078 Pozzuoli (NA) * > * Italy * > * tel +390818675054 * > * fax +390818675326 * > ------------------------------------------- > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > _______________________________________________ > 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 Fri Jan 14 09:48:13 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 09:48:13 +0100 Subject: [FieldTrip] Question about wavelet analysis In-Reply-To: References: Message-ID: <0CECFFCC-6802-42DE-81C3-B8FD25E5F1F2@donders.ru.nl> Dear Inbal, > 1. Just wanted to make sure: > When I use [res] = ft_freqanalysis(cfg,data) with data that have > several trials - and I define cfg.keeptrials = 'yes'; > I get an analysis for each trial in [res]. Then I use > ft_multiplotTFR(cfg,res) with cfg.trials = 'all'; > The result is an average on the wavelet result of all trials? (and > not a wavelet on the averaged signal of all trials) > Yes, ft_multiplotTFR computes an average spectrogram over observations/ trials > 2. Is there a way for me to see the wavelet analysis result of each > trial and to browse easily between them? > rather than calling ft_multiplotTFR(cfg,res) each time with > cfg.trials = i ; where i is the desired trial number? > At the moment, no. I never really thought of looking at single trial multiplots but I can imagine the need for this functionality. Your workaround indeed works, but may be a bit tedioius. > 3. How can I use other mother wavelet? (and not just Morlet wavelets) > What kind of wavelet would you like to use? If the wavelet consists of a tapered cosine/sine wave in which the Gaussian taper will be replaced by something else, you could use cfg.method = 'mtmconvol'. This is an efficient implementation of a wavelet-like analysis, where there is some freedom to define your own taper. At present this relies on matlab's window-function (or on the slepian sequences; different story), so the different tapers are limited to those available in matlab. However, it is relatively straightforward to tap into the code here, and provide your own taper. A dangerous, but possible option is to temporarily overload the matlab window-function with your own, spitting out the requested taper. > 4. How can I control the colormap min and max values so that they > will be similar in all figures? (like doing imagesc(pic,clim))? > I guess cfg.zlim should do the trick. Best, JM > Thank you very much > > Inbal > _______________________________________________ > 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 jungky at korea.ac.kr Fri Jan 14 09:58:38 2011 From: jungky at korea.ac.kr (Jung, Ki-Young) Date: Fri, 14 Jan 2011 00:58:38 -0800 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: Message-ID: Dear all, I'd like to do statistical comparison using cluster based permuation between two groups on ERP data. But I am receiving following error messages ??? Undefined function or method 'bwlabeln' for input arguments of type 'double'. Error in ==> findcluster at 89  [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :),  nfreq, ntime), 4); Error in ==> clusterstat at 194     posclusobs = findcluster(reshape(postailobs,     [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); Error in ==> statistics_montecarlo at 321  [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); Error in ==> statistics_wrapper at 285   [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 125 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); My configuration for ft_freqstatistics are cfg = []; cfg.channel          = 'all'; cfg.latency          = 'all'; cfg.frequency        = [30 50]; cfg.method           = 'montecarlo'; cfg.statistic        = 'indepsamplesT'; cfg.correctm         = 'cluster'; cfg.clusteralpha     = 0.025; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan        = 2; cfg.tail             = 0; cfg.clustertail      = 0; cfg.alpha            = 0.025; cfg.numrandomization = 500; cfg.neighbours       = [ ]; design = [ones(1, 16), ones(1, 16)*2]; cfg.design           = design; cfg.ivar             = 1; [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); Data structure of con_grand_avg are con_grand_avg =       label: {27x1 cell}        freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50]        time: [1x21 double]      dimord: 'subj_chan_freq_time'   powspctrm: [4-D double]         cfg: [1x1 struct] Any comment helps me. Best regards, Ki-Young Jung From julian.keil at gmail.com Fri Jan 14 10:04:19 2011 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 14 Jan 2011 10:04:19 +0100 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: Message-ID: <5CAF6334-C41B-429B-8575-E3CAAA20EB37@gmail.com> Hi, did you check with 'which bwlabeln' if you have the respcetive function? It's part of the image processing toolbox for matlab. Good Luck. Julian Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > Dear all, > > I'd like to do statistical comparison using cluster based permuation > between two groups on ERP data. > But I am receiving following error messages > ??? Undefined function or method 'bwlabeln' for input arguments of > type 'double'. > > Error in ==> findcluster at 89 > [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), > nfreq, ntime), 4); > > Error in ==> clusterstat at 194 > posclusobs = findcluster(reshape(postailobs, > [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); > > Error in ==> statistics_montecarlo at 321 > [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_freqstatistics at 125 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > My configuration for ft_freqstatistics are > cfg = []; > cfg.channel = 'all'; > cfg.latency = 'all'; > cfg.frequency = [30 50]; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.025; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > cfg.numrandomization = 500; > cfg.neighbours = [ ]; > design = [ones(1, 16), ones(1, 16)*2]; > cfg.design = design; > cfg.ivar = 1; > [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); > > > Data structure of con_grand_avg are > > con_grand_avg = > label: {27x1 cell} > freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50] > time: [1x21 double] > dimord: 'subj_chan_freq_time' > powspctrm: [4-D double] > cfg: [1x1 struct] > > > Any comment helps me. > > > Best regards, > > Ki-Young Jung > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From s.rombetto at cib.na.cnr.it Fri Jan 14 11:03:18 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Fri, 14 Jan 2011 11:03:18 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> Message-ID: <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> Hello yes I'm referring to the example script 'fixing a missing sensor'. Even if you consider the structure grad, you also load LABEL275.mat and GRAD275.mat, that is the layout in someway. What I do is to process my data: I define trials and preprocess them. Then I use ft_rejectvisual to remove artifacts and noisy channels. After this my data are ok, but I have some missing channels. In order to solve the inverse problem, I'm using a software that needs all the channels....and this is the reason why I'm trying to "fix the missing sensor". Sara > Cara Sara, > > I am not sure whether I totally understand your question. Are you > referring to the example script 'fixing a missing sensor'? > When I look at it on our (renewed) wiki (still brings tears to my > eyes), I don't see any mention of a layout. > > I agree with you that the example however can be made a bit more clear. > This is my take on it, starting from the back of the pipeline: > > The 'fixing' algorithm replaces a 'dead' channel with the average > signal recorded at its neighbours. In the current implementation, the > description of the sensors and the data (=the grad-structure and the > data.trial) which go into ft_channelrepair need to contain a full > description of the sensor-array, including the faulty one. In other > words, if your sensor array has 10 sensors, one of which you want to > have repaired, the input to ft_channelrepair needs a data-structure > containing data from the spatial location of those 10 sensors (this is > in data.grad, and needed to determine which channels are the > neighbours). For consistency, the time course of the faulty channel > also needs to be there. The actual time courses of the faulty channel > will not be used, and these can take any value. Depending on the > hardware and recording protocol, a faulty channel is either present or > not in the data. In the example script, the faulty channel was not even > recorded, and this is the reason for the first part of the script: the > creation of a dummy channel, initialized with 0's in order to make > ft_channelrepair work. If, however, your dataset actually contains data > on the faulty channel (which may look very noisy), you can skip the > first part of the script, and directly go to the second part. > > Best wishes, > > Jan-Mathijs > > > On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: > >> Hello >> can anybody spend some more words on the chapter "Fixing a missing sensor"? >> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >> cannot understand how to use it. I've several troubles when I've to >> declare the layout, since I don't have a layout file, but I construct >> that starting from grad... >> Do you have any hint for me? >> >> Sara Rombetto >> >> >> ------------------------------------------- >> * Dott.ssa Sara Rombetto * >> * Istituto di Cibernetica "E. Caianiello" * >> * Via Campi Flegrei, 34 * >> * 80078 Pozzuoli (NA) * >> * Italy * >> * tel +390818675054 * >> * fax +390818675326 * >> ------------------------------------------- >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> _______________________________________________ >> 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 ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From jan.schoffelen at donders.ru.nl Fri Jan 14 11:30:45 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 14 Jan 2011 11:30:45 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> Message-ID: <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> Cara Sara, OK. Indeed, if you have run ft_rejectvisual and removed some channels, these are missing from your actual data. The original data.grad should however still contain the labels of all channels, and you can use grad.label as 'LABEL275', provided the order of the remaining channels did not change. Alternatively, you could define cfg.keepchannel = 'nan', before calling ft_rejectvisual. The noisy channels will then still be 'present' in your data (but set to NaN). I believe that this would take away the need to do the first part of the script. Best JM PS: please note that it is not optimal to do source reconstruction after replacing noisy channels with an average of their neighbours. At least you need to take this into account in the creation of the leadfields. On Jan 14, 2011, at 11:03 AM, s.rombetto at cib.na.cnr.it wrote: > Hello > yes I'm referring to the example script 'fixing a missing sensor'. > Even if you consider the structure grad, you also load LABEL275.mat > and GRAD275.mat, that is the layout in someway. > > What I do is to process my data: I define trials and preprocess > them. Then I use ft_rejectvisual to remove artifacts and noisy > channels. > After this my data are ok, but I have some missing channels. > In order to solve the inverse problem, I'm using a software that > needs all the channels....and this is the reason why I'm trying to > "fix the missing sensor". > > Sara > >> Cara Sara, >> >> I am not sure whether I totally understand your question. Are you >> referring to the example script 'fixing a missing sensor'? >> When I look at it on our (renewed) wiki (still brings tears to my >> eyes), I don't see any mention of a layout. >> >> I agree with you that the example however can be made a bit more >> clear. >> This is my take on it, starting from the back of the pipeline: >> >> The 'fixing' algorithm replaces a 'dead' channel with the average >> signal recorded at its neighbours. In the current implementation, the >> description of the sensors and the data (=the grad-structure and the >> data.trial) which go into ft_channelrepair need to contain a full >> description of the sensor-array, including the faulty one. In other >> words, if your sensor array has 10 sensors, one of which you want to >> have repaired, the input to ft_channelrepair needs a data-structure >> containing data from the spatial location of those 10 sensors (this >> is >> in data.grad, and needed to determine which channels are the >> neighbours). For consistency, the time course of the faulty channel >> also needs to be there. The actual time courses of the faulty channel >> will not be used, and these can take any value. Depending on the >> hardware and recording protocol, a faulty channel is either present >> or >> not in the data. In the example script, the faulty channel was not >> even >> recorded, and this is the reason for the first part of the script: >> the >> creation of a dummy channel, initialized with 0's in order to make >> ft_channelrepair work. If, however, your dataset actually contains >> data >> on the faulty channel (which may look very noisy), you can skip the >> first part of the script, and directly go to the second part. >> >> Best wishes, >> >> Jan-Mathijs >> >> >> On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: >> >>> Hello >>> can anybody spend some more words on the chapter "Fixing a missing >>> sensor"? >>> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >>> cannot understand how to use it. I've several troubles when I've to >>> declare the layout, since I don't have a layout file, but I >>> construct >>> that starting from grad... >>> Do you have any hint for me? >>> >>> Sara Rombetto >>> >>> >>> ------------------------------------------- >>> * Dott.ssa Sara Rombetto * >>> * Istituto di Cibernetica "E. Caianiello" * >>> * Via Campi Flegrei, 34 * >>> * 80078 Pozzuoli (NA) * >>> * Italy * >>> * tel +390818675054 * >>> * fax +390818675326 * >>> ------------------------------------------- >>> >>> ---------------------------------------------------------------- >>> This message was sent using IMP, the Internet Messaging Program. >>> >>> >>> _______________________________________________ >>> 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 > > > > ------------------------------------------- > * Dott.ssa Sara Rombetto * > * Istituto di Cibernetica "E. Caianiello" * > * Via Campi Flegrei, 34 * > * 80078 Pozzuoli (NA) * > * Italy * > * tel +390818675054 * > * fax +390818675326 * > ------------------------------------------- > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program. > > > > _______________________________________________ > 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 s.rombetto at cib.na.cnr.it Fri Jan 14 11:40:09 2011 From: s.rombetto at cib.na.cnr.it (s.rombetto at cib.na.cnr.it) Date: Fri, 14 Jan 2011 11:40:09 +0100 Subject: [FieldTrip] fieldtrip question - help needed In-Reply-To: <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> References: <20110113160911.920ivb5pcgco4osw@arco.cib.na.cnr.it> <1C6EFE2A-77A0-41F7-A7B2-6E980C7B2FCE@donders.ru.nl> <20110114110318.h1vsbz8z4o4kco0w@arco.cib.na.cnr.it> <7B1CC02A-D12C-4A63-8E64-8993C353B3A3@donders.ru.nl> Message-ID: <20110114114009.bkaw65hmaog880g4@arco.cib.na.cnr.it> thanks that's right. But we also fabricate squids, so the broken channels can change. So I was looking for a temporary solution. best regards Sara > Cara Sara, > > OK. Indeed, if you have run ft_rejectvisual and removed some channels, > these are missing from your actual data. The original data.grad should > however still contain the labels of all channels, and you can use > grad.label as 'LABEL275', provided the order of the remaining channels > did not change. Alternatively, you could define cfg.keepchannel = > 'nan', before calling ft_rejectvisual. The noisy channels will then > still be 'present' in your data (but set to NaN). I believe that this > would take away the need to do the first part of the script. > > Best > > JM > > PS: please note that it is not optimal to do source reconstruction > after replacing noisy channels with an average of their neighbours. At > least you need to take this into account in the creation of the > leadfields. > > > On Jan 14, 2011, at 11:03 AM, s.rombetto at cib.na.cnr.it wrote: > >> Hello >> yes I'm referring to the example script 'fixing a missing sensor'. >> Even if you consider the structure grad, you also load LABEL275.mat >> and GRAD275.mat, that is the layout in someway. >> >> What I do is to process my data: I define trials and preprocess >> them. Then I use ft_rejectvisual to remove artifacts and noisy >> channels. >> After this my data are ok, but I have some missing channels. >> In order to solve the inverse problem, I'm using a software that >> needs all the channels....and this is the reason why I'm trying to >> "fix the missing sensor". >> >> Sara >> >>> Cara Sara, >>> >>> I am not sure whether I totally understand your question. Are you >>> referring to the example script 'fixing a missing sensor'? >>> When I look at it on our (renewed) wiki (still brings tears to my >>> eyes), I don't see any mention of a layout. >>> >>> I agree with you that the example however can be made a bit more clear. >>> This is my take on it, starting from the back of the pipeline: >>> >>> The 'fixing' algorithm replaces a 'dead' channel with the average >>> signal recorded at its neighbours. In the current implementation, the >>> description of the sensors and the data (=the grad-structure and the >>> data.trial) which go into ft_channelrepair need to contain a full >>> description of the sensor-array, including the faulty one. In other >>> words, if your sensor array has 10 sensors, one of which you want to >>> have repaired, the input to ft_channelrepair needs a data-structure >>> containing data from the spatial location of those 10 sensors (this is >>> in data.grad, and needed to determine which channels are the >>> neighbours). For consistency, the time course of the faulty channel >>> also needs to be there. The actual time courses of the faulty channel >>> will not be used, and these can take any value. Depending on the >>> hardware and recording protocol, a faulty channel is either present or >>> not in the data. In the example script, the faulty channel was not even >>> recorded, and this is the reason for the first part of the script: the >>> creation of a dummy channel, initialized with 0's in order to make >>> ft_channelrepair work. If, however, your dataset actually contains data >>> on the faulty channel (which may look very noisy), you can skip the >>> first part of the script, and directly go to the second part. >>> >>> Best wishes, >>> >>> Jan-Mathijs >>> >>> >>> On Jan 13, 2011, at 4:09 PM, s.rombetto at cib.na.cnr.it wrote: >>> >>>> Hello >>>> can anybody spend some more words on the chapter "Fixing a >>>> missing sensor"? >>>> I'm trying to use it with a AtB (like ITAB-Chieti) device...but I >>>> cannot understand how to use it. I've several troubles when I've to >>>> declare the layout, since I don't have a layout file, but I construct >>>> that starting from grad... >>>> Do you have any hint for me? >>>> >>>> Sara Rombetto >>>> >>>> >>>> ------------------------------------------- >>>> * Dott.ssa Sara Rombetto * >>>> * Istituto di Cibernetica "E. Caianiello" * >>>> * Via Campi Flegrei, 34 * >>>> * 80078 Pozzuoli (NA) * >>>> * Italy * >>>> * tel +390818675054 * >>>> * fax +390818675326 * >>>> ------------------------------------------- >>>> >>>> ---------------------------------------------------------------- >>>> This message was sent using IMP, the Internet Messaging Program. >>>> >>>> >>>> _______________________________________________ >>>> 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 >> >> >> >> ------------------------------------------- >> * Dott.ssa Sara Rombetto * >> * Istituto di Cibernetica "E. Caianiello" * >> * Via Campi Flegrei, 34 * >> * 80078 Pozzuoli (NA) * >> * Italy * >> * tel +390818675054 * >> * fax +390818675326 * >> ------------------------------------------- >> >> ---------------------------------------------------------------- >> This message was sent using IMP, the Internet Messaging Program. >> >> >> >> _______________________________________________ >> 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 ------------------------------------------- * Dott.ssa Sara Rombetto * * Istituto di Cibernetica "E. Caianiello" * * Via Campi Flegrei, 34 * * 80078 Pozzuoli (NA) * * Italy * * tel +390818675054 * * fax +390818675326 * ------------------------------------------- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From julian.keil at gmail.com Fri Jan 14 12:51:14 2011 From: julian.keil at gmail.com (Julian Keil) Date: Fri, 14 Jan 2011 12:51:14 +0100 Subject: [FieldTrip] grid - bug in ft_prepare_leadfield Message-ID: <78914DC7-8F9C-41C6-9FA1-853ABFA19B5C@gmail.com> Hi, there might be a bug in the latest release of ft_prepare leadfield (version 20110113): In line 172: [sourcegrid, tmpcfg] ... but later on, the code only refers to "grid" not "sourcegrid". Changing "sourcegrid" to "grid" solves the problem. By the way, I get a conflict with the graph2d-toolbox, as this toolbox has a function called grid.m Greetings 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 jungky at korea.ac.kr Fri Jan 14 18:58:23 2011 From: jungky at korea.ac.kr (Jung, Ki-Young) Date: Fri, 14 Jan 2011 09:58:23 -0800 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: <1294996134883354.0.mail@mail> References: <1294996134883354.0.mail@mail> Message-ID: Thanks! But I have still trouble with this message. ??? Error using ==> statistics_montecarlo Too many input arguments. Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 125 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Best regards, KY On Fri, Jan 14, 2011 at 1:04 AM, Julian Keil wrote: > Hi, > > did you check with 'which bwlabeln' if you have the respcetive function? > It's part of the image processing toolbox for matlab. > > Good Luck. > > Julian > > Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > >> Dear all, >> >> I'd like to do statistical comparison using cluster based permuation >> between two groups on ERP data. >> But I am receiving following error messages >> ??? Undefined function or method 'bwlabeln' for input arguments of >> type 'double'. >> >> Error in ==> findcluster at 89 >>  [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, :, :), >>  nfreq, ntime), 4); >> >> Error in ==> clusterstat at 194 >>     posclusobs = findcluster(reshape(postailobs, >>     [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); >> >> Error in ==> statistics_montecarlo at 321 >>  [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); >> >> Error in ==> statistics_wrapper at 285 >>   [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); >> >> Error in ==> ft_freqstatistics at 125 >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); >> >> My configuration for ft_freqstatistics are >> cfg = []; >> cfg.channel          = 'all'; >> cfg.latency          = 'all'; >> cfg.frequency        = [30 50]; >> cfg.method           = 'montecarlo'; >> cfg.statistic        = 'indepsamplesT'; >> cfg.correctm         = 'cluster'; >> cfg.clusteralpha     = 0.025; >> cfg.clusterstatistic = 'maxsum'; >> cfg.minnbchan        = 2; >> cfg.tail             = 0; >> cfg.clustertail      = 0; >> cfg.alpha            = 0.025; >> cfg.numrandomization = 500; >> cfg.neighbours       = [ ]; >> design = [ones(1, 16), ones(1, 16)*2]; >> cfg.design           = design; >> cfg.ivar             = 1; >> [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); >> >> >> Data structure of con_grand_avg are >> >> con_grand_avg = >>       label: {27x1 cell} >>        freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50] >>        time: [1x21 double] >>      dimord: 'subj_chan_freq_time' >>   powspctrm: [4-D double] >>         cfg: [1x1 struct] >> >> >> Any comment helps me. >> >> >> Best regards, >> >> Ki-Young Jung >> >> _______________________________________________ >> 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 batrod at gmail.com Fri Jan 14 22:29:41 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Fri, 14 Jan 2011 15:29:41 -0600 Subject: [FieldTrip] Fwd: question about ft_statistics errors In-Reply-To: References: <1294996134883354.0.mail@mail> Message-ID: I may be wrong but as far as i remember, the cluster analysis can only be done on one value of frequency, average or not. There is no cfg.avgoverfreq option n your script. But again i might be wrong. Rodolphe On Fri, Jan 14, 2011 at 11:58 AM, Jung, Ki-Young wrote: > Thanks! But I have still trouble with this message. > > ??? Error using ==> statistics_montecarlo > Too many input arguments. > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > > Error in ==> ft_freqstatistics at 125 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Best regards, > > KY > > On Fri, Jan 14, 2011 at 1:04 AM, Julian Keil > wrote: > > Hi, > > > > did you check with 'which bwlabeln' if you have the respcetive function? > > It's part of the image processing toolbox for matlab. > > > > Good Luck. > > > > Julian > > > > Am 14.01.2011 um 09:58 schrieb Jung, Ki-Young: > > > >> Dear all, > >> > >> I'd like to do statistical comparison using cluster based permuation > >> between two groups on ERP data. > >> But I am receiving following error messages > >> ??? Undefined function or method 'bwlabeln' for input arguments of > >> type 'double'. > >> > >> Error in ==> findcluster at 89 > >> [labelmat(spatdimlev, :, :), num] = bwlabeln(reshape(onoff(spatdimlev, > :, :), > >> nfreq, ntime), 4); > >> > >> Error in ==> clusterstat at 194 > >> posclusobs = findcluster(reshape(postailobs, > >> [cfg.dim,1]),channeighbstructmat,cfg.minnbchan); > >> > >> Error in ==> statistics_montecarlo at 321 > >> [stat, cfg] = clusterstat(cfg, statrand, statobs,'issource',issource); > >> > >> Error in ==> statistics_wrapper at 285 > >> [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); > >> > >> Error in ==> ft_freqstatistics at 125 > >> [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > >> > >> My configuration for ft_freqstatistics are > >> cfg = []; > >> cfg.channel = 'all'; > >> cfg.latency = 'all'; > >> cfg.frequency = [30 50]; > >> cfg.method = 'montecarlo'; > >> cfg.statistic = 'indepsamplesT'; > >> cfg.correctm = 'cluster'; > >> cfg.clusteralpha = 0.025; > >> cfg.clusterstatistic = 'maxsum'; > >> cfg.minnbchan = 2; > >> cfg.tail = 0; > >> cfg.clustertail = 0; > >> cfg.alpha = 0.025; > >> cfg.numrandomization = 500; > >> cfg.neighbours = [ ]; > >> design = [ones(1, 16), ones(1, 16)*2]; > >> cfg.design = design; > >> cfg.ivar = 1; > >> [stat] = ft_freqstatistics(cfg, mig_grand_avg, con_grand_avg); > >> > >> > >> Data structure of con_grand_avg are > >> > >> con_grand_avg = > >> label: {27x1 cell} > >> freq: [30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 > 49 50] > >> time: [1x21 double] > >> dimord: 'subj_chan_freq_time' > >> powspctrm: [4-D double] > >> cfg: [1x1 struct] > >> > >> > >> Any comment helps me. > >> > >> > >> Best regards, > >> > >> Ki-Young Jung > >> > >> _______________________________________________ > >> 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 dgroppe at cogsci.ucsd.edu Fri Jan 14 22:36:13 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 14 Jan 2011 13:36:13 -0800 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout Message-ID: Hi Fieldtripians, I'm trying to export some EEGLAB data to Fieldtrip and am having trouble plotting the data topographically. I constructed a layout file for my 31 electrodes (see attached) and tried to plot the topography of my data using ft_topoplotER.m. This produced the attached figures all_chans.jpg and just_scalp_chans.jpg. The topography should look like that in the attached image, eeglab_topo.jpg. As you can see, the electrodes are shrunk too far into the head and can be off center. Trying to change the channel layout file to fix this has little effect because ft_prepare_layout.m automatically normalizes the electrode coordinates to fill a unit circle. Given the topoplots in the fieldtrip tutorial, there's obviously a way around this problem but save for editing the ft_prepare_layout.m, I don't know what to do. thanks in advance for your help, -David -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ -------------- next part -------------- A non-text attachment was scrubbed... Name: eeglab_topo.jpg Type: image/jpeg Size: 92401 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: all_chans.jpg Type: image/jpeg Size: 92441 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: just_scalp_chans.jpg Type: image/jpeg Size: 82349 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 31chan.lay Type: application/octet-stream Size: 1067 bytes Desc: not available URL: From batrod at gmail.com Fri Jan 14 22:52:48 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Fri, 14 Jan 2011 15:52:48 -0600 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout In-Reply-To: References: Message-ID: David, i had the same issue with my own layout. The position of my electrodes was not fitting the head, even if the proportion were right, like in your first image. I solved this problem by multiplying the position with different numbers until i found the perfect one. This is the part of code that does this: lay = ft_prepare_layout(cfg); lay.pos(:,1) = 1.5*lay.pos(:,1); Replace 1.5 by something that works for you. Hope this helps, Rodolphe. On Fri, Jan 14, 2011 at 3:36 PM, David Groppe wrote: > Hi Fieldtripians, > I'm trying to export some EEGLAB data to Fieldtrip and am having > trouble plotting the data topographically. I constructed a layout file > for my 31 electrodes (see attached) and tried to plot the topography > of my data using ft_topoplotER.m. This produced the attached figures > all_chans.jpg and just_scalp_chans.jpg. The topography should look > like that in the attached image, eeglab_topo.jpg. As you can see, the > electrodes are shrunk too far into the head and can be off center. > Trying to change the channel layout file to fix this has little effect > because ft_prepare_layout.m automatically normalizes the electrode > coordinates to fill a unit circle. Given the topoplots in the > fieldtrip tutorial, there's obviously a way around this problem but > save for editing the ft_prepare_layout.m, I don't know what to do. > thanks in advance for your help, > -David > > -- > David Groppe, Ph.D. > dgroppe at cogsci.ucsd.edu > http://www.cogsci.ucsd.edu/~dgroppe/ > > _______________________________________________ > 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 karl.doron at gmail.com Sat Jan 15 18:05:46 2011 From: karl.doron at gmail.com (Karl Doron) Date: Sat, 15 Jan 2011 09:05:46 -0800 Subject: [FieldTrip] singleplotTFR error Message-ID: Hello, Has anyone else reported a problem with ft_singleplotTFR and output of the new specest module? multiplotTFR works, but 'interactive' method fails. It looks like the error occurs when trying to mask NaNs % masking only possible for evenly spaced axis if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) warning('(one of the) axis are not evenly spaced -> nans cannot be masked out -> cfg.masknans is set to ''no'';') cfg.masknans = 'no'; end Thank you, karl doron UCSB -------------- next part -------------- An HTML attachment was scrubbed... URL: From dgroppe at cogsci.ucsd.edu Sat Jan 15 18:49:09 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Sat, 15 Jan 2011 09:49:09 -0800 Subject: [FieldTrip] problems with channel layout autoscaling by ft_prepare_layout In-Reply-To: References: Message-ID: Thanks for the email Rodolphe. It's good to know I'm not the only one who has had this problem. I was hoping for a solution that didn't involve editing the code, since that makes it a pain to update our version of fieldtrip when a new version is released. It looks like that might be the only way though. cheers, -David On Fri, Jan 14, 2011 at 1:52 PM, Rodolphe Nenert wrote: > David, > i had the same issue with my own layout. The position of my electrodes was > not fitting the head, even if the proportion were right, like in your first > image. > I solved this problem by multiplying the position with different numbers > until i found the perfect one. > This is the part of code that does this: > lay = ft_prepare_layout(cfg); > lay.pos(:,1) = 1.5*lay.pos(:,1); > Replace 1.5 by something that works for you. > Hope this helps, > Rodolphe. > > On Fri, Jan 14, 2011 at 3:36 PM, David Groppe > wrote: >> >> Hi Fieldtripians, >>   I'm trying to export some EEGLAB data to Fieldtrip and am having >> trouble plotting the data topographically. I constructed a layout file >> for my 31 electrodes (see attached) and tried to plot the topography >> of my data using ft_topoplotER.m.  This produced the attached figures >> all_chans.jpg and just_scalp_chans.jpg.  The topography should look >> like that in the attached image, eeglab_topo.jpg.  As you can see, the >> electrodes are shrunk too far into the head and can be off center. >> Trying to change the channel layout file to fix this has little effect >> because ft_prepare_layout.m automatically normalizes the electrode >> coordinates to fill a unit circle.  Given the topoplots in the >> fieldtrip tutorial, there's obviously a way around this problem but >> save for editing the ft_prepare_layout.m, I don't know what to do. >>     thanks in advance for your help, >>            -David >> >> -- >> David Groppe, Ph.D. >> dgroppe at cogsci.ucsd.edu >> http://www.cogsci.ucsd.edu/~dgroppe/ >> >> _______________________________________________ >> 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. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From dgroppe at cogsci.ucsd.edu Sat Jan 15 23:43:29 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Sat, 15 Jan 2011 14:43:29 -0800 Subject: [FieldTrip] logic behind normalizing tapers Message-ID: Hi again Fieldtrippers, I noticed that when estimating power spectra ft_specest_mtmfft.m scales tapers such that their sum squared value is 1 before applying them to the data. For example: %lines 106-108 of ft_specest_mtmfft.m case 'hanning' tap = hanning(ndatsample)'; tap = tap./norm(tap, 'fro'); I realize this simply scales the power spectrum, but what's the rationale for this? Other EEG analysis software and tutorials I've read don't do this. much thanks, -David -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From TAVABIK at email.chop.edu Sun Jan 16 07:58:50 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Sun, 16 Jan 2011 01:58:50 -0500 Subject: [FieldTrip] MEG Artifact removal Message-ID: Greetings - Would someone please comment on the following procedure: (1) dummy=ft_rejectvisual(cfg,raw-data) where cfg.method='trial', cfg.channel='MEG' (2) dummy2=ft_rejectvisual(cfg,dummy) where cfg.method='channel', cfg.channel='MEG' (3) save artifact-rejected-data dummy2 Is this what is actually recommended by the visual artifact rejection tutorial, if not, then is it correct to assume that the final data structure (artifact-rejected-data) is the 'clean' data? Also, are there any automatic artifact rejection options available for trial (CTF) MEG data? Thanks in advance. -K. ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- From r.vandermeij at donders.ru.nl Sun Jan 16 11:20:11 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Sun, 16 Jan 2011 11:20:11 +0100 Subject: [FieldTrip] singleplotTFR error In-Reply-To: References: Message-ID: <4D32C65B.5020304@donders.ru.nl> Hi Karl, Could you give some more information on the errors? Could you also post your cfg's? That will help in finding and fixing the bug. What FieldTrip version are you using? Best, Roemer On 15-1-2011 18:05, Karl Doron wrote: > Hello, > > Has anyone else reported a problem with ft_singleplotTFR and output of > the new specest module? > > multiplotTFR works, but 'interactive' method fails. > > It looks like the error occurs when trying to mask NaNs > > % masking only possible for evenly spaced axis > > if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) > > warning('(one of the) axis are not evenly spaced -> nans cannot be > masked out -> cfg.masknans is set to ''no'';') > > cfg.masknans = 'no'; > > end > > > > Thank you, > karl doron > UCSB > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From karl.doron at gmail.com Mon Jan 17 02:51:13 2011 From: karl.doron at gmail.com (Karl Doron) Date: Sun, 16 Jan 2011 17:51:13 -0800 Subject: [FieldTrip] singleplotTFR error In-Reply-To: <4D32C65B.5020304@donders.ru.nl> References: <4D32C65B.5020304@donders.ru.nl> Message-ID: Hello Roemer, Here's the cfg's and output from calls to ft_freqanalysis with method='wavelet' and the subsequent call to ft_singleplotTFR and the resulting error. The imagesc command will however plot the data at that channel imagesc(squeeze(wvpow.powspctrm(strmatch('A177',label),:,:))) Thanks for any help! cfg = []; cfg.output = 'pow'; cfg.channel = 'MEG'; cfg.method = 'wavelet'; cfg.foi = 10:2:30; cfg.toi = 0.0:0.05:2.75; wvpow = ft_freqanalysis(cfg, data_spctrm); wvpow = label: {246x1 cell} dimord: 'chan_freq_time' freq: [1x11 double] time: [1x56 double] powspctrm: [246x11x56 double] grad: [1x1 struct] cfg: [1x1 struct] %Singleplot results cfg = []; cfg.channel = 'A177'; cfg.grad = grad; cfg.xlim = [0.6 2.5]; cfg.ylim = [10 20]; figure; ft_singleplotTFR(cfg, wvpow) Warning: (one of the) axis are not evenly spaced -> nans cannot be masked out -> cfg.masknans is set to 'no'; > In ft_singleplotTFR at 296 ??? Attempted to access c(6,1); index out of bounds because size(c)=[5,37]. Error in ==> uimage at 124 ce(j,i) = c(indi(end), indj(end)); Error in ==> uimagesc at 46 hh = uimage(varargin{:},'CDataMapping','scaled'); Error in ==> ft_plot_matrix at 192 h = uimagesc(hdat, vdat, cdat, clim); Error in ==> ft_singleplotTFR at 327 ft_plot_matrix(data.(cfg.xparam)(xidc),data.(cfg.yparam)(yidc), TFR, 'clim',[zmin,zmax],'tag','cip') On Sun, Jan 16, 2011 at 2:20 AM, Roemer van der Meij < r.vandermeij at donders.ru.nl> wrote: > Hi Karl, > > Could you give some more information on the errors? Could you also post > your cfg's? That will help in finding and fixing the bug. What FieldTrip > version are you using? > > Best, > Roemer > > > > On 15-1-2011 18:05, Karl Doron wrote: > > Hello, > > Has anyone else reported a problem with ft_singleplotTFR and output of > the new specest module? > > multiplotTFR works, but 'interactive' method fails. > > It looks like the error occurs when trying to mask NaNs > > % masking only possible for evenly spaced axis > > if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) > > warning('(one of the) axis are not evenly spaced -> nans cannot be > masked out -> cfg.masknans is set to ''no'';') > > cfg.masknans = 'no'; > > end > > > Thank you, > karl doron > UCSB > > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > 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 mcregar at upo.es Mon Jan 17 15:42:43 2011 From: mcregar at upo.es (Maite Crespo Garcia) Date: Mon, 17 Jan 2011 15:42:43 +0100 Subject: [FieldTrip] Noise projection for coherence estimates... Message-ID: <4374c5456d2776bd.4d346373@upo.es> Hello all, I would like to know if beamformer coherence estimates should be normalized dividing them by an equivalent noise projection as for power estimates. My experiment has a baseline. Would it be correct to divide coherence during active state by baseline coherence? What would be the better approach? Thank you very much in advance. Best regards, Maité -------------- next part -------------- An HTML attachment was scrubbed... URL: From sangita.dandekar at gmail.com Mon Jan 17 17:44:52 2011 From: sangita.dandekar at gmail.com (Sangita Dandekar) Date: Mon, 17 Jan 2011 11:44:52 -0500 Subject: [FieldTrip] searchable email discussion archive? Message-ID: The new fieldtrip page looks good. I was just wondering whether there is a method in place to search the discussion list email archives using keywords? The page at: http://mailman.science.ru.nl/pipermail/fieldtrip/ is sortable by field but I haven't been able to figure out how to do a keyword search. The old webpage's searchable email archive was extremely useful. Are there plans to create the same sort searchable archive for the new page? Thanks in advance for any help, Sangi -------------- next part -------------- An HTML attachment was scrubbed... URL: From matt.mollison at gmail.com Mon Jan 17 18:08:11 2011 From: matt.mollison at gmail.com (Matt Mollison) Date: Mon, 17 Jan 2011 10:08:11 -0700 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: References: Message-ID: Sangi, I agree that the search functionality at the old site was quite useful. One method that I've used for searching the new archives is to go to google.comand include "site: http://mailman.science.ru.nl/pipermail/fieldtrip/" with the terms that you wish to search for. Hope that helps. Matt -- Univ. of Colorado at Boulder Dept. of Psychology and Neuroscience matthew.mollison at colorado.edu http://psych.colorado.edu/~mollison/ On Mon, Jan 17, 2011 at 9:44 AM, Sangita Dandekar < sangita.dandekar at gmail.com> wrote: > The new fieldtrip page looks good. I was just wondering whether there is a > method in place to search the discussion list email archives using keywords? > > The page at: > http://mailman.science.ru.nl/pipermail/fieldtrip/ > > is sortable by field but I haven't been able to figure out how to do a > keyword search. The old webpage's searchable email archive was extremely > useful. Are there > plans to create the same sort searchable archive for the new page? > > Thanks in advance for any help, > Sangi > > _______________________________________________ > 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 mcregar at upo.es Mon Jan 17 18:13:18 2011 From: mcregar at upo.es (Maite Crespo Garcia) Date: Mon, 17 Jan 2011 18:13:18 +0100 Subject: [FieldTrip] Noise projection for coherence estimates... In-Reply-To: <4374c5456d2776bd.4d346373@upo.es> References: <4374c5456d2776bd.4d346373@upo.es> Message-ID: <45d37fe857bb6844.4d3486be@upo.es> I realized after writing the previous post that the coherence estimate is a ratio itself. Likely, using projected noise has no sense. But I'm still not sure about the right approach (compare to baseline and then between conditions?). Any suggestion? Thanks, Maité ----- Mensaje original ----- De: Maite Crespo Garcia Fecha: Lunes, 17 de Enero de 2011, 4:25 pm Asunto: [FieldTrip] Noise projection for coherence estimates... A: fieldtrip at donders.ru.nl > Hello all, > > I would like to know if beamformer coherence estimates should be normalized dividing them by an equivalent noise projection as for power estimates. My experiment has a baseline. Would it be correct to divide coherence during active state by baseline coherence? What would be the better approach? > > Thank you very much in advance. > > Best regards, > Maité > _______________________________________________ > 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.oosthoek at donders.ru.nl Tue Jan 18 09:18:46 2011 From: s.oosthoek at donders.ru.nl (Simon Oosthoek) Date: Tue, 18 Jan 2011 09:18:46 +0100 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: References: Message-ID: <4D354CE6.8000009@donders.ru.nl> Matt Mollison wrote: > Sangi, > > I agree that the search functionality at the old site was quite > useful. One method that I've used for searching the new archives is to > go to google.com and include > "site:http://mailman.science.ru.nl/pipermail/fieldtrip/" with the > terms that you wish to search for. > I think this is the best method to use, because I doubt the search functionality can easily be included on the mailman site. Perhaps I can fabricate a search box using google on the wiki for the mailinglist... Cheers Simon From stephen.whitmarsh at gmail.com Tue Jan 18 10:37:55 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Tue, 18 Jan 2011 10:37:55 +0100 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: <-6003509403171258621@unknownmsgid> References: <-6003509403171258621@unknownmsgid> Message-ID: Dear All, We will be giving a weekend FieldTrip workshop at the City College New York soon (February 5th – 6th) and still have a couple of last-minute spaces left for those in the NYC region interested in joining. Please see attachment for details. Sincerely, Stephen Whitmarsh -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: FieldTrip Weekend Workshop NYC.pdf Type: application/pdf Size: 86868 bytes Desc: not available URL: From eelke.spaak at donders.ru.nl Tue Jan 18 10:39:12 2011 From: eelke.spaak at donders.ru.nl (Eelke Spaak) Date: Tue, 18 Jan 2011 10:39:12 +0100 Subject: [FieldTrip] searchable email discussion archive? In-Reply-To: <4D354CE6.8000009@donders.ru.nl> References: <4D354CE6.8000009@donders.ru.nl> Message-ID: Hello everyone, I've just added a Google Custom search box to the Discussion list page on the wiki (http://fieldtrip.fcdonders.nl/discussion_list). (Note that we are having a bit of trouble with some of our fileservers at the moment, and therefore the wiki might be offline every now and then. We hope to have these problems fixed shortly.) Best, Eelke 2011/1/18 Simon Oosthoek : > Matt Mollison wrote: >> >> Sangi, >> >> I agree that the search functionality at the old site was quite useful. >> One method that I've used for searching the new archives is to go to >> google.com and include >> "site:http://mailman.science.ru.nl/pipermail/fieldtrip/" with the terms that >> you wish to search for. >> > I think this is the best method to use, because I doubt the search > functionality can easily be included on the mailman site. > Perhaps I can fabricate a search box using google on the wiki for the > mailinglist... > > Cheers > > Simon > From venug001 at crimson.ua.edu Tue Jan 18 14:39:36 2011 From: venug001 at crimson.ua.edu (Gopakumar Venugopalan) Date: Tue, 18 Jan 2011 04:39:36 -0900 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, and just finished my post doc last week. I wonder what options might be open to me. Thanks in advance. Warm regards gopa On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < stephen.whitmarsh at gmail.com> wrote: > Dear All, > > > > We will be giving a weekend FieldTrip workshop at the City College New York > soon (February 5th – 6th) and still have a couple of last-minute spaces > left for those in the NYC region interested in joining. Please see > attachment for details. > > > > Sincerely, > > Stephen Whitmarsh > > > _______________________________________________ > 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 venug001 at crimson.ua.edu Tue Jan 18 14:40:48 2011 From: venug001 at crimson.ua.edu (Gopakumar Venugopalan) Date: Tue, 18 Jan 2011 04:40:48 -0900 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: I responded to the fieldtrip listserv by mistake, would you please delete it and NOT include it in your digest or forward. Warm regards gopa On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan < venug001 at crimson.ua.edu> wrote: > Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, > and just finished my post doc last week. I wonder what options might be open > to me. Thanks in advance. > Warm regards > gopa > > On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < > stephen.whitmarsh at gmail.com> wrote: > >> Dear All, >> >> >> >> We will be giving a weekend FieldTrip workshop at the City College New >> York soon (February 5th – 6th) and still have a couple of last-minute >> spaces left for those in the NYC region interested in joining. Please see >> attachment for details. >> >> >> >> Sincerely, >> >> Stephen Whitmarsh >> >> >> _______________________________________________ >> 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 Tue Jan 18 18:43:11 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 18 Jan 2011 11:43:11 -0600 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Dear Fieldtrip users, i just received the info about the NY workshop taking place on 5th and 6th february. Unfortunately, its too late for me to make it. As i'd like to participate to such workshop/formation, is there a webpage or a place where i can find such informations about future events? Rodolphe On Tue, Jan 18, 2011 at 7:40 AM, Gopakumar Venugopalan < venug001 at crimson.ua.edu> wrote: > I responded to the fieldtrip listserv by mistake, would you please delete > it and NOT include it in your digest or forward. > Warm regards > gopa > > On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan < > venug001 at crimson.ua.edu> wrote: > >> Dear Stepben Whitmarsh, I would be interested, don't live in the NYC area, >> and just finished my post doc last week. I wonder what options might be open >> to me. Thanks in advance. >> Warm regards >> gopa >> >> On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh < >> stephen.whitmarsh at gmail.com> wrote: >> >>> Dear All, >>> >>> >>> >>> We will be giving a weekend FieldTrip workshop at the City College New >>> York soon (February 5th – 6th) and still have a couple of last-minute >>> spaces left for those in the NYC region interested in joining. Please see >>> attachment for details. >>> >>> >>> >>> Sincerely, >>> >>> Stephen Whitmarsh >>> >>> >>> _______________________________________________ >>> 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 m.chait at ucl.ac.uk Wed Jan 19 11:48:37 2011 From: m.chait at ucl.ac.uk (Maria Chait) Date: Wed, 19 Jan 2011 10:48:37 -0000 Subject: [FieldTrip] RA position at the UCL Ear Institute - MEG & auditory change detection Message-ID: <079f01cbb7c6$6d996c50$48cc44f0$@chait@ucl.ac.uk> Dear Colleagues, I am writing to point your attention to a research assistant job opening at the UCL Ear Institute and would be grateful if you could distribute the advert to relevant students in your department. Please note that it is possible to undertake a UCL PhD degree within the context of this research work. Research Assistant - Ref: 1174144 Closing Date: 17/02/2011 Apply on: www.ucl.ac.uk/hr/jobs A research assistant position (salary £27,796 - £29,318 per annum Inclusive of London allowance) is available to work on a Wellcome Trust funded project that will use MEG functional brain imaging to investigate the neural systems that support auditory change detection in the human brain. You will be supervised by Dr Maria Chait (UCL Ear Institute) and Prof. Tim Griffiths (Newcastle University). The post holder will be based at UCL Ear Institute, and report to Dr Maria Chait. MEG scanning will be carried out at UCL’s Wellcome Trust Centre for Neuroimaging. Initial funding for this post is available for 36 months. There is the possibility (if UCL eligibility criteria are satisfied) to undertake a UCL PhD degree within the context of this research work. Your main duties and responsibilities will be: 1. Design and execute MEG brain imaging experiments. 2. Develop MatLab software for running the experiments and for data analysis 3. Train subjects in preparation for relevant experiments. 4. Record and analyze imaging data. 5. Assist in the preparation of manuscripts. The UCL Ear Institute provides state-of-the-art research facilities across a wide range of disciplines and is one of the foremost centres for hearing, speech and language-related research within Europe. The Wellcome Trust Centre for Neuroimaging is a leading centre for brain imaging, bringing together clinicians and scientists who study higher cognitive function using neuroimaging techniques. Key Requirements Applicants should hold a 1St class, or upper 2nd (or equivalent) bachelor’s degree (masters degree an advantage) in an engineering or scientific subject and have substantial experience in digital signal processing and computer programming. Previous experience with functional brain imaging and/or acoustics is desirable. Further Details You should apply for this post (Ref #: 1174144) through UCL's online recruitment website, www.ucl.ac.uk/hr/jobs, where you can download a job description and person specification. If you have any queries please contact Dr. Maria Chait (email m.chait at ucl.ac.uk) Maria Chait PhD m.chait at ucl.ac.uk Research Fellow UCL Ear Institute 332 Gray's Inn Road London WC1X 8EE -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Thu Jan 20 10:51:48 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 20 Jan 2011 10:51:48 +0100 Subject: [FieldTrip] FieldtripR? In-Reply-To: References: Message-ID: <87C19057-05F3-4A69-85A4-0B932BA8FC6A@donders.ru.nl> Dear Mike, [CCed to the fieldtrip email discussion list]] On 19 Jan 2011, at 23:39, Mike Lawrence wrote: > I just came across your Fieldtrip software and it looks very > impressive. However, I'm not a MATLAB user; I feel that scientific > software needs to be both free and open source for the purposes of > replication and extension, so I use R instead (well, I also use R > because it's the lingua franca of statistics, so it provides access to > cutting edge routines). I therefore thought I'd request that the > Fieldtrip team work to port the Fieldtrip code to R. There is > currently a paucity of EEG analysis packages for R and a port of > Fieldtrip would make a great contribution. Thanks for your constructive suggestion. The FieldTrip software is open source, but indeed requires commercial software (MATLAB) to run. Most people run it on Windows or Apple OSX, even further commercial dependencies for those users. Requests for porting FieldTrip to free languages (other than Matlab) come up regularly, e.g. to make a compiled C/C++ version, an Octave version, a Python version or an R version. Regretfully, we are not able to honor these requests. FieldTrip is developped for, and by scientists that are mostly funded by national and international scientific projects. Those projects require our contributors to focus on their scientific results, and FieldTrip can be considered as just spinoff. For people that want to use FieldTrip without Matlab, pragmatically I would first suggest to look into Octave: large parts (but not all parts) of our code will execute properly in Octave with no or little changes. An alternative that requires MATLAB for development, but does not require MATLAB for running it, would be to use the MATLAB compiler to compile it into a stand-alone version that can be distributed free of charge. Contributions in either the direction of Octave or a compiled version, or contributions in porting it to another language, are most certainly welcome and would receive our support. If you feel that we should receive funding from our national or from international research funding agency to do the work that is required in porting it to a free platform, please consider contacting http://www.nwo.nl and similar agencies to make a plea for this. best regards, Robert PS please also see my "coffee machine" email at http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003339.html , which is part of a similar thread. --- FieldTrip project leader Senior Researcher and MEG physicist at the Donders Centre for Cognitive Neuroimaging From michael.wibral at web.de Thu Jan 20 10:51:59 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 20 Jan 2011 10:51:59 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection Message-ID: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> Deal Fieldtrip users, there is something else I do not understand in the tutorial: if you read in the data in trials (as it is done) how can you do padding later as it is suggested. I tried to run the example code on teh website reading in the data such that it contains trials. If I then try to search for muscle artifacts I get the 'subscript indices must be positive or logical ... values', indicating that the code tries to access data that aren't there. If I set the padding to zero (instead of 0.1) it works. So I am wondering wether somehow one should actually run these things on continuous data (contrary to what is indicated in the tutorial)? Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From michael.wibral at web.de Thu Jan 20 10:52:17 2011 From: michael.wibral at web.de (Michael Wibral) Date: Thu, 20 Jan 2011 10:52:17 +0100 (CET) Subject: [FieldTrip] error in the artifact rejection tutorial? Message-ID: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> Dear fieldtrip community, there seems to be a slight inconsistency in the tutorial section on artifact removal (which I otherwise like a lot because it calrifies a lot of the 'black-boxiness' of these particular fieldtrip functions (thanks a lot). The part I am referring to is in the jump removal section. It starts with the lines: % jump cfg = []; if isfield(cfg, 'padding') && cfg.padding~=0 padding = cfg.padding; else padding = 0; end I wonder whther these lines should go somewhere else as after clearing cfg the code will alwazs end up in the second part if the if condition, as there can be no 'padding' field. Didn't want to change this my self, as I might misunderstand something. Michael -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From r.oostenveld at donders.ru.nl Thu Jan 20 15:06:33 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Thu, 20 Jan 2011 15:06:33 +0100 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: <5E34E57B-F699-4267-858B-D903CE79F61C@donders.ru.nl> Dear Rodolphe We will host a toolkit course on "Advanced MEG and EEG analysis" at the Donders in Nijmegen. Please have a look at http://www.ru.nl/donders/agenda-events/courses/toolkits-2011/ . Note that it only contains the preliminary program (simply copied from last year) and that the final programm will look slightly different. The registation has just openend this week, and a formal annoucement will follow. Please do note that it tends to be oversubscribed: we select the participants on their motivation and background and not on who registers first. best regards, Robert On 18 Jan 2011, at 18:43, Rodolphe Nenert wrote: > Dear Fieldtrip users, > > i just received the info about the NY workshop taking place on 5th > and 6th february. Unfortunately, its too late for me to make it. As > i'd like to participate to such workshop/formation, is there a > webpage or a place where i can find such informations about future > events? > > Rodolphe From jan.schoffelen at donders.ru.nl Fri Jan 21 09:52:23 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 21 Jan 2011 09:52:23 +0100 Subject: [FieldTrip] error in the artifact rejection tutorial? In-Reply-To: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> References: <32784113.398892.1295517137562.JavaMail.fmail@mwmweb056> Message-ID: Dear Michael, Please feel free to delete this particular line (and/or edit any other line) from the wiki. Declaring cfg empty before the conditional statements indeed does not makes sense. Best wishes, JM On Jan 20, 2011, at 10:52 AM, Michael Wibral wrote: > Dear fieldtrip community, > > there seems to be a slight inconsistency in the tutorial section on > artifact removal (which I otherwise like a lot because it calrifies > a lot of the 'black-boxiness' of these particular fieldtrip > functions (thanks a lot). > The part I am referring to is in the jump removal section. > > It starts with the lines: > > > % jump > cfg = []; > if isfield(cfg, 'padding') && cfg.padding~=0 > padding = cfg.padding; > else > padding = 0; > end > > > I wonder whther these lines should go somewhere else as after > clearing cfg the code will alwazs end up in the second part if the > if condition, as there can be no 'padding' field. > Didn't want to change this my self, as I might misunderstand > something. > > Michael > Wibral.vcf>_______________________________________________ > 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 Fri Jan 21 09:55:48 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Fri, 21 Jan 2011 09:55:48 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> Message-ID: Dear Michael, Yes, I agree with you here as well. In principle the ft_artifact_zvalue supports data as a second input argument, but in such case the different types of padding in the cfg do not make sense. I would indeed remove the second input arguments in the example code snippets. Could I ask you to take care of that? Thanks, JM On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: > Deal Fieldtrip users, > > there is something else I do not understand in the tutorial: if you > read in the data in trials (as it is done) how can you do padding > later as it is suggested. I tried to run the example code on teh > website reading in the data such that it contains trials. If I then > try to search for muscle artifacts I get the 'subscript indices must > be positive or logical ... values', indicating that the code tries > to access data that aren't there. If I set the padding to zero > (instead of 0.1) it works. So I am wondering wether somehow one > should actually run these things on continuous data (contrary to > what is indicated in the tutorial)? > > Michael > Wibral.vcf>_______________________________________________ > 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 karch at mpib-berlin.mpg.de Fri Jan 21 16:49:20 2011 From: karch at mpib-berlin.mpg.de (Karch, Julian) Date: Fri, 21 Jan 2011 16:49:20 +0100 Subject: [FieldTrip] WG: References: <82EE999347EBF142A8D78EF16FB83D8D01C82524@MPIBMAIL01.mpib-berlin.mpg.de> Message-ID: <82EE999347EBF142A8D78EF16FB83D8D01C82525@MPIBMAIL01.mpib-berlin.mpg.de> Hello, i just tried to go through the Multivariates Tutorial (http://fieldtrip.fcdonders.nl/tutorial/multivariateanalysis) unluckly when i typed "stat = ft_timelockstatistics(cfg,tleft,tright);" matlab aborted with the exit code: ??? Error using ==> tprod at 119 unable to compile MEX version of 'E:/julian/matlab/fieldtrip/multivariate/external/farquhar/tprod/tprod', please make sure your MEX compiler is set up correctly (try 'mex -setup'). I'm using MATLAB 7.10.0 64 Bit on Windows 7. I definitively have a working mex compiler as compiling the example yprime.c is working perfectly. I also tried to compile the files manually by typing mex('ddtprod.c','dstprod.c','sdtprod.c','sstprod.c','tprod_util.c','tprod_mex.c','mxInfo.c');. This resulted in the following output: ddtprod.c e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(249) : error C2143: syntax error : missing ';' before 'type' e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(250) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(276) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(277) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(278) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(279) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(280) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(283) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(284) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier e:\julian\matlab\fieldtrip\multivariate\external\farquhar\tprod\tprod.def(285) : error C2065: 'd' : undeclared identifier C:\PROGRA~1\MATLAB\R2010A\BIN\MEX.PL: Error: Compile of 'ddtprod.c' failed. Any suggestions? Julian Karch Research Assistant Max Planck Institute for Human Development Department Lifespan Psychology Lentzeallee 94 14195 Berlin Tel.: 030 / 82406-294 Email: karch at mpib-berlin.mpg.de Internet: www.mpib-berlin.mpg.de -------------- next part -------------- An HTML attachment was scrubbed... URL: From frank.ye.mei at gmail.com Fri Jan 21 20:07:17 2011 From: frank.ye.mei at gmail.com (Frank (Ye) Mei) Date: Fri, 21 Jan 2011 14:07:17 -0500 Subject: [FieldTrip] problem downloading fieldtrip Message-ID: <4D39D965.20601@gmail.com> I cann't download the fieldtrip toolbox. I didn't get the email with download instructions. Thank you for your download request, an email with download instructions has been sent to ............ If you object to giving your real email address, please consider using a service like http://www.spamgourmet.com, http://www.mailinator.com or http://10minutemail.com. -------------- next part -------------- An HTML attachment was scrubbed... URL: From todavidkim at gmail.com Fri Jan 21 20:21:27 2011 From: todavidkim at gmail.com (David Kim) Date: Fri, 21 Jan 2011 11:21:27 -0800 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: <4D39D965.20601@gmail.com> References: <4D39D965.20601@gmail.com> Message-ID: Hi Frank, While you are awaiting the official response from fieldtrip folks you might try this: http://code.google.com/p/fieldtrip/source/checkout If you have a working understanding of of how to use svn, I found this to be a great way to install and update fieldtrip software. On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: > I cann't download the fieldtrip toolbox. I didn't get the email with > download instructions. > > Thank you for your download request, an email with download instructions > has been sent to ............ > > If you object to giving your real email address, please consider using a > service like http://www.spamgourmet.com, http://www.mailinator.com or > http://10minutemail.com. > > > _______________________________________________ > 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 dgroppe at cogsci.ucsd.edu Sat Jan 22 08:29:00 2011 From: dgroppe at cogsci.ucsd.edu (David Groppe) Date: Fri, 21 Jan 2011 23:29:00 -0800 Subject: [FieldTrip] FieldTrip weekend toolkit NYC, Feb 5-6 In-Reply-To: References: <-6003509403171258621@unknownmsgid> Message-ID: Speaking of workshops, Fieldtrip users might be interested in some of the talks from the 12th EEGLAB workshop that took place a couple of months ago. Videos of the talks were just posted online: http://thesciencenetwork.org/programs/12th-eeglab-workshop Talk slides and supportive material are available on the EEGLAB wiki as well: http://sccn.ucsd.edu/wiki/Twelfth_EEGLAB_Workshop Although the talks obviously don't cover the logistics of using Fieldtrip, some of the methods implemented by Fieldtrip (e.g., time-frequency analysis, independent components analysis) are and might be of use to those of you just getting started with these techniques. Moreover, there are some neat talks on future directions in EEG technology (e.g., dry electrodes and EEG recording from moving participants). cheers, -David On Tue, Jan 18, 2011 at 9:43 AM, Rodolphe Nenert wrote: > Dear Fieldtrip users, > i just received the info about the NY workshop taking place on 5th and 6th > february. Unfortunately, its too late for me to make it. As i'd like to > participate to such workshop/formation, is there a webpage or a place where > i can find such informations about future events? > Rodolphe > > On Tue, Jan 18, 2011 at 7:40 AM, Gopakumar Venugopalan > wrote: >> >> I responded to the fieldtrip listserv by mistake, would you please delete >> it and NOT include it in your digest or forward. >> Warm regards >> gopa >> >> On Tue, Jan 18, 2011 at 4:39 AM, Gopakumar Venugopalan >> wrote: >>> >>> Dear Stepben Whitmarsh, I would be interested, don't live in the NYC >>> area, and just finished my post doc last week. I wonder what options might >>> be open to me. Thanks in advance. >>> Warm regards >>> gopa >>> >>> On Tue, Jan 18, 2011 at 12:37 AM, Stephen Whitmarsh >>> wrote: >>>> >>>> Dear All, >>>> >>>> >>>> >>>> We will be giving a weekend FieldTrip workshop at the City College New >>>> York soon (February 5th – 6th) and still have a couple of last-minute spaces >>>> left for those in the NYC region interested in joining. Please see >>>> attachment for details. >>>> >>>> >>>> >>>> Sincerely, >>>> >>>> Stephen Whitmarsh >>>> >>>> _______________________________________________ >>>> 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 > -- David Groppe, Ph.D. dgroppe at cogsci.ucsd.edu http://www.cogsci.ucsd.edu/~dgroppe/ From kassayag at gmail.com Sat Jan 22 08:45:07 2011 From: kassayag at gmail.com (karen assayag) Date: Sat, 22 Jan 2011 09:45:07 +0200 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: References: <4D39D965.20601@gmail.com> Message-ID: is the download good for mac ? On Fri, Jan 21, 2011 at 9:21 PM, David Kim wrote: > Hi Frank, > > While you are awaiting the official response from fieldtrip folks you might > try this: > > http://code.google.com/p/fieldtrip/source/checkout > > If you have a working understanding of of how to use svn, > I found this to be a great way to install and update fieldtrip software. > > On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: > >> I cann't download the fieldtrip toolbox. I didn't get the email with >> download instructions. >> >> Thank you for your download request, an email with download instructions >> has been sent to ............ >> >> If you object to giving your real email address, please consider using a >> service like http://www.spamgourmet.com, http://www.mailinator.com or >> http://10minutemail.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 > -- Karen -------------- next part -------------- An HTML attachment was scrubbed... URL: From todavidkim at gmail.com Sat Jan 22 08:54:42 2011 From: todavidkim at gmail.com (David Kim) Date: Fri, 21 Jan 2011 23:54:42 -0800 Subject: [FieldTrip] problem downloading fieldtrip In-Reply-To: References: <4D39D965.20601@gmail.com> Message-ID: Hi Karen, Again, you might want to hear the official response from the fieldtrip folks, but I've successfully used svn on several OS platforms without an issue (WinXP, Win7, CentOs, Ubuntu). So I'm assuming it works across platforms. I just did a search on my CentOs machine, and it looks like the svn version includes all the mexmac files. I would give it a try. On Fri, Jan 21, 2011 at 11:45 PM, karen assayag wrote: > is the download good for mac ? > > > On Fri, Jan 21, 2011 at 9:21 PM, David Kim wrote: > >> Hi Frank, >> >> While you are awaiting the official response from fieldtrip folks you >> might try this: >> >> http://code.google.com/p/fieldtrip/source/checkout >> >> If you have a working understanding of of how to use svn, >> I found this to be a great way to install and update fieldtrip software. >> >> On Fri, Jan 21, 2011 at 11:07 AM, Frank (Ye) Mei wrote: >> >>> I cann't download the fieldtrip toolbox. I didn't get the email with >>> download instructions. >>> >>> Thank you for your download request, an email with download instructions >>> has been sent to ............ >>> >>> If you object to giving your real email address, please consider using a >>> service like http://www.spamgourmet.com, http://www.mailinator.com or >>> http://10minutemail.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 >> > > > > -- > Karen > > > > _______________________________________________ > 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 Marcel.Bastiaansen at mpi.nl Mon Jan 24 11:44:07 2011 From: Marcel.Bastiaansen at mpi.nl (Bastiaansen, Marcel) Date: Mon, 24 Jan 2011 11:44:07 +0100 Subject: [FieldTrip] question on beamformers Message-ID: <4D3D57F7.8090504@mpi.nl> Dear all, I have the following conceptual issue with using beamforming: I have data from 2 conditions, A and B. Both contain a prestimulus interval and a poststimulus interval. When plotting the TF representations of power, using a *relative* baseline (poststimulus interval / prestimulus interval), a strong difference emerges between the conditions in the beta frequency range. Especially if I plot the *difference between the conditions*, the beta effect is long-lasting, narrow-band and topographically focused. Ideal for beamforming, I'd say. In setting up the beamformer analysis, I am faced with the following issue: the effect is most clearly present in the *relative* power changes, so I would want to compute spatial filters for both the pre and the post time intervals. My hunch would be to compute common spatial filters for both pre intervals (preA and preB), and common filters for both post intervals (postA and postB). Then, (after projecting the trials through the filters), compute the relative power again (pre/post for each condition). Does this approach make sense? Next question is then, at which point in the analysis pipeline should one do the condition subtraction? (I'd want to do that because at the TFR level the effect comes out most clearly in the condition difference) Best, Marcel -- dr. Marcel C.M. Bastiaansen. Max Planck Institute for Psycholinguistics Visiting Adress: Wundtlaan 1, 6525 XD Nijmegen, the Netherlands Mailing adress: P.O. Box 310, 6500 AH Nijmegen, the Netherlands phone: +31 24 3521 347 fax: +31 24 3521 213 mail: marcel.bastiaansen at mpi.nl http://www.mpi.nl/people/bastiaansen-marcel and Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Visiting address: Kapittelweg 29, 6525 EN Nijmegen, the Netherlands Mailing address: PO Box 9101, 6500 HB Nijmegen, the Netherlands phone: + 31 24 3610 882 fax: + 31 24 3610 989 mail: marcel.bastiaansen at fcdonders.ru.nl web: http://www.ru.nl/neuroimaging/staff/neurocognition_of/marcel_bastiaansen/ -- From michael.wibral at web.de Mon Jan 24 11:48:47 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 11:48:47 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056>, Message-ID: <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> Hi Jan-Mathijs, I am a bit unsure how to proceed: (1) sketch the artifact correction way like this ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> ft_preprocessing OR (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. I think I should go for option (1) as this seems to be the standard use on continuous data. Sometime in the futrure one should then add a tutorial for those that have data in trials to start with. Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 21, 2011 9:55:48 AM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Dear Michael, > >Yes, I agree with you here as well. In principle the >ft_artifact_zvalue supports data as a second input argument, but in >such case the different types of padding in the cfg do not make sense. >I would indeed remove the second input arguments in the example code >snippets. Could I ask you to take care of that? > >Thanks, > >JM > > >On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: > >> Deal Fieldtrip users, >> >> there is something else I do not understand in the tutorial: if you >> read in the data in trials (as it is done) how can you do padding >> later as it is suggested. I tried to run the example code on teh >> website reading in the data such that it contains trials. If I then >> try to search for muscle artifacts I get the 'subscript indices must >> be positive or logical ... values', indicating that the code tries >> to access data that aren't there. If I set the padding to zero >> (instead of 0.1) it works. So I am wondering wether somehow one >> should actually run these things on continuous data (contrary to >> what is indicated in the tutorial)? >> >> Michael >> > Wibral.vcf>_______________________________________________ >> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Mon Jan 24 12:12:57 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 24 Jan 2011 12:12:57 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> Message-ID: <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> Dear Michael, I agree. The tutorial should be 'de'-confused by sketching option 1, and another one should be describing option 2, or the original should be clearly making the distinction. Best, JM On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: > Hi Jan-Mathijs, > > I am a bit unsure how to proceed: > > (1) sketch the artifact correction way like this > ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> > ft_preprocessing > OR > (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> > artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. > > I think I should go for option (1) as this seems to be the standard > use on continuous data. Sometime in the futrure one should then add > a tutorial for those that have data in trials to start with. > > Michael > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 21, 2011 9:55:48 AM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Dear Michael, >> >> Yes, I agree with you here as well. In principle the >> ft_artifact_zvalue supports data as a second input argument, but in >> such case the different types of padding in the cfg do not make >> sense. >> I would indeed remove the second input arguments in the example code >> snippets. Could I ask you to take care of that? >> >> Thanks, >> >> JM >> >> >> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >> >>> Deal Fieldtrip users, >>> >>> there is something else I do not understand in the tutorial: if you >>> read in the data in trials (as it is done) how can you do padding >>> later as it is suggested. I tried to run the example code on teh >>> website reading in the data such that it contains trials. If I then >>> try to search for muscle artifacts I get the 'subscript indices must >>> be positive or logical ... values', indicating that the code tries >>> to access data that aren't there. If I set the padding to zero >>> (instead of 0.1) it works. So I am wondering wether somehow one >>> should actually run these things on continuous data (contrary to >>> what is indicated in the tutorial)? >>> >>> Michael >>> >> Wibral.vcf>_______________________________________________ >>> 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 stephen.whitmarsh at gmail.com Mon Jan 24 12:18:47 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Mon, 24 Jan 2011 12:18:47 +0100 Subject: [FieldTrip] question on beamformers In-Reply-To: <4D3D57F7.8090504@mpi.nl> References: <4D3D57F7.8090504@mpi.nl> Message-ID: Dear Marcel, My two cents are the following: I would recommend to compute common filter over ALL conditions, pre AND post. This will make sure you use as much information as possible to calculate your cross-spectral density matrix and subsequent filter. I assume you assume that the location/orientation of the sources do not change before and after stimulus. Also, in the case that you are looking for a post-stimulus beta DECREASE it will help you to accurately determine post-stimulus activity based on a filter calculated from of a period where there is most (beta) signal. Then, for your contrast project your conditions, pre and post *separately* and do your relative contrast then: e.g. projected post-stimulus activity A / projected pre-stimulus activity A, and same for B. Then compare relative A - or / by B. Bottom line, do your common filter on everything, project and compare everything separately after that. Hope that helps, Stephen On 24 January 2011 11:44, Bastiaansen, Marcel wrote: > Dear all, > > I have the following conceptual issue with using beamforming: > > I have data from 2 conditions, A and B. Both contain a prestimulus interval > and a poststimulus interval. > > When plotting the TF representations of power, using a *relative* baseline > (poststimulus interval / prestimulus interval), a strong difference emerges > between the conditions in the beta frequency range. Especially if I plot the > *difference between the conditions*, the beta effect is long-lasting, > narrow-band and topographically focused. Ideal for beamforming, I'd say. > > In setting up the beamformer analysis, I am faced with the following issue: > the effect is most clearly present in the *relative* power changes, so I > would want to compute spatial filters for both the pre and the post time > intervals. My hunch would be to compute common spatial filters for both pre > intervals (preA and preB), and common filters for both post intervals (postA > and postB). Then, (after projecting the trials through the filters), compute > the relative power again (pre/post for each condition). Does this approach > make sense? > > Next question is then, at which point in the analysis pipeline should one > do the condition subtraction? (I'd want to do that because at the TFR level > the effect comes out most clearly in the condition difference) > > > Best, > Marcel > > > > -- > dr. Marcel C.M. Bastiaansen. > > Max Planck Institute for Psycholinguistics > Visiting Adress: Wundtlaan 1, 6525 XD Nijmegen, the Netherlands > Mailing adress: P.O. Box 310, 6500 AH Nijmegen, the Netherlands > phone: +31 24 3521 347 > fax: +31 24 3521 213 > mail: marcel.bastiaansen at mpi.nl > http://www.mpi.nl/people/bastiaansen-marcel > > and > > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognitive Neuroimaging > Visiting address: Kapittelweg 29, 6525 EN Nijmegen, the Netherlands > Mailing address: PO Box 9101, 6500 HB Nijmegen, the Netherlands > phone: + 31 24 3610 882 > fax: + 31 24 3610 989 > mail: marcel.bastiaansen at fcdonders.ru.nl > web: > http://www.ru.nl/neuroimaging/staff/neurocognition_of/marcel_bastiaansen/ > -- > _______________________________________________ > 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 Mon Jan 24 13:51:38 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 13:51:38 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054>, <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> Message-ID: <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> Hi Jan mathijs, I tried to get option1 running, stumbled over the following little obstacle however: I tried to keep one cfg throughout the steps ft_definetrial; ft_artifact_zvalue, ft_rejectartifcat (with option complete and some tracking of where artfecats were found), ft_preprocessing (cutting out the clean trials from the cont. data). IMHO this used to be the way most people did this kind of procesing a while ago. However, I can't get ft_artifact_zvalue to run with different settings one after another for jump/musvle/EOG. FT claims after the first run of ft_artifact_zvalue that the z-value thing has been performed and refuse to detect other artifacts with new settings. >From here I only see two alternative: specifying a really lengthy cfg every time a new (also struggling with the cfg.dataset versus cfg.datafile issue) and do the bookkeeping of cfg.trl and related things myself or manually removing the cfg.artdef.zvalue.artifct field to get the z-value based detection to run again. This seems a bit odd to me. Any suggestions? Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 12:12:57 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Dear Michael, > >I agree. The tutorial should be 'de'-confused by sketching option 1, >and another one should be describing option 2, or the original should >be clearly making the distinction. > >Best, > >JM > > >On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: > >> Hi Jan-Mathijs, >> >> I am a bit unsure how to proceed: >> >> (1) sketch the artifact correction way like this >> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >> ft_preprocessing >> OR >> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> ft_preprocessing. >> >> I think I should go for option (1) as this seems to be the standard >> use on continuous data. Sometime in the futrure one should then add >> a tutorial for those that have data in trials to start with. >> >> Michael >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 21, 2011 9:55:48 AM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> Yes, I agree with you here as well. In principle the >>> ft_artifact_zvalue supports data as a second input argument, but in >>> such case the different types of padding in the cfg do not make >>> sense. >>> I would indeed remove the second input arguments in the example code >>> snippets. Could I ask you to take care of that? >>> >>> Thanks, >>> >>> JM >>> >>> >>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>> >>>> Deal Fieldtrip users, >>>> >>>> there is something else I do not understand in the tutorial: if you >>>> read in the data in trials (as it is done) how can you do padding >>>> later as it is suggested. I tried to run the example code on teh >>>> website reading in the data such that it contains trials. If I then >>>> try to search for muscle artifacts I get the 'subscript indices must >>>> be positive or logical ... values', indicating that the code tries >>>> to access data that aren't there. If I set the padding to zero >>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>> should actually run these things on continuous data (contrary to >>>> what is indicated in the tutorial)? >>>> >>>> Michael >>>> >>> Wibral.vcf>_______________________________________________ >>>> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Mon Jan 24 16:41:09 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Mon, 24 Jan 2011 16:41:09 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> Message-ID: Hmmm, apparently this approach needs to be ironed out a bit (also from our side). For now, I'd say that it should work if you keep per type of artifact the artifact field in the output configuration, and just concatenate these prior to calling ft_rejectartifact. I will moreover CC this e-mail to the people involved in creating the first version of the renewed tutorial, and will bring up the issue in this week's FieldTrip developers meeting. Best, JM On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > Hi Jan mathijs, > > I tried to get option1 running, stumbled over the following little > obstacle however: > > I tried to keep one cfg throughout the steps ft_definetrial; > ft_artifact_zvalue, ft_rejectartifcat (with option complete and some > tracking of where artfecats were found), ft_preprocessing (cutting > out the clean trials from the cont. data). IMHO this used to be the > way most people did this kind of procesing a while ago. > > However, I can't get ft_artifact_zvalue to run with different > settings one after another for jump/musvle/EOG. FT claims after the > first run of ft_artifact_zvalue that the z-value thing has been > performed and refuse to detect other artifacts with new settings. > >> From here I only see two alternative: specifying a really lengthy >> cfg every time a new (also struggling with the cfg.dataset versus >> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >> things myself or manually removing the cfg.artdef.zvalue.artifct >> field to get the z-value based detection to run again. This seems a >> bit odd to me. > > Any suggestions? > > Michael > > > > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 24, 2011 12:12:57 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Dear Michael, >> >> I agree. The tutorial should be 'de'-confused by sketching option 1, >> and another one should be describing option 2, or the original should >> be clearly making the distinction. >> >> Best, >> >> JM >> >> >> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >> >>> Hi Jan-Mathijs, >>> >>> I am a bit unsure how to proceed: >>> >>> (1) sketch the artifact correction way like this >>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>> ft_preprocessing >>> OR >>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>> ft_preprocessing. >>> >>> I think I should go for option (1) as this seems to be the standard >>> use on continuous data. Sometime in the futrure one should then add >>> a tutorial for those that have data in trials to start with. >>> >>> Michael >>> >>> -----Ursprüngliche Nachricht----- >>> Von: "jan-mathijs schoffelen" >>> Gesendet: Jan 21, 2011 9:55:48 AM >>> An: "Email discussion list for the FieldTrip project" >>> >>> Betreff: Re: [FieldTrip] more on artfifact rejection >>> >>>> Dear Michael, >>>> >>>> Yes, I agree with you here as well. In principle the >>>> ft_artifact_zvalue supports data as a second input argument, but in >>>> such case the different types of padding in the cfg do not make >>>> sense. >>>> I would indeed remove the second input arguments in the example >>>> code >>>> snippets. Could I ask you to take care of that? >>>> >>>> Thanks, >>>> >>>> JM >>>> >>>> >>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>> >>>>> Deal Fieldtrip users, >>>>> >>>>> there is something else I do not understand in the tutorial: if >>>>> you >>>>> read in the data in trials (as it is done) how can you do padding >>>>> later as it is suggested. I tried to run the example code on teh >>>>> website reading in the data such that it contains trials. If I >>>>> then >>>>> try to search for muscle artifacts I get the 'subscript indices >>>>> must >>>>> be positive or logical ... values', indicating that the code tries >>>>> to access data that aren't there. If I set the padding to zero >>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>> should actually run these things on continuous data (contrary to >>>>> what is indicated in the tutorial)? >>>>> >>>>> Michael >>>>> >>>> Wibral.vcf>_______________________________________________ >>>>> 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 Patricia.Wollstadt at gmx.de Mon Jan 24 17:47:26 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Mon, 24 Jan 2011 17:47:26 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction Message-ID: <20110124164726.247880@gmx.net> Dear Fieldtrip-users, I'm currently trying to calculate freqstatistics for four experimental groups, using the following options: groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) length(subjects{4})]; design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; % 1 to N subjects design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group membership cfg=[]; cfg.design=design; cfg.uvar = 1; cfg.ivar = 2; cfg.method = 'montecarlo'; cfg.statistic = 'indepsamplesF'; cfg.correctm = 'fdr'; cfg.numrandomization = 180000; cfg.alpha = 0.01/7; cfg.tail = 1; cfg.design = design; cfg.channels = myChannels; cfg.avgovertime = 'yes'; cfg.avgoverfreq = 'yes'; cfg.frequency = [1 3]; stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); With these settings, the coputation itself runs fine, but the resulting 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists of only ones). This would mean, that I found significant effects for all channels. Is this possible or rather due to an error somewhere in my script? Is it likely, that these are 'real' zeroes or rather very small values, close to zero? Any hints and suggestions are very welcome, thank you in advance, Kind regards Patricia Wollstadt -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl From michael.wibral at web.de Mon Jan 24 18:27:08 2011 From: michael.wibral at web.de (Michael Wibral) Date: Mon, 24 Jan 2011 18:27:08 +0100 (CET) Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054>, Message-ID: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Hi Jan-Mathijs, this is basically what we do at the moment, i.e. fooling artifcat_zvalue by removing the one field it complains about amnd using rejetartefact only at the very last. See the attched code - I really do not want to post this code on the tutorial website as I am not fully sure what I am doing :-). Michael %% CODE ft_defaults; Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/DATASETS/'; Design={ 'DMG13_NewMooney_20110120_0', [2 3], 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; } for ss=1:size(Design,1) % over subjects for cc=1:length(Design{ss,4}) % over conditions for ff=1:length(Design{ss,2}) % over .ds datasets/runs FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), '.ds') FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) % core data reading cfg=[]; cfg.dataset=FullFileName; cfg.headerformat = 'ctf_ds'; % for you to check whether still necessary ctf.dataformat = 'ctf_ds'; cfg.cond=Design{ss,4}(cc) cfg.continuous='yes'; cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? cfg.trialfun=Design{ss,3}; cfg=ft_definetrial(cfg); cfg.trl(end,:)=[]; trl=cfg.trl; % keep track of the trials padding=0.75 % 750 ms %%%%%%%%% artifact rejection section %%% jump % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 35; cfg.artfctdef.zvalue.trlpadding = 0.5*padding; cfg.artfctdef.zvalue.artpadding = 0.5*padding; cfg.artfctdef.zvalue.fltpadding = 0; % algorithmic parameters cfg.artfctdef.zvalue.medianfilter = 'yes'; cfg.artfctdef.zvalue.medianfiltord = 9; % in samples cfg.artfctdef.zvalue.absdiff = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'jump'; [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); % cfg.artfctdef.jump.artifact = artifact_jump; % cfg = ft_rejectartifact(cfg); %%% muscle cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % remove field from structure otherwise this won't run ?? % cutoff and padding  cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 15; cfg.artfctdef.zvalue.trlpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; cfg.artfctdef.zvalue.artpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfreq = [110 140]; cfg.artfctdef.zvalue.bpfiltord = 6; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.boxcar = 0.2; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'muscle'; [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); %%% EOG cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % cutoff and padding cfg.artfctdef.zvalue.channel = 'MRT41'; cfg.artfctdef.zvalue.cutoff = 10; cfg.artfctdef.zvalue.trlpadding = 0.5; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 3; cfg.artfctdef.zvalue.hilbert = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'EOG'; [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); cfg.trl=trl; cfg.artfctdef.reject = 'complete'; % this rejects complete trials, use 'partial' if you want to do partial artifact rejection % collect all the info about the artifacts that were found cfg.artfctdef.eog.artifact =artifact_EOG; cfg.artfctdef.jump.artifact = artifact_jump; cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); Data_no_artifacts=ft_preprocessing(cfg); % some additional filtering for DC removal and detrending cfg=[]; cfg.detrend='yes' cfg.hpfilt='yes' cfg.hpfreq=1; TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); clear Data_no_artifacts;  end ... ... end end -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 4:41:09 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Hmmm, apparently this approach needs to be ironed out a bit (also from >our side). For now, I'd say that it should work if you keep per type >of artifact the artifact field in the output configuration, and just >concatenate these prior to calling ft_rejectartifact. I will moreover >CC this e-mail to the people involved in creating the first version of >the renewed tutorial, and will bring up the issue in this week's >FieldTrip developers meeting. > >Best, > >JM > >On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > >> Hi Jan mathijs, >> >> I tried to get option1 running, stumbled over the following little >> obstacle however: >> >> I tried to keep one cfg throughout the steps ft_definetrial; >> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >> tracking of where artfecats were found), ft_preprocessing (cutting >> out the clean trials from the cont. data). IMHO this used to be the >> way most people did this kind of procesing a while ago. >> >> However, I can't get ft_artifact_zvalue to run with different >> settings one after another for jump/musvle/EOG. FT claims after the >> first run of ft_artifact_zvalue that the z-value thing has been >> performed and refuse to detect other artifacts with new settings. >> >>> From here I only see two alternative: specifying a really lengthy >>> cfg every time a new (also struggling with the cfg.dataset versus >>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>> things myself or manually removing the cfg.artdef.zvalue.artifct >>> field to get the z-value based detection to run again. This seems a >>> bit odd to me. >> >> Any suggestions? >> >> Michael >> >> >> >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 24, 2011 12:12:57 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> I agree. The tutorial should be 'de'-confused by sketching option 1, >>> and another one should be describing option 2, or the original should >>> be clearly making the distinction. >>> >>> Best, >>> >>> JM >>> >>> >>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>> >>>> Hi Jan-Mathijs, >>>> >>>> I am a bit unsure how to proceed: >>>> >>>> (1) sketch the artifact correction way like this >>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>> ft_preprocessing >>>> OR >>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>> ft_preprocessing. >>>> >>>> I think I should go for option (1) as this seems to be the standard >>>> use on continuous data. Sometime in the futrure one should then add >>>> a tutorial for those that have data in trials to start with. >>>> >>>> Michael >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: "jan-mathijs schoffelen" >>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>> An: "Email discussion list for the FieldTrip project" >>>> >>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>> >>>>> Dear Michael, >>>>> >>>>> Yes, I agree with you here as well. In principle the >>>>> ft_artifact_zvalue supports data as a second input argument, but in >>>>> such case the different types of padding in the cfg do not make >>>>> sense. >>>>> I would indeed remove the second input arguments in the example >>>>> code >>>>> snippets. Could I ask you to take care of that? >>>>> >>>>> Thanks, >>>>> >>>>> JM >>>>> >>>>> >>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>> >>>>>> Deal Fieldtrip users, >>>>>> >>>>>> there is something else I do not understand in the tutorial: if >>>>>> you >>>>>> read in the data in trials (as it is done) how can you do padding >>>>>> later as it is suggested. I tried to run the example code on teh >>>>>> website reading in the data such that it contains trials. If I >>>>>> then >>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>> must >>>>>> be positive or logical ... values', indicating that the code tries >>>>>> to access data that aren't there. If I set the padding to zero >>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>> should actually run these things on continuous data (contrary to >>>>>> what is indicated in the tutorial)? >>>>>> >>>>>> Michael >>>>>> >>>>> Wibral.vcf>_______________________________________________ >>>>>> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From batrod at gmail.com Mon Jan 24 18:39:31 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Mon, 24 Jan 2011 11:39:31 -0600 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110124164726.247880@gmx.net> References: <20110124164726.247880@gmx.net> Message-ID: Dear Patricia, Your alpha seems a little bit low, why taking 0.01/7= 0.0014 ? I may be wrong but i guess that a fdr correction on a such value of alpha will be very hard with your data. Rodolphe N., PhD. On Mon, Jan 24, 2011 at 10:47 AM, Patricia Wollstadt < Patricia.Wollstadt at gmx.de> wrote: > Dear Fieldtrip-users, > > I'm currently trying to calculate freqstatistics for four experimental > groups, using the following options: > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > length(subjects{4})]; > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > % 1 to N subjects > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group > membership > > > cfg=[]; > cfg.design=design; > cfg.uvar = 1; > cfg.ivar = 2; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; > cfg.correctm = 'fdr'; > cfg.numrandomization = 180000; > cfg.alpha = 0.01/7; > cfg.tail = 1; > cfg.design = design; > cfg.channels = myChannels; > cfg.avgovertime = 'yes'; > cfg.avgoverfreq = 'yes'; > cfg.frequency = [1 3]; > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); > > With these settings, the coputation itself runs fine, but the resulting > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists > of only ones). This would mean, that I found significant effects for all > channels. Is this possible or rather due to an error somewhere in my script? > Is it likely, that these are 'real' zeroes or rather very small values, > close to zero? > Any hints and suggestions are very welcome, thank you in advance, > > Kind regards > > Patricia Wollstadt > > > -- > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > _______________________________________________ > 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 Patricia.Wollstadt at gmx.de Mon Jan 24 19:25:15 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Mon, 24 Jan 2011 19:25:15 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: References: <20110124164726.247880@gmx.net> Message-ID: <20110124182515.12260@gmx.net> Hi Rodolphe, usually I compute this statistic for seven individual frequency bands (I left this part of the script out to keep the example-code short), so I did an additional correction of my alpha niveau. Regards, Patricia -------- Original-Nachricht -------- > Datum: Mon, 24 Jan 2011 11:39:31 -0600 > Von: Rodolphe Nenert > An: Email discussion list for the FieldTrip project > Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction > Dear Patricia, > > Your alpha seems a little bit low, why taking 0.01/7= 0.0014 ? > I may be wrong but i guess that a fdr correction on a such value of alpha > will be very hard with your data. > > Rodolphe N., PhD. > > On Mon, Jan 24, 2011 at 10:47 AM, Patricia Wollstadt < > Patricia.Wollstadt at gmx.de> wrote: > > > Dear Fieldtrip-users, > > > > I'm currently trying to calculate freqstatistics for four experimental > > groups, using the following options: > > > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > > length(subjects{4})]; > > > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > > % 1 to N subjects > > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group > > membership > > > > > > cfg=[]; > > cfg.design=design; > > cfg.uvar = 1; > > cfg.ivar = 2; > > cfg.method = 'montecarlo'; > > cfg.statistic = 'indepsamplesF'; > > cfg.correctm = 'fdr'; > > cfg.numrandomization = 180000; > > cfg.alpha = 0.01/7; > > cfg.tail = 1; > > cfg.design = design; > > cfg.channels = myChannels; > > cfg.avgovertime = 'yes'; > > cfg.avgoverfreq = 'yes'; > > cfg.frequency = [1 3]; > > > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, > group4avg); > > > > With these settings, the coputation itself runs fine, but the resulting > > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix > consists > > of only ones). This would mean, that I found significant effects for all > > channels. Is this possible or rather due to an error somewhere in my > script? > > Is it likely, that these are 'real' zeroes or rather very small values, > > close to zero? > > Any hints and suggestions are very welcome, thank you in advance, > > > > Kind regards > > > > Patricia Wollstadt > > > > > > -- > > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail From ekanal at cmu.edu Mon Jan 24 21:26:09 2011 From: ekanal at cmu.edu (Kanal Eliezer) Date: Mon, 24 Jan 2011 15:26:09 -0500 Subject: [FieldTrip] questions about averaging/clustering tutorial Message-ID: <4233AF54-D71B-423D-A509-F225C92049C1@cmu.edu> Hello Fieldtrippers - Two unrelated questions about the averaging and clustering tutorials: 1) By the end of the averaging routine, there were only ~75 useful trials per condition left, which seems to be quite small to me. I understand that different studies will require different numbers of trials, but I was wondering whether you could go into a little detail as to why you chose to complete the study with (seemingly) so few trials. 2) In the cluster tutorial, you specify "cfg.clusteralpha = 0.05" and "cfg.clustertail = 0". If the tail is double-sided, wouldn't you want to use a cluster alpha of 0.025? Thanks - Elli Kanal From r.vandermeij at donders.ru.nl Tue Jan 25 17:40:02 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 25 Jan 2011 17:40:02 +0100 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper In-Reply-To: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> References: <021F1DDB-AA8E-4DC3-ADE4-6ADB052CCBEE@npsych.med.kyushu-u.ac.jp> Message-ID: <4D3EFCE2.2010209@donders.ru.nl> Hi Shogo, Haven't earned that title yet ;). My apologies for my late reply. > In your 2nd step, I should compute cluster-level-statistics from > random permutation data. > Here, I have an question. > When I define clusters from random permutation data, which should I > define where clusters are the same place (e.g. time, sensor and so on) > as "observed clasters" or should I define newly where clusters are > from random permutation data regardless of the places of "observed > clasters"? The idea is that for every random permutation of data, you calculate your statistics and cluster over them. Then, select the largest of these, whether it occurs at different time-points than your observed clusters or not. The null-hypothesis that your are trying to refute is not of the form "this cluster is significant is bigger than zero", but of the form "the data is interchangeable between conditions". Therefore, you gather 'largest-clusters' from 1000 random combinations of data. If your biggest cluster is bigger than 95% of the biggest clusters (alpha = 0.05, single-sided test), than the data is /not /interchangeable, and thus significantly different between conditions. This is exemplified by /all /clusters that surpass the test based on the /same /permutation-distribution of 'biggest-clusters'. Your data is different between conditions, and all peaks in the mountain-range are representing this (if they surpass the cluster-level test) (my favorite analogy). > I think the latter is right, this is OK? Yes. > > Second, If I have interests in the cluster that has the second or > third... non first largest cluster-level-statistics from the > experimental hypothesis, how should I test these clusters? All clusters are tested against the permutation-distribution of 'biggest-clusters'. Any of the smaller observed-clusters that are still bigger than 95% of your distribution-of-biggest-clusters (alpha = 0.05, single-sided), are part of /*all* /the clusters that /*together *show that the data differs between conditions/. Best, Roemer -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From Patricia.Wollstadt at gmx.de Tue Jan 25 18:08:38 2011 From: Patricia.Wollstadt at gmx.de (Patricia Wollstadt) Date: Tue, 25 Jan 2011 18:08:38 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110124164726.247880@gmx.net> References: <20110124164726.247880@gmx.net> Message-ID: <20110125170838.254600@gmx.net> Dear all, I'm still trying to identify the underlying reason for the issue described below. I ran the analysis in debug mode (I'm using Matlab2008b and the Fieldtrip-release from the 16th of January 2011) and found that the matrix 'resample', that is generated in 'statistics_montecarlo', line 187: resample = resampledesign(cfg, design); doesn't contain actual permutations of my initial design, but rather sorted rowvectors from 1 to 80 (no of subjects). So (since there is no permutation of the units of observation) the 'randstat' that is subsequently calculated for each row of the resample-matrix is always the same. Is this maybe due to my design and my units of observations respectively? I am looking at age-dependent variations in resting-state data, so my UO are 80 subjects, divided into four age groups. The commandline-output of the 'resampledesign'-function is as follows: total number of measurements = 80 total number of variables = 2 number of independent variables = 1 number of unit variables = 1 number of within-cell variables = 0 number of control variables = 0 using a permutation resampling approach repeated measurement in variable 1 over 80 levels number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Is this correct? Shouldn't this read 'repeated measurement in variable 2 over 4 levels' with the number of subjects per group as repeated measurements within a condition? Still I am pretty sure about my design matrix, which contains the indices 1 to 80 (for all subjects) in the first row (this is my cfg.uvar) with the corresponding age groups (1 to 4) in the second row (cfg.ivar, see my previous email below). I use an 'indepsamplesF'-statistic, since I am comparing between four groups of different subjects (averaged over trials). I hope, I got the settings and my design right. Any suggestions, whether this is a problem due to wrong configurations in my script are very welcome. Right now I work around this issue by replacing line 279 in 'statistics_montecarlo': tmpdesign = design(:,resample(i,:)); with: tmpdesign = design(:,randperm(size(design,2))); creating permutations of my design 'by hand'. Is this acceptable or is there anything I'm maybe missing. Thank you very much, kind regards, Patricia -------- Original-Nachricht -------- > Datum: Mon, 24 Jan 2011 17:47:26 +0100 > Von: "Patricia Wollstadt" > An: fieldtrip at donders.ru.nl > Betreff: [FieldTrip] ft_freqstatistics and FDR-correction > Dear Fieldtrip-users, > > I'm currently trying to calculate freqstatistics for four experimental > groups, using the following options: > > groupSize=[length(subjects{1}) length(subjects{2}) length(subjects{3}) > length(subjects{4})]; > > design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; > % 1 to N subjects > design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) > 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> group membership > > > cfg=[]; > cfg.design=design; > cfg.uvar = 1; > cfg.ivar = 2; > cfg.method = 'montecarlo'; > cfg.statistic = 'indepsamplesF'; > cfg.correctm = 'fdr'; > cfg.numrandomization = 180000; > cfg.alpha = 0.01/7; > cfg.tail = 1; > cfg.design = design; > cfg.channels = myChannels; > cfg.avgovertime = 'yes'; > cfg.avgoverfreq = 'yes'; > cfg.frequency = [1 3]; > > stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, group4avg); > > With these settings, the coputation itself runs fine, but the resulting > 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix consists of > only ones). This would mean, that I found significant effects for all > channels. Is this possible or rather due to an error somewhere in my script? Is > it likely, that these are 'real' zeroes or rather very small values, close > to zero? > Any hints and suggestions are very welcome, thank you in advance, > > Kind regards > > Patricia Wollstadt > > > -- > GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit > gratis Handy-Flat! http://portal.gmx.net/de/go/dsl > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de From r.vandermeij at donders.ru.nl Tue Jan 25 17:53:53 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Tue, 25 Jan 2011 17:53:53 +0100 Subject: [FieldTrip] singleplotTFR error In-Reply-To: References: <4D32C65B.5020304@donders.ru.nl> Message-ID: <4D3F0021.2060701@donders.ru.nl> Hi Karl, Sorry for my late reply. We are looking for a proper fix for this issue, it occurs in several situations. Any axes that are not monotonously increasing causes a crash in uimagesc, because it cannot determine how to plot the data (if I recall correctly, uimagesc plots multiple copies of the same data when axes are not evenly spaced). For the moment, you can try to hack the frequency axis to conform to the monotonously increasing part/(in most cases a simple round() would do it)/. Or, you can hack it by changing it to a linear index, and then add the axis-labels by hand afterwards /(by using set(gca,'ytick', [index vector], 'yticklabel', string-array of num2str(freq-axis))/. Best, Roemer On 17-01-11 2:51, Karl Doron wrote: > Hello Roemer, > > Here's the cfg's and output from calls to ft_freqanalysis with > method='wavelet' and the subsequent call to ft_singleplotTFR and the > resulting error. The imagesc command will however plot the data at > that > channel imagesc(squeeze(wvpow.powspctrm(strmatch('A177',label),:,:))) > Thanks for any help! > > cfg = []; > > cfg.output = 'pow'; > > cfg.channel = 'MEG'; > > cfg.method = 'wavelet'; > > cfg.foi = 10:2:30; > > cfg.toi = 0.0:0.05:2.75; > > wvpow = ft_freqanalysis(cfg, data_spctrm); > > wvpow = > > label: {246x1 cell} > > dimord: 'chan_freq_time' > > freq: [1x11 double] > > time: [1x56 double] > > powspctrm: [246x11x56 double] > > grad: [1x1 struct] > > cfg: [1x1 struct] > > %Singleplot results > > cfg = []; > > cfg.channel = 'A177'; > > cfg.grad = grad; > > cfg.xlim = [0.6 2.5]; > > cfg.ylim = [10 20]; > > figure; > > ft_singleplotTFR(cfg, wvpow) > > Warning: (one of the) axis are not evenly spaced -> nans cannot > > be maskedout->cfg.masknansissetto'no'; > > > In ft_singleplotTFR at 296 > > ??? Attempted toaccessc(6,1); index outofboundsbecause > > size(c)=[5,37]. > > Error in==>uimageat124 > > ce(j,i) = c(indi(end), indj(end)); > > Error in==>uimagescat46 > > hh = uimage(varargin{:},'CDataMapping','scaled'); > > Error in==>ft_plot_matrixat192 > > h = uimagesc(hdat, vdat, cdat, clim); > > Error in==>ft_singleplotTFRat327 > > ft_plot_matrix(data.(cfg.xparam)(xidc),data.(cfg.yparam)(yidc), > > TFR, 'clim',[zmin,zmax],'tag','cip') > > > > On Sun, Jan 16, 2011 at 2:20 AM, Roemer van der Meij > > wrote: > > Hi Karl, > > Could you give some more information on the errors? Could you also > post your cfg's? That will help in finding and fixing the bug. > What FieldTrip version are you using? > > Best, > Roemer > > > > On 15-1-2011 18:05, Karl Doron wrote: >> Hello, >> >> Has anyone else reported a problem with ft_singleplotTFR and >> output of the new specest module? >> >> multiplotTFR works, but 'interactive' method fails. >> >> It looks like the error occurs when trying to mask NaNs >> >> % masking only possible for evenly spaced axis >> >> if strcmp(cfg.masknans, 'yes') && (~evenx || ~eveny) >> >> warning('(one of the) axis are not evenly spaced -> nans cannot >> be masked out -> cfg.masknans is set to ''no'';') >> >> cfg.masknans = 'no'; >> >> end >> >> >> >> Thank you, >> karl doron >> UCSB >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > Roemer van der Meij M.Sc. > PhD student > Donders Institute for Brain, Cognition and Behaviour > Centre for Cognition > P.O. Box 9104 > 6500 HE Nijmegen > The Netherlands > Tel: +31(0)24 3655932 > E-mail: r.vandermeij at donders.ru.nl > > _______________________________________________ > 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 -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 25 20:57:03 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 25 Jan 2011 20:57:03 +0100 Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <20110125170838.254600@gmx.net> References: <20110124164726.247880@gmx.net> <20110125170838.254600@gmx.net> Message-ID: <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> Hi Patricia, I don't really understand what is going on, but could you try to specify your design only in a single row (design = design(2,:) in your case), specify cfg.ivar = 1; and cfg=rmfield(cfg,'uvar'), and see how it runs? As such the uvar row is not relevant in an independent samples design. Best, Jan-Mathijs On Jan 25, 2011, at 6:08 PM, Patricia Wollstadt wrote: > Dear all, > > I'm still trying to identify the underlying reason for the issue > described below. I ran the analysis in debug mode (I'm using > Matlab2008b and the Fieldtrip-release from the 16th of January 2011) > and found that the matrix 'resample', that is generated in > 'statistics_montecarlo', line 187: > > resample = resampledesign(cfg, design); > > doesn't contain actual permutations of my initial design, but rather > sorted rowvectors from 1 to 80 (no of subjects). So (since there is > no permutation of the units of observation) the 'randstat' that is > subsequently calculated for each row of the resample-matrix is > always the same. > Is this maybe due to my design and my units of observations > respectively? I am looking at age-dependent variations in resting- > state data, so my UO are 80 subjects, divided into four age groups. > The commandline-output of the 'resampledesign'-function is as follows: > > total number of measurements = 80 > total number of variables = 2 > number of independent variables = 1 > number of unit variables = 1 > number of within-cell variables = 0 > number of control variables = 0 > using a permutation resampling approach > repeated measurement in variable 1 over 80 levels > number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 > 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > 1 1 > > > Is this correct? Shouldn't this read 'repeated measurement in > variable 2 over 4 levels' with the number of subjects per group as > repeated measurements within a condition? Still I am pretty sure > about my design matrix, which contains the indices 1 to 80 (for all > subjects) in the first row (this is my cfg.uvar) with the > corresponding age groups (1 to 4) in the second row (cfg.ivar, see > my previous email below). I use an 'indepsamplesF'-statistic, since > I am comparing between four groups of different subjects (averaged > over trials). > > I hope, I got the settings and my design right. Any suggestions, > whether this is a problem due to wrong configurations in my script > are very welcome. > > Right now I work around this issue by replacing line 279 in > 'statistics_montecarlo': > > tmpdesign = design(:,resample(i,:)); > > with: > > tmpdesign = design(:,randperm(size(design,2))); > > creating permutations of my design 'by hand'. Is this acceptable or > is there anything I'm maybe missing. > > Thank you very much, kind regards, > > Patricia > > > > > -------- Original-Nachricht -------- >> Datum: Mon, 24 Jan 2011 17:47:26 +0100 >> Von: "Patricia Wollstadt" >> An: fieldtrip at donders.ru.nl >> Betreff: [FieldTrip] ft_freqstatistics and FDR-correction > >> Dear Fieldtrip-users, >> >> I'm currently trying to calculate freqstatistics for four >> experimental >> groups, using the following options: >> >> groupSize=[length(subjects{1}) length(subjects{2}) >> length(subjects{3}) >> length(subjects{4})]; >> >> design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; >> % 1 to N subjects >> design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) >> 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> >> group membership >> >> >> cfg=[]; >> cfg.design=design; >> cfg.uvar = 1; >> cfg.ivar = 2; >> cfg.method = 'montecarlo'; >> cfg.statistic = 'indepsamplesF'; >> cfg.correctm = 'fdr'; >> cfg.numrandomization = 180000; >> cfg.alpha = 0.01/7; >> cfg.tail = 1; >> cfg.design = design; >> cfg.channels = myChannels; >> cfg.avgovertime = 'yes'; >> cfg.avgoverfreq = 'yes'; >> cfg.frequency = [1 3]; >> >> stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, >> group4avg); >> >> With these settings, the coputation itself runs fine, but the >> resulting >> 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix >> consists of >> only ones). This would mean, that I found significant effects for all >> channels. Is this possible or rather due to an error somewhere in >> my script? Is >> it likely, that these are 'real' zeroes or rather very small >> values, close >> to zero? >> Any hints and suggestions are very welcome, thank you in advance, >> >> Kind regards >> >> Patricia Wollstadt >> >> >> -- >> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit >> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > -- > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > _______________________________________________ > 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 batrod at gmail.com Tue Jan 25 21:02:02 2011 From: batrod at gmail.com (Rodolphe Nenert) Date: Tue, 25 Jan 2011 14:02:02 -0600 Subject: [FieldTrip] Error in correlation analysis with ft_freqstatistics Message-ID: Dear Fieldtrip Users, im actually trying to do a correlation analysis between frequency power and behavioral results. The problem is when i change the design matrix containing the classical independent variables to behavioral scores, as indicate in the walktrough section of the fieldtrip website : cfg.design = [ .1 .2 .4 .3 etc...]; cfg.ivar = 1; Then, Matlab gives me the following errors: ??? Error using ==> statfun_indepsamplesF at 55 Invalid specification of the independent variable in the design array. Error in ==> statistics_montecarlo at 241 [statobs, cfg] = statfun(cfg, dat, design); Error in ==> statistics_wrapper at 285 [stat, cfg] = statmethod(cfg, dat, cfg.design, 'issource',issource); Error in ==> ft_freqstatistics at 127 [stat, cfg] = statistics_wrapper(cfg, varargin{:}); Does anyone have an example of a script for such analysis that works? Thanks, Rodolphe. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Tue Jan 25 21:16:38 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Tue, 25 Jan 2011 21:16:38 +0100 Subject: [FieldTrip] Error in correlation analysis with ft_freqstatistics In-Reply-To: References: Message-ID: <196CB43E-E377-449F-ABB4-BA02DED6BF0A@donders.ru.nl> Dear Rodolphe, The trick here is not to specify cfg.statistic = 'indepsamplesF'; You need to specify cfg.statistic = 'yourownfunction', and create an m- file 'statfun_yourownfunction.m' that computes a correlation. That could look like function s = statfun_yourownfunction(cfg, dat, design) % mean subtract mdat = mean(dat,2); dat = dat - mdat(:,ones(1,size(dat,2))); mdesign = mean(design); design = design - mean(design); % covariance covdat = dat*design'; % variance vdat = sum(dat.^2,2); vdes = sum(design.^2); % correlation s.stat = covdat./sqrt(vdat.*vdes); This is just typed down in half a minute so don't take it for granted. Best, Jan-Mathijs On Jan 25, 2011, at 9:02 PM, Rodolphe Nenert wrote: > Dear Fieldtrip Users, > > im actually trying to do a correlation analysis between frequency > power and behavioral results. > The problem is when i change the design matrix containing the > classical independent variables to behavioral scores, as indicate in > the walktrough section of the fieldtrip website : > > cfg.design = [ .1 .2 .4 .3 etc...]; > cfg.ivar = 1; > > Then, Matlab gives me the following errors: > > ??? Error using ==> statfun_indepsamplesF at 55 > Invalid specification of the independent variable in the design array. > > Error in ==> statistics_montecarlo at 241 > [statobs, cfg] = statfun(cfg, dat, design); > > Error in ==> statistics_wrapper at 285 > [stat, cfg] = statmethod(cfg, dat, cfg.design, > 'issource',issource); > > Error in ==> ft_freqstatistics at 127 > [stat, cfg] = statistics_wrapper(cfg, varargin{:}); > > Does anyone have an example of a script for such analysis that works? > > Thanks, > > Rodolphe. > _______________________________________________ > 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 shhirano at npsych.med.kyushu-u.ac.jp Wed Jan 26 00:45:28 2011 From: shhirano at npsych.med.kyushu-u.ac.jp (=?ISO-2022-JP?B?GyRCSj9MbhsoQiAbJEI+PDhjGyhC?=) Date: Wed, 26 Jan 2011 08:45:28 +0900 Subject: [FieldTrip] Question about Dr Eric Maris et al. paper Message-ID: <10E711DB-D7B4-4E82-AEEB-310C773BBD60@npsych.med.kyushu-u.ac.jp> Dear Roemer I really appreciate your very clear-cut answer. I'm going to test my data. Thank you very much for your kindness! Best regards, Shogo -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SpamAssassinReport.txt URL: From michael.wibral at web.de Wed Jan 26 10:08:51 2011 From: michael.wibral at web.de (Michael Wibral) Date: Wed, 26 Jan 2011 10:08:51 +0100 (CET) Subject: [FieldTrip] ft_freqstatistics and FDR-correction In-Reply-To: <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> References: <20110124164726.247880@gmx.net> <20110125170838.254600@gmx.net>, <1C530F16-9067-4FDF-A526-20513EE05C79@donders.ru.nl> Message-ID: <1367146600.2032784.1296032931966.JavaMail.fmail@mwmweb056> Hi Patricia, I also would have thought your design to be correct. Maybe the unneccessary specification of the uvar screws thinsg up?? However, you really do not have any repeated measures in your design - here the output of FT is correct. I interpret it in the following way: You specified cfg.uvar - indicating to FT the possibility that this might be a repeated measures design. FT identified the units of observation as being 80 (correct), and then checked how many repeated measures you ran in each UO and found just 1 - which is also correct. I agree that naming the units of observation (UO) as 'levels' of the UO variable is a bit odd, should rather be 'units of observation'. The concept of repeated measures is also very often misunderstood: in repated measures you do not actually repeat anything, rather you perform different measurements (treatments) WITHIN a unit of observation - so a repated measures design is a within UO design. Your subjects just have one age, so there are no different treatments (levels of the indep variable) per subjects and, hence, no 'repeated measures'. Hope this clarifies terminology for further discussion. Michael -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 25, 2011 8:57:03 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] ft_freqstatistics and FDR-correction >Hi Patricia, > >I don't really understand what is going on, but could you try to >specify your design only in a single row (design = design(2,:) in your >case), specify cfg.ivar = 1; and cfg=rmfield(cfg,'uvar'), and see how >it runs? As such the uvar row is not relevant in an independent >samples design. > >Best, > >Jan-Mathijs > > > >On Jan 25, 2011, at 6:08 PM, Patricia Wollstadt wrote: > >> Dear all, >> >> I'm still trying to identify the underlying reason for the issue >> described below. I ran the analysis in debug mode (I'm using >> Matlab2008b and the Fieldtrip-release from the 16th of January 2011) >> and found that the matrix 'resample', that is generated in >> 'statistics_montecarlo', line 187: >> >> resample = resampledesign(cfg, design); >> >> doesn't contain actual permutations of my initial design, but rather >> sorted rowvectors from 1 to 80 (no of subjects). So (since there is >> no permutation of the units of observation) the 'randstat' that is >> subsequently calculated for each row of the resample-matrix is >> always the same. >> Is this maybe due to my design and my units of observations >> respectively? I am looking at age-dependent variations in resting- >> state data, so my UO are 80 subjects, divided into four age groups. >> The commandline-output of the 'resampledesign'-function is as follows: >> >> total number of measurements = 80 >> total number of variables = 2 >> number of independent variables = 1 >> number of unit variables = 1 >> number of within-cell variables = 0 >> number of control variables = 0 >> using a permutation resampling approach >> repeated measurement in variable 1 over 80 levels >> number of repeated measurements in each level is 1 1 1 1 1 1 1 1 1 1 >> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >> 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 >> 1 1 >> >> >> Is this correct? Shouldn't this read 'repeated measurement in >> variable 2 over 4 levels' with the number of subjects per group as >> repeated measurements within a condition? Still I am pretty sure >> about my design matrix, which contains the indices 1 to 80 (for all >> subjects) in the first row (this is my cfg.uvar) with the >> corresponding age groups (1 to 4) in the second row (cfg.ivar, see >> my previous email below). I use an 'indepsamplesF'-statistic, since >> I am comparing between four groups of different subjects (averaged >> over trials). >> >> I hope, I got the settings and my design right. Any suggestions, >> whether this is a problem due to wrong configurations in my script >> are very welcome. >> >> Right now I work around this issue by replacing line 279 in >> 'statistics_montecarlo': >> >> tmpdesign = design(:,resample(i,:)); >> >> with: >> >> tmpdesign = design(:,randperm(size(design,2))); >> >> creating permutations of my design 'by hand'. Is this acceptable or >> is there anything I'm maybe missing. >> >> Thank you very much, kind regards, >> >> Patricia >> >> >> >> >> -------- Original-Nachricht -------- >>> Datum: Mon, 24 Jan 2011 17:47:26 +0100 >>> Von: "Patricia Wollstadt" >>> An: fieldtrip at donders.ru.nl >>> Betreff: [FieldTrip] ft_freqstatistics and FDR-correction >> >>> Dear Fieldtrip-users, >>> >>> I'm currently trying to calculate freqstatistics for four >>> experimental >>> groups, using the following options: >>> >>> groupSize=[length(subjects{1}) length(subjects{2}) >>> length(subjects{3}) >>> length(subjects{4})]; >>> >>> design = [1:groupSize(1)+groupSize(2)+groupSize(3)+groupSize(4)]; >>> % 1 to N subjects >>> design(2,:) = [ones(1,groupSize(1)) 2*ones(1,groupSize(2)) >>> 3*ones(1,groupSize(3)) 4*ones(1,groupSize(4))]; % indep var -> >>> group membership >>> >>> >>> cfg=[]; >>> cfg.design=design; >>> cfg.uvar = 1; >>> cfg.ivar = 2; >>> cfg.method = 'montecarlo'; >>> cfg.statistic = 'indepsamplesF'; >>> cfg.correctm = 'fdr'; >>> cfg.numrandomization = 180000; >>> cfg.alpha = 0.01/7; >>> cfg.tail = 1; >>> cfg.design = design; >>> cfg.channels = myChannels; >>> cfg.avgovertime = 'yes'; >>> cfg.avgoverfreq = 'yes'; >>> cfg.frequency = [1 3]; >>> >>> stat = ft_freqstatistics(cfg, group1avg, group2avg, group3avg, >>> group4avg); >>> >>> With these settings, the coputation itself runs fine, but the >>> resulting >>> 'prob'-matrix contains only zeros (accordingly the 'mask'-matrix >>> consists of >>> only ones). This would mean, that I found significant effects for all >>> channels. Is this possible or rather due to an error somewhere in >>> my script? Is >>> it likely, that these are 'real' zeroes or rather very small >>> values, close >>> to zero? >>> Any hints and suggestions are very welcome, thank you in advance, >>> >>> Kind regards >>> >>> Patricia Wollstadt >>> >>> >>> -- >>> GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit >>> gratis Handy-Flat! http://portal.gmx.net/de/go/dsl >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> -- >> Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir >> belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de >> _______________________________________________ >> 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 637 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Wed Jan 26 11:45:23 2011 From: jan.schoffelen at donders.ru.nl (jan-mathijs schoffelen) Date: Wed, 26 Jan 2011 11:45:23 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: <9B00A155-4D0A-493D-A617-2F9E90439E35@donders.ru.nl> Dear Michael and the rest of the world, I updated the documentation page on artifact rejection with a more explicit statement that specifying the padding only works with data on disk (and removed the second input arguments in the code examples). I'll discuss the other issue with the rest soon. Best JM On Jan 24, 2011, at 6:27 PM, Michael Wibral wrote: > Hi Jan-Mathijs, > > this is basically what we do at the moment, i.e. fooling > artifcat_zvalue by removing the one field it complains about amnd > using rejetartefact only at the very last. > See the attched code - I really do not want to post this code on the > tutorial website as I am not fully sure what I am doing :-). > > Michael > > %% CODE > ft_defaults; > Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/ > DATASETS/'; > Design={ > 'DMG13_NewMooney_20110120_0', [2 3], > 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; > } > > > for ss=1:size(Design,1) % over subjects > for cc=1:length(Design{ss,4}) % over conditions > for ff=1:length(Design{ss,2}) % over .ds datasets/runs > > FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), > '.ds') > FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) > % core data reading > cfg=[]; > cfg.dataset=FullFileName; > cfg.headerformat = 'ctf_ds'; % for you to check whether still > necessary > ctf.dataformat = 'ctf_ds'; > cfg.cond=Design{ss,4}(cc) > cfg.continuous='yes'; > > cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '- > MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? > cfg.trialfun=Design{ss,3}; > cfg=ft_definetrial(cfg); > cfg.trl(end,:)=[]; > trl=cfg.trl; % keep track of the trials > > padding=0.75 % 750 ms > > > %%%%%%%%% artifact rejection section > %%% jump > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MEG'; > cfg.artfctdef.zvalue.cutoff = 35; > cfg.artfctdef.zvalue.trlpadding = 0.5*padding; > cfg.artfctdef.zvalue.artpadding = 0.5*padding; > cfg.artfctdef.zvalue.fltpadding = 0; > > % algorithmic parameters > cfg.artfctdef.zvalue.medianfilter = 'yes'; > cfg.artfctdef.zvalue.medianfiltord = 9; % in samples > cfg.artfctdef.zvalue.absdiff = 'yes'; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'jump'; > [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); > % cfg.artfctdef.jump.artifact = artifact_jump; > % cfg = ft_rejectartifact(cfg); > > %%% muscle > cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % > remove field from structure otherwise this won't run ?? > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MEG'; > cfg.artfctdef.zvalue.cutoff = 15; > cfg.artfctdef.zvalue.trlpadding = 0.1; > cfg.artfctdef.zvalue.fltpadding = 0.1; > cfg.artfctdef.zvalue.artpadding = 0.1; > > % algorithmic parameters > cfg.artfctdef.zvalue.bpfilter = 'yes'; > cfg.artfctdef.zvalue.bpfreq = [110 140]; > cfg.artfctdef.zvalue.bpfiltord = 6; > cfg.artfctdef.zvalue.bpfilttype = 'but'; > cfg.artfctdef.zvalue.hilbert = 'yes'; > cfg.artfctdef.zvalue.boxcar = 0.2; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'muscle'; > [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); > cfg.artfctdef.muscle.artifact = artifact_muscle; > cfg = ft_rejectartifact(cfg); > > %%% EOG > > > cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); > % cutoff and padding > cfg.artfctdef.zvalue.channel = 'MRT41'; > cfg.artfctdef.zvalue.cutoff = 10; > cfg.artfctdef.zvalue.trlpadding = 0.5; > cfg.artfctdef.zvalue.artpadding = 0.1; > cfg.artfctdef.zvalue.fltpadding = 0.1; > % algorithmic parameters > cfg.artfctdef.zvalue.bpfilter = 'yes'; > cfg.artfctdef.zvalue.bpfilttype = 'but'; > cfg.artfctdef.zvalue.bpfreq = [1 15]; > cfg.artfctdef.zvalue.bpfiltord = 3; > cfg.artfctdef.zvalue.hilbert = 'yes'; > > % feedback > cfg.artfctdef.zvalue.feedback = 'no'; > cfg.artfctdef.reject = 'EOG'; > [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); > > cfg.trl=trl; > cfg.artfctdef.reject = 'complete'; % this rejects complete trials, > use 'partial' if you want to do partial artifact rejection > % collect all the info about the artifacts that were found > cfg.artfctdef.eog.artifact =artifact_EOG; > cfg.artfctdef.jump.artifact = artifact_jump; > cfg.artfctdef.muscle.artifact = artifact_muscle; > cfg = ft_rejectartifact(cfg); > > Data_no_artifacts=ft_preprocessing(cfg); > > % some additional filtering for DC removal and detrending > cfg=[]; > cfg.detrend='yes' > cfg.hpfilt='yes' > cfg.hpfreq=1; > TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); > clear Data_no_artifacts; > > end > ... > ... > end > end > > > > > > -----Ursprüngliche Nachricht----- > Von: "jan-mathijs schoffelen" > Gesendet: Jan 24, 2011 4:41:09 PM > An: "Email discussion list for the FieldTrip project" > > Betreff: Re: [FieldTrip] more on artfifact rejection > >> Hmmm, apparently this approach needs to be ironed out a bit (also >> from >> our side). For now, I'd say that it should work if you keep per type >> of artifact the artifact field in the output configuration, and just >> concatenate these prior to calling ft_rejectartifact. I will moreover >> CC this e-mail to the people involved in creating the first version >> of >> the renewed tutorial, and will bring up the issue in this week's >> FieldTrip developers meeting. >> >> Best, >> >> JM >> >> On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: >> >>> Hi Jan mathijs, >>> >>> I tried to get option1 running, stumbled over the following little >>> obstacle however: >>> >>> I tried to keep one cfg throughout the steps ft_definetrial; >>> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >>> tracking of where artfecats were found), ft_preprocessing (cutting >>> out the clean trials from the cont. data). IMHO this used to be the >>> way most people did this kind of procesing a while ago. >>> >>> However, I can't get ft_artifact_zvalue to run with different >>> settings one after another for jump/musvle/EOG. FT claims after the >>> first run of ft_artifact_zvalue that the z-value thing has been >>> performed and refuse to detect other artifacts with new settings. >>> >>>> From here I only see two alternative: specifying a really lengthy >>>> cfg every time a new (also struggling with the cfg.dataset versus >>>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>>> things myself or manually removing the cfg.artdef.zvalue.artifct >>>> field to get the z-value based detection to run again. This seems a >>>> bit odd to me. >>> >>> Any suggestions? >>> >>> Michael >>> >>> >>> >>> >>> -----Ursprüngliche Nachricht----- >>> Von: "jan-mathijs schoffelen" >>> Gesendet: Jan 24, 2011 12:12:57 PM >>> An: "Email discussion list for the FieldTrip project" >>> >>> Betreff: Re: [FieldTrip] more on artfifact rejection >>> >>>> Dear Michael, >>>> >>>> I agree. The tutorial should be 'de'-confused by sketching option >>>> 1, >>>> and another one should be describing option 2, or the original >>>> should >>>> be clearly making the distinction. >>>> >>>> Best, >>>> >>>> JM >>>> >>>> >>>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>>> >>>>> Hi Jan-Mathijs, >>>>> >>>>> I am a bit unsure how to proceed: >>>>> >>>>> (1) sketch the artifact correction way like this >>>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>>> ft_preprocessing >>>>> OR >>>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>>> ft_preprocessing. >>>>> >>>>> I think I should go for option (1) as this seems to be the >>>>> standard >>>>> use on continuous data. Sometime in the futrure one should then >>>>> add >>>>> a tutorial for those that have data in trials to start with. >>>>> >>>>> Michael >>>>> >>>>> -----Ursprüngliche Nachricht----- >>>>> Von: "jan-mathijs schoffelen" >>>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>>> An: "Email discussion list for the FieldTrip project" >>>>> >>>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>>> >>>>>> Dear Michael, >>>>>> >>>>>> Yes, I agree with you here as well. In principle the >>>>>> ft_artifact_zvalue supports data as a second input argument, >>>>>> but in >>>>>> such case the different types of padding in the cfg do not make >>>>>> sense. >>>>>> I would indeed remove the second input arguments in the example >>>>>> code >>>>>> snippets. Could I ask you to take care of that? >>>>>> >>>>>> Thanks, >>>>>> >>>>>> JM >>>>>> >>>>>> >>>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>>> >>>>>>> Deal Fieldtrip users, >>>>>>> >>>>>>> there is something else I do not understand in the tutorial: if >>>>>>> you >>>>>>> read in the data in trials (as it is done) how can you do >>>>>>> padding >>>>>>> later as it is suggested. I tried to run the example code on teh >>>>>>> website reading in the data such that it contains trials. If I >>>>>>> then >>>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>>> must >>>>>>> be positive or logical ... values', indicating that the code >>>>>>> tries >>>>>>> to access data that aren't there. If I set the padding to zero >>>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>>> should actually run these things on continuous data (contrary to >>>>>>> what is indicated in the tutorial)? >>>>>>> >>>>>>> Michael >>>>>>> >>>>>> Wibral.vcf>_______________________________________________ >>>>>>> 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 >>>>> >>>> Wibral.vcf>_______________________________________________ >>>>> 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 tom_campbell75 at hotmail.com Thu Jan 27 00:26:27 2011 From: tom_campbell75 at hotmail.com (Tom Campbell) Date: Wed, 26 Jan 2011 23:26:27 +0000 Subject: [FieldTrip] depsamplesF Message-ID: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. -------------- next part -------------- An HTML attachment was scrubbed... URL: From olga at graphicmind.info Thu Jan 27 04:16:51 2011 From: olga at graphicmind.info (Olga Sysoeva) Date: Thu, 27 Jan 2011 06:16:51 +0300 Subject: [FieldTrip] depsamplesF In-Reply-To: References: Message-ID: <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: > Dear Eric Maris, Robert Oostenveld and colleagues, > > I write with some queries with reference to your previous > correspondence on the Fieldtrip listserv and would very much > appreciate if you could please answer them. > > I am trying to use Fieldtrip to analyse timelocked ERP data from > what is a 16(participant: [1:16]) X2(Background: congruent, > incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to > runing well treating this as a 16(participant: [1:16]) X4(Visual > stimulus: animal-congruent background, animal-incongruent > background, vehicle-congruent, vehicle-incongruent )design with 4 > conditions, though I haven't looked at the results of the tests yet. > If I then run cluster analyses of differences of theoretical > interest via depsamplest, please how would I bonferroni correct? I > am interested in what clusters exist in the background and stimulus > main effects and their background X stimulus interaction. Please is > this possible in fieldtrip to use depsamplesF to work with a > Participant X "2-way" design? > > Best regards, > > Tom Campbell. > > > > > _______________________________________________ > 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 tom_campbell75 at hotmail.com Thu Jan 27 06:02:29 2011 From: tom_campbell75 at hotmail.com (Tom Campbell) Date: Thu, 27 Jan 2011 05:02:29 +0000 Subject: [FieldTrip] depsamplesF In-Reply-To: <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> References: , <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Message-ID: Thank you very much for this helpful advice Olga. That would have also been my impression until I found this discussion between Maya Zuckerman and Eric Maris: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003335.html http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html , which I may have misunderstood. I can see from the list that people are interested in using depsampleF to investigate interactions between two independent variables (e.g., background: I,II x stimulus: a,b) in experiments with multiple participants. I can also see a several people have had problems with this. Given for datasets I_a, I_b, II_a, II_b I'd like to do something like: cfg.design =????; ... cfg.statistic ='depsamplesF'; ... [stat] = ft_timelockstatistics(cfg, I_a, I_b, II_a, II_b); to find the tests of of main effect clusters for each factor and interaction clusters. How to specify up cfg.design could be one of the problems, as could be what other cfg parameters need to be specified. I may be barking up completely the wrong tree. Assuming the interaction is significant, there are 4 differences that would be of theoretical interest: I_a vs I_b, II_a vs II_b,I_a vs II_a,I_b vs II_b). For instance, a "classical" interaction might exhibit the abolition of significance of an effect ab seen at I at level II of that factor. So, if I understand the Zuckerman-Maris dialogue, if I used the permutation test to test such I_a vd II_b differences as in the tutorial: cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; ... [I_avsb_stat] = ft_timelockstatistics(cfg, I_a, I_b); [II_avsb_stat] = ft_timelockstatistics(cfg, II_a, II_b); [IvsII_a_stat] = ft_timelockstatistics(cfg, I_a, II_a); [IvsII_b_stat] = ft_timelockstatistics(cfg, I_a, II_b); ,I may have to either do some bonferonni correction: -at the cluster level (cluster.alpha) -or at the level at which each t-test can be included in a cluster (cfg.alpha). Please would you verify which, if at all? If I am testing 4 such differences with 4 permutation tests then if the bonferroni correction is to be at the cluster level, please should the correction depend upon the number of clusters as well as the number of such differences tested? Please, I look forward to any clarifications. With best regards, Tom Campbell. From: olga at graphicmind.info To: tom_campbell75 at hotmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] depsamplesF Date: Thu, 27 Jan 2011 06:16:51 +0300 Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. _______________________________________________ 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 lumatobu2 at hotmail.com Fri Jan 28 04:52:09 2011 From: lumatobu2 at hotmail.com (Ludwing Torres) Date: Thu, 27 Jan 2011 22:52:09 -0500 Subject: [FieldTrip] help with inverse computing Message-ID: Hello, I have the next script that computes the forward model of the brain activity: clear all close all clc % load electrodes positions elec = []; load electrodes1020 % array of electrode positions i_elec=[4 6 18 19 21 23 25 27 28 31 33 35 37 40 41 43 45 47 49 50 53 55 57 59 62 63 65 67 69 71 72 84 86]; % load concentric spheres or bem load standard_vol.mat % vol.cond = [1 1/80 1]; % load spheric_vol_162.mat %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% cfg = []; cfg.vol = vol; % cfg.elec = elec; cfg.elec.pnt = elec.pnt(i_elec,1:3); cfg.elec.label = elec.label(i_elec); fs=250; ns=250; cfg.fsample = fs; time = (1:ns)/fs; signal1 = 1*sin(2*time*6*pi); signal2 = 1*cos(2*time*12*pi); signal3 = 1*cos(2*time*8*pi); % head model [vols, sens, cfg] = prepare_headmodel(cfg, []); dipin=[]; [x,y,z]=meshgrid(linspace(-40,40,4), linspace(-40,40,4), linspace(0,30,3) ); dipin.pos=[x(:) y(:) z(:)]; mom_t=zeros(3*length(dipin.pos),ns); x_orig=mom_t; n_orig=mom_t; n_orig(20,:)=signal1; n_orig(80,:)=signal2; n_orig(40,:)=signal3; a11=1.2; b11=0.05; M11=3*length(dipin.pos); A = a11*diag(ones(M11,1)) + b11*(diag(ones(M11-1,1),1) + diag(ones(M11-1,1),-1)); b12=0; b13=0; c11=-0.9; for b=1:ns, if b==1, x_orig(:,b)=n_orig(:,b); end if b==2, x_orig(:,b)=A*x_orig(:,b-1)+b12*x_orig(:,b-1).^2-b13*x_orig(:,b-1).^3+n_orig(:,b); end if b>2, x_orig(:,b)=A*x_orig(:,b-1)+b12*x_orig(:,b-1).^2+b13*x_orig(:,b-1).^3+c11*x_orig(:,b-2)+n_orig(:,b); end end C=compute_leadfield(dipin.pos, sens, vols); dat=C*x_orig; now I have to compute the inverse model, that is, I have to obtain the x_orig data, knowing only the data stored in dat and C. For that, I made the next script (After runing the previous) In which I use different functions of FieldTrip to recover the x data: [vol1,sens1]=prepare_vol_sens(vol, sens); inside=inside_vol(dipin.pos,vol1); %After that I get 48 dipoles inside and 0 outside dipin.outside=[]; dipin.inside=1:48; %Inverse computing using MNE dipout=minimumnormestimate(dipin,sens1,vol1,dat); % I store the dipole moments obtained as a matrix Xres=[]; for ii=1:48 Xres=[Xres;dipout.mom{ii}]; end % I compute a relative error between the original x and the obtained x to compare error1=norm(Xres-x_orig,'fro')/norm(x_orig,'fro') %Using Residual variance [dipout2] = residualvariance(dipin, sens1, vol1, dat); Xres2=[]; for ii=1:48 Xres2=[Xres2;dipout2.mom{ii}]; end error2=norm(Xres2-x_orig,'fro')/norm(x_orig,'fro') %Using dipole fitting [dipout4] = dipole_fit(dipin, sens1, vol1, dat) error4=norm(dipout4.mom-x_orig,'fro')/norm(x_orig,'fro') The error obtained using residual variance is very different to the error of the two other methods. Besides, I get a very big error (92%) with the other two methods. I don't know if I'm doing something wrong, please If anyone could help me, I could pay you. Thanks C=compute_leadfield(dipin.pos, sens, vols); dat=C*x_orig; -------------- next part -------------- An HTML attachment was scrubbed... URL: From TAVABIK at email.chop.edu Fri Jan 28 06:06:41 2011 From: TAVABIK at email.chop.edu (Tavabi, Kambiz) Date: Fri, 28 Jan 2011 00:06:41 -0500 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054>, , <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: Greetings - this has been an informative discussion. My question remains is , what is the consensus on an approach for automatic artifact rejection with trial (CTF) data? E.g., could one use the artifact rejection section of Michael's code without any padding? I have not found any tutorials or suggestions on how to use the artifact rejection tools on trial data...have I missed something. -Kambiz ------------------------------------------------------------- Kambiz Tavabi PhD Biomedical Imaging Laboratory The Children's Hospital of Philadelphia 34th Street and Civic Center Boulevard Philadelphia, Pa. 19104 Tel: 267.426.0302 email: tavabik at email.chop.edu ------------------------------------------------------------- ________________________________________ 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, January 24, 2011 12:27 PM To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] more on artfifact rejection Hi Jan-Mathijs, this is basically what we do at the moment, i.e. fooling artifcat_zvalue by removing the one field it complains about amnd using rejetartefact only at the very last. See the attched code - I really do not want to post this code on the tutorial website as I am not fully sure what I am doing :-). Michael %% CODE ft_defaults; Datapath='/data/MEGArchive/data/meg/CTF_Data/NewMooney.proc/DATASETS/'; Design={ 'DMG13_NewMooney_20110120_0', [2 3], 'mytrialfun_New_MooneyMEEG_StandardButtons2',[4 5 6 7 8]; } for ss=1:size(Design,1) % over subjects for cc=1:length(Design{ss,4}) % over conditions for ff=1:length(Design{ss,2}) % over .ds datasets/runs FullFileName=strcat(Datapath,Design{ss,1},num2str(Design{ss,2}(ff)), '.ds') FullHeaderFile=FullFileName; %strcat(FullFileName,'/',) % core data reading cfg=[]; cfg.dataset=FullFileName; cfg.headerformat = 'ctf_ds'; % for you to check whether still necessary ctf.dataformat = 'ctf_ds'; cfg.cond=Design{ss,4}(cc) cfg.continuous='yes'; cfg.channel={'MEG','EEG','-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-MLO21', '-MRO44', '-MRT47'}; % add bad channels ? cfg.trialfun=Design{ss,3}; cfg=ft_definetrial(cfg); cfg.trl(end,:)=[]; trl=cfg.trl; % keep track of the trials padding=0.75 % 750 ms %%%%%%%%% artifact rejection section %%% jump % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 35; cfg.artfctdef.zvalue.trlpadding = 0.5*padding; cfg.artfctdef.zvalue.artpadding = 0.5*padding; cfg.artfctdef.zvalue.fltpadding = 0; % algorithmic parameters cfg.artfctdef.zvalue.medianfilter = 'yes'; cfg.artfctdef.zvalue.medianfiltord = 9; % in samples cfg.artfctdef.zvalue.absdiff = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'jump'; [cfg, artifact_jump] = ft_artifact_zvalue(cfg); %, Data); % cfg.artfctdef.jump.artifact = artifact_jump; % cfg = ft_rejectartifact(cfg); %%% muscle cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % remove field from structure otherwise this won't run ?? % cutoff and padding cfg.artfctdef.zvalue.channel = 'MEG'; cfg.artfctdef.zvalue.cutoff = 15; cfg.artfctdef.zvalue.trlpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; cfg.artfctdef.zvalue.artpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfreq = [110 140]; cfg.artfctdef.zvalue.bpfiltord = 6; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.hilbert = 'yes'; cfg.artfctdef.zvalue.boxcar = 0.2; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'muscle'; [cfg, artifact_muscle] = ft_artifact_zvalue(cfg); cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); %%% EOG cfg.artfctdef.zvalue=rmfield(cfg.artfctdef.zvalue, 'artifact'); % cutoff and padding cfg.artfctdef.zvalue.channel = 'MRT41'; cfg.artfctdef.zvalue.cutoff = 10; cfg.artfctdef.zvalue.trlpadding = 0.5; cfg.artfctdef.zvalue.artpadding = 0.1; cfg.artfctdef.zvalue.fltpadding = 0.1; % algorithmic parameters cfg.artfctdef.zvalue.bpfilter = 'yes'; cfg.artfctdef.zvalue.bpfilttype = 'but'; cfg.artfctdef.zvalue.bpfreq = [1 15]; cfg.artfctdef.zvalue.bpfiltord = 3; cfg.artfctdef.zvalue.hilbert = 'yes'; % feedback cfg.artfctdef.zvalue.feedback = 'no'; cfg.artfctdef.reject = 'EOG'; [cfg, artifact_EOG] = ft_artifact_zvalue(cfg); % Data); cfg.trl=trl; cfg.artfctdef.reject = 'complete'; % this rejects complete trials, use 'partial' if you want to do partial artifact rejection % collect all the info about the artifacts that were found cfg.artfctdef.eog.artifact =artifact_EOG; cfg.artfctdef.jump.artifact = artifact_jump; cfg.artfctdef.muscle.artifact = artifact_muscle; cfg = ft_rejectartifact(cfg); Data_no_artifacts=ft_preprocessing(cfg); % some additional filtering for DC removal and detrending cfg=[]; cfg.detrend='yes' cfg.hpfilt='yes' cfg.hpfreq=1; TrialData{ff}=ft_preprocessing(cfg,Data_no_artifacts); clear Data_no_artifacts; end ... ... end end -----Ursprüngliche Nachricht----- Von: "jan-mathijs schoffelen" Gesendet: Jan 24, 2011 4:41:09 PM An: "Email discussion list for the FieldTrip project" Betreff: Re: [FieldTrip] more on artfifact rejection >Hmmm, apparently this approach needs to be ironed out a bit (also from >our side). For now, I'd say that it should work if you keep per type >of artifact the artifact field in the output configuration, and just >concatenate these prior to calling ft_rejectartifact. I will moreover >CC this e-mail to the people involved in creating the first version of >the renewed tutorial, and will bring up the issue in this week's >FieldTrip developers meeting. > >Best, > >JM > >On Jan 24, 2011, at 1:51 PM, Michael Wibral wrote: > >> Hi Jan mathijs, >> >> I tried to get option1 running, stumbled over the following little >> obstacle however: >> >> I tried to keep one cfg throughout the steps ft_definetrial; >> ft_artifact_zvalue, ft_rejectartifcat (with option complete and some >> tracking of where artfecats were found), ft_preprocessing (cutting >> out the clean trials from the cont. data). IMHO this used to be the >> way most people did this kind of procesing a while ago. >> >> However, I can't get ft_artifact_zvalue to run with different >> settings one after another for jump/musvle/EOG. FT claims after the >> first run of ft_artifact_zvalue that the z-value thing has been >> performed and refuse to detect other artifacts with new settings. >> >>> From here I only see two alternative: specifying a really lengthy >>> cfg every time a new (also struggling with the cfg.dataset versus >>> cfg.datafile issue) and do the bookkeeping of cfg.trl and related >>> things myself or manually removing the cfg.artdef.zvalue.artifct >>> field to get the z-value based detection to run again. This seems a >>> bit odd to me. >> >> Any suggestions? >> >> Michael >> >> >> >> >> -----Ursprüngliche Nachricht----- >> Von: "jan-mathijs schoffelen" >> Gesendet: Jan 24, 2011 12:12:57 PM >> An: "Email discussion list for the FieldTrip project" > > >> Betreff: Re: [FieldTrip] more on artfifact rejection >> >>> Dear Michael, >>> >>> I agree. The tutorial should be 'de'-confused by sketching option 1, >>> and another one should be describing option 2, or the original should >>> be clearly making the distinction. >>> >>> Best, >>> >>> JM >>> >>> >>> On Jan 24, 2011, at 11:48 AM, Michael Wibral wrote: >>> >>>> Hi Jan-Mathijs, >>>> >>>> I am a bit unsure how to proceed: >>>> >>>> (1) sketch the artifact correction way like this >>>> ft-definetrial -> artifact.XXX.YYY -> ft_rejectartifact -> >>>> ft_preprocessing >>>> OR >>>> (2) ft-definetrial -> ft_preprocessing (with cfg.padding) -> >>>> artifact.XXX.YYY -> ft_rejectartifact(cfg, data) -> >>>> ft_preprocessing. >>>> >>>> I think I should go for option (1) as this seems to be the standard >>>> use on continuous data. Sometime in the futrure one should then add >>>> a tutorial for those that have data in trials to start with. >>>> >>>> Michael >>>> >>>> -----Ursprüngliche Nachricht----- >>>> Von: "jan-mathijs schoffelen" >>>> Gesendet: Jan 21, 2011 9:55:48 AM >>>> An: "Email discussion list for the FieldTrip project" >>>> >>>> Betreff: Re: [FieldTrip] more on artfifact rejection >>>> >>>>> Dear Michael, >>>>> >>>>> Yes, I agree with you here as well. In principle the >>>>> ft_artifact_zvalue supports data as a second input argument, but in >>>>> such case the different types of padding in the cfg do not make >>>>> sense. >>>>> I would indeed remove the second input arguments in the example >>>>> code >>>>> snippets. Could I ask you to take care of that? >>>>> >>>>> Thanks, >>>>> >>>>> JM >>>>> >>>>> >>>>> On Jan 20, 2011, at 10:51 AM, Michael Wibral wrote: >>>>> >>>>>> Deal Fieldtrip users, >>>>>> >>>>>> there is something else I do not understand in the tutorial: if >>>>>> you >>>>>> read in the data in trials (as it is done) how can you do padding >>>>>> later as it is suggested. I tried to run the example code on teh >>>>>> website reading in the data such that it contains trials. If I >>>>>> then >>>>>> try to search for muscle artifacts I get the 'subscript indices >>>>>> must >>>>>> be positive or logical ... values', indicating that the code tries >>>>>> to access data that aren't there. If I set the padding to zero >>>>>> (instead of 0.1) it works. So I am wondering wether somehow one >>>>>> should actually run these things on continuous data (contrary to >>>>>> what is indicated in the tutorial)? >>>>>> >>>>>> Michael >>>>>> >>>>> Wibral.vcf>_______________________________________________ >>>>>> 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 e.maris at donders.ru.nl Fri Jan 28 10:43:42 2011 From: e.maris at donders.ru.nl (Eric Maris) Date: Fri, 28 Jan 2011 10:43:42 +0100 Subject: [FieldTrip] depsamplesF In-Reply-To: References: , <6FF942DE-E2EC-47D0-BC81-CEDCD9B12410@graphicmind.info> Message-ID: <001001cbbecf$dc470260$94d50720$@maris@donders.ru.nl> Hi Tom, To test main and interaction effects in your 2x2 within subjects design, you have to perform 3 tests, each using the statfun desamplesT. Say you have the output of ft_timelockanalysis for all four conditions: tlout_Ia, tlout_Ib, tlout_IIa, tlout_IIb. Your then proceed as follows: 1. Main effect of I versus II: calculate the mean of tlout_Ia.avg and tlout_Ib.avg and put this is a a new struct variable tlout_I, which has the same fields as tlout_Ia and tlout_Ib. Do the same with tlout_IIa.avg and tlout_IIb.avg and make a new struct variable tlout_II. Then run ft_timelockstatistics with input arguments tlout_I and tlout_II. With this analysis you will test the main effect of I-versus-II. 2. In the same way, you now test the main effect of a versus b. In your calculations, the roles of (I,II) and (a,b) are now reversed. 3. Interaction of I-vs-II and a-vs-b. Calculate the differences (tlout_Ia.avg-tlout_Ib.avg) and (tlout_IIa.avg-tlout_IIb.avg), put them in output structures and statistically compare them using ft_timelockstatistics. With this analysis, you test the interaction of I-vs-II and a-vs-b. There is no need for Bonferroni correction or an adjustment of cfg.clusteralpha (which does not affect the false alarm rate anyhow) and cfg.alpha. Best, Eric Mari Thank you very much for this helpful advice Olga. That would have also been my impression until I found this discussion between Maya Zuckerman and Eric Maris: http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003335.html http://mailman.science.ru.nl/pipermail/fieldtrip/2010-December/003338.html , which I may have misunderstood. I can see from the list that people are interested in using depsampleF to investigate interactions between two independent variables (e.g., background: I,II x stimulus: a,b) in experiments with multiple participants. I can also see a several people have had problems with this. Given for datasets I_a, I_b, II_a, II_b I'd like to do something like: cfg.design =????; ... cfg.statistic ='depsamplesF'; ... [stat] = ft_timelockstatistics(cfg, I_a, I_b, II_a, II_b); to find the tests of of main effect clusters for each factor and interaction clusters. How to specify up cfg.design could be one of the problems, as could be what other cfg parameters need to be specified. I may be barking up completely the wrong tree. Assuming the interaction is significant, there are 4 differences that would be of theoretical interest: I_a vs I_b, II_a vs II_b,I_a vs II_a,I_b vs II_b). For instance, a "classical" interaction might exhibit the abolition of significance of an effect ab seen at I at level II of that factor. So, if I understand the Zuckerman-Maris dialogue, if I used the permutation test to test such I_a vd II_b differences as in the tutorial: cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; cfg.numrandomization = 500; ... [I_avsb_stat] = ft_timelockstatistics(cfg, I_a, I_b); [II_avsb_stat] = ft_timelockstatistics(cfg, II_a, II_b); [IvsII_a_stat] = ft_timelockstatistics(cfg, I_a, II_a); [IvsII_b_stat] = ft_timelockstatistics(cfg, I_a, II_b); ,I may have to either do some bonferonni correction: -at the cluster level (cluster.alpha) -or at the level at which each t-test can be included in a cluster (cfg.alpha). Please would you verify which, if at all? If I am testing 4 such differences with 4 permutation tests then if the bonferroni correction is to be at the cluster level, please should the correction depend upon the number of clusters as well as the number of such differences tested? Please, I look forward to any clarifications. With best regards, Tom Campbell. _____ From: olga at graphicmind.info To: tom_campbell75 at hotmail.com; fieldtrip at donders.ru.nl Subject: Re: [FieldTrip] depsamplesF Date: Thu, 27 Jan 2011 06:16:51 +0300 Hi, Tom, I guess if you do cluster analysis, which is based on permutation tests you do not need any correction like. Cluster-based statistics just deal with multiple comparison problem differently (Monte-Carlo randomization, permutation tests and examine the probability of your cluster among the random ones). Clusters may be formed based on time, space/frequency adjacency. Best Regards, Olga. On 27.01.2011, at 2:26, Tom Campbell wrote: Dear Eric Maris, Robert Oostenveld and colleagues, I write with some queries with reference to your previous correspondence on the Fieldtrip listserv and would very much appreciate if you could please answer them. I am trying to use Fieldtrip to analyse timelocked ERP data from what is a 16(participant: [1:16]) X2(Background: congruent, incongruent)x2(Stimulus: Animal, Vehicle) design. The code seems to runing well treating this as a 16(participant: [1:16]) X4(Visual stimulus: animal-congruent background, animal-incongruent background, vehicle-congruent, vehicle-incongruent )design with 4 conditions, though I haven't looked at the results of the tests yet. If I then run cluster analyses of differences of theoretical interest via depsamplest, please how would I bonferroni correct? I am interested in what clusters exist in the background and stimulus main effects and their background X stimulus interaction. Please is this possible in fieldtrip to use depsamplesF to work with a Participant X "2-way" design? Best regards, Tom Campbell. _______________________________________________ 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 hanneke.meeren at uvt.nl Fri Jan 28 13:03:34 2011 From: hanneke.meeren at uvt.nl (Meeren.H.K.M. ) Date: Fri, 28 Jan 2011 13:03:34 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha Message-ID: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> Dear Fieldtrippers, I am relatively new to fieldtrip, and just starting to make some serious use of the cluster-based permutation routines, and I would just like to (double)check something before I continu. I use ft_timelockstatistics with the following configuration structure: cfg.parameter = 'individual'; cfg.method = 'montecarlo'; cfg.statistic = 'depsamplesT'; cfg.correctm = 'cluster'; cfg.clusteralpha = 0.05; cfg.clusterstatistic = 'maxsum'; cfg.minnbchan = 2; cfg.tail = 0; cfg.clustertail = 0; cfg.alpha = 0.025; etc. >From my understanding of the tutorial the "cfg.clusteralpha" stands for the alpha-value used for the initial test-statistic (in my case a paired t-test) for thresholding the data, and that the "cfg.alpha" field contains the alpha-value for the second step, i.e. selecting clusters after the permutation tests. However, the naming of the parameters seems rather contraintuitive to me. I would have expected it to be the other way around, i.e "cfg.clusteralpha" for my clusters (second step), and not the initial t-test. Could anyone confirm (or deny) the way it is written in the tutorial? Thanks a lot, Hanneke Meeren ---------------------------------- Hanneke K.M. Meeren, PhD. Researcher and Lecturer Medical Psychology and Cognitive Neuroscience Tilburg University P.O. Box 90153 5000 LE Tilburg The Netherlands email: hanneke.meeren at uvt.nl From r.oostenveld at donders.ru.nl Fri Jan 28 13:43:06 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 28 Jan 2011 13:43:06 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> Message-ID: <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> Dear Kambiz Although other people's preferences might differ, I would suggest that you use visual inspection to detect your artifacts. For trial-based data you cannot apply filter padding. The consequence is that the automatic artifact detection routine implemented in fieldtrip is likely to suffer from false alarms at the edges of your trials, and reduced sensitivity away from the edges. Visual detection of artifacts can be done using ft_rejectvisual (check out the three options it has), and using ft_databrowser. best regards, Robert On 28 Jan 2011, at 6:06, Tavabi, Kambiz wrote: > Greetings - this has been an informative discussion. My question remains is , what is the consensus on an approach for automatic artifact rejection with trial (CTF) data? E.g., could one use the artifact rejection section of Michael's code without any padding? I have not found any tutorials or suggestions on how to use the artifact rejection tools on trial data...have I missed something. > -Kambiz From e.maris at donders.ru.nl Fri Jan 28 14:05:07 2011 From: e.maris at donders.ru.nl (Eric Maris) Date: Fri, 28 Jan 2011 14:05:07 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha In-Reply-To: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> Message-ID: <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> Hi Hanneke, > I am relatively new to fieldtrip, and just starting to make some > serious use of the cluster-based permutation routines, and I would just > like to (double)check something before I continu. > > I use ft_timelockstatistics with the following configuration structure: > cfg.parameter = 'individual'; > cfg.method = 'montecarlo'; > cfg.statistic = 'depsamplesT'; > cfg.correctm = 'cluster'; > cfg.clusteralpha = 0.05; > cfg.clusterstatistic = 'maxsum'; > cfg.minnbchan = 2; > cfg.tail = 0; > cfg.clustertail = 0; > cfg.alpha = 0.025; > etc. > > >From my understanding of the tutorial the "cfg.clusteralpha" stands > for the alpha-value used for the initial test-statistic (in my case a > paired t-test) for thresholding the data, This is correct. and that the "cfg.alpha" > field contains the alpha-value for the second step, i.e. selecting > clusters after the permutation tests. This is not correct. Actually, cfg.alpha is superfluous. In the output, every cluster has a p-value assigned to it, and if there is one or more cluster with a p-value less than your critical alpha-level (mostly 0.05 for a one-sided and 0.025 for a two-sided test), then you have found a significant difference. Best, Eric > > However, the naming of the parameters seems rather contraintuitive to > me. I would have expected it to be the other way around, i.e > "cfg.clusteralpha" for my clusters (second step), and not the initial > t-test. > > Could anyone confirm (or deny) the way it is written in the tutorial? > > Thanks a lot, > > Hanneke Meeren > > ---------------------------------- > Hanneke K.M. Meeren, PhD. > Researcher and Lecturer > Medical Psychology and Cognitive Neuroscience > Tilburg University > P.O. Box 90153 > 5000 LE Tilburg > The Netherlands > email: hanneke.meeren at uvt.nl > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From r.vandermeij at donders.ru.nl Fri Jan 28 14:32:56 2011 From: r.vandermeij at donders.ru.nl (Roemer van der Meij) Date: Fri, 28 Jan 2011 14:32:56 +0100 Subject: [FieldTrip] doublecheck significance cfg.alpha and cfg.clusteralpha In-Reply-To: <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> Message-ID: <4D42C588.4080709@donders.ru.nl> > This is not correct. Actually, cfg.alpha is superfluous. In the output, > every cluster has a p-value assigned to it, and if there is one or more > cluster with a p-value less than your critical alpha-level (mostly 0.05 for > a one-sided and 0.025 for a two-sided test), then you have found a > significant difference. > It does affect the output.mask field, which can be used for plotting. This will have a 0 for a time-frequency-channel triplet if its p-value is above cfg.alpha, and a 1 when it is below it. Other than that, it is superfluous. Best, Roemer -- Roemer van der Meij M.Sc. PhD student Donders Institute for Brain, Cognition and Behaviour Centre for Cognition P.O. Box 9104 6500 HE Nijmegen The Netherlands Tel: +31(0)24 3655932 E-mail: r.vandermeij at donders.ru.nl -------------- next part -------------- An HTML attachment was scrubbed... URL: From stephen.whitmarsh at gmail.com Fri Jan 28 17:58:35 2011 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Fri, 28 Jan 2011 17:58:35 +0100 Subject: [FieldTrip] more on artfifact rejection In-Reply-To: <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> References: <130162082.398663.1295517119314.JavaMail.fmail@mwmweb056> <798636036.1010010.1295866127742.JavaMail.fmail@mwmweb054> <582327D5-6E85-4962-B7CD-00597C9F53F0@donders.ru.nl> <73800219.1087625.1295873498667.JavaMail.fmail@mwmweb054> <2024762473.1276448.1295890028620.JavaMail.fmail@mwmweb054> <6CB8CE20-4754-467F-871B-627BB2D4E53A@donders.ru.nl> Message-ID: Dear Kambiz, Please note there is a short description of the use of ft_databrowser in the walkthrough: http://fieldtrip.fcdonders.nl/walkthrough#visual_data_inspection As well as some documentation on visual artifact rejection http://fieldtrip.fcdonders.nl/tutorial/visual_artifact_rejection Best, Stephen On 28 January 2011 13:43, Robert Oostenveld wrote: > Dear Kambiz > > Although other people's preferences might differ, I would suggest that you > use visual inspection to detect your artifacts. For trial-based data you > cannot apply filter padding. The consequence is that the automatic artifact > detection routine implemented in fieldtrip is likely to suffer from false > alarms at the edges of your trials, and reduced sensitivity away from the > edges. > > Visual detection of artifacts can be done using ft_rejectvisual (check out > the three options it has), and using ft_databrowser. > > best regards, > Robert > > > On 28 Jan 2011, at 6:06, Tavabi, Kambiz wrote: > > > Greetings - this has been an informative discussion. My question remains > is , what is the consensus on an approach for automatic artifact rejection > with trial (CTF) data? E.g., could one use the artifact rejection section of > Michael's code without any padding? I have not found any tutorials or > suggestions on how to use the artifact rejection tools on trial data...have > I missed something. > > -Kambiz > > > _______________________________________________ > 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 hanneke.meeren at uvt.nl Mon Jan 31 10:41:51 2011 From: hanneke.meeren at uvt.nl (H.K.M. Meeren) Date: Mon, 31 Jan 2011 10:41:51 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <4D42C588.4080709@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$@maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> Message-ID: <000f01cbc12b$163b4a50$42b1def0$@meeren@uvt.nl> Dear Developers, I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. Could someone quickly send me a download link? Thanks a lot! Hanneke ----------------------------- Hanneke K.M. Meeren, Ph.D. Lecturer and Researcher Cognitive Neuroscience University of Tilburg Room P 614 P.O.Box 90153 5000 LE Tilburg The Netherlands Phone: +31 (0)13 466 3005 Fax: +31 (0)13 466 2067 email: hanneke.meeren at uvt.nl ----------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Mon Jan 31 15:31:07 2011 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Mon, 31 Jan 2011 15:31:07 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$%maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> Message-ID: <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> Hi Hanneke I hope you (and potential others searching for it) have found it by now, if not, please go to http://fieldtrip.fcdonders.nl/download.php There are some problems with the new wiki layout rendering on older versions of MS Internet Explorer which we try to fix a.s.a.p. best regards, Robert On 31 Jan 2011, at 10:41, H.K.M. Meeren wrote: > Dear Developers, > > I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. > Could someone quickly send me a download link? > &n bsp;Thanks a lot! > > Hanneke > ----------------------------- > Hanneke K.M. Meeren, Ph.D. > Lecturer and Researcher > Cognitive Neuroscience > University of Tilburg > Room P 614 > P.O.Box 90153 > 5000 LE Tilburg > The Netherlands > Phone: +31 (0)13 466 3005 > Fax: +31 (0)13 466 2067 > email: hanneke.meeren at uvt.nl > ----------------------------- > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From hanneke.meeren at uvt.nl Mon Jan 31 16:29:19 2011 From: hanneke.meeren at uvt.nl (H.K.M. Meeren) Date: Mon, 31 Jan 2011 16:29:19 +0100 Subject: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website In-Reply-To: <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> References: <1296216214.4b8f41cHkmeeren@atommail.uvt.nl> <003801cbbeeb$ffd8c760$ff8a5620$%maris@donders.ru.nl> <4D42C588.4080709@donders.ru.nl> <000f01cbc12b$163b4a50$42b1def0$%meeren@uvt.nl> <0DB806FC-E13D-4559-81C4-CF0FAFE9B914@donders.ru.nl> Message-ID: <001a01cbc15b$a1049d50$e30dd7f0$@meeren@uvt.nl> Hi Robert and others, Yes, the problem has been solved, thanks a lot. I have already downloaded by now. Stephen Whitmarsh sent me the exact same link earlier. Apparantly I replied to him personally, and not the whole discussion forum... Best regards, Hanneke --------------------------- Hanneke K.M. Meeren, Ph.D. University of Tilburg Room P 614 Tel: +31 (0)13 466 3005 --------------------------- From: fieldtrip-bounces at donders.ru.nl [mailto:fieldtrip-bounces at donders.ru.nl] On Behalf Of Robert Oostenveld Sent: maandag 31 januari 2011 15:31 To: Email discussion list for the FieldTrip project Subject: Re: [FieldTrip] Help wanted with downloading Fieldtrip!!! Can't find link on new Website Importance: High Hi Hanneke I hope you (and potential others searching for it) have found it by now, if not, please go to http://fieldtrip.fcdonders.nl/download.php There are some problems with the new wiki layout rendering on older versions of MS Internet Explorer which we try to fix a.s.a.p. best regards, Robert On 31 Jan 2011, at 10:41, H.K.M. Meeren wrote: Dear Developers, I would like to download Fieldtrip, but I cannot find any download link on your website. It looks as if the nice photograph with the mug is hiding the top half of all the pages. Could someone quickly send me a download link? &n bsp;Thanks a lot! Hanneke ----------------------------- Hanneke K.M. Meeren, Ph.D. Lecturer and Researcher Cognitive Neuroscience University of Tilburg Room P 614 P.O.Box 90153 5000 LE Tilburg The Netherlands Phone: +31 (0)13 466 3005 Fax: +31 (0)13 466 2067 email: hanneke.meeren at uvt.nl ----------------------------- _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: