From r.oostenveld at FCDONDERS.RU.NL Mon Mar 2 11:56:26 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 2 Mar 2009 11:56:26 +0100 Subject: default neuromag fif reader changed Message-ID: Dear neuromag+fieldtrip users, Summary: I have changed the default reading functions for Neuromag *.fif data. Instead of calling the mex files, it now relies on the Matlab functions from the MNE toolbox. Details: It used to be that the meg-pd mex functions were called on continuous data. These mex functions turned out to be quite problematic on a variety of matlab versions and operating systems. An alternative and pure-matlab (i.e. no compiled mex files) implementation for reading data from fif files has been made available by Matti Hamalainen. Laurence Hunt from Oxford has been working on getting these functions implemented in FieldTrip as alternative to the mex file dependencies. The functions from the MNE toolbox themselves are not incldued in the FieldTrip release, because the MNE license does not allow that. You should download the MNE toolbox yourself and install it under fieldtrip/external/mne or somewhere else and add it to your matlab path. If you want to continue using the mex files in fieldtrip/preprocessing you can specify cfg.dataformat and cfg.headerformat fields. You can specify either 'neuromag_mex' or 'neuromag_mne' to pick the low-level reading functions of your choise. The auto-detected default value for the data and headerformat of 'neuromag_fif' will use the MNE functions. See http://www.kolumbus.fi/kuutela/programs/meg-pd and http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php for details on the two external dependencies that FieldTrip has for reading Neuromag fif data. best regards, Robert ----------------------------------------------------------- Robert Oostenveld Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From cornelia.kranczioch at MED.UNI-JENA.DE Mon Mar 2 13:26:57 2009 From: cornelia.kranczioch at MED.UNI-JENA.DE (Conny Kranczioch) Date: Mon, 2 Mar 2009 13:26:57 +0100 Subject: 2 PhD Positions in the Biomagnetic Center Jena Message-ID: 2 PhD Positions in Junior Research Group "Neurocognition of temporal attention", Biomagnetic Center Jena, Germany Two three-year PhD positions (TV-L 13 50%) are available in the Junior Research Group "Neurocognition of temporal attention", headed by Dr. Cornelia Kranczioch. The first post will focus on studying the influence of cognitive states on temporal attention, the second post will study the role of alpha activity on perceptual performance and visual temporal attention. Candidates will have a Diplom or Master's degree in psychology, biology, neurosciences or a related discipline. Candidates should have a strong interest in experimental and cognitive neuroscience and expertise in EEG or MEG recordings. Fluent English is highly desirable. Some background in programming and/or biosignal processing is desirable but not mandatory. The Junior Research Group is affiliated with the Biomagnetic Center Jena. Biomagnetism has a long-standing tradition in Jena and the center consists of a young, interdisciplinary and international research team and a new head of department (Prof. S. Debener). The Biomag Center comprises several labs, including a new 306/128-channel whole-head MEG/EEG system (Neuromag). Areas of research are multisensory processing, somatosensory and pain research, cortical re-organization after cochlear implantation, neurocognition of temporal attention, and EEG-fMRI integration. For further enquiries, please contact Conny Kranczioch. International applications are welcome. Please send your application (application letter, CV, contact information for two references) to cornelia.kranczioch at med.uni-jena.de. Closing date is March 31, 2009. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From wibral at BIC.UNI-FRANKFURT.DE Mon Mar 2 14:02:17 2009 From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral) Date: Mon, 2 Mar 2009 14:02:17 +0100 Subject: incomplete CSD Matrix Message-ID: Hi Frederic, I suspect that the configuration of channels (electrodes / gradiometers) used for preprocessing the data and computing the CSD matrix is different from the one used in the creation of the grid / headmodel / leadfield. At least I have seen such a setup result in a very similar error. Michael > -----Ursprüngliche Nachricht----- > Von: "Frederic Roux" > Gesendet: 27.02.09 11:02:47 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: [FIELDTRIP] incomplete CSD Matrix Dear fieldtrip users, > > I am running sourceanalysis for different subjects. In 18 of 20 > sujbects everything works out, however for 2 subjects in particular I > am getting the following error message: > > ???Error using==>fieldtrip-20081208/private/prepare_freq_matrices > at201 > > The cross-spectral-density matrix is not complete > > Error in==>sourceanalysis at 723 > [Cf, Cr, Pr, Ntrials , cfg] = prepare_freq_matrices(cfg, data); > > Error in==>computeLead fields at 105 > [pressource]= sourceanalysis(cfg,preTFdata); > > I checked the Cf matrix and found out that it contains 2 NaN entries. > Does anyone have an idea what this could possibly be related to or > what > I should check my data for? I used exactly the same parameters as for > all the other subjects. > > Best, > > Frederic > Brand neu: Top Videos auf MSN ClipClub! Schau Dir die besten > > Playlists an >> Play now! ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From tbardouille at ROTMAN-BAYCREST.ON.CA Tue Mar 3 14:50:55 2009 From: tbardouille at ROTMAN-BAYCREST.ON.CA (Tim Bardouille) Date: Tue, 3 Mar 2009 08:50:55 -0500 Subject: Source coherence spectrum Message-ID: Hi there, I'm using fieldtrip to look at corticomuscular coherence (CMC) based on MEG data. I've managed to get source estimates of the CMC in contralateral MI using the DICS method, but I would like to look at the CMC spectrum at this site (over the bandwidth used for source estimation). Is there a way to get out a CMC spectrum (similar to the MEG-EMG spectrum that is output from freqanalysis and freqdescriptives) for a given location in the brain? I've attached the function I wrote to get out the CMC at one frequency. Cheers, Tim Bardouille. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: FldT_source_coherence.m Type: text/x-matlab Size: 1788 bytes Desc: not available URL: From tineke.snijders at DONDERS.RU.NL Tue Mar 3 15:35:18 2009 From: tineke.snijders at DONDERS.RU.NL (Tineke Snijders) Date: Tue, 3 Mar 2009 15:35:18 +0100 Subject: Toolkit course on EEG/MEG data analysis/Nijmegen In-Reply-To: <53972.39517.qm@web15201.mail.cnb.yahoo.com> Message-ID: Hi Luqiang, You should be able to login on the ftp server with username 'anonymous' and your e-mail address as password. Your problem might arise because the computer server (or more specific the spam-filter) has problems with non-western characters. (Sorry about that, we can not change it). You might try to change the settings of your e-mail address (name, etc) to western characters and see if you can login then. Hope this helps, Tineke -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of xu luqiang Sent: Friday, February 27, 2009 8:22 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: !!!!!SPAM!!!!! [FIELDTRIP] [FIELDTRIP] Toolkit course on EEG/MEG data analysis/Nijmegen Dear sir, I hope to download tutorial data from your website. I try to login with username 'anonymous' and use my email address "luqiangxu at yahoo.com.cn"as password,but It does not work. Can I login with username 'anonymous' and use my email address "luqiangxu at yahoo.com.cn"as password? thanks luqiang ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From victimontes at HOTMAIL.COM Thu Mar 5 22:20:30 2009 From: victimontes at HOTMAIL.COM (Victoria Eugenia Montes Restrepo) Date: Thu, 5 Mar 2009 16:20:30 -0500 Subject: Source localization with minimum norm Message-ID: Hello all, I'm using the minimumnormestimate() function from the Forwinv toolbox with a four-shell spherical head model, and assuming orthogonal dipoles orientation. When applying this function, I obtain the strengths and power at each source location. If my objective is choosing a single source, which procedure should I use after estimation of these current densities? Thanks in advance, Victoria Eugenia Montes Universidad Nacional de Colombia - Manizales ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saskia.haegens at DONDERS.RU.NL Fri Mar 6 14:21:19 2009 From: saskia.haegens at DONDERS.RU.NL (Saskia Haegens) Date: Fri, 6 Mar 2009 14:21:19 +0100 Subject: change of default in sourceanalysis: cfg.projectnoise='no' Message-ID: Dear all, For all of you using sourceanalysis: the default setting cfg.projectnoise='yes' has just been changed to cfg.projectnoise='no'. In case you are using the noise estimate (e.g. for the neural activity index), please be aware of this and add cfg.projectnoise='yes' to your scripts. Best, Saskia =============================================== Saskia Haegens PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging P.O. Box 9101 6500 HB Nijmegen The Netherlands tel. : +31 24 36 14731 e-mail: saskia.haegens at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From iversen at NSI.EDU Sat Mar 7 09:57:02 2009 From: iversen at NSI.EDU (John Iversen) Date: Sat, 7 Mar 2009 00:57:02 -0800 Subject: 4D data reading In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl> Message-ID: Hello, I haven't found this 4D148.lay file in recent versions of Fieldtrip. Could someone please send it to me? Thank you. Best, John On Oct 7, 2008, at 12:19 AM, Robert Oostenveld wrote: > Dear all, > > I have received the layout from Almu and have added the 4D148.lay > layout to the fieldtirp/template directory (where the other layouts > are now also to be found). See attached for how it looks. > > thanks, > Robert > > > On 6 Oct 2008, at 15:02, Almudena Capilla wrote: > >> Dear Gopa, >> >> I have got a template for the 4D - 148 channels system. I could >> give it to >> the Fieldtrip developers if this is helpful for other users of this >> system. >> >> Best, >> Almu > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Mar 9 10:49:32 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 9 Mar 2009 09:49:32 +0000 Subject: 4D data reading In-Reply-To: Message-ID: Dear John, Please see attached file. It seems the file was in fieldtrip's cvs- repository but not yet mentioned in the shellscripts controlling which files from the repository end up in the release version of fieldtrip. I changed this, and hopefully all will be well again as of tomorrow. Best, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: 4D148.lay Type: application/octet-stream Size: 4608 bytes Desc: not available URL: -------------- next part -------------- On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > Hello, > > I haven't found this 4D148.lay file in recent versions of > Fieldtrip. Could someone please send it to me? > > Thank you. > > Best, > > John ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From iversen at NSI.EDU Mon Mar 9 17:11:55 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 9 Mar 2009 09:11:55 -0700 Subject: 4D data reading In-Reply-To: <2BC1183D-2927-4290-A91C-5790F5191423@psy.gla.ac.uk> Message-ID: Many thanks, Jan-Mathijs. John On Mar 9, 2009, at 2:49 AM, jan-mathijs schoffelen wrote: > Dear John, > > Please see attached file. It seems the file was in fieldtrip's cvs- > repository but not yet mentioned in the shellscripts controlling > which files from the repository end up in the release version of > fieldtrip. I changed this, and hopefully all will be well again as > of tomorrow. > > Best, > > Jan-Mathijs > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > <4D148.lay> > > > On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > >> Hello, >> >> I haven't found this 4D148.lay file in recent versions of >> Fieldtrip. Could someone please send it to me? >> >> Thank you. >> >> Best, >> >> John > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ghocepie at ULB.AC.BE Mon Mar 9 18:12:38 2009 From: ghocepie at ULB.AC.BE (Gatien Hocepied) Date: Mon, 9 Mar 2009 18:12:38 +0100 Subject: Source localization with minimum norm In-Reply-To: Message-ID: Hello all, I ‘m facing serious problems with this function How can I define the dip.inside and dip.outside ? Besides, for 2 dipoles, this line seems to be incorrect : dip.leadfield{i} = compute_leadfield(dip.pos(i,:), grad, vol, 'reducerank', reducerank, 'normalize', normalize, 'normalizeparam', normalizeparam) * dip.mom(:,i); It seems to be a dimension problem between the matrix given by compute_leadfield and dip.mom (1x6 in case of 2 dipoles ) Thx in advance, Gatien Hocepied De : FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] De la part de Victoria Eugenia Montes Restrepo Envoyé : jeudi 5 mars 2009 22:21 À : FIELDTRIP at NIC.SURFNET.NL Objet : [FIELDTRIP] Source localization with minimum norm Hello all, I'm using the minimumnormestimate() function from the Forwinv toolbox with a four-shell spherical head model, and assuming orthogonal dipoles orientation. When applying this function, I obtain the strengths and power at each source location. If my objective is choosing a single source, which procedure should I use after estimation of these current densities? Thanks in advance, Victoria Eugenia Montes Universidad Nacional de Colombia - Manizales ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From venug001 at BAMA.UA.EDU Mon Mar 9 18:34:54 2009 From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan) Date: Mon, 9 Mar 2009 12:34:54 -0500 Subject: 4D data reading In-Reply-To: Message-ID: Hello all, I was told that each system has its own xyz locations, which may or may not differ, very slightly, from other machines. Maybe it is best to create your own 148.lay using the channels names, and x,y,z locations that are idiosyncratic to your own machine. regards gopa Quoting John Iversen : > Many thanks, Jan-Mathijs. > > John > > On Mar 9, 2009, at 2:49 AM, jan-mathijs schoffelen wrote: > > > Dear John, > > > > Please see attached file. It seems the file was in fieldtrip's cvs- > > > repository but not yet mentioned in the shellscripts controlling > > which files from the repository end up in the release version of > > fieldtrip. I changed this, and hopefully all will be well again as > > > of tomorrow. > > > > Best, > > > > Jan-Mathijs > > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > > > of the FieldTrip toolbox, to share experiences and to discuss new > > > ideas for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html > > and http://www.ru.nl/neuroimaging/fieldtrip. > > <4D148.lay> > > > > > > On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > > > >> Hello, > >> > >> I haven't found this 4D148.lay file in recent versions of > >> Fieldtrip. Could someone please send it to me? > >> > >> Thank you. > >> > >> Best, > >> > >> John > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > > > of the FieldTrip toolbox, to share experiences and to discuss new > > > ideas for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html > > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lhunt at FMRIB.OX.AC.UK Wed Mar 11 15:58:03 2009 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Wed, 11 Mar 2009 14:58:03 +0000 Subject: TopoplotER for Neuromag 306 Message-ID: Hi all, Quick question from a Fieldtrip newbie - when using topoplotER on neuromag 306 data, it appears to give unreasonable results. I suspect this is most likely because two out of three sensors are magnetometers, whereas every third sensor is a planar gradiometer, and the scales on these two types of sensor are different by a factor of ten. One thing I could do is edit prepare_layout to only return planar gradiometers or magnetometers, but before I do this, do people have any other solutions for combining these two different types of sensor that they already use for neuromag data? Apologies if this has already been discussed elsewhere. Cheers, Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Fri Mar 13 17:32:02 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Fri, 13 Mar 2009 17:32:02 +0100 Subject: freqstatistics, Message-ID: ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From michael.wibral at WEB.DE Fri Mar 13 17:35:33 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Fri, 13 Mar 2009 17:35:33 +0100 Subject: freqstatistics; data 1versus data 2 Message-ID: Dear all, I have a quick question concerning freqstatistics(cfg, data1, data2): If I get a positive raw effect at some time t and frequency f that means that: data2(t,f) > data1(t,f), correct? It's a bit difficult to follow the transformation of data1, data2 and the design variables through the code of the various layers of statfuns. Best Regards, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:07:23 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:07:23 +0100 Subject: TopoplotER for Neuromag 306 In-Reply-To: <6CCFCB69-51E0-45B0-A87C-459181B54D9F@fmrib.ox.ac.uk> Message-ID: Hi Laurence, On 11 Mar 2009, at 15:58, Laurence Hunt wrote: > Quick question from a Fieldtrip newbie - when using topoplotER on > neuromag 306 data, it appears to give unreasonable results. I > suspect this is most likely because two out of three sensors are > magnetometers, whereas every third sensor is a planar gradiometer, > and the scales on these two types of sensor are different by a > factor of ten. That is most likely correct. If you are plotting physical data (i.e. not some sort of normalized statistic), the planar gradiometers have T/ m units and the magnetometers have T units. > One thing I could do is edit prepare_layout to only return planar > gradiometers or magnetometers, but before I do this, do people have > any other solutions for combining these two different types of > sensor that they already use for neuromag data? you can use chantype to select the planar and magnetometers. It would indeed be nice to have a cfg.chantype option in plrepare layout, where if specified different from 'all' would use a subset of channels. Another function that you shoudl look into is combineplanar. We use that for the ctf data, where in megplanar we convert the axial gradients in planar gradients. Then we do spectral estimation, and after that we do combineplanar to combine the power of the 2 planar (horizontal and vertical) channel at each location. I am not sure whether it will work out of the box for neuromag data (it was initially written for ctf data), but rudimentary support for neuromag is present. That should not be difficult to improve if needed, see line 205 where the two planar channel sets are determined. The planarchannelset helper function contaimns hard-coded lists, from which I am not sure whether they apply precisely the same to all neuromag systems (this list was determined from a particular system). best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:19:15 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:19:15 +0100 Subject: Source localization with minimum norm In-Reply-To: <001e01c9a0da$3f5ca280$be15e780$@ac.be> Message-ID: Hi Gatien, On 9 Mar 2009, at 18:12, Gatien Hocepied wrote: > I ‘m facing serious problems with this function… How can I define > the dip.inside and dip.outside ? If you access the functino through the fieldtrip sourceanalysis function (and not directly as low-level function), the prepare_dipole_grid function will set up the 3D grid with all dipoles and for each dipole determine whether it is insode or outside the brain (based on the volume conduction model). The function that is notmally called to determine the inside/outide aspect of each gridpoiunt is the inside_vol function (see forwinv/private). If you know that all dipoles are inside the brain, then you can specify the dip.inside vector as a boolean NdipolesX1 vector with all elements being true. Grid positions taht are outside the brain (and that therefore should not be included in the inverse estimate) should be marked as false. To understand this, please consider a 3D box-like grid encompassing the complete brain. The corners of the box will always be outside the brain, so using a 3D box-like grid means that ~30% of the considered grid points is outside the brain and should not be scanned (in case of a beamformer method) or included in the distributed model (in your case). > Besides, for 2 dipoles, this line seems to be incorrect : > > dip.leadfield{i} = compute_leadfield(dip.pos(i,:), grad, vol, > 'reducerank', reducerank,'normalize', normalize, 'normalizeparam', > normalizeparam) * dip.mom(:,i); dip.pos should be a Ndipoles*3 matrix, causing the leadfield to become Nchans*3. That is then (optionally) multiplied with the 3*1 fixed dipole orientation (e.g. constrained by the orientation of the cortical sheet). The concatenation of the leadfields to NchansX(3*Ndipoles) or NchansXNdipoles (in case of fixed orientation) is done from line 109 onwards. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:22:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:22:47 +0100 Subject: Source localization with minimum norm In-Reply-To: Message-ID: On 5 Mar 2009, at 22:20, Victoria Eugenia Montes Restrepo wrote: > I'm using the minimumnormestimate() function from the Forwinv > toolbox with a four-shell spherical head model, and assuming > orthogonal dipoles orientation. When applying this function, I > obtain the strengths and power at each source location. If my > objective is choosing a single source, which procedure should I use > after estimation of these current densities? Hi Victoria, Why do you start with a distributed source model (which is what minimumnormestimate is for) if you are interested in modelling the data with a single dipole? If you think that a single dipole is able to explain the data, you should search for a single dipole solution. That may mean that you also shoudl search for the optimal position and not only the optimal strength of all dipoles at the same time (which is only what MNE does). Perhaps you should look at the fieldtrip/ dipolefitting function. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From christine.gruetzner at GOOGLEMAIL.COM Fri Mar 20 10:47:17 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Fri, 20 Mar 2009 10:47:17 +0100 Subject: timelockstatistics Message-ID: Dear Fieldtrippers, I have some trouble using 'timelockstatistics' for task vs baseline comparisons (the code I'm using is pasted below). In the output of timelockstatistics, I get only one (!) time sample (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, it is possible to plot the whole time window I specified in cfg.latency - even though the topography seems to be the same for each time bin... The steps I do before computing timelockstatistics are the following: 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately 2) Compute timelockgrandaverage for task and baseline 3) Use the code below to compute timelockstatistics Can anybody help me with this issue? I would be very glad about any suggestions on what is going wrong here!! Best Christine cfg = []; cfg.grad = timelockUprightTask{1}.grad; cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; cfg.statistic = 'actvsblT'; cfg.clusterthreshold = 'parametric'; cfg.clusteralpha = 0.05; cfg.alpha = 0.05; cfg.makeclusters = 'yes'; cfg.minnbchan = 3; cfg.parameter = 'individual'; cfg.clusterstatistic = 'maxsum'; cfg.onetwo = 'twosided'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.numrandomization = 1000; cfg.latency = [0 0.2]; nSubjects = length(filesUprightTask); a = [1:nSubjects]; b = ones(1,nSubjects); cfg.design = [a a; b (2*b)]; cfg.uvar = 1; cfg.ivar = 2; timelockstat = timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Fri Mar 20 11:30:25 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Fri, 20 Mar 2009 11:30:25 +0100 Subject: timelockstatistics In-Reply-To: <841d3140903200247v185dd15eo57345d197a1a147b@mail.gmail.com> Message-ID: Hi Christine, I have some trouble using 'timelockstatistics' for task vs baseline comparisons (the code I'm using is pasted below). In the output of timelockstatistics, I get only one (!) time sample (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, it is possible to plot the whole time window I specified in cfg.latency - even though the topography seems to be the same for each time bin... The steps I do before computing timelockstatistics are the following: 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately 2) Compute timelockgrandaverage for task and baseline 3) Use the code below to compute timelockstatistics Can anybody help me with this issue? I would be very glad about any suggestions on what is going wrong here!! For permutation statistics with actvsblT to make sense, the number of time samples in the activation and the baseline data must be equal. This does not appear to be the case in your configuration for timelockanalysis. Good luck, Eric Maris Best Christine cfg = []; cfg.grad = timelockUprightTask{1}.grad; cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; cfg.statistic = 'actvsblT'; cfg.clusterthreshold = 'parametric'; cfg.clusteralpha = 0.05; cfg.alpha = 0.05; cfg.makeclusters = 'yes'; cfg.minnbchan = 3; cfg.parameter = 'individual'; cfg.clusterstatistic = 'maxsum'; cfg.onetwo = 'twosided'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.numrandomization = 1000; cfg.latency = [0 0.2]; nSubjects = length(filesUprightTask); a = [1:nSubjects]; b = ones(1,nSubjects); cfg.design = [a a; b (2*b)]; cfg.uvar = 1; cfg.ivar = 2; timelockstat = timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.gruetzner at GOOGLEMAIL.COM Fri Mar 20 14:52:46 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Fri, 20 Mar 2009 14:52:46 +0100 Subject: timelockstatistics In-Reply-To: <20090320103024.776BFE6AA9@smtp.ru.nl> Message-ID: Hi Eric, Sorry, this was just a little mistake in writing in my mail; I actually use the same number of time samples for the task and the baseline (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.05])!! Best Christine 2009/3/20 Eric Maris > Hi Christine, > > > > > > > > I have some trouble using 'timelockstatistics' for task vs baseline > comparisons (the code I'm using is pasted below). > > In the output of timelockstatistics, I get only one (!) time sample (prob, > stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter > cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, > it is possible to plot the whole time window I specified in cfg.latency - > even though the topography seems to be the same for each time bin... > > The steps I do before computing timelockstatistics are the following: > 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 > 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately > 2) Compute timelockgrandaverage for task and baseline > 3) Use the code below to compute timelockstatistics > > Can anybody help me with this issue? > I would be very glad about any suggestions on what is going wrong here!! > > > > For permutation statistics with actvsblT to make sense, the number of time > samples in the activation and the baseline data must be equal. This does not > appear to be the case in your configuration for timelockanalysis. > > > > Good luck, > > > > Eric Maris > > > > > > > > > > > > > Best > Christine > > > cfg = []; > cfg.grad = timelockUprightTask{1}.grad; > cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', > '-MRT21', '-ML021', '-MRO44', '-MRT47'}; > cfg.statistic = 'actvsblT'; > cfg.clusterthreshold = 'parametric'; > cfg.clusteralpha = 0.05; > cfg.alpha = 0.05; > cfg.makeclusters = 'yes'; > cfg.minnbchan = 3; > cfg.parameter = 'individual'; > cfg.clusterstatistic = 'maxsum'; > cfg.onetwo = 'twosided'; > cfg.method = 'montecarlo'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 1000; > cfg.latency = [0 0.2]; > nSubjects = length(filesUprightTask); > a = [1:nSubjects]; > b = ones(1,nSubjects); > cfg.design = [a a; b (2*b)]; > cfg.uvar = 1; > cfg.ivar = 2; > timelockstat = > timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); > > > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lulswinnik at GMAIL.COM Mon Mar 23 19:19:23 2009 From: lulswinnik at GMAIL.COM (Katya Vinnik) Date: Mon, 23 Mar 2009 19:19:23 +0100 Subject: plots and stats with biosemi128.lay Message-ID: Dear FT users, has anyone of you encountered this warning? Duplicate x-y data points detected: using average of the z values. I'm simply plotting my data with cfg.layout = 'biosemi128.lay'; and it gives me strange plots like the one here: http://picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink basically data from channels B19 and 21 and D22 and 24 are overlayed (circled in red on the pictures). This message appears also with topoplot functions. In the layout file, howether ,positions of this electrodes are different (see below). Do you think it can affect cluster-based multiple comparison correction? For example, if I use cfg.layout = 'biosemi128.lay'; cfg.correctm = 'cluster'; [stat] = freqstatistics(cfg,x,y) does it calcultate it properly? Thank you, Best regards, Katya P.S. positions of this electrodes from biosemi128.lay: 51 0.521467 -0.301069 0.180000 0.140000 B19 53 0.602139 0.000000 0.180000 0.140000 B21 118 -1.404990 -0.000000 0.180000 0.140000 D22 120 -1.527114 -0.496189 0.180000 0.140000 D24 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanna.Renvall at PSYCHOLOGY.UNIMAAS.NL Tue Mar 24 08:44:31 2009 From: Hanna.Renvall at PSYCHOLOGY.UNIMAAS.NL (Renvall Hanna (PSYCHOLOGY)) Date: Tue, 24 Mar 2009 08:44:31 +0100 Subject: VL: aivoAALTO/open positions in Finland Message-ID: Dear Colleagues Our newly established multidisciplinary "aivoAALTO" research project opens positions in the field of systems-level human brain imaging and related research, with a strong focus on social interaction in natural settings, including economic decision making, cinema viewing, and methodological development. http://www.aaltoyliopisto.info/en/news/funding-to-aalto-university-s-aivoaalto-research-project The project involves Helsinki University of Technology (TKK, www.tkk.fi ), Helsinki School of Economics (HSE, www.hse.fi ) and Helsinki University of Art and Design (TAIK, www.taik.fi ). These three schools are just merging to form a new Aalto University ("Aalto", meaning wave, honors the famous Finnish architect Alvar Aalto). The positions, available immediately for up to 3 years, are the following: . 1 PhD student in neuroeconomics and decision making . 1 PhD student in neurocinematics . 1 PhD student in brain-imaging-related signal analysis . 3 postdoctoral positions in human brain imaging and related research . 2 senior scientist positions in human brain imaging and related research For further information, see http://neuro.ltl.hut.fi/~hari/aivoAALTO_positions_March2009.pdf -- Riitta Hari, prof. Brain Research Unit Low Temperature Laboratory Helsinki University of Technology Puumiehenkuja 2, room #250 02015 TKK, Espoo, Finland tel +358 9 451 2959, fax +358 9 451 3508 hari at neuro.hut.fi http://neuro.hut.fi (Brain Research Unit) http://ltl.tkk.fi/wiki/LTL/Contact_information (How to find us) Advanced Magnetic Imaging Centre (AMI) Helsinki University of Technology http://www.ami.hut.fi ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Tue Mar 24 14:55:45 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 24 Mar 2009 14:55:45 +0100 Subject: timelockstatistics In-Reply-To: <841d3140903200652m794c3eb7x4ce8bae7a8c84c7f@mail.gmail.com> Message-ID: Hi Christine With timelockstatsistics you can only test the exchangeability for data points that can be exchanged one-to-one. The data is usually arranged in a Ntrials*Nchans*Ntime matrix and you should have such a matrix both for the baseline and activation window. You should prepare your data in such a way that the channels (of course) but also that the timepoints match. The underlying function will make the data selection based on the overlap bwteen the two input datasets that you hand over to timelockstatistics. So if you want to compare paired data, also the time-axis of the two datasets should be the same. Resegmenting the data can be done using redefinetrial, i.e. cfg = [] cfg.toilim = [0.050 0.400]; dataA = redefinetrial(cfg, data_org) cfg.toilim = [-0.400 -0.050]; dataB = redefinetrial(cfg, data_org) Subsequently you can assign the same time axis to both, either by shifting the time-axis of each trial for i=1:ntrials dataA.time{i} = dataA.time{i} - min(dataA.time{i}) dataB.time{i} = dataB.time{i} - min(dataB.time{i}) end or simply by copying the one time-axis into the other dataB.time = dataA.time In the second case you should be carefull that you don't have a mismatch in the number of samples in the data and in the time axis. A single sample is sometimes easy to loose due to rounding off errors. After that, you can do cfg = [] cfg.keeptrials = 'yes' avgA = timelockanalysis(cfg, dataA); avgB = timelockanalysis(cfg, dataB); and test the two conditions against each other. I am not sure about the applicability of actvsblT as statistic here, but the trick above applies in general and hence should work with any statistic. Depending on the statistic that you use, you might have to be carefull about a difference in the baselining for the pre- and post- stimulus window. I.e. if you subtract the baseline estimated on the pre-stimulus window, then the pre-stimulus window will have less variance over trials regardless of the presence of an effect. best regards, Robert On 20 Mar 2009, at 14:52, Christine Gruetzner wrote: > Hi Eric, > > Sorry, this was just a little mistake in writing in my mail; I > actually use the same number of time samples for the task and the > baseline (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = > [-0.4 -0.05])!! > > Best > Christine > > > > 2009/3/20 Eric Maris > Hi Christine, > > > > > I have some trouble using 'timelockstatistics' for task vs baseline > comparisons (the code I'm using is pasted below). > > In the output of timelockstatistics, I get only one (!) time sample > (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the > parameter cfg.latency (e.g. [0 0.2]). However, when I plot the > statistics afterwards, it is possible to plot the whole time window > I specified in cfg.latency - even though the topography seems to be > the same for each time bin... > > The steps I do before computing timelockstatistics are the following: > 1) Compute timelockanalyis separately for the task (cfg.latency = > [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately > 2) Compute timelockgrandaverage for task and baseline > 3) Use the code below to compute timelockstatistics > > Can anybody help me with this issue? > I would be very glad about any suggestions on what is going wrong > here!! > > > For permutation statistics with actvsblT to make sense, the number > of time samples in the activation and the baseline data must be > equal. This does not appear to be the case in your configuration for > timelockanalysis. > > > Good luck, > > > Eric Maris > > > > > > > > Best > Christine > > > cfg = []; > cfg.grad = timelockUprightTask{1}.grad; > cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '- > MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; > cfg.statistic = 'actvsblT'; > cfg.clusterthreshold = 'parametric'; > cfg.clusteralpha = 0.05; > cfg.alpha = 0.05; > cfg.makeclusters = 'yes'; > cfg.minnbchan = 3; > cfg.parameter = 'individual'; > cfg.clusterstatistic = 'maxsum'; > cfg.onetwo = 'twosided'; > cfg.method = 'montecarlo'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 1000; > cfg.latency = [0 0.2]; > nSubjects = length(filesUprightTask); > a = [1:nSubjects]; > b = ones(1,nSubjects); > cfg.design = [a a; b (2*b)]; > cfg.uvar = 1; > cfg.ivar = 2; > timelockstat = > timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Mar 24 15:01:20 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 24 Mar 2009 15:01:20 +0100 Subject: freqstatistics; data 1versus data 2 In-Reply-To: <920739784@web.de> Message-ID: Hi Michael On 13 Mar 2009, at 17:35, Michael Wibral wrote: > Dear all, > > I have a quick question concerning freqstatistics(cfg, data1, data2): > If I get a positive raw effect at some time t and frequency f that > means that: data2(t,f) > data1(t,f), correct? > It's a bit difficult to follow the transformation of data1, data2 > and the design variables through the code of the various layers of > statfuns. The raw effect (i.e. the difference in the mean value in both conditions) is not computed by freqstatistics, only the statistic of the effect (usually the t-value) and its significance. But a positive t-value means that htere is a positive effect in the difference of the mean values. You could simply add the raw effect to the statfun, e.g. in statfun_indepsamplesT by changing line 109 into s.stat = (avg1 - avg2)./sqrt(varc); % this is the t-value s.effect = (avg1 - avg2); % this is the raw effect any parameter that is returned by the statfun and that has the correct size (meaning that it can be reshaped into the original 3D array) will be automatically passed along to the outside of the function, i.e. to the command line on which you call freqstatistics. best regards Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From katharina.matz at UNI-KONSTANZ.DE Wed Mar 25 09:48:52 2009 From: katharina.matz at UNI-KONSTANZ.DE (Katharina Matz) Date: Wed, 25 Mar 2009 09:48:52 +0100 Subject: how to interpolate bad channels?? Message-ID: Dear FT users, does anyone of you know how to interpolate bad channels? Interactive preprocessing allows me to exclude channels but I'd like to keep them. Thank you! Best regards, Katharina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From rmontefusco at MED.UCHILE.CL Wed Mar 25 22:51:12 2009 From: rmontefusco at MED.UCHILE.CL (Rodrigo A. Montefusco Siegmund) Date: Wed, 25 Mar 2009 17:51:12 -0400 Subject: eog artifact rejection Message-ID: Hello everyone I'm trying to implement a script to detect and remove artifacts. One using artifact_eog to eliminate artifacts in the EOG channels. I'm also looking to eliminate a very large amplitudes in the signal. The problem is that the script artifact_eog doesn't work on my dataset derived from my own trialfun script. Error in ==> fieldtrip-20080701\private\filetype at 225 [p, f, x] = fileparts(filename); Error in ==> fieldtrip-20080701\private\dataset2files at 66 switch filetype(cfg.dataset) Error in ==> artifact_zvalue at 155 cfg = dataset2files(cfg); Error in ==> artifact_eog at 137 [tmpcfg, artifact] = artifact_zvalue(tmpcfg); My raw data is obtained from an amplifier built in my laboratory, so we collect data very raw, without file header or anything similar. The file .dat is turned to .mat, then that file is loaded to the workspace, and then I process it with my trialfun. with that, I create a structure "data" which contains data = trial: (1x60 cell) label: (1x24 cell) fsample: 250 time: (1x60 cell) in the format for fieldtrip. also generates a hdr hdr = Fs: 250 nChans: 24 nSamples: 750 nSamplesPre: 250 nTrials: 60 label: (1x24 cell) FirstTimeStamp: 1 TimeStampPerSample: 1 and the trl that is requested by the documentation. How can I use the artifact_eog on data generated in the format that I mentioned above? Thanks a lot and excuse my english best regards Rodrigo -- ============================================================== Rodrigo A. Montefusco Siegmund Doctorado en Ciencias Biomédicas Programa de Fisiología y Biofí­sica I. C. B. M. Facultad de Medicina Universidad de Chile Centro de Neurociencias Integradas Iniciativa Cientí­fica Milenio Fono: 56 09 82793847 email: rmontefusco at med.uchile.cl =============================================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Wed Mar 25 22:34:05 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 25 Mar 2009 21:34:05 +0000 Subject: eog artifact rejection In-Reply-To: <1976.172.16.72.117.1238017872.squirrel@correo.med.uchile.cl> Message-ID: Dear Rodrigo, It looks as if you are almost there! I suspect the problem occurs because you use a version of fieldtrip which cannot do artifact identification on data which is already present in memory. This version always tries to read in data from a file, and fails in your case. Probably the problem solves itself when you download the most recent version. I assume that you call artifact_eog as follows: cfg = artifact_eog(cfg, data) The second input argument data is of course crucial here. Keep up the good work! Cheers, Jan-Mathijs On Mar 25, 2009, at 9:51 PM, Rodrigo A. Montefusco Siegmund wrote: > Hello everyone > > I'm trying to implement a script to detect and remove artifacts. > One using > artifact_eog to eliminate artifacts in the EOG channels. I'm also > looking > to eliminate a very large amplitudes in the signal. > > The problem is that the script artifact_eog doesn't work on my dataset > derived from my own trialfun script. > > Error in ==> fieldtrip-20080701\private\filetype at 225 > [p, f, x] = fileparts(filename); > > Error in ==> fieldtrip-20080701\private\dataset2files at 66 > switch filetype(cfg.dataset) > > Error in ==> artifact_zvalue at 155 > cfg = dataset2files(cfg); > > Error in ==> artifact_eog at 137 > [tmpcfg, artifact] = artifact_zvalue(tmpcfg); > > > My raw data is obtained from an amplifier built in my laboratory, > so we > collect data very raw, without file header or anything similar. > > The file .dat is turned to .mat, then that file is loaded to the > workspace, and then I process it with my trialfun. with that, I > create a > structure "data" which contains > > data = > trial: (1x60 cell) > label: (1x24 cell) > fsample: 250 > time: (1x60 cell) > > in the format for fieldtrip. also generates a hdr > > hdr = > Fs: 250 > nChans: 24 > nSamples: 750 > nSamplesPre: 250 > nTrials: 60 > label: (1x24 cell) > FirstTimeStamp: 1 > TimeStampPerSample: 1 > > and the trl that is requested by the documentation. > > How can I use the artifact_eog on data generated in the format that I > mentioned above? > > Thanks a lot and excuse my english > > best regards > > Rodrigo > > -- > ============================================================== > Rodrigo A. Montefusco Siegmund > Doctorado en Ciencias Biomédicas > Programa de Fisiología y Biofí sica > I. C. B. M. Facultad de Medicina > Universidad de Chile > Centro de Neurociencias Integradas > Iniciativa Cientí fica Milenio > Fono: 56 09 82793847 > email: rmontefusco at med.uchile.cl > =============================================================== > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Mar 26 09:35:51 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 26 Mar 2009 09:35:51 +0100 Subject: how to interpolate bad channels?? In-Reply-To: <1F841765-BFCA-4154-B7CE-A7421D77D1A4@uni-konstanz.de> Message-ID: Dear Katharina You can use the channelrepair function for that. best regards, Robert On 25 Mar 2009, at 9:48, Katharina Matz wrote: > Dear FT users, > > does anyone of you know how to interpolate bad channels? Interactive > preprocessing allows me to exclude channels but I'd like to keep them. > > Thank you! > Best regards, > Katharina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Mar 26 18:01:57 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 26 Mar 2009 18:01:57 +0100 Subject: multisphere and CTF 3rd order gradients Message-ID: Dear FieldTrip/CTF users, I have extended the prepare_vol_sens function (which is a helper function for sourceanalysis and dipolefitting) so that it can also prepare multisphere ("local spheres") models in case the gradiometer array is synthetically balanced (e.g. CTF 3rd gradients). The change also required an update to the read_ctf_hdm function. The updates will be available in the public release version of fieldtrip on the ftp server this evening. best regards, Robert PS at the moment it will not yet work for multisphere models created using fieldtrip/prepare_localspheres, but only for the ones created using the CTF software and stored in a *.hdm file. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From sdmuthu at CARDIFF.AC.UK Fri Mar 27 17:20:36 2009 From: sdmuthu at CARDIFF.AC.UK (Suresh Muthukumaraswamy) Date: Fri, 27 Mar 2009 17:20:36 +0100 Subject: ICA on 275ch MEG... removing artifacts Message-ID: Hi Everybody, I have started playing with the componentanalysis and rejectcomponent functions to try to remove eye artefacts from CTF 275 channel MEG data. The aim is to try to remove eye artefacts and then run SAM analyses. Technically, I have the approach working fine and it does seem to reduce the eye artefact in the MEG channels near the front of the helmet (I have EOG traces as well) Specifically I was wondering Typically how many components do people normally estimate and then how many of these would normally get rejected as containing eye artefact? 270 components is alot to look through! I see one can limit the number of components the function can return.... Do people normally reject solely on topography or do they do a frequency analysis of the component time-course or perhaps other things? Moreoever, I was also wondering if anyone had carried out any kind of systematic comparison between this approach for MEG compared to traditional EEG approaches to this problem (e.g. projecting out the EOG channels)? Thanks in advance Suresh ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From soren.r.christensen at GSK.COM Fri Mar 27 18:05:43 2009 From: soren.r.christensen at GSK.COM (Soren Rahn Christensen) Date: Fri, 27 Mar 2009 17:05:43 +0000 Subject: Soren R Christensen is out of the office. Message-ID: I will be out of the office starting 27-Mar-2009 and will not return until 30-Mar-2009. I'll be back Tuesday 31st ----------------------------------------------------------- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wibral at BIC.UNI-FRANKFURT.DE Fri Mar 27 18:41:54 2009 From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral) Date: Fri, 27 Mar 2009 18:41:54 +0100 Subject: ICA on 275ch MEG... removing artifacts Message-ID: Dear Suresh, I will try to answer your questions to my best knowledge (we are doing both MEG and EEG ICA here) below. Sorry if the response got a bit lengthy. Best, Michael > -----Ursprüngliche Nachricht----- > Von: "Suresh Muthukumaraswamy" > Gesendet: 27.03.09 17:22:35 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: [FIELDTRIP] ICA on 275ch MEG... removing artifacts > Hi Everybody, > I have started playing with the componentanalysis and rejectcomponent > functions to try to remove eye artefacts from CTF 275 channel MEG data. The > aim is to try to remove eye artefacts and then run SAM analyses. > Technically, I have the approach working fine and it does seem to reduce the > eye artefact in the MEG channels near the front of the helmet (I have EOG > traces as well) > Specifically I was wondering > > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... In EEG we saw a definite improvement of the removal of blink artifacts when going from 64 to 128 channels - this suggests to do as many components as possible. There is a second reason to do as many components as possible: In order to search less components than sensors you need to reduce the dimensionality of your data - typically using PCA as a preprocessing step. The directions of PCA dimensions that you remove are at odd angles with the later ICA component axes - hence by doing PCA you change every later IC a little bit, something that doesn't happen when not using PCA. This information is lost, because the data you'll backproject for beamforming are the cleaned data and have a dimensionality of (number of sensors)-(dimensions removed by PCA)-(dimensions removed as artefact components). There are algorithms that can reduce dimensions by taking out ICs during the estimation process - in fact we're working on those and you may consider trying those (contact Georg Turi: turi at mpih-frankfurt.mpg.de). Note that deflationary ICA - only run up to the desired number of components - is NOT a option, as the order in which components are found is undefined. By backprojecting these lower dimensional data to your sensors you encounter an additional mathematical problem, when planning to do beamforming: technically the covariance matrix of your data is rank deficient, because you have more sensors (aka columns or rows of the cov-matrix) than dimensions in your data (because you removed some of them). This theoretically would cause an error in your analysis. The fact that you did not encounter such an error is because you most likely use regularization (lambda in Fieldtrip). This adds a scaled unity matrix to your cov-matrix and helps you to get full dimensionality again. How many components should be removed for eyeartefacts? Difficult to say, there is usually one or two blink components. Eye movements are a totally different story. The signals from eye-movements VIOLATE the ICA mixing model which uses stationany, not moving sources - i.e. in theory they can't be modeled as independent components at all. Sometimes you may be lucky that exact rotations of the eyeball can be modelled as two orthogonal sationary sources with sinusoidal modulations - if that is the case you should get roughly 4 components:2 for each principal axis of rotation. But be careful, because this really means abusing the ICA mixing model! How many components can you estimate at all? For algorithms like Fastica or INFOMAX a stable estimation requires a number of samples bigger than 20*(number of sensors)^2. That's what it says as a rule of thumb in the EEGLAB tutorial. The mathematical limit is 3*(number of sensors)^2 (this is the Cramer-Rao lower bound). Below this an estimation is mathematically impossible. Some more modern algorithms (EFICA) claim to almost reach the Cramer-Rao lower bound, you may consider using these. If you get close to this threshold I we strongly recommend using a statistical validation of your results, e.g. using ICASSO. or RICE (you could contact Georg Turi for this as well). To sum up, use all possible components if you can afford it - i.e. if you have enough meaningful samples. If not, consider using a non-PCA approach for dimension reduction. If you're close to the Cramer-Rao lower bound you should do a statistical validation of your results by doing ICA from random starting points several hundred times (e.g. in ICASSO). And be careful with contributions from eye-movements - moving sources are not considered in the ICA mixing model that you try to estimate - so anything is possible there. > > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? You would reject on the basis of topography and IC timecourse. > > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? For blinks ICA works as well on MEG as it does on EEG, and it works very well! Projecting out the EOG channels will definitely distort the signal (a detailed discussion of what to expect can be found in the BESA help for example). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From s.debener at UKE.UNI-HAMBURG.DE Fri Mar 27 21:54:28 2009 From: s.debener at UKE.UNI-HAMBURG.DE (Stefan Debener) Date: Fri, 27 Mar 2009 20:54:28 +0000 Subject: ICA on 275ch MEG... removing artifacts In-Reply-To: Message-ID: Hi Suresh, > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... > Be careful with assuming a fixed number of components to explain eye blinks. In EEG, it largely (but not solely!) depends on the number of channels/components; so, while most 32 channel decompositions return 1 eye blink component, this cannot always be expected, and in 128 channel data it can be anything between, roughly, 1 and 6. The problem with ICA of course is that we have no clue about the number of sources contributing to the data, so over/underfitting seems the rule rather than the exception. Therefore (and for other reasons), one should evaluate the quality of the decomposition, which usually includes evaluating the time course information as well as the reliability of a decomposition. With regard to spatial stationarity, as mentioned by Michael already, it seems important to recognize that many artefacts violate this assumption to some more or less relevant extent. Eye blinks, for instance, seem to be caused primarily by the movement of the eye lids (not so much of the eye balls; there is a wonderful paper published on this in Clin Neurophysiol, but I keep forgetting the reference, sorry). So, it is a moving source which often can be 'perfectly' modelled with ICA. In my experience, the same holds for lateral eye movements, which also can be nicely modelled with ICA: these components show a very robust topography, that is, you need not much data to find such ICs quite quickly and reliably, and they show up in nearly all datasets. Thus, ICA seems to tolerate to some extent stationarity violations. My speculation is that this is related to the relatively poor spatial sampling of these artefacts in conventional EEG/MEG recordings: imagine decomposing from 100 channels that covered the whole face: I would not be surprised if those recordings would be more sensitive to stationarity violations contributed by these artefacts. A case where the violation of stationarity typically messes up ICA is for inside scanner EEG recordings. Here, it is my experience that ICA cannot deal well with the ballistocardiogram, which contributes a very complex, dynamically moving signal to the EEG (but see plenty other published papers proposing just the opposite). The reason for this inconsistency seems that the ballistocardiogram scales with the scanner B0 field: in the case of 1.5T, ICA sometimes still pulls out a more or less reasonable decomposition, but at 3T, or even 7T, it performs poorly, under otherwise identical conditions (Debener et al., 2008, Int J Psychophysiol). > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? > Depends. As it happens, there is a paper in press (Viola et al., Clin Neurophysiology, will be available online in a few days) evaluating the use of topographical information for eye blink and eye movement component identification and clustering (across datasets). This works surprisingly well, from 30 to 128 channel EEG recordings. Temporal correlations of component activations with aux channels have also been used for component identification (e.g., Srivastava et al., 2005, Neurimage) but I have mixed experience with this approach and would not recommend it. However, it really depends on the type of artefact you are after: there are cases where topographical information is not of much help, while temporal information gives a detailed picture of which component reflects artefact and which does not (e.g., Sandmann et al.,in press in Brain; or Ohla et al., in press in Brain Topography; both available online). > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to > traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? > Interesting you mention this - that's one of the issues we are very much interested in. Hope this helps, Stefan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Mar 30 16:15:38 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 30 Mar 2009 15:15:38 +0100 Subject: handling of 4D-data: update Message-ID: Dear 4D-neuroimagers, I just committed an updated version of read_4d_hdr to fieldtrip's release which I would like to draw your attention to. The reason for this is twofold: it handles some fields in the header in a different way, which might lead to backward compatitibility problems, and it has some functional improvements. Moreover, even though this new version works alright on the data acquired in Glasgow, I am not sure whether this holds true for all 4D-systems. Specifically, what changed is the following: user_block_data which are stored in the run-specific config file are now stored differently in fieldtrip's hdr-structure. Originally, it was stored as a structure-array in hdr.orig.user_block_data. I changed this into a cell-array. Moreover, I made some efforts to make sense of the content of these user_blocks, so some of these now actually contain some data (such as digitized positions of the coils- on-head, estimated coil-on-head positions in dewar space etc). Most consequentially, read_4d_hdr now attempts to read in the weight table used during acquisition of the data. The digital weights from this table are subsequently incorporated into the balancing matrix of the gradiometer-array (this is now done in bti2grad). This is necessary for correct computation of the leadfields. I'd like to ask you to keep your eyes open and to check whether it also works for data acquired at your system. Please let me know of any problems arising from these changes. Moreover, if you would like to contribute to perfecting read_4d_hdr, just let me know. Yours, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From sdmuthu at CARDIFF.AC.UK Tue Mar 31 13:01:01 2009 From: sdmuthu at CARDIFF.AC.UK (Suresh Muthukumaraswamy) Date: Tue, 31 Mar 2009 12:01:01 +0100 Subject: ICA on 275ch MEG... removing artifacts In-Reply-To: <49CD3D04.2060806@uke.uni-hamburg.de> Message-ID: Thanks Stefan and Michael for your help with this! All the best, Suresh Suresh Muthukumaraswamy, PhD CUBRIC Cardiff University Park Place Cardiff, CF10 3AT United Kingdom email: sdmuthu at cardiff.ac.uk Phone: +44 (0)29 2087 0353 >>> Stefan Debener 03/27/09 8:54 pm >>> Hi Suresh, > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... > Be careful with assuming a fixed number of components to explain eye blinks. In EEG, it largely (but not solely!) depends on the number of channels/components; so, while most 32 channel decompositions return 1 eye blink component, this cannot always be expected, and in 128 channel data it can be anything between, roughly, 1 and 6. The problem with ICA of course is that we have no clue about the number of sources contributing to the data, so over/underfitting seems the rule rather than the exception. Therefore (and for other reasons), one should evaluate the quality of the decomposition, which usually includes evaluating the time course information as well as the reliability of a decomposition. With regard to spatial stationarity, as mentioned by Michael already, it seems important to recognize that many artefacts violate this assumption to some more or less relevant extent. Eye blinks, for instance, seem to be caused primarily by the movement of the eye lids (not so much of the eye balls; there is a wonderful paper published on this in Clin Neurophysiol, but I keep forgetting the reference, sorry). So, it is a moving source which often can be 'perfectly' modelled with ICA. In my experience, the same holds for lateral eye movements, which also can be nicely modelled with ICA: these components show a very robust topography, that is, you need not much data to find such ICs quite quickly and reliably, and they show up in nearly all datasets. Thus, ICA seems to tolerate to some extent stationarity violations. My speculation is that this is related to the relatively poor spatial sampling of these artefacts in conventional EEG/MEG recordings: imagine decomposing from 100 channels that covered the whole face: I would not be surprised if those recordings would be more sensitive to stationarity violations contributed by these artefacts. A case where the violation of stationarity typically messes up ICA is for inside scanner EEG recordings. Here, it is my experience that ICA cannot deal well with the ballistocardiogram, which contributes a very complex, dynamically moving signal to the EEG (but see plenty other published papers proposing just the opposite). The reason for this inconsistency seems that the ballistocardiogram scales with the scanner B0 field: in the case of 1.5T, ICA sometimes still pulls out a more or less reasonable decomposition, but at 3T, or even 7T, it performs poorly, under otherwise identical conditions (Debener et al., 2008, Int J Psychophysiol). > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? > Depends. As it happens, there is a paper in press (Viola et al., Clin Neurophysiology, will be available online in a few days) evaluating the use of topographical information for eye blink and eye movement component identification and clustering (across datasets). This works surprisingly well, from 30 to 128 channel EEG recordings. Temporal correlations of component activations with aux channels have also been used for component identification (e.g., Srivastava et al., 2005, Neurimage) but I have mixed experience with this approach and would not recommend it. However, it really depends on the type of artefact you are after: there are cases where topographical information is not of much help, while temporal information gives a detailed picture of which component reflects artefact and which does not (e.g., Sandmann et al.,in press in Brain; or Ohla et al., in press in Brain Topography; both available online). > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to > traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? > Interesting you mention this - that's one of the issues we are very much interested in. Hope this helps, Stefan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Martijn.Barendregt at PHIL.UU.NL Tue Mar 31 15:23:06 2009 From: Martijn.Barendregt at PHIL.UU.NL (Martijn Barendregt) Date: Tue, 31 Mar 2009 15:23:06 +0200 Subject: Need help with BVA files Message-ID: Hi, I'm trying to process some E.E.G. data that I've exported from BrainVision Analyzer. But when I run my script (see below) I don't get any errors but the 'time' field in the raw_data struct will be all zeros. Because of this I can't do anything with the data. What can I do to get the time values in correctly? Kinds regards, Martijn Barendregt My code: cfg = []; cfg.datafile = 'somefile.dat'; cfg.headerfile = 'somefile.vhdr'; cfg.trialdef.trgfile = 'somefile.vmkr'; cfg.trialdef.eventtype = 'Stimulus'; cfg.trialdef.eventvalue = 'M22'; cfg.traildef.prestim = 3; cfg.traildef.poststim = 3; cfg.trialdef.segment = 'no'; cfg.trialdef.timezero = 'no'; [cfg] = definetrial(cfg); raw_data = preprocessing(cfg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Mar 2 11:56:26 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 2 Mar 2009 11:56:26 +0100 Subject: default neuromag fif reader changed Message-ID: Dear neuromag+fieldtrip users, Summary: I have changed the default reading functions for Neuromag *.fif data. Instead of calling the mex files, it now relies on the Matlab functions from the MNE toolbox. Details: It used to be that the meg-pd mex functions were called on continuous data. These mex functions turned out to be quite problematic on a variety of matlab versions and operating systems. An alternative and pure-matlab (i.e. no compiled mex files) implementation for reading data from fif files has been made available by Matti Hamalainen. Laurence Hunt from Oxford has been working on getting these functions implemented in FieldTrip as alternative to the mex file dependencies. The functions from the MNE toolbox themselves are not incldued in the FieldTrip release, because the MNE license does not allow that. You should download the MNE toolbox yourself and install it under fieldtrip/external/mne or somewhere else and add it to your matlab path. If you want to continue using the mex files in fieldtrip/preprocessing you can specify cfg.dataformat and cfg.headerformat fields. You can specify either 'neuromag_mex' or 'neuromag_mne' to pick the low-level reading functions of your choise. The auto-detected default value for the data and headerformat of 'neuromag_fif' will use the MNE functions. See http://www.kolumbus.fi/kuutela/programs/meg-pd and http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php for details on the two external dependencies that FieldTrip has for reading Neuromag fif data. best regards, Robert ----------------------------------------------------------- Robert Oostenveld Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From cornelia.kranczioch at MED.UNI-JENA.DE Mon Mar 2 13:26:57 2009 From: cornelia.kranczioch at MED.UNI-JENA.DE (Conny Kranczioch) Date: Mon, 2 Mar 2009 13:26:57 +0100 Subject: 2 PhD Positions in the Biomagnetic Center Jena Message-ID: 2 PhD Positions in Junior Research Group "Neurocognition of temporal attention", Biomagnetic Center Jena, Germany Two three-year PhD positions (TV-L 13 50%) are available in the Junior Research Group "Neurocognition of temporal attention", headed by Dr. Cornelia Kranczioch. The first post will focus on studying the influence of cognitive states on temporal attention, the second post will study the role of alpha activity on perceptual performance and visual temporal attention. Candidates will have a Diplom or Master's degree in psychology, biology, neurosciences or a related discipline. Candidates should have a strong interest in experimental and cognitive neuroscience and expertise in EEG or MEG recordings. Fluent English is highly desirable. Some background in programming and/or biosignal processing is desirable but not mandatory. The Junior Research Group is affiliated with the Biomagnetic Center Jena. Biomagnetism has a long-standing tradition in Jena and the center consists of a young, interdisciplinary and international research team and a new head of department (Prof. S. Debener). The Biomag Center comprises several labs, including a new 306/128-channel whole-head MEG/EEG system (Neuromag). Areas of research are multisensory processing, somatosensory and pain research, cortical re-organization after cochlear implantation, neurocognition of temporal attention, and EEG-fMRI integration. For further enquiries, please contact Conny Kranczioch. International applications are welcome. Please send your application (application letter, CV, contact information for two references) to cornelia.kranczioch at med.uni-jena.de. Closing date is March 31, 2009. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From wibral at BIC.UNI-FRANKFURT.DE Mon Mar 2 14:02:17 2009 From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral) Date: Mon, 2 Mar 2009 14:02:17 +0100 Subject: incomplete CSD Matrix Message-ID: Hi Frederic, I suspect that the configuration of channels (electrodes / gradiometers) used for preprocessing the data and computing the CSD matrix is different from the one used in the creation of the grid / headmodel / leadfield. At least I have seen such a setup result in a very similar error. Michael > -----Ursprüngliche Nachricht----- > Von: "Frederic Roux" > Gesendet: 27.02.09 11:02:47 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: [FIELDTRIP] incomplete CSD Matrix Dear fieldtrip users, > > I am running sourceanalysis for different subjects. In 18 of 20 > sujbects everything works out, however for 2 subjects in particular I > am getting the following error message: > > ???Error using==>fieldtrip-20081208/private/prepare_freq_matrices > at201 > > The cross-spectral-density matrix is not complete > > Error in==>sourceanalysis at 723 > [Cf, Cr, Pr, Ntrials , cfg] = prepare_freq_matrices(cfg, data); > > Error in==>computeLead fields at 105 > [pressource]= sourceanalysis(cfg,preTFdata); > > I checked the Cf matrix and found out that it contains 2 NaN entries. > Does anyone have an idea what this could possibly be related to or > what > I should check my data for? I used exactly the same parameters as for > all the other subjects. > > Best, > > Frederic > Brand neu: Top Videos auf MSN ClipClub! Schau Dir die besten > > Playlists an >> Play now! ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From tbardouille at ROTMAN-BAYCREST.ON.CA Tue Mar 3 14:50:55 2009 From: tbardouille at ROTMAN-BAYCREST.ON.CA (Tim Bardouille) Date: Tue, 3 Mar 2009 08:50:55 -0500 Subject: Source coherence spectrum Message-ID: Hi there, I'm using fieldtrip to look at corticomuscular coherence (CMC) based on MEG data. I've managed to get source estimates of the CMC in contralateral MI using the DICS method, but I would like to look at the CMC spectrum at this site (over the bandwidth used for source estimation). Is there a way to get out a CMC spectrum (similar to the MEG-EMG spectrum that is output from freqanalysis and freqdescriptives) for a given location in the brain? I've attached the function I wrote to get out the CMC at one frequency. Cheers, Tim Bardouille. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: FldT_source_coherence.m Type: text/x-matlab Size: 1788 bytes Desc: not available URL: From tineke.snijders at DONDERS.RU.NL Tue Mar 3 15:35:18 2009 From: tineke.snijders at DONDERS.RU.NL (Tineke Snijders) Date: Tue, 3 Mar 2009 15:35:18 +0100 Subject: Toolkit course on EEG/MEG data analysis/Nijmegen In-Reply-To: <53972.39517.qm@web15201.mail.cnb.yahoo.com> Message-ID: Hi Luqiang, You should be able to login on the ftp server with username 'anonymous' and your e-mail address as password. Your problem might arise because the computer server (or more specific the spam-filter) has problems with non-western characters. (Sorry about that, we can not change it). You might try to change the settings of your e-mail address (name, etc) to western characters and see if you can login then. Hope this helps, Tineke -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of xu luqiang Sent: Friday, February 27, 2009 8:22 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: !!!!!SPAM!!!!! [FIELDTRIP] [FIELDTRIP] Toolkit course on EEG/MEG data analysis/Nijmegen Dear sir, I hope to download tutorial data from your website. I try to login with username 'anonymous' and use my email address "luqiangxu at yahoo.com.cn"as password,but It does not work. Can I login with username 'anonymous' and use my email address "luqiangxu at yahoo.com.cn"as password? thanks luqiang ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From victimontes at HOTMAIL.COM Thu Mar 5 22:20:30 2009 From: victimontes at HOTMAIL.COM (Victoria Eugenia Montes Restrepo) Date: Thu, 5 Mar 2009 16:20:30 -0500 Subject: Source localization with minimum norm Message-ID: Hello all, I'm using the minimumnormestimate() function from the Forwinv toolbox with a four-shell spherical head model, and assuming orthogonal dipoles orientation. When applying this function, I obtain the strengths and power at each source location. If my objective is choosing a single source, which procedure should I use after estimation of these current densities? Thanks in advance, Victoria Eugenia Montes Universidad Nacional de Colombia - Manizales ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saskia.haegens at DONDERS.RU.NL Fri Mar 6 14:21:19 2009 From: saskia.haegens at DONDERS.RU.NL (Saskia Haegens) Date: Fri, 6 Mar 2009 14:21:19 +0100 Subject: change of default in sourceanalysis: cfg.projectnoise='no' Message-ID: Dear all, For all of you using sourceanalysis: the default setting cfg.projectnoise='yes' has just been changed to cfg.projectnoise='no'. In case you are using the noise estimate (e.g. for the neural activity index), please be aware of this and add cfg.projectnoise='yes' to your scripts. Best, Saskia =============================================== Saskia Haegens PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging P.O. Box 9101 6500 HB Nijmegen The Netherlands tel. : +31 24 36 14731 e-mail: saskia.haegens at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From iversen at NSI.EDU Sat Mar 7 09:57:02 2009 From: iversen at NSI.EDU (John Iversen) Date: Sat, 7 Mar 2009 00:57:02 -0800 Subject: 4D data reading In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl> Message-ID: Hello, I haven't found this 4D148.lay file in recent versions of Fieldtrip. Could someone please send it to me? Thank you. Best, John On Oct 7, 2008, at 12:19 AM, Robert Oostenveld wrote: > Dear all, > > I have received the layout from Almu and have added the 4D148.lay > layout to the fieldtirp/template directory (where the other layouts > are now also to be found). See attached for how it looks. > > thanks, > Robert > > > On 6 Oct 2008, at 15:02, Almudena Capilla wrote: > >> Dear Gopa, >> >> I have got a template for the 4D - 148 channels system. I could >> give it to >> the Fieldtrip developers if this is helpful for other users of this >> system. >> >> Best, >> Almu > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Mar 9 10:49:32 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 9 Mar 2009 09:49:32 +0000 Subject: 4D data reading In-Reply-To: Message-ID: Dear John, Please see attached file. It seems the file was in fieldtrip's cvs- repository but not yet mentioned in the shellscripts controlling which files from the repository end up in the release version of fieldtrip. I changed this, and hopefully all will be well again as of tomorrow. Best, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: 4D148.lay Type: application/octet-stream Size: 4608 bytes Desc: not available URL: -------------- next part -------------- On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > Hello, > > I haven't found this 4D148.lay file in recent versions of > Fieldtrip. Could someone please send it to me? > > Thank you. > > Best, > > John ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From iversen at NSI.EDU Mon Mar 9 17:11:55 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 9 Mar 2009 09:11:55 -0700 Subject: 4D data reading In-Reply-To: <2BC1183D-2927-4290-A91C-5790F5191423@psy.gla.ac.uk> Message-ID: Many thanks, Jan-Mathijs. John On Mar 9, 2009, at 2:49 AM, jan-mathijs schoffelen wrote: > Dear John, > > Please see attached file. It seems the file was in fieldtrip's cvs- > repository but not yet mentioned in the shellscripts controlling > which files from the repository end up in the release version of > fieldtrip. I changed this, and hopefully all will be well again as > of tomorrow. > > Best, > > Jan-Mathijs > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > <4D148.lay> > > > On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > >> Hello, >> >> I haven't found this 4D148.lay file in recent versions of >> Fieldtrip. Could someone please send it to me? >> >> Thank you. >> >> Best, >> >> John > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ghocepie at ULB.AC.BE Mon Mar 9 18:12:38 2009 From: ghocepie at ULB.AC.BE (Gatien Hocepied) Date: Mon, 9 Mar 2009 18:12:38 +0100 Subject: Source localization with minimum norm In-Reply-To: Message-ID: Hello all, I ‘m facing serious problems with this function How can I define the dip.inside and dip.outside ? Besides, for 2 dipoles, this line seems to be incorrect : dip.leadfield{i} = compute_leadfield(dip.pos(i,:), grad, vol, 'reducerank', reducerank, 'normalize', normalize, 'normalizeparam', normalizeparam) * dip.mom(:,i); It seems to be a dimension problem between the matrix given by compute_leadfield and dip.mom (1x6 in case of 2 dipoles ) Thx in advance, Gatien Hocepied De : FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] De la part de Victoria Eugenia Montes Restrepo Envoyé : jeudi 5 mars 2009 22:21 À : FIELDTRIP at NIC.SURFNET.NL Objet : [FIELDTRIP] Source localization with minimum norm Hello all, I'm using the minimumnormestimate() function from the Forwinv toolbox with a four-shell spherical head model, and assuming orthogonal dipoles orientation. When applying this function, I obtain the strengths and power at each source location. If my objective is choosing a single source, which procedure should I use after estimation of these current densities? Thanks in advance, Victoria Eugenia Montes Universidad Nacional de Colombia - Manizales ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From venug001 at BAMA.UA.EDU Mon Mar 9 18:34:54 2009 From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan) Date: Mon, 9 Mar 2009 12:34:54 -0500 Subject: 4D data reading In-Reply-To: Message-ID: Hello all, I was told that each system has its own xyz locations, which may or may not differ, very slightly, from other machines. Maybe it is best to create your own 148.lay using the channels names, and x,y,z locations that are idiosyncratic to your own machine. regards gopa Quoting John Iversen : > Many thanks, Jan-Mathijs. > > John > > On Mar 9, 2009, at 2:49 AM, jan-mathijs schoffelen wrote: > > > Dear John, > > > > Please see attached file. It seems the file was in fieldtrip's cvs- > > > repository but not yet mentioned in the shellscripts controlling > > which files from the repository end up in the release version of > > fieldtrip. I changed this, and hopefully all will be well again as > > > of tomorrow. > > > > Best, > > > > Jan-Mathijs > > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > > > of the FieldTrip toolbox, to share experiences and to discuss new > > > ideas for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html > > and http://www.ru.nl/neuroimaging/fieldtrip. > > <4D148.lay> > > > > > > On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > > > >> Hello, > >> > >> I haven't found this 4D148.lay file in recent versions of > >> Fieldtrip. Could someone please send it to me? > >> > >> Thank you. > >> > >> Best, > >> > >> John > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > > > of the FieldTrip toolbox, to share experiences and to discuss new > > > ideas for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html > > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lhunt at FMRIB.OX.AC.UK Wed Mar 11 15:58:03 2009 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Wed, 11 Mar 2009 14:58:03 +0000 Subject: TopoplotER for Neuromag 306 Message-ID: Hi all, Quick question from a Fieldtrip newbie - when using topoplotER on neuromag 306 data, it appears to give unreasonable results. I suspect this is most likely because two out of three sensors are magnetometers, whereas every third sensor is a planar gradiometer, and the scales on these two types of sensor are different by a factor of ten. One thing I could do is edit prepare_layout to only return planar gradiometers or magnetometers, but before I do this, do people have any other solutions for combining these two different types of sensor that they already use for neuromag data? Apologies if this has already been discussed elsewhere. Cheers, Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Fri Mar 13 17:32:02 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Fri, 13 Mar 2009 17:32:02 +0100 Subject: freqstatistics, Message-ID: ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From michael.wibral at WEB.DE Fri Mar 13 17:35:33 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Fri, 13 Mar 2009 17:35:33 +0100 Subject: freqstatistics; data 1versus data 2 Message-ID: Dear all, I have a quick question concerning freqstatistics(cfg, data1, data2): If I get a positive raw effect at some time t and frequency f that means that: data2(t,f) > data1(t,f), correct? It's a bit difficult to follow the transformation of data1, data2 and the design variables through the code of the various layers of statfuns. Best Regards, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:07:23 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:07:23 +0100 Subject: TopoplotER for Neuromag 306 In-Reply-To: <6CCFCB69-51E0-45B0-A87C-459181B54D9F@fmrib.ox.ac.uk> Message-ID: Hi Laurence, On 11 Mar 2009, at 15:58, Laurence Hunt wrote: > Quick question from a Fieldtrip newbie - when using topoplotER on > neuromag 306 data, it appears to give unreasonable results. I > suspect this is most likely because two out of three sensors are > magnetometers, whereas every third sensor is a planar gradiometer, > and the scales on these two types of sensor are different by a > factor of ten. That is most likely correct. If you are plotting physical data (i.e. not some sort of normalized statistic), the planar gradiometers have T/ m units and the magnetometers have T units. > One thing I could do is edit prepare_layout to only return planar > gradiometers or magnetometers, but before I do this, do people have > any other solutions for combining these two different types of > sensor that they already use for neuromag data? you can use chantype to select the planar and magnetometers. It would indeed be nice to have a cfg.chantype option in plrepare layout, where if specified different from 'all' would use a subset of channels. Another function that you shoudl look into is combineplanar. We use that for the ctf data, where in megplanar we convert the axial gradients in planar gradients. Then we do spectral estimation, and after that we do combineplanar to combine the power of the 2 planar (horizontal and vertical) channel at each location. I am not sure whether it will work out of the box for neuromag data (it was initially written for ctf data), but rudimentary support for neuromag is present. That should not be difficult to improve if needed, see line 205 where the two planar channel sets are determined. The planarchannelset helper function contaimns hard-coded lists, from which I am not sure whether they apply precisely the same to all neuromag systems (this list was determined from a particular system). best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:19:15 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:19:15 +0100 Subject: Source localization with minimum norm In-Reply-To: <001e01c9a0da$3f5ca280$be15e780$@ac.be> Message-ID: Hi Gatien, On 9 Mar 2009, at 18:12, Gatien Hocepied wrote: > I ‘m facing serious problems with this function… How can I define > the dip.inside and dip.outside ? If you access the functino through the fieldtrip sourceanalysis function (and not directly as low-level function), the prepare_dipole_grid function will set up the 3D grid with all dipoles and for each dipole determine whether it is insode or outside the brain (based on the volume conduction model). The function that is notmally called to determine the inside/outide aspect of each gridpoiunt is the inside_vol function (see forwinv/private). If you know that all dipoles are inside the brain, then you can specify the dip.inside vector as a boolean NdipolesX1 vector with all elements being true. Grid positions taht are outside the brain (and that therefore should not be included in the inverse estimate) should be marked as false. To understand this, please consider a 3D box-like grid encompassing the complete brain. The corners of the box will always be outside the brain, so using a 3D box-like grid means that ~30% of the considered grid points is outside the brain and should not be scanned (in case of a beamformer method) or included in the distributed model (in your case). > Besides, for 2 dipoles, this line seems to be incorrect : > > dip.leadfield{i} = compute_leadfield(dip.pos(i,:), grad, vol, > 'reducerank', reducerank,'normalize', normalize, 'normalizeparam', > normalizeparam) * dip.mom(:,i); dip.pos should be a Ndipoles*3 matrix, causing the leadfield to become Nchans*3. That is then (optionally) multiplied with the 3*1 fixed dipole orientation (e.g. constrained by the orientation of the cortical sheet). The concatenation of the leadfields to NchansX(3*Ndipoles) or NchansXNdipoles (in case of fixed orientation) is done from line 109 onwards. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:22:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:22:47 +0100 Subject: Source localization with minimum norm In-Reply-To: Message-ID: On 5 Mar 2009, at 22:20, Victoria Eugenia Montes Restrepo wrote: > I'm using the minimumnormestimate() function from the Forwinv > toolbox with a four-shell spherical head model, and assuming > orthogonal dipoles orientation. When applying this function, I > obtain the strengths and power at each source location. If my > objective is choosing a single source, which procedure should I use > after estimation of these current densities? Hi Victoria, Why do you start with a distributed source model (which is what minimumnormestimate is for) if you are interested in modelling the data with a single dipole? If you think that a single dipole is able to explain the data, you should search for a single dipole solution. That may mean that you also shoudl search for the optimal position and not only the optimal strength of all dipoles at the same time (which is only what MNE does). Perhaps you should look at the fieldtrip/ dipolefitting function. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From christine.gruetzner at GOOGLEMAIL.COM Fri Mar 20 10:47:17 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Fri, 20 Mar 2009 10:47:17 +0100 Subject: timelockstatistics Message-ID: Dear Fieldtrippers, I have some trouble using 'timelockstatistics' for task vs baseline comparisons (the code I'm using is pasted below). In the output of timelockstatistics, I get only one (!) time sample (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, it is possible to plot the whole time window I specified in cfg.latency - even though the topography seems to be the same for each time bin... The steps I do before computing timelockstatistics are the following: 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately 2) Compute timelockgrandaverage for task and baseline 3) Use the code below to compute timelockstatistics Can anybody help me with this issue? I would be very glad about any suggestions on what is going wrong here!! Best Christine cfg = []; cfg.grad = timelockUprightTask{1}.grad; cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; cfg.statistic = 'actvsblT'; cfg.clusterthreshold = 'parametric'; cfg.clusteralpha = 0.05; cfg.alpha = 0.05; cfg.makeclusters = 'yes'; cfg.minnbchan = 3; cfg.parameter = 'individual'; cfg.clusterstatistic = 'maxsum'; cfg.onetwo = 'twosided'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.numrandomization = 1000; cfg.latency = [0 0.2]; nSubjects = length(filesUprightTask); a = [1:nSubjects]; b = ones(1,nSubjects); cfg.design = [a a; b (2*b)]; cfg.uvar = 1; cfg.ivar = 2; timelockstat = timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Fri Mar 20 11:30:25 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Fri, 20 Mar 2009 11:30:25 +0100 Subject: timelockstatistics In-Reply-To: <841d3140903200247v185dd15eo57345d197a1a147b@mail.gmail.com> Message-ID: Hi Christine, I have some trouble using 'timelockstatistics' for task vs baseline comparisons (the code I'm using is pasted below). In the output of timelockstatistics, I get only one (!) time sample (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, it is possible to plot the whole time window I specified in cfg.latency - even though the topography seems to be the same for each time bin... The steps I do before computing timelockstatistics are the following: 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately 2) Compute timelockgrandaverage for task and baseline 3) Use the code below to compute timelockstatistics Can anybody help me with this issue? I would be very glad about any suggestions on what is going wrong here!! For permutation statistics with actvsblT to make sense, the number of time samples in the activation and the baseline data must be equal. This does not appear to be the case in your configuration for timelockanalysis. Good luck, Eric Maris Best Christine cfg = []; cfg.grad = timelockUprightTask{1}.grad; cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; cfg.statistic = 'actvsblT'; cfg.clusterthreshold = 'parametric'; cfg.clusteralpha = 0.05; cfg.alpha = 0.05; cfg.makeclusters = 'yes'; cfg.minnbchan = 3; cfg.parameter = 'individual'; cfg.clusterstatistic = 'maxsum'; cfg.onetwo = 'twosided'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.numrandomization = 1000; cfg.latency = [0 0.2]; nSubjects = length(filesUprightTask); a = [1:nSubjects]; b = ones(1,nSubjects); cfg.design = [a a; b (2*b)]; cfg.uvar = 1; cfg.ivar = 2; timelockstat = timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.gruetzner at GOOGLEMAIL.COM Fri Mar 20 14:52:46 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Fri, 20 Mar 2009 14:52:46 +0100 Subject: timelockstatistics In-Reply-To: <20090320103024.776BFE6AA9@smtp.ru.nl> Message-ID: Hi Eric, Sorry, this was just a little mistake in writing in my mail; I actually use the same number of time samples for the task and the baseline (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.05])!! Best Christine 2009/3/20 Eric Maris > Hi Christine, > > > > > > > > I have some trouble using 'timelockstatistics' for task vs baseline > comparisons (the code I'm using is pasted below). > > In the output of timelockstatistics, I get only one (!) time sample (prob, > stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter > cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, > it is possible to plot the whole time window I specified in cfg.latency - > even though the topography seems to be the same for each time bin... > > The steps I do before computing timelockstatistics are the following: > 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 > 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately > 2) Compute timelockgrandaverage for task and baseline > 3) Use the code below to compute timelockstatistics > > Can anybody help me with this issue? > I would be very glad about any suggestions on what is going wrong here!! > > > > For permutation statistics with actvsblT to make sense, the number of time > samples in the activation and the baseline data must be equal. This does not > appear to be the case in your configuration for timelockanalysis. > > > > Good luck, > > > > Eric Maris > > > > > > > > > > > > > Best > Christine > > > cfg = []; > cfg.grad = timelockUprightTask{1}.grad; > cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', > '-MRT21', '-ML021', '-MRO44', '-MRT47'}; > cfg.statistic = 'actvsblT'; > cfg.clusterthreshold = 'parametric'; > cfg.clusteralpha = 0.05; > cfg.alpha = 0.05; > cfg.makeclusters = 'yes'; > cfg.minnbchan = 3; > cfg.parameter = 'individual'; > cfg.clusterstatistic = 'maxsum'; > cfg.onetwo = 'twosided'; > cfg.method = 'montecarlo'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 1000; > cfg.latency = [0 0.2]; > nSubjects = length(filesUprightTask); > a = [1:nSubjects]; > b = ones(1,nSubjects); > cfg.design = [a a; b (2*b)]; > cfg.uvar = 1; > cfg.ivar = 2; > timelockstat = > timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); > > > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lulswinnik at GMAIL.COM Mon Mar 23 19:19:23 2009 From: lulswinnik at GMAIL.COM (Katya Vinnik) Date: Mon, 23 Mar 2009 19:19:23 +0100 Subject: plots and stats with biosemi128.lay Message-ID: Dear FT users, has anyone of you encountered this warning? Duplicate x-y data points detected: using average of the z values. I'm simply plotting my data with cfg.layout = 'biosemi128.lay'; and it gives me strange plots like the one here: http://picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink basically data from channels B19 and 21 and D22 and 24 are overlayed (circled in red on the pictures). This message appears also with topoplot functions. In the layout file, howether ,positions of this electrodes are different (see below). Do you think it can affect cluster-based multiple comparison correction? For example, if I use cfg.layout = 'biosemi128.lay'; cfg.correctm = 'cluster'; [stat] = freqstatistics(cfg,x,y) does it calcultate it properly? Thank you, Best regards, Katya P.S. positions of this electrodes from biosemi128.lay: 51 0.521467 -0.301069 0.180000 0.140000 B19 53 0.602139 0.000000 0.180000 0.140000 B21 118 -1.404990 -0.000000 0.180000 0.140000 D22 120 -1.527114 -0.496189 0.180000 0.140000 D24 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanna.Renvall at PSYCHOLOGY.UNIMAAS.NL Tue Mar 24 08:44:31 2009 From: Hanna.Renvall at PSYCHOLOGY.UNIMAAS.NL (Renvall Hanna (PSYCHOLOGY)) Date: Tue, 24 Mar 2009 08:44:31 +0100 Subject: VL: aivoAALTO/open positions in Finland Message-ID: Dear Colleagues Our newly established multidisciplinary "aivoAALTO" research project opens positions in the field of systems-level human brain imaging and related research, with a strong focus on social interaction in natural settings, including economic decision making, cinema viewing, and methodological development. http://www.aaltoyliopisto.info/en/news/funding-to-aalto-university-s-aivoaalto-research-project The project involves Helsinki University of Technology (TKK, www.tkk.fi ), Helsinki School of Economics (HSE, www.hse.fi ) and Helsinki University of Art and Design (TAIK, www.taik.fi ). These three schools are just merging to form a new Aalto University ("Aalto", meaning wave, honors the famous Finnish architect Alvar Aalto). The positions, available immediately for up to 3 years, are the following: . 1 PhD student in neuroeconomics and decision making . 1 PhD student in neurocinematics . 1 PhD student in brain-imaging-related signal analysis . 3 postdoctoral positions in human brain imaging and related research . 2 senior scientist positions in human brain imaging and related research For further information, see http://neuro.ltl.hut.fi/~hari/aivoAALTO_positions_March2009.pdf -- Riitta Hari, prof. Brain Research Unit Low Temperature Laboratory Helsinki University of Technology Puumiehenkuja 2, room #250 02015 TKK, Espoo, Finland tel +358 9 451 2959, fax +358 9 451 3508 hari at neuro.hut.fi http://neuro.hut.fi (Brain Research Unit) http://ltl.tkk.fi/wiki/LTL/Contact_information (How to find us) Advanced Magnetic Imaging Centre (AMI) Helsinki University of Technology http://www.ami.hut.fi ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Tue Mar 24 14:55:45 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 24 Mar 2009 14:55:45 +0100 Subject: timelockstatistics In-Reply-To: <841d3140903200652m794c3eb7x4ce8bae7a8c84c7f@mail.gmail.com> Message-ID: Hi Christine With timelockstatsistics you can only test the exchangeability for data points that can be exchanged one-to-one. The data is usually arranged in a Ntrials*Nchans*Ntime matrix and you should have such a matrix both for the baseline and activation window. You should prepare your data in such a way that the channels (of course) but also that the timepoints match. The underlying function will make the data selection based on the overlap bwteen the two input datasets that you hand over to timelockstatistics. So if you want to compare paired data, also the time-axis of the two datasets should be the same. Resegmenting the data can be done using redefinetrial, i.e. cfg = [] cfg.toilim = [0.050 0.400]; dataA = redefinetrial(cfg, data_org) cfg.toilim = [-0.400 -0.050]; dataB = redefinetrial(cfg, data_org) Subsequently you can assign the same time axis to both, either by shifting the time-axis of each trial for i=1:ntrials dataA.time{i} = dataA.time{i} - min(dataA.time{i}) dataB.time{i} = dataB.time{i} - min(dataB.time{i}) end or simply by copying the one time-axis into the other dataB.time = dataA.time In the second case you should be carefull that you don't have a mismatch in the number of samples in the data and in the time axis. A single sample is sometimes easy to loose due to rounding off errors. After that, you can do cfg = [] cfg.keeptrials = 'yes' avgA = timelockanalysis(cfg, dataA); avgB = timelockanalysis(cfg, dataB); and test the two conditions against each other. I am not sure about the applicability of actvsblT as statistic here, but the trick above applies in general and hence should work with any statistic. Depending on the statistic that you use, you might have to be carefull about a difference in the baselining for the pre- and post- stimulus window. I.e. if you subtract the baseline estimated on the pre-stimulus window, then the pre-stimulus window will have less variance over trials regardless of the presence of an effect. best regards, Robert On 20 Mar 2009, at 14:52, Christine Gruetzner wrote: > Hi Eric, > > Sorry, this was just a little mistake in writing in my mail; I > actually use the same number of time samples for the task and the > baseline (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = > [-0.4 -0.05])!! > > Best > Christine > > > > 2009/3/20 Eric Maris > Hi Christine, > > > > > I have some trouble using 'timelockstatistics' for task vs baseline > comparisons (the code I'm using is pasted below). > > In the output of timelockstatistics, I get only one (!) time sample > (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the > parameter cfg.latency (e.g. [0 0.2]). However, when I plot the > statistics afterwards, it is possible to plot the whole time window > I specified in cfg.latency - even though the topography seems to be > the same for each time bin... > > The steps I do before computing timelockstatistics are the following: > 1) Compute timelockanalyis separately for the task (cfg.latency = > [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately > 2) Compute timelockgrandaverage for task and baseline > 3) Use the code below to compute timelockstatistics > > Can anybody help me with this issue? > I would be very glad about any suggestions on what is going wrong > here!! > > > For permutation statistics with actvsblT to make sense, the number > of time samples in the activation and the baseline data must be > equal. This does not appear to be the case in your configuration for > timelockanalysis. > > > Good luck, > > > Eric Maris > > > > > > > > Best > Christine > > > cfg = []; > cfg.grad = timelockUprightTask{1}.grad; > cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '- > MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; > cfg.statistic = 'actvsblT'; > cfg.clusterthreshold = 'parametric'; > cfg.clusteralpha = 0.05; > cfg.alpha = 0.05; > cfg.makeclusters = 'yes'; > cfg.minnbchan = 3; > cfg.parameter = 'individual'; > cfg.clusterstatistic = 'maxsum'; > cfg.onetwo = 'twosided'; > cfg.method = 'montecarlo'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 1000; > cfg.latency = [0 0.2]; > nSubjects = length(filesUprightTask); > a = [1:nSubjects]; > b = ones(1,nSubjects); > cfg.design = [a a; b (2*b)]; > cfg.uvar = 1; > cfg.ivar = 2; > timelockstat = > timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Mar 24 15:01:20 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 24 Mar 2009 15:01:20 +0100 Subject: freqstatistics; data 1versus data 2 In-Reply-To: <920739784@web.de> Message-ID: Hi Michael On 13 Mar 2009, at 17:35, Michael Wibral wrote: > Dear all, > > I have a quick question concerning freqstatistics(cfg, data1, data2): > If I get a positive raw effect at some time t and frequency f that > means that: data2(t,f) > data1(t,f), correct? > It's a bit difficult to follow the transformation of data1, data2 > and the design variables through the code of the various layers of > statfuns. The raw effect (i.e. the difference in the mean value in both conditions) is not computed by freqstatistics, only the statistic of the effect (usually the t-value) and its significance. But a positive t-value means that htere is a positive effect in the difference of the mean values. You could simply add the raw effect to the statfun, e.g. in statfun_indepsamplesT by changing line 109 into s.stat = (avg1 - avg2)./sqrt(varc); % this is the t-value s.effect = (avg1 - avg2); % this is the raw effect any parameter that is returned by the statfun and that has the correct size (meaning that it can be reshaped into the original 3D array) will be automatically passed along to the outside of the function, i.e. to the command line on which you call freqstatistics. best regards Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From katharina.matz at UNI-KONSTANZ.DE Wed Mar 25 09:48:52 2009 From: katharina.matz at UNI-KONSTANZ.DE (Katharina Matz) Date: Wed, 25 Mar 2009 09:48:52 +0100 Subject: how to interpolate bad channels?? Message-ID: Dear FT users, does anyone of you know how to interpolate bad channels? Interactive preprocessing allows me to exclude channels but I'd like to keep them. Thank you! Best regards, Katharina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From rmontefusco at MED.UCHILE.CL Wed Mar 25 22:51:12 2009 From: rmontefusco at MED.UCHILE.CL (Rodrigo A. Montefusco Siegmund) Date: Wed, 25 Mar 2009 17:51:12 -0400 Subject: eog artifact rejection Message-ID: Hello everyone I'm trying to implement a script to detect and remove artifacts. One using artifact_eog to eliminate artifacts in the EOG channels. I'm also looking to eliminate a very large amplitudes in the signal. The problem is that the script artifact_eog doesn't work on my dataset derived from my own trialfun script. Error in ==> fieldtrip-20080701\private\filetype at 225 [p, f, x] = fileparts(filename); Error in ==> fieldtrip-20080701\private\dataset2files at 66 switch filetype(cfg.dataset) Error in ==> artifact_zvalue at 155 cfg = dataset2files(cfg); Error in ==> artifact_eog at 137 [tmpcfg, artifact] = artifact_zvalue(tmpcfg); My raw data is obtained from an amplifier built in my laboratory, so we collect data very raw, without file header or anything similar. The file .dat is turned to .mat, then that file is loaded to the workspace, and then I process it with my trialfun. with that, I create a structure "data" which contains data = trial: (1x60 cell) label: (1x24 cell) fsample: 250 time: (1x60 cell) in the format for fieldtrip. also generates a hdr hdr = Fs: 250 nChans: 24 nSamples: 750 nSamplesPre: 250 nTrials: 60 label: (1x24 cell) FirstTimeStamp: 1 TimeStampPerSample: 1 and the trl that is requested by the documentation. How can I use the artifact_eog on data generated in the format that I mentioned above? Thanks a lot and excuse my english best regards Rodrigo -- ============================================================== Rodrigo A. Montefusco Siegmund Doctorado en Ciencias Biomédicas Programa de Fisiología y Biofí­sica I. C. B. M. Facultad de Medicina Universidad de Chile Centro de Neurociencias Integradas Iniciativa Cientí­fica Milenio Fono: 56 09 82793847 email: rmontefusco at med.uchile.cl =============================================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Wed Mar 25 22:34:05 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 25 Mar 2009 21:34:05 +0000 Subject: eog artifact rejection In-Reply-To: <1976.172.16.72.117.1238017872.squirrel@correo.med.uchile.cl> Message-ID: Dear Rodrigo, It looks as if you are almost there! I suspect the problem occurs because you use a version of fieldtrip which cannot do artifact identification on data which is already present in memory. This version always tries to read in data from a file, and fails in your case. Probably the problem solves itself when you download the most recent version. I assume that you call artifact_eog as follows: cfg = artifact_eog(cfg, data) The second input argument data is of course crucial here. Keep up the good work! Cheers, Jan-Mathijs On Mar 25, 2009, at 9:51 PM, Rodrigo A. Montefusco Siegmund wrote: > Hello everyone > > I'm trying to implement a script to detect and remove artifacts. > One using > artifact_eog to eliminate artifacts in the EOG channels. I'm also > looking > to eliminate a very large amplitudes in the signal. > > The problem is that the script artifact_eog doesn't work on my dataset > derived from my own trialfun script. > > Error in ==> fieldtrip-20080701\private\filetype at 225 > [p, f, x] = fileparts(filename); > > Error in ==> fieldtrip-20080701\private\dataset2files at 66 > switch filetype(cfg.dataset) > > Error in ==> artifact_zvalue at 155 > cfg = dataset2files(cfg); > > Error in ==> artifact_eog at 137 > [tmpcfg, artifact] = artifact_zvalue(tmpcfg); > > > My raw data is obtained from an amplifier built in my laboratory, > so we > collect data very raw, without file header or anything similar. > > The file .dat is turned to .mat, then that file is loaded to the > workspace, and then I process it with my trialfun. with that, I > create a > structure "data" which contains > > data = > trial: (1x60 cell) > label: (1x24 cell) > fsample: 250 > time: (1x60 cell) > > in the format for fieldtrip. also generates a hdr > > hdr = > Fs: 250 > nChans: 24 > nSamples: 750 > nSamplesPre: 250 > nTrials: 60 > label: (1x24 cell) > FirstTimeStamp: 1 > TimeStampPerSample: 1 > > and the trl that is requested by the documentation. > > How can I use the artifact_eog on data generated in the format that I > mentioned above? > > Thanks a lot and excuse my english > > best regards > > Rodrigo > > -- > ============================================================== > Rodrigo A. Montefusco Siegmund > Doctorado en Ciencias Biomédicas > Programa de Fisiología y Biofí sica > I. C. B. M. Facultad de Medicina > Universidad de Chile > Centro de Neurociencias Integradas > Iniciativa Cientí fica Milenio > Fono: 56 09 82793847 > email: rmontefusco at med.uchile.cl > =============================================================== > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Mar 26 09:35:51 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 26 Mar 2009 09:35:51 +0100 Subject: how to interpolate bad channels?? In-Reply-To: <1F841765-BFCA-4154-B7CE-A7421D77D1A4@uni-konstanz.de> Message-ID: Dear Katharina You can use the channelrepair function for that. best regards, Robert On 25 Mar 2009, at 9:48, Katharina Matz wrote: > Dear FT users, > > does anyone of you know how to interpolate bad channels? Interactive > preprocessing allows me to exclude channels but I'd like to keep them. > > Thank you! > Best regards, > Katharina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Mar 26 18:01:57 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 26 Mar 2009 18:01:57 +0100 Subject: multisphere and CTF 3rd order gradients Message-ID: Dear FieldTrip/CTF users, I have extended the prepare_vol_sens function (which is a helper function for sourceanalysis and dipolefitting) so that it can also prepare multisphere ("local spheres") models in case the gradiometer array is synthetically balanced (e.g. CTF 3rd gradients). The change also required an update to the read_ctf_hdm function. The updates will be available in the public release version of fieldtrip on the ftp server this evening. best regards, Robert PS at the moment it will not yet work for multisphere models created using fieldtrip/prepare_localspheres, but only for the ones created using the CTF software and stored in a *.hdm file. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From sdmuthu at CARDIFF.AC.UK Fri Mar 27 17:20:36 2009 From: sdmuthu at CARDIFF.AC.UK (Suresh Muthukumaraswamy) Date: Fri, 27 Mar 2009 17:20:36 +0100 Subject: ICA on 275ch MEG... removing artifacts Message-ID: Hi Everybody, I have started playing with the componentanalysis and rejectcomponent functions to try to remove eye artefacts from CTF 275 channel MEG data. The aim is to try to remove eye artefacts and then run SAM analyses. Technically, I have the approach working fine and it does seem to reduce the eye artefact in the MEG channels near the front of the helmet (I have EOG traces as well) Specifically I was wondering Typically how many components do people normally estimate and then how many of these would normally get rejected as containing eye artefact? 270 components is alot to look through! I see one can limit the number of components the function can return.... Do people normally reject solely on topography or do they do a frequency analysis of the component time-course or perhaps other things? Moreoever, I was also wondering if anyone had carried out any kind of systematic comparison between this approach for MEG compared to traditional EEG approaches to this problem (e.g. projecting out the EOG channels)? Thanks in advance Suresh ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From soren.r.christensen at GSK.COM Fri Mar 27 18:05:43 2009 From: soren.r.christensen at GSK.COM (Soren Rahn Christensen) Date: Fri, 27 Mar 2009 17:05:43 +0000 Subject: Soren R Christensen is out of the office. Message-ID: I will be out of the office starting 27-Mar-2009 and will not return until 30-Mar-2009. I'll be back Tuesday 31st ----------------------------------------------------------- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wibral at BIC.UNI-FRANKFURT.DE Fri Mar 27 18:41:54 2009 From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral) Date: Fri, 27 Mar 2009 18:41:54 +0100 Subject: ICA on 275ch MEG... removing artifacts Message-ID: Dear Suresh, I will try to answer your questions to my best knowledge (we are doing both MEG and EEG ICA here) below. Sorry if the response got a bit lengthy. Best, Michael > -----Ursprüngliche Nachricht----- > Von: "Suresh Muthukumaraswamy" > Gesendet: 27.03.09 17:22:35 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: [FIELDTRIP] ICA on 275ch MEG... removing artifacts > Hi Everybody, > I have started playing with the componentanalysis and rejectcomponent > functions to try to remove eye artefacts from CTF 275 channel MEG data. The > aim is to try to remove eye artefacts and then run SAM analyses. > Technically, I have the approach working fine and it does seem to reduce the > eye artefact in the MEG channels near the front of the helmet (I have EOG > traces as well) > Specifically I was wondering > > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... In EEG we saw a definite improvement of the removal of blink artifacts when going from 64 to 128 channels - this suggests to do as many components as possible. There is a second reason to do as many components as possible: In order to search less components than sensors you need to reduce the dimensionality of your data - typically using PCA as a preprocessing step. The directions of PCA dimensions that you remove are at odd angles with the later ICA component axes - hence by doing PCA you change every later IC a little bit, something that doesn't happen when not using PCA. This information is lost, because the data you'll backproject for beamforming are the cleaned data and have a dimensionality of (number of sensors)-(dimensions removed by PCA)-(dimensions removed as artefact components). There are algorithms that can reduce dimensions by taking out ICs during the estimation process - in fact we're working on those and you may consider trying those (contact Georg Turi: turi at mpih-frankfurt.mpg.de). Note that deflationary ICA - only run up to the desired number of components - is NOT a option, as the order in which components are found is undefined. By backprojecting these lower dimensional data to your sensors you encounter an additional mathematical problem, when planning to do beamforming: technically the covariance matrix of your data is rank deficient, because you have more sensors (aka columns or rows of the cov-matrix) than dimensions in your data (because you removed some of them). This theoretically would cause an error in your analysis. The fact that you did not encounter such an error is because you most likely use regularization (lambda in Fieldtrip). This adds a scaled unity matrix to your cov-matrix and helps you to get full dimensionality again. How many components should be removed for eyeartefacts? Difficult to say, there is usually one or two blink components. Eye movements are a totally different story. The signals from eye-movements VIOLATE the ICA mixing model which uses stationany, not moving sources - i.e. in theory they can't be modeled as independent components at all. Sometimes you may be lucky that exact rotations of the eyeball can be modelled as two orthogonal sationary sources with sinusoidal modulations - if that is the case you should get roughly 4 components:2 for each principal axis of rotation. But be careful, because this really means abusing the ICA mixing model! How many components can you estimate at all? For algorithms like Fastica or INFOMAX a stable estimation requires a number of samples bigger than 20*(number of sensors)^2. That's what it says as a rule of thumb in the EEGLAB tutorial. The mathematical limit is 3*(number of sensors)^2 (this is the Cramer-Rao lower bound). Below this an estimation is mathematically impossible. Some more modern algorithms (EFICA) claim to almost reach the Cramer-Rao lower bound, you may consider using these. If you get close to this threshold I we strongly recommend using a statistical validation of your results, e.g. using ICASSO. or RICE (you could contact Georg Turi for this as well). To sum up, use all possible components if you can afford it - i.e. if you have enough meaningful samples. If not, consider using a non-PCA approach for dimension reduction. If you're close to the Cramer-Rao lower bound you should do a statistical validation of your results by doing ICA from random starting points several hundred times (e.g. in ICASSO). And be careful with contributions from eye-movements - moving sources are not considered in the ICA mixing model that you try to estimate - so anything is possible there. > > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? You would reject on the basis of topography and IC timecourse. > > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? For blinks ICA works as well on MEG as it does on EEG, and it works very well! Projecting out the EOG channels will definitely distort the signal (a detailed discussion of what to expect can be found in the BESA help for example). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From s.debener at UKE.UNI-HAMBURG.DE Fri Mar 27 21:54:28 2009 From: s.debener at UKE.UNI-HAMBURG.DE (Stefan Debener) Date: Fri, 27 Mar 2009 20:54:28 +0000 Subject: ICA on 275ch MEG... removing artifacts In-Reply-To: Message-ID: Hi Suresh, > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... > Be careful with assuming a fixed number of components to explain eye blinks. In EEG, it largely (but not solely!) depends on the number of channels/components; so, while most 32 channel decompositions return 1 eye blink component, this cannot always be expected, and in 128 channel data it can be anything between, roughly, 1 and 6. The problem with ICA of course is that we have no clue about the number of sources contributing to the data, so over/underfitting seems the rule rather than the exception. Therefore (and for other reasons), one should evaluate the quality of the decomposition, which usually includes evaluating the time course information as well as the reliability of a decomposition. With regard to spatial stationarity, as mentioned by Michael already, it seems important to recognize that many artefacts violate this assumption to some more or less relevant extent. Eye blinks, for instance, seem to be caused primarily by the movement of the eye lids (not so much of the eye balls; there is a wonderful paper published on this in Clin Neurophysiol, but I keep forgetting the reference, sorry). So, it is a moving source which often can be 'perfectly' modelled with ICA. In my experience, the same holds for lateral eye movements, which also can be nicely modelled with ICA: these components show a very robust topography, that is, you need not much data to find such ICs quite quickly and reliably, and they show up in nearly all datasets. Thus, ICA seems to tolerate to some extent stationarity violations. My speculation is that this is related to the relatively poor spatial sampling of these artefacts in conventional EEG/MEG recordings: imagine decomposing from 100 channels that covered the whole face: I would not be surprised if those recordings would be more sensitive to stationarity violations contributed by these artefacts. A case where the violation of stationarity typically messes up ICA is for inside scanner EEG recordings. Here, it is my experience that ICA cannot deal well with the ballistocardiogram, which contributes a very complex, dynamically moving signal to the EEG (but see plenty other published papers proposing just the opposite). The reason for this inconsistency seems that the ballistocardiogram scales with the scanner B0 field: in the case of 1.5T, ICA sometimes still pulls out a more or less reasonable decomposition, but at 3T, or even 7T, it performs poorly, under otherwise identical conditions (Debener et al., 2008, Int J Psychophysiol). > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? > Depends. As it happens, there is a paper in press (Viola et al., Clin Neurophysiology, will be available online in a few days) evaluating the use of topographical information for eye blink and eye movement component identification and clustering (across datasets). This works surprisingly well, from 30 to 128 channel EEG recordings. Temporal correlations of component activations with aux channels have also been used for component identification (e.g., Srivastava et al., 2005, Neurimage) but I have mixed experience with this approach and would not recommend it. However, it really depends on the type of artefact you are after: there are cases where topographical information is not of much help, while temporal information gives a detailed picture of which component reflects artefact and which does not (e.g., Sandmann et al.,in press in Brain; or Ohla et al., in press in Brain Topography; both available online). > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to > traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? > Interesting you mention this - that's one of the issues we are very much interested in. Hope this helps, Stefan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Mar 30 16:15:38 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 30 Mar 2009 15:15:38 +0100 Subject: handling of 4D-data: update Message-ID: Dear 4D-neuroimagers, I just committed an updated version of read_4d_hdr to fieldtrip's release which I would like to draw your attention to. The reason for this is twofold: it handles some fields in the header in a different way, which might lead to backward compatitibility problems, and it has some functional improvements. Moreover, even though this new version works alright on the data acquired in Glasgow, I am not sure whether this holds true for all 4D-systems. Specifically, what changed is the following: user_block_data which are stored in the run-specific config file are now stored differently in fieldtrip's hdr-structure. Originally, it was stored as a structure-array in hdr.orig.user_block_data. I changed this into a cell-array. Moreover, I made some efforts to make sense of the content of these user_blocks, so some of these now actually contain some data (such as digitized positions of the coils- on-head, estimated coil-on-head positions in dewar space etc). Most consequentially, read_4d_hdr now attempts to read in the weight table used during acquisition of the data. The digital weights from this table are subsequently incorporated into the balancing matrix of the gradiometer-array (this is now done in bti2grad). This is necessary for correct computation of the leadfields. I'd like to ask you to keep your eyes open and to check whether it also works for data acquired at your system. Please let me know of any problems arising from these changes. Moreover, if you would like to contribute to perfecting read_4d_hdr, just let me know. Yours, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From sdmuthu at CARDIFF.AC.UK Tue Mar 31 13:01:01 2009 From: sdmuthu at CARDIFF.AC.UK (Suresh Muthukumaraswamy) Date: Tue, 31 Mar 2009 12:01:01 +0100 Subject: ICA on 275ch MEG... removing artifacts In-Reply-To: <49CD3D04.2060806@uke.uni-hamburg.de> Message-ID: Thanks Stefan and Michael for your help with this! All the best, Suresh Suresh Muthukumaraswamy, PhD CUBRIC Cardiff University Park Place Cardiff, CF10 3AT United Kingdom email: sdmuthu at cardiff.ac.uk Phone: +44 (0)29 2087 0353 >>> Stefan Debener 03/27/09 8:54 pm >>> Hi Suresh, > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... > Be careful with assuming a fixed number of components to explain eye blinks. In EEG, it largely (but not solely!) depends on the number of channels/components; so, while most 32 channel decompositions return 1 eye blink component, this cannot always be expected, and in 128 channel data it can be anything between, roughly, 1 and 6. The problem with ICA of course is that we have no clue about the number of sources contributing to the data, so over/underfitting seems the rule rather than the exception. Therefore (and for other reasons), one should evaluate the quality of the decomposition, which usually includes evaluating the time course information as well as the reliability of a decomposition. With regard to spatial stationarity, as mentioned by Michael already, it seems important to recognize that many artefacts violate this assumption to some more or less relevant extent. Eye blinks, for instance, seem to be caused primarily by the movement of the eye lids (not so much of the eye balls; there is a wonderful paper published on this in Clin Neurophysiol, but I keep forgetting the reference, sorry). So, it is a moving source which often can be 'perfectly' modelled with ICA. In my experience, the same holds for lateral eye movements, which also can be nicely modelled with ICA: these components show a very robust topography, that is, you need not much data to find such ICs quite quickly and reliably, and they show up in nearly all datasets. Thus, ICA seems to tolerate to some extent stationarity violations. My speculation is that this is related to the relatively poor spatial sampling of these artefacts in conventional EEG/MEG recordings: imagine decomposing from 100 channels that covered the whole face: I would not be surprised if those recordings would be more sensitive to stationarity violations contributed by these artefacts. A case where the violation of stationarity typically messes up ICA is for inside scanner EEG recordings. Here, it is my experience that ICA cannot deal well with the ballistocardiogram, which contributes a very complex, dynamically moving signal to the EEG (but see plenty other published papers proposing just the opposite). The reason for this inconsistency seems that the ballistocardiogram scales with the scanner B0 field: in the case of 1.5T, ICA sometimes still pulls out a more or less reasonable decomposition, but at 3T, or even 7T, it performs poorly, under otherwise identical conditions (Debener et al., 2008, Int J Psychophysiol). > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? > Depends. As it happens, there is a paper in press (Viola et al., Clin Neurophysiology, will be available online in a few days) evaluating the use of topographical information for eye blink and eye movement component identification and clustering (across datasets). This works surprisingly well, from 30 to 128 channel EEG recordings. Temporal correlations of component activations with aux channels have also been used for component identification (e.g., Srivastava et al., 2005, Neurimage) but I have mixed experience with this approach and would not recommend it. However, it really depends on the type of artefact you are after: there are cases where topographical information is not of much help, while temporal information gives a detailed picture of which component reflects artefact and which does not (e.g., Sandmann et al.,in press in Brain; or Ohla et al., in press in Brain Topography; both available online). > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to > traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? > Interesting you mention this - that's one of the issues we are very much interested in. Hope this helps, Stefan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Martijn.Barendregt at PHIL.UU.NL Tue Mar 31 15:23:06 2009 From: Martijn.Barendregt at PHIL.UU.NL (Martijn Barendregt) Date: Tue, 31 Mar 2009 15:23:06 +0200 Subject: Need help with BVA files Message-ID: Hi, I'm trying to process some E.E.G. data that I've exported from BrainVision Analyzer. But when I run my script (see below) I don't get any errors but the 'time' field in the raw_data struct will be all zeros. Because of this I can't do anything with the data. What can I do to get the time values in correctly? Kinds regards, Martijn Barendregt My code: cfg = []; cfg.datafile = 'somefile.dat'; cfg.headerfile = 'somefile.vhdr'; cfg.trialdef.trgfile = 'somefile.vmkr'; cfg.trialdef.eventtype = 'Stimulus'; cfg.trialdef.eventvalue = 'M22'; cfg.traildef.prestim = 3; cfg.traildef.poststim = 3; cfg.trialdef.segment = 'no'; cfg.trialdef.timezero = 'no'; [cfg] = definetrial(cfg); raw_data = preprocessing(cfg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Mar 2 11:56:26 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 2 Mar 2009 11:56:26 +0100 Subject: default neuromag fif reader changed Message-ID: Dear neuromag+fieldtrip users, Summary: I have changed the default reading functions for Neuromag *.fif data. Instead of calling the mex files, it now relies on the Matlab functions from the MNE toolbox. Details: It used to be that the meg-pd mex functions were called on continuous data. These mex functions turned out to be quite problematic on a variety of matlab versions and operating systems. An alternative and pure-matlab (i.e. no compiled mex files) implementation for reading data from fif files has been made available by Matti Hamalainen. Laurence Hunt from Oxford has been working on getting these functions implemented in FieldTrip as alternative to the mex file dependencies. The functions from the MNE toolbox themselves are not incldued in the FieldTrip release, because the MNE license does not allow that. You should download the MNE toolbox yourself and install it under fieldtrip/external/mne or somewhere else and add it to your matlab path. If you want to continue using the mex files in fieldtrip/preprocessing you can specify cfg.dataformat and cfg.headerformat fields. You can specify either 'neuromag_mex' or 'neuromag_mne' to pick the low-level reading functions of your choise. The auto-detected default value for the data and headerformat of 'neuromag_fif' will use the MNE functions. See http://www.kolumbus.fi/kuutela/programs/meg-pd and http://www.nmr.mgh.harvard.edu/martinos/userInfo/data/sofMNE.php for details on the two external dependencies that FieldTrip has for reading Neuromag fif data. best regards, Robert ----------------------------------------------------------- Robert Oostenveld Senior Researcher Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen tel.: +31 (0)24 3619695 e-mail: r.oostenveld at donders.ru.nl web: http://www.ru.nl/neuroimaging skype: r.oostenveld ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From cornelia.kranczioch at MED.UNI-JENA.DE Mon Mar 2 13:26:57 2009 From: cornelia.kranczioch at MED.UNI-JENA.DE (Conny Kranczioch) Date: Mon, 2 Mar 2009 13:26:57 +0100 Subject: 2 PhD Positions in the Biomagnetic Center Jena Message-ID: 2 PhD Positions in Junior Research Group "Neurocognition of temporal attention", Biomagnetic Center Jena, Germany Two three-year PhD positions (TV-L 13 50%) are available in the Junior Research Group "Neurocognition of temporal attention", headed by Dr. Cornelia Kranczioch. The first post will focus on studying the influence of cognitive states on temporal attention, the second post will study the role of alpha activity on perceptual performance and visual temporal attention. Candidates will have a Diplom or Master's degree in psychology, biology, neurosciences or a related discipline. Candidates should have a strong interest in experimental and cognitive neuroscience and expertise in EEG or MEG recordings. Fluent English is highly desirable. Some background in programming and/or biosignal processing is desirable but not mandatory. The Junior Research Group is affiliated with the Biomagnetic Center Jena. Biomagnetism has a long-standing tradition in Jena and the center consists of a young, interdisciplinary and international research team and a new head of department (Prof. S. Debener). The Biomag Center comprises several labs, including a new 306/128-channel whole-head MEG/EEG system (Neuromag). Areas of research are multisensory processing, somatosensory and pain research, cortical re-organization after cochlear implantation, neurocognition of temporal attention, and EEG-fMRI integration. For further enquiries, please contact Conny Kranczioch. International applications are welcome. Please send your application (application letter, CV, contact information for two references) to cornelia.kranczioch at med.uni-jena.de. Closing date is March 31, 2009. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. From wibral at BIC.UNI-FRANKFURT.DE Mon Mar 2 14:02:17 2009 From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral) Date: Mon, 2 Mar 2009 14:02:17 +0100 Subject: incomplete CSD Matrix Message-ID: Hi Frederic, I suspect that the configuration of channels (electrodes / gradiometers) used for preprocessing the data and computing the CSD matrix is different from the one used in the creation of the grid / headmodel / leadfield. At least I have seen such a setup result in a very similar error. Michael > -----Ursprüngliche Nachricht----- > Von: "Frederic Roux" > Gesendet: 27.02.09 11:02:47 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: [FIELDTRIP] incomplete CSD Matrix Dear fieldtrip users, > > I am running sourceanalysis for different subjects. In 18 of 20 > sujbects everything works out, however for 2 subjects in particular I > am getting the following error message: > > ???Error using==>fieldtrip-20081208/private/prepare_freq_matrices > at201 > > The cross-spectral-density matrix is not complete > > Error in==>sourceanalysis at 723 > [Cf, Cr, Pr, Ntrials , cfg] = prepare_freq_matrices(cfg, data); > > Error in==>computeLead fields at 105 > [pressource]= sourceanalysis(cfg,preTFdata); > > I checked the Cf matrix and found out that it contains 2 NaN entries. > Does anyone have an idea what this could possibly be related to or > what > I should check my data for? I used exactly the same parameters as for > all the other subjects. > > Best, > > Frederic > Brand neu: Top Videos auf MSN ClipClub! Schau Dir die besten > > Playlists an >> Play now! ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From tbardouille at ROTMAN-BAYCREST.ON.CA Tue Mar 3 14:50:55 2009 From: tbardouille at ROTMAN-BAYCREST.ON.CA (Tim Bardouille) Date: Tue, 3 Mar 2009 08:50:55 -0500 Subject: Source coherence spectrum Message-ID: Hi there, I'm using fieldtrip to look at corticomuscular coherence (CMC) based on MEG data. I've managed to get source estimates of the CMC in contralateral MI using the DICS method, but I would like to look at the CMC spectrum at this site (over the bandwidth used for source estimation). Is there a way to get out a CMC spectrum (similar to the MEG-EMG spectrum that is output from freqanalysis and freqdescriptives) for a given location in the brain? I've attached the function I wrote to get out the CMC at one frequency. Cheers, Tim Bardouille. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: FldT_source_coherence.m Type: text/x-matlab Size: 1788 bytes Desc: not available URL: From tineke.snijders at DONDERS.RU.NL Tue Mar 3 15:35:18 2009 From: tineke.snijders at DONDERS.RU.NL (Tineke Snijders) Date: Tue, 3 Mar 2009 15:35:18 +0100 Subject: Toolkit course on EEG/MEG data analysis/Nijmegen In-Reply-To: <53972.39517.qm@web15201.mail.cnb.yahoo.com> Message-ID: Hi Luqiang, You should be able to login on the ftp server with username 'anonymous' and your e-mail address as password. Your problem might arise because the computer server (or more specific the spam-filter) has problems with non-western characters. (Sorry about that, we can not change it). You might try to change the settings of your e-mail address (name, etc) to western characters and see if you can login then. Hope this helps, Tineke -----Original Message----- From: FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] On Behalf Of xu luqiang Sent: Friday, February 27, 2009 8:22 AM To: FIELDTRIP at NIC.SURFNET.NL Subject: !!!!!SPAM!!!!! [FIELDTRIP] [FIELDTRIP] Toolkit course on EEG/MEG data analysis/Nijmegen Dear sir, I hope to download tutorial data from your website. I try to login with username 'anonymous' and use my email address "luqiangxu at yahoo.com.cn"as password,but It does not work. Can I login with username 'anonymous' and use my email address "luqiangxu at yahoo.com.cn"as password? thanks luqiang ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From victimontes at HOTMAIL.COM Thu Mar 5 22:20:30 2009 From: victimontes at HOTMAIL.COM (Victoria Eugenia Montes Restrepo) Date: Thu, 5 Mar 2009 16:20:30 -0500 Subject: Source localization with minimum norm Message-ID: Hello all, I'm using the minimumnormestimate() function from the Forwinv toolbox with a four-shell spherical head model, and assuming orthogonal dipoles orientation. When applying this function, I obtain the strengths and power at each source location. If my objective is choosing a single source, which procedure should I use after estimation of these current densities? Thanks in advance, Victoria Eugenia Montes Universidad Nacional de Colombia - Manizales ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From saskia.haegens at DONDERS.RU.NL Fri Mar 6 14:21:19 2009 From: saskia.haegens at DONDERS.RU.NL (Saskia Haegens) Date: Fri, 6 Mar 2009 14:21:19 +0100 Subject: change of default in sourceanalysis: cfg.projectnoise='no' Message-ID: Dear all, For all of you using sourceanalysis: the default setting cfg.projectnoise='yes' has just been changed to cfg.projectnoise='no'. In case you are using the noise estimate (e.g. for the neural activity index), please be aware of this and add cfg.projectnoise='yes' to your scripts. Best, Saskia =============================================== Saskia Haegens PhD student Donders Institute for Brain, Cognition and Behaviour, Centre for Cognitive Neuroimaging P.O. Box 9101 6500 HB Nijmegen The Netherlands tel. : +31 24 36 14731 e-mail: saskia.haegens at donders.ru.nl ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From iversen at NSI.EDU Sat Mar 7 09:57:02 2009 From: iversen at NSI.EDU (John Iversen) Date: Sat, 7 Mar 2009 00:57:02 -0800 Subject: 4D data reading In-Reply-To: <5E2A6C3F-3335-4B61-A24E-D608947C471D@fcdonders.ru.nl> Message-ID: Hello, I haven't found this 4D148.lay file in recent versions of Fieldtrip. Could someone please send it to me? Thank you. Best, John On Oct 7, 2008, at 12:19 AM, Robert Oostenveld wrote: > Dear all, > > I have received the layout from Almu and have added the 4D148.lay > layout to the fieldtirp/template directory (where the other layouts > are now also to be found). See attached for how it looks. > > thanks, > Robert > > > On 6 Oct 2008, at 15:02, Almudena Capilla wrote: > >> Dear Gopa, >> >> I have got a template for the 4D - 148 channels system. I could >> give it to >> the Fieldtrip developers if this is helpful for other users of this >> system. >> >> Best, >> Almu > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/fcdonders/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Mar 9 10:49:32 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 9 Mar 2009 09:49:32 +0000 Subject: 4D data reading In-Reply-To: Message-ID: Dear John, Please see attached file. It seems the file was in fieldtrip's cvs- repository but not yet mentioned in the shellscripts controlling which files from the repository end up in the release version of fieldtrip. I changed this, and hopefully all will be well again as of tomorrow. Best, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: 4D148.lay Type: application/octet-stream Size: 4608 bytes Desc: not available URL: -------------- next part -------------- On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > Hello, > > I haven't found this 4D148.lay file in recent versions of > Fieldtrip. Could someone please send it to me? > > Thank you. > > Best, > > John ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From iversen at NSI.EDU Mon Mar 9 17:11:55 2009 From: iversen at NSI.EDU (John Iversen) Date: Mon, 9 Mar 2009 09:11:55 -0700 Subject: 4D data reading In-Reply-To: <2BC1183D-2927-4290-A91C-5790F5191423@psy.gla.ac.uk> Message-ID: Many thanks, Jan-Mathijs. John On Mar 9, 2009, at 2:49 AM, jan-mathijs schoffelen wrote: > Dear John, > > Please see attached file. It seems the file was in fieldtrip's cvs- > repository but not yet mentioned in the shellscripts controlling > which files from the repository end up in the release version of > fieldtrip. I changed this, and hopefully all will be well again as > of tomorrow. > > Best, > > Jan-Mathijs > > > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. > <4D148.lay> > > > On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > >> Hello, >> >> I haven't found this 4D148.lay file in recent versions of >> Fieldtrip. Could someone please send it to me? >> >> Thank you. >> >> Best, >> >> John > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html > and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From ghocepie at ULB.AC.BE Mon Mar 9 18:12:38 2009 From: ghocepie at ULB.AC.BE (Gatien Hocepied) Date: Mon, 9 Mar 2009 18:12:38 +0100 Subject: Source localization with minimum norm In-Reply-To: Message-ID: Hello all, I ‘m facing serious problems with this function How can I define the dip.inside and dip.outside ? Besides, for 2 dipoles, this line seems to be incorrect : dip.leadfield{i} = compute_leadfield(dip.pos(i,:), grad, vol, 'reducerank', reducerank, 'normalize', normalize, 'normalizeparam', normalizeparam) * dip.mom(:,i); It seems to be a dimension problem between the matrix given by compute_leadfield and dip.mom (1x6 in case of 2 dipoles ) Thx in advance, Gatien Hocepied De : FieldTrip discussion list [mailto:FIELDTRIP at NIC.SURFNET.NL] De la part de Victoria Eugenia Montes Restrepo Envoyé : jeudi 5 mars 2009 22:21 À : FIELDTRIP at NIC.SURFNET.NL Objet : [FIELDTRIP] Source localization with minimum norm Hello all, I'm using the minimumnormestimate() function from the Forwinv toolbox with a four-shell spherical head model, and assuming orthogonal dipoles orientation. When applying this function, I obtain the strengths and power at each source location. If my objective is choosing a single source, which procedure should I use after estimation of these current densities? Thanks in advance, Victoria Eugenia Montes Universidad Nacional de Colombia - Manizales ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From venug001 at BAMA.UA.EDU Mon Mar 9 18:34:54 2009 From: venug001 at BAMA.UA.EDU (Gopakumar Venugopalan) Date: Mon, 9 Mar 2009 12:34:54 -0500 Subject: 4D data reading In-Reply-To: Message-ID: Hello all, I was told that each system has its own xyz locations, which may or may not differ, very slightly, from other machines. Maybe it is best to create your own 148.lay using the channels names, and x,y,z locations that are idiosyncratic to your own machine. regards gopa Quoting John Iversen : > Many thanks, Jan-Mathijs. > > John > > On Mar 9, 2009, at 2:49 AM, jan-mathijs schoffelen wrote: > > > Dear John, > > > > Please see attached file. It seems the file was in fieldtrip's cvs- > > > repository but not yet mentioned in the shellscripts controlling > > which files from the repository end up in the release version of > > fieldtrip. I changed this, and hopefully all will be well again as > > > of tomorrow. > > > > Best, > > > > Jan-Mathijs > > > > > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > > > of the FieldTrip toolbox, to share experiences and to discuss new > > > ideas for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html > > and http://www.ru.nl/neuroimaging/fieldtrip. > > <4D148.lay> > > > > > > On Mar 7, 2009, at 8:57 AM, John Iversen wrote: > > > >> Hello, > >> > >> I haven't found this 4D148.lay file in recent versions of > >> Fieldtrip. Could someone please send it to me? > >> > >> Thank you. > >> > >> Best, > >> > >> John > > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > > > of the FieldTrip toolbox, to share experiences and to discuss new > > > ideas for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html > > and http://www.ru.nl/neuroimaging/fieldtrip. > > ---------------------------------- > The aim of this list is to facilitate the discussion between users of > the FieldTrip toolbox, to share experiences and to discuss new ideas > for MEG and EEG analysis. See also > http://listserv.surfnet.nl/archives/fieldtrip.html and > http://www.ru.nl/neuroimaging/fieldtrip. > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From lhunt at FMRIB.OX.AC.UK Wed Mar 11 15:58:03 2009 From: lhunt at FMRIB.OX.AC.UK (Laurence Hunt) Date: Wed, 11 Mar 2009 14:58:03 +0000 Subject: TopoplotER for Neuromag 306 Message-ID: Hi all, Quick question from a Fieldtrip newbie - when using topoplotER on neuromag 306 data, it appears to give unreasonable results. I suspect this is most likely because two out of three sensors are magnetometers, whereas every third sensor is a planar gradiometer, and the scales on these two types of sensor are different by a factor of ten. One thing I could do is edit prepare_layout to only return planar gradiometers or magnetometers, but before I do this, do people have any other solutions for combining these two different types of sensor that they already use for neuromag data? Apologies if this has already been discussed elsewhere. Cheers, Laurence =========================================== Laurence Hunt, DPhil Student Centre for Functional MRI of the Brain (FMRIB), University of Oxford lhunt at fmrib.ox.ac.uk Phone: (+44)1865-(2)22738 =========================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From michael.wibral at WEB.DE Fri Mar 13 17:32:02 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Fri, 13 Mar 2009 17:32:02 +0100 Subject: freqstatistics, Message-ID: ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From michael.wibral at WEB.DE Fri Mar 13 17:35:33 2009 From: michael.wibral at WEB.DE (Michael Wibral) Date: Fri, 13 Mar 2009 17:35:33 +0100 Subject: freqstatistics; data 1versus data 2 Message-ID: Dear all, I have a quick question concerning freqstatistics(cfg, data1, data2): If I get a positive raw effect at some time t and frequency f that means that: data2(t,f) > data1(t,f), correct? It's a bit difficult to follow the transformation of data1, data2 and the design variables through the code of the various layers of statfuns. Best Regards, Michael ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:07:23 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:07:23 +0100 Subject: TopoplotER for Neuromag 306 In-Reply-To: <6CCFCB69-51E0-45B0-A87C-459181B54D9F@fmrib.ox.ac.uk> Message-ID: Hi Laurence, On 11 Mar 2009, at 15:58, Laurence Hunt wrote: > Quick question from a Fieldtrip newbie - when using topoplotER on > neuromag 306 data, it appears to give unreasonable results. I > suspect this is most likely because two out of three sensors are > magnetometers, whereas every third sensor is a planar gradiometer, > and the scales on these two types of sensor are different by a > factor of ten. That is most likely correct. If you are plotting physical data (i.e. not some sort of normalized statistic), the planar gradiometers have T/ m units and the magnetometers have T units. > One thing I could do is edit prepare_layout to only return planar > gradiometers or magnetometers, but before I do this, do people have > any other solutions for combining these two different types of > sensor that they already use for neuromag data? you can use chantype to select the planar and magnetometers. It would indeed be nice to have a cfg.chantype option in plrepare layout, where if specified different from 'all' would use a subset of channels. Another function that you shoudl look into is combineplanar. We use that for the ctf data, where in megplanar we convert the axial gradients in planar gradients. Then we do spectral estimation, and after that we do combineplanar to combine the power of the 2 planar (horizontal and vertical) channel at each location. I am not sure whether it will work out of the box for neuromag data (it was initially written for ctf data), but rudimentary support for neuromag is present. That should not be difficult to improve if needed, see line 205 where the two planar channel sets are determined. The planarchannelset helper function contaimns hard-coded lists, from which I am not sure whether they apply precisely the same to all neuromag systems (this list was determined from a particular system). best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:19:15 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:19:15 +0100 Subject: Source localization with minimum norm In-Reply-To: <001e01c9a0da$3f5ca280$be15e780$@ac.be> Message-ID: Hi Gatien, On 9 Mar 2009, at 18:12, Gatien Hocepied wrote: > I ‘m facing serious problems with this function… How can I define > the dip.inside and dip.outside ? If you access the functino through the fieldtrip sourceanalysis function (and not directly as low-level function), the prepare_dipole_grid function will set up the 3D grid with all dipoles and for each dipole determine whether it is insode or outside the brain (based on the volume conduction model). The function that is notmally called to determine the inside/outide aspect of each gridpoiunt is the inside_vol function (see forwinv/private). If you know that all dipoles are inside the brain, then you can specify the dip.inside vector as a boolean NdipolesX1 vector with all elements being true. Grid positions taht are outside the brain (and that therefore should not be included in the inverse estimate) should be marked as false. To understand this, please consider a 3D box-like grid encompassing the complete brain. The corners of the box will always be outside the brain, so using a 3D box-like grid means that ~30% of the considered grid points is outside the brain and should not be scanned (in case of a beamformer method) or included in the distributed model (in your case). > Besides, for 2 dipoles, this line seems to be incorrect : > > dip.leadfield{i} = compute_leadfield(dip.pos(i,:), grad, vol, > 'reducerank', reducerank,'normalize', normalize, 'normalizeparam', > normalizeparam) * dip.mom(:,i); dip.pos should be a Ndipoles*3 matrix, causing the leadfield to become Nchans*3. That is then (optionally) multiplied with the 3*1 fixed dipole orientation (e.g. constrained by the orientation of the cortical sheet). The concatenation of the leadfields to NchansX(3*Ndipoles) or NchansXNdipoles (in case of fixed orientation) is done from line 109 onwards. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Mon Mar 16 22:22:47 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Mon, 16 Mar 2009 22:22:47 +0100 Subject: Source localization with minimum norm In-Reply-To: Message-ID: On 5 Mar 2009, at 22:20, Victoria Eugenia Montes Restrepo wrote: > I'm using the minimumnormestimate() function from the Forwinv > toolbox with a four-shell spherical head model, and assuming > orthogonal dipoles orientation. When applying this function, I > obtain the strengths and power at each source location. If my > objective is choosing a single source, which procedure should I use > after estimation of these current densities? Hi Victoria, Why do you start with a distributed source model (which is what minimumnormestimate is for) if you are interested in modelling the data with a single dipole? If you think that a single dipole is able to explain the data, you should search for a single dipole solution. That may mean that you also shoudl search for the optimal position and not only the optimal strength of all dipoles at the same time (which is only what MNE does). Perhaps you should look at the fieldtrip/ dipolefitting function. best regards, Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From christine.gruetzner at GOOGLEMAIL.COM Fri Mar 20 10:47:17 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Fri, 20 Mar 2009 10:47:17 +0100 Subject: timelockstatistics Message-ID: Dear Fieldtrippers, I have some trouble using 'timelockstatistics' for task vs baseline comparisons (the code I'm using is pasted below). In the output of timelockstatistics, I get only one (!) time sample (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, it is possible to plot the whole time window I specified in cfg.latency - even though the topography seems to be the same for each time bin... The steps I do before computing timelockstatistics are the following: 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately 2) Compute timelockgrandaverage for task and baseline 3) Use the code below to compute timelockstatistics Can anybody help me with this issue? I would be very glad about any suggestions on what is going wrong here!! Best Christine cfg = []; cfg.grad = timelockUprightTask{1}.grad; cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; cfg.statistic = 'actvsblT'; cfg.clusterthreshold = 'parametric'; cfg.clusteralpha = 0.05; cfg.alpha = 0.05; cfg.makeclusters = 'yes'; cfg.minnbchan = 3; cfg.parameter = 'individual'; cfg.clusterstatistic = 'maxsum'; cfg.onetwo = 'twosided'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.numrandomization = 1000; cfg.latency = [0 0.2]; nSubjects = length(filesUprightTask); a = [1:nSubjects]; b = ones(1,nSubjects); cfg.design = [a a; b (2*b)]; cfg.uvar = 1; cfg.ivar = 2; timelockstat = timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From e.maris at DONDERS.RU.NL Fri Mar 20 11:30:25 2009 From: e.maris at DONDERS.RU.NL (Eric Maris) Date: Fri, 20 Mar 2009 11:30:25 +0100 Subject: timelockstatistics In-Reply-To: <841d3140903200247v185dd15eo57345d197a1a147b@mail.gmail.com> Message-ID: Hi Christine, I have some trouble using 'timelockstatistics' for task vs baseline comparisons (the code I'm using is pasted below). In the output of timelockstatistics, I get only one (!) time sample (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, it is possible to plot the whole time window I specified in cfg.latency - even though the topography seems to be the same for each time bin... The steps I do before computing timelockstatistics are the following: 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately 2) Compute timelockgrandaverage for task and baseline 3) Use the code below to compute timelockstatistics Can anybody help me with this issue? I would be very glad about any suggestions on what is going wrong here!! For permutation statistics with actvsblT to make sense, the number of time samples in the activation and the baseline data must be equal. This does not appear to be the case in your configuration for timelockanalysis. Good luck, Eric Maris Best Christine cfg = []; cfg.grad = timelockUprightTask{1}.grad; cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; cfg.statistic = 'actvsblT'; cfg.clusterthreshold = 'parametric'; cfg.clusteralpha = 0.05; cfg.alpha = 0.05; cfg.makeclusters = 'yes'; cfg.minnbchan = 3; cfg.parameter = 'individual'; cfg.clusterstatistic = 'maxsum'; cfg.onetwo = 'twosided'; cfg.method = 'montecarlo'; cfg.correctm = 'cluster'; cfg.numrandomization = 1000; cfg.latency = [0 0.2]; nSubjects = length(filesUprightTask); a = [1:nSubjects]; b = ones(1,nSubjects); cfg.design = [a a; b (2*b)]; cfg.uvar = 1; cfg.ivar = 2; timelockstat = timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. http://listserv.surfnet.nl/archives/fieldtrip.html http://www.ru.nl/fcdonders/fieldtrip/ ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.gruetzner at GOOGLEMAIL.COM Fri Mar 20 14:52:46 2009 From: christine.gruetzner at GOOGLEMAIL.COM (Christine Gruetzner) Date: Fri, 20 Mar 2009 14:52:46 +0100 Subject: timelockstatistics In-Reply-To: <20090320103024.776BFE6AA9@smtp.ru.nl> Message-ID: Hi Eric, Sorry, this was just a little mistake in writing in my mail; I actually use the same number of time samples for the task and the baseline (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.05])!! Best Christine 2009/3/20 Eric Maris > Hi Christine, > > > > > > > > I have some trouble using 'timelockstatistics' for task vs baseline > comparisons (the code I'm using is pasted below). > > In the output of timelockstatistics, I get only one (!) time sample (prob, > stat, mask: 266 (channels) x 1 (time)), even if I specify the parameter > cfg.latency (e.g. [0 0.2]). However, when I plot the statistics afterwards, > it is possible to plot the whole time window I specified in cfg.latency - > even though the topography seems to be the same for each time bin... > > The steps I do before computing timelockstatistics are the following: > 1) Compute timelockanalyis separately for the task (cfg.latency = [0.05 > 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately > 2) Compute timelockgrandaverage for task and baseline > 3) Use the code below to compute timelockstatistics > > Can anybody help me with this issue? > I would be very glad about any suggestions on what is going wrong here!! > > > > For permutation statistics with actvsblT to make sense, the number of time > samples in the activation and the baseline data must be equal. This does not > appear to be the case in your configuration for timelockanalysis. > > > > Good luck, > > > > Eric Maris > > > > > > > > > > > > > Best > Christine > > > cfg = []; > cfg.grad = timelockUprightTask{1}.grad; > cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '-MRP56', > '-MRT21', '-ML021', '-MRO44', '-MRT47'}; > cfg.statistic = 'actvsblT'; > cfg.clusterthreshold = 'parametric'; > cfg.clusteralpha = 0.05; > cfg.alpha = 0.05; > cfg.makeclusters = 'yes'; > cfg.minnbchan = 3; > cfg.parameter = 'individual'; > cfg.clusterstatistic = 'maxsum'; > cfg.onetwo = 'twosided'; > cfg.method = 'montecarlo'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 1000; > cfg.latency = [0 0.2]; > nSubjects = length(filesUprightTask); > a = [1:nSubjects]; > b = ones(1,nSubjects); > cfg.design = [a a; b (2*b)]; > cfg.uvar = 1; > cfg.ivar = 2; > timelockstat = > timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); > > > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users of the > FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and > EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > -- Christine Gruetzner, geb.Tillmann Max-Planck-Institut für Hirnforschung Abt. Neurophysiologie Deutschordenstr. 46 60528 Frankfurt am Main Germany Phone: +49 (0)69/6301-83225 E-Mail: tillmann at mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From lulswinnik at GMAIL.COM Mon Mar 23 19:19:23 2009 From: lulswinnik at GMAIL.COM (Katya Vinnik) Date: Mon, 23 Mar 2009 19:19:23 +0100 Subject: plots and stats with biosemi128.lay Message-ID: Dear FT users, has anyone of you encountered this warning? Duplicate x-y data points detected: using average of the z values. I'm simply plotting my data with cfg.layout = 'biosemi128.lay'; and it gives me strange plots like the one here: http://picasaweb.google.com/lh/photo/qmd3BgpeEDegPo4kHdRW0w?feat=directlink basically data from channels B19 and 21 and D22 and 24 are overlayed (circled in red on the pictures). This message appears also with topoplot functions. In the layout file, howether ,positions of this electrodes are different (see below). Do you think it can affect cluster-based multiple comparison correction? For example, if I use cfg.layout = 'biosemi128.lay'; cfg.correctm = 'cluster'; [stat] = freqstatistics(cfg,x,y) does it calcultate it properly? Thank you, Best regards, Katya P.S. positions of this electrodes from biosemi128.lay: 51 0.521467 -0.301069 0.180000 0.140000 B19 53 0.602139 0.000000 0.180000 0.140000 B21 118 -1.404990 -0.000000 0.180000 0.140000 D22 120 -1.527114 -0.496189 0.180000 0.140000 D24 ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Hanna.Renvall at PSYCHOLOGY.UNIMAAS.NL Tue Mar 24 08:44:31 2009 From: Hanna.Renvall at PSYCHOLOGY.UNIMAAS.NL (Renvall Hanna (PSYCHOLOGY)) Date: Tue, 24 Mar 2009 08:44:31 +0100 Subject: VL: aivoAALTO/open positions in Finland Message-ID: Dear Colleagues Our newly established multidisciplinary "aivoAALTO" research project opens positions in the field of systems-level human brain imaging and related research, with a strong focus on social interaction in natural settings, including economic decision making, cinema viewing, and methodological development. http://www.aaltoyliopisto.info/en/news/funding-to-aalto-university-s-aivoaalto-research-project The project involves Helsinki University of Technology (TKK, www.tkk.fi ), Helsinki School of Economics (HSE, www.hse.fi ) and Helsinki University of Art and Design (TAIK, www.taik.fi ). These three schools are just merging to form a new Aalto University ("Aalto", meaning wave, honors the famous Finnish architect Alvar Aalto). The positions, available immediately for up to 3 years, are the following: . 1 PhD student in neuroeconomics and decision making . 1 PhD student in neurocinematics . 1 PhD student in brain-imaging-related signal analysis . 3 postdoctoral positions in human brain imaging and related research . 2 senior scientist positions in human brain imaging and related research For further information, see http://neuro.ltl.hut.fi/~hari/aivoAALTO_positions_March2009.pdf -- Riitta Hari, prof. Brain Research Unit Low Temperature Laboratory Helsinki University of Technology Puumiehenkuja 2, room #250 02015 TKK, Espoo, Finland tel +358 9 451 2959, fax +358 9 451 3508 hari at neuro.hut.fi http://neuro.hut.fi (Brain Research Unit) http://ltl.tkk.fi/wiki/LTL/Contact_information (How to find us) Advanced Magnetic Imaging Centre (AMI) Helsinki University of Technology http://www.ami.hut.fi ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at FCDONDERS.RU.NL Tue Mar 24 14:55:45 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 24 Mar 2009 14:55:45 +0100 Subject: timelockstatistics In-Reply-To: <841d3140903200652m794c3eb7x4ce8bae7a8c84c7f@mail.gmail.com> Message-ID: Hi Christine With timelockstatsistics you can only test the exchangeability for data points that can be exchanged one-to-one. The data is usually arranged in a Ntrials*Nchans*Ntime matrix and you should have such a matrix both for the baseline and activation window. You should prepare your data in such a way that the channels (of course) but also that the timepoints match. The underlying function will make the data selection based on the overlap bwteen the two input datasets that you hand over to timelockstatistics. So if you want to compare paired data, also the time-axis of the two datasets should be the same. Resegmenting the data can be done using redefinetrial, i.e. cfg = [] cfg.toilim = [0.050 0.400]; dataA = redefinetrial(cfg, data_org) cfg.toilim = [-0.400 -0.050]; dataB = redefinetrial(cfg, data_org) Subsequently you can assign the same time axis to both, either by shifting the time-axis of each trial for i=1:ntrials dataA.time{i} = dataA.time{i} - min(dataA.time{i}) dataB.time{i} = dataB.time{i} - min(dataB.time{i}) end or simply by copying the one time-axis into the other dataB.time = dataA.time In the second case you should be carefull that you don't have a mismatch in the number of samples in the data and in the time axis. A single sample is sometimes easy to loose due to rounding off errors. After that, you can do cfg = [] cfg.keeptrials = 'yes' avgA = timelockanalysis(cfg, dataA); avgB = timelockanalysis(cfg, dataB); and test the two conditions against each other. I am not sure about the applicability of actvsblT as statistic here, but the trick above applies in general and hence should work with any statistic. Depending on the statistic that you use, you might have to be carefull about a difference in the baselining for the pre- and post- stimulus window. I.e. if you subtract the baseline estimated on the pre-stimulus window, then the pre-stimulus window will have less variance over trials regardless of the presence of an effect. best regards, Robert On 20 Mar 2009, at 14:52, Christine Gruetzner wrote: > Hi Eric, > > Sorry, this was just a little mistake in writing in my mail; I > actually use the same number of time samples for the task and the > baseline (cfg.latency = [0.05 0.4]) and the baseline (cfg.latency = > [-0.4 -0.05])!! > > Best > Christine > > > > 2009/3/20 Eric Maris > Hi Christine, > > > > > I have some trouble using 'timelockstatistics' for task vs baseline > comparisons (the code I'm using is pasted below). > > In the output of timelockstatistics, I get only one (!) time sample > (prob, stat, mask: 266 (channels) x 1 (time)), even if I specify the > parameter cfg.latency (e.g. [0 0.2]). However, when I plot the > statistics afterwards, it is possible to plot the whole time window > I specified in cfg.latency - even though the topography seems to be > the same for each time bin... > > The steps I do before computing timelockstatistics are the following: > 1) Compute timelockanalyis separately for the task (cfg.latency = > [0.05 0.4]) and the baseline (cfg.latency = [-0.4 -0.5]) separately > 2) Compute timelockgrandaverage for task and baseline > 3) Use the code below to compute timelockstatistics > > Can anybody help me with this issue? > I would be very glad about any suggestions on what is going wrong > here!! > > > For permutation statistics with actvsblT to make sense, the number > of time samples in the activation and the baseline data must be > equal. This does not appear to be the case in your configuration for > timelockanalysis. > > > Good luck, > > > Eric Maris > > > > > > > > Best > Christine > > > cfg = []; > cfg.grad = timelockUprightTask{1}.grad; > cfg.channel = {'MEG', '-MLP12', '-MRC14', '-MLT41', '-MRC25', '- > MRP56', '-MRT21', '-ML021', '-MRO44', '-MRT47'}; > cfg.statistic = 'actvsblT'; > cfg.clusterthreshold = 'parametric'; > cfg.clusteralpha = 0.05; > cfg.alpha = 0.05; > cfg.makeclusters = 'yes'; > cfg.minnbchan = 3; > cfg.parameter = 'individual'; > cfg.clusterstatistic = 'maxsum'; > cfg.onetwo = 'twosided'; > cfg.method = 'montecarlo'; > cfg.correctm = 'cluster'; > cfg.numrandomization = 1000; > cfg.latency = [0 0.2]; > nSubjects = length(filesUprightTask); > a = [1:nSubjects]; > b = ones(1,nSubjects); > cfg.design = [a a; b (2*b)]; > cfg.uvar = 1; > cfg.ivar = 2; > timelockstat = > timelockstatistics(cfg,timelockUprightTaskGA,timelockUprightBaseGA); > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > > > > > -- > Christine Gruetzner, geb.Tillmann > Max-Planck-Institut für Hirnforschung > Abt. Neurophysiologie > Deutschordenstr. 46 > 60528 Frankfurt am Main > Germany > > Phone: +49 (0)69/6301-83225 > E-Mail: tillmann at mpih-frankfurt.mpg.de > http://www.mpih-frankfurt.mpg.de/global/Np/Staff/tillmann.htm > > > ---------------------------------- > > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. > > http://listserv.surfnet.nl/archives/fieldtrip.html > > http://www.ru.nl/fcdonders/fieldtrip/ > ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Tue Mar 24 15:01:20 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Tue, 24 Mar 2009 15:01:20 +0100 Subject: freqstatistics; data 1versus data 2 In-Reply-To: <920739784@web.de> Message-ID: Hi Michael On 13 Mar 2009, at 17:35, Michael Wibral wrote: > Dear all, > > I have a quick question concerning freqstatistics(cfg, data1, data2): > If I get a positive raw effect at some time t and frequency f that > means that: data2(t,f) > data1(t,f), correct? > It's a bit difficult to follow the transformation of data1, data2 > and the design variables through the code of the various layers of > statfuns. The raw effect (i.e. the difference in the mean value in both conditions) is not computed by freqstatistics, only the statistic of the effect (usually the t-value) and its significance. But a positive t-value means that htere is a positive effect in the difference of the mean values. You could simply add the raw effect to the statfun, e.g. in statfun_indepsamplesT by changing line 109 into s.stat = (avg1 - avg2)./sqrt(varc); % this is the t-value s.effect = (avg1 - avg2); % this is the raw effect any parameter that is returned by the statfun and that has the correct size (meaning that it can be reshaped into the original 3D array) will be automatically passed along to the outside of the function, i.e. to the command line on which you call freqstatistics. best regards Robert ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From katharina.matz at UNI-KONSTANZ.DE Wed Mar 25 09:48:52 2009 From: katharina.matz at UNI-KONSTANZ.DE (Katharina Matz) Date: Wed, 25 Mar 2009 09:48:52 +0100 Subject: how to interpolate bad channels?? Message-ID: Dear FT users, does anyone of you know how to interpolate bad channels? Interactive preprocessing allows me to exclude channels but I'd like to keep them. Thank you! Best regards, Katharina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From rmontefusco at MED.UCHILE.CL Wed Mar 25 22:51:12 2009 From: rmontefusco at MED.UCHILE.CL (Rodrigo A. Montefusco Siegmund) Date: Wed, 25 Mar 2009 17:51:12 -0400 Subject: eog artifact rejection Message-ID: Hello everyone I'm trying to implement a script to detect and remove artifacts. One using artifact_eog to eliminate artifacts in the EOG channels. I'm also looking to eliminate a very large amplitudes in the signal. The problem is that the script artifact_eog doesn't work on my dataset derived from my own trialfun script. Error in ==> fieldtrip-20080701\private\filetype at 225 [p, f, x] = fileparts(filename); Error in ==> fieldtrip-20080701\private\dataset2files at 66 switch filetype(cfg.dataset) Error in ==> artifact_zvalue at 155 cfg = dataset2files(cfg); Error in ==> artifact_eog at 137 [tmpcfg, artifact] = artifact_zvalue(tmpcfg); My raw data is obtained from an amplifier built in my laboratory, so we collect data very raw, without file header or anything similar. The file .dat is turned to .mat, then that file is loaded to the workspace, and then I process it with my trialfun. with that, I create a structure "data" which contains data = trial: (1x60 cell) label: (1x24 cell) fsample: 250 time: (1x60 cell) in the format for fieldtrip. also generates a hdr hdr = Fs: 250 nChans: 24 nSamples: 750 nSamplesPre: 250 nTrials: 60 label: (1x24 cell) FirstTimeStamp: 1 TimeStampPerSample: 1 and the trl that is requested by the documentation. How can I use the artifact_eog on data generated in the format that I mentioned above? Thanks a lot and excuse my english best regards Rodrigo -- ============================================================== Rodrigo A. Montefusco Siegmund Doctorado en Ciencias Biomédicas Programa de Fisiología y Biofí­sica I. C. B. M. Facultad de Medicina Universidad de Chile Centro de Neurociencias Integradas Iniciativa Cientí­fica Milenio Fono: 56 09 82793847 email: rmontefusco at med.uchile.cl =============================================================== ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Wed Mar 25 22:34:05 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Wed, 25 Mar 2009 21:34:05 +0000 Subject: eog artifact rejection In-Reply-To: <1976.172.16.72.117.1238017872.squirrel@correo.med.uchile.cl> Message-ID: Dear Rodrigo, It looks as if you are almost there! I suspect the problem occurs because you use a version of fieldtrip which cannot do artifact identification on data which is already present in memory. This version always tries to read in data from a file, and fails in your case. Probably the problem solves itself when you download the most recent version. I assume that you call artifact_eog as follows: cfg = artifact_eog(cfg, data) The second input argument data is of course crucial here. Keep up the good work! Cheers, Jan-Mathijs On Mar 25, 2009, at 9:51 PM, Rodrigo A. Montefusco Siegmund wrote: > Hello everyone > > I'm trying to implement a script to detect and remove artifacts. > One using > artifact_eog to eliminate artifacts in the EOG channels. I'm also > looking > to eliminate a very large amplitudes in the signal. > > The problem is that the script artifact_eog doesn't work on my dataset > derived from my own trialfun script. > > Error in ==> fieldtrip-20080701\private\filetype at 225 > [p, f, x] = fileparts(filename); > > Error in ==> fieldtrip-20080701\private\dataset2files at 66 > switch filetype(cfg.dataset) > > Error in ==> artifact_zvalue at 155 > cfg = dataset2files(cfg); > > Error in ==> artifact_eog at 137 > [tmpcfg, artifact] = artifact_zvalue(tmpcfg); > > > My raw data is obtained from an amplifier built in my laboratory, > so we > collect data very raw, without file header or anything similar. > > The file .dat is turned to .mat, then that file is loaded to the > workspace, and then I process it with my trialfun. with that, I > create a > structure "data" which contains > > data = > trial: (1x60 cell) > label: (1x24 cell) > fsample: 250 > time: (1x60 cell) > > in the format for fieldtrip. also generates a hdr > > hdr = > Fs: 250 > nChans: 24 > nSamples: 750 > nSamplesPre: 250 > nTrials: 60 > label: (1x24 cell) > FirstTimeStamp: 1 > TimeStampPerSample: 1 > > and the trl that is requested by the documentation. > > How can I use the artifact_eog on data generated in the format that I > mentioned above? > > Thanks a lot and excuse my english > > best regards > > Rodrigo > > -- > ============================================================== > Rodrigo A. Montefusco Siegmund > Doctorado en Ciencias Biomédicas > Programa de Fisiología y Biofí sica > I. C. B. M. Facultad de Medicina > Universidad de Chile > Centro de Neurociencias Integradas > Iniciativa Cientí fica Milenio > Fono: 56 09 82793847 > email: rmontefusco at med.uchile.cl > =============================================================== > > ---------------------------------- > The aim of this list is to facilitate the discussion between users > of the FieldTrip toolbox, to share experiences and to discuss new > ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/ > archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Mar 26 09:35:51 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 26 Mar 2009 09:35:51 +0100 Subject: how to interpolate bad channels?? In-Reply-To: <1F841765-BFCA-4154-B7CE-A7421D77D1A4@uni-konstanz.de> Message-ID: Dear Katharina You can use the channelrepair function for that. best regards, Robert On 25 Mar 2009, at 9:48, Katharina Matz wrote: > Dear FT users, > > does anyone of you know how to interpolate bad channels? Interactive > preprocessing allows me to exclude channels but I'd like to keep them. > > Thank you! > Best regards, > Katharina ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From r.oostenveld at FCDONDERS.RU.NL Thu Mar 26 18:01:57 2009 From: r.oostenveld at FCDONDERS.RU.NL (Robert Oostenveld) Date: Thu, 26 Mar 2009 18:01:57 +0100 Subject: multisphere and CTF 3rd order gradients Message-ID: Dear FieldTrip/CTF users, I have extended the prepare_vol_sens function (which is a helper function for sourceanalysis and dipolefitting) so that it can also prepare multisphere ("local spheres") models in case the gradiometer array is synthetically balanced (e.g. CTF 3rd gradients). The change also required an update to the read_ctf_hdm function. The updates will be available in the public release version of fieldtrip on the ftp server this evening. best regards, Robert PS at the moment it will not yet work for multisphere models created using fieldtrip/prepare_localspheres, but only for the ones created using the CTF software and stored in a *.hdm file. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From sdmuthu at CARDIFF.AC.UK Fri Mar 27 17:20:36 2009 From: sdmuthu at CARDIFF.AC.UK (Suresh Muthukumaraswamy) Date: Fri, 27 Mar 2009 17:20:36 +0100 Subject: ICA on 275ch MEG... removing artifacts Message-ID: Hi Everybody, I have started playing with the componentanalysis and rejectcomponent functions to try to remove eye artefacts from CTF 275 channel MEG data. The aim is to try to remove eye artefacts and then run SAM analyses. Technically, I have the approach working fine and it does seem to reduce the eye artefact in the MEG channels near the front of the helmet (I have EOG traces as well) Specifically I was wondering Typically how many components do people normally estimate and then how many of these would normally get rejected as containing eye artefact? 270 components is alot to look through! I see one can limit the number of components the function can return.... Do people normally reject solely on topography or do they do a frequency analysis of the component time-course or perhaps other things? Moreoever, I was also wondering if anyone had carried out any kind of systematic comparison between this approach for MEG compared to traditional EEG approaches to this problem (e.g. projecting out the EOG channels)? Thanks in advance Suresh ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From soren.r.christensen at GSK.COM Fri Mar 27 18:05:43 2009 From: soren.r.christensen at GSK.COM (Soren Rahn Christensen) Date: Fri, 27 Mar 2009 17:05:43 +0000 Subject: Soren R Christensen is out of the office. Message-ID: I will be out of the office starting 27-Mar-2009 and will not return until 30-Mar-2009. I'll be back Tuesday 31st ----------------------------------------------------------- This e-mail was sent by GlaxoSmithKline Services Unlimited (registered in England and Wales No. 1047315), which is a member of the GlaxoSmithKline group of companies. The registered address of GlaxoSmithKline Services Unlimited is 980 Great West Road, Brentford, Middlesex TW8 9GS. ----------------------------------------------------------- ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wibral at BIC.UNI-FRANKFURT.DE Fri Mar 27 18:41:54 2009 From: wibral at BIC.UNI-FRANKFURT.DE (Michael Wibral) Date: Fri, 27 Mar 2009 18:41:54 +0100 Subject: ICA on 275ch MEG... removing artifacts Message-ID: Dear Suresh, I will try to answer your questions to my best knowledge (we are doing both MEG and EEG ICA here) below. Sorry if the response got a bit lengthy. Best, Michael > -----Ursprüngliche Nachricht----- > Von: "Suresh Muthukumaraswamy" > Gesendet: 27.03.09 17:22:35 > An: FIELDTRIP at NIC.SURFNET.NL > Betreff: [FIELDTRIP] ICA on 275ch MEG... removing artifacts > Hi Everybody, > I have started playing with the componentanalysis and rejectcomponent > functions to try to remove eye artefacts from CTF 275 channel MEG data. The > aim is to try to remove eye artefacts and then run SAM analyses. > Technically, I have the approach working fine and it does seem to reduce the > eye artefact in the MEG channels near the front of the helmet (I have EOG > traces as well) > Specifically I was wondering > > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... In EEG we saw a definite improvement of the removal of blink artifacts when going from 64 to 128 channels - this suggests to do as many components as possible. There is a second reason to do as many components as possible: In order to search less components than sensors you need to reduce the dimensionality of your data - typically using PCA as a preprocessing step. The directions of PCA dimensions that you remove are at odd angles with the later ICA component axes - hence by doing PCA you change every later IC a little bit, something that doesn't happen when not using PCA. This information is lost, because the data you'll backproject for beamforming are the cleaned data and have a dimensionality of (number of sensors)-(dimensions removed by PCA)-(dimensions removed as artefact components). There are algorithms that can reduce dimensions by taking out ICs during the estimation process - in fact we're working on those and you may consider trying those (contact Georg Turi: turi at mpih-frankfurt.mpg.de). Note that deflationary ICA - only run up to the desired number of components - is NOT a option, as the order in which components are found is undefined. By backprojecting these lower dimensional data to your sensors you encounter an additional mathematical problem, when planning to do beamforming: technically the covariance matrix of your data is rank deficient, because you have more sensors (aka columns or rows of the cov-matrix) than dimensions in your data (because you removed some of them). This theoretically would cause an error in your analysis. The fact that you did not encounter such an error is because you most likely use regularization (lambda in Fieldtrip). This adds a scaled unity matrix to your cov-matrix and helps you to get full dimensionality again. How many components should be removed for eyeartefacts? Difficult to say, there is usually one or two blink components. Eye movements are a totally different story. The signals from eye-movements VIOLATE the ICA mixing model which uses stationany, not moving sources - i.e. in theory they can't be modeled as independent components at all. Sometimes you may be lucky that exact rotations of the eyeball can be modelled as two orthogonal sationary sources with sinusoidal modulations - if that is the case you should get roughly 4 components:2 for each principal axis of rotation. But be careful, because this really means abusing the ICA mixing model! How many components can you estimate at all? For algorithms like Fastica or INFOMAX a stable estimation requires a number of samples bigger than 20*(number of sensors)^2. That's what it says as a rule of thumb in the EEGLAB tutorial. The mathematical limit is 3*(number of sensors)^2 (this is the Cramer-Rao lower bound). Below this an estimation is mathematically impossible. Some more modern algorithms (EFICA) claim to almost reach the Cramer-Rao lower bound, you may consider using these. If you get close to this threshold I we strongly recommend using a statistical validation of your results, e.g. using ICASSO. or RICE (you could contact Georg Turi for this as well). To sum up, use all possible components if you can afford it - i.e. if you have enough meaningful samples. If not, consider using a non-PCA approach for dimension reduction. If you're close to the Cramer-Rao lower bound you should do a statistical validation of your results by doing ICA from random starting points several hundred times (e.g. in ICASSO). And be careful with contributions from eye-movements - moving sources are not considered in the ICA mixing model that you try to estimate - so anything is possible there. > > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? You would reject on the basis of topography and IC timecourse. > > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? For blinks ICA works as well on MEG as it does on EEG, and it works very well! Projecting out the EOG channels will definitely distort the signal (a detailed discussion of what to expect can be found in the BESA help for example). ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. -------------- next part -------------- A non-text attachment was scrubbed... Name: Michael Wibral.vcf Type: text/x-vcard Size: 344 bytes Desc: not available URL: From s.debener at UKE.UNI-HAMBURG.DE Fri Mar 27 21:54:28 2009 From: s.debener at UKE.UNI-HAMBURG.DE (Stefan Debener) Date: Fri, 27 Mar 2009 20:54:28 +0000 Subject: ICA on 275ch MEG... removing artifacts In-Reply-To: Message-ID: Hi Suresh, > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... > Be careful with assuming a fixed number of components to explain eye blinks. In EEG, it largely (but not solely!) depends on the number of channels/components; so, while most 32 channel decompositions return 1 eye blink component, this cannot always be expected, and in 128 channel data it can be anything between, roughly, 1 and 6. The problem with ICA of course is that we have no clue about the number of sources contributing to the data, so over/underfitting seems the rule rather than the exception. Therefore (and for other reasons), one should evaluate the quality of the decomposition, which usually includes evaluating the time course information as well as the reliability of a decomposition. With regard to spatial stationarity, as mentioned by Michael already, it seems important to recognize that many artefacts violate this assumption to some more or less relevant extent. Eye blinks, for instance, seem to be caused primarily by the movement of the eye lids (not so much of the eye balls; there is a wonderful paper published on this in Clin Neurophysiol, but I keep forgetting the reference, sorry). So, it is a moving source which often can be 'perfectly' modelled with ICA. In my experience, the same holds for lateral eye movements, which also can be nicely modelled with ICA: these components show a very robust topography, that is, you need not much data to find such ICs quite quickly and reliably, and they show up in nearly all datasets. Thus, ICA seems to tolerate to some extent stationarity violations. My speculation is that this is related to the relatively poor spatial sampling of these artefacts in conventional EEG/MEG recordings: imagine decomposing from 100 channels that covered the whole face: I would not be surprised if those recordings would be more sensitive to stationarity violations contributed by these artefacts. A case where the violation of stationarity typically messes up ICA is for inside scanner EEG recordings. Here, it is my experience that ICA cannot deal well with the ballistocardiogram, which contributes a very complex, dynamically moving signal to the EEG (but see plenty other published papers proposing just the opposite). The reason for this inconsistency seems that the ballistocardiogram scales with the scanner B0 field: in the case of 1.5T, ICA sometimes still pulls out a more or less reasonable decomposition, but at 3T, or even 7T, it performs poorly, under otherwise identical conditions (Debener et al., 2008, Int J Psychophysiol). > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? > Depends. As it happens, there is a paper in press (Viola et al., Clin Neurophysiology, will be available online in a few days) evaluating the use of topographical information for eye blink and eye movement component identification and clustering (across datasets). This works surprisingly well, from 30 to 128 channel EEG recordings. Temporal correlations of component activations with aux channels have also been used for component identification (e.g., Srivastava et al., 2005, Neurimage) but I have mixed experience with this approach and would not recommend it. However, it really depends on the type of artefact you are after: there are cases where topographical information is not of much help, while temporal information gives a detailed picture of which component reflects artefact and which does not (e.g., Sandmann et al.,in press in Brain; or Ohla et al., in press in Brain Topography; both available online). > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to > traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? > Interesting you mention this - that's one of the issues we are very much interested in. Hope this helps, Stefan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From j.schoffelen at PSY.GLA.AC.UK Mon Mar 30 16:15:38 2009 From: j.schoffelen at PSY.GLA.AC.UK (jan-mathijs schoffelen) Date: Mon, 30 Mar 2009 15:15:38 +0100 Subject: handling of 4D-data: update Message-ID: Dear 4D-neuroimagers, I just committed an updated version of read_4d_hdr to fieldtrip's release which I would like to draw your attention to. The reason for this is twofold: it handles some fields in the header in a different way, which might lead to backward compatitibility problems, and it has some functional improvements. Moreover, even though this new version works alright on the data acquired in Glasgow, I am not sure whether this holds true for all 4D-systems. Specifically, what changed is the following: user_block_data which are stored in the run-specific config file are now stored differently in fieldtrip's hdr-structure. Originally, it was stored as a structure-array in hdr.orig.user_block_data. I changed this into a cell-array. Moreover, I made some efforts to make sense of the content of these user_blocks, so some of these now actually contain some data (such as digitized positions of the coils- on-head, estimated coil-on-head positions in dewar space etc). Most consequentially, read_4d_hdr now attempts to read in the weight table used during acquisition of the data. The digital weights from this table are subsequently incorporated into the balancing matrix of the gradiometer-array (this is now done in bti2grad). This is necessary for correct computation of the leadfields. I'd like to ask you to keep your eyes open and to check whether it also works for data acquired at your system. Please let me know of any problems arising from these changes. Moreover, if you would like to contribute to perfecting read_4d_hdr, just let me know. Yours, Jan-Mathijs ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From sdmuthu at CARDIFF.AC.UK Tue Mar 31 13:01:01 2009 From: sdmuthu at CARDIFF.AC.UK (Suresh Muthukumaraswamy) Date: Tue, 31 Mar 2009 12:01:01 +0100 Subject: ICA on 275ch MEG... removing artifacts In-Reply-To: <49CD3D04.2060806@uke.uni-hamburg.de> Message-ID: Thanks Stefan and Michael for your help with this! All the best, Suresh Suresh Muthukumaraswamy, PhD CUBRIC Cardiff University Park Place Cardiff, CF10 3AT United Kingdom email: sdmuthu at cardiff.ac.uk Phone: +44 (0)29 2087 0353 >>> Stefan Debener 03/27/09 8:54 pm >>> Hi Suresh, > Typically how many components do people normally estimate and then how > many of these would normally get rejected as containing eye artefact? 270 > components is alot to look through! I see one can limit the number of > components the function can return.... > Be careful with assuming a fixed number of components to explain eye blinks. In EEG, it largely (but not solely!) depends on the number of channels/components; so, while most 32 channel decompositions return 1 eye blink component, this cannot always be expected, and in 128 channel data it can be anything between, roughly, 1 and 6. The problem with ICA of course is that we have no clue about the number of sources contributing to the data, so over/underfitting seems the rule rather than the exception. Therefore (and for other reasons), one should evaluate the quality of the decomposition, which usually includes evaluating the time course information as well as the reliability of a decomposition. With regard to spatial stationarity, as mentioned by Michael already, it seems important to recognize that many artefacts violate this assumption to some more or less relevant extent. Eye blinks, for instance, seem to be caused primarily by the movement of the eye lids (not so much of the eye balls; there is a wonderful paper published on this in Clin Neurophysiol, but I keep forgetting the reference, sorry). So, it is a moving source which often can be 'perfectly' modelled with ICA. In my experience, the same holds for lateral eye movements, which also can be nicely modelled with ICA: these components show a very robust topography, that is, you need not much data to find such ICs quite quickly and reliably, and they show up in nearly all datasets. Thus, ICA seems to tolerate to some extent stationarity violations. My speculation is that this is related to the relatively poor spatial sampling of these artefacts in conventional EEG/MEG recordings: imagine decomposing from 100 channels that covered the whole face: I would not be surprised if those recordings would be more sensitive to stationarity violations contributed by these artefacts. A case where the violation of stationarity typically messes up ICA is for inside scanner EEG recordings. Here, it is my experience that ICA cannot deal well with the ballistocardiogram, which contributes a very complex, dynamically moving signal to the EEG (but see plenty other published papers proposing just the opposite). The reason for this inconsistency seems that the ballistocardiogram scales with the scanner B0 field: in the case of 1.5T, ICA sometimes still pulls out a more or less reasonable decomposition, but at 3T, or even 7T, it performs poorly, under otherwise identical conditions (Debener et al., 2008, Int J Psychophysiol). > Do people normally reject solely on topography or do they do a frequency > analysis of the component time-course or perhaps other things? > Depends. As it happens, there is a paper in press (Viola et al., Clin Neurophysiology, will be available online in a few days) evaluating the use of topographical information for eye blink and eye movement component identification and clustering (across datasets). This works surprisingly well, from 30 to 128 channel EEG recordings. Temporal correlations of component activations with aux channels have also been used for component identification (e.g., Srivastava et al., 2005, Neurimage) but I have mixed experience with this approach and would not recommend it. However, it really depends on the type of artefact you are after: there are cases where topographical information is not of much help, while temporal information gives a detailed picture of which component reflects artefact and which does not (e.g., Sandmann et al.,in press in Brain; or Ohla et al., in press in Brain Topography; both available online). > Moreoever, I was also wondering if anyone had carried out any kind of > systematic comparison between this approach for MEG compared to > traditional > EEG approaches to this problem (e.g. projecting out the EOG channels)? > Interesting you mention this - that's one of the issues we are very much interested in. Hope this helps, Stefan ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip. From Martijn.Barendregt at PHIL.UU.NL Tue Mar 31 15:23:06 2009 From: Martijn.Barendregt at PHIL.UU.NL (Martijn Barendregt) Date: Tue, 31 Mar 2009 15:23:06 +0200 Subject: Need help with BVA files Message-ID: Hi, I'm trying to process some E.E.G. data that I've exported from BrainVision Analyzer. But when I run my script (see below) I don't get any errors but the 'time' field in the raw_data struct will be all zeros. Because of this I can't do anything with the data. What can I do to get the time values in correctly? Kinds regards, Martijn Barendregt My code: cfg = []; cfg.datafile = 'somefile.dat'; cfg.headerfile = 'somefile.vhdr'; cfg.trialdef.trgfile = 'somefile.vmkr'; cfg.trialdef.eventtype = 'Stimulus'; cfg.trialdef.eventvalue = 'M22'; cfg.traildef.prestim = 3; cfg.traildef.poststim = 3; cfg.trialdef.segment = 'no'; cfg.trialdef.timezero = 'no'; [cfg] = definetrial(cfg); raw_data = preprocessing(cfg); ---------------------------------- The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/neuroimaging/fieldtrip.