From r.oostenveld at donders.ru.nl Fri May 1 09:44:26 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 1 May 2015 09:44:26 +0200 Subject: [FieldTrip] postdoc position at NatMEG: Alzheimer's disease diagnostics and treatment evaluation with MEG Message-ID: Post doc, Stockholm, Sweden The position as postdoctoral researcher at NatMEG Applications are invited for a postdoctoral position in MEG within a project aiming at new diagnostics and (evaluation of) treatment for the neuropathological conditions Alzheimer´s disease (AD), Parkinson´s disease (PD) and related prodromal and at-risk stages of these conditions. The position is for 2 years, with the possibility of extension for a maximum of another 2 years. Duties The successful candidate will use MEG during emotion/cognition tasks, activation (motor), stimulation (visual, auditory, somatosensory, olfactory) and resting state protocols to explore functional connectivity measures for characterizing individuals with AD and PD, and for detecting individuals at risk of developing either of these conditions. The successful candidate will also work with methods for evaluating treatment effects within AD, PD and related prodromal cohorts. NatMEG –The National Facility for Magnetoencephalography (MEG) As of September 2013, Karolinska Institutet hosts a superbly equipped MEG lab. The lab, NatMEG, is a national facility, open for researchers from all across Sweden. The fact that NatMEG is a national facility is reflected by the wide array of projects currently ongoing/under initiation at NatMEG, covering areas such as next-generation SQUIDS, computational modelling, epilepsy work-ups, and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson’s and Alzheimer’s disease, and more. The latest equipment installations, entailing microneurography and next-generation high-Tc SQUIDS, makes NatMEG very uniquely equipped. NatMEG offers an open and friendly working environment, in the middle of Karolinska Institutet campus, Stockholm. Please visit http://natmeg.se for more information. Entry requirements A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. It is required that a candidate: A. Has extensive MEG hands-on experience (preferably on an Elekta Neuromag TRIUX or Vectorview system), from MEG data collection, including setting up experiments and peripheral stimulators. B. Has strong skills and expertise in MEG analysis (preferably in at least FieldTrip and/or MNE). C. Has a background and research interest within the cognitive neuroscience domain. D. Is independent, professional, and service minded, and enjoys interacting with researchers and research subjects. E. Masters academic English. It is also highly valued if a candidate: F. Has experience and/or expertise regarding Alzheimer’s disease. G. Has experience and/or expertise regarding Parkinson’s disease. H. Has an expertise in / experience with psychophysiology (e.g. EMG, facial EMG, GSR, HR, respiration) measurements and analysis. H. Karolinska Institutet Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 percent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. See http://ki.se/en/ for more information. The Department of Clinical Neuroscience The Department of Clinical Neuroscience (CNS) conducts research and education in the field of neuroscience from the molecular level to the society level. The clinical research and education is conducted in collaboration with other research groups from the Karolinska Institutet, with other universities as well as the Stockholm County Council. Please visit our website for more information: http://ki.se/en/cns Application process Read more about the application process at https://ki.mynetworkglobal.com/en/what:job/jobID:63833/. Applications are to be submitted in the recruitment system MyNetwork. Application deadline 2015-05-24 Contact information Daniel Lundqvist, Head of Unit daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri May 1 09:44:29 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 1 May 2015 09:44:29 +0200 Subject: [FieldTrip] postdoc position at NatMEG: combined MEG and microneurography Message-ID: <2F1892F1-A625-4919-AB37-43AE8C571093@donders.ru.nl> Post doc, Stockholm, Sweden The position as postdoctoral researcher at NatMEG Applications are invited for a postdoctoral position within two unique and overlapping projects at NatMEG: 1. combined MEG and microneurography (recording and stimulation inside peripheral nerve fibres) measurements, and 2. benchmarking of next-generation high-Tc SQUIDS (head-adjustable, nitrogen-cooled MEG sensors with millimetre sensor-to-scalp-proximity) against today’s state of the art MEG system (Elekta Triux). The position is for a maximum of 4 years. Duties The successful candidate will explore: 1. the (1a) physiology of touch and the (1b) autonomic nervous system by means of combined MEG and microneurography recordings. 2. the spatiotemporal precision and MEG signal characteristics of focal High-TC SQUIDS, benchmarked against the present (a conventional helium-cooled) MEG system for application such as (2a) sensory stimulation (visual, auditory, somatosensory, olfactory) and clinical applications such as (2b) interictal epileptogenic spike detection and (2c) functional mapping. NatMEG –The National Facility for Magnetoencephalography (MEG) As of September 2013, Karolinska Institutet hosts a superbly equipped MEG lab. The lab, NatMEG, is a national facility, open for researchers from all across Sweden. The fact that NatMEG is a national facility is reflected by the wide array of projects currently ongoing/under initiation at NatMEG, covering areas such as next-generation SQUIDS, computational modelling, epilepsy work-ups, and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson’s and Alzheimer’s disease, and more. The latest equipment installations, entailing microneurography and next-generation high-Tc SQUIDS, makes NatMEG very uniquely equipped. NatMEG offers an open and friendly working environment, in the middle of Karolinska Institutet campus, Stockholm. Please visit http://natmeg.se for more information. Entry requirements A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. It is required that a candidate: A. Has a background and research interest within the cognitive neuroscience domain. B. Has extensive MEG hands-on experience (preferably on an Elekta Neuromag TRIUX or Vectorview system), from MEG data collection, including setting up experiments and peripheral stimulators. C. Has very strong skills and expertise in MEG analysis (preferably in at least FieldTrip and/or MNE). D. Is independent, professional, and service minded, and enjoys interacting with researchers and research subjects. E. Masters academic English. It is also highly valued if a candidate: F. Has an expertise in the primary sensory system in one or several sensory modalities. G. Has an expertise in / experience from high-Tc SQUIDS. H. Has an expertise in / experience from microneurography measurements and analysis. I. Has an expertise in / experience with psychophysiology (e.g. EMG, facial EMG, GSR, HR, respiration) measurements and analysis. I. Karolinska Institutet Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 percent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. See http://ki.se/en/ for more information. The Department of Clinical Neuroscience The Department of Clinical Neuroscience (CNS) conducts research and education in the field of neuroscience from the molecular level to the society level. The clinical research and education is conducted in collaboration with other research groups from the Karolinska Institutet, with other universities as well as the Stockholm County Council. Please visit our website for more information: http://ki.se/en/cns Application process Read more about the application process at https://ki.mynetworkglobal.com/what:job/jobID:63834/. Applications are to be submitted in the recruitment system MyNetwork. Application deadline 2015-05-24 Contact information Daniel Lundqvist, Head of Unit daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Fri May 1 20:29:09 2015 From: elam4hcp at gmail.com (Jennifer Elam) Date: Fri, 1 May 2015 13:29:09 -0500 Subject: [FieldTrip] Still time to register for the 2015 HCP Course! Message-ID: A reminder that it’s not too late to register for the 2015 HCP Course: “Exploring the Human Connectome” , to be held June 8-12, 2015 at the Marriott Resort Waikiki Beach, in Honolulu, Hawaii, USA. Also, a reminder that you might try http://www.vrbo.com/ or https://www.airbnb.com/ for affordable accommodations in the Waikiki Beach area, near the Marriott. This 5-day intensive course is designed for investigators who are interested in: - using data being collected and distributed by HCP - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - learning to use Connectome Workbench tools and the CIFTI connectivity data format - learning HCP multi-modal neuroimaging analysis methods, including those that combine MEG and MRI data - positioning yourself to capitalize on HCP-style data from forthcoming large-scale projects (e.g., Lifespan HCP and Connectomes Related to Human Disease) Visit the HCP Course website to register and for Faculty listings and the full schedule of covered topics. We hope to see you in Hawaii! Best, 2015 HCP Course Organizers -------------- next part -------------- An HTML attachment was scrubbed... URL: From haristz at umn.edu Fri May 1 21:58:02 2015 From: haristz at umn.edu (Haris Tzagarakis) Date: Fri, 1 May 2015 14:58:02 -0500 Subject: [FieldTrip] Problems using fieldtrip with Matlab Distributed Computing Server Message-ID: Hi There, I have been trying to use fieldrtip in conjunction with Matlab Distributed Computing Server on a supercomputing resource and have been running into a problem that seems to come from paths/global variables? in detail: I use fieldtrip in conjunction with my own code for an analysis. The analysis works fine on a "normal"/non-parallel call. I then set out to parallelize the code and split the analysis to a different node for every subject I have. I have access to a supercomputing cluster (not uniquely for matlab/biomed use), which runs Matlab Distributed Computing Server, so job scheduling etc can happen from within matlab. I believe this is different from the 'peer distributed' approach described in the faq. I prepared a script which is then run with the matlab 'batch' command : job = batch('parscript3b', 'Profile', 'Itasca_MSI', 'Pool', 10); I attach the script in its current form here. This call should pass the script to a top level node that then distributes the loop in 10 nodes, one for each subject. What always happens however is that I get an error at the top level node saying: Error using ft_hastoolbox (line 469) the FREESURFER toolbox is not installed, see http://surfer.nmr.mgh.harvard.edu/fswiki I have read the help/comments text and some of the code in ft_hastoolbox and ft_defaults (I in fact always call ft_defaults at startup - my startup file is also attached here). This in conjunction with what is mentioned in MATLAB help makes me think that there is something about the way paths and global variables are handled by MDCS that does not agree with Fieldtrip. I have been trying to go around the problem by liberally using ft_defaults in my script code (as can be seen) and I also added some lines to the ft_hastoolbox function (in all its 4 instances in the private folders) to check explicitly for the fieldtrip locations in my system but none of this has worked. I would be grateful for any insight you might have. With Thanks and Best Wishes, Haris -- Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych Senior Research Associate University of Minnesota Dept of Neuroscience office: Brain Sciences Center Minneapolis VA Medical Center Tel:612-467-1363 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: parscript3b.m Type: text/x-csrc Size: 679 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: startup_current.m Type: text/x-csrc Size: 552 bytes Desc: not available URL: From e.maris at donders.ru.nl Mon May 4 17:42:17 2015 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Mon, 4 May 2015 15:42:17 +0000 Subject: [FieldTrip] symposium on model-based and model-inspired analysis of electrophysiological data Message-ID: <30e5b4c636464fafb45f7de18ae20de5@EXPRD03.hosting.ru.nl> Dear colleague, On June 1, I will organise a symposium on model-based and model-inspired analysis of electrophysiological data, to which I would like to invite you and your colleagues. You can find the program and additional information in the attachment. Please send around this invitation to everyone who might profit from this symposium. About a week before the symposium, I will send around directions on how the get here. best, Eric Maris -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2015-06-01.Model-based and Model-inspired Analysis of Electrophysiological Data.pdf Type: application/pdf Size: 27061 bytes Desc: 2015-06-01.Model-based and Model-inspired Analysis of Electrophysiological Data.pdf URL: From mark.woolrich at ohba.ox.ac.uk Tue May 5 13:14:50 2015 From: mark.woolrich at ohba.ox.ac.uk (Mark Woolrich) Date: Tue, 5 May 2015 11:14:50 +0000 Subject: [FieldTrip] Research postdoc positions in neuroimage analysis and computational neuroscience. Message-ID: <0229ABEF-5744-43AD-8130-CC2567B50AD5@ohba.ox.ac.uk> Applications are invited for two postdoctoral scientists to work on a Wellcome Trust funded project to advance understanding of spontaneous whole-brain activity. The project will use a combination of MRI, M/EEG / LFP recordings, methods development and biophysical modeling to advance understanding of spontaneous whole-brain activity, and provide new insights into the underlying mechanisms. This research will be conducted within the OHBA Analysis Group headed by Mark Woolrich and based at the Oxford Centre for Human Brain Activity (http://www.ohba.ox.ac.uk), and will be in collaboration with colleagues at FMRIB (http://www.fmrib.ox.ac.uk/analysis) and the Centre for Neural Circuits and Behaviour (http://www.cncb.ox.ac.uk). We are looking for excellent researchers with a strong technical background, ideally in computational neuroscience and/or in developing neuroimaging analysis methods, but also with experience in other areas of Engineering/Applied Mathematics, Statistics, Computer Science and Physics (e.g. Machine Learning and Pattern Recognition). Post in Neuroimaging Analysis https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=117895 Post in computational biophysical model development https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=118123 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmuehl at gmail.com Tue May 5 17:20:32 2015 From: cmuehl at gmail.com (Christian Muehl) Date: Tue, 5 May 2015 15:20:32 +0000 Subject: [FieldTrip] 2nd Call for Papers - 4th Workshop on Affective Brain-Computer Interfaces @ ACII2015 Message-ID: ** 2nd Call for Papers ** 4th Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2015 (September 21-24), Xi'an, China, September 21, 2015 http://www.affective-sciences.org/aBCI2015 http://www.acii2015.org/ The goal of the aBCI workshop series is to connect researchers from the communities of affective computing, social signal processing, brain-computer interfacing, neuro-ergonomics, and neuroscience around the federating theme of affective brain computer interfaces (aBCI). Affective BCI aim at the development of human-computer interfaces able to react and adapt to users' emotions and related cognitive states as measured from neurophysiological signals. Besides the general solicitation of work toward adaptive HCI applications based on aBCI, this 4th edition of the workshop will focus on two specific aspects of aBCI. Firstly, we welcome papers on ways to alleviate current aBCI limitations, through work on the physiological basis of aBCI, innovative applications resilient to classification error, and methods to increase the robustness of aBCI. Secondly, we would like to explore the social aspects and applications of aBCI by welcoming submissions on topics such as multi-user aBCI and the assessment of social processes from brain signals. The workshop topics include, but are not limited to, * effective emotion elicitation and data collection in social settings; * identification of robust and specific markers of emotional, cognitive and social processes; * methods for the assessment of emotions, cognitive states and social interactions; * methods to measure and process multiple people physiological activity; * applications of central and peripheral signal processing to social situations; * innovative concepts for adaptive interfaces and affective BCI; * demos of affective BCI systems. Submission Instructions: * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors. * Papers will be published electronically in the proceedings of ACII 2015 by IEEE Xplore. Papers should be limited to 6 pages+1page references. The review is double blind - please remove all author information from the manuscripts. * Further details about the submission instructions and format can be found on the website of ACII 2015. Important Dates: June 5, 2015: Submission of manuscripts July 3, 2015: Acceptance/Rejection notification July 24, 2015: Submission of camera-ready papers September 21, 2015: Date of the Workshop For further information, see our website or contact abci at ewi.utwente.nl Programme Chairs: * Fabien Lotte, Inria Bordeaux Sud-Ouest, Talance, France * Guillaume Chanel, Swiss Center for Affective Sciences, Geneva, Switzerland * Christian Mühl, German Aerospace Center, Cologne, Germany * Anton Nijholt, Universiteit Twente, the Netherlands Programme Committee: Egon L. van den Broek, University of Utrecht, the Netherlands Anne-Marie Brouwer, TNO Perceptual and Cognitive Systems, Soesterberg, the Netherlands Stephen Dunne, Starlab Barcelona, Spain Touradj Ebrahimi, École polytechnique fédérale de Lausanne, Switzerland Stephen Fairclough, John Moores University, Liverpool, UK Tiago H. Falk, Institut National de la Recherche Scientifique (INRS), Montreal, Canada Hayrettin Gürkök, University of Twente, Enschede, the Netherlands Dominic Heger, Karlsruhe Institute of Technology, Germany Klas Ihme, German Aerospace Center, Brunswick, Germany Jonghwa Kim, University of Augsburg, Germany Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA, Grace Leslie, MIT Media Lab, Boston, USA Giulia Liberati, Université catholique de Louvain, Belgium Gary Garcia Molina, Philips Research North America, Briarcliff, USA Scott Makeig, University of California San Diego, USA Tim Mullen, University of California San Diego, USA Domen Novak, University of Wyoming, Laramie, USA Ioannis Patras, Queen Mary University, London, UK Evan Peck, Bucknell University, Lewisburg, USA Mannes Poel, University of Twente, Enschede, the Netherlands Alan Pope, NASA Langley Research Center, Norfolk, USA Thierry Pun, University of Geneva, Switzerland Erin Solovey, Drexel University, Philadelphia, USA Mohammad Soleymani, University of Geneva, Switzerland Aureli Soria-Frisch, Starlab Barcelona, Spain Olga Sourina, NanYang Technological University, Singapore Aleksander Valjamae, Linköping University, Sweden Jan van Erp, University of Twente, Enschede, the Netherlands Chi Thanh Vi, University of Bristol, UK Thorsten Zander, Technische Universität Berlin, Germany From hamzaf at sabanciuniv.edu Tue May 5 18:40:23 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Tue, 5 May 2015 18:40:23 +0200 Subject: [FieldTrip] brick0 Message-ID: Hello, While trying to plot all tissues in one image using ft_sourceplot function as in seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); I faced the following error: Reference to non-existent field 'brick0' This brick0 is defined in atlas_lookup.m as brick0_val = atlas.brick0(ijk(1), ijk(2), ijk(3)); But the atlas variable that is called for this function is defined as: dim: [256 256 256] transform: [4x4 double] coordsys: 'ctf' unit: 'mm' cfg: [1x1 struct] seg: [256x256x256 double] seglabel: {'gray' 'white' 'csf' 'skull' 'scalp'} I wonder from where this brick0 come? Thanks for help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Wed May 6 00:01:40 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Tue, 5 May 2015 23:01:40 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy Message-ID: <55493DC4.90601@glasgow.ac.uk> An HTML attachment was scrubbed... URL: From nadine.dijkstra92 at gmail.com Wed May 6 14:20:58 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Wed, 6 May 2015 14:20:58 +0200 Subject: [FieldTrip] labels per grid point Message-ID: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Dear Fieldtrip Users, I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? Thanks in advance for your help, Nadine From tzvetan.popov at uni-konstanz.de Wed May 6 14:37:56 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 6 May 2015 14:37:56 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: Hi Nadine, maybe this is what you need? http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations best tzvetan > Dear Fieldtrip Users, > > I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? > > Thanks in advance for your help, > Nadine > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 14:43:08 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 14:43:08 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: <018c01d087fa$34fa3150$9eee93f0$@artinis.com> Hi Nadine, does the second exercise in this section help (i.e. defining a lookup atlas for source plotting): http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_source s_of_oscillatory_gamma-band_activity ? Best, Jörn -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Nadine > Sent: Wednesday, May 6, 2015 2:21 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] labels per grid point > > Dear Fieldtrip Users, > > I am trying to get anatomical labels for individual source grid points. I can only > find how to parcellate the grid points to get an averaged value of sources for > certain parcellations (e.g. Brodmann areas). But I would like to get an > anatomical label per grid point, so that I can see which grid points belong to > which area. Does anybody have any solution for this? > > Thanks in advance for your help, > Nadine > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 14:49:32 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 14:49:32 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <018c01d087fa$34fa3150$9eee93f0$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> Message-ID: <018f01d087fb$19d25460$4d76fd20$@artinis.com> the correct link is: http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_source s_of_oscillatory_gamma-band_activity not sure why there was a line break introduced... -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > Sent: Wednesday, May 6, 2015 2:43 PM > To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] labels per grid point > > Hi Nadine, > > does the second exercise in this section help (i.e. defining a lookup atlas for > source plotting): > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > ource > s_of_oscillatory_gamma-band_activity > ? > > Best, > Jörn > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems  |  +31 481 350 980 > > > -----Original Message----- > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > bounces at science.ru.nl] On Behalf Of Nadine > > Sent: Wednesday, May 6, 2015 2:21 PM > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] labels per grid point > > > > Dear Fieldtrip Users, > > > > I am trying to get anatomical labels for individual source grid > > points. I > can only > > find how to parcellate the grid points to get an averaged value of > > sources > for > > certain parcellations (e.g. Brodmann areas). But I would like to get > > an anatomical label per grid point, so that I can see which grid > > points > belong to > > which area. Does anybody have any solution for this? > > > > Thanks in advance for your help, > > Nadine > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 15:07:24 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 15:07:24 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <018f01d087fb$19d25460$4d76fd20$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> <018f01d087fb$19d25460$4d76fd20$@artinis.com> Message-ID: <019001d087fd$98c7f020$ca57d060$@artinis.com> haha ok, I give up, the link still appears to be broken - please copy the link together yourself or click on 'Plotting sources of oscillatory gamma-band activity' on the navigation tab to the left and look for the second exercise in that section. -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > Sent: Wednesday, May 6, 2015 2:50 PM > To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] labels per grid point > > the correct link is: > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > ource > s_of_oscillatory_gamma-band_activity > not sure why there was a line break introduced... > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems  |  +31 481 350 980 > > > -----Original Message----- > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > > Sent: Wednesday, May 6, 2015 2:43 PM > > To: 'FieldTrip discussion list' > > Subject: Re: [FieldTrip] labels per grid point > > > > Hi Nadine, > > > > does the second exercise in this section help (i.e. defining a lookup > atlas for > > source plotting): > > > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ > > s > > ource > > s_of_oscillatory_gamma-band_activity > > ? > > > > Best, > > Jörn > > > > > > -- > > > > Jörn M. Horschig, Software Engineer > > Artinis Medical Systems  |  +31 481 350 980 > > > > > -----Original Message----- > > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > > bounces at science.ru.nl] On Behalf Of Nadine > > > Sent: Wednesday, May 6, 2015 2:21 PM > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] labels per grid point > > > > > > Dear Fieldtrip Users, > > > > > > I am trying to get anatomical labels for individual source grid > > > points. I > > can only > > > find how to parcellate the grid points to get an averaged value of > > > sources > > for > > > certain parcellations (e.g. Brodmann areas). But I would like to get > > > an anatomical label per grid point, so that I can see which grid > > > points > > belong to > > > which area. Does anybody have any solution for this? > > > > > > Thanks in advance for your help, > > > Nadine > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nadine.dijkstra92 at gmail.com Wed May 6 15:51:59 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Wed, 6 May 2015 15:51:59 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <019001d087fd$98c7f020$ca57d060$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> <018f01d087fb$19d25460$4d76fd20$@artinis.com> <019001d087fd$98c7f020$ca57d060$@artinis.com> Message-ID: Thanks, the link works fine for me! I am not sure if this solves the problem however, because it only gives the labels for some points in the plot, while I want to have the label for every individual grid point in a list so that I can see which grid points belong to the same area etc. However, this might be a good place to start. Thanks anyway! Best, Nadine On 06 May 2015, at 15:07, Jörn M. Horschig wrote: > haha ok, I give up, the link still appears to be broken - please copy the > link together yourself or click on 'Plotting sources of oscillatory > gamma-band activity' on the navigation tab to the left and look for the > second exercise in that section. > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems | +31 481 350 980 > >> -----Original Message----- >> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >> bounces at science.ru.nl] On Behalf Of Jörn M. Horschig >> Sent: Wednesday, May 6, 2015 2:50 PM >> To: 'FieldTrip discussion list' >> Subject: Re: [FieldTrip] labels per grid point >> >> the correct link is: >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s >> ource >> s_of_oscillatory_gamma-band_activity >> not sure why there was a line break introduced... >> >> >> -- >> >> Jörn M. Horschig, Software Engineer >> Artinis Medical Systems | +31 481 350 980 >> >>> -----Original Message----- >>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >>> bounces at science.ru.nl] On Behalf Of Jörn M. Horschig >>> Sent: Wednesday, May 6, 2015 2:43 PM >>> To: 'FieldTrip discussion list' >>> Subject: Re: [FieldTrip] labels per grid point >>> >>> Hi Nadine, >>> >>> does the second exercise in this section help (i.e. defining a lookup >> atlas for >>> source plotting): >>> >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ >>> s >>> ource >>> s_of_oscillatory_gamma-band_activity >>> ? >>> >>> Best, >>> Jörn >>> >>> >>> -- >>> >>> Jörn M. Horschig, Software Engineer >>> Artinis Medical Systems | +31 481 350 980 >>> >>>> -----Original Message----- >>>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >>>> bounces at science.ru.nl] On Behalf Of Nadine >>>> Sent: Wednesday, May 6, 2015 2:21 PM >>>> To: fieldtrip at science.ru.nl >>>> Subject: [FieldTrip] labels per grid point >>>> >>>> Dear Fieldtrip Users, >>>> >>>> I am trying to get anatomical labels for individual source grid >>>> points. I >>> can only >>>> find how to parcellate the grid points to get an averaged value of >>>> sources >>> for >>>> certain parcellations (e.g. Brodmann areas). But I would like to get >>>> an anatomical label per grid point, so that I can see which grid >>>> points >>> belong to >>>> which area. Does anybody have any solution for this? >>>> >>>> Thanks in advance for your help, >>>> Nadine >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nadine.dijkstra92 at gmail.com Thu May 7 09:36:34 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Thu, 7 May 2015 09:36:34 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: <306CCF9F-01AC-4036-8B14-C4FFC99AA54E@gmail.com> Hi Tzvetan, Yes, thank you, this is perfect! Best, Nadine On 06 May 2015, at 14:37, Tzvetan Popov wrote: > Hi Nadine, > > maybe this is what you need? > http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations > > best > tzvetan > >> Dear Fieldtrip Users, >> >> I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? >> >> Thanks in advance for your help, >> Nadine >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From guiraudh at gmail.com Thu May 7 10:21:19 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Thu, 7 May 2015 10:21:19 +0200 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi Till and John, Thank you, this is perfect! Best regards, Hélène 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > We have a template for children‹actually have for infants from 2 weeks > through adults at 89 years. We also have average electrode positions for > EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented > priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have > been using this recently with FT for infants and child/adolescent/adult > ages. > > WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > Fro www site: This is a database of average MRIs and associated MRI > volumes for developmental MRI work. It consists of average MRI templates, > segmented partial volume estimate volumes for GM, WM, T2W-derived CSF > (Description > > > ). The database is separated into head-based and brain-based averages. The > data are separated by ages in months, years, 6-month, or 5-year intervals > (Ages and Templates > < > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm > l>). The templates are grouped into first year (2 weeks through 12 > months), early childhood (15 months through 4 years), childhood (4 years > through 10 years), adolescence (10.5 years through 17.5 years) and adults > (18 years through 89 years). > Tools for cortical source analysis of EEG and ERP are provided. These > tools are based on the average MRI templates, segmenting, and atlases. > > Also see my www site, jerlab.psych.sc.edu for publications describing > this. We have a recent chapter that has a good description of the issues > behind the database (with Wanze Xie). We have a paper accepted at > Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, > Michelle Phillips-Meek, and Wanze Xie). > > John > > > *********************************************** > John E. Richards Carolina Distinguished Professor > Department of Psychology > University of South Carolina > Columbia, SC 29208 > Dept Phone: 803 777 2079 > Fax: 803 777 9558 > Email: richards-john at sc.edu > HTTP: jerlab.psych.sc.edu > *********************************************** > > > > > > > > > On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" > wrote: > > >Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > >To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > >You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > >When replying, please edit your Subject line so it is more specific > >than "Re: Contents of fieldtrip digest..." > > > > > >Today's Topics: > > > > 1. Search for a template children. (H?l?ne Guiraud) > > 2. Re: Search for a template children. (Till Schneider) > > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > > > > >---------------------------------------------------------------------- > > > >Message: 1 > >Date: Wed, 29 Apr 2015 14:45:56 +0200 > >From: H?l?ne Guiraud > >To: fieldtrip at science.ru.nl > >Subject: [FieldTrip] Search for a template children. > >Message-ID: > > < > CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> > >Content-Type: text/plain; charset="utf-8" > > > >Dear community, > > > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on > >speech perception in children using MEG. > >The children involved in the study don't pass MRI. We want to achieve > >source reconstruction from a template. However I can't find a template > >corresponding to the anatomy of a child (8-12 years). > >Can someone tell me if there are template children and where I can find > >them? > > > >Best, > > > >H?l?ne Guiraud > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e > >9b53e/attachment-0001.html> > > > >------------------------------ > > > >Message: 2 > >Date: Wed, 29 Apr 2015 15:53:13 +0200 > >From: Till Schneider > >To: FieldTrip discussion list > >Subject: Re: [FieldTrip] Search for a template children. > >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> > >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > > >Dear Helene, > > > >McGill University provides MNI brains for different age groups between > >4.5y to 18y. > >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 > >You will probably find the template brain you are searching for in this > >database. > > > >Best regards, > >Till > > > >-- > > > >Till Schneider, PhD > > > >Cognitive and Clinical Neurophysiology Group > >Dept. of Neurophysiology and Pathophysiology > >University Medical Center Hamburg-Eppendorf > >Martinistr. 52 > >20246 Hamburg > >Germany > > > >phone +49-40-7410-53188 > >fax +49-40-7410-57126 > >www.uke.de/neurophysiologie > > > > > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: > >> Dear community, > >> > >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) > >> on speech perception in children using MEG. > >> The children involved in the study don't pass MRI. We want to achieve > >> source reconstruction from a template. However I can't find a template > >> corresponding to the anatomy of a child (8-12 years). > >> Can someone tell me if there are template children and where I can > >> find them? > >> > >> Best, > >> > >> H?l?ne Guiraud > >> > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > >-- > > > >_____________________________________________________________________ > > > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen > >Rechts; Gerichtsstand: Hamburg | www.uke.de > >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. > >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik > >_____________________________________________________________________ > > > >SAVE PAPER - THINK BEFORE PRINTING > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e > >44937/attachment-0001.html> > > > >------------------------------ > > > >Message: 3 > >Date: Wed, 29 Apr 2015 16:25:35 +0200 > >From: Keyvan Mahjoory > >To: FieldTrip discussion list > >Subject: [FieldTrip] ICBM 152 templates in FT > >Message-ID: > > UJp6-+4+7fA at mail.gmail.com> > >Content-Type: text/plain; charset="iso-8859-1" > > > >Dear Fieldtrip Users, > > > >I perform source analysis in Fieldtrip with a template head model ( > >standard_bem ) and a > >template source model (cortex_5124.surf.gii > >) to constarin > >estimated sources on cortex. These templates are based on Colin27, But I > >prefere to use the template ICBM152 instead. > >Does FT include ICBM template? I mean templates for both head model and > >cortical surfe. > > > >Many Thanks in advance, > >Keyvan > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 > >9daf3/attachment-0001.html> > > > >------------------------------ > > > >_______________________________________________ > >fieldtrip mailing list > >fieldtrip at donders.ru.nl > >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > >End of fieldtrip Digest, Vol 53, Issue 23 > >***************************************** > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hélène Guiraud Doctorante Université Lyon 2 Laboratoire Dynamique Du Langage CNRS, UMR 5596 Tel : 04 72 72 65 34 guiraudh at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From sander at mpib-berlin.mpg.de Thu May 7 10:29:39 2015 From: sander at mpib-berlin.mpg.de (Sander, Myriam) Date: Thu, 7 May 2015 08:29:39 +0000 Subject: [FieldTrip] Vacant Predoctoral Position in Lifespan Psychology at the MPI for Human Development in Berlin, Germany Message-ID: ********************************************************* PREDOCTORAL POSITION: CENTER FOR LIFESPAN PSYCHOLOGY, MPI BERLIN The new MINERVA research group headed by Dr. Myriam Sander at the Max Planck Institute for Human Development, Center for Lifespan Psychology (Director: Prof. Dr. Ulman Lindenberger), is seeking applications for a PREDOCTORAL POSITION The doctoral contract will last for 3 years. The position is available from October 1, 2015 or later. Job Description: Future research of the new MINERVA research group (PI: Dr. Myriam Sander) will use a multi-modal imaging approach (EEG with a focus on oscillatory measures in combination with structural and functional MRI) to uncover lifespan differences in the interplay between sensory (visual and auditory) and cognitive abilities influencing memory performance. The MINERVA research group is part of the project „Cognitive and Neural Dynamics of Memory Across the Lifespan (CONMEM)” which investigates lifespan changes in the interplay between associative and strategic components of memory functioning on neural and cognitive levels, with a focus on working and episodic memory (see Sander, et al., Neurosci. Biobehav. Rev., 2012; Shing, et al., Neurosci. Biobehav. Rev., 2010). The successful predoctoral fellow will plan and conduct empirical studies in this domain, analyze the behavioral, EEG, and MRI data, and prepare scientific manuscripts for publication. For further information, please contact: Dr. Myriam Sander (sander at mpib-berlin.mpg.de) Requirements: A successful applicant needs to hold (or expect by summer 2015) a diploma/master degree in psychology, cognitive neuroscience, or related fields. Applicants should have experience with conducting experimental research, knowledge in neuroimaging methods (EEG and/or MRI), and a solid background in at least one programming language (preferably Matlab or R). In addition, the ability to work independently as well as a high proficiency of the English language is required. Experience with age-comparative studies is an advantage. The Max Planck Society is interested in increasing the number of women on its scientific staff. We strongly encourage applications from women and members of minority groups. In addition, the Max Planck Society is committed to employing more handicapped individuals and encourages them to apply. To apply, please send (as ONE FILE and via email only) a statement of research interests, a CV, a copy of relevant certificates, (p)reprints of publications, and a list of two references to Dr. Myriam Sander, MPI for Human Development, Lentzeallee 94, 14195 Berlin (sander at mpib-berlin.mpg.de) preferably by June 30th, 2015. Later applications will be considered until the position is filled. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu May 7 11:11:54 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Thu, 7 May 2015 11:11:54 +0200 Subject: [FieldTrip] Vgrid Message-ID: Hello, I got the following error when I run these lines: (found in http://www.fieldtriptoolbox.org/development/simbio) cfg = []; cfg.shift = 0.3; cfg.method = 'hexahedral'; mesh = ft_prepare_mesh(cfg,segmentedmri); Error using vgrid (line 16) the vgrid executable is not available for your platform, it was expected to be located at ***\external\vgrid\bin\pcwin64\vgrid.exe I don't have a folder called pcwin64! I have only glnx86 (empty folder) glnxa64 and maci64 in ***\external\vgrid\bin\ I also downloaded a newer version of fieldtrip, but I did not find it! >From where I can get vgrid.exe? Thank you -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.vorw01 at gmail.com Thu May 7 11:40:17 2015 From: j.vorw01 at gmail.com (Johannes Vorwerk) Date: Thu, 07 May 2015 11:40:17 +0200 Subject: [FieldTrip] Vgrid In-Reply-To: References: Message-ID: <1430991617.11932.23.camel@biomag43> Hi, vgrid should no longer be needed in recent fieldtrip-versions. It was replaced by a fully matlab-based function (prepare_mesh_hexahedral), that should now also work under windows. A vgrid.exe never existed, it was only available for mac and linux. Did you try updating your fieldtrip-version to a recent release? Best, Johannes Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi Altakroury (Alumni): > Hello, > > > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was > expected to be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > > I don't have a folder called pcwin64! I have only glnx86 (empty > folder) glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > From where I can get vgrid.exe? > > > Thank you > > > > -- > > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dipl.-Math. Johannes Vorwerk e-mail: j.vorwerk at uni-muenster.de Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters Institute for Biomagnetism and Biosignalanalysis, University of Muenster www: http://campus.uni-muenster.de/index.php?id=919&L=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Thu May 7 12:21:40 2015 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Thu, 7 May 2015 12:21:40 +0200 Subject: [FieldTrip] labels per grid point (Nadine) Message-ID: Hi Nadine, Following up Tzvetan's response , you get the label for every grid by doing this : clear all; clc; % read the atlas atlas = ft_read_atlas('/home/common/matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii'); load('standard_sourcemodel3d10mm.mat'); % mni template source model % and call ft_sourceinterpolate: cfg = []; cfg.interpmethod = 'nearest'; cfg.parameter = 'tissue'; sourcemodel2 = ft_sourceinterpolate(cfg, atlas, sourcemodel); % replace NAN with 0 ; sourcemodel2.tissue(isnan(sourcemodel2.tissue)) =0; ids =find(sourcemodel2.tissue); % all interpolate regions id =sourcemodel2.tissue(ids); % all interpolate regions index ROI =atlas.tissuelabel(id); if you want to find Occipital for instance , you just call a few more lines code : occid =find(strncmpi(ROI,'Occipital',9)); % indice OCC =ROI(occid); % label Hope this helps, Hatieng > Message: 6 > Date: Wed, 6 May 2015 15:51:59 +0200 > From: Nadine > To: FieldTrip discussion list > Subject: Re: [FieldTrip] labels per grid point > Message-ID: > Content-Type: text/plain; charset=iso-8859-1 > > Thanks, the link works fine for me! > I am not sure if this solves the problem however, because it only gives > the labels for some points in the plot, while I want to have the label for > every individual grid point in a list so that I can see which grid points > belong to the same area etc. However, this might be a good place to start. > Thanks anyway! > > Best, > Nadine > > On 06 May 2015, at 15:07, J?rn M. Horschig wrote: > > > haha ok, I give up, the link still appears to be broken - please copy the > > link together yourself or click on 'Plotting sources of oscillatory > > gamma-band activity' on the navigation tab to the left and look for the > > second exercise in that section. > > > > > > -- > > > > J?rn M. Horschig, Software Engineer > > Artinis Medical Systems | +31 481 350 980 > > > >> -----Original Message----- > >> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >> bounces at science.ru.nl] On Behalf Of J?rn M. Horschig > >> Sent: Wednesday, May 6, 2015 2:50 PM > >> To: 'FieldTrip discussion list' > >> Subject: Re: [FieldTrip] labels per grid point > >> > >> the correct link is: > >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > >> ource > >> s_of_oscillatory_gamma-band_activity > >> not sure why there was a line break introduced... > >> > >> > >> -- > >> > >> J?rn M. Horschig, Software Engineer > >> Artinis Medical Systems | +31 481 350 980 > >> > >>> -----Original Message----- > >>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >>> bounces at science.ru.nl] On Behalf Of J?rn M. Horschig > >>> Sent: Wednesday, May 6, 2015 2:43 PM > >>> To: 'FieldTrip discussion list' > >>> Subject: Re: [FieldTrip] labels per grid point > >>> > >>> Hi Nadine, > >>> > >>> does the second exercise in this section help (i.e. defining a lookup > >> atlas for > >>> source plotting): > >>> > >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ > >>> s > >>> ource > >>> s_of_oscillatory_gamma-band_activity > >>> ? > >>> > >>> Best, > >>> J?rn > >>> > >>> > >>> -- > >>> > >>> J?rn M. Horschig, Software Engineer > >>> Artinis Medical Systems | +31 481 350 980 > >>> > >>>> -----Original Message----- > >>>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >>>> bounces at science.ru.nl] On Behalf Of Nadine > >>>> Sent: Wednesday, May 6, 2015 2:21 PM > >>>> To: fieldtrip at science.ru.nl > >>>> Subject: [FieldTrip] labels per grid point > >>>> > >>>> Dear Fieldtrip Users, > >>>> > >>>> I am trying to get anatomical labels for individual source grid > >>>> points. I > >>> can only > >>>> find how to parcellate the grid points to get an averaged value of > >>>> sources > >>> for > >>>> certain parcellations (e.g. Brodmann areas). But I would like to get > >>>> an anatomical label per grid point, so that I can see which grid > >>>> points > >>> belong to > >>>> which area. Does anybody have any solution for this? > >>>> > >>>> Thanks in advance for your help, > >>>> Nadine > >>>> > >>>> _______________________________________________ > >>>> fieldtrip mailing list > >>>> fieldtrip at donders.ru.nl > >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >>> > >>> > >>> _______________________________________________ > >>> fieldtrip mailing list > >>> fieldtrip at donders.ru.nl > >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > ------------------------------ > > Message: 7 > Date: Thu, 7 May 2015 09:36:34 +0200 > From: Nadine > To: FieldTrip discussion list > Subject: Re: [FieldTrip] labels per grid point > Message-ID: <306CCF9F-01AC-4036-8B14-C4FFC99AA54E at gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi Tzvetan, > > Yes, thank you, this is perfect! > > Best, > Nadine > On 06 May 2015, at 14:37, Tzvetan Popov > wrote: > > > Hi Nadine, > > > > maybe this is what you need? > > > http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations > > > > best > > tzvetan > > > >> Dear Fieldtrip Users, > >> > >> I am trying to get anatomical labels for individual source grid points. > I can only find how to parcellate the grid points to get an averaged value > of sources for certain parcellations (e.g. Brodmann areas). But I would > like to get an anatomical label per grid point, so that I can see which > grid points belong to which area. Does anybody have any solution for this? > >> > >> Thanks in advance for your help, > >> Nadine > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > ------------------------------ > > Message: 8 > Date: Thu, 7 May 2015 10:21:19 +0200 > From: H?l?ne Guiraud > To: FieldTrip discussion list > Subject: Re: [FieldTrip] re template for children > Message-ID: > < > CAJ16KS8BwyAttHC2E23tsdisvjE+Y_T5NAjpMm4F8--0H6HN8g at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Till and John, > > Thank you, this is perfect! > > Best regards, > H?l?ne > > 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > > > We have a template for children?actually have for infants from 2 weeks > > through adults at 89 years. We also have average electrode positions for > > EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented > > priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have > > been using this recently with FT for infants and child/adolescent/adult > > ages. > > > > WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > Fro www site: This is a database of average MRIs and associated MRI > > volumes for developmental MRI work. It consists of average MRI templates, > > segmented partial volume estimate volumes for GM, WM, T2W-derived CSF > > (Description > > < > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html > > > > > ). The database is separated into head-based and brain-based averages. > The > > data are separated by ages in months, years, 6-month, or 5-year intervals > > (Ages and Templates > > < > > > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm > > l>). The templates are grouped into first year (2 weeks through 12 > > months), early childhood (15 months through 4 years), childhood (4 years > > through 10 years), adolescence (10.5 years through 17.5 years) and adults > > (18 years through 89 years). > > Tools for cortical source analysis of EEG and ERP are provided. These > > tools are based on the average MRI templates, segmenting, and atlases. > > > > Also see my www site, jerlab.psych.sc.edu for publications describing > > this. We have a recent chapter that has a good description of the issues > > behind the database (with Wanze Xie). We have a paper accepted at > > Neuroimage for their upcoming ?Data Sharing? issue (with Carmen Sanchez, > > Michelle Phillips-Meek, and Wanze Xie). > > > > John > > > > > > *********************************************** > > John E. Richards Carolina Distinguished Professor > > Department of Psychology > > University of South Carolina > > Columbia, SC 29208 > > Dept Phone: 803 777 2079 > > Fax: 803 777 9558 > > Email: richards-john at sc.edu > > HTTP: jerlab.psych.sc.edu > > *********************************************** > > > > > > > > > > > > > > > > > > On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" > > wrote: > > > > >Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > >To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > >You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > >When replying, please edit your Subject line so it is more specific > > >than "Re: Contents of fieldtrip digest..." > > > > > > > > >Today's Topics: > > > > > > 1. Search for a template children. (H?l?ne Guiraud) > > > 2. Re: Search for a template children. (Till Schneider) > > > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > > > > > > > >---------------------------------------------------------------------- > > > > > >Message: 1 > > >Date: Wed, 29 Apr 2015 14:45:56 +0200 > > >From: H?l?ne Guiraud > > >To: fieldtrip at science.ru.nl > > >Subject: [FieldTrip] Search for a template children. > > >Message-ID: > > > < > > CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> > > >Content-Type: text/plain; charset="utf-8" > > > > > >Dear community, > > > > > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on > > >speech perception in children using MEG. > > >The children involved in the study don't pass MRI. We want to achieve > > >source reconstruction from a template. However I can't find a template > > >corresponding to the anatomy of a child (8-12 years). > > >Can someone tell me if there are template children and where I can find > > >them? > > > > > >Best, > > > > > >H?l?ne Guiraud > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e > > >9b53e/attachment-0001.html> > > > > > >------------------------------ > > > > > >Message: 2 > > >Date: Wed, 29 Apr 2015 15:53:13 +0200 > > >From: Till Schneider > > >To: FieldTrip discussion list > > >Subject: Re: [FieldTrip] Search for a template children. > > >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> > > >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > > > > >Dear Helene, > > > > > >McGill University provides MNI brains for different age groups between > > >4.5y to 18y. > > >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 > > >You will probably find the template brain you are searching for in this > > >database. > > > > > >Best regards, > > >Till > > > > > >-- > > > > > >Till Schneider, PhD > > > > > >Cognitive and Clinical Neurophysiology Group > > >Dept. of Neurophysiology and Pathophysiology > > >University Medical Center Hamburg-Eppendorf > > >Martinistr. 52 > > >20246 Hamburg > > >Germany > > > > > >phone +49-40-7410-53188 > > >fax +49-40-7410-57126 > > >www.uke.de/neurophysiologie > > > > > > > > > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: > > >> Dear community, > > >> > > >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) > > >> on speech perception in children using MEG. > > >> The children involved in the study don't pass MRI. We want to achieve > > >> source reconstruction from a template. However I can't find a template > > >> corresponding to the anatomy of a child (8-12 years). > > >> Can someone tell me if there are template children and where I can > > >> find them? > > >> > > >> Best, > > >> > > >> H?l?ne Guiraud > > >> > > >> > > >> _______________________________________________ > > >> fieldtrip mailing list > > >> fieldtrip at donders.ru.nl > > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > >-- > > > > > >_____________________________________________________________________ > > > > > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen > > >Rechts; Gerichtsstand: Hamburg | www.uke.de > > >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. > > >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik > > >_____________________________________________________________________ > > > > > >SAVE PAPER - THINK BEFORE PRINTING > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e > > >44937/attachment-0001.html> > > > > > >------------------------------ > > > > > >Message: 3 > > >Date: Wed, 29 Apr 2015 16:25:35 +0200 > > >From: Keyvan Mahjoory > > >To: FieldTrip discussion list > > >Subject: [FieldTrip] ICBM 152 templates in FT > > >Message-ID: > > > > UJp6-+4+7fA at mail.gmail.com> > > >Content-Type: text/plain; charset="iso-8859-1" > > > > > >Dear Fieldtrip Users, > > > > > >I perform source analysis in Fieldtrip with a template head model ( > > >standard_bem ) and > a > > >template source model (cortex_5124.surf.gii > > >) to constarin > > >estimated sources on cortex. These templates are based on Colin27, But > I > > >prefere to use the template ICBM152 instead. > > >Does FT include ICBM template? I mean templates for both head model and > > >cortical surfe. > > > > > >Many Thanks in advance, > > >Keyvan > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 > > >9daf3/attachment-0001.html> > > > > > >------------------------------ > > > > > >_______________________________________________ > > >fieldtrip mailing list > > >fieldtrip at donders.ru.nl > > >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > >End of fieldtrip Digest, Vol 53, Issue 23 > > >***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > H?l?ne Guiraud > Doctorante > Universit? Lyon 2 > Laboratoire Dynamique Du Langage > CNRS, UMR 5596 > Tel : 04 72 72 65 34 > guiraudh at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/0bd0dea8/attachment-0001.html > > > > ------------------------------ > > Message: 9 > Date: Thu, 7 May 2015 08:29:39 +0000 > From: "Sander, Myriam" > To: FieldTrip discussion list ?[fieldtrip at science.ru.nl]? > > Subject: [FieldTrip] Vacant Predoctoral Position in Lifespan > Psychology at the MPI for Human Development in Berlin, Germany > Message-ID: > < > D12CFACF574CEA4498D72B949FF5631C9B20628E at MaxMail04.mpib-berlin.mpg.de> > > Content-Type: text/plain; charset="cp1256" > > ********************************************************* > > PREDOCTORAL POSITION: CENTER FOR LIFESPAN PSYCHOLOGY, MPI BERLIN > > The new MINERVA research group headed by Dr. Myriam Sander at the Max > Planck Institute for Human Development, Center for Lifespan Psychology > (Director: Prof. Dr. Ulman Lindenberger), is seeking applications for a > > PREDOCTORAL POSITION > > The doctoral contract will last for 3 years. The position is available > from October 1, 2015 or later. > > Job Description: Future research of the new MINERVA research group (PI: > Dr. Myriam Sander) will use a multi-modal imaging approach (EEG with a > focus on oscillatory measures in combination with structural and functional > MRI) to uncover lifespan differences in the interplay between sensory > (visual and auditory) and cognitive abilities influencing memory > performance. The MINERVA research group is part of the project ?Cognitive > and Neural Dynamics of Memory Across the Lifespan (CONMEM)? which > investigates lifespan changes in the interplay between associative and > strategic components of memory functioning on neural and cognitive levels, > with a focus on working and episodic memory (see Sander, et al., Neurosci. > Biobehav. Rev., 2012; Shing, et al., Neurosci. Biobehav. Rev., 2010). The > successful predoctoral fellow will plan and conduct empirical studies in > this domain, analyze the behavioral, EEG, and MRI data, and prepare > scientific manuscripts for publication. > > For further information, please contact: Dr. Myriam Sander ( > sander at mpib-berlin.mpg.de) > > Requirements: A successful applicant needs to hold (or expect by summer > 2015) a diploma/master degree in psychology, cognitive neuroscience, or > related fields. Applicants should have experience with conducting > experimental research, knowledge in neuroimaging methods (EEG and/or MRI), > and a solid background in at least one programming language (preferably > Matlab or R). In addition, the ability to work independently as well as a > high proficiency of the English language is required. Experience with > age-comparative studies is an advantage. > > The Max Planck Society is interested in increasing the number of women on > its scientific staff. We strongly encourage applications from women and > members of minority groups. In addition, the Max Planck Society is > committed to employing more handicapped individuals and encourages them to > apply. > > To apply, please send (as ONE FILE and via email only) a statement of > research interests, a CV, a copy of relevant certificates, (p)reprints of > publications, and a list of two references to Dr. Myriam Sander, MPI for > Human Development, Lentzeallee 94, 14195 Berlin (sander at mpib-berlin.mpg.de) > preferably by June 30th, 2015. Later applications will be considered until > the position is filled. > > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/0579250d/attachment-0001.html > > > > ------------------------------ > > Message: 10 > Date: Thu, 7 May 2015 11:11:54 +0200 > From: "Hamza Fawzi Altakroury (Alumni)" > To: FieldTrip discussion list > Subject: [FieldTrip] Vgrid > Message-ID: > < > CADB5qVBgnCciEmuwJ8ZR3MPRrEuHeWdysTQWek9+aTabP6-GMg at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was expected to > be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > I don't have a folder called pcwin64! I have only glnx86 (empty folder) > glnxa64 and maci64 in ***\external\vgrid\bin\ > > I also downloaded a newer version of fieldtrip, but I did not find it! > > >From where I can get vgrid.exe? > > Thank you > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabanc? University > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/793650e7/attachment-0001.html > > > > ------------------------------ > > Message: 11 > Date: Thu, 07 May 2015 11:40:17 +0200 > From: Johannes Vorwerk > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] Vgrid > Message-ID: <1430991617.11932.23.camel at biomag43> > Content-Type: text/plain; charset="utf-8" > > Hi, > > vgrid should no longer be needed in recent fieldtrip-versions. It was > replaced by a fully matlab-based function (prepare_mesh_hexahedral), > that should now also work under windows. A vgrid.exe never existed, it > was only available for mac and linux. Did you try updating your > fieldtrip-version to a recent release? > > Best, > Johannes > > Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi > Altakroury (Alumni): > > Hello, > > > > > > > > I got the following error when I run these lines: (found in > > http://www.fieldtriptoolbox.org/development/simbio) > > > > cfg = []; > > cfg.shift = 0.3; > > cfg.method = 'hexahedral'; > > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > Error using vgrid (line 16) > > the vgrid executable is not available for your platform, it was > > expected to be > > located at > > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > > > > > > I don't have a folder called pcwin64! I have only glnx86 (empty > > folder) glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > > > > From where I can get vgrid.exe? > > > > > > Thank you > > > > > > > > -- > > > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabanc? University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Dipl.-Math. Johannes Vorwerk > e-mail: j.vorwerk at uni-muenster.de > > Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters > Institute for Biomagnetism and Biosignalanalysis, University of Muenster > www: http://campus.uni-muenster.de/index.php?id=919&L=1 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/6c43fe26/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 5 > **************************************** > -- Haiteng Jiang PhD candidate Donders Institute for Brain, Cognition and Behaviour Neuronal Oscillations Group Computational Cognitive Neuroscience Lab https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.wunderle at esi-frankfurt.de Thu May 7 12:56:27 2015 From: thomas.wunderle at esi-frankfurt.de (Wunderle, Thomas) Date: Thu, 7 May 2015 10:56:27 +0000 Subject: [FieldTrip] Statistics on spike rate Message-ID: <27E5CAD9145EEC41BB9B34C01716A1987FB3B3B3@UM-EXCDAG-A01.um.gwdg.de> Dear community, I’m working on spike/ spike-field analysis and I was wondering if there are statistical comparisons in field trip for spikes. In particular, I would like to test if the spike rate after a stimulus onset is significantly different from the spike rate before stimulus onset (that is, the recorded neurons responds to the stimulus). I tried around with “ft_timelockstatistics”, “ft_statistics_stats” and “ft_spike_rate”, bud did not succeed. I’m not very familiar with statistical testing in FT in general, so I don’t know if statistics for spike rate are implemented in field trip at all. Thanks in advance, Thomas ----- Dr. Thomas Wunderle Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society Deutschordenstrasse 46 60528 Frankfurt am Main, Germany www.esi-frankfurt.de thomas.wunderle at esi-frankfurt.de Tel: +49 69 96769 516 Fax: +49 69 96769 555 Sitz der Gesellschaft: Frankfurt am Main Registergericht: Amtsgericht Frankfurt - HRB 84266 Geschäftsführer: Prof. Dr. Pascal Fries -------------- next part -------------- An HTML attachment was scrubbed... URL: From berdakho at gmail.com Thu May 7 15:56:04 2015 From: berdakho at gmail.com (Berdakh Abibullaev) Date: Thu, 7 May 2015 08:56:04 -0500 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi, I am also using the Dr. Richard's infant database. It took us sometime to figure out to how prepare forward models in FT. If you need I have scripts ready to use to get you started smoothly. ​Just let me know. ​ ​​ Thanks, Berdakh Abibullaev, Postdoctoral Research Scholar , Laboratory for Non-invasive Brain-Machine Interfaces, Department of Electrical Eng. & Computer Science, University of Houston, E413, Engineering Building II, Houston, Texas, 77204-4005. https://www.facebook.com/UHBMIST On Thu, May 7, 2015 at 3:21 AM, Hélène Guiraud wrote: > Hi Till and John, > > Thank you, this is perfect! > > Best regards, > Hélène > > 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > >> We have a template for children‹actually have for infants from 2 weeks >> through adults at 89 years. We also have average electrode positions for >> EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented >> priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have >> been using this recently with FT for infants and child/adolescent/adult >> ages. >> >> WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ >> Fro www site: This is a database of average MRIs and associated MRI >> volumes for developmental MRI work. It consists of average MRI templates, >> segmented partial volume estimate volumes for GM, WM, T2W-derived CSF >> (Description >> < >> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html >> > >> ). The database is separated into head-based and brain-based averages. The >> data are separated by ages in months, years, 6-month, or 5-year intervals >> (Ages and Templates >> < >> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm >> l>). The templates are grouped into first year (2 weeks through 12 >> months), early childhood (15 months through 4 years), childhood (4 years >> through 10 years), adolescence (10.5 years through 17.5 years) and adults >> (18 years through 89 years). >> Tools for cortical source analysis of EEG and ERP are provided. These >> tools are based on the average MRI templates, segmenting, and atlases. >> >> Also see my www site, jerlab.psych.sc.edu for publications describing >> this. We have a recent chapter that has a good description of the issues >> behind the database (with Wanze Xie). We have a paper accepted at >> Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, >> Michelle Phillips-Meek, and Wanze Xie). >> >> John >> >> >> *********************************************** >> John E. Richards Carolina Distinguished Professor >> Department of Psychology >> University of South Carolina >> Columbia, SC 29208 >> Dept Phone: 803 777 2079 >> Fax: 803 777 9558 >> Email: richards-john at sc.edu >> HTTP: jerlab.psych.sc.edu >> *********************************************** >> >> >> >> >> >> >> >> >> On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" >> wrote: >> >> >Send fieldtrip mailing list submissions to >> > fieldtrip at science.ru.nl >> > >> >To subscribe or unsubscribe via the World Wide Web, visit >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >or, via email, send a message with subject or body 'help' to >> > fieldtrip-request at science.ru.nl >> > >> >You can reach the person managing the list at >> > fieldtrip-owner at science.ru.nl >> > >> >When replying, please edit your Subject line so it is more specific >> >than "Re: Contents of fieldtrip digest..." >> > >> > >> >Today's Topics: >> > >> > 1. Search for a template children. (H?l?ne Guiraud) >> > 2. Re: Search for a template children. (Till Schneider) >> > 3. ICBM 152 templates in FT (Keyvan Mahjoory) >> > >> > >> >---------------------------------------------------------------------- >> > >> >Message: 1 >> >Date: Wed, 29 Apr 2015 14:45:56 +0200 >> >From: H?l?ne Guiraud >> >To: fieldtrip at science.ru.nl >> >Subject: [FieldTrip] Search for a template children. >> >Message-ID: >> > < >> CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> >> >Content-Type: text/plain; charset="utf-8" >> > >> >Dear community, >> > >> >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >> >speech perception in children using MEG. >> >The children involved in the study don't pass MRI. We want to achieve >> >source reconstruction from a template. However I can't find a template >> >corresponding to the anatomy of a child (8-12 years). >> >Can someone tell me if there are template children and where I can find >> >them? >> > >> >Best, >> > >> >H?l?ne Guiraud >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e >> >9b53e/attachment-0001.html> >> > >> >------------------------------ >> > >> >Message: 2 >> >Date: Wed, 29 Apr 2015 15:53:13 +0200 >> >From: Till Schneider >> >To: FieldTrip discussion list >> >Subject: Re: [FieldTrip] Search for a template children. >> >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" >> > >> >Dear Helene, >> > >> >McGill University provides MNI brains for different age groups between >> >4.5y to 18y. >> >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >> >You will probably find the template brain you are searching for in this >> >database. >> > >> >Best regards, >> >Till >> > >> >-- >> > >> >Till Schneider, PhD >> > >> >Cognitive and Clinical Neurophysiology Group >> >Dept. of Neurophysiology and Pathophysiology >> >University Medical Center Hamburg-Eppendorf >> >Martinistr. 52 >> >20246 Hamburg >> >Germany >> > >> >phone +49-40-7410-53188 >> >fax +49-40-7410-57126 >> >www.uke.de/neurophysiologie >> > >> > >> > >> >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >> >> Dear community, >> >> >> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >> >> on speech perception in children using MEG. >> >> The children involved in the study don't pass MRI. We want to achieve >> >> source reconstruction from a template. However I can't find a template >> >> corresponding to the anatomy of a child (8-12 years). >> >> Can someone tell me if there are template children and where I can >> >> find them? >> >> >> >> Best, >> >> >> >> H?l?ne Guiraud >> >> >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> > >> >-- >> > >> >_____________________________________________________________________ >> > >> >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >> >Rechts; Gerichtsstand: Hamburg | www.uke.de >> >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >> >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >> >_____________________________________________________________________ >> > >> >SAVE PAPER - THINK BEFORE PRINTING >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e >> >44937/attachment-0001.html> >> > >> >------------------------------ >> > >> >Message: 3 >> >Date: Wed, 29 Apr 2015 16:25:35 +0200 >> >From: Keyvan Mahjoory >> >To: FieldTrip discussion list >> >Subject: [FieldTrip] ICBM 152 templates in FT >> >Message-ID: >> > > UJp6-+4+7fA at mail.gmail.com> >> >Content-Type: text/plain; charset="iso-8859-1" >> > >> >Dear Fieldtrip Users, >> > >> >I perform source analysis in Fieldtrip with a template head model ( >> >standard_bem ) and a >> >template source model (cortex_5124.surf.gii >> >) to constarin >> >estimated sources on cortex. These templates are based on Colin27, But I >> >prefere to use the template ICBM152 instead. >> >Does FT include ICBM template? I mean templates for both head model and >> >cortical surfe. >> > >> >Many Thanks in advance, >> >Keyvan >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 >> >9daf3/attachment-0001.html> >> > >> >------------------------------ >> > >> >_______________________________________________ >> >fieldtrip mailing list >> >fieldtrip at donders.ru.nl >> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> >End of fieldtrip Digest, Vol 53, Issue 23 >> >***************************************** >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Hélène Guiraud > Doctorante > Université Lyon 2 > Laboratoire Dynamique Du Langage > CNRS, UMR 5596 > Tel : 04 72 72 65 34 > guiraudh at gmail.com > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guiraudh at gmail.com Thu May 7 16:23:54 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Thu, 7 May 2015 16:23:54 +0200 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi, Thank you. I'm just trying to develop my scripts. A little help would be welcome! I'm taking, thank! Hélène 2015-05-07 15:56 GMT+02:00 Berdakh Abibullaev : > Hi, > > I am also using the Dr. Richard's infant database. It took us sometime to > figure out to how prepare forward models in FT. > If you need I have scripts ready to use to get you started smoothly. > > ​Just let me know. ​ > > ​​ > Thanks, > > Berdakh Abibullaev, > > Postdoctoral Research Scholar , > Laboratory for Non-invasive Brain-Machine Interfaces, > Department of Electrical Eng. & Computer Science, > University of Houston, E413, Engineering Building II, > Houston, Texas, 77204-4005. > https://www.facebook.com/UHBMIST > > On Thu, May 7, 2015 at 3:21 AM, Hélène Guiraud wrote: > >> Hi Till and John, >> >> Thank you, this is perfect! >> >> Best regards, >> Hélène >> >> 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : >> >>> We have a template for children‹actually have for infants from 2 weeks >>> through adults at 89 years. We also have average electrode positions for >>> EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented >>> priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have >>> been using this recently with FT for infants and child/adolescent/adult >>> ages. >>> >>> WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ >>> Fro www site: This is a database of average MRIs and associated MRI >>> volumes for developmental MRI work. It consists of average MRI templates, >>> segmented partial volume estimate volumes for GM, WM, T2W-derived CSF >>> (Description >>> < >>> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html >>> > >>> ). The database is separated into head-based and brain-based averages. >>> The >>> data are separated by ages in months, years, 6-month, or 5-year intervals >>> (Ages and Templates >>> < >>> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm >>> l>). The templates are grouped into first year (2 weeks through 12 >>> months), early childhood (15 months through 4 years), childhood (4 years >>> through 10 years), adolescence (10.5 years through 17.5 years) and adults >>> (18 years through 89 years). >>> Tools for cortical source analysis of EEG and ERP are provided. These >>> tools are based on the average MRI templates, segmenting, and atlases. >>> >>> Also see my www site, jerlab.psych.sc.edu for publications describing >>> this. We have a recent chapter that has a good description of the issues >>> behind the database (with Wanze Xie). We have a paper accepted at >>> Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, >>> Michelle Phillips-Meek, and Wanze Xie). >>> >>> John >>> >>> >>> *********************************************** >>> John E. Richards Carolina Distinguished Professor >>> Department of Psychology >>> University of South Carolina >>> Columbia, SC 29208 >>> Dept Phone: 803 777 2079 >>> Fax: 803 777 9558 >>> Email: richards-john at sc.edu >>> HTTP: jerlab.psych.sc.edu >>> *********************************************** >>> >>> >>> >>> >>> >>> >>> >>> >>> On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" >>> wrote: >>> >>> >Send fieldtrip mailing list submissions to >>> > fieldtrip at science.ru.nl >>> > >>> >To subscribe or unsubscribe via the World Wide Web, visit >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >or, via email, send a message with subject or body 'help' to >>> > fieldtrip-request at science.ru.nl >>> > >>> >You can reach the person managing the list at >>> > fieldtrip-owner at science.ru.nl >>> > >>> >When replying, please edit your Subject line so it is more specific >>> >than "Re: Contents of fieldtrip digest..." >>> > >>> > >>> >Today's Topics: >>> > >>> > 1. Search for a template children. (H?l?ne Guiraud) >>> > 2. Re: Search for a template children. (Till Schneider) >>> > 3. ICBM 152 templates in FT (Keyvan Mahjoory) >>> > >>> > >>> >---------------------------------------------------------------------- >>> > >>> >Message: 1 >>> >Date: Wed, 29 Apr 2015 14:45:56 +0200 >>> >From: H?l?ne Guiraud >>> >To: fieldtrip at science.ru.nl >>> >Subject: [FieldTrip] Search for a template children. >>> >Message-ID: >>> > < >>> CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> >>> >Content-Type: text/plain; charset="utf-8" >>> > >>> >Dear community, >>> > >>> >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >>> >speech perception in children using MEG. >>> >The children involved in the study don't pass MRI. We want to achieve >>> >source reconstruction from a template. However I can't find a template >>> >corresponding to the anatomy of a child (8-12 years). >>> >Can someone tell me if there are template children and where I can find >>> >them? >>> > >>> >Best, >>> > >>> >H?l?ne Guiraud >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e >>> >9b53e/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >Message: 2 >>> >Date: Wed, 29 Apr 2015 15:53:13 +0200 >>> >From: Till Schneider >>> >To: FieldTrip discussion list >>> >Subject: Re: [FieldTrip] Search for a template children. >>> >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >>> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" >>> > >>> >Dear Helene, >>> > >>> >McGill University provides MNI brains for different age groups between >>> >4.5y to 18y. >>> >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >>> >You will probably find the template brain you are searching for in this >>> >database. >>> > >>> >Best regards, >>> >Till >>> > >>> >-- >>> > >>> >Till Schneider, PhD >>> > >>> >Cognitive and Clinical Neurophysiology Group >>> >Dept. of Neurophysiology and Pathophysiology >>> >University Medical Center Hamburg-Eppendorf >>> >Martinistr. 52 >>> >20246 Hamburg >>> >Germany >>> > >>> >phone +49-40-7410-53188 >>> >fax +49-40-7410-57126 >>> >www.uke.de/neurophysiologie >>> > >>> > >>> > >>> >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >>> >> Dear community, >>> >> >>> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >>> >> on speech perception in children using MEG. >>> >> The children involved in the study don't pass MRI. We want to achieve >>> >> source reconstruction from a template. However I can't find a template >>> >> corresponding to the anatomy of a child (8-12 years). >>> >> Can someone tell me if there are template children and where I can >>> >> find them? >>> >> >>> >> Best, >>> >> >>> >> H?l?ne Guiraud >>> >> >>> >> >>> >> _______________________________________________ >>> >> fieldtrip mailing list >>> >> fieldtrip at donders.ru.nl >>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> > >>> > >>> >-- >>> > >>> >_____________________________________________________________________ >>> > >>> >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >>> >Rechts; Gerichtsstand: Hamburg | www.uke.de >>> >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >>> >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >>> >_____________________________________________________________________ >>> > >>> >SAVE PAPER - THINK BEFORE PRINTING >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e >>> >44937/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >Message: 3 >>> >Date: Wed, 29 Apr 2015 16:25:35 +0200 >>> >From: Keyvan Mahjoory >>> >To: FieldTrip discussion list >>> >Subject: [FieldTrip] ICBM 152 templates in FT >>> >Message-ID: >>> > >> UJp6-+4+7fA at mail.gmail.com> >>> >Content-Type: text/plain; charset="iso-8859-1" >>> > >>> >Dear Fieldtrip Users, >>> > >>> >I perform source analysis in Fieldtrip with a template head model ( >>> >standard_bem ) and >>> a >>> >template source model (cortex_5124.surf.gii >>> >) to constarin >>> >estimated sources on cortex. These templates are based on Colin27, But >>> I >>> >prefere to use the template ICBM152 instead. >>> >Does FT include ICBM template? I mean templates for both head model and >>> >cortical surfe. >>> > >>> >Many Thanks in advance, >>> >Keyvan >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 >>> >9daf3/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >_______________________________________________ >>> >fieldtrip mailing list >>> >fieldtrip at donders.ru.nl >>> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> > >>> >End of fieldtrip Digest, Vol 53, Issue 23 >>> >***************************************** >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Hélène Guiraud >> Doctorante >> Université Lyon 2 >> Laboratoire Dynamique Du Langage >> CNRS, UMR 5596 >> Tel : 04 72 72 65 34 >> guiraudh at gmail.com >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hélène Guiraud Doctorante Université Lyon 2 Laboratoire Dynamique Du Langage CNRS, UMR 5596 Tel : 04 72 72 65 34 guiraudh at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu May 7 16:39:59 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Thu, 7 May 2015 17:39:59 +0300 Subject: [FieldTrip] Vgrid In-Reply-To: <1430991617.11932.23.camel@biomag43> References: <1430991617.11932.23.camel@biomag43> Message-ID: Thank you Johannes, I'll try to run it using a newer version of fieldtrip. Best, Hamza On Thu, May 7, 2015 at 12:40 PM, Johannes Vorwerk wrote: > Hi, > > vgrid should no longer be needed in recent fieldtrip-versions. It was > replaced by a fully matlab-based function (prepare_mesh_hexahedral), that > should now also work under windows. A vgrid.exe never existed, it was only > available for mac and linux. Did you try updating your fieldtrip-version to > a recent release? > > Best, > Johannes > > Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi Altakroury > (Alumni): > > Hello, > > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was expected > to be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > I don't have a folder called pcwin64! I have only glnx86 (empty folder) > glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > From where I can get vgrid.exe? > > > Thank you > > > > -- > > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Dipl.-Math. Johannes Vorwerk > e-mail: j.vorwerk at uni-muenster.de > > Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters > Institute for Biomagnetism and Biosignalanalysis, University of Muenster > www: http://campus.uni-muenster.de/index.php?id=919&L=1 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Fri May 8 13:22:56 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Fri, 8 May 2015 12:22:56 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy Message-ID: <554C9C90.4090702@glasgow.ac.uk> An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri May 8 13:38:48 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 8 May 2015 11:38:48 +0000 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy In-Reply-To: <554C9C90.4090702@glasgow.ac.uk> References: <554C9C90.4090702@glasgow.ac.uk> Message-ID: <524BB694-AB68-4A2A-BC8B-9A9F515CC75B@fcdonders.ru.nl> May, Have you ensured that the stat.pos field contains the dipole positions, coregistered to the template brain? Best, Jan-Mathijs On May 8, 2015, at 1:22 PM, Heng-Ru May Tan > wrote: Hi Fieldtrippers [The previous email didn't display properly so resending this again.] I am having trouble running ft_sourceinterpolate... I didn't seem to have this issue before. =( The anatomy seems to be missing and so when I subsequently call ft_sourceplot, the brain anatomy is not 'available' for plotting. Here are some example of the things I tried and the errors in hope that someone might be able help! Many thanks in advance, May -- this is a stat structure used: stat = prob: [33480x1 double] cirange: [33480x1 double] mask: [33480x1 logical] stat: [33480x1 double] ref: [33480x1 double] df: 185 critval: [-1.9729 1.9729] dim: [33480 1] inside: [10354x1 double] outside: [23126x1 double] pos: [33480x3 double] freq: 64.9309 cfg: [1x1 struct] grid = xgrid: [1x31 double] ygrid: [1x36 double] zgrid: [1x30 double] dim: [31 36 30] pos: [33480x3 double] inside: [12773x1 double] outside: [20707x1 double] anatpath2 = [unixANALYSEpath 'Matlab_scripts/fieldtrip-20140114/template/anatomy/single_subj_T1.nii'] template_mri = ft_read_mri(anatpath2); cfg = []; cfg.parameter = 'stat'; cfg.interpmethod = 'nearest'; statplot2 = ft_sourceinterpolate(cfg,stat, template_mri); the input is volume data with dimensions [91 109 91] Warning: sphereradius is not used for projmethod 'nearest' > In fieldtrip-20140114/private/interp_ungridded at 86 In ft_sourceinterpolate at 216 the call to "ft_sourceinterpolate" took 37 seconds and required the additional allocation of an estimated 96 MB -- somehow anatomy structure is lost... ?! statplot2 = freq: 64.9309 stat: [902629x1 double] pos: [902629x3 double] dim: [91 109 91] inside: [1x902629 double] outside: [1x0 double] unit: 'mm' cfg: [1x1 struct] cfg = []; cfg.method ='slice'; cfg.nslices = 30 cfg.funparameter = 'stat'; % cfg.maskparameter = 'mask'; cfg.maskparameter = cfg.funparameter; cfg.anaparameter = 'anatomy'; cfg.opacitymap = 'rampup'; ft_sourceplot(cfg, statplot2); the input is source data with 902629 positions on a [91 109 91] grid Warning: do not understand cfg.anaparameter, not plotting anatomy\n > In ft_sourceplot at 350 the call to "ft_sourceplot" took 2 seconds and required the additional allocation of an estimated 3 MB -- If using fieldtrip_new on server --> revision = '$Id: ft_sourceinterpolate.m 10221 2015-02-12 08:28:20Z roboos $'; cfg = parameter: 'stat' interpmethod: 'nearest' statplot1 = ft_sourceinterpolate(stat, template_mri) Undefined function or variable 'abort'. Error in ft_sourceinterpolate (line 106) if abort -- ________________________________________________________________________________________________________________________________________ Heng-Ru May Tan Centre for Cognitive Neuroimaging (CCNi) ▫Institute of Neuroscience and Psychology (INP) ▫ College of Medical, Veterinary and Life Sciences & College of Science and Engineering ▫ University of Glasgow ▫ 58 Hillhead Street, Glasgow G12 8QB, United Kingdom ▫ +44 (0)141-330-5090 ▫ Heng-RuMay.Tan at glasgow.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From christophe.grova at mcgill.ca Sat May 9 12:38:09 2015 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Sat, 9 May 2015 10:38:09 +0000 Subject: [FieldTrip] MSc/PhD positions in Biomedical Physics and at the PERFORM Centre, Concordia University Message-ID: <9E1647EDA3EBB44AADA162CEC4C4222E7510052D@exmbx2010-9.campus.MCGILL.CA> Now available, MSc/PhD positions in Biomedical Physics and at the PERFORM Centre, Concordia University [multi_funkin] We offer two very interesting opportunities for M.Sc or PhD projects in the context of the new Biomedical Physics program proposed at Concordia University by the Department of Physics and at PERFORM. Project 1: Multimodal characterization of resting state functional connectivity. Supervisor: C. Grova, Department of Physics and PERFORM Center The overall project aims at assessing the organization of fluctuations of neuronal bioelectrical signals measured from the scalp using either Electro-EncephaloGraphy (EEG) or Magneto-EncephaloGraphy (MEG), while the subject is resting. The main methodological originality of this project is to consider time-frequency based source localization of EEG and MEG data, using wavelet-based Maximum on the Mean wMEM (Lina et al IEEE TBME 2014) in order to investigate resting state functional connectivity from simultaneous EEG/MEG data and also from simultaneous high-density EEG/fMRI data. These multimodal data will be considered in order to investigate the dynamic of resting state functional connectivity patterns in healthy controls The candidates will join a multidisciplinary team composed of neurologists and methodologists within the Multimodal Functional Imaging Laboratory, directed by Pr. Christophe Grova. Simultaneous EEG/fMRI data will be acquired at PERFORM, while simultaneous EEG/MEG data will be acquired at the Montreal Neurological Institute, McGill University. The key component of this project consists in adapting and validating the performance of EEG/MEG source localization of resting state data in healthy subjects, in order to build a normative database. Requirements: The candidate should have some knowledge in image and signal processing, linear algebra and statistics, as well as experience in computation and programmation, using notably Matlab software. Any experience with neuroimaging softwares would be an asset. Project 2: Multimodal characterization of functional hubs. Supervisor: C. Gauthier, Department of Physics and PERFORM Center Co-Supervisor: C. Grova, Department of Physics and PERFORM Center In the overall context of understanding the organization of brain activity during rest, as in the analysis of any network, the notion of “hub”, their detection and characterization is a key and challenging objective. This project will propose and evaluate new methods to detect these hubs and to charactrize their underlying metabolism using quantitative Magnetic Resonance Imaging (MRI) techniques. Using a new method based on sparse modeling to extract the hubs of such network organization from resting state functional MRI data acquired simultaneously with EEG data, the project will consist in combining these techniques with quantitative MRI to measure the metabolic rate of oxygen consumption. To do so, gas manipulations, i.e. breathing controlled amount of CO2 and O2, will be needed during the MRI acquisition. The objective will be to assess hemodynamic fluctuations, neuronal bioelectrical oscillations and local oxygen consumption of these hubs, within a population of healthy controls of different age ranges. Requirements: The candidate should have some knowledge in image and signal processing, linear algebra and statistics, as well as experience in computation and programmation, using notably Matlab software. Any experience of neuroimaging softwares and in experimental sciences would be an asset More details on the Multimodal Functional Imaging Lab can be found at: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage More details on PERFORM centre can be found at: http://www.concordia.ca/research/perform.html Please send your CV and motivation letter to: christophe.grova at concordia.ca and claudine.gauthier at concordia.ca *************************** Christophe Grova, PhD Assistant Professor, Physics Dpt, Concordia University PERFORM centre, Concordia University, Chair of PERFORM Applied Bio-Imaging Committee (ABC) Adjunct Prof in Biomedical Engineering, and Neurology and Neurosurgery Dpt, McGill University Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute - epilepsy group Centre de Recherches en Mathématiques Physics Dpt Concordia University - Loyola Campus - Office SP 365.12 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Phone: (514) 848-2424 ext.4221 Biomedical Engineering Department McGill University - Room 304 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 Phone : (514) 398 2516 Fax : (514) 398 7461 email : christophe.grova at concordia.ca , christophe.grova at mcgill.ca web: Explore Concordia: http://explore.concordia.ca/christophe-grova Physics, Concordia University: http://physics.concordia.ca/facultyandresearch/bios/grova.php McGill University: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** [X] -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Mon May 11 13:29:03 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Mon, 11 May 2015 12:29:03 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy In-Reply-To: References: Message-ID: <5550927F.7080609@glasgow.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hjcjfgji.png Type: image/png Size: 213443 bytes Desc: not available URL: From anna.wieczorek.taraday at gmail.com Tue May 12 10:17:40 2015 From: anna.wieczorek.taraday at gmail.com (Anna Wieczorek-Taraday) Date: Tue, 12 May 2015 08:17:40 +0000 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip Message-ID: Dear Fieldtrippers, I have a problem while reading EEG (EGI) electrode location file to FieldTrip. I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? Any support will be appreciated. I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. *************************************** Here is code I used to read these locations: cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; cfg.feedback = 'yes'; layout = ft_prepare_layout(cfg); Here is the code that I used to preprocess my data in Fieldtrip: cfg = []; cfg.trialfun = 'ft_trialfun_general'; cfg.dataset = '136.set'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'DIN8' cfg.trialdef.prestim = 0.5; cfg.trialdef.poststim = 2.5; cfg = ft_definetrial(cfg); cfg.lpfilter = 'no'; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.3; data = ft_preprocessing(cfg); Anna Wieczorek-Taraday. PhD Student Nencki Institute of Experimental Biology Pasteur Street 3, 02-093 Warsaw, Poland Warsaw University of Social Sciences and Humanities Chodakowska Street 19/31, 03-815 Warsaw, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 12 11:05:09 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 12 May 2015 11:05:09 +0200 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip In-Reply-To: References: Message-ID: Hi Ana The ft_prepare_layout function reads the electrode positions and scales them such that they fit in the sphere that represents the head. I suggest you do cfg.layout = ‘yourfilename’ lay = ft_prepare_layout(cfg); cfg = []; cfg.layout = lay; ft_layoutplot(cfg); and then modify lay.pos repeatedly, every time plotting it again, until you are happy with the result. You probably want to do this for the vertical direction lay.pos(:,2) = (lay.pos(:,2)+shift) .* scale; to shift and scale the electrodes to a better fit inside/outside the sphere, and this for the horizontal lay.pos(:,1) = lay.pos(:,1) .* scale; as they seem to be properly centred along the x-axis alreadly. After this, you can save yourlayout.mat lay and specify “yourlayout.mat” as the layout filename for your future figures. best regards Robert On 12 May 2015, at 10:17, Anna Wieczorek-Taraday wrote: > Dear Fieldtrippers, > > I have a problem while reading EEG (EGI) electrode location file to FieldTrip. > I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. > > When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. > When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). > However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. > > I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? > Any support will be appreciated. > > I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. > > *************************************** > > > Here is code I used to read these locations: > > cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; > cfg.feedback = 'yes'; > layout = ft_prepare_layout(cfg); > > > Here is the code that I used to preprocess my data in Fieldtrip: > > cfg = []; > cfg.trialfun = 'ft_trialfun_general'; > cfg.dataset = '136.set'; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'DIN8' > cfg.trialdef.prestim = 0.5; > cfg.trialdef.poststim = 2.5; > cfg = ft_definetrial(cfg); > > cfg.lpfilter = 'no'; > cfg.hpfilter = 'yes'; > cfg.hpfreq = 0.3; > data = ft_preprocessing(cfg); > > Anna Wieczorek-Taraday. > > PhD Student > Nencki Institute of Experimental Biology > Pasteur Street 3, 02-093 Warsaw, Poland > > Warsaw University of Social Sciences and Humanities > Chodakowska Street 19/31, 03-815 Warsaw, Poland > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From anna.wieczorek.taraday at gmail.com Tue May 12 17:25:43 2015 From: anna.wieczorek.taraday at gmail.com (Anna Wieczorek-Taraday) Date: Tue, 12 May 2015 17:25:43 +0200 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip In-Reply-To: References: Message-ID: <72EDF4F9-1F07-42A1-B1B3-72174896C8A2@gmail.com> Hi Robert, Thank you for your help. Indeed, the location on the sphere looks good after adjusting these parameters. Thank you a lot. Best regards, Anna Sent from my iPad > On 12 May 2015, at 11:05, Robert Oostenveld wrote: > > Hi Ana > > The ft_prepare_layout function reads the electrode positions and scales them such that they fit in the sphere that represents the head. > > I suggest you do > > cfg.layout = ‘yourfilename’ > lay = ft_prepare_layout(cfg); > > cfg = []; > cfg.layout = lay; > ft_layoutplot(cfg); > > and then modify lay.pos repeatedly, every time plotting it again, until you are happy with the result. You probably want to do this for the vertical direction > lay.pos(:,2) = (lay.pos(:,2)+shift) .* scale; > to shift and scale the electrodes to a better fit inside/outside the sphere, and this for the horizontal > lay.pos(:,1) = lay.pos(:,1) .* scale; > as they seem to be properly centred along the x-axis alreadly. > > After this, you can > save yourlayout.mat lay > and specify “yourlayout.mat” as the layout filename for your future figures. > > > best regards > Robert > > > >> On 12 May 2015, at 10:17, Anna Wieczorek-Taraday wrote: >> >> Dear Fieldtrippers, >> >> I have a problem while reading EEG (EGI) electrode location file to FieldTrip. >> I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. >> >> When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. >> When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). >> However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. >> >> I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? >> Any support will be appreciated. >> >> I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. >> >> *************************************** >> >> >> Here is code I used to read these locations: >> >> cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; >> cfg.feedback = 'yes'; >> layout = ft_prepare_layout(cfg); >> >> >> Here is the code that I used to preprocess my data in Fieldtrip: >> >> cfg = []; >> cfg.trialfun = 'ft_trialfun_general'; >> cfg.dataset = '136.set'; >> cfg.trialdef.eventtype = 'trigger'; >> cfg.trialdef.eventvalue = 'DIN8' >> cfg.trialdef.prestim = 0.5; >> cfg.trialdef.poststim = 2.5; >> cfg = ft_definetrial(cfg); >> >> cfg.lpfilter = 'no'; >> cfg.hpfilter = 'yes'; >> cfg.hpfreq = 0.3; >> data = ft_preprocessing(cfg); >> >> Anna Wieczorek-Taraday. >> >> PhD Student >> Nencki Institute of Experimental Biology >> Pasteur Street 3, 02-093 Warsaw, Poland >> >> Warsaw University of Social Sciences and Humanities >> Chodakowska Street 19/31, 03-815 Warsaw, Poland >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Wed May 13 17:28:39 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Wed, 13 May 2015 17:28:39 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI Message-ID: Dear all, I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? If I am right, which command shall I use to organize individual WPLI data, in order to create a correct input for ‘ft_freqstatistics’. According to the tutorial, in case of time-frequency data it is ft_freqgrandaverage. However, if I use it for WPLI data, I have the following error: “This function requires freq data as input”. Could you please recommend me a tutorial, reference documentation or some comment on this issue? Thanks for any suggestions in advanced and let me know if the description of my problem is not clear! Zsolt -- ************************************************************ Ph.D. student Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Wed May 13 19:14:45 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 13 May 2015 19:14:45 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: Message-ID: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Hi Zsolt, > Dear all, > > > I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. > > > I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > You could. Stick with the tutorial you are currently working with. You should organize your data into cell arrays and call ft_freqstatistics like this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise ft_freqstatistics will default to ‘powspctrm’ which will be not present in the data. good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: From zerr.paul at googlemail.com Thu May 14 14:01:07 2015 From: zerr.paul at googlemail.com (Paul Zerr) Date: Thu, 14 May 2015 14:01:07 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found Message-ID: Hi all, I'm new to fieldtrip so forgive me if my mistake is obvious. I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with *cfg = []; * *cfg.dataset = '2.bdf';* *data = ft_preprocessing(cfg)* However, I get *reading and preprocessing* *error opening file: 2.bdf* *One or more output arguments not assigned during call to "read_24bit".* *Error in read_biosemi_bdf>readLowLevel (line 274)* * buf = read_24bit(filename, offset, numwords);* *Error in read_biosemi_bdf (line 242)* * buf = readLowLevel(filename, offset, epochlength); % see below in subfunction* *Error in ft_read_data (line 321)* * dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx);* *Error in ft_preprocessing (line 578)* * dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample,* * 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',* * strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat)* *Error in Untitled (line 19)* *data = ft_preprocessing(cfg) * Using *cfg.trialdef.eventtype = '?';* outputs *"no events were found in the datafile"* for *ft_definetrial* even for datasets with many markers. Converting to EDF+ did not help as it then says *"channels with different sampling rate not supported"*. Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Defining only one channel to preprocess gives the same error. I couldn't find a solution in the archives, the faq, wiki or documentation. I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. Any ideas? Much appreciated, Paul Zerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Thu May 14 16:15:09 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Thu, 14 May 2015 16:15:09 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Message-ID: Hi Tzvetan, thanks for your suggestions. I am still stucked at the ft_freqstatistics, as I keep on receiving the following error and would be glad if you could make a comment on this as well: #### Reference to non-existent field 'label'. Error in ft_freqgrandaverage (line 123) cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); ### Is it because I have labelcomb in the WPLI data? labelcmb: {9x2 cell} dimord: 'chan_freq_time' wplispctrm: [9x7x16 double] freq: [3 4 5 6 7 8 9] time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] cfg: [1x1 struct] And this is my specification (I couldn't fine the option cfg.channelcmb for ft_freqgrandaverage in the reference documentation): cfg = []; cfg.keepindividual = 'yes'; cfg.cfg.foilim = 'all'; cfg.toilim = 'all'; cfg.channel = 'all'; cfg.parameter = 'wplispctrm'; Thanks again for the answer in advance! Best, Zsolt ps.I can provide other parts of my code but I don't want to make this mail too long : 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > > Dear all, > > > I would like to perform a cluster-based permutation test on weighted phase > lag index values by using a within-subjects experimental design. I have two > conditions (congruent and incongruent one) and my goal is to compute WPLI > between certain channel combinations (FCz and F3 for instance) and see the > WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two > conditions. > > > I experienced some difficulties after the point when I calculated the > WPLI data for each participant. To perform the above-mentioned comparison, > shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > > You could. Stick with the tutorial you are currently working with. You > should organize your data into cell arrays and call ft_freqstatistics like > this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). > Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise > ft_freqstatistics will default to ‘powspctrm’ which will be not present in > the data. > good luck > tzvetan > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Fri May 15 10:26:45 2015 From: B.Haendel at gmx.net (Barbara Haendel) Date: Fri, 15 May 2015 10:26:45 +0200 Subject: [FieldTrip] leadfields MNI-coordinates Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: warp_location.JPG Type: image/jpeg Size: 95511 bytes Desc: not available URL: From alexandra.bendixen at physik.tu-chemnitz.de Fri May 15 11:49:52 2015 From: alexandra.bendixen at physik.tu-chemnitz.de (Alexandra Bendixen) Date: Fri, 15 May 2015 11:49:52 +0200 Subject: [FieldTrip] Postdoc position in Chemnitz, Germany: Auditory perception & cognition Message-ID: Dear list, A postdoc position is available in my newly established Cognitive Systems Lab at Chemnitz University of Technology (https://www.tu-chemnitz.de/physik/SFKS/index.html.en). The lab is part of an interdisciplinary research center at the intersection of physics and psychology. Our research is centered around auditory perception and cognition, with extensions towards multisensory processing as well as towards effects of cognitive aging. Within this general framework, there is a great deal of flexibility in the specific research topic(s) pursued by the postdoc. We are looking for candidates with an academic university degree (M.Sc. equivalent) as well as a Ph.D. degree in psychology, neuroscience, cognitive science, or a related field. Good programming skills, good command of English, and prior publications in peer-reviewed journals are required. We use and combine EEG, eyetracking, and psychophysics methods. Candidates should have a strong background in at least one of these methods, or a complementary profile in cognitive/computational modeling. The position involves 4 hours of teaching per week at Bachelor or Master level, covering psychophysics and psychophysiology topics. To fulfill teaching requirements, knowledge of German is advantageous (but not strictly necessary). The position can be filled immediately and runs until March 31, 2018. Salary is determined by German public service regulations for full-term employment with a Ph.D. degree. Chemnitz University of Technology is dedicated to increasing the percentage of women in science. Therefore, female candidates are particularly encouraged to apply. Applicants with disabilities will be employed preferentially if equally qualified. This call is open until June 2nd, 2015. Anybody interested is welcome to contact me (alexandra.bendixen at physik.tu-chemnitz.de). For more information on the position and on how to apply, please visit https://www.tu-chemnitz.de/verwaltung/personal/stellen/212067_4_Ku.php I would be grateful if you could distribute this advert to anyone potentially interested. Many thanks, Alexandra Bendixen --- Prof. Dr. Alexandra Bendixen Cognitive Systems Lab Chemnitz University of Technology Faculty of Natural Sciences Institute of Physics New Physics Building, Room P137 Reichenhainer Str. 70 D-09126 Chemnitz, Germany Tel.: +49-(0)371-531-31681 Fax: +49-(0)371-531-831681 E-mail: alexandra.bendixen at physik.tu-chemnitz.de WWW: https://www.tu-chemnitz.de/physik/SFKS/alexandrabendixen.html.en From michelic72 at gmail.com Sat May 16 16:17:25 2015 From: michelic72 at gmail.com (Cristiano Micheli) Date: Sat, 16 May 2015 16:17:25 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: Message-ID: Dear Zsolt I experienced difficulties and encountered many pitfalls along the way too. What exactly will your metric be? wPLI of post onset versus baseline difference/ratio? wPLI difference of the two conditions? Do you common average re-reference your data before? The statistics that you will use will depend on your design. I would personally try a non-parametric design where you shuffle the index of the trials of one condition (if you do wPLI1-wPLI2) and consider the proportion of iterations exceeding the measured wPLI difference. Please consider though that both conditions should have the same number of trials. Could you attach the programming attempts that you tried so far together with the exact error outputs? I hope this helps so far. Cris Micheli On Wed, May 13, 2015 at 5:28 PM, Zsolt Turi wrote: > Dear all, > > > > I would like to perform a cluster-based permutation test on weighted phase > lag index values by using a within-subjects experimental design. I have two > conditions (congruent and incongruent one) and my goal is to compute WPLI > between certain channel combinations (FCz and F3 for instance) and see the > WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two > conditions. > > > I experienced some difficulties after the point when I calculated the > WPLI data for each participant. To perform the above-mentioned comparison, > shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > > > > If I am right, which command shall I use to organize individual WPLI data, > in order to create a correct input for ‘ft_freqstatistics’. According to > the tutorial, in case of time-frequency data it is ft_freqgrandaverage. > However, if I use it for WPLI data, I have the following error: “This > function requires freq data as input”. > > > > Could you please recommend me a tutorial, reference documentation or some > comment on this issue? > > > > Thanks for any suggestions in advanced and let me know if the description > of my problem is not clear! > > > > Zsolt > > -- > ************************************************************ > Ph.D. student > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 08:18:54 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 08:18:54 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Message-ID: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Hi Zsolt, > Hi Tzvetan, > > thanks for your suggestions. > I am still stucked at the ft_freqstatistics, as I keep on receiving the following error and would be glad if you could make a comment on this as well: > > #### > Reference to non-existent field 'label'. > > Error in ft_freqgrandaverage (line 123) > cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); > ### > > Is it because I have labelcomb in the WPLI data? yes > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x7x16 double] > freq: [3 4 5 6 7 8 9] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > And this is my specification (I couldn't fine the option cfg.channelcmb for ft_freqgrandaverage in the reference documentation): again try to give cell arrays as input to ft_freqanalysis. I’m still considering the case you mentioned in your initial e-mail, one channel etc. e.g. cfg.channel = ‘FCzF3’; cfg.parameter = ‘wplispctrm’; cfg.neighbours = []; % this will force clustering over time and freq dimension best tzvetan > > cfg = []; > cfg.keepindividual = 'yes'; > cfg.cfg.foilim = 'all'; > cfg.toilim = 'all'; > cfg.channel = 'all'; > cfg.parameter = 'wplispctrm'; > > Thanks again for the answer in advance! > > Best, > Zsolt > > ps.I can provide other parts of my code but I don't want to make this mail too long : > > > > 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > >> Dear all, >> >> >> I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. >> >> >> I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >> > You could. Stick with the tutorial you are currently working with. You should organize your data into cell arrays and call ft_freqstatistics like this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise ft_freqstatistics will default to ‘powspctrm’ which will be not present in the data. > good luck > tzvetan > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 08:19:41 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 08:19:41 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: > > again try to give cell arrays as input to ft_freqanalysis I’m sorry I meant ft_freqstatistics here tz From zsoltturi at gmail.com Mon May 18 11:33:48 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Mon, 18 May 2015 11:33:48 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Hi Tzvetan and Chris, thanks for your emails. Removing channelcmb and adding a new one called label solved my problem. Chris: I'ld like to compare the WPLI difference of two conditions, congruent and incongruent ones by using a within-subjects design (so not a between trials comparison). >From your email I may infer that after running wpli, I should still have my trials. However, I do not have repetitions (trials) anymore in the output structure. Am I doing an illegitimate step during wPLI calculation or miss one specification? cfg = []; cfg.method = 'wpli'; dataWPLI = ft_connectivityanalysis(cfg,TFRhann); labelcmb: {9x2 cell} dimord: 'chan_freq_time' wplispctrm: [9x43x16 double] freq: [1x43 double] time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] cfg: [1x1 struct] Thanks for your help! Best, Zsolt 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > > Hi Tzvetan, > > thanks for your suggestions. > I am still stucked at the ft_freqstatistics, as I keep on receiving the > following error and would be glad if you could make a comment on this as > well: > > #### > Reference to non-existent field 'label'. > > Error in ft_freqgrandaverage (line 123) > cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); > ### > > Is it because I have labelcomb in the WPLI data? > > yes > > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x7x16 double] > freq: [3 4 5 6 7 8 9] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 > 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > And this is my specification (I couldn't fine the option cfg.channelcmb > for ft_freqgrandaverage in the reference documentation): > > again try to give cell arrays as input to ft_freqanalysis. I’m still > considering the case you mentioned in your initial e-mail, one channel etc. > e.g. cfg.channel = ‘FCzF3’; > cfg.parameter = ‘wplispctrm’; > cfg.neighbours = []; % this will force clustering over time and > freq dimension > > best > tzvetan > > > cfg = []; > cfg.keepindividual = 'yes'; > cfg.cfg.foilim = 'all'; > cfg.toilim = 'all'; > cfg.channel = 'all'; > cfg.parameter = 'wplispctrm'; > > Thanks again for the answer in advance! > > Best, > Zsolt > > ps.I can provide other parts of my code but I don't want to make this mail > too long : > > > > 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > >> Hi Zsolt, >> >> >> Dear all, >> >> >> I would like to perform a cluster-based permutation test on weighted >> phase lag index values by using a within-subjects experimental design. I >> have two conditions (congruent and incongruent one) and my goal is to >> compute WPLI between certain channel combinations (FCz and F3 for instance) >> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >> two conditions. >> >> >> I experienced some difficulties after the point when I calculated the >> WPLI data for each participant. To perform the above-mentioned comparison, >> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >> >> You could. Stick with the tutorial you are currently working with. You >> should organize your data into cell arrays and call ft_freqstatistics like >> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >> the data. >> good luck >> tzvetan >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Mon May 18 18:30:03 2015 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Mon, 18 May 2015 16:30:03 +0000 Subject: [FieldTrip] Source Reconstruction: MNI or subject space Message-ID: <1431966603032.7006@nin.knaw.nl> Dear FieldTrippers, When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 20:02:05 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 20:02:05 +0200 Subject: [FieldTrip] Source Reconstruction: MNI or subject space In-Reply-To: <1431966603032.7006@nin.knaw.nl> References: <1431966603032.7006@nin.knaw.nl> Message-ID: Dear Rajat, one option that is widely used by FieldTrip users, I believe, is the computation of source model aligned in MNI space while retaining the individual head model. This FAQ explains how to do this. http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space best tzvetan > Dear FieldTrippers, > > When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? > > > Thank you. > Rajat > > > > > > Rajat Mani Thomas > Social Brain Lab > Netherlands Institute for Neuroscience > Amsterdam > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 18 21:54:08 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 18 May 2015 19:54:08 +0000 Subject: [FieldTrip] problem reading bdf-file References: Message-ID: <4C5E591D-C0B8-4161-8070-80CA60521DB3@fcdonders.ru.nl> Dear all, I want to import a raw, markerless datafile (http://www.filedropper.com/1_20) by using cfg = []; cfg.dataset = '2.bdf'; data = ft_preprocessing(cfg) However, I get reading and preprocessing error opening file: 2.bdf One or more output arguments not assigned during call to "read_24bit". Error in read_biosemi_bdf>readLowLevel (line 274) buf = read_24bit(filename, offset, numwords); Error in read_biosemi_bdf (line 242) buf = readLowLevel(filename, offset, epochlength); % see below in subfunction Error in ft_read_data (line 321) dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 578) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Error in Untitled (line 19) data = ft_preprocessing(cfg) Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Tue May 19 10:23:19 2015 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Tue, 19 May 2015 08:23:19 +0000 Subject: [FieldTrip] using SPM to transform EEG electrode location Message-ID: <1432023799396.61888@nin.knaw.nl> Hi FieldTrippers and users of SPM I have, (i) the coordinates of my EEG electrodes in MNI space (ii) the y_*.nii and iy_*.nii files (deformation fields from SPM segmentation that is used to transform back and forth from subj->MNI. Does anyone know how to use the deformation fields on the 3D coordinates in MNI space to get the electrode locations in subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Tue May 19 11:09:09 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Tue, 19 May 2015 09:09:09 +0000 Subject: [FieldTrip] leadfields MNI-coordinates In-Reply-To: References: Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> Hi Barbara, Your code actually looks fine to me. Some things that I could think of: 1. Did you specify cfg.coordinates=’mni’ before applying ft_volumenormalise? 2. Did you select the right volumes for plotting? So a. For CTF head space: % make a figure of the single subject headmodel cfg=[]; cfg.location=ctfpos(i,:); cfg.locationcoordinates='head'; ft_sourceplot(cfg,mri_realign) b. And for MNI-space: cfg=[]; cfg.location=targets(i,:); cfg.locationcoordinates='head'; ft_sourceplot(cfg,mri_realign_mni) This should lead to the same anatomical locations. Hope this helps! Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Barbara Haendel Sent: vrijdag 15 mei 2015 10:27 To: fieldtrip at science.ru.nl Subject: [FieldTrip] leadfields MNI-coordinates Hi there, I found this very nice thread on warping between spm and ctf space (thanks Jan-Mathijs and Stan) and at first sight it seems to work fine (numbers match after applying warping back and forth) but when I try to navigate to the spot in the plotted figure the point of interest seems not to be the same. mri_realign_mni=ft_volumenormalise([],mri_realign) % Inverse warping mnipos=[-48 -75 8]; % [46 -78 6]; MT posback=ft_warp_apply(mri_realign_mni.params,mnipos,'sn2individual') ctfpos= ft_warp_apply(pinv(mri_realign_mni.initial),posback) -8.6110 55.6190 50.0473 I plotted either (see .jpg) A. the source (source = ft_sourceanalysis(cfg, freq)); B. the interpolated source (sourceInt = ft_sourceinterpolate(cfg, source , mri_realign); C. the normalized source (sourceIntNorm = ft_volumenormalise(cfg, sourceInt); and manually navigated to the respective coordinates. While for the normalized source the location makes sense (area MT) the location for A and B seems different. Is there any obvious mistake I’m overlooking? Thanks a lot! Barbara -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Tue May 19 11:17:25 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Tue, 19 May 2015 09:17:25 +0000 Subject: [FieldTrip] Source Reconstruction: MNI or subject space In-Reply-To: References: <1431966603032.7006@nin.knaw.nl> Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C1793D04F@exprd03.hosting.ru.nl> Dear Rajat, Both options are fine in principle. The only thing to keep in mind is that you used a non-warped volume (with either a CTF or MNI-grid) when computing the leadfields. It is crucial that these are computed based on the actual physical proportions/relations of the brain and sensors. Best, Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Tzvetan Popov Sent: maandag 18 mei 2015 20:02 To: FieldTrip discussion list Subject: Re: [FieldTrip] Source Reconstruction: MNI or subject space Dear Rajat, one option that is widely used by FieldTrip users, I believe, is the computation of source model aligned in MNI space while retaining the individual head model. This FAQ explains how to do this. http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space best tzvetan Dear FieldTrippers, When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue May 19 12:47:43 2015 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 May 2015 12:47:43 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Dear Zsolt, please find an answer below. Regards Cris On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > Hi Tzvetan and Chris, > > thanks for your emails. > Removing channelcmb and adding a new one called label solved my problem. > > Chris: > I'ld like to compare the WPLI difference of two conditions, congruent and > incongruent ones by using a within-subjects design (so not a between trials > comparison). > From your email I may infer that after running wpli, I should still have > my trials. However, I do not have repetitions (trials) anymore in the > output structure. Am I doing an illegitimate step during wPLI calculation > or miss one specification? > You did it correctly. After running the wPLI metric ( I suggest the unbiased version of it, use the 'wpli_debiased' method in ft_connectivityanalysis) you are left with no trials. This is because the trials dimension (and tapers) are used to estimate the phase lag index. If I left that implied in the previous mail, I did not communicate it very well. What I meant to say is to be careful in the contrast of two conditions, because the subtraction (or ratio, or else...) will generate fake effects (or false positives) if the trials in condition 1 and condition 2 BEFORE wPLI calculation are different. I hope this helps Cris > cfg = []; > cfg.method = 'wpli'; > dataWPLI = ft_connectivityanalysis(cfg,TFRhann); > > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x43x16 double] > freq: [1x43 double] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 > 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > Thanks for your help! > > Best, > Zsolt > > > > > 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : > >> Hi Zsolt, >> >> >> Hi Tzvetan, >> >> thanks for your suggestions. >> I am still stucked at the ft_freqstatistics, as I keep on receiving the >> following error and would be glad if you could make a comment on this as >> well: >> >> #### >> Reference to non-existent field 'label'. >> >> Error in ft_freqgrandaverage (line 123) >> cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); >> ### >> >> Is it because I have labelcomb in the WPLI data? >> >> yes >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x7x16 double] >> freq: [3 4 5 6 7 8 9] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> And this is my specification (I couldn't fine the option cfg.channelcmb >> for ft_freqgrandaverage in the reference documentation): >> >> again try to give cell arrays as input to ft_freqanalysis. I’m still >> considering the case you mentioned in your initial e-mail, one channel etc. >> e.g. cfg.channel = ‘FCzF3’; >> cfg.parameter = ‘wplispctrm’; >> cfg.neighbours = []; % this will force clustering over time and >> freq dimension >> >> best >> tzvetan >> >> >> cfg = []; >> cfg.keepindividual = 'yes'; >> cfg.cfg.foilim = 'all'; >> cfg.toilim = 'all'; >> cfg.channel = 'all'; >> cfg.parameter = 'wplispctrm'; >> >> Thanks again for the answer in advance! >> >> Best, >> Zsolt >> >> ps.I can provide other parts of my code but I don't want to make this >> mail too long : >> >> >> >> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Dear all, >>> >>> >>> I would like to perform a cluster-based permutation test on weighted >>> phase lag index values by using a within-subjects experimental design. I >>> have two conditions (congruent and incongruent one) and my goal is to >>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >>> two conditions. >>> >>> >>> I experienced some difficulties after the point when I calculated the >>> WPLI data for each participant. To perform the above-mentioned comparison, >>> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >>> >>> You could. Stick with the tutorial you are currently working with. You >>> should organize your data into cell arrays and call ft_freqstatistics like >>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >>> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >>> the data. >>> good luck >>> tzvetan >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, Göttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Wed May 20 08:20:09 2015 From: B.Haendel at gmx.net (Barbara Haendel) Date: Wed, 20 May 2015 08:20:09 +0200 Subject: [FieldTrip] leadfields MNI-coordinates In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> References: , <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> Message-ID: An HTML attachment was scrubbed... URL: From e.caspar at ucl.ac.uk Wed May 20 10:20:57 2015 From: e.caspar at ucl.ac.uk (Caspar, Emilie) Date: Wed, 20 May 2015 08:20:57 +0000 Subject: [FieldTrip] Tiggers added manually Message-ID: Dear Fieldtrippers, I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. Many thanks in advance! Emilie From rb643 at medschl.cam.ac.uk Wed May 20 12:34:32 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Wed, 20 May 2015 10:34:32 +0000 Subject: [FieldTrip] data segmenting and frequency analysis Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> Dear Fieldtrippers, Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. Thus, my questions are: 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? If a: how does freqanalysis handle multiple trials? I currently use this: cfg.method = 'wavelet'; cfg.output = 'powandcsd'; cfg.channel = 1:64; cfg.foilim = [0 70]; cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: cfg.method = 'wpli'; wpli_data = ft_connectivityanalysis(cfg, freq_data); 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? Any help would be much appreciated! Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From spa268 at nyu.edu Wed May 20 12:44:22 2015 From: spa268 at nyu.edu (Stephen Politzer-Ahles) Date: Wed, 20 May 2015 06:44:22 -0400 Subject: [FieldTrip] Tiggers added manually Message-ID: Hi Emilie, You could add new rows to the trial definition matrix (cfg.trl) to add new triggers. See http://www.fieldtriptoolbox.org/reference/ft_definetrial for information on how cfg.trl is organized. There might be more efficient built-in ways to do it, but this is how I add triggers at least. Best, Steve > ------------------------------ > > Message: 3 > Date: Wed, 20 May 2015 08:20:57 +0000 > From: "Caspar, Emilie" > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Tiggers added manually > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. > > Many thanks in advance! > > Emilie > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 17 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From melissa.ralston at gmail.com Wed May 20 20:34:33 2015 From: melissa.ralston at gmail.com (Melissa Smith) Date: Wed, 20 May 2015 11:34:33 -0700 Subject: [FieldTrip] Reading/importing .daq files Message-ID: Hi Fieldtrip community, My name is Melissa and I have a very basic question as I am just starting to use the Fieldtrip toolbox. I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 channels. So, each trial has four .daq data files (one for each amplifier containing 16 channels). What is the best way to import and read this data for analysis using Fieldtrip? Thanks in advance for your time! Best, Melissa -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Wed May 20 20:51:02 2015 From: mcantor at umich.edu (Max Cantor) Date: Wed, 20 May 2015 14:51:02 -0400 Subject: [FieldTrip] Reading/importing .daq files In-Reply-To: References: Message-ID: I don't know about g.tec amps or .daq files specifically, but one way I can think to do it would be to load them each in separately and then use ft_appenddata. Coincidentally, I'm actually heading to Seattle tomorrow to visit a friend of mine at University of Washington! Great place :) Best, Max On Wed, May 20, 2015 at 2:34 PM, Melissa Smith wrote: > Hi Fieldtrip community, > > My name is Melissa and I have a very basic question as I am just starting > to use the Fieldtrip toolbox. > > I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 > channels. So, each trial has four .daq data files (one for each amplifier > containing 16 channels). > > What is the best way to import and read this data for analysis using > Fieldtrip? > > Thanks in advance for your time! > > Best, > Melissa > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Lab Manager Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Wed May 20 21:23:26 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 20 May 2015 21:23:26 +0200 Subject: [FieldTrip] data segmenting and frequency analysis In-Reply-To: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> References: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> Message-ID: Dear Richard, > Dear Fieldtrippers, > > Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. you might check this page that illustrates a way to do this. It is in source space yet in your case you’ll stay on the electrode level. http://www.fieldtriptoolbox.org/tutorial/networkanalysis Keep in mind that sensor/electrode level connectivity metrics, regardless of the metric, come with some difficulties that are not trivial to solve. Maybe is good if you consult this lecture first: https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. cfg = []; cfg.dataset = ‘yourdataset'; cfg.trialdef.triallength = 4; cfg.trialdef.ntrials = Inf; cfg = ft_definetrial(cfg); cfg.channel = {‘EEG'}; data = ft_preprocessing(cfg); If you generate several of these data structures corresponding to your 1-minute epochs you can do data = ft_appenddata([],data1,data2). This way you combine them in one data structure. > After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. > > Thus, my questions are: > 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? > If a: how does freqanalysis handle multiple trials? I currently use this: > cfg.method = 'wavelet'; > cfg.output = 'powandcsd'; > cfg.channel = 1:64; > cfg.foilim = [0 70]; > cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] > [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data > > Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? Then for a given frequency in this example 8-12 Hz you could do this: cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.tapsmofrq = 2; cfg.foi = 10; freq_data = ft_freqanalysis(cfg, data); and subsequently use ft_connectivityanalysis with the metric of your choice. > > If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? there are two functions you might want to check: ft_redefinetrial and ft_selectdata > > 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? I would definitely remove the channel but there are certainly other opinions on that. > > 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? You can- cfg.foi = [0:1:100] gives you 0 to 100 Hz in steps of 1 Hz. Whether or not your frequency resolution is 1 Hz is different issue. You might check out this lecture too: https://www.youtube.com/watch?v=vwPpSglPJTE > > 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: > > cfg.method = 'wpli'; > wpli_data = ft_connectivityanalysis(cfg, freq_data); see above > > 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? no, you have to decide what value corresponds to a connection = 1 and what not =0 > Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? ft_selectdata with cfg.avgoverfreq = ‘yes' > Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? I don’t get that one. Good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Wed May 20 22:24:38 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Wed, 20 May 2015 22:24:38 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Dear Chris, thanks again for your comment. Cheers, Zsolt 2015-05-19 12:47 GMT+02:00 Cristiano Micheli : > > Dear Zsolt, > please find an answer below. > Regards > Cris > > On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > >> Hi Tzvetan and Chris, >> >> thanks for your emails. >> Removing channelcmb and adding a new one called label solved my problem. >> >> Chris: >> I'ld like to compare the WPLI difference of two conditions, congruent and >> incongruent ones by using a within-subjects design (so not a between trials >> comparison). >> From your email I may infer that after running wpli, I should still have >> my trials. However, I do not have repetitions (trials) anymore in the >> output structure. Am I doing an illegitimate step during wPLI calculation >> or miss one specification? >> > > You did it correctly. > After running the wPLI metric ( I suggest the unbiased version of it, use > the 'wpli_debiased' method in ft_connectivityanalysis) you are left with > no trials. This is because the trials dimension (and tapers) are used to > estimate the phase lag index. If I left that implied in the previous mail, > I did not communicate it very well. What I meant to say is to be careful in > the contrast of two conditions, because the subtraction (or ratio, or > else...) will generate fake effects (or false positives) if the trials in > condition 1 and condition 2 BEFORE wPLI calculation are different. > > I hope this helps > Cris > > >> cfg = []; >> cfg.method = 'wpli'; >> dataWPLI = ft_connectivityanalysis(cfg,TFRhann); >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x43x16 double] >> freq: [1x43 double] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> Thanks for your help! >> >> Best, >> Zsolt >> >> >> >> >> 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Hi Tzvetan, >>> >>> thanks for your suggestions. >>> I am still stucked at the ft_freqstatistics, as I keep on receiving the >>> following error and would be glad if you could make a comment on this as >>> well: >>> >>> #### >>> Reference to non-existent field 'label'. >>> >>> Error in ft_freqgrandaverage (line 123) >>> cfg.channel = ft_channelselection(cfg.channel, >>> varargin{i}.label); >>> ### >>> >>> Is it because I have labelcomb in the WPLI data? >>> >>> yes >>> >>> >>> labelcmb: {9x2 cell} >>> dimord: 'chan_freq_time' >>> wplispctrm: [9x7x16 double] >>> freq: [3 4 5 6 7 8 9] >>> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >>> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >>> cfg: [1x1 struct] >>> >>> And this is my specification (I couldn't fine the option cfg.channelcmb >>> for ft_freqgrandaverage in the reference documentation): >>> >>> again try to give cell arrays as input to ft_freqanalysis. I’m still >>> considering the case you mentioned in your initial e-mail, one channel etc. >>> e.g. cfg.channel = ‘FCzF3’; >>> cfg.parameter = ‘wplispctrm’; >>> cfg.neighbours = []; % this will force clustering over time and >>> freq dimension >>> >>> best >>> tzvetan >>> >>> >>> cfg = []; >>> cfg.keepindividual = 'yes'; >>> cfg.cfg.foilim = 'all'; >>> cfg.toilim = 'all'; >>> cfg.channel = 'all'; >>> cfg.parameter = 'wplispctrm'; >>> >>> Thanks again for the answer in advance! >>> >>> Best, >>> Zsolt >>> >>> ps.I can provide other parts of my code but I don't want to make this >>> mail too long : >>> >>> >>> >>> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov >>> : >>> >>>> Hi Zsolt, >>>> >>>> >>>> Dear all, >>>> >>>> >>>> I would like to perform a cluster-based permutation test on weighted >>>> phase lag index values by using a within-subjects experimental design. I >>>> have two conditions (congruent and incongruent one) and my goal is to >>>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>>> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >>>> two conditions. >>>> >>>> >>>> I experienced some difficulties after the point when I calculated the >>>> WPLI data for each participant. To perform the above-mentioned comparison, >>>> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >>>> >>>> You could. Stick with the tutorial you are currently working with. You >>>> should organize your data into cell arrays and call ft_freqstatistics like >>>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>>> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >>>> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >>>> the data. >>>> good luck >>>> tzvetan >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> ************************************************************ >>> Ph.D. >>> Department of Clinical Neurophysiology >>> Georg-August University, Göttingen >>> Robert-Koch-Str. 40 >>> 37075 Goettingen >>> Web: http://www.uni-goettingen.de/en/222525.html >>> ************************************************************ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, Göttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Thu May 21 14:02:53 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Thu, 21 May 2015 12:02:53 +0000 Subject: [FieldTrip] data segmenting and frequency analysis (Tzvetan Popov) Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF47FDCE@me-mbx3.medschl.cam.ac.uk> Hi Tzvetan and others, Thanks for all the wonderful feedback and links to resources! I did manage to sort out the redefine trials issue now to split the trial up in smaller segments. As for faulty channels, I found the option to repair channels (which I would prefer to keep the matrix sizes the same). When looking at the data this does seem to adequately resolve the one faulty channel I had with the specific subject I was looking at. For some reason however this seems to cause some errors in later on displaying the ICA topoplots (the ICA itself still seems to run fine, but when inspecting the components I only see the timecourses and not the topoplots)? An error in matlabs surf function in using complex numbers is all I get back? As for the frequencies of interest: I would ideally like to use wavelet decomposition rather than fourier transformations to obtain a specific power. I assume I can set this in cfg_foi and then run ft_freqanalysis on the different bands, but at what point would you collapse or average the windows together? As for the connectivity analysis, the reason I would like to use wpli is precisely to get around the volume conduction issue and the fact that I only have the elecrode level metrics. It does seem however as though something is missing in my pipeline before that as the cross and power spectra contains a lot of NaN's? I am also not sure about when to average over the wavelet windows or frequency 'timepoints' (going from the 3D wpli spectrum to a vector or a 2 matrix)? Related to that last point was my question about the adjacency matrix, the connectivity analysis output just list all the wpl indices per channel pair, but I would rather have the 2D matrix (with nothing trilled off) that lists all channels against all channels? Just to sum up my remaining questions: 1. Why would channelrepair result in issues with ICA's topoplot and how to fix that (it would be good to see if the noise from the one faulty channel is really gone)? 2. How to obtain a metric per frequency band (using wavelets)/or alternatively at what point in the analysis should the wavelet decomposition be averaged? 3. How to obtain a 64*64 matrix (all channels*all channels) of the wpl indices? For reference, my entire (under construction) code is here: https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m Cheers, Richard ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] Sent: 21 May 2015 11:00 To: fieldtrip at science.ru.nl Subject: fieldtrip Digest, Vol 54, Issue 18 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit http://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. data segmenting and frequency analysis (Richard Bethlehem) 2. Re: Tiggers added manually (Stephen Politzer-Ahles) 3. Reading/importing .daq files (Melissa Smith) 4. Re: Reading/importing .daq files (Max Cantor) 5. Re: data segmenting and frequency analysis (Tzvetan Popov) 6. Re: cluster-based permutation test on WPLI (Zsolt Turi) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 May 2015 10:34:32 +0000 From: Richard Bethlehem To: "fieldtrip at science.ru.nl" Subject: [FieldTrip] data segmenting and frequency analysis Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4759E5 at me-mbx3.medschl.cam.ac.uk> Content-Type: text/plain; charset="iso-8859-1" Dear Fieldtrippers, Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. Thus, my questions are: 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? If a: how does freqanalysis handle multiple trials? I currently use this: cfg.method = 'wavelet'; cfg.output = 'powandcsd'; cfg.channel = 1:64; cfg.foilim = [0 70]; cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: cfg.method = 'wpli'; wpli_data = ft_connectivityanalysis(cfg, freq_data); 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? Any help would be much appreciated! Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 20 May 2015 06:44:22 -0400 From: Stephen Politzer-Ahles To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Tiggers added manually Message-ID: Content-Type: text/plain; charset="utf-8" Hi Emilie, You could add new rows to the trial definition matrix (cfg.trl) to add new triggers. See http://www.fieldtriptoolbox.org/reference/ft_definetrial for information on how cfg.trl is organized. There might be more efficient built-in ways to do it, but this is how I add triggers at least. Best, Steve > ------------------------------ > > Message: 3 > Date: Wed, 20 May 2015 08:20:57 +0000 > From: "Caspar, Emilie" > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Tiggers added manually > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. > > Many thanks in advance! > > Emilie > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 17 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 20 May 2015 11:34:33 -0700 From: Melissa Smith To: fieldtrip at science.ru.nl Subject: [FieldTrip] Reading/importing .daq files Message-ID: Content-Type: text/plain; charset="utf-8" Hi Fieldtrip community, My name is Melissa and I have a very basic question as I am just starting to use the Fieldtrip toolbox. I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 channels. So, each trial has four .daq data files (one for each amplifier containing 16 channels). What is the best way to import and read this data for analysis using Fieldtrip? Thanks in advance for your time! Best, Melissa -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 4 Date: Wed, 20 May 2015 14:51:02 -0400 From: Max Cantor To: FieldTrip discussion list Subject: Re: [FieldTrip] Reading/importing .daq files Message-ID: Content-Type: text/plain; charset="utf-8" I don't know about g.tec amps or .daq files specifically, but one way I can think to do it would be to load them each in separately and then use ft_appenddata. Coincidentally, I'm actually heading to Seattle tomorrow to visit a friend of mine at University of Washington! Great place :) Best, Max On Wed, May 20, 2015 at 2:34 PM, Melissa Smith wrote: > Hi Fieldtrip community, > > My name is Melissa and I have a very basic question as I am just starting > to use the Fieldtrip toolbox. > > I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 > channels. So, each trial has four .daq data files (one for each amplifier > containing 16 channels). > > What is the best way to import and read this data for analysis using > Fieldtrip? > > Thanks in advance for your time! > > Best, > Melissa > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Lab Manager Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 5 Date: Wed, 20 May 2015 21:23:26 +0200 From: Tzvetan Popov To: FieldTrip discussion list Subject: Re: [FieldTrip] data segmenting and frequency analysis Message-ID: Content-Type: text/plain; charset="windows-1252" Dear Richard, > Dear Fieldtrippers, > > Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. you might check this page that illustrates a way to do this. It is in source space yet in your case you?ll stay on the electrode level. http://www.fieldtriptoolbox.org/tutorial/networkanalysis Keep in mind that sensor/electrode level connectivity metrics, regardless of the metric, come with some difficulties that are not trivial to solve. Maybe is good if you consult this lecture first: https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. cfg = []; cfg.dataset = ?yourdataset'; cfg.trialdef.triallength = 4; cfg.trialdef.ntrials = Inf; cfg = ft_definetrial(cfg); cfg.channel = {?EEG'}; data = ft_preprocessing(cfg); If you generate several of these data structures corresponding to your 1-minute epochs you can do data = ft_appenddata([],data1,data2). This way you combine them in one data structure. > After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. > > Thus, my questions are: > 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? > If a: how does freqanalysis handle multiple trials? I currently use this: > cfg.method = 'wavelet'; > cfg.output = 'powandcsd'; > cfg.channel = 1:64; > cfg.foilim = [0 70]; > cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] > [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data > > Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? Then for a given frequency in this example 8-12 Hz you could do this: cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.tapsmofrq = 2; cfg.foi = 10; freq_data = ft_freqanalysis(cfg, data); and subsequently use ft_connectivityanalysis with the metric of your choice. > > If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? there are two functions you might want to check: ft_redefinetrial and ft_selectdata > > 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? I would definitely remove the channel but there are certainly other opinions on that. > > 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? You can- cfg.foi = [0:1:100] gives you 0 to 100 Hz in steps of 1 Hz. Whether or not your frequency resolution is 1 Hz is different issue. You might check out this lecture too: https://www.youtube.com/watch?v=vwPpSglPJTE > > 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: > > cfg.method = 'wpli'; > wpli_data = ft_connectivityanalysis(cfg, freq_data); see above > > 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? no, you have to decide what value corresponds to a connection = 1 and what not =0 > Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? ft_selectdata with cfg.avgoverfreq = ?yes' > Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? I don?t get that one. Good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 6 Date: Wed, 20 May 2015 22:24:38 +0200 From: Zsolt Turi To: FieldTrip discussion list Subject: Re: [FieldTrip] cluster-based permutation test on WPLI Message-ID: Content-Type: text/plain; charset="utf-8" Dear Chris, thanks again for your comment. Cheers, Zsolt 2015-05-19 12:47 GMT+02:00 Cristiano Micheli : > > Dear Zsolt, > please find an answer below. > Regards > Cris > > On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > >> Hi Tzvetan and Chris, >> >> thanks for your emails. >> Removing channelcmb and adding a new one called label solved my problem. >> >> Chris: >> I'ld like to compare the WPLI difference of two conditions, congruent and >> incongruent ones by using a within-subjects design (so not a between trials >> comparison). >> From your email I may infer that after running wpli, I should still have >> my trials. However, I do not have repetitions (trials) anymore in the >> output structure. Am I doing an illegitimate step during wPLI calculation >> or miss one specification? >> > > You did it correctly. > After running the wPLI metric ( I suggest the unbiased version of it, use > the 'wpli_debiased' method in ft_connectivityanalysis) you are left with > no trials. This is because the trials dimension (and tapers) are used to > estimate the phase lag index. If I left that implied in the previous mail, > I did not communicate it very well. What I meant to say is to be careful in > the contrast of two conditions, because the subtraction (or ratio, or > else...) will generate fake effects (or false positives) if the trials in > condition 1 and condition 2 BEFORE wPLI calculation are different. > > I hope this helps > Cris > > >> cfg = []; >> cfg.method = 'wpli'; >> dataWPLI = ft_connectivityanalysis(cfg,TFRhann); >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x43x16 double] >> freq: [1x43 double] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> Thanks for your help! >> >> Best, >> Zsolt >> >> >> >> >> 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Hi Tzvetan, >>> >>> thanks for your suggestions. >>> I am still stucked at the ft_freqstatistics, as I keep on receiving the >>> following error and would be glad if you could make a comment on this as >>> well: >>> >>> #### >>> Reference to non-existent field 'label'. >>> >>> Error in ft_freqgrandaverage (line 123) >>> cfg.channel = ft_channelselection(cfg.channel, >>> varargin{i}.label); >>> ### >>> >>> Is it because I have labelcomb in the WPLI data? >>> >>> yes >>> >>> >>> labelcmb: {9x2 cell} >>> dimord: 'chan_freq_time' >>> wplispctrm: [9x7x16 double] >>> freq: [3 4 5 6 7 8 9] >>> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >>> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >>> cfg: [1x1 struct] >>> >>> And this is my specification (I couldn't fine the option cfg.channelcmb >>> for ft_freqgrandaverage in the reference documentation): >>> >>> again try to give cell arrays as input to ft_freqanalysis. I?m still >>> considering the case you mentioned in your initial e-mail, one channel etc. >>> e.g. cfg.channel = ?FCzF3?; >>> cfg.parameter = ?wplispctrm?; >>> cfg.neighbours = []; % this will force clustering over time and >>> freq dimension >>> >>> best >>> tzvetan >>> >>> >>> cfg = []; >>> cfg.keepindividual = 'yes'; >>> cfg.cfg.foilim = 'all'; >>> cfg.toilim = 'all'; >>> cfg.channel = 'all'; >>> cfg.parameter = 'wplispctrm'; >>> >>> Thanks again for the answer in advance! >>> >>> Best, >>> Zsolt >>> >>> ps.I can provide other parts of my code but I don't want to make this >>> mail too long : >>> >>> >>> >>> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov >>> : >>> >>>> Hi Zsolt, >>>> >>>> >>>> Dear all, >>>> >>>> >>>> I would like to perform a cluster-based permutation test on weighted >>>> phase lag index values by using a within-subjects experimental design. I >>>> have two conditions (congruent and incongruent one) and my goal is to >>>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>>> and see the WPLI change let?s say in 3-9 Hz and -100 to 500 ms between the >>>> two conditions. >>>> >>>> >>>> I experienced some difficulties after the point when I calculated the >>>> WPLI data for each participant. To perform the above-mentioned comparison, >>>> shall I use ?ft_freqstatistics?for the cluster-based permutation test? >>>> >>>> You could. Stick with the tutorial you are currently working with. You >>>> should organize your data into cell arrays and call ft_freqstatistics like >>>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>>> Furthermore you should specify cfg.parameter = ?wplispctrm? otherwise >>>> ft_freqstatistics will default to ?powspctrm? which will be not present in >>>> the data. >>>> good luck >>>> tzvetan >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> ************************************************************ >>> Ph.D. >>> Department of Clinical Neurophysiology >>> Georg-August University, G?ttingen >>> Robert-Koch-Str. 40 >>> 37075 Goettingen >>> Web: http://www.uni-goettingen.de/en/222525.html >>> ************************************************************ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, G?ttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, G?ttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 54, Issue 18 ***************************************** From l.garcia.d at gmail.com Thu May 21 20:02:04 2015 From: l.garcia.d at gmail.com (Luis Garcia Dominguez) Date: Thu, 21 May 2015 14:02:04 -0400 Subject: [FieldTrip] Fwd: clusterplot not plotting for gradiometeres In-Reply-To: References: Message-ID: Dear All, Has anyone been successful in combining magnetometers and gradiometers in dipole fitting. In my experience the results obtained using either grad or mag are very similar and accurate, but the combination of both did not work.... I can offer more details, code and data if needed. Any updates on this? Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: From mor2451 at gmail.com Fri May 22 14:00:47 2015 From: mor2451 at gmail.com (moran abilea) Date: Fri, 22 May 2015 15:00:47 +0300 Subject: [FieldTrip] what should i do between two stimulations P300 speller Message-ID: hi there everyone, so quick update and a problem that i need some advice from you guys. as I've already mentioned i'm doing a final project of MALAB p300 speller, i'm currently at the part of the experiment which means recording raw data on my partner's scalp while showing him the flashing 6X6 matrix of letters. we are using Emotiv EPOC device which means that it records 128 samples per sec. so now for my question: in the raw data itself that i record, between two stimulations i have 128 recorded raw data and i don't know what to do with it in order to continue the next step of using p300 detection method. what should i do with the 128 recorded data? should i average it or maybe use any band pass filter on the data i'm stuck and i need ideas in order to continue my project. any help will be welcomed, best regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.llera at donders.ru.nl Fri May 22 17:34:25 2015 From: a.llera at donders.ru.nl (Llera Arenas, A. (Alberto)) Date: Fri, 22 May 2015 15:34:25 +0000 Subject: [FieldTrip] what should i do between two stimulations P300 speller In-Reply-To: References: Message-ID: <6F2BEAB2DB977640884026115886A9B3247F9F@exprd01.hosting.ru.nl> Hi Hereby some starting points: I first would recommend reading the following paper: Single-Trial Analysis and Classification of ERP Components – a Tutorial. You can download it for free at http://doc.ml.tu-berlin.de/bbci/publications/BlaLemTreHauMue10.pdf If you want more, check for example: Interactions between pre-processing and classification methods for event-related-potential classification: best-practice guidelines for brain-computer interfacing. http://www.ncbi.nlm.nih.gov/pubmed/23250668 a free pre print of this last one is available at research gate http://www.researchgate.net/publication/234112682_FarquharHill_ERP_Classification_Best_Practice_Author_Pre-print Good luck Alberto Llera ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of moran abilea [mor2451 at gmail.com] Sent: Friday, May 22, 2015 2:00 PM To: FieldTrip discussion list Subject: [FieldTrip] what should i do between two stimulations P300 speller hi there everyone, so quick update and a problem that i need some advice from you guys. as I've already mentioned i'm doing a final project of MALAB p300 speller, i'm currently at the part of the experiment which means recording raw data on my partner's scalp while showing him the flashing 6X6 matrix of letters. we are using Emotiv EPOC device which means that it records 128 samples per sec. so now for my question: in the raw data itself that i record, between two stimulations i have 128 recorded raw data and i don't know what to do with it in order to continue the next step of using p300 detection method. what should i do with the 128 recorded data? should i average it or maybe use any band pass filter on the data i'm stuck and i need ideas in order to continue my project. any help will be welcomed, best regards, Moran Abilea From greg at think-now.com Sat May 23 02:11:58 2015 From: greg at think-now.com (Greg Simpson) Date: Fri, 22 May 2015 17:11:58 -0700 Subject: [FieldTrip] RA Position Open Message-ID: Dear Colleagues, I would like to announce an opening for a Research Associate (see ad below). Please spread the word. Thank you, Greg Research Associate – Cognitive Training Think Now Incorporated is seeking a research associate to work on a NIMH funded project testing the effects of mobile software training on attention in adults with ADHD. Duties will include recruiting, screening and testing (both behavioral tests and EEG tests) of adults with ADHD, before and after they train their attention with the mobile software. We are seeking candidates with direct hands-on experience in conducting cognitive/psychological tests or related experience. Experience with collecting EEG data is not required but would be great. Also, experience with MatLab and statistical packages such as SPSS would be a plus. We prefer strongly self-directed individuals with great people-skills to take on this work. The position reports directly to Greg Simpson, Ph.D., a cognitive neuroscientist and Chief Scientific Officer of Think Now. Think Now is located in San Francisco and our research partners for this effort are located at UCLA in Los Angeles. Candidates need to be located in the Los Angeles area. Think Now is focused on creating solutions for the diagnosis and amelioration of neurological disorders with a focus on attention and its control. Please send your CV to jobs at think-now.com with a letter describing your prior experience with conducting studies with adults (and any EEG experience) and your reason for being interested in this position. Gregory V. Simpson, Ph.D. Think Now, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ad_Staff Research Associate TNI 2015.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 15847 bytes Desc: not available URL: From sjaak10101 at gmail.com Sat May 23 21:54:42 2015 From: sjaak10101 at gmail.com (Sjaak Zwart) Date: Sat, 23 May 2015 21:54:42 +0200 Subject: [FieldTrip] EDF+C annotations Message-ID: Dear all, I have an .edf file, according to the header, I think the precise format is EDF+C, and my goal is to convert this file in SPM and see the data with annotations. SPM is able to convert the file, although it does give a warning: Warning: Skipping "EDF Annotations" as continuous data channel because of > inconsistent sampling frequency > > In fileio/private/read_edf at 235 > In ft_read_header at 616 > In spm_eeg_convert at 97 > In spm_eeg_convert at 92 > In spm_eeg_convert_ui at 26 > In spm at 1054 > I further noticed that the EDFBrowser application is able to read the data *and* show the annotations. I could now try to figure out from the source what the EDFBrowser is doing exactly, and try to do something similar in the fieldtrip methods that read the edf. Not sure how far I'd get then. An additional complexity is that I do not have a full Matlab license, so I have the Matlab compiler and I have octave installed. (I'm not 100% sure but I think that means I cannot run Matlab code, but only pre-compiled code). >From the EDFBrowser I am able to export the events. But I don't know how to read that file together with the original file when I convert the edf file in SPM to get everything to show up right. Would be great if anybody has some experience with this already, or somebody who just knows how to get me further, Thanks, Sjaak. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at gmail.com Sat May 23 22:06:40 2015 From: bibi.raquel at gmail.com (bibi.raquel at gmail.com) Date: Sat, 23 May 2015 20:06:40 +0000 Subject: [FieldTrip] =?utf-8?q?biosemi_bdf_=3E=3E_read=5F24bit_error_+_no_?= =?utf-8?q?events_found?= In-Reply-To: References: Message-ID: <5560dddf.0b91340a.2dab.ffffdae5@mx.google.com> Have you resolved this issue? From: Paul Zerr Sent: ‎Thursday‎, ‎May‎ ‎14‎, ‎2015 ‎8‎:‎01‎ ‎AM To: FieldTrip discussion list Hi all, I'm new to fieldtrip so forgive me if my mistake is obvious. I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with cfg = []; cfg.dataset = '2.bdf'; data = ft_preprocessing(cfg) However, I get reading and preprocessing error opening file: 2.bdf One or more output arguments not assigned during call to "read_24bit". Error in read_biosemi_bdf>readLowLevel (line 274) buf = read_24bit(filename, offset, numwords); Error in read_biosemi_bdf (line 242) buf = readLowLevel(filename, offset, epochlength); % see below in subfunction Error in ft_read_data (line 321) dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 578) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Error in Untitled (line 19) data = ft_preprocessing(cfg) Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Defining only one channel to preprocess gives the same error. I couldn't find a solution in the archives, the faq, wiki or documentation. I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. Any ideas? Much appreciated, Paul Zerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From Andreas.Horn at charite.de Sun May 24 10:55:55 2015 From: Andreas.Horn at charite.de (Horn, Andreas) Date: Sun, 24 May 2015 08:55:55 +0000 Subject: [FieldTrip] Elements have wrong orientation or are degenerated Message-ID: Hello everybody, I am new to fieldtrip and want to use it (and simbio) to forward model the current spread of a known dipole. I consider only a small cubic fraction of brain tissue which I so far have divided in gray and white matter. I pass that cubic volume into ft_prepare_mesh and get a hexahedral mesh without error. ft_plot_mesh also shows the correct mesh. However, once I pass the mesh into ft_headmodel_simbio, I get the error ‘Elements have wrong orientation or are degenerated’ Does anyone have an idea of why this could happen and how I could potentially fix the issue? Thanks a lot, Andreas From alizadeh.arezoo88 at gmail.com Sun May 24 22:00:11 2015 From: alizadeh.arezoo88 at gmail.com (Arezoo Alizadeh) Date: Sun, 24 May 2015 09:00:11 -1100 Subject: [FieldTrip] User pass Message-ID: Hello, I have forget both my user name and pass word to ask question from fieldtriper. Could you please help me. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Sun May 24 22:03:46 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Sun, 24 May 2015 22:03:46 +0200 Subject: [FieldTrip] User pass In-Reply-To: References: Message-ID: http://mailman.science.ru.nl/mailman/listinfo/fieldtrip On Sun, May 24, 2015 at 10:00 PM, Arezoo Alizadeh < alizadeh.arezoo88 at gmail.com> wrote: > Hello, > > I have forget both my user name and pass word to ask question from > fieldtriper. Could you please help me. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.pedrosa at ndcn.ox.ac.uk Mon May 25 11:19:00 2015 From: david.pedrosa at ndcn.ox.ac.uk (David Pedrosa) Date: Mon, 25 May 2015 09:19:00 +0000 Subject: [FieldTrip] Statistics of coherence (DICS) Message-ID: Dear list, I would be very grateful if someone might answer some questions on the statistics of coherence. Maybe first of all an outline to our experiment. We have measured a 128 channel EEG with additional peripheral signals from the most affected arm on 20 subjects suffering from tremor and the same number of healthy control subjects with a simple motor paradigm (activation condition). In another condition, rest (baseline condition) was also measured (we have about 20-35 trials per condition). For the data analysis we have preprocessed the EEG in a rather standard way. For localizing the cortical sources we created a headmodel from individual MRI and the source reconstruction was obtained using the DICS beamformer (with the peripheral signal as 'refchan' and after computing a common spatial filter). Everything works out well and regarding the activation condition by itself the sources appear to be where we you would suspect it (motor areas) in all individuals. Of course coherence is much bigger during activation (about 1-3 dimensions). But otherwise coherence is never 0, not even in the rest condition (as to be expected). This makes us suspect a permutation test much more valid for testing the 'null-hypothesis' of interchangeable coherence between the conditions. Now we are struggling with the stats of the individual but also the group results. My first question is am I right that averageing over trials per condition is not necessary? And do I need to normalise the coherence after computing it with ft_freqanalysis? I was thinking of computing (activation - baseline)/baseline. And, finally, regarding the stats. The idea is to look individually at differences between the conditions and in a second step perform a group analysis. But what to test if we are not assuming a null-hypothesis, or am I completely on the wrong track? Thanks in advance. Best, David From zerr.paul at googlemail.com Mon May 25 15:51:15 2015 From: zerr.paul at googlemail.com (Paul Zerr) Date: Mon, 25 May 2015 15:51:15 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found Message-ID: I have not. I can read in the header but that's about it. I don't have any older matlab versions here to test it with either. >From what I understand ft_preprocessing should be capable of reading bdf's directly with only the file name as input arg. Greetings, Paul Zerr From: > To: FieldTrip discussion list > Subject: Re: [FieldTrip] biosemi bdf >> read_24bit error + no events > found > Message-ID: <5560dddf.0b91340a.2dab.ffffdae5 at mx.google.com> > Content-Type: text/plain; charset="utf-8" > > Have you resolved this issue? > > > From: Paul Zerr > Sent: ?Thursday?, ?May? ?14?, ?2015 ?8?:?01? ?AM > To: FieldTrip discussion list > > > Hi all, > > I'm new to fieldtrip so forgive me if my mistake is obvious. > I want to import my raw, markerless dataset ( > http://www.filedropper.com/1_20) with > > cfg = []; > cfg.dataset = '2.bdf'; > data = ft_preprocessing(cfg) > > However, I get > > reading and preprocessing > error opening file: 2.bdf > One or more output arguments not assigned during call to "read_24bit". > > Error in read_biosemi_bdf>readLowLevel (line 274) > buf = read_24bit(filename, offset, numwords); > > Error in read_biosemi_bdf (line 242) > buf = readLowLevel(filename, offset, epochlength); % see below in > subfunction > > Error in ft_read_data (line 321) > dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); > > Error in ft_preprocessing (line 578) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, > 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) > > Error in Untitled (line 19) > data = ft_preprocessing(cfg) > > Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the > datafile" for ft_definetrial even for datasets with many markers. > Converting to EDF+ did not help as it then says "channels with different > sampling rate not supported". Specifying only one channel makes no > difference. The file itself is fine (opens well in BvA). > > Defining only one channel to preprocess gives the same error. > > I couldn't find a solution in the archives, the faq, wiki or documentation. > > I'm using debian stable & matlab 2014a. Same issue at DCC computers > running windows & matlab 2013a. > > Any ideas? > > Much appreciated, > > Paul Zerr > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Mon May 25 20:15:04 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Mon, 25 May 2015 18:15:04 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at: https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 25 20:52:56 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 25 May 2015 18:52:56 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR In-Reply-To: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> References: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> Message-ID: <0D293943-40CA-45B3-B6E6-0CA403FCFA0B@fcdonders.ru.nl> Hi Richard, Is there a specific reason you would want to do a time-frequency type of analysis (with averaging across ‘epochs’ for resting state data? Since there’s no external event, such analysis does not really make sense. Yet, if you insist on doing this, you need to ensure that the individual ‘pseudo-trial’ time axis (i.e. data_iccleaned.time{x}) contains a ‘pseudo-time-axis’ such that it goes from 0 to 4. Best, Jan-Mathijs On May 25, 2015, at 8:15 PM, Richard Bethlehem > wrote: Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at:https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Tue May 26 11:27:38 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Tue, 26 May 2015 09:27:38 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4AAB5C@me-mbx3.medschl.cam.ac.uk> Hi Jan-Mathijs, Essentially I want to do connectivity analysis using the wpli measure for connectivity and use wavelets to get to the frequency domain, I gathered I needed to do frequency analysis to get the power and crosspectrum info for computing wpli (and to decompose into the different frequency bands), but please let me know if this should be done differently? I thought with such analysis selecting epochs would be fairly standard practice (following van Diessen et al. 2014), but again please do correct me if I misunderstood. If not, what would be the alternative for getting epochs/trials? Following you suggestion I have replaced the time axis with the same 0-4second interval as used in the freqanalysis input: stepSize = 1/1024; timeVector = 0:stepSize:(epochLength-stepSize); for i = 1:size(data_iccleaned.time,2) data_iccleaned.time{:,i} = timeVector; end Unfortunately this still gives me NaN's in the output... Cheers, Richard Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl ________________________________ Hi Richard, Is there a specific reason you would want to do a time-frequency type of analysis (with averaging across ‘epochs’ for resting state data? Since there’s no external event, such analysis does not really make sense. Yet, if you insist on doing this, you need to ensure that the individual ‘pseudo-trial’ time axis (i.e. data_iccleaned.time{x}) contains a ‘pseudo-time-axis’ such that it goes from 0 to 4. Best, Jan-Mathijs On May 25, 2015, at 8:15 PM, Richard Bethlehem >> wrote: Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at:https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed May 27 11:28:27 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 27 May 2015 11:28:27 +0200 Subject: [FieldTrip] Power Spectra - averaging across samples Message-ID: Dear all, I have a question about spectral power computation. I'm using this code cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 5:1:40; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; freqfourier = ft_freqanalysis(cfg, eeg); and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) X 36 (frequencies), for each subject. My question is: is it correct to average the data across the samples dimension? Thank you in advance! Best, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Wed May 27 11:46:25 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Wed, 27 May 2015 09:46:25 +0000 Subject: [FieldTrip] Power Spectra - averaging across samples In-Reply-To: References: Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> Dear Fedrica, Yes it is. You can get to the same outcome directly by just specifying cfg.keeptrials=’no’ (the default), but I assume you want to do some single-trial analysis later on. Best, Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Federica Mauro Sent: woensdag 27 mei 2015 11:28 To: FieldTrip discussion list Subject: [FieldTrip] Power Spectra - averaging across samples Dear all, I have a question about spectral power computation. I'm using this code cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 5:1:40; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; freqfourier = ft_freqanalysis(cfg, eeg); and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) X 36 (frequencies), for each subject. My question is: is it correct to average the data across the samples dimension? Thank you in advance! Best, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed May 27 12:09:43 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 27 May 2015 12:09:43 +0200 Subject: [FieldTrip] Power Spectra - averaging across samples In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> References: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> Message-ID: ok, great, thanks! 2015-05-27 11:46 GMT+02:00 Pelt, S. van (Stan) : > Dear Fedrica, > > > > Yes it is. You can get to the same outcome directly by just specifying > cfg.keeptrials=’no’ (the default), but I assume you want to do some > single-trial analysis later on. > > > > Best, > > Stan > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Federica Mauro > *Sent:* woensdag 27 mei 2015 11:28 > *To:* FieldTrip discussion list > *Subject:* [FieldTrip] Power Spectra - averaging across samples > > > > Dear all, > > I have a question about spectral power computation. > > I'm using this code > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.foi = 5:1:40; > cfg.t_ftimwin = 5./cfg.foi; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' > 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; > freqfourier = ft_freqanalysis(cfg, eeg); > > and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) > X 36 (frequencies), for each subject. > > My question is: is it correct to average the data across the samples > dimension? > > Thank you in advance! > > Best, > > Federica > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.schubert at gmail.com Wed May 27 16:33:26 2015 From: jonathan.schubert at gmail.com (Jonathan Schubert) Date: Wed, 27 May 2015 16:33:26 +0200 Subject: [FieldTrip] postdoc position in Hamburg In-Reply-To: <4E102991-AB38-44E6-AA60-780A723AFCE2@gmail.com> References: <4E102991-AB38-44E6-AA60-780A723AFCE2@gmail.com> Message-ID: <5565D5B6.8020805@gmail.com> Dear all, I'd like to advertise the following postdoc postion. If you have any questions, please do not hesitate to contact Tobias Heed (tobias.heed at uni-hamburg.de). Cheers, Jonathan -------- Weitergeleitete Nachricht -------- Dear friends and colleagues, The Reach & Touch Lab at the University of Hamburg is hiring a PostDoc for a 4-year project about brain connectivity in tactile-visual processing involving EEG, TMS, and eye tracking. I would be thankful if you could pass on this link: http://goo.gl/zhlk4p to anyone who might be interested. Application deadline is June 15, 2015. Thanks! Tobias Heed — Follow the Reach & Touch Lab (@HeedLab ) and myself (@TobiasHeed ) on Twitter Read our news and blog posts on www.reachtouchlab.com View our publications Dr. Tobias Heed Reach & Touch Lab of the Biological Psychology and Neuropsychology Faculty of Psychology & Human Movement Science | University of Hamburg Von-Melle-Park 11, Room 206 | D-20146 Hamburg, Germany Phone: (49) 40 - 42838 5831 | Fax: (49) 40 - 42838 6591 tobias.heed at uni-hamburg.de | Website | Twitter | Google Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: From lauri.parkkonen at aalto.fi Thu May 28 14:51:18 2015 From: lauri.parkkonen at aalto.fi (Parkkonen Lauri) Date: Thu, 28 May 2015 12:51:18 +0000 Subject: [FieldTrip] Post-doc position in Bayesian estimation & MEG Message-ID: Postdoctoral researcher in Bayesian estimation of functional connectivity from MEG data at Department of Neuroscience and Biomedical Engineering (NBE) of Aalto University School of Science, Finland. The work will be carried out jointly in the teams of prof. Lauri Parkkonen and prof. Simo Särkkä. More information on the position can be found here: http://www.aalto.fi/en/about/careers/jobs/view/515/ Cheers, Lauri -- ----------------------------------------------- Dr. Lauri Parkkonen Assistant Professor (Medical Imaging) Dept. of Neuroscience and Biomedical Engineering (NBE) Aalto University School of Science Street address: Rakentajanaukio 2 C, FI-02150 ESPOO, Finland Postal address: P.O. Box 12200, FI-00076 AALTO, Finland Tel: +358-40-5089712, mailto:lauri.parkkonen at aalto.fi http://nbe.aalto.fi/en -------------- next part -------------- An HTML attachment was scrubbed... URL: From mor2451 at gmail.com Thu May 28 16:56:51 2015 From: mor2451 at gmail.com (moran abilea) Date: Thu, 28 May 2015 17:56:51 +0300 Subject: [FieldTrip] using triggers building my own function Message-ID: hi everyone, so i'm trying to create my own function for using triggers with EEG raw data. i used this tutorial: http://www.fieldtriptoolbox.org/tutorial/preprocessing my question is if i can somehow specify the time i want to record my EEG data? for example i would like my function to get 'time' as parameter to the function and returns the EEG raw data of this specific time+one second. if so, can some one give me a piece of code for example to understand what to do? also 2 more little questions: 1. cfg.trialdef.eventvalue = [3 5 9]; what does the 3 5 9 stands for? i don't understand what is the meaning of those (or any other) numbers. can i get definition for what is event value? 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; does it means it takes exactly one second for the buffer to give me the EEG raw data? or does it means wait one second and then take the data from the buffer or something like that (1 second the trigger will "pop out" and finish taking the data from the buffer after 2 seconds) the triggers are new to me, so i have some problems to understand the concept of it, thus my questions for you guys. i hope i explained myself as clear as possible, i really would like to understand what i'm doing. regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From bmaniscalco at gmail.com Thu May 28 17:30:17 2015 From: bmaniscalco at gmail.com (Brian Maniscalco) Date: Thu, 28 May 2015 11:30:17 -0400 Subject: [FieldTrip] Inverse warping vs interpolating & normalizing for across-subject source space analysis Message-ID: When it comes to conducting across-subject analysis on source space data, I've seen two approaches described on the Field Trip web site and mailing list. 1) for each subject, interpolate the source space data onto the subject's brain anatomy and then normalize the result to a standard template before conducting across-subject analysis 2) for each subject, perform an inverse warp to a template as described in the following link, which then allows across-subject analysis without having to interpolate and normalize http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space I have seen approach (2) recommended for Field Trip users but I have not been able to find an in depth discussion of the pros and cons of doing (1) vs (2). I gather that (2) is computationally simpler and may save computation time. But aside from computational considerations, is there any theoretical or statistical benefit to using approach (2) over approach (1) or vice versa? thanks, Brian -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Fri May 29 11:59:33 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Fri, 29 May 2015 09:59:33 +0000 Subject: [FieldTrip] using triggers building my own function In-Reply-To: References: Message-ID: Hi Moran, It was a bit difficult to understand your question, but I've tried to answer them below. For your main question: Yes, it is possible to cut up your EEG data into individual trials, with the time (i.e. 1 second) that you specify. The function that cuts up your EEG data is known as ft_definetrial. However, ft_definetrial needs to read information from another function that explicitly tells it how to do the cutting. Usually, that function is "ft_trialfun_general" (this is the tutorial link you mentioned). However, if you have a complicated set of triggers or ways you want to cut up your data, you will be better off writing your own trialfun (" trial function"). If you need to write your trialfun, you should check out these example scripts / tutorials: http://www.fieldtriptoolbox.org/example/making_your_own_trialfun_for_conditional_trial_definitionhttp://www.fieldtriptoolbox.org/example/making_your_own_trialfun_for_conditional_trial_definition http://www.fieldtriptoolbox.org/tutorial/eeg_preprocessing_erphttp://www.fieldtriptoolbox.org/tutorial/eeg_preprocessing_erp To answer your " little " questions 1. cfg.trialdef.eventvalue = [3 5 9]; 3 5 9 are trigger codes. This tells your function to go into your data, look for these trigger codes, and cut your data with respect to the location of these triggers E.g., your data trigger codes look like this ----1 ----- 3 ------ 4 ------5 ----- 9 ----. In this case, the ft_definetrial will only use triggers 3, 5, and 9 as relative points for cutting your data, trigger 1 and 4 will be ignored. N.B. The data at trigger 1 might end up in your time window that contains trigger 3 if you define your time window to be very. To understand this, see below. 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; These 2 parameters are important. The values are defined in seconds. So cfg.trialdef.prestim refers to 1s before your trigger (i.e. prestim = prestimulus onset, where stimulus onset is referred to the sample point of your chosen trigger). cfg.trialdef.poststim refers to 2s after your trigger. In this way you would end up with a 3 second time window (1 second before trigger, and 2 seconds after). You mentioned you wanted " specific time [in data] + one second". So you 1) determine which triggers mark the " specific time [in your data]" 2) specify cfg.trialdef.poststim = 1. Hope this helps and good luck, Nietzsche ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of moran abilea [mor2451 at gmail.com] Sent: 28 May 2015 16:56 To: FieldTrip discussion list Subject: [FieldTrip] using triggers building my own function hi everyone, so i'm trying to create my own function for using triggers with EEG raw data. i used this tutorial: http://www.fieldtriptoolbox.org/tutorial/preprocessing my question is if i can somehow specify the time i want to record my EEG data? for example i would like my function to get 'time' as parameter to the function and returns the EEG raw data of this specific time+one second. if so, can some one give me a piece of code for example to understand what to do? also 2 more little questions: 1. cfg.trialdef.eventvalue = [3 5 9]; what does the 3 5 9 stands for? i don't understand what is the meaning of those (or any other) numbers. can i get definition for what is event value? 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; does it means it takes exactly one second for the buffer to give me the EEG raw data? or does it means wait one second and then take the data from the buffer or something like that (1 second the trigger will "pop out" and finish taking the data from the buffer after 2 seconds) the triggers are new to me, so i have some problems to understand the concept of it, thus my questions for you guys. i hope i explained myself as clear as possible, i really would like to understand what i'm doing. regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun May 31 22:16:45 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 31 May 2015 22:16:45 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found In-Reply-To: References: Message-ID: <82B38BFA-DF5F-4364-B7A5-7D1D754A75F7@donders.ru.nl> Hi Paul, I suppose it is an incompatibility between your particular BDF file and the code. I suggest you use MATLAB debugging facilities to check what is wrong in the lower-level code. See http://tinyurl.com/oy7b496. best regards, Robert On 25 May 2015, at 15:51, Paul Zerr wrote: > I have not. I can read in the header but that's about it. > I don't have any older matlab versions here to test it with either. > > From what I understand ft_preprocessing should be capable of reading bdf's directly with only the file name as input arg. > > Greetings, > Paul Zerr > > > From: > To: FieldTrip discussion list > Subject: Re: [FieldTrip] biosemi bdf >> read_24bit error + no events > found > Message-ID: <5560dddf.0b91340a.2dab.ffffdae5 at mx.google.com> > Content-Type: text/plain; charset="utf-8" > > Have you resolved this issue? > > > From: Paul Zerr > Sent: ?Thursday?, ?May? ?14?, ?2015 ?8?:?01? ?AM > To: FieldTrip discussion list > > > Hi all, > > I'm new to fieldtrip so forgive me if my mistake is obvious. > I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with > > cfg = []; > cfg.dataset = '2.bdf'; > data = ft_preprocessing(cfg) > > However, I get > > reading and preprocessing > error opening file: 2.bdf > One or more output arguments not assigned during call to "read_24bit". > > Error in read_biosemi_bdf>readLowLevel (line 274) > buf = read_24bit(filename, offset, numwords); > > Error in read_biosemi_bdf (line 242) > buf = readLowLevel(filename, offset, epochlength); % see below in subfunction > > Error in ft_read_data (line 321) > dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); > > Error in ft_preprocessing (line 578) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, > 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) > > Error in Untitled (line 19) > data = ft_preprocessing(cfg) > > Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). > > Defining only one channel to preprocess gives the same error. > > I couldn't find a solution in the archives, the faq, wiki or documentation. > > I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. > > Any ideas? > > Much appreciated, > > Paul Zerr > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun May 31 22:18:38 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 31 May 2015 22:18:38 +0200 Subject: [FieldTrip] Research Scientist Position at University of Washington References: Message-ID: Please see the message below on behalf of Chris Bishop. Begin forwarded message: > We are looking for qualified applicants for a Senior Research Scientist position at the University of Washington. Applicants will need to have a background in EEG and MATLAB. > > The requisition number is 120420. Full description and application details can be found at the link below. > > https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szCategory=jobprofile&szOrderID=120420&szCandidateID=0&szSearchWords=&szReturnToSearch=1 > > Thank you > -Chris Bishop -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri May 1 09:44:26 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 1 May 2015 09:44:26 +0200 Subject: [FieldTrip] postdoc position at NatMEG: Alzheimer's disease diagnostics and treatment evaluation with MEG Message-ID: Post doc, Stockholm, Sweden The position as postdoctoral researcher at NatMEG Applications are invited for a postdoctoral position in MEG within a project aiming at new diagnostics and (evaluation of) treatment for the neuropathological conditions Alzheimer´s disease (AD), Parkinson´s disease (PD) and related prodromal and at-risk stages of these conditions. The position is for 2 years, with the possibility of extension for a maximum of another 2 years. Duties The successful candidate will use MEG during emotion/cognition tasks, activation (motor), stimulation (visual, auditory, somatosensory, olfactory) and resting state protocols to explore functional connectivity measures for characterizing individuals with AD and PD, and for detecting individuals at risk of developing either of these conditions. The successful candidate will also work with methods for evaluating treatment effects within AD, PD and related prodromal cohorts. NatMEG –The National Facility for Magnetoencephalography (MEG) As of September 2013, Karolinska Institutet hosts a superbly equipped MEG lab. The lab, NatMEG, is a national facility, open for researchers from all across Sweden. The fact that NatMEG is a national facility is reflected by the wide array of projects currently ongoing/under initiation at NatMEG, covering areas such as next-generation SQUIDS, computational modelling, epilepsy work-ups, and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson’s and Alzheimer’s disease, and more. The latest equipment installations, entailing microneurography and next-generation high-Tc SQUIDS, makes NatMEG very uniquely equipped. NatMEG offers an open and friendly working environment, in the middle of Karolinska Institutet campus, Stockholm. Please visit http://natmeg.se for more information. Entry requirements A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. It is required that a candidate: A. Has extensive MEG hands-on experience (preferably on an Elekta Neuromag TRIUX or Vectorview system), from MEG data collection, including setting up experiments and peripheral stimulators. B. Has strong skills and expertise in MEG analysis (preferably in at least FieldTrip and/or MNE). C. Has a background and research interest within the cognitive neuroscience domain. D. Is independent, professional, and service minded, and enjoys interacting with researchers and research subjects. E. Masters academic English. It is also highly valued if a candidate: F. Has experience and/or expertise regarding Alzheimer’s disease. G. Has experience and/or expertise regarding Parkinson’s disease. H. Has an expertise in / experience with psychophysiology (e.g. EMG, facial EMG, GSR, HR, respiration) measurements and analysis. H. Karolinska Institutet Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 percent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. See http://ki.se/en/ for more information. The Department of Clinical Neuroscience The Department of Clinical Neuroscience (CNS) conducts research and education in the field of neuroscience from the molecular level to the society level. The clinical research and education is conducted in collaboration with other research groups from the Karolinska Institutet, with other universities as well as the Stockholm County Council. Please visit our website for more information: http://ki.se/en/cns Application process Read more about the application process at https://ki.mynetworkglobal.com/en/what:job/jobID:63833/. Applications are to be submitted in the recruitment system MyNetwork. Application deadline 2015-05-24 Contact information Daniel Lundqvist, Head of Unit daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri May 1 09:44:29 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 1 May 2015 09:44:29 +0200 Subject: [FieldTrip] postdoc position at NatMEG: combined MEG and microneurography Message-ID: <2F1892F1-A625-4919-AB37-43AE8C571093@donders.ru.nl> Post doc, Stockholm, Sweden The position as postdoctoral researcher at NatMEG Applications are invited for a postdoctoral position within two unique and overlapping projects at NatMEG: 1. combined MEG and microneurography (recording and stimulation inside peripheral nerve fibres) measurements, and 2. benchmarking of next-generation high-Tc SQUIDS (head-adjustable, nitrogen-cooled MEG sensors with millimetre sensor-to-scalp-proximity) against today’s state of the art MEG system (Elekta Triux). The position is for a maximum of 4 years. Duties The successful candidate will explore: 1. the (1a) physiology of touch and the (1b) autonomic nervous system by means of combined MEG and microneurography recordings. 2. the spatiotemporal precision and MEG signal characteristics of focal High-TC SQUIDS, benchmarked against the present (a conventional helium-cooled) MEG system for application such as (2a) sensory stimulation (visual, auditory, somatosensory, olfactory) and clinical applications such as (2b) interictal epileptogenic spike detection and (2c) functional mapping. NatMEG –The National Facility for Magnetoencephalography (MEG) As of September 2013, Karolinska Institutet hosts a superbly equipped MEG lab. The lab, NatMEG, is a national facility, open for researchers from all across Sweden. The fact that NatMEG is a national facility is reflected by the wide array of projects currently ongoing/under initiation at NatMEG, covering areas such as next-generation SQUIDS, computational modelling, epilepsy work-ups, and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson’s and Alzheimer’s disease, and more. The latest equipment installations, entailing microneurography and next-generation high-Tc SQUIDS, makes NatMEG very uniquely equipped. NatMEG offers an open and friendly working environment, in the middle of Karolinska Institutet campus, Stockholm. Please visit http://natmeg.se for more information. Entry requirements A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. It is required that a candidate: A. Has a background and research interest within the cognitive neuroscience domain. B. Has extensive MEG hands-on experience (preferably on an Elekta Neuromag TRIUX or Vectorview system), from MEG data collection, including setting up experiments and peripheral stimulators. C. Has very strong skills and expertise in MEG analysis (preferably in at least FieldTrip and/or MNE). D. Is independent, professional, and service minded, and enjoys interacting with researchers and research subjects. E. Masters academic English. It is also highly valued if a candidate: F. Has an expertise in the primary sensory system in one or several sensory modalities. G. Has an expertise in / experience from high-Tc SQUIDS. H. Has an expertise in / experience from microneurography measurements and analysis. I. Has an expertise in / experience with psychophysiology (e.g. EMG, facial EMG, GSR, HR, respiration) measurements and analysis. I. Karolinska Institutet Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 percent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. See http://ki.se/en/ for more information. The Department of Clinical Neuroscience The Department of Clinical Neuroscience (CNS) conducts research and education in the field of neuroscience from the molecular level to the society level. The clinical research and education is conducted in collaboration with other research groups from the Karolinska Institutet, with other universities as well as the Stockholm County Council. Please visit our website for more information: http://ki.se/en/cns Application process Read more about the application process at https://ki.mynetworkglobal.com/what:job/jobID:63834/. Applications are to be submitted in the recruitment system MyNetwork. Application deadline 2015-05-24 Contact information Daniel Lundqvist, Head of Unit daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Fri May 1 20:29:09 2015 From: elam4hcp at gmail.com (Jennifer Elam) Date: Fri, 1 May 2015 13:29:09 -0500 Subject: [FieldTrip] Still time to register for the 2015 HCP Course! Message-ID: A reminder that it’s not too late to register for the 2015 HCP Course: “Exploring the Human Connectome” , to be held June 8-12, 2015 at the Marriott Resort Waikiki Beach, in Honolulu, Hawaii, USA. Also, a reminder that you might try http://www.vrbo.com/ or https://www.airbnb.com/ for affordable accommodations in the Waikiki Beach area, near the Marriott. This 5-day intensive course is designed for investigators who are interested in: - using data being collected and distributed by HCP - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - learning to use Connectome Workbench tools and the CIFTI connectivity data format - learning HCP multi-modal neuroimaging analysis methods, including those that combine MEG and MRI data - positioning yourself to capitalize on HCP-style data from forthcoming large-scale projects (e.g., Lifespan HCP and Connectomes Related to Human Disease) Visit the HCP Course website to register and for Faculty listings and the full schedule of covered topics. We hope to see you in Hawaii! Best, 2015 HCP Course Organizers -------------- next part -------------- An HTML attachment was scrubbed... URL: From haristz at umn.edu Fri May 1 21:58:02 2015 From: haristz at umn.edu (Haris Tzagarakis) Date: Fri, 1 May 2015 14:58:02 -0500 Subject: [FieldTrip] Problems using fieldtrip with Matlab Distributed Computing Server Message-ID: Hi There, I have been trying to use fieldrtip in conjunction with Matlab Distributed Computing Server on a supercomputing resource and have been running into a problem that seems to come from paths/global variables? in detail: I use fieldtrip in conjunction with my own code for an analysis. The analysis works fine on a "normal"/non-parallel call. I then set out to parallelize the code and split the analysis to a different node for every subject I have. I have access to a supercomputing cluster (not uniquely for matlab/biomed use), which runs Matlab Distributed Computing Server, so job scheduling etc can happen from within matlab. I believe this is different from the 'peer distributed' approach described in the faq. I prepared a script which is then run with the matlab 'batch' command : job = batch('parscript3b', 'Profile', 'Itasca_MSI', 'Pool', 10); I attach the script in its current form here. This call should pass the script to a top level node that then distributes the loop in 10 nodes, one for each subject. What always happens however is that I get an error at the top level node saying: Error using ft_hastoolbox (line 469) the FREESURFER toolbox is not installed, see http://surfer.nmr.mgh.harvard.edu/fswiki I have read the help/comments text and some of the code in ft_hastoolbox and ft_defaults (I in fact always call ft_defaults at startup - my startup file is also attached here). This in conjunction with what is mentioned in MATLAB help makes me think that there is something about the way paths and global variables are handled by MDCS that does not agree with Fieldtrip. I have been trying to go around the problem by liberally using ft_defaults in my script code (as can be seen) and I also added some lines to the ft_hastoolbox function (in all its 4 instances in the private folders) to check explicitly for the fieldtrip locations in my system but none of this has worked. I would be grateful for any insight you might have. With Thanks and Best Wishes, Haris -- Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych Senior Research Associate University of Minnesota Dept of Neuroscience office: Brain Sciences Center Minneapolis VA Medical Center Tel:612-467-1363 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: parscript3b.m Type: text/x-csrc Size: 679 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: startup_current.m Type: text/x-csrc Size: 552 bytes Desc: not available URL: From e.maris at donders.ru.nl Mon May 4 17:42:17 2015 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Mon, 4 May 2015 15:42:17 +0000 Subject: [FieldTrip] symposium on model-based and model-inspired analysis of electrophysiological data Message-ID: <30e5b4c636464fafb45f7de18ae20de5@EXPRD03.hosting.ru.nl> Dear colleague, On June 1, I will organise a symposium on model-based and model-inspired analysis of electrophysiological data, to which I would like to invite you and your colleagues. You can find the program and additional information in the attachment. Please send around this invitation to everyone who might profit from this symposium. About a week before the symposium, I will send around directions on how the get here. best, Eric Maris -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2015-06-01.Model-based and Model-inspired Analysis of Electrophysiological Data.pdf Type: application/pdf Size: 27061 bytes Desc: 2015-06-01.Model-based and Model-inspired Analysis of Electrophysiological Data.pdf URL: From mark.woolrich at ohba.ox.ac.uk Tue May 5 13:14:50 2015 From: mark.woolrich at ohba.ox.ac.uk (Mark Woolrich) Date: Tue, 5 May 2015 11:14:50 +0000 Subject: [FieldTrip] Research postdoc positions in neuroimage analysis and computational neuroscience. Message-ID: <0229ABEF-5744-43AD-8130-CC2567B50AD5@ohba.ox.ac.uk> Applications are invited for two postdoctoral scientists to work on a Wellcome Trust funded project to advance understanding of spontaneous whole-brain activity. The project will use a combination of MRI, M/EEG / LFP recordings, methods development and biophysical modeling to advance understanding of spontaneous whole-brain activity, and provide new insights into the underlying mechanisms. This research will be conducted within the OHBA Analysis Group headed by Mark Woolrich and based at the Oxford Centre for Human Brain Activity (http://www.ohba.ox.ac.uk), and will be in collaboration with colleagues at FMRIB (http://www.fmrib.ox.ac.uk/analysis) and the Centre for Neural Circuits and Behaviour (http://www.cncb.ox.ac.uk). We are looking for excellent researchers with a strong technical background, ideally in computational neuroscience and/or in developing neuroimaging analysis methods, but also with experience in other areas of Engineering/Applied Mathematics, Statistics, Computer Science and Physics (e.g. Machine Learning and Pattern Recognition). Post in Neuroimaging Analysis https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=117895 Post in computational biophysical model development https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=118123 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmuehl at gmail.com Tue May 5 17:20:32 2015 From: cmuehl at gmail.com (Christian Muehl) Date: Tue, 5 May 2015 15:20:32 +0000 Subject: [FieldTrip] 2nd Call for Papers - 4th Workshop on Affective Brain-Computer Interfaces @ ACII2015 Message-ID: ** 2nd Call for Papers ** 4th Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2015 (September 21-24), Xi'an, China, September 21, 2015 http://www.affective-sciences.org/aBCI2015 http://www.acii2015.org/ The goal of the aBCI workshop series is to connect researchers from the communities of affective computing, social signal processing, brain-computer interfacing, neuro-ergonomics, and neuroscience around the federating theme of affective brain computer interfaces (aBCI). Affective BCI aim at the development of human-computer interfaces able to react and adapt to users' emotions and related cognitive states as measured from neurophysiological signals. Besides the general solicitation of work toward adaptive HCI applications based on aBCI, this 4th edition of the workshop will focus on two specific aspects of aBCI. Firstly, we welcome papers on ways to alleviate current aBCI limitations, through work on the physiological basis of aBCI, innovative applications resilient to classification error, and methods to increase the robustness of aBCI. Secondly, we would like to explore the social aspects and applications of aBCI by welcoming submissions on topics such as multi-user aBCI and the assessment of social processes from brain signals. The workshop topics include, but are not limited to, * effective emotion elicitation and data collection in social settings; * identification of robust and specific markers of emotional, cognitive and social processes; * methods for the assessment of emotions, cognitive states and social interactions; * methods to measure and process multiple people physiological activity; * applications of central and peripheral signal processing to social situations; * innovative concepts for adaptive interfaces and affective BCI; * demos of affective BCI systems. Submission Instructions: * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors. * Papers will be published electronically in the proceedings of ACII 2015 by IEEE Xplore. Papers should be limited to 6 pages+1page references. The review is double blind - please remove all author information from the manuscripts. * Further details about the submission instructions and format can be found on the website of ACII 2015. Important Dates: June 5, 2015: Submission of manuscripts July 3, 2015: Acceptance/Rejection notification July 24, 2015: Submission of camera-ready papers September 21, 2015: Date of the Workshop For further information, see our website or contact abci at ewi.utwente.nl Programme Chairs: * Fabien Lotte, Inria Bordeaux Sud-Ouest, Talance, France * Guillaume Chanel, Swiss Center for Affective Sciences, Geneva, Switzerland * Christian Mühl, German Aerospace Center, Cologne, Germany * Anton Nijholt, Universiteit Twente, the Netherlands Programme Committee: Egon L. van den Broek, University of Utrecht, the Netherlands Anne-Marie Brouwer, TNO Perceptual and Cognitive Systems, Soesterberg, the Netherlands Stephen Dunne, Starlab Barcelona, Spain Touradj Ebrahimi, École polytechnique fédérale de Lausanne, Switzerland Stephen Fairclough, John Moores University, Liverpool, UK Tiago H. Falk, Institut National de la Recherche Scientifique (INRS), Montreal, Canada Hayrettin Gürkök, University of Twente, Enschede, the Netherlands Dominic Heger, Karlsruhe Institute of Technology, Germany Klas Ihme, German Aerospace Center, Brunswick, Germany Jonghwa Kim, University of Augsburg, Germany Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA, Grace Leslie, MIT Media Lab, Boston, USA Giulia Liberati, Université catholique de Louvain, Belgium Gary Garcia Molina, Philips Research North America, Briarcliff, USA Scott Makeig, University of California San Diego, USA Tim Mullen, University of California San Diego, USA Domen Novak, University of Wyoming, Laramie, USA Ioannis Patras, Queen Mary University, London, UK Evan Peck, Bucknell University, Lewisburg, USA Mannes Poel, University of Twente, Enschede, the Netherlands Alan Pope, NASA Langley Research Center, Norfolk, USA Thierry Pun, University of Geneva, Switzerland Erin Solovey, Drexel University, Philadelphia, USA Mohammad Soleymani, University of Geneva, Switzerland Aureli Soria-Frisch, Starlab Barcelona, Spain Olga Sourina, NanYang Technological University, Singapore Aleksander Valjamae, Linköping University, Sweden Jan van Erp, University of Twente, Enschede, the Netherlands Chi Thanh Vi, University of Bristol, UK Thorsten Zander, Technische Universität Berlin, Germany From hamzaf at sabanciuniv.edu Tue May 5 18:40:23 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Tue, 5 May 2015 18:40:23 +0200 Subject: [FieldTrip] brick0 Message-ID: Hello, While trying to plot all tissues in one image using ft_sourceplot function as in seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); I faced the following error: Reference to non-existent field 'brick0' This brick0 is defined in atlas_lookup.m as brick0_val = atlas.brick0(ijk(1), ijk(2), ijk(3)); But the atlas variable that is called for this function is defined as: dim: [256 256 256] transform: [4x4 double] coordsys: 'ctf' unit: 'mm' cfg: [1x1 struct] seg: [256x256x256 double] seglabel: {'gray' 'white' 'csf' 'skull' 'scalp'} I wonder from where this brick0 come? Thanks for help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Wed May 6 00:01:40 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Tue, 5 May 2015 23:01:40 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy Message-ID: <55493DC4.90601@glasgow.ac.uk> An HTML attachment was scrubbed... URL: From nadine.dijkstra92 at gmail.com Wed May 6 14:20:58 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Wed, 6 May 2015 14:20:58 +0200 Subject: [FieldTrip] labels per grid point Message-ID: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Dear Fieldtrip Users, I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? Thanks in advance for your help, Nadine From tzvetan.popov at uni-konstanz.de Wed May 6 14:37:56 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 6 May 2015 14:37:56 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: Hi Nadine, maybe this is what you need? http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations best tzvetan > Dear Fieldtrip Users, > > I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? > > Thanks in advance for your help, > Nadine > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 14:43:08 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 14:43:08 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: <018c01d087fa$34fa3150$9eee93f0$@artinis.com> Hi Nadine, does the second exercise in this section help (i.e. defining a lookup atlas for source plotting): http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_source s_of_oscillatory_gamma-band_activity ? Best, Jörn -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Nadine > Sent: Wednesday, May 6, 2015 2:21 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] labels per grid point > > Dear Fieldtrip Users, > > I am trying to get anatomical labels for individual source grid points. I can only > find how to parcellate the grid points to get an averaged value of sources for > certain parcellations (e.g. Brodmann areas). But I would like to get an > anatomical label per grid point, so that I can see which grid points belong to > which area. Does anybody have any solution for this? > > Thanks in advance for your help, > Nadine > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 14:49:32 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 14:49:32 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <018c01d087fa$34fa3150$9eee93f0$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> Message-ID: <018f01d087fb$19d25460$4d76fd20$@artinis.com> the correct link is: http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_source s_of_oscillatory_gamma-band_activity not sure why there was a line break introduced... -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > Sent: Wednesday, May 6, 2015 2:43 PM > To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] labels per grid point > > Hi Nadine, > > does the second exercise in this section help (i.e. defining a lookup atlas for > source plotting): > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > ource > s_of_oscillatory_gamma-band_activity > ? > > Best, > Jörn > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems  |  +31 481 350 980 > > > -----Original Message----- > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > bounces at science.ru.nl] On Behalf Of Nadine > > Sent: Wednesday, May 6, 2015 2:21 PM > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] labels per grid point > > > > Dear Fieldtrip Users, > > > > I am trying to get anatomical labels for individual source grid > > points. I > can only > > find how to parcellate the grid points to get an averaged value of > > sources > for > > certain parcellations (e.g. Brodmann areas). But I would like to get > > an anatomical label per grid point, so that I can see which grid > > points > belong to > > which area. Does anybody have any solution for this? > > > > Thanks in advance for your help, > > Nadine > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 15:07:24 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 15:07:24 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <018f01d087fb$19d25460$4d76fd20$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> <018f01d087fb$19d25460$4d76fd20$@artinis.com> Message-ID: <019001d087fd$98c7f020$ca57d060$@artinis.com> haha ok, I give up, the link still appears to be broken - please copy the link together yourself or click on 'Plotting sources of oscillatory gamma-band activity' on the navigation tab to the left and look for the second exercise in that section. -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > Sent: Wednesday, May 6, 2015 2:50 PM > To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] labels per grid point > > the correct link is: > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > ource > s_of_oscillatory_gamma-band_activity > not sure why there was a line break introduced... > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems  |  +31 481 350 980 > > > -----Original Message----- > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > > Sent: Wednesday, May 6, 2015 2:43 PM > > To: 'FieldTrip discussion list' > > Subject: Re: [FieldTrip] labels per grid point > > > > Hi Nadine, > > > > does the second exercise in this section help (i.e. defining a lookup > atlas for > > source plotting): > > > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ > > s > > ource > > s_of_oscillatory_gamma-band_activity > > ? > > > > Best, > > Jörn > > > > > > -- > > > > Jörn M. Horschig, Software Engineer > > Artinis Medical Systems  |  +31 481 350 980 > > > > > -----Original Message----- > > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > > bounces at science.ru.nl] On Behalf Of Nadine > > > Sent: Wednesday, May 6, 2015 2:21 PM > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] labels per grid point > > > > > > Dear Fieldtrip Users, > > > > > > I am trying to get anatomical labels for individual source grid > > > points. I > > can only > > > find how to parcellate the grid points to get an averaged value of > > > sources > > for > > > certain parcellations (e.g. Brodmann areas). But I would like to get > > > an anatomical label per grid point, so that I can see which grid > > > points > > belong to > > > which area. Does anybody have any solution for this? > > > > > > Thanks in advance for your help, > > > Nadine > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nadine.dijkstra92 at gmail.com Wed May 6 15:51:59 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Wed, 6 May 2015 15:51:59 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <019001d087fd$98c7f020$ca57d060$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> <018f01d087fb$19d25460$4d76fd20$@artinis.com> <019001d087fd$98c7f020$ca57d060$@artinis.com> Message-ID: Thanks, the link works fine for me! I am not sure if this solves the problem however, because it only gives the labels for some points in the plot, while I want to have the label for every individual grid point in a list so that I can see which grid points belong to the same area etc. However, this might be a good place to start. Thanks anyway! Best, Nadine On 06 May 2015, at 15:07, Jörn M. Horschig wrote: > haha ok, I give up, the link still appears to be broken - please copy the > link together yourself or click on 'Plotting sources of oscillatory > gamma-band activity' on the navigation tab to the left and look for the > second exercise in that section. > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems | +31 481 350 980 > >> -----Original Message----- >> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >> bounces at science.ru.nl] On Behalf Of Jörn M. Horschig >> Sent: Wednesday, May 6, 2015 2:50 PM >> To: 'FieldTrip discussion list' >> Subject: Re: [FieldTrip] labels per grid point >> >> the correct link is: >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s >> ource >> s_of_oscillatory_gamma-band_activity >> not sure why there was a line break introduced... >> >> >> -- >> >> Jörn M. Horschig, Software Engineer >> Artinis Medical Systems | +31 481 350 980 >> >>> -----Original Message----- >>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >>> bounces at science.ru.nl] On Behalf Of Jörn M. Horschig >>> Sent: Wednesday, May 6, 2015 2:43 PM >>> To: 'FieldTrip discussion list' >>> Subject: Re: [FieldTrip] labels per grid point >>> >>> Hi Nadine, >>> >>> does the second exercise in this section help (i.e. defining a lookup >> atlas for >>> source plotting): >>> >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ >>> s >>> ource >>> s_of_oscillatory_gamma-band_activity >>> ? >>> >>> Best, >>> Jörn >>> >>> >>> -- >>> >>> Jörn M. Horschig, Software Engineer >>> Artinis Medical Systems | +31 481 350 980 >>> >>>> -----Original Message----- >>>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >>>> bounces at science.ru.nl] On Behalf Of Nadine >>>> Sent: Wednesday, May 6, 2015 2:21 PM >>>> To: fieldtrip at science.ru.nl >>>> Subject: [FieldTrip] labels per grid point >>>> >>>> Dear Fieldtrip Users, >>>> >>>> I am trying to get anatomical labels for individual source grid >>>> points. I >>> can only >>>> find how to parcellate the grid points to get an averaged value of >>>> sources >>> for >>>> certain parcellations (e.g. Brodmann areas). But I would like to get >>>> an anatomical label per grid point, so that I can see which grid >>>> points >>> belong to >>>> which area. Does anybody have any solution for this? >>>> >>>> Thanks in advance for your help, >>>> Nadine >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nadine.dijkstra92 at gmail.com Thu May 7 09:36:34 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Thu, 7 May 2015 09:36:34 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: <306CCF9F-01AC-4036-8B14-C4FFC99AA54E@gmail.com> Hi Tzvetan, Yes, thank you, this is perfect! Best, Nadine On 06 May 2015, at 14:37, Tzvetan Popov wrote: > Hi Nadine, > > maybe this is what you need? > http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations > > best > tzvetan > >> Dear Fieldtrip Users, >> >> I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? >> >> Thanks in advance for your help, >> Nadine >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From guiraudh at gmail.com Thu May 7 10:21:19 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Thu, 7 May 2015 10:21:19 +0200 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi Till and John, Thank you, this is perfect! Best regards, Hélène 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > We have a template for children‹actually have for infants from 2 weeks > through adults at 89 years. We also have average electrode positions for > EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented > priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have > been using this recently with FT for infants and child/adolescent/adult > ages. > > WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > Fro www site: This is a database of average MRIs and associated MRI > volumes for developmental MRI work. It consists of average MRI templates, > segmented partial volume estimate volumes for GM, WM, T2W-derived CSF > (Description > > > ). The database is separated into head-based and brain-based averages. The > data are separated by ages in months, years, 6-month, or 5-year intervals > (Ages and Templates > < > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm > l>). The templates are grouped into first year (2 weeks through 12 > months), early childhood (15 months through 4 years), childhood (4 years > through 10 years), adolescence (10.5 years through 17.5 years) and adults > (18 years through 89 years). > Tools for cortical source analysis of EEG and ERP are provided. These > tools are based on the average MRI templates, segmenting, and atlases. > > Also see my www site, jerlab.psych.sc.edu for publications describing > this. We have a recent chapter that has a good description of the issues > behind the database (with Wanze Xie). We have a paper accepted at > Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, > Michelle Phillips-Meek, and Wanze Xie). > > John > > > *********************************************** > John E. Richards Carolina Distinguished Professor > Department of Psychology > University of South Carolina > Columbia, SC 29208 > Dept Phone: 803 777 2079 > Fax: 803 777 9558 > Email: richards-john at sc.edu > HTTP: jerlab.psych.sc.edu > *********************************************** > > > > > > > > > On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" > wrote: > > >Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > >To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > >You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > >When replying, please edit your Subject line so it is more specific > >than "Re: Contents of fieldtrip digest..." > > > > > >Today's Topics: > > > > 1. Search for a template children. (H?l?ne Guiraud) > > 2. Re: Search for a template children. (Till Schneider) > > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > > > > >---------------------------------------------------------------------- > > > >Message: 1 > >Date: Wed, 29 Apr 2015 14:45:56 +0200 > >From: H?l?ne Guiraud > >To: fieldtrip at science.ru.nl > >Subject: [FieldTrip] Search for a template children. > >Message-ID: > > < > CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> > >Content-Type: text/plain; charset="utf-8" > > > >Dear community, > > > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on > >speech perception in children using MEG. > >The children involved in the study don't pass MRI. We want to achieve > >source reconstruction from a template. However I can't find a template > >corresponding to the anatomy of a child (8-12 years). > >Can someone tell me if there are template children and where I can find > >them? > > > >Best, > > > >H?l?ne Guiraud > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e > >9b53e/attachment-0001.html> > > > >------------------------------ > > > >Message: 2 > >Date: Wed, 29 Apr 2015 15:53:13 +0200 > >From: Till Schneider > >To: FieldTrip discussion list > >Subject: Re: [FieldTrip] Search for a template children. > >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> > >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > > >Dear Helene, > > > >McGill University provides MNI brains for different age groups between > >4.5y to 18y. > >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 > >You will probably find the template brain you are searching for in this > >database. > > > >Best regards, > >Till > > > >-- > > > >Till Schneider, PhD > > > >Cognitive and Clinical Neurophysiology Group > >Dept. of Neurophysiology and Pathophysiology > >University Medical Center Hamburg-Eppendorf > >Martinistr. 52 > >20246 Hamburg > >Germany > > > >phone +49-40-7410-53188 > >fax +49-40-7410-57126 > >www.uke.de/neurophysiologie > > > > > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: > >> Dear community, > >> > >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) > >> on speech perception in children using MEG. > >> The children involved in the study don't pass MRI. We want to achieve > >> source reconstruction from a template. However I can't find a template > >> corresponding to the anatomy of a child (8-12 years). > >> Can someone tell me if there are template children and where I can > >> find them? > >> > >> Best, > >> > >> H?l?ne Guiraud > >> > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > >-- > > > >_____________________________________________________________________ > > > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen > >Rechts; Gerichtsstand: Hamburg | www.uke.de > >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. > >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik > >_____________________________________________________________________ > > > >SAVE PAPER - THINK BEFORE PRINTING > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e > >44937/attachment-0001.html> > > > >------------------------------ > > > >Message: 3 > >Date: Wed, 29 Apr 2015 16:25:35 +0200 > >From: Keyvan Mahjoory > >To: FieldTrip discussion list > >Subject: [FieldTrip] ICBM 152 templates in FT > >Message-ID: > > UJp6-+4+7fA at mail.gmail.com> > >Content-Type: text/plain; charset="iso-8859-1" > > > >Dear Fieldtrip Users, > > > >I perform source analysis in Fieldtrip with a template head model ( > >standard_bem ) and a > >template source model (cortex_5124.surf.gii > >) to constarin > >estimated sources on cortex. These templates are based on Colin27, But I > >prefere to use the template ICBM152 instead. > >Does FT include ICBM template? I mean templates for both head model and > >cortical surfe. > > > >Many Thanks in advance, > >Keyvan > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 > >9daf3/attachment-0001.html> > > > >------------------------------ > > > >_______________________________________________ > >fieldtrip mailing list > >fieldtrip at donders.ru.nl > >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > >End of fieldtrip Digest, Vol 53, Issue 23 > >***************************************** > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hélène Guiraud Doctorante Université Lyon 2 Laboratoire Dynamique Du Langage CNRS, UMR 5596 Tel : 04 72 72 65 34 guiraudh at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From sander at mpib-berlin.mpg.de Thu May 7 10:29:39 2015 From: sander at mpib-berlin.mpg.de (Sander, Myriam) Date: Thu, 7 May 2015 08:29:39 +0000 Subject: [FieldTrip] Vacant Predoctoral Position in Lifespan Psychology at the MPI for Human Development in Berlin, Germany Message-ID: ********************************************************* PREDOCTORAL POSITION: CENTER FOR LIFESPAN PSYCHOLOGY, MPI BERLIN The new MINERVA research group headed by Dr. Myriam Sander at the Max Planck Institute for Human Development, Center for Lifespan Psychology (Director: Prof. Dr. Ulman Lindenberger), is seeking applications for a PREDOCTORAL POSITION The doctoral contract will last for 3 years. The position is available from October 1, 2015 or later. Job Description: Future research of the new MINERVA research group (PI: Dr. Myriam Sander) will use a multi-modal imaging approach (EEG with a focus on oscillatory measures in combination with structural and functional MRI) to uncover lifespan differences in the interplay between sensory (visual and auditory) and cognitive abilities influencing memory performance. The MINERVA research group is part of the project „Cognitive and Neural Dynamics of Memory Across the Lifespan (CONMEM)” which investigates lifespan changes in the interplay between associative and strategic components of memory functioning on neural and cognitive levels, with a focus on working and episodic memory (see Sander, et al., Neurosci. Biobehav. Rev., 2012; Shing, et al., Neurosci. Biobehav. Rev., 2010). The successful predoctoral fellow will plan and conduct empirical studies in this domain, analyze the behavioral, EEG, and MRI data, and prepare scientific manuscripts for publication. For further information, please contact: Dr. Myriam Sander (sander at mpib-berlin.mpg.de) Requirements: A successful applicant needs to hold (or expect by summer 2015) a diploma/master degree in psychology, cognitive neuroscience, or related fields. Applicants should have experience with conducting experimental research, knowledge in neuroimaging methods (EEG and/or MRI), and a solid background in at least one programming language (preferably Matlab or R). In addition, the ability to work independently as well as a high proficiency of the English language is required. Experience with age-comparative studies is an advantage. The Max Planck Society is interested in increasing the number of women on its scientific staff. We strongly encourage applications from women and members of minority groups. In addition, the Max Planck Society is committed to employing more handicapped individuals and encourages them to apply. To apply, please send (as ONE FILE and via email only) a statement of research interests, a CV, a copy of relevant certificates, (p)reprints of publications, and a list of two references to Dr. Myriam Sander, MPI for Human Development, Lentzeallee 94, 14195 Berlin (sander at mpib-berlin.mpg.de) preferably by June 30th, 2015. Later applications will be considered until the position is filled. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu May 7 11:11:54 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Thu, 7 May 2015 11:11:54 +0200 Subject: [FieldTrip] Vgrid Message-ID: Hello, I got the following error when I run these lines: (found in http://www.fieldtriptoolbox.org/development/simbio) cfg = []; cfg.shift = 0.3; cfg.method = 'hexahedral'; mesh = ft_prepare_mesh(cfg,segmentedmri); Error using vgrid (line 16) the vgrid executable is not available for your platform, it was expected to be located at ***\external\vgrid\bin\pcwin64\vgrid.exe I don't have a folder called pcwin64! I have only glnx86 (empty folder) glnxa64 and maci64 in ***\external\vgrid\bin\ I also downloaded a newer version of fieldtrip, but I did not find it! >From where I can get vgrid.exe? Thank you -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.vorw01 at gmail.com Thu May 7 11:40:17 2015 From: j.vorw01 at gmail.com (Johannes Vorwerk) Date: Thu, 07 May 2015 11:40:17 +0200 Subject: [FieldTrip] Vgrid In-Reply-To: References: Message-ID: <1430991617.11932.23.camel@biomag43> Hi, vgrid should no longer be needed in recent fieldtrip-versions. It was replaced by a fully matlab-based function (prepare_mesh_hexahedral), that should now also work under windows. A vgrid.exe never existed, it was only available for mac and linux. Did you try updating your fieldtrip-version to a recent release? Best, Johannes Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi Altakroury (Alumni): > Hello, > > > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was > expected to be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > > I don't have a folder called pcwin64! I have only glnx86 (empty > folder) glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > From where I can get vgrid.exe? > > > Thank you > > > > -- > > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dipl.-Math. Johannes Vorwerk e-mail: j.vorwerk at uni-muenster.de Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters Institute for Biomagnetism and Biosignalanalysis, University of Muenster www: http://campus.uni-muenster.de/index.php?id=919&L=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Thu May 7 12:21:40 2015 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Thu, 7 May 2015 12:21:40 +0200 Subject: [FieldTrip] labels per grid point (Nadine) Message-ID: Hi Nadine, Following up Tzvetan's response , you get the label for every grid by doing this : clear all; clc; % read the atlas atlas = ft_read_atlas('/home/common/matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii'); load('standard_sourcemodel3d10mm.mat'); % mni template source model % and call ft_sourceinterpolate: cfg = []; cfg.interpmethod = 'nearest'; cfg.parameter = 'tissue'; sourcemodel2 = ft_sourceinterpolate(cfg, atlas, sourcemodel); % replace NAN with 0 ; sourcemodel2.tissue(isnan(sourcemodel2.tissue)) =0; ids =find(sourcemodel2.tissue); % all interpolate regions id =sourcemodel2.tissue(ids); % all interpolate regions index ROI =atlas.tissuelabel(id); if you want to find Occipital for instance , you just call a few more lines code : occid =find(strncmpi(ROI,'Occipital',9)); % indice OCC =ROI(occid); % label Hope this helps, Hatieng > Message: 6 > Date: Wed, 6 May 2015 15:51:59 +0200 > From: Nadine > To: FieldTrip discussion list > Subject: Re: [FieldTrip] labels per grid point > Message-ID: > Content-Type: text/plain; charset=iso-8859-1 > > Thanks, the link works fine for me! > I am not sure if this solves the problem however, because it only gives > the labels for some points in the plot, while I want to have the label for > every individual grid point in a list so that I can see which grid points > belong to the same area etc. However, this might be a good place to start. > Thanks anyway! > > Best, > Nadine > > On 06 May 2015, at 15:07, J?rn M. Horschig wrote: > > > haha ok, I give up, the link still appears to be broken - please copy the > > link together yourself or click on 'Plotting sources of oscillatory > > gamma-band activity' on the navigation tab to the left and look for the > > second exercise in that section. > > > > > > -- > > > > J?rn M. Horschig, Software Engineer > > Artinis Medical Systems | +31 481 350 980 > > > >> -----Original Message----- > >> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >> bounces at science.ru.nl] On Behalf Of J?rn M. Horschig > >> Sent: Wednesday, May 6, 2015 2:50 PM > >> To: 'FieldTrip discussion list' > >> Subject: Re: [FieldTrip] labels per grid point > >> > >> the correct link is: > >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > >> ource > >> s_of_oscillatory_gamma-band_activity > >> not sure why there was a line break introduced... > >> > >> > >> -- > >> > >> J?rn M. Horschig, Software Engineer > >> Artinis Medical Systems | +31 481 350 980 > >> > >>> -----Original Message----- > >>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >>> bounces at science.ru.nl] On Behalf Of J?rn M. Horschig > >>> Sent: Wednesday, May 6, 2015 2:43 PM > >>> To: 'FieldTrip discussion list' > >>> Subject: Re: [FieldTrip] labels per grid point > >>> > >>> Hi Nadine, > >>> > >>> does the second exercise in this section help (i.e. defining a lookup > >> atlas for > >>> source plotting): > >>> > >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ > >>> s > >>> ource > >>> s_of_oscillatory_gamma-band_activity > >>> ? > >>> > >>> Best, > >>> J?rn > >>> > >>> > >>> -- > >>> > >>> J?rn M. Horschig, Software Engineer > >>> Artinis Medical Systems | +31 481 350 980 > >>> > >>>> -----Original Message----- > >>>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >>>> bounces at science.ru.nl] On Behalf Of Nadine > >>>> Sent: Wednesday, May 6, 2015 2:21 PM > >>>> To: fieldtrip at science.ru.nl > >>>> Subject: [FieldTrip] labels per grid point > >>>> > >>>> Dear Fieldtrip Users, > >>>> > >>>> I am trying to get anatomical labels for individual source grid > >>>> points. I > >>> can only > >>>> find how to parcellate the grid points to get an averaged value of > >>>> sources > >>> for > >>>> certain parcellations (e.g. Brodmann areas). But I would like to get > >>>> an anatomical label per grid point, so that I can see which grid > >>>> points > >>> belong to > >>>> which area. Does anybody have any solution for this? > >>>> > >>>> Thanks in advance for your help, > >>>> Nadine > >>>> > >>>> _______________________________________________ > >>>> fieldtrip mailing list > >>>> fieldtrip at donders.ru.nl > >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >>> > >>> > >>> _______________________________________________ > >>> fieldtrip mailing list > >>> fieldtrip at donders.ru.nl > >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > ------------------------------ > > Message: 7 > Date: Thu, 7 May 2015 09:36:34 +0200 > From: Nadine > To: FieldTrip discussion list > Subject: Re: [FieldTrip] labels per grid point > Message-ID: <306CCF9F-01AC-4036-8B14-C4FFC99AA54E at gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi Tzvetan, > > Yes, thank you, this is perfect! > > Best, > Nadine > On 06 May 2015, at 14:37, Tzvetan Popov > wrote: > > > Hi Nadine, > > > > maybe this is what you need? > > > http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations > > > > best > > tzvetan > > > >> Dear Fieldtrip Users, > >> > >> I am trying to get anatomical labels for individual source grid points. > I can only find how to parcellate the grid points to get an averaged value > of sources for certain parcellations (e.g. Brodmann areas). But I would > like to get an anatomical label per grid point, so that I can see which > grid points belong to which area. Does anybody have any solution for this? > >> > >> Thanks in advance for your help, > >> Nadine > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > ------------------------------ > > Message: 8 > Date: Thu, 7 May 2015 10:21:19 +0200 > From: H?l?ne Guiraud > To: FieldTrip discussion list > Subject: Re: [FieldTrip] re template for children > Message-ID: > < > CAJ16KS8BwyAttHC2E23tsdisvjE+Y_T5NAjpMm4F8--0H6HN8g at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Till and John, > > Thank you, this is perfect! > > Best regards, > H?l?ne > > 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > > > We have a template for children?actually have for infants from 2 weeks > > through adults at 89 years. We also have average electrode positions for > > EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented > > priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have > > been using this recently with FT for infants and child/adolescent/adult > > ages. > > > > WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > Fro www site: This is a database of average MRIs and associated MRI > > volumes for developmental MRI work. It consists of average MRI templates, > > segmented partial volume estimate volumes for GM, WM, T2W-derived CSF > > (Description > > < > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html > > > > > ). The database is separated into head-based and brain-based averages. > The > > data are separated by ages in months, years, 6-month, or 5-year intervals > > (Ages and Templates > > < > > > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm > > l>). The templates are grouped into first year (2 weeks through 12 > > months), early childhood (15 months through 4 years), childhood (4 years > > through 10 years), adolescence (10.5 years through 17.5 years) and adults > > (18 years through 89 years). > > Tools for cortical source analysis of EEG and ERP are provided. These > > tools are based on the average MRI templates, segmenting, and atlases. > > > > Also see my www site, jerlab.psych.sc.edu for publications describing > > this. We have a recent chapter that has a good description of the issues > > behind the database (with Wanze Xie). We have a paper accepted at > > Neuroimage for their upcoming ?Data Sharing? issue (with Carmen Sanchez, > > Michelle Phillips-Meek, and Wanze Xie). > > > > John > > > > > > *********************************************** > > John E. Richards Carolina Distinguished Professor > > Department of Psychology > > University of South Carolina > > Columbia, SC 29208 > > Dept Phone: 803 777 2079 > > Fax: 803 777 9558 > > Email: richards-john at sc.edu > > HTTP: jerlab.psych.sc.edu > > *********************************************** > > > > > > > > > > > > > > > > > > On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" > > wrote: > > > > >Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > >To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > >You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > >When replying, please edit your Subject line so it is more specific > > >than "Re: Contents of fieldtrip digest..." > > > > > > > > >Today's Topics: > > > > > > 1. Search for a template children. (H?l?ne Guiraud) > > > 2. Re: Search for a template children. (Till Schneider) > > > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > > > > > > > >---------------------------------------------------------------------- > > > > > >Message: 1 > > >Date: Wed, 29 Apr 2015 14:45:56 +0200 > > >From: H?l?ne Guiraud > > >To: fieldtrip at science.ru.nl > > >Subject: [FieldTrip] Search for a template children. > > >Message-ID: > > > < > > CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> > > >Content-Type: text/plain; charset="utf-8" > > > > > >Dear community, > > > > > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on > > >speech perception in children using MEG. > > >The children involved in the study don't pass MRI. We want to achieve > > >source reconstruction from a template. However I can't find a template > > >corresponding to the anatomy of a child (8-12 years). > > >Can someone tell me if there are template children and where I can find > > >them? > > > > > >Best, > > > > > >H?l?ne Guiraud > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e > > >9b53e/attachment-0001.html> > > > > > >------------------------------ > > > > > >Message: 2 > > >Date: Wed, 29 Apr 2015 15:53:13 +0200 > > >From: Till Schneider > > >To: FieldTrip discussion list > > >Subject: Re: [FieldTrip] Search for a template children. > > >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> > > >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > > > > >Dear Helene, > > > > > >McGill University provides MNI brains for different age groups between > > >4.5y to 18y. > > >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 > > >You will probably find the template brain you are searching for in this > > >database. > > > > > >Best regards, > > >Till > > > > > >-- > > > > > >Till Schneider, PhD > > > > > >Cognitive and Clinical Neurophysiology Group > > >Dept. of Neurophysiology and Pathophysiology > > >University Medical Center Hamburg-Eppendorf > > >Martinistr. 52 > > >20246 Hamburg > > >Germany > > > > > >phone +49-40-7410-53188 > > >fax +49-40-7410-57126 > > >www.uke.de/neurophysiologie > > > > > > > > > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: > > >> Dear community, > > >> > > >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) > > >> on speech perception in children using MEG. > > >> The children involved in the study don't pass MRI. We want to achieve > > >> source reconstruction from a template. However I can't find a template > > >> corresponding to the anatomy of a child (8-12 years). > > >> Can someone tell me if there are template children and where I can > > >> find them? > > >> > > >> Best, > > >> > > >> H?l?ne Guiraud > > >> > > >> > > >> _______________________________________________ > > >> fieldtrip mailing list > > >> fieldtrip at donders.ru.nl > > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > >-- > > > > > >_____________________________________________________________________ > > > > > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen > > >Rechts; Gerichtsstand: Hamburg | www.uke.de > > >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. > > >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik > > >_____________________________________________________________________ > > > > > >SAVE PAPER - THINK BEFORE PRINTING > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e > > >44937/attachment-0001.html> > > > > > >------------------------------ > > > > > >Message: 3 > > >Date: Wed, 29 Apr 2015 16:25:35 +0200 > > >From: Keyvan Mahjoory > > >To: FieldTrip discussion list > > >Subject: [FieldTrip] ICBM 152 templates in FT > > >Message-ID: > > > > UJp6-+4+7fA at mail.gmail.com> > > >Content-Type: text/plain; charset="iso-8859-1" > > > > > >Dear Fieldtrip Users, > > > > > >I perform source analysis in Fieldtrip with a template head model ( > > >standard_bem ) and > a > > >template source model (cortex_5124.surf.gii > > >) to constarin > > >estimated sources on cortex. These templates are based on Colin27, But > I > > >prefere to use the template ICBM152 instead. > > >Does FT include ICBM template? I mean templates for both head model and > > >cortical surfe. > > > > > >Many Thanks in advance, > > >Keyvan > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 > > >9daf3/attachment-0001.html> > > > > > >------------------------------ > > > > > >_______________________________________________ > > >fieldtrip mailing list > > >fieldtrip at donders.ru.nl > > >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > >End of fieldtrip Digest, Vol 53, Issue 23 > > >***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > H?l?ne Guiraud > Doctorante > Universit? Lyon 2 > Laboratoire Dynamique Du Langage > CNRS, UMR 5596 > Tel : 04 72 72 65 34 > guiraudh at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/0bd0dea8/attachment-0001.html > > > > ------------------------------ > > Message: 9 > Date: Thu, 7 May 2015 08:29:39 +0000 > From: "Sander, Myriam" > To: FieldTrip discussion list ?[fieldtrip at science.ru.nl]? > > Subject: [FieldTrip] Vacant Predoctoral Position in Lifespan > Psychology at the MPI for Human Development in Berlin, Germany > Message-ID: > < > D12CFACF574CEA4498D72B949FF5631C9B20628E at MaxMail04.mpib-berlin.mpg.de> > > Content-Type: text/plain; charset="cp1256" > > ********************************************************* > > PREDOCTORAL POSITION: CENTER FOR LIFESPAN PSYCHOLOGY, MPI BERLIN > > The new MINERVA research group headed by Dr. Myriam Sander at the Max > Planck Institute for Human Development, Center for Lifespan Psychology > (Director: Prof. Dr. Ulman Lindenberger), is seeking applications for a > > PREDOCTORAL POSITION > > The doctoral contract will last for 3 years. The position is available > from October 1, 2015 or later. > > Job Description: Future research of the new MINERVA research group (PI: > Dr. Myriam Sander) will use a multi-modal imaging approach (EEG with a > focus on oscillatory measures in combination with structural and functional > MRI) to uncover lifespan differences in the interplay between sensory > (visual and auditory) and cognitive abilities influencing memory > performance. The MINERVA research group is part of the project ?Cognitive > and Neural Dynamics of Memory Across the Lifespan (CONMEM)? which > investigates lifespan changes in the interplay between associative and > strategic components of memory functioning on neural and cognitive levels, > with a focus on working and episodic memory (see Sander, et al., Neurosci. > Biobehav. Rev., 2012; Shing, et al., Neurosci. Biobehav. Rev., 2010). The > successful predoctoral fellow will plan and conduct empirical studies in > this domain, analyze the behavioral, EEG, and MRI data, and prepare > scientific manuscripts for publication. > > For further information, please contact: Dr. Myriam Sander ( > sander at mpib-berlin.mpg.de) > > Requirements: A successful applicant needs to hold (or expect by summer > 2015) a diploma/master degree in psychology, cognitive neuroscience, or > related fields. Applicants should have experience with conducting > experimental research, knowledge in neuroimaging methods (EEG and/or MRI), > and a solid background in at least one programming language (preferably > Matlab or R). In addition, the ability to work independently as well as a > high proficiency of the English language is required. Experience with > age-comparative studies is an advantage. > > The Max Planck Society is interested in increasing the number of women on > its scientific staff. We strongly encourage applications from women and > members of minority groups. In addition, the Max Planck Society is > committed to employing more handicapped individuals and encourages them to > apply. > > To apply, please send (as ONE FILE and via email only) a statement of > research interests, a CV, a copy of relevant certificates, (p)reprints of > publications, and a list of two references to Dr. Myriam Sander, MPI for > Human Development, Lentzeallee 94, 14195 Berlin (sander at mpib-berlin.mpg.de) > preferably by June 30th, 2015. Later applications will be considered until > the position is filled. > > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/0579250d/attachment-0001.html > > > > ------------------------------ > > Message: 10 > Date: Thu, 7 May 2015 11:11:54 +0200 > From: "Hamza Fawzi Altakroury (Alumni)" > To: FieldTrip discussion list > Subject: [FieldTrip] Vgrid > Message-ID: > < > CADB5qVBgnCciEmuwJ8ZR3MPRrEuHeWdysTQWek9+aTabP6-GMg at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was expected to > be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > I don't have a folder called pcwin64! I have only glnx86 (empty folder) > glnxa64 and maci64 in ***\external\vgrid\bin\ > > I also downloaded a newer version of fieldtrip, but I did not find it! > > >From where I can get vgrid.exe? > > Thank you > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabanc? University > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/793650e7/attachment-0001.html > > > > ------------------------------ > > Message: 11 > Date: Thu, 07 May 2015 11:40:17 +0200 > From: Johannes Vorwerk > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] Vgrid > Message-ID: <1430991617.11932.23.camel at biomag43> > Content-Type: text/plain; charset="utf-8" > > Hi, > > vgrid should no longer be needed in recent fieldtrip-versions. It was > replaced by a fully matlab-based function (prepare_mesh_hexahedral), > that should now also work under windows. A vgrid.exe never existed, it > was only available for mac and linux. Did you try updating your > fieldtrip-version to a recent release? > > Best, > Johannes > > Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi > Altakroury (Alumni): > > Hello, > > > > > > > > I got the following error when I run these lines: (found in > > http://www.fieldtriptoolbox.org/development/simbio) > > > > cfg = []; > > cfg.shift = 0.3; > > cfg.method = 'hexahedral'; > > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > Error using vgrid (line 16) > > the vgrid executable is not available for your platform, it was > > expected to be > > located at > > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > > > > > > I don't have a folder called pcwin64! I have only glnx86 (empty > > folder) glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > > > > From where I can get vgrid.exe? > > > > > > Thank you > > > > > > > > -- > > > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabanc? University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Dipl.-Math. Johannes Vorwerk > e-mail: j.vorwerk at uni-muenster.de > > Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters > Institute for Biomagnetism and Biosignalanalysis, University of Muenster > www: http://campus.uni-muenster.de/index.php?id=919&L=1 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/6c43fe26/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 5 > **************************************** > -- Haiteng Jiang PhD candidate Donders Institute for Brain, Cognition and Behaviour Neuronal Oscillations Group Computational Cognitive Neuroscience Lab https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.wunderle at esi-frankfurt.de Thu May 7 12:56:27 2015 From: thomas.wunderle at esi-frankfurt.de (Wunderle, Thomas) Date: Thu, 7 May 2015 10:56:27 +0000 Subject: [FieldTrip] Statistics on spike rate Message-ID: <27E5CAD9145EEC41BB9B34C01716A1987FB3B3B3@UM-EXCDAG-A01.um.gwdg.de> Dear community, I’m working on spike/ spike-field analysis and I was wondering if there are statistical comparisons in field trip for spikes. In particular, I would like to test if the spike rate after a stimulus onset is significantly different from the spike rate before stimulus onset (that is, the recorded neurons responds to the stimulus). I tried around with “ft_timelockstatistics”, “ft_statistics_stats” and “ft_spike_rate”, bud did not succeed. I’m not very familiar with statistical testing in FT in general, so I don’t know if statistics for spike rate are implemented in field trip at all. Thanks in advance, Thomas ----- Dr. Thomas Wunderle Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society Deutschordenstrasse 46 60528 Frankfurt am Main, Germany www.esi-frankfurt.de thomas.wunderle at esi-frankfurt.de Tel: +49 69 96769 516 Fax: +49 69 96769 555 Sitz der Gesellschaft: Frankfurt am Main Registergericht: Amtsgericht Frankfurt - HRB 84266 Geschäftsführer: Prof. Dr. Pascal Fries -------------- next part -------------- An HTML attachment was scrubbed... URL: From berdakho at gmail.com Thu May 7 15:56:04 2015 From: berdakho at gmail.com (Berdakh Abibullaev) Date: Thu, 7 May 2015 08:56:04 -0500 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi, I am also using the Dr. Richard's infant database. It took us sometime to figure out to how prepare forward models in FT. If you need I have scripts ready to use to get you started smoothly. ​Just let me know. ​ ​​ Thanks, Berdakh Abibullaev, Postdoctoral Research Scholar , Laboratory for Non-invasive Brain-Machine Interfaces, Department of Electrical Eng. & Computer Science, University of Houston, E413, Engineering Building II, Houston, Texas, 77204-4005. https://www.facebook.com/UHBMIST On Thu, May 7, 2015 at 3:21 AM, Hélène Guiraud wrote: > Hi Till and John, > > Thank you, this is perfect! > > Best regards, > Hélène > > 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > >> We have a template for children‹actually have for infants from 2 weeks >> through adults at 89 years. We also have average electrode positions for >> EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented >> priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have >> been using this recently with FT for infants and child/adolescent/adult >> ages. >> >> WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ >> Fro www site: This is a database of average MRIs and associated MRI >> volumes for developmental MRI work. It consists of average MRI templates, >> segmented partial volume estimate volumes for GM, WM, T2W-derived CSF >> (Description >> < >> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html >> > >> ). The database is separated into head-based and brain-based averages. The >> data are separated by ages in months, years, 6-month, or 5-year intervals >> (Ages and Templates >> < >> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm >> l>). The templates are grouped into first year (2 weeks through 12 >> months), early childhood (15 months through 4 years), childhood (4 years >> through 10 years), adolescence (10.5 years through 17.5 years) and adults >> (18 years through 89 years). >> Tools for cortical source analysis of EEG and ERP are provided. These >> tools are based on the average MRI templates, segmenting, and atlases. >> >> Also see my www site, jerlab.psych.sc.edu for publications describing >> this. We have a recent chapter that has a good description of the issues >> behind the database (with Wanze Xie). We have a paper accepted at >> Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, >> Michelle Phillips-Meek, and Wanze Xie). >> >> John >> >> >> *********************************************** >> John E. Richards Carolina Distinguished Professor >> Department of Psychology >> University of South Carolina >> Columbia, SC 29208 >> Dept Phone: 803 777 2079 >> Fax: 803 777 9558 >> Email: richards-john at sc.edu >> HTTP: jerlab.psych.sc.edu >> *********************************************** >> >> >> >> >> >> >> >> >> On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" >> wrote: >> >> >Send fieldtrip mailing list submissions to >> > fieldtrip at science.ru.nl >> > >> >To subscribe or unsubscribe via the World Wide Web, visit >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >or, via email, send a message with subject or body 'help' to >> > fieldtrip-request at science.ru.nl >> > >> >You can reach the person managing the list at >> > fieldtrip-owner at science.ru.nl >> > >> >When replying, please edit your Subject line so it is more specific >> >than "Re: Contents of fieldtrip digest..." >> > >> > >> >Today's Topics: >> > >> > 1. Search for a template children. (H?l?ne Guiraud) >> > 2. Re: Search for a template children. (Till Schneider) >> > 3. ICBM 152 templates in FT (Keyvan Mahjoory) >> > >> > >> >---------------------------------------------------------------------- >> > >> >Message: 1 >> >Date: Wed, 29 Apr 2015 14:45:56 +0200 >> >From: H?l?ne Guiraud >> >To: fieldtrip at science.ru.nl >> >Subject: [FieldTrip] Search for a template children. >> >Message-ID: >> > < >> CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> >> >Content-Type: text/plain; charset="utf-8" >> > >> >Dear community, >> > >> >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >> >speech perception in children using MEG. >> >The children involved in the study don't pass MRI. We want to achieve >> >source reconstruction from a template. However I can't find a template >> >corresponding to the anatomy of a child (8-12 years). >> >Can someone tell me if there are template children and where I can find >> >them? >> > >> >Best, >> > >> >H?l?ne Guiraud >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e >> >9b53e/attachment-0001.html> >> > >> >------------------------------ >> > >> >Message: 2 >> >Date: Wed, 29 Apr 2015 15:53:13 +0200 >> >From: Till Schneider >> >To: FieldTrip discussion list >> >Subject: Re: [FieldTrip] Search for a template children. >> >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" >> > >> >Dear Helene, >> > >> >McGill University provides MNI brains for different age groups between >> >4.5y to 18y. >> >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >> >You will probably find the template brain you are searching for in this >> >database. >> > >> >Best regards, >> >Till >> > >> >-- >> > >> >Till Schneider, PhD >> > >> >Cognitive and Clinical Neurophysiology Group >> >Dept. of Neurophysiology and Pathophysiology >> >University Medical Center Hamburg-Eppendorf >> >Martinistr. 52 >> >20246 Hamburg >> >Germany >> > >> >phone +49-40-7410-53188 >> >fax +49-40-7410-57126 >> >www.uke.de/neurophysiologie >> > >> > >> > >> >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >> >> Dear community, >> >> >> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >> >> on speech perception in children using MEG. >> >> The children involved in the study don't pass MRI. We want to achieve >> >> source reconstruction from a template. However I can't find a template >> >> corresponding to the anatomy of a child (8-12 years). >> >> Can someone tell me if there are template children and where I can >> >> find them? >> >> >> >> Best, >> >> >> >> H?l?ne Guiraud >> >> >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> > >> >-- >> > >> >_____________________________________________________________________ >> > >> >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >> >Rechts; Gerichtsstand: Hamburg | www.uke.de >> >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >> >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >> >_____________________________________________________________________ >> > >> >SAVE PAPER - THINK BEFORE PRINTING >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e >> >44937/attachment-0001.html> >> > >> >------------------------------ >> > >> >Message: 3 >> >Date: Wed, 29 Apr 2015 16:25:35 +0200 >> >From: Keyvan Mahjoory >> >To: FieldTrip discussion list >> >Subject: [FieldTrip] ICBM 152 templates in FT >> >Message-ID: >> > > UJp6-+4+7fA at mail.gmail.com> >> >Content-Type: text/plain; charset="iso-8859-1" >> > >> >Dear Fieldtrip Users, >> > >> >I perform source analysis in Fieldtrip with a template head model ( >> >standard_bem ) and a >> >template source model (cortex_5124.surf.gii >> >) to constarin >> >estimated sources on cortex. These templates are based on Colin27, But I >> >prefere to use the template ICBM152 instead. >> >Does FT include ICBM template? I mean templates for both head model and >> >cortical surfe. >> > >> >Many Thanks in advance, >> >Keyvan >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 >> >9daf3/attachment-0001.html> >> > >> >------------------------------ >> > >> >_______________________________________________ >> >fieldtrip mailing list >> >fieldtrip at donders.ru.nl >> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> >End of fieldtrip Digest, Vol 53, Issue 23 >> >***************************************** >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Hélène Guiraud > Doctorante > Université Lyon 2 > Laboratoire Dynamique Du Langage > CNRS, UMR 5596 > Tel : 04 72 72 65 34 > guiraudh at gmail.com > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guiraudh at gmail.com Thu May 7 16:23:54 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Thu, 7 May 2015 16:23:54 +0200 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi, Thank you. I'm just trying to develop my scripts. A little help would be welcome! I'm taking, thank! Hélène 2015-05-07 15:56 GMT+02:00 Berdakh Abibullaev : > Hi, > > I am also using the Dr. Richard's infant database. It took us sometime to > figure out to how prepare forward models in FT. > If you need I have scripts ready to use to get you started smoothly. > > ​Just let me know. ​ > > ​​ > Thanks, > > Berdakh Abibullaev, > > Postdoctoral Research Scholar , > Laboratory for Non-invasive Brain-Machine Interfaces, > Department of Electrical Eng. & Computer Science, > University of Houston, E413, Engineering Building II, > Houston, Texas, 77204-4005. > https://www.facebook.com/UHBMIST > > On Thu, May 7, 2015 at 3:21 AM, Hélène Guiraud wrote: > >> Hi Till and John, >> >> Thank you, this is perfect! >> >> Best regards, >> Hélène >> >> 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : >> >>> We have a template for children‹actually have for infants from 2 weeks >>> through adults at 89 years. We also have average electrode positions for >>> EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented >>> priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have >>> been using this recently with FT for infants and child/adolescent/adult >>> ages. >>> >>> WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ >>> Fro www site: This is a database of average MRIs and associated MRI >>> volumes for developmental MRI work. It consists of average MRI templates, >>> segmented partial volume estimate volumes for GM, WM, T2W-derived CSF >>> (Description >>> < >>> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html >>> > >>> ). The database is separated into head-based and brain-based averages. >>> The >>> data are separated by ages in months, years, 6-month, or 5-year intervals >>> (Ages and Templates >>> < >>> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm >>> l>). The templates are grouped into first year (2 weeks through 12 >>> months), early childhood (15 months through 4 years), childhood (4 years >>> through 10 years), adolescence (10.5 years through 17.5 years) and adults >>> (18 years through 89 years). >>> Tools for cortical source analysis of EEG and ERP are provided. These >>> tools are based on the average MRI templates, segmenting, and atlases. >>> >>> Also see my www site, jerlab.psych.sc.edu for publications describing >>> this. We have a recent chapter that has a good description of the issues >>> behind the database (with Wanze Xie). We have a paper accepted at >>> Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, >>> Michelle Phillips-Meek, and Wanze Xie). >>> >>> John >>> >>> >>> *********************************************** >>> John E. Richards Carolina Distinguished Professor >>> Department of Psychology >>> University of South Carolina >>> Columbia, SC 29208 >>> Dept Phone: 803 777 2079 >>> Fax: 803 777 9558 >>> Email: richards-john at sc.edu >>> HTTP: jerlab.psych.sc.edu >>> *********************************************** >>> >>> >>> >>> >>> >>> >>> >>> >>> On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" >>> wrote: >>> >>> >Send fieldtrip mailing list submissions to >>> > fieldtrip at science.ru.nl >>> > >>> >To subscribe or unsubscribe via the World Wide Web, visit >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >or, via email, send a message with subject or body 'help' to >>> > fieldtrip-request at science.ru.nl >>> > >>> >You can reach the person managing the list at >>> > fieldtrip-owner at science.ru.nl >>> > >>> >When replying, please edit your Subject line so it is more specific >>> >than "Re: Contents of fieldtrip digest..." >>> > >>> > >>> >Today's Topics: >>> > >>> > 1. Search for a template children. (H?l?ne Guiraud) >>> > 2. Re: Search for a template children. (Till Schneider) >>> > 3. ICBM 152 templates in FT (Keyvan Mahjoory) >>> > >>> > >>> >---------------------------------------------------------------------- >>> > >>> >Message: 1 >>> >Date: Wed, 29 Apr 2015 14:45:56 +0200 >>> >From: H?l?ne Guiraud >>> >To: fieldtrip at science.ru.nl >>> >Subject: [FieldTrip] Search for a template children. >>> >Message-ID: >>> > < >>> CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> >>> >Content-Type: text/plain; charset="utf-8" >>> > >>> >Dear community, >>> > >>> >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >>> >speech perception in children using MEG. >>> >The children involved in the study don't pass MRI. We want to achieve >>> >source reconstruction from a template. However I can't find a template >>> >corresponding to the anatomy of a child (8-12 years). >>> >Can someone tell me if there are template children and where I can find >>> >them? >>> > >>> >Best, >>> > >>> >H?l?ne Guiraud >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e >>> >9b53e/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >Message: 2 >>> >Date: Wed, 29 Apr 2015 15:53:13 +0200 >>> >From: Till Schneider >>> >To: FieldTrip discussion list >>> >Subject: Re: [FieldTrip] Search for a template children. >>> >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >>> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" >>> > >>> >Dear Helene, >>> > >>> >McGill University provides MNI brains for different age groups between >>> >4.5y to 18y. >>> >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >>> >You will probably find the template brain you are searching for in this >>> >database. >>> > >>> >Best regards, >>> >Till >>> > >>> >-- >>> > >>> >Till Schneider, PhD >>> > >>> >Cognitive and Clinical Neurophysiology Group >>> >Dept. of Neurophysiology and Pathophysiology >>> >University Medical Center Hamburg-Eppendorf >>> >Martinistr. 52 >>> >20246 Hamburg >>> >Germany >>> > >>> >phone +49-40-7410-53188 >>> >fax +49-40-7410-57126 >>> >www.uke.de/neurophysiologie >>> > >>> > >>> > >>> >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >>> >> Dear community, >>> >> >>> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >>> >> on speech perception in children using MEG. >>> >> The children involved in the study don't pass MRI. We want to achieve >>> >> source reconstruction from a template. However I can't find a template >>> >> corresponding to the anatomy of a child (8-12 years). >>> >> Can someone tell me if there are template children and where I can >>> >> find them? >>> >> >>> >> Best, >>> >> >>> >> H?l?ne Guiraud >>> >> >>> >> >>> >> _______________________________________________ >>> >> fieldtrip mailing list >>> >> fieldtrip at donders.ru.nl >>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> > >>> > >>> >-- >>> > >>> >_____________________________________________________________________ >>> > >>> >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >>> >Rechts; Gerichtsstand: Hamburg | www.uke.de >>> >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >>> >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >>> >_____________________________________________________________________ >>> > >>> >SAVE PAPER - THINK BEFORE PRINTING >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e >>> >44937/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >Message: 3 >>> >Date: Wed, 29 Apr 2015 16:25:35 +0200 >>> >From: Keyvan Mahjoory >>> >To: FieldTrip discussion list >>> >Subject: [FieldTrip] ICBM 152 templates in FT >>> >Message-ID: >>> > >> UJp6-+4+7fA at mail.gmail.com> >>> >Content-Type: text/plain; charset="iso-8859-1" >>> > >>> >Dear Fieldtrip Users, >>> > >>> >I perform source analysis in Fieldtrip with a template head model ( >>> >standard_bem ) and >>> a >>> >template source model (cortex_5124.surf.gii >>> >) to constarin >>> >estimated sources on cortex. These templates are based on Colin27, But >>> I >>> >prefere to use the template ICBM152 instead. >>> >Does FT include ICBM template? I mean templates for both head model and >>> >cortical surfe. >>> > >>> >Many Thanks in advance, >>> >Keyvan >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 >>> >9daf3/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >_______________________________________________ >>> >fieldtrip mailing list >>> >fieldtrip at donders.ru.nl >>> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> > >>> >End of fieldtrip Digest, Vol 53, Issue 23 >>> >***************************************** >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Hélène Guiraud >> Doctorante >> Université Lyon 2 >> Laboratoire Dynamique Du Langage >> CNRS, UMR 5596 >> Tel : 04 72 72 65 34 >> guiraudh at gmail.com >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hélène Guiraud Doctorante Université Lyon 2 Laboratoire Dynamique Du Langage CNRS, UMR 5596 Tel : 04 72 72 65 34 guiraudh at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu May 7 16:39:59 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Thu, 7 May 2015 17:39:59 +0300 Subject: [FieldTrip] Vgrid In-Reply-To: <1430991617.11932.23.camel@biomag43> References: <1430991617.11932.23.camel@biomag43> Message-ID: Thank you Johannes, I'll try to run it using a newer version of fieldtrip. Best, Hamza On Thu, May 7, 2015 at 12:40 PM, Johannes Vorwerk wrote: > Hi, > > vgrid should no longer be needed in recent fieldtrip-versions. It was > replaced by a fully matlab-based function (prepare_mesh_hexahedral), that > should now also work under windows. A vgrid.exe never existed, it was only > available for mac and linux. Did you try updating your fieldtrip-version to > a recent release? > > Best, > Johannes > > Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi Altakroury > (Alumni): > > Hello, > > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was expected > to be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > I don't have a folder called pcwin64! I have only glnx86 (empty folder) > glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > From where I can get vgrid.exe? > > > Thank you > > > > -- > > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Dipl.-Math. Johannes Vorwerk > e-mail: j.vorwerk at uni-muenster.de > > Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters > Institute for Biomagnetism and Biosignalanalysis, University of Muenster > www: http://campus.uni-muenster.de/index.php?id=919&L=1 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Fri May 8 13:22:56 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Fri, 8 May 2015 12:22:56 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy Message-ID: <554C9C90.4090702@glasgow.ac.uk> An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri May 8 13:38:48 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 8 May 2015 11:38:48 +0000 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy In-Reply-To: <554C9C90.4090702@glasgow.ac.uk> References: <554C9C90.4090702@glasgow.ac.uk> Message-ID: <524BB694-AB68-4A2A-BC8B-9A9F515CC75B@fcdonders.ru.nl> May, Have you ensured that the stat.pos field contains the dipole positions, coregistered to the template brain? Best, Jan-Mathijs On May 8, 2015, at 1:22 PM, Heng-Ru May Tan > wrote: Hi Fieldtrippers [The previous email didn't display properly so resending this again.] I am having trouble running ft_sourceinterpolate... I didn't seem to have this issue before. =( The anatomy seems to be missing and so when I subsequently call ft_sourceplot, the brain anatomy is not 'available' for plotting. Here are some example of the things I tried and the errors in hope that someone might be able help! Many thanks in advance, May -- this is a stat structure used: stat = prob: [33480x1 double] cirange: [33480x1 double] mask: [33480x1 logical] stat: [33480x1 double] ref: [33480x1 double] df: 185 critval: [-1.9729 1.9729] dim: [33480 1] inside: [10354x1 double] outside: [23126x1 double] pos: [33480x3 double] freq: 64.9309 cfg: [1x1 struct] grid = xgrid: [1x31 double] ygrid: [1x36 double] zgrid: [1x30 double] dim: [31 36 30] pos: [33480x3 double] inside: [12773x1 double] outside: [20707x1 double] anatpath2 = [unixANALYSEpath 'Matlab_scripts/fieldtrip-20140114/template/anatomy/single_subj_T1.nii'] template_mri = ft_read_mri(anatpath2); cfg = []; cfg.parameter = 'stat'; cfg.interpmethod = 'nearest'; statplot2 = ft_sourceinterpolate(cfg,stat, template_mri); the input is volume data with dimensions [91 109 91] Warning: sphereradius is not used for projmethod 'nearest' > In fieldtrip-20140114/private/interp_ungridded at 86 In ft_sourceinterpolate at 216 the call to "ft_sourceinterpolate" took 37 seconds and required the additional allocation of an estimated 96 MB -- somehow anatomy structure is lost... ?! statplot2 = freq: 64.9309 stat: [902629x1 double] pos: [902629x3 double] dim: [91 109 91] inside: [1x902629 double] outside: [1x0 double] unit: 'mm' cfg: [1x1 struct] cfg = []; cfg.method ='slice'; cfg.nslices = 30 cfg.funparameter = 'stat'; % cfg.maskparameter = 'mask'; cfg.maskparameter = cfg.funparameter; cfg.anaparameter = 'anatomy'; cfg.opacitymap = 'rampup'; ft_sourceplot(cfg, statplot2); the input is source data with 902629 positions on a [91 109 91] grid Warning: do not understand cfg.anaparameter, not plotting anatomy\n > In ft_sourceplot at 350 the call to "ft_sourceplot" took 2 seconds and required the additional allocation of an estimated 3 MB -- If using fieldtrip_new on server --> revision = '$Id: ft_sourceinterpolate.m 10221 2015-02-12 08:28:20Z roboos $'; cfg = parameter: 'stat' interpmethod: 'nearest' statplot1 = ft_sourceinterpolate(stat, template_mri) Undefined function or variable 'abort'. Error in ft_sourceinterpolate (line 106) if abort -- ________________________________________________________________________________________________________________________________________ Heng-Ru May Tan Centre for Cognitive Neuroimaging (CCNi) ▫Institute of Neuroscience and Psychology (INP) ▫ College of Medical, Veterinary and Life Sciences & College of Science and Engineering ▫ University of Glasgow ▫ 58 Hillhead Street, Glasgow G12 8QB, United Kingdom ▫ +44 (0)141-330-5090 ▫ Heng-RuMay.Tan at glasgow.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From christophe.grova at mcgill.ca Sat May 9 12:38:09 2015 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Sat, 9 May 2015 10:38:09 +0000 Subject: [FieldTrip] MSc/PhD positions in Biomedical Physics and at the PERFORM Centre, Concordia University Message-ID: <9E1647EDA3EBB44AADA162CEC4C4222E7510052D@exmbx2010-9.campus.MCGILL.CA> Now available, MSc/PhD positions in Biomedical Physics and at the PERFORM Centre, Concordia University [multi_funkin] We offer two very interesting opportunities for M.Sc or PhD projects in the context of the new Biomedical Physics program proposed at Concordia University by the Department of Physics and at PERFORM. Project 1: Multimodal characterization of resting state functional connectivity. Supervisor: C. Grova, Department of Physics and PERFORM Center The overall project aims at assessing the organization of fluctuations of neuronal bioelectrical signals measured from the scalp using either Electro-EncephaloGraphy (EEG) or Magneto-EncephaloGraphy (MEG), while the subject is resting. The main methodological originality of this project is to consider time-frequency based source localization of EEG and MEG data, using wavelet-based Maximum on the Mean wMEM (Lina et al IEEE TBME 2014) in order to investigate resting state functional connectivity from simultaneous EEG/MEG data and also from simultaneous high-density EEG/fMRI data. These multimodal data will be considered in order to investigate the dynamic of resting state functional connectivity patterns in healthy controls The candidates will join a multidisciplinary team composed of neurologists and methodologists within the Multimodal Functional Imaging Laboratory, directed by Pr. Christophe Grova. Simultaneous EEG/fMRI data will be acquired at PERFORM, while simultaneous EEG/MEG data will be acquired at the Montreal Neurological Institute, McGill University. The key component of this project consists in adapting and validating the performance of EEG/MEG source localization of resting state data in healthy subjects, in order to build a normative database. Requirements: The candidate should have some knowledge in image and signal processing, linear algebra and statistics, as well as experience in computation and programmation, using notably Matlab software. Any experience with neuroimaging softwares would be an asset. Project 2: Multimodal characterization of functional hubs. Supervisor: C. Gauthier, Department of Physics and PERFORM Center Co-Supervisor: C. Grova, Department of Physics and PERFORM Center In the overall context of understanding the organization of brain activity during rest, as in the analysis of any network, the notion of “hub”, their detection and characterization is a key and challenging objective. This project will propose and evaluate new methods to detect these hubs and to charactrize their underlying metabolism using quantitative Magnetic Resonance Imaging (MRI) techniques. Using a new method based on sparse modeling to extract the hubs of such network organization from resting state functional MRI data acquired simultaneously with EEG data, the project will consist in combining these techniques with quantitative MRI to measure the metabolic rate of oxygen consumption. To do so, gas manipulations, i.e. breathing controlled amount of CO2 and O2, will be needed during the MRI acquisition. The objective will be to assess hemodynamic fluctuations, neuronal bioelectrical oscillations and local oxygen consumption of these hubs, within a population of healthy controls of different age ranges. Requirements: The candidate should have some knowledge in image and signal processing, linear algebra and statistics, as well as experience in computation and programmation, using notably Matlab software. Any experience of neuroimaging softwares and in experimental sciences would be an asset More details on the Multimodal Functional Imaging Lab can be found at: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage More details on PERFORM centre can be found at: http://www.concordia.ca/research/perform.html Please send your CV and motivation letter to: christophe.grova at concordia.ca and claudine.gauthier at concordia.ca *************************** Christophe Grova, PhD Assistant Professor, Physics Dpt, Concordia University PERFORM centre, Concordia University, Chair of PERFORM Applied Bio-Imaging Committee (ABC) Adjunct Prof in Biomedical Engineering, and Neurology and Neurosurgery Dpt, McGill University Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute - epilepsy group Centre de Recherches en Mathématiques Physics Dpt Concordia University - Loyola Campus - Office SP 365.12 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Phone: (514) 848-2424 ext.4221 Biomedical Engineering Department McGill University - Room 304 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 Phone : (514) 398 2516 Fax : (514) 398 7461 email : christophe.grova at concordia.ca , christophe.grova at mcgill.ca web: Explore Concordia: http://explore.concordia.ca/christophe-grova Physics, Concordia University: http://physics.concordia.ca/facultyandresearch/bios/grova.php McGill University: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** [X] -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Mon May 11 13:29:03 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Mon, 11 May 2015 12:29:03 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy In-Reply-To: References: Message-ID: <5550927F.7080609@glasgow.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hjcjfgji.png Type: image/png Size: 213443 bytes Desc: not available URL: From anna.wieczorek.taraday at gmail.com Tue May 12 10:17:40 2015 From: anna.wieczorek.taraday at gmail.com (Anna Wieczorek-Taraday) Date: Tue, 12 May 2015 08:17:40 +0000 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip Message-ID: Dear Fieldtrippers, I have a problem while reading EEG (EGI) electrode location file to FieldTrip. I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? Any support will be appreciated. I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. *************************************** Here is code I used to read these locations: cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; cfg.feedback = 'yes'; layout = ft_prepare_layout(cfg); Here is the code that I used to preprocess my data in Fieldtrip: cfg = []; cfg.trialfun = 'ft_trialfun_general'; cfg.dataset = '136.set'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'DIN8' cfg.trialdef.prestim = 0.5; cfg.trialdef.poststim = 2.5; cfg = ft_definetrial(cfg); cfg.lpfilter = 'no'; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.3; data = ft_preprocessing(cfg); Anna Wieczorek-Taraday. PhD Student Nencki Institute of Experimental Biology Pasteur Street 3, 02-093 Warsaw, Poland Warsaw University of Social Sciences and Humanities Chodakowska Street 19/31, 03-815 Warsaw, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 12 11:05:09 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 12 May 2015 11:05:09 +0200 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip In-Reply-To: References: Message-ID: Hi Ana The ft_prepare_layout function reads the electrode positions and scales them such that they fit in the sphere that represents the head. I suggest you do cfg.layout = ‘yourfilename’ lay = ft_prepare_layout(cfg); cfg = []; cfg.layout = lay; ft_layoutplot(cfg); and then modify lay.pos repeatedly, every time plotting it again, until you are happy with the result. You probably want to do this for the vertical direction lay.pos(:,2) = (lay.pos(:,2)+shift) .* scale; to shift and scale the electrodes to a better fit inside/outside the sphere, and this for the horizontal lay.pos(:,1) = lay.pos(:,1) .* scale; as they seem to be properly centred along the x-axis alreadly. After this, you can save yourlayout.mat lay and specify “yourlayout.mat” as the layout filename for your future figures. best regards Robert On 12 May 2015, at 10:17, Anna Wieczorek-Taraday wrote: > Dear Fieldtrippers, > > I have a problem while reading EEG (EGI) electrode location file to FieldTrip. > I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. > > When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. > When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). > However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. > > I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? > Any support will be appreciated. > > I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. > > *************************************** > > > Here is code I used to read these locations: > > cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; > cfg.feedback = 'yes'; > layout = ft_prepare_layout(cfg); > > > Here is the code that I used to preprocess my data in Fieldtrip: > > cfg = []; > cfg.trialfun = 'ft_trialfun_general'; > cfg.dataset = '136.set'; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'DIN8' > cfg.trialdef.prestim = 0.5; > cfg.trialdef.poststim = 2.5; > cfg = ft_definetrial(cfg); > > cfg.lpfilter = 'no'; > cfg.hpfilter = 'yes'; > cfg.hpfreq = 0.3; > data = ft_preprocessing(cfg); > > Anna Wieczorek-Taraday. > > PhD Student > Nencki Institute of Experimental Biology > Pasteur Street 3, 02-093 Warsaw, Poland > > Warsaw University of Social Sciences and Humanities > Chodakowska Street 19/31, 03-815 Warsaw, Poland > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From anna.wieczorek.taraday at gmail.com Tue May 12 17:25:43 2015 From: anna.wieczorek.taraday at gmail.com (Anna Wieczorek-Taraday) Date: Tue, 12 May 2015 17:25:43 +0200 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip In-Reply-To: References: Message-ID: <72EDF4F9-1F07-42A1-B1B3-72174896C8A2@gmail.com> Hi Robert, Thank you for your help. Indeed, the location on the sphere looks good after adjusting these parameters. Thank you a lot. Best regards, Anna Sent from my iPad > On 12 May 2015, at 11:05, Robert Oostenveld wrote: > > Hi Ana > > The ft_prepare_layout function reads the electrode positions and scales them such that they fit in the sphere that represents the head. > > I suggest you do > > cfg.layout = ‘yourfilename’ > lay = ft_prepare_layout(cfg); > > cfg = []; > cfg.layout = lay; > ft_layoutplot(cfg); > > and then modify lay.pos repeatedly, every time plotting it again, until you are happy with the result. You probably want to do this for the vertical direction > lay.pos(:,2) = (lay.pos(:,2)+shift) .* scale; > to shift and scale the electrodes to a better fit inside/outside the sphere, and this for the horizontal > lay.pos(:,1) = lay.pos(:,1) .* scale; > as they seem to be properly centred along the x-axis alreadly. > > After this, you can > save yourlayout.mat lay > and specify “yourlayout.mat” as the layout filename for your future figures. > > > best regards > Robert > > > >> On 12 May 2015, at 10:17, Anna Wieczorek-Taraday wrote: >> >> Dear Fieldtrippers, >> >> I have a problem while reading EEG (EGI) electrode location file to FieldTrip. >> I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. >> >> When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. >> When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). >> However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. >> >> I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? >> Any support will be appreciated. >> >> I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. >> >> *************************************** >> >> >> Here is code I used to read these locations: >> >> cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; >> cfg.feedback = 'yes'; >> layout = ft_prepare_layout(cfg); >> >> >> Here is the code that I used to preprocess my data in Fieldtrip: >> >> cfg = []; >> cfg.trialfun = 'ft_trialfun_general'; >> cfg.dataset = '136.set'; >> cfg.trialdef.eventtype = 'trigger'; >> cfg.trialdef.eventvalue = 'DIN8' >> cfg.trialdef.prestim = 0.5; >> cfg.trialdef.poststim = 2.5; >> cfg = ft_definetrial(cfg); >> >> cfg.lpfilter = 'no'; >> cfg.hpfilter = 'yes'; >> cfg.hpfreq = 0.3; >> data = ft_preprocessing(cfg); >> >> Anna Wieczorek-Taraday. >> >> PhD Student >> Nencki Institute of Experimental Biology >> Pasteur Street 3, 02-093 Warsaw, Poland >> >> Warsaw University of Social Sciences and Humanities >> Chodakowska Street 19/31, 03-815 Warsaw, Poland >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Wed May 13 17:28:39 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Wed, 13 May 2015 17:28:39 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI Message-ID: Dear all, I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? If I am right, which command shall I use to organize individual WPLI data, in order to create a correct input for ‘ft_freqstatistics’. According to the tutorial, in case of time-frequency data it is ft_freqgrandaverage. However, if I use it for WPLI data, I have the following error: “This function requires freq data as input”. Could you please recommend me a tutorial, reference documentation or some comment on this issue? Thanks for any suggestions in advanced and let me know if the description of my problem is not clear! Zsolt -- ************************************************************ Ph.D. student Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Wed May 13 19:14:45 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 13 May 2015 19:14:45 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: Message-ID: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Hi Zsolt, > Dear all, > > > I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. > > > I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > You could. Stick with the tutorial you are currently working with. You should organize your data into cell arrays and call ft_freqstatistics like this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise ft_freqstatistics will default to ‘powspctrm’ which will be not present in the data. good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: From zerr.paul at googlemail.com Thu May 14 14:01:07 2015 From: zerr.paul at googlemail.com (Paul Zerr) Date: Thu, 14 May 2015 14:01:07 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found Message-ID: Hi all, I'm new to fieldtrip so forgive me if my mistake is obvious. I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with *cfg = []; * *cfg.dataset = '2.bdf';* *data = ft_preprocessing(cfg)* However, I get *reading and preprocessing* *error opening file: 2.bdf* *One or more output arguments not assigned during call to "read_24bit".* *Error in read_biosemi_bdf>readLowLevel (line 274)* * buf = read_24bit(filename, offset, numwords);* *Error in read_biosemi_bdf (line 242)* * buf = readLowLevel(filename, offset, epochlength); % see below in subfunction* *Error in ft_read_data (line 321)* * dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx);* *Error in ft_preprocessing (line 578)* * dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample,* * 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',* * strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat)* *Error in Untitled (line 19)* *data = ft_preprocessing(cfg) * Using *cfg.trialdef.eventtype = '?';* outputs *"no events were found in the datafile"* for *ft_definetrial* even for datasets with many markers. Converting to EDF+ did not help as it then says *"channels with different sampling rate not supported"*. Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Defining only one channel to preprocess gives the same error. I couldn't find a solution in the archives, the faq, wiki or documentation. I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. Any ideas? Much appreciated, Paul Zerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Thu May 14 16:15:09 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Thu, 14 May 2015 16:15:09 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Message-ID: Hi Tzvetan, thanks for your suggestions. I am still stucked at the ft_freqstatistics, as I keep on receiving the following error and would be glad if you could make a comment on this as well: #### Reference to non-existent field 'label'. Error in ft_freqgrandaverage (line 123) cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); ### Is it because I have labelcomb in the WPLI data? labelcmb: {9x2 cell} dimord: 'chan_freq_time' wplispctrm: [9x7x16 double] freq: [3 4 5 6 7 8 9] time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] cfg: [1x1 struct] And this is my specification (I couldn't fine the option cfg.channelcmb for ft_freqgrandaverage in the reference documentation): cfg = []; cfg.keepindividual = 'yes'; cfg.cfg.foilim = 'all'; cfg.toilim = 'all'; cfg.channel = 'all'; cfg.parameter = 'wplispctrm'; Thanks again for the answer in advance! Best, Zsolt ps.I can provide other parts of my code but I don't want to make this mail too long : 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > > Dear all, > > > I would like to perform a cluster-based permutation test on weighted phase > lag index values by using a within-subjects experimental design. I have two > conditions (congruent and incongruent one) and my goal is to compute WPLI > between certain channel combinations (FCz and F3 for instance) and see the > WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two > conditions. > > > I experienced some difficulties after the point when I calculated the > WPLI data for each participant. To perform the above-mentioned comparison, > shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > > You could. Stick with the tutorial you are currently working with. You > should organize your data into cell arrays and call ft_freqstatistics like > this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). > Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise > ft_freqstatistics will default to ‘powspctrm’ which will be not present in > the data. > good luck > tzvetan > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Fri May 15 10:26:45 2015 From: B.Haendel at gmx.net (Barbara Haendel) Date: Fri, 15 May 2015 10:26:45 +0200 Subject: [FieldTrip] leadfields MNI-coordinates Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: warp_location.JPG Type: image/jpeg Size: 95511 bytes Desc: not available URL: From alexandra.bendixen at physik.tu-chemnitz.de Fri May 15 11:49:52 2015 From: alexandra.bendixen at physik.tu-chemnitz.de (Alexandra Bendixen) Date: Fri, 15 May 2015 11:49:52 +0200 Subject: [FieldTrip] Postdoc position in Chemnitz, Germany: Auditory perception & cognition Message-ID: Dear list, A postdoc position is available in my newly established Cognitive Systems Lab at Chemnitz University of Technology (https://www.tu-chemnitz.de/physik/SFKS/index.html.en). The lab is part of an interdisciplinary research center at the intersection of physics and psychology. Our research is centered around auditory perception and cognition, with extensions towards multisensory processing as well as towards effects of cognitive aging. Within this general framework, there is a great deal of flexibility in the specific research topic(s) pursued by the postdoc. We are looking for candidates with an academic university degree (M.Sc. equivalent) as well as a Ph.D. degree in psychology, neuroscience, cognitive science, or a related field. Good programming skills, good command of English, and prior publications in peer-reviewed journals are required. We use and combine EEG, eyetracking, and psychophysics methods. Candidates should have a strong background in at least one of these methods, or a complementary profile in cognitive/computational modeling. The position involves 4 hours of teaching per week at Bachelor or Master level, covering psychophysics and psychophysiology topics. To fulfill teaching requirements, knowledge of German is advantageous (but not strictly necessary). The position can be filled immediately and runs until March 31, 2018. Salary is determined by German public service regulations for full-term employment with a Ph.D. degree. Chemnitz University of Technology is dedicated to increasing the percentage of women in science. Therefore, female candidates are particularly encouraged to apply. Applicants with disabilities will be employed preferentially if equally qualified. This call is open until June 2nd, 2015. Anybody interested is welcome to contact me (alexandra.bendixen at physik.tu-chemnitz.de). For more information on the position and on how to apply, please visit https://www.tu-chemnitz.de/verwaltung/personal/stellen/212067_4_Ku.php I would be grateful if you could distribute this advert to anyone potentially interested. Many thanks, Alexandra Bendixen --- Prof. Dr. Alexandra Bendixen Cognitive Systems Lab Chemnitz University of Technology Faculty of Natural Sciences Institute of Physics New Physics Building, Room P137 Reichenhainer Str. 70 D-09126 Chemnitz, Germany Tel.: +49-(0)371-531-31681 Fax: +49-(0)371-531-831681 E-mail: alexandra.bendixen at physik.tu-chemnitz.de WWW: https://www.tu-chemnitz.de/physik/SFKS/alexandrabendixen.html.en From michelic72 at gmail.com Sat May 16 16:17:25 2015 From: michelic72 at gmail.com (Cristiano Micheli) Date: Sat, 16 May 2015 16:17:25 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: Message-ID: Dear Zsolt I experienced difficulties and encountered many pitfalls along the way too. What exactly will your metric be? wPLI of post onset versus baseline difference/ratio? wPLI difference of the two conditions? Do you common average re-reference your data before? The statistics that you will use will depend on your design. I would personally try a non-parametric design where you shuffle the index of the trials of one condition (if you do wPLI1-wPLI2) and consider the proportion of iterations exceeding the measured wPLI difference. Please consider though that both conditions should have the same number of trials. Could you attach the programming attempts that you tried so far together with the exact error outputs? I hope this helps so far. Cris Micheli On Wed, May 13, 2015 at 5:28 PM, Zsolt Turi wrote: > Dear all, > > > > I would like to perform a cluster-based permutation test on weighted phase > lag index values by using a within-subjects experimental design. I have two > conditions (congruent and incongruent one) and my goal is to compute WPLI > between certain channel combinations (FCz and F3 for instance) and see the > WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two > conditions. > > > I experienced some difficulties after the point when I calculated the > WPLI data for each participant. To perform the above-mentioned comparison, > shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > > > > If I am right, which command shall I use to organize individual WPLI data, > in order to create a correct input for ‘ft_freqstatistics’. According to > the tutorial, in case of time-frequency data it is ft_freqgrandaverage. > However, if I use it for WPLI data, I have the following error: “This > function requires freq data as input”. > > > > Could you please recommend me a tutorial, reference documentation or some > comment on this issue? > > > > Thanks for any suggestions in advanced and let me know if the description > of my problem is not clear! > > > > Zsolt > > -- > ************************************************************ > Ph.D. student > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 08:18:54 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 08:18:54 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Message-ID: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Hi Zsolt, > Hi Tzvetan, > > thanks for your suggestions. > I am still stucked at the ft_freqstatistics, as I keep on receiving the following error and would be glad if you could make a comment on this as well: > > #### > Reference to non-existent field 'label'. > > Error in ft_freqgrandaverage (line 123) > cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); > ### > > Is it because I have labelcomb in the WPLI data? yes > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x7x16 double] > freq: [3 4 5 6 7 8 9] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > And this is my specification (I couldn't fine the option cfg.channelcmb for ft_freqgrandaverage in the reference documentation): again try to give cell arrays as input to ft_freqanalysis. I’m still considering the case you mentioned in your initial e-mail, one channel etc. e.g. cfg.channel = ‘FCzF3’; cfg.parameter = ‘wplispctrm’; cfg.neighbours = []; % this will force clustering over time and freq dimension best tzvetan > > cfg = []; > cfg.keepindividual = 'yes'; > cfg.cfg.foilim = 'all'; > cfg.toilim = 'all'; > cfg.channel = 'all'; > cfg.parameter = 'wplispctrm'; > > Thanks again for the answer in advance! > > Best, > Zsolt > > ps.I can provide other parts of my code but I don't want to make this mail too long : > > > > 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > >> Dear all, >> >> >> I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. >> >> >> I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >> > You could. Stick with the tutorial you are currently working with. You should organize your data into cell arrays and call ft_freqstatistics like this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise ft_freqstatistics will default to ‘powspctrm’ which will be not present in the data. > good luck > tzvetan > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 08:19:41 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 08:19:41 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: > > again try to give cell arrays as input to ft_freqanalysis I’m sorry I meant ft_freqstatistics here tz From zsoltturi at gmail.com Mon May 18 11:33:48 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Mon, 18 May 2015 11:33:48 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Hi Tzvetan and Chris, thanks for your emails. Removing channelcmb and adding a new one called label solved my problem. Chris: I'ld like to compare the WPLI difference of two conditions, congruent and incongruent ones by using a within-subjects design (so not a between trials comparison). >From your email I may infer that after running wpli, I should still have my trials. However, I do not have repetitions (trials) anymore in the output structure. Am I doing an illegitimate step during wPLI calculation or miss one specification? cfg = []; cfg.method = 'wpli'; dataWPLI = ft_connectivityanalysis(cfg,TFRhann); labelcmb: {9x2 cell} dimord: 'chan_freq_time' wplispctrm: [9x43x16 double] freq: [1x43 double] time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] cfg: [1x1 struct] Thanks for your help! Best, Zsolt 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > > Hi Tzvetan, > > thanks for your suggestions. > I am still stucked at the ft_freqstatistics, as I keep on receiving the > following error and would be glad if you could make a comment on this as > well: > > #### > Reference to non-existent field 'label'. > > Error in ft_freqgrandaverage (line 123) > cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); > ### > > Is it because I have labelcomb in the WPLI data? > > yes > > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x7x16 double] > freq: [3 4 5 6 7 8 9] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 > 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > And this is my specification (I couldn't fine the option cfg.channelcmb > for ft_freqgrandaverage in the reference documentation): > > again try to give cell arrays as input to ft_freqanalysis. I’m still > considering the case you mentioned in your initial e-mail, one channel etc. > e.g. cfg.channel = ‘FCzF3’; > cfg.parameter = ‘wplispctrm’; > cfg.neighbours = []; % this will force clustering over time and > freq dimension > > best > tzvetan > > > cfg = []; > cfg.keepindividual = 'yes'; > cfg.cfg.foilim = 'all'; > cfg.toilim = 'all'; > cfg.channel = 'all'; > cfg.parameter = 'wplispctrm'; > > Thanks again for the answer in advance! > > Best, > Zsolt > > ps.I can provide other parts of my code but I don't want to make this mail > too long : > > > > 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > >> Hi Zsolt, >> >> >> Dear all, >> >> >> I would like to perform a cluster-based permutation test on weighted >> phase lag index values by using a within-subjects experimental design. I >> have two conditions (congruent and incongruent one) and my goal is to >> compute WPLI between certain channel combinations (FCz and F3 for instance) >> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >> two conditions. >> >> >> I experienced some difficulties after the point when I calculated the >> WPLI data for each participant. To perform the above-mentioned comparison, >> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >> >> You could. Stick with the tutorial you are currently working with. You >> should organize your data into cell arrays and call ft_freqstatistics like >> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >> the data. >> good luck >> tzvetan >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Mon May 18 18:30:03 2015 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Mon, 18 May 2015 16:30:03 +0000 Subject: [FieldTrip] Source Reconstruction: MNI or subject space Message-ID: <1431966603032.7006@nin.knaw.nl> Dear FieldTrippers, When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 20:02:05 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 20:02:05 +0200 Subject: [FieldTrip] Source Reconstruction: MNI or subject space In-Reply-To: <1431966603032.7006@nin.knaw.nl> References: <1431966603032.7006@nin.knaw.nl> Message-ID: Dear Rajat, one option that is widely used by FieldTrip users, I believe, is the computation of source model aligned in MNI space while retaining the individual head model. This FAQ explains how to do this. http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space best tzvetan > Dear FieldTrippers, > > When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? > > > Thank you. > Rajat > > > > > > Rajat Mani Thomas > Social Brain Lab > Netherlands Institute for Neuroscience > Amsterdam > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 18 21:54:08 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 18 May 2015 19:54:08 +0000 Subject: [FieldTrip] problem reading bdf-file References: Message-ID: <4C5E591D-C0B8-4161-8070-80CA60521DB3@fcdonders.ru.nl> Dear all, I want to import a raw, markerless datafile (http://www.filedropper.com/1_20) by using cfg = []; cfg.dataset = '2.bdf'; data = ft_preprocessing(cfg) However, I get reading and preprocessing error opening file: 2.bdf One or more output arguments not assigned during call to "read_24bit". Error in read_biosemi_bdf>readLowLevel (line 274) buf = read_24bit(filename, offset, numwords); Error in read_biosemi_bdf (line 242) buf = readLowLevel(filename, offset, epochlength); % see below in subfunction Error in ft_read_data (line 321) dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 578) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Error in Untitled (line 19) data = ft_preprocessing(cfg) Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Tue May 19 10:23:19 2015 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Tue, 19 May 2015 08:23:19 +0000 Subject: [FieldTrip] using SPM to transform EEG electrode location Message-ID: <1432023799396.61888@nin.knaw.nl> Hi FieldTrippers and users of SPM I have, (i) the coordinates of my EEG electrodes in MNI space (ii) the y_*.nii and iy_*.nii files (deformation fields from SPM segmentation that is used to transform back and forth from subj->MNI. Does anyone know how to use the deformation fields on the 3D coordinates in MNI space to get the electrode locations in subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Tue May 19 11:09:09 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Tue, 19 May 2015 09:09:09 +0000 Subject: [FieldTrip] leadfields MNI-coordinates In-Reply-To: References: Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> Hi Barbara, Your code actually looks fine to me. Some things that I could think of: 1. Did you specify cfg.coordinates=’mni’ before applying ft_volumenormalise? 2. Did you select the right volumes for plotting? So a. For CTF head space: % make a figure of the single subject headmodel cfg=[]; cfg.location=ctfpos(i,:); cfg.locationcoordinates='head'; ft_sourceplot(cfg,mri_realign) b. And for MNI-space: cfg=[]; cfg.location=targets(i,:); cfg.locationcoordinates='head'; ft_sourceplot(cfg,mri_realign_mni) This should lead to the same anatomical locations. Hope this helps! Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Barbara Haendel Sent: vrijdag 15 mei 2015 10:27 To: fieldtrip at science.ru.nl Subject: [FieldTrip] leadfields MNI-coordinates Hi there, I found this very nice thread on warping between spm and ctf space (thanks Jan-Mathijs and Stan) and at first sight it seems to work fine (numbers match after applying warping back and forth) but when I try to navigate to the spot in the plotted figure the point of interest seems not to be the same. mri_realign_mni=ft_volumenormalise([],mri_realign) % Inverse warping mnipos=[-48 -75 8]; % [46 -78 6]; MT posback=ft_warp_apply(mri_realign_mni.params,mnipos,'sn2individual') ctfpos= ft_warp_apply(pinv(mri_realign_mni.initial),posback) -8.6110 55.6190 50.0473 I plotted either (see .jpg) A. the source (source = ft_sourceanalysis(cfg, freq)); B. the interpolated source (sourceInt = ft_sourceinterpolate(cfg, source , mri_realign); C. the normalized source (sourceIntNorm = ft_volumenormalise(cfg, sourceInt); and manually navigated to the respective coordinates. While for the normalized source the location makes sense (area MT) the location for A and B seems different. Is there any obvious mistake I’m overlooking? Thanks a lot! Barbara -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Tue May 19 11:17:25 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Tue, 19 May 2015 09:17:25 +0000 Subject: [FieldTrip] Source Reconstruction: MNI or subject space In-Reply-To: References: <1431966603032.7006@nin.knaw.nl> Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C1793D04F@exprd03.hosting.ru.nl> Dear Rajat, Both options are fine in principle. The only thing to keep in mind is that you used a non-warped volume (with either a CTF or MNI-grid) when computing the leadfields. It is crucial that these are computed based on the actual physical proportions/relations of the brain and sensors. Best, Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Tzvetan Popov Sent: maandag 18 mei 2015 20:02 To: FieldTrip discussion list Subject: Re: [FieldTrip] Source Reconstruction: MNI or subject space Dear Rajat, one option that is widely used by FieldTrip users, I believe, is the computation of source model aligned in MNI space while retaining the individual head model. This FAQ explains how to do this. http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space best tzvetan Dear FieldTrippers, When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue May 19 12:47:43 2015 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 May 2015 12:47:43 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Dear Zsolt, please find an answer below. Regards Cris On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > Hi Tzvetan and Chris, > > thanks for your emails. > Removing channelcmb and adding a new one called label solved my problem. > > Chris: > I'ld like to compare the WPLI difference of two conditions, congruent and > incongruent ones by using a within-subjects design (so not a between trials > comparison). > From your email I may infer that after running wpli, I should still have > my trials. However, I do not have repetitions (trials) anymore in the > output structure. Am I doing an illegitimate step during wPLI calculation > or miss one specification? > You did it correctly. After running the wPLI metric ( I suggest the unbiased version of it, use the 'wpli_debiased' method in ft_connectivityanalysis) you are left with no trials. This is because the trials dimension (and tapers) are used to estimate the phase lag index. If I left that implied in the previous mail, I did not communicate it very well. What I meant to say is to be careful in the contrast of two conditions, because the subtraction (or ratio, or else...) will generate fake effects (or false positives) if the trials in condition 1 and condition 2 BEFORE wPLI calculation are different. I hope this helps Cris > cfg = []; > cfg.method = 'wpli'; > dataWPLI = ft_connectivityanalysis(cfg,TFRhann); > > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x43x16 double] > freq: [1x43 double] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 > 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > Thanks for your help! > > Best, > Zsolt > > > > > 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : > >> Hi Zsolt, >> >> >> Hi Tzvetan, >> >> thanks for your suggestions. >> I am still stucked at the ft_freqstatistics, as I keep on receiving the >> following error and would be glad if you could make a comment on this as >> well: >> >> #### >> Reference to non-existent field 'label'. >> >> Error in ft_freqgrandaverage (line 123) >> cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); >> ### >> >> Is it because I have labelcomb in the WPLI data? >> >> yes >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x7x16 double] >> freq: [3 4 5 6 7 8 9] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> And this is my specification (I couldn't fine the option cfg.channelcmb >> for ft_freqgrandaverage in the reference documentation): >> >> again try to give cell arrays as input to ft_freqanalysis. I’m still >> considering the case you mentioned in your initial e-mail, one channel etc. >> e.g. cfg.channel = ‘FCzF3’; >> cfg.parameter = ‘wplispctrm’; >> cfg.neighbours = []; % this will force clustering over time and >> freq dimension >> >> best >> tzvetan >> >> >> cfg = []; >> cfg.keepindividual = 'yes'; >> cfg.cfg.foilim = 'all'; >> cfg.toilim = 'all'; >> cfg.channel = 'all'; >> cfg.parameter = 'wplispctrm'; >> >> Thanks again for the answer in advance! >> >> Best, >> Zsolt >> >> ps.I can provide other parts of my code but I don't want to make this >> mail too long : >> >> >> >> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Dear all, >>> >>> >>> I would like to perform a cluster-based permutation test on weighted >>> phase lag index values by using a within-subjects experimental design. I >>> have two conditions (congruent and incongruent one) and my goal is to >>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >>> two conditions. >>> >>> >>> I experienced some difficulties after the point when I calculated the >>> WPLI data for each participant. To perform the above-mentioned comparison, >>> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >>> >>> You could. Stick with the tutorial you are currently working with. You >>> should organize your data into cell arrays and call ft_freqstatistics like >>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >>> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >>> the data. >>> good luck >>> tzvetan >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, Göttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Wed May 20 08:20:09 2015 From: B.Haendel at gmx.net (Barbara Haendel) Date: Wed, 20 May 2015 08:20:09 +0200 Subject: [FieldTrip] leadfields MNI-coordinates In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> References: , <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> Message-ID: An HTML attachment was scrubbed... URL: From e.caspar at ucl.ac.uk Wed May 20 10:20:57 2015 From: e.caspar at ucl.ac.uk (Caspar, Emilie) Date: Wed, 20 May 2015 08:20:57 +0000 Subject: [FieldTrip] Tiggers added manually Message-ID: Dear Fieldtrippers, I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. Many thanks in advance! Emilie From rb643 at medschl.cam.ac.uk Wed May 20 12:34:32 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Wed, 20 May 2015 10:34:32 +0000 Subject: [FieldTrip] data segmenting and frequency analysis Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> Dear Fieldtrippers, Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. Thus, my questions are: 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? If a: how does freqanalysis handle multiple trials? I currently use this: cfg.method = 'wavelet'; cfg.output = 'powandcsd'; cfg.channel = 1:64; cfg.foilim = [0 70]; cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: cfg.method = 'wpli'; wpli_data = ft_connectivityanalysis(cfg, freq_data); 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? Any help would be much appreciated! Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From spa268 at nyu.edu Wed May 20 12:44:22 2015 From: spa268 at nyu.edu (Stephen Politzer-Ahles) Date: Wed, 20 May 2015 06:44:22 -0400 Subject: [FieldTrip] Tiggers added manually Message-ID: Hi Emilie, You could add new rows to the trial definition matrix (cfg.trl) to add new triggers. See http://www.fieldtriptoolbox.org/reference/ft_definetrial for information on how cfg.trl is organized. There might be more efficient built-in ways to do it, but this is how I add triggers at least. Best, Steve > ------------------------------ > > Message: 3 > Date: Wed, 20 May 2015 08:20:57 +0000 > From: "Caspar, Emilie" > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Tiggers added manually > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. > > Many thanks in advance! > > Emilie > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 17 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From melissa.ralston at gmail.com Wed May 20 20:34:33 2015 From: melissa.ralston at gmail.com (Melissa Smith) Date: Wed, 20 May 2015 11:34:33 -0700 Subject: [FieldTrip] Reading/importing .daq files Message-ID: Hi Fieldtrip community, My name is Melissa and I have a very basic question as I am just starting to use the Fieldtrip toolbox. I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 channels. So, each trial has four .daq data files (one for each amplifier containing 16 channels). What is the best way to import and read this data for analysis using Fieldtrip? Thanks in advance for your time! Best, Melissa -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Wed May 20 20:51:02 2015 From: mcantor at umich.edu (Max Cantor) Date: Wed, 20 May 2015 14:51:02 -0400 Subject: [FieldTrip] Reading/importing .daq files In-Reply-To: References: Message-ID: I don't know about g.tec amps or .daq files specifically, but one way I can think to do it would be to load them each in separately and then use ft_appenddata. Coincidentally, I'm actually heading to Seattle tomorrow to visit a friend of mine at University of Washington! Great place :) Best, Max On Wed, May 20, 2015 at 2:34 PM, Melissa Smith wrote: > Hi Fieldtrip community, > > My name is Melissa and I have a very basic question as I am just starting > to use the Fieldtrip toolbox. > > I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 > channels. So, each trial has four .daq data files (one for each amplifier > containing 16 channels). > > What is the best way to import and read this data for analysis using > Fieldtrip? > > Thanks in advance for your time! > > Best, > Melissa > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Lab Manager Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Wed May 20 21:23:26 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 20 May 2015 21:23:26 +0200 Subject: [FieldTrip] data segmenting and frequency analysis In-Reply-To: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> References: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> Message-ID: Dear Richard, > Dear Fieldtrippers, > > Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. you might check this page that illustrates a way to do this. It is in source space yet in your case you’ll stay on the electrode level. http://www.fieldtriptoolbox.org/tutorial/networkanalysis Keep in mind that sensor/electrode level connectivity metrics, regardless of the metric, come with some difficulties that are not trivial to solve. Maybe is good if you consult this lecture first: https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. cfg = []; cfg.dataset = ‘yourdataset'; cfg.trialdef.triallength = 4; cfg.trialdef.ntrials = Inf; cfg = ft_definetrial(cfg); cfg.channel = {‘EEG'}; data = ft_preprocessing(cfg); If you generate several of these data structures corresponding to your 1-minute epochs you can do data = ft_appenddata([],data1,data2). This way you combine them in one data structure. > After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. > > Thus, my questions are: > 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? > If a: how does freqanalysis handle multiple trials? I currently use this: > cfg.method = 'wavelet'; > cfg.output = 'powandcsd'; > cfg.channel = 1:64; > cfg.foilim = [0 70]; > cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] > [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data > > Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? Then for a given frequency in this example 8-12 Hz you could do this: cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.tapsmofrq = 2; cfg.foi = 10; freq_data = ft_freqanalysis(cfg, data); and subsequently use ft_connectivityanalysis with the metric of your choice. > > If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? there are two functions you might want to check: ft_redefinetrial and ft_selectdata > > 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? I would definitely remove the channel but there are certainly other opinions on that. > > 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? You can- cfg.foi = [0:1:100] gives you 0 to 100 Hz in steps of 1 Hz. Whether or not your frequency resolution is 1 Hz is different issue. You might check out this lecture too: https://www.youtube.com/watch?v=vwPpSglPJTE > > 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: > > cfg.method = 'wpli'; > wpli_data = ft_connectivityanalysis(cfg, freq_data); see above > > 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? no, you have to decide what value corresponds to a connection = 1 and what not =0 > Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? ft_selectdata with cfg.avgoverfreq = ‘yes' > Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? I don’t get that one. Good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Wed May 20 22:24:38 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Wed, 20 May 2015 22:24:38 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Dear Chris, thanks again for your comment. Cheers, Zsolt 2015-05-19 12:47 GMT+02:00 Cristiano Micheli : > > Dear Zsolt, > please find an answer below. > Regards > Cris > > On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > >> Hi Tzvetan and Chris, >> >> thanks for your emails. >> Removing channelcmb and adding a new one called label solved my problem. >> >> Chris: >> I'ld like to compare the WPLI difference of two conditions, congruent and >> incongruent ones by using a within-subjects design (so not a between trials >> comparison). >> From your email I may infer that after running wpli, I should still have >> my trials. However, I do not have repetitions (trials) anymore in the >> output structure. Am I doing an illegitimate step during wPLI calculation >> or miss one specification? >> > > You did it correctly. > After running the wPLI metric ( I suggest the unbiased version of it, use > the 'wpli_debiased' method in ft_connectivityanalysis) you are left with > no trials. This is because the trials dimension (and tapers) are used to > estimate the phase lag index. If I left that implied in the previous mail, > I did not communicate it very well. What I meant to say is to be careful in > the contrast of two conditions, because the subtraction (or ratio, or > else...) will generate fake effects (or false positives) if the trials in > condition 1 and condition 2 BEFORE wPLI calculation are different. > > I hope this helps > Cris > > >> cfg = []; >> cfg.method = 'wpli'; >> dataWPLI = ft_connectivityanalysis(cfg,TFRhann); >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x43x16 double] >> freq: [1x43 double] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> Thanks for your help! >> >> Best, >> Zsolt >> >> >> >> >> 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Hi Tzvetan, >>> >>> thanks for your suggestions. >>> I am still stucked at the ft_freqstatistics, as I keep on receiving the >>> following error and would be glad if you could make a comment on this as >>> well: >>> >>> #### >>> Reference to non-existent field 'label'. >>> >>> Error in ft_freqgrandaverage (line 123) >>> cfg.channel = ft_channelselection(cfg.channel, >>> varargin{i}.label); >>> ### >>> >>> Is it because I have labelcomb in the WPLI data? >>> >>> yes >>> >>> >>> labelcmb: {9x2 cell} >>> dimord: 'chan_freq_time' >>> wplispctrm: [9x7x16 double] >>> freq: [3 4 5 6 7 8 9] >>> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >>> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >>> cfg: [1x1 struct] >>> >>> And this is my specification (I couldn't fine the option cfg.channelcmb >>> for ft_freqgrandaverage in the reference documentation): >>> >>> again try to give cell arrays as input to ft_freqanalysis. I’m still >>> considering the case you mentioned in your initial e-mail, one channel etc. >>> e.g. cfg.channel = ‘FCzF3’; >>> cfg.parameter = ‘wplispctrm’; >>> cfg.neighbours = []; % this will force clustering over time and >>> freq dimension >>> >>> best >>> tzvetan >>> >>> >>> cfg = []; >>> cfg.keepindividual = 'yes'; >>> cfg.cfg.foilim = 'all'; >>> cfg.toilim = 'all'; >>> cfg.channel = 'all'; >>> cfg.parameter = 'wplispctrm'; >>> >>> Thanks again for the answer in advance! >>> >>> Best, >>> Zsolt >>> >>> ps.I can provide other parts of my code but I don't want to make this >>> mail too long : >>> >>> >>> >>> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov >>> : >>> >>>> Hi Zsolt, >>>> >>>> >>>> Dear all, >>>> >>>> >>>> I would like to perform a cluster-based permutation test on weighted >>>> phase lag index values by using a within-subjects experimental design. I >>>> have two conditions (congruent and incongruent one) and my goal is to >>>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>>> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >>>> two conditions. >>>> >>>> >>>> I experienced some difficulties after the point when I calculated the >>>> WPLI data for each participant. To perform the above-mentioned comparison, >>>> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >>>> >>>> You could. Stick with the tutorial you are currently working with. You >>>> should organize your data into cell arrays and call ft_freqstatistics like >>>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>>> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >>>> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >>>> the data. >>>> good luck >>>> tzvetan >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> ************************************************************ >>> Ph.D. >>> Department of Clinical Neurophysiology >>> Georg-August University, Göttingen >>> Robert-Koch-Str. 40 >>> 37075 Goettingen >>> Web: http://www.uni-goettingen.de/en/222525.html >>> ************************************************************ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, Göttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Thu May 21 14:02:53 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Thu, 21 May 2015 12:02:53 +0000 Subject: [FieldTrip] data segmenting and frequency analysis (Tzvetan Popov) Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF47FDCE@me-mbx3.medschl.cam.ac.uk> Hi Tzvetan and others, Thanks for all the wonderful feedback and links to resources! I did manage to sort out the redefine trials issue now to split the trial up in smaller segments. As for faulty channels, I found the option to repair channels (which I would prefer to keep the matrix sizes the same). When looking at the data this does seem to adequately resolve the one faulty channel I had with the specific subject I was looking at. For some reason however this seems to cause some errors in later on displaying the ICA topoplots (the ICA itself still seems to run fine, but when inspecting the components I only see the timecourses and not the topoplots)? An error in matlabs surf function in using complex numbers is all I get back? As for the frequencies of interest: I would ideally like to use wavelet decomposition rather than fourier transformations to obtain a specific power. I assume I can set this in cfg_foi and then run ft_freqanalysis on the different bands, but at what point would you collapse or average the windows together? As for the connectivity analysis, the reason I would like to use wpli is precisely to get around the volume conduction issue and the fact that I only have the elecrode level metrics. It does seem however as though something is missing in my pipeline before that as the cross and power spectra contains a lot of NaN's? I am also not sure about when to average over the wavelet windows or frequency 'timepoints' (going from the 3D wpli spectrum to a vector or a 2 matrix)? Related to that last point was my question about the adjacency matrix, the connectivity analysis output just list all the wpl indices per channel pair, but I would rather have the 2D matrix (with nothing trilled off) that lists all channels against all channels? Just to sum up my remaining questions: 1. Why would channelrepair result in issues with ICA's topoplot and how to fix that (it would be good to see if the noise from the one faulty channel is really gone)? 2. How to obtain a metric per frequency band (using wavelets)/or alternatively at what point in the analysis should the wavelet decomposition be averaged? 3. How to obtain a 64*64 matrix (all channels*all channels) of the wpl indices? For reference, my entire (under construction) code is here: https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m Cheers, Richard ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] Sent: 21 May 2015 11:00 To: fieldtrip at science.ru.nl Subject: fieldtrip Digest, Vol 54, Issue 18 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit http://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. data segmenting and frequency analysis (Richard Bethlehem) 2. Re: Tiggers added manually (Stephen Politzer-Ahles) 3. Reading/importing .daq files (Melissa Smith) 4. Re: Reading/importing .daq files (Max Cantor) 5. Re: data segmenting and frequency analysis (Tzvetan Popov) 6. Re: cluster-based permutation test on WPLI (Zsolt Turi) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 May 2015 10:34:32 +0000 From: Richard Bethlehem To: "fieldtrip at science.ru.nl" Subject: [FieldTrip] data segmenting and frequency analysis Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4759E5 at me-mbx3.medschl.cam.ac.uk> Content-Type: text/plain; charset="iso-8859-1" Dear Fieldtrippers, Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. Thus, my questions are: 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? If a: how does freqanalysis handle multiple trials? I currently use this: cfg.method = 'wavelet'; cfg.output = 'powandcsd'; cfg.channel = 1:64; cfg.foilim = [0 70]; cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: cfg.method = 'wpli'; wpli_data = ft_connectivityanalysis(cfg, freq_data); 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? Any help would be much appreciated! Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 20 May 2015 06:44:22 -0400 From: Stephen Politzer-Ahles To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Tiggers added manually Message-ID: Content-Type: text/plain; charset="utf-8" Hi Emilie, You could add new rows to the trial definition matrix (cfg.trl) to add new triggers. See http://www.fieldtriptoolbox.org/reference/ft_definetrial for information on how cfg.trl is organized. There might be more efficient built-in ways to do it, but this is how I add triggers at least. Best, Steve > ------------------------------ > > Message: 3 > Date: Wed, 20 May 2015 08:20:57 +0000 > From: "Caspar, Emilie" > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Tiggers added manually > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. > > Many thanks in advance! > > Emilie > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 17 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 20 May 2015 11:34:33 -0700 From: Melissa Smith To: fieldtrip at science.ru.nl Subject: [FieldTrip] Reading/importing .daq files Message-ID: Content-Type: text/plain; charset="utf-8" Hi Fieldtrip community, My name is Melissa and I have a very basic question as I am just starting to use the Fieldtrip toolbox. I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 channels. So, each trial has four .daq data files (one for each amplifier containing 16 channels). What is the best way to import and read this data for analysis using Fieldtrip? Thanks in advance for your time! Best, Melissa -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 4 Date: Wed, 20 May 2015 14:51:02 -0400 From: Max Cantor To: FieldTrip discussion list Subject: Re: [FieldTrip] Reading/importing .daq files Message-ID: Content-Type: text/plain; charset="utf-8" I don't know about g.tec amps or .daq files specifically, but one way I can think to do it would be to load them each in separately and then use ft_appenddata. Coincidentally, I'm actually heading to Seattle tomorrow to visit a friend of mine at University of Washington! Great place :) Best, Max On Wed, May 20, 2015 at 2:34 PM, Melissa Smith wrote: > Hi Fieldtrip community, > > My name is Melissa and I have a very basic question as I am just starting > to use the Fieldtrip toolbox. > > I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 > channels. So, each trial has four .daq data files (one for each amplifier > containing 16 channels). > > What is the best way to import and read this data for analysis using > Fieldtrip? > > Thanks in advance for your time! > > Best, > Melissa > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Lab Manager Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 5 Date: Wed, 20 May 2015 21:23:26 +0200 From: Tzvetan Popov To: FieldTrip discussion list Subject: Re: [FieldTrip] data segmenting and frequency analysis Message-ID: Content-Type: text/plain; charset="windows-1252" Dear Richard, > Dear Fieldtrippers, > > Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. you might check this page that illustrates a way to do this. It is in source space yet in your case you?ll stay on the electrode level. http://www.fieldtriptoolbox.org/tutorial/networkanalysis Keep in mind that sensor/electrode level connectivity metrics, regardless of the metric, come with some difficulties that are not trivial to solve. Maybe is good if you consult this lecture first: https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. cfg = []; cfg.dataset = ?yourdataset'; cfg.trialdef.triallength = 4; cfg.trialdef.ntrials = Inf; cfg = ft_definetrial(cfg); cfg.channel = {?EEG'}; data = ft_preprocessing(cfg); If you generate several of these data structures corresponding to your 1-minute epochs you can do data = ft_appenddata([],data1,data2). This way you combine them in one data structure. > After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. > > Thus, my questions are: > 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? > If a: how does freqanalysis handle multiple trials? I currently use this: > cfg.method = 'wavelet'; > cfg.output = 'powandcsd'; > cfg.channel = 1:64; > cfg.foilim = [0 70]; > cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] > [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data > > Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? Then for a given frequency in this example 8-12 Hz you could do this: cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.tapsmofrq = 2; cfg.foi = 10; freq_data = ft_freqanalysis(cfg, data); and subsequently use ft_connectivityanalysis with the metric of your choice. > > If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? there are two functions you might want to check: ft_redefinetrial and ft_selectdata > > 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? I would definitely remove the channel but there are certainly other opinions on that. > > 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? You can- cfg.foi = [0:1:100] gives you 0 to 100 Hz in steps of 1 Hz. Whether or not your frequency resolution is 1 Hz is different issue. You might check out this lecture too: https://www.youtube.com/watch?v=vwPpSglPJTE > > 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: > > cfg.method = 'wpli'; > wpli_data = ft_connectivityanalysis(cfg, freq_data); see above > > 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? no, you have to decide what value corresponds to a connection = 1 and what not =0 > Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? ft_selectdata with cfg.avgoverfreq = ?yes' > Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? I don?t get that one. Good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 6 Date: Wed, 20 May 2015 22:24:38 +0200 From: Zsolt Turi To: FieldTrip discussion list Subject: Re: [FieldTrip] cluster-based permutation test on WPLI Message-ID: Content-Type: text/plain; charset="utf-8" Dear Chris, thanks again for your comment. Cheers, Zsolt 2015-05-19 12:47 GMT+02:00 Cristiano Micheli : > > Dear Zsolt, > please find an answer below. > Regards > Cris > > On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > >> Hi Tzvetan and Chris, >> >> thanks for your emails. >> Removing channelcmb and adding a new one called label solved my problem. >> >> Chris: >> I'ld like to compare the WPLI difference of two conditions, congruent and >> incongruent ones by using a within-subjects design (so not a between trials >> comparison). >> From your email I may infer that after running wpli, I should still have >> my trials. However, I do not have repetitions (trials) anymore in the >> output structure. Am I doing an illegitimate step during wPLI calculation >> or miss one specification? >> > > You did it correctly. > After running the wPLI metric ( I suggest the unbiased version of it, use > the 'wpli_debiased' method in ft_connectivityanalysis) you are left with > no trials. This is because the trials dimension (and tapers) are used to > estimate the phase lag index. If I left that implied in the previous mail, > I did not communicate it very well. What I meant to say is to be careful in > the contrast of two conditions, because the subtraction (or ratio, or > else...) will generate fake effects (or false positives) if the trials in > condition 1 and condition 2 BEFORE wPLI calculation are different. > > I hope this helps > Cris > > >> cfg = []; >> cfg.method = 'wpli'; >> dataWPLI = ft_connectivityanalysis(cfg,TFRhann); >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x43x16 double] >> freq: [1x43 double] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> Thanks for your help! >> >> Best, >> Zsolt >> >> >> >> >> 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Hi Tzvetan, >>> >>> thanks for your suggestions. >>> I am still stucked at the ft_freqstatistics, as I keep on receiving the >>> following error and would be glad if you could make a comment on this as >>> well: >>> >>> #### >>> Reference to non-existent field 'label'. >>> >>> Error in ft_freqgrandaverage (line 123) >>> cfg.channel = ft_channelselection(cfg.channel, >>> varargin{i}.label); >>> ### >>> >>> Is it because I have labelcomb in the WPLI data? >>> >>> yes >>> >>> >>> labelcmb: {9x2 cell} >>> dimord: 'chan_freq_time' >>> wplispctrm: [9x7x16 double] >>> freq: [3 4 5 6 7 8 9] >>> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >>> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >>> cfg: [1x1 struct] >>> >>> And this is my specification (I couldn't fine the option cfg.channelcmb >>> for ft_freqgrandaverage in the reference documentation): >>> >>> again try to give cell arrays as input to ft_freqanalysis. I?m still >>> considering the case you mentioned in your initial e-mail, one channel etc. >>> e.g. cfg.channel = ?FCzF3?; >>> cfg.parameter = ?wplispctrm?; >>> cfg.neighbours = []; % this will force clustering over time and >>> freq dimension >>> >>> best >>> tzvetan >>> >>> >>> cfg = []; >>> cfg.keepindividual = 'yes'; >>> cfg.cfg.foilim = 'all'; >>> cfg.toilim = 'all'; >>> cfg.channel = 'all'; >>> cfg.parameter = 'wplispctrm'; >>> >>> Thanks again for the answer in advance! >>> >>> Best, >>> Zsolt >>> >>> ps.I can provide other parts of my code but I don't want to make this >>> mail too long : >>> >>> >>> >>> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov >>> : >>> >>>> Hi Zsolt, >>>> >>>> >>>> Dear all, >>>> >>>> >>>> I would like to perform a cluster-based permutation test on weighted >>>> phase lag index values by using a within-subjects experimental design. I >>>> have two conditions (congruent and incongruent one) and my goal is to >>>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>>> and see the WPLI change let?s say in 3-9 Hz and -100 to 500 ms between the >>>> two conditions. >>>> >>>> >>>> I experienced some difficulties after the point when I calculated the >>>> WPLI data for each participant. To perform the above-mentioned comparison, >>>> shall I use ?ft_freqstatistics?for the cluster-based permutation test? >>>> >>>> You could. Stick with the tutorial you are currently working with. You >>>> should organize your data into cell arrays and call ft_freqstatistics like >>>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>>> Furthermore you should specify cfg.parameter = ?wplispctrm? otherwise >>>> ft_freqstatistics will default to ?powspctrm? which will be not present in >>>> the data. >>>> good luck >>>> tzvetan >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> ************************************************************ >>> Ph.D. >>> Department of Clinical Neurophysiology >>> Georg-August University, G?ttingen >>> Robert-Koch-Str. 40 >>> 37075 Goettingen >>> Web: http://www.uni-goettingen.de/en/222525.html >>> ************************************************************ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, G?ttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, G?ttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 54, Issue 18 ***************************************** From l.garcia.d at gmail.com Thu May 21 20:02:04 2015 From: l.garcia.d at gmail.com (Luis Garcia Dominguez) Date: Thu, 21 May 2015 14:02:04 -0400 Subject: [FieldTrip] Fwd: clusterplot not plotting for gradiometeres In-Reply-To: References: Message-ID: Dear All, Has anyone been successful in combining magnetometers and gradiometers in dipole fitting. In my experience the results obtained using either grad or mag are very similar and accurate, but the combination of both did not work.... I can offer more details, code and data if needed. Any updates on this? Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: From mor2451 at gmail.com Fri May 22 14:00:47 2015 From: mor2451 at gmail.com (moran abilea) Date: Fri, 22 May 2015 15:00:47 +0300 Subject: [FieldTrip] what should i do between two stimulations P300 speller Message-ID: hi there everyone, so quick update and a problem that i need some advice from you guys. as I've already mentioned i'm doing a final project of MALAB p300 speller, i'm currently at the part of the experiment which means recording raw data on my partner's scalp while showing him the flashing 6X6 matrix of letters. we are using Emotiv EPOC device which means that it records 128 samples per sec. so now for my question: in the raw data itself that i record, between two stimulations i have 128 recorded raw data and i don't know what to do with it in order to continue the next step of using p300 detection method. what should i do with the 128 recorded data? should i average it or maybe use any band pass filter on the data i'm stuck and i need ideas in order to continue my project. any help will be welcomed, best regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.llera at donders.ru.nl Fri May 22 17:34:25 2015 From: a.llera at donders.ru.nl (Llera Arenas, A. (Alberto)) Date: Fri, 22 May 2015 15:34:25 +0000 Subject: [FieldTrip] what should i do between two stimulations P300 speller In-Reply-To: References: Message-ID: <6F2BEAB2DB977640884026115886A9B3247F9F@exprd01.hosting.ru.nl> Hi Hereby some starting points: I first would recommend reading the following paper: Single-Trial Analysis and Classification of ERP Components – a Tutorial. You can download it for free at http://doc.ml.tu-berlin.de/bbci/publications/BlaLemTreHauMue10.pdf If you want more, check for example: Interactions between pre-processing and classification methods for event-related-potential classification: best-practice guidelines for brain-computer interfacing. http://www.ncbi.nlm.nih.gov/pubmed/23250668 a free pre print of this last one is available at research gate http://www.researchgate.net/publication/234112682_FarquharHill_ERP_Classification_Best_Practice_Author_Pre-print Good luck Alberto Llera ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of moran abilea [mor2451 at gmail.com] Sent: Friday, May 22, 2015 2:00 PM To: FieldTrip discussion list Subject: [FieldTrip] what should i do between two stimulations P300 speller hi there everyone, so quick update and a problem that i need some advice from you guys. as I've already mentioned i'm doing a final project of MALAB p300 speller, i'm currently at the part of the experiment which means recording raw data on my partner's scalp while showing him the flashing 6X6 matrix of letters. we are using Emotiv EPOC device which means that it records 128 samples per sec. so now for my question: in the raw data itself that i record, between two stimulations i have 128 recorded raw data and i don't know what to do with it in order to continue the next step of using p300 detection method. what should i do with the 128 recorded data? should i average it or maybe use any band pass filter on the data i'm stuck and i need ideas in order to continue my project. any help will be welcomed, best regards, Moran Abilea From greg at think-now.com Sat May 23 02:11:58 2015 From: greg at think-now.com (Greg Simpson) Date: Fri, 22 May 2015 17:11:58 -0700 Subject: [FieldTrip] RA Position Open Message-ID: Dear Colleagues, I would like to announce an opening for a Research Associate (see ad below). Please spread the word. Thank you, Greg Research Associate – Cognitive Training Think Now Incorporated is seeking a research associate to work on a NIMH funded project testing the effects of mobile software training on attention in adults with ADHD. Duties will include recruiting, screening and testing (both behavioral tests and EEG tests) of adults with ADHD, before and after they train their attention with the mobile software. We are seeking candidates with direct hands-on experience in conducting cognitive/psychological tests or related experience. Experience with collecting EEG data is not required but would be great. Also, experience with MatLab and statistical packages such as SPSS would be a plus. We prefer strongly self-directed individuals with great people-skills to take on this work. The position reports directly to Greg Simpson, Ph.D., a cognitive neuroscientist and Chief Scientific Officer of Think Now. Think Now is located in San Francisco and our research partners for this effort are located at UCLA in Los Angeles. Candidates need to be located in the Los Angeles area. Think Now is focused on creating solutions for the diagnosis and amelioration of neurological disorders with a focus on attention and its control. Please send your CV to jobs at think-now.com with a letter describing your prior experience with conducting studies with adults (and any EEG experience) and your reason for being interested in this position. Gregory V. Simpson, Ph.D. Think Now, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ad_Staff Research Associate TNI 2015.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 15847 bytes Desc: not available URL: From sjaak10101 at gmail.com Sat May 23 21:54:42 2015 From: sjaak10101 at gmail.com (Sjaak Zwart) Date: Sat, 23 May 2015 21:54:42 +0200 Subject: [FieldTrip] EDF+C annotations Message-ID: Dear all, I have an .edf file, according to the header, I think the precise format is EDF+C, and my goal is to convert this file in SPM and see the data with annotations. SPM is able to convert the file, although it does give a warning: Warning: Skipping "EDF Annotations" as continuous data channel because of > inconsistent sampling frequency > > In fileio/private/read_edf at 235 > In ft_read_header at 616 > In spm_eeg_convert at 97 > In spm_eeg_convert at 92 > In spm_eeg_convert_ui at 26 > In spm at 1054 > I further noticed that the EDFBrowser application is able to read the data *and* show the annotations. I could now try to figure out from the source what the EDFBrowser is doing exactly, and try to do something similar in the fieldtrip methods that read the edf. Not sure how far I'd get then. An additional complexity is that I do not have a full Matlab license, so I have the Matlab compiler and I have octave installed. (I'm not 100% sure but I think that means I cannot run Matlab code, but only pre-compiled code). >From the EDFBrowser I am able to export the events. But I don't know how to read that file together with the original file when I convert the edf file in SPM to get everything to show up right. Would be great if anybody has some experience with this already, or somebody who just knows how to get me further, Thanks, Sjaak. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at gmail.com Sat May 23 22:06:40 2015 From: bibi.raquel at gmail.com (bibi.raquel at gmail.com) Date: Sat, 23 May 2015 20:06:40 +0000 Subject: [FieldTrip] =?utf-8?q?biosemi_bdf_=3E=3E_read=5F24bit_error_+_no_?= =?utf-8?q?events_found?= In-Reply-To: References: Message-ID: <5560dddf.0b91340a.2dab.ffffdae5@mx.google.com> Have you resolved this issue? From: Paul Zerr Sent: ‎Thursday‎, ‎May‎ ‎14‎, ‎2015 ‎8‎:‎01‎ ‎AM To: FieldTrip discussion list Hi all, I'm new to fieldtrip so forgive me if my mistake is obvious. I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with cfg = []; cfg.dataset = '2.bdf'; data = ft_preprocessing(cfg) However, I get reading and preprocessing error opening file: 2.bdf One or more output arguments not assigned during call to "read_24bit". Error in read_biosemi_bdf>readLowLevel (line 274) buf = read_24bit(filename, offset, numwords); Error in read_biosemi_bdf (line 242) buf = readLowLevel(filename, offset, epochlength); % see below in subfunction Error in ft_read_data (line 321) dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 578) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Error in Untitled (line 19) data = ft_preprocessing(cfg) Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Defining only one channel to preprocess gives the same error. I couldn't find a solution in the archives, the faq, wiki or documentation. I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. Any ideas? Much appreciated, Paul Zerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From Andreas.Horn at charite.de Sun May 24 10:55:55 2015 From: Andreas.Horn at charite.de (Horn, Andreas) Date: Sun, 24 May 2015 08:55:55 +0000 Subject: [FieldTrip] Elements have wrong orientation or are degenerated Message-ID: Hello everybody, I am new to fieldtrip and want to use it (and simbio) to forward model the current spread of a known dipole. I consider only a small cubic fraction of brain tissue which I so far have divided in gray and white matter. I pass that cubic volume into ft_prepare_mesh and get a hexahedral mesh without error. ft_plot_mesh also shows the correct mesh. However, once I pass the mesh into ft_headmodel_simbio, I get the error ‘Elements have wrong orientation or are degenerated’ Does anyone have an idea of why this could happen and how I could potentially fix the issue? Thanks a lot, Andreas From alizadeh.arezoo88 at gmail.com Sun May 24 22:00:11 2015 From: alizadeh.arezoo88 at gmail.com (Arezoo Alizadeh) Date: Sun, 24 May 2015 09:00:11 -1100 Subject: [FieldTrip] User pass Message-ID: Hello, I have forget both my user name and pass word to ask question from fieldtriper. Could you please help me. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Sun May 24 22:03:46 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Sun, 24 May 2015 22:03:46 +0200 Subject: [FieldTrip] User pass In-Reply-To: References: Message-ID: http://mailman.science.ru.nl/mailman/listinfo/fieldtrip On Sun, May 24, 2015 at 10:00 PM, Arezoo Alizadeh < alizadeh.arezoo88 at gmail.com> wrote: > Hello, > > I have forget both my user name and pass word to ask question from > fieldtriper. Could you please help me. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.pedrosa at ndcn.ox.ac.uk Mon May 25 11:19:00 2015 From: david.pedrosa at ndcn.ox.ac.uk (David Pedrosa) Date: Mon, 25 May 2015 09:19:00 +0000 Subject: [FieldTrip] Statistics of coherence (DICS) Message-ID: Dear list, I would be very grateful if someone might answer some questions on the statistics of coherence. Maybe first of all an outline to our experiment. We have measured a 128 channel EEG with additional peripheral signals from the most affected arm on 20 subjects suffering from tremor and the same number of healthy control subjects with a simple motor paradigm (activation condition). In another condition, rest (baseline condition) was also measured (we have about 20-35 trials per condition). For the data analysis we have preprocessed the EEG in a rather standard way. For localizing the cortical sources we created a headmodel from individual MRI and the source reconstruction was obtained using the DICS beamformer (with the peripheral signal as 'refchan' and after computing a common spatial filter). Everything works out well and regarding the activation condition by itself the sources appear to be where we you would suspect it (motor areas) in all individuals. Of course coherence is much bigger during activation (about 1-3 dimensions). But otherwise coherence is never 0, not even in the rest condition (as to be expected). This makes us suspect a permutation test much more valid for testing the 'null-hypothesis' of interchangeable coherence between the conditions. Now we are struggling with the stats of the individual but also the group results. My first question is am I right that averageing over trials per condition is not necessary? And do I need to normalise the coherence after computing it with ft_freqanalysis? I was thinking of computing (activation - baseline)/baseline. And, finally, regarding the stats. The idea is to look individually at differences between the conditions and in a second step perform a group analysis. But what to test if we are not assuming a null-hypothesis, or am I completely on the wrong track? Thanks in advance. Best, David From zerr.paul at googlemail.com Mon May 25 15:51:15 2015 From: zerr.paul at googlemail.com (Paul Zerr) Date: Mon, 25 May 2015 15:51:15 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found Message-ID: I have not. I can read in the header but that's about it. I don't have any older matlab versions here to test it with either. >From what I understand ft_preprocessing should be capable of reading bdf's directly with only the file name as input arg. Greetings, Paul Zerr From: > To: FieldTrip discussion list > Subject: Re: [FieldTrip] biosemi bdf >> read_24bit error + no events > found > Message-ID: <5560dddf.0b91340a.2dab.ffffdae5 at mx.google.com> > Content-Type: text/plain; charset="utf-8" > > Have you resolved this issue? > > > From: Paul Zerr > Sent: ?Thursday?, ?May? ?14?, ?2015 ?8?:?01? ?AM > To: FieldTrip discussion list > > > Hi all, > > I'm new to fieldtrip so forgive me if my mistake is obvious. > I want to import my raw, markerless dataset ( > http://www.filedropper.com/1_20) with > > cfg = []; > cfg.dataset = '2.bdf'; > data = ft_preprocessing(cfg) > > However, I get > > reading and preprocessing > error opening file: 2.bdf > One or more output arguments not assigned during call to "read_24bit". > > Error in read_biosemi_bdf>readLowLevel (line 274) > buf = read_24bit(filename, offset, numwords); > > Error in read_biosemi_bdf (line 242) > buf = readLowLevel(filename, offset, epochlength); % see below in > subfunction > > Error in ft_read_data (line 321) > dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); > > Error in ft_preprocessing (line 578) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, > 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) > > Error in Untitled (line 19) > data = ft_preprocessing(cfg) > > Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the > datafile" for ft_definetrial even for datasets with many markers. > Converting to EDF+ did not help as it then says "channels with different > sampling rate not supported". Specifying only one channel makes no > difference. The file itself is fine (opens well in BvA). > > Defining only one channel to preprocess gives the same error. > > I couldn't find a solution in the archives, the faq, wiki or documentation. > > I'm using debian stable & matlab 2014a. Same issue at DCC computers > running windows & matlab 2013a. > > Any ideas? > > Much appreciated, > > Paul Zerr > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Mon May 25 20:15:04 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Mon, 25 May 2015 18:15:04 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at: https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 25 20:52:56 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 25 May 2015 18:52:56 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR In-Reply-To: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> References: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> Message-ID: <0D293943-40CA-45B3-B6E6-0CA403FCFA0B@fcdonders.ru.nl> Hi Richard, Is there a specific reason you would want to do a time-frequency type of analysis (with averaging across ‘epochs’ for resting state data? Since there’s no external event, such analysis does not really make sense. Yet, if you insist on doing this, you need to ensure that the individual ‘pseudo-trial’ time axis (i.e. data_iccleaned.time{x}) contains a ‘pseudo-time-axis’ such that it goes from 0 to 4. Best, Jan-Mathijs On May 25, 2015, at 8:15 PM, Richard Bethlehem > wrote: Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at:https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Tue May 26 11:27:38 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Tue, 26 May 2015 09:27:38 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4AAB5C@me-mbx3.medschl.cam.ac.uk> Hi Jan-Mathijs, Essentially I want to do connectivity analysis using the wpli measure for connectivity and use wavelets to get to the frequency domain, I gathered I needed to do frequency analysis to get the power and crosspectrum info for computing wpli (and to decompose into the different frequency bands), but please let me know if this should be done differently? I thought with such analysis selecting epochs would be fairly standard practice (following van Diessen et al. 2014), but again please do correct me if I misunderstood. If not, what would be the alternative for getting epochs/trials? Following you suggestion I have replaced the time axis with the same 0-4second interval as used in the freqanalysis input: stepSize = 1/1024; timeVector = 0:stepSize:(epochLength-stepSize); for i = 1:size(data_iccleaned.time,2) data_iccleaned.time{:,i} = timeVector; end Unfortunately this still gives me NaN's in the output... Cheers, Richard Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl ________________________________ Hi Richard, Is there a specific reason you would want to do a time-frequency type of analysis (with averaging across ‘epochs’ for resting state data? Since there’s no external event, such analysis does not really make sense. Yet, if you insist on doing this, you need to ensure that the individual ‘pseudo-trial’ time axis (i.e. data_iccleaned.time{x}) contains a ‘pseudo-time-axis’ such that it goes from 0 to 4. Best, Jan-Mathijs On May 25, 2015, at 8:15 PM, Richard Bethlehem >> wrote: Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at:https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed May 27 11:28:27 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 27 May 2015 11:28:27 +0200 Subject: [FieldTrip] Power Spectra - averaging across samples Message-ID: Dear all, I have a question about spectral power computation. I'm using this code cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 5:1:40; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; freqfourier = ft_freqanalysis(cfg, eeg); and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) X 36 (frequencies), for each subject. My question is: is it correct to average the data across the samples dimension? Thank you in advance! Best, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Wed May 27 11:46:25 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Wed, 27 May 2015 09:46:25 +0000 Subject: [FieldTrip] Power Spectra - averaging across samples In-Reply-To: References: Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> Dear Fedrica, Yes it is. You can get to the same outcome directly by just specifying cfg.keeptrials=’no’ (the default), but I assume you want to do some single-trial analysis later on. Best, Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Federica Mauro Sent: woensdag 27 mei 2015 11:28 To: FieldTrip discussion list Subject: [FieldTrip] Power Spectra - averaging across samples Dear all, I have a question about spectral power computation. I'm using this code cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 5:1:40; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; freqfourier = ft_freqanalysis(cfg, eeg); and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) X 36 (frequencies), for each subject. My question is: is it correct to average the data across the samples dimension? Thank you in advance! Best, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed May 27 12:09:43 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 27 May 2015 12:09:43 +0200 Subject: [FieldTrip] Power Spectra - averaging across samples In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> References: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> Message-ID: ok, great, thanks! 2015-05-27 11:46 GMT+02:00 Pelt, S. van (Stan) : > Dear Fedrica, > > > > Yes it is. You can get to the same outcome directly by just specifying > cfg.keeptrials=’no’ (the default), but I assume you want to do some > single-trial analysis later on. > > > > Best, > > Stan > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Federica Mauro > *Sent:* woensdag 27 mei 2015 11:28 > *To:* FieldTrip discussion list > *Subject:* [FieldTrip] Power Spectra - averaging across samples > > > > Dear all, > > I have a question about spectral power computation. > > I'm using this code > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.foi = 5:1:40; > cfg.t_ftimwin = 5./cfg.foi; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' > 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; > freqfourier = ft_freqanalysis(cfg, eeg); > > and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) > X 36 (frequencies), for each subject. > > My question is: is it correct to average the data across the samples > dimension? > > Thank you in advance! > > Best, > > Federica > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.schubert at gmail.com Wed May 27 16:33:26 2015 From: jonathan.schubert at gmail.com (Jonathan Schubert) Date: Wed, 27 May 2015 16:33:26 +0200 Subject: [FieldTrip] postdoc position in Hamburg In-Reply-To: <4E102991-AB38-44E6-AA60-780A723AFCE2@gmail.com> References: <4E102991-AB38-44E6-AA60-780A723AFCE2@gmail.com> Message-ID: <5565D5B6.8020805@gmail.com> Dear all, I'd like to advertise the following postdoc postion. If you have any questions, please do not hesitate to contact Tobias Heed (tobias.heed at uni-hamburg.de). Cheers, Jonathan -------- Weitergeleitete Nachricht -------- Dear friends and colleagues, The Reach & Touch Lab at the University of Hamburg is hiring a PostDoc for a 4-year project about brain connectivity in tactile-visual processing involving EEG, TMS, and eye tracking. I would be thankful if you could pass on this link: http://goo.gl/zhlk4p to anyone who might be interested. Application deadline is June 15, 2015. Thanks! Tobias Heed — Follow the Reach & Touch Lab (@HeedLab ) and myself (@TobiasHeed ) on Twitter Read our news and blog posts on www.reachtouchlab.com View our publications Dr. Tobias Heed Reach & Touch Lab of the Biological Psychology and Neuropsychology Faculty of Psychology & Human Movement Science | University of Hamburg Von-Melle-Park 11, Room 206 | D-20146 Hamburg, Germany Phone: (49) 40 - 42838 5831 | Fax: (49) 40 - 42838 6591 tobias.heed at uni-hamburg.de | Website | Twitter | Google Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: From lauri.parkkonen at aalto.fi Thu May 28 14:51:18 2015 From: lauri.parkkonen at aalto.fi (Parkkonen Lauri) Date: Thu, 28 May 2015 12:51:18 +0000 Subject: [FieldTrip] Post-doc position in Bayesian estimation & MEG Message-ID: Postdoctoral researcher in Bayesian estimation of functional connectivity from MEG data at Department of Neuroscience and Biomedical Engineering (NBE) of Aalto University School of Science, Finland. The work will be carried out jointly in the teams of prof. Lauri Parkkonen and prof. Simo Särkkä. More information on the position can be found here: http://www.aalto.fi/en/about/careers/jobs/view/515/ Cheers, Lauri -- ----------------------------------------------- Dr. Lauri Parkkonen Assistant Professor (Medical Imaging) Dept. of Neuroscience and Biomedical Engineering (NBE) Aalto University School of Science Street address: Rakentajanaukio 2 C, FI-02150 ESPOO, Finland Postal address: P.O. Box 12200, FI-00076 AALTO, Finland Tel: +358-40-5089712, mailto:lauri.parkkonen at aalto.fi http://nbe.aalto.fi/en -------------- next part -------------- An HTML attachment was scrubbed... URL: From mor2451 at gmail.com Thu May 28 16:56:51 2015 From: mor2451 at gmail.com (moran abilea) Date: Thu, 28 May 2015 17:56:51 +0300 Subject: [FieldTrip] using triggers building my own function Message-ID: hi everyone, so i'm trying to create my own function for using triggers with EEG raw data. i used this tutorial: http://www.fieldtriptoolbox.org/tutorial/preprocessing my question is if i can somehow specify the time i want to record my EEG data? for example i would like my function to get 'time' as parameter to the function and returns the EEG raw data of this specific time+one second. if so, can some one give me a piece of code for example to understand what to do? also 2 more little questions: 1. cfg.trialdef.eventvalue = [3 5 9]; what does the 3 5 9 stands for? i don't understand what is the meaning of those (or any other) numbers. can i get definition for what is event value? 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; does it means it takes exactly one second for the buffer to give me the EEG raw data? or does it means wait one second and then take the data from the buffer or something like that (1 second the trigger will "pop out" and finish taking the data from the buffer after 2 seconds) the triggers are new to me, so i have some problems to understand the concept of it, thus my questions for you guys. i hope i explained myself as clear as possible, i really would like to understand what i'm doing. regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From bmaniscalco at gmail.com Thu May 28 17:30:17 2015 From: bmaniscalco at gmail.com (Brian Maniscalco) Date: Thu, 28 May 2015 11:30:17 -0400 Subject: [FieldTrip] Inverse warping vs interpolating & normalizing for across-subject source space analysis Message-ID: When it comes to conducting across-subject analysis on source space data, I've seen two approaches described on the Field Trip web site and mailing list. 1) for each subject, interpolate the source space data onto the subject's brain anatomy and then normalize the result to a standard template before conducting across-subject analysis 2) for each subject, perform an inverse warp to a template as described in the following link, which then allows across-subject analysis without having to interpolate and normalize http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space I have seen approach (2) recommended for Field Trip users but I have not been able to find an in depth discussion of the pros and cons of doing (1) vs (2). I gather that (2) is computationally simpler and may save computation time. But aside from computational considerations, is there any theoretical or statistical benefit to using approach (2) over approach (1) or vice versa? thanks, Brian -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Fri May 29 11:59:33 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Fri, 29 May 2015 09:59:33 +0000 Subject: [FieldTrip] using triggers building my own function In-Reply-To: References: Message-ID: Hi Moran, It was a bit difficult to understand your question, but I've tried to answer them below. For your main question: Yes, it is possible to cut up your EEG data into individual trials, with the time (i.e. 1 second) that you specify. The function that cuts up your EEG data is known as ft_definetrial. However, ft_definetrial needs to read information from another function that explicitly tells it how to do the cutting. Usually, that function is "ft_trialfun_general" (this is the tutorial link you mentioned). However, if you have a complicated set of triggers or ways you want to cut up your data, you will be better off writing your own trialfun (" trial function"). If you need to write your trialfun, you should check out these example scripts / tutorials: http://www.fieldtriptoolbox.org/example/making_your_own_trialfun_for_conditional_trial_definitionhttp://www.fieldtriptoolbox.org/example/making_your_own_trialfun_for_conditional_trial_definition http://www.fieldtriptoolbox.org/tutorial/eeg_preprocessing_erphttp://www.fieldtriptoolbox.org/tutorial/eeg_preprocessing_erp To answer your " little " questions 1. cfg.trialdef.eventvalue = [3 5 9]; 3 5 9 are trigger codes. This tells your function to go into your data, look for these trigger codes, and cut your data with respect to the location of these triggers E.g., your data trigger codes look like this ----1 ----- 3 ------ 4 ------5 ----- 9 ----. In this case, the ft_definetrial will only use triggers 3, 5, and 9 as relative points for cutting your data, trigger 1 and 4 will be ignored. N.B. The data at trigger 1 might end up in your time window that contains trigger 3 if you define your time window to be very. To understand this, see below. 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; These 2 parameters are important. The values are defined in seconds. So cfg.trialdef.prestim refers to 1s before your trigger (i.e. prestim = prestimulus onset, where stimulus onset is referred to the sample point of your chosen trigger). cfg.trialdef.poststim refers to 2s after your trigger. In this way you would end up with a 3 second time window (1 second before trigger, and 2 seconds after). You mentioned you wanted " specific time [in data] + one second". So you 1) determine which triggers mark the " specific time [in your data]" 2) specify cfg.trialdef.poststim = 1. Hope this helps and good luck, Nietzsche ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of moran abilea [mor2451 at gmail.com] Sent: 28 May 2015 16:56 To: FieldTrip discussion list Subject: [FieldTrip] using triggers building my own function hi everyone, so i'm trying to create my own function for using triggers with EEG raw data. i used this tutorial: http://www.fieldtriptoolbox.org/tutorial/preprocessing my question is if i can somehow specify the time i want to record my EEG data? for example i would like my function to get 'time' as parameter to the function and returns the EEG raw data of this specific time+one second. if so, can some one give me a piece of code for example to understand what to do? also 2 more little questions: 1. cfg.trialdef.eventvalue = [3 5 9]; what does the 3 5 9 stands for? i don't understand what is the meaning of those (or any other) numbers. can i get definition for what is event value? 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; does it means it takes exactly one second for the buffer to give me the EEG raw data? or does it means wait one second and then take the data from the buffer or something like that (1 second the trigger will "pop out" and finish taking the data from the buffer after 2 seconds) the triggers are new to me, so i have some problems to understand the concept of it, thus my questions for you guys. i hope i explained myself as clear as possible, i really would like to understand what i'm doing. regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun May 31 22:16:45 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 31 May 2015 22:16:45 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found In-Reply-To: References: Message-ID: <82B38BFA-DF5F-4364-B7A5-7D1D754A75F7@donders.ru.nl> Hi Paul, I suppose it is an incompatibility between your particular BDF file and the code. I suggest you use MATLAB debugging facilities to check what is wrong in the lower-level code. See http://tinyurl.com/oy7b496. best regards, Robert On 25 May 2015, at 15:51, Paul Zerr wrote: > I have not. I can read in the header but that's about it. > I don't have any older matlab versions here to test it with either. > > From what I understand ft_preprocessing should be capable of reading bdf's directly with only the file name as input arg. > > Greetings, > Paul Zerr > > > From: > To: FieldTrip discussion list > Subject: Re: [FieldTrip] biosemi bdf >> read_24bit error + no events > found > Message-ID: <5560dddf.0b91340a.2dab.ffffdae5 at mx.google.com> > Content-Type: text/plain; charset="utf-8" > > Have you resolved this issue? > > > From: Paul Zerr > Sent: ?Thursday?, ?May? ?14?, ?2015 ?8?:?01? ?AM > To: FieldTrip discussion list > > > Hi all, > > I'm new to fieldtrip so forgive me if my mistake is obvious. > I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with > > cfg = []; > cfg.dataset = '2.bdf'; > data = ft_preprocessing(cfg) > > However, I get > > reading and preprocessing > error opening file: 2.bdf > One or more output arguments not assigned during call to "read_24bit". > > Error in read_biosemi_bdf>readLowLevel (line 274) > buf = read_24bit(filename, offset, numwords); > > Error in read_biosemi_bdf (line 242) > buf = readLowLevel(filename, offset, epochlength); % see below in subfunction > > Error in ft_read_data (line 321) > dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); > > Error in ft_preprocessing (line 578) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, > 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) > > Error in Untitled (line 19) > data = ft_preprocessing(cfg) > > Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). > > Defining only one channel to preprocess gives the same error. > > I couldn't find a solution in the archives, the faq, wiki or documentation. > > I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. > > Any ideas? > > Much appreciated, > > Paul Zerr > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun May 31 22:18:38 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 31 May 2015 22:18:38 +0200 Subject: [FieldTrip] Research Scientist Position at University of Washington References: Message-ID: Please see the message below on behalf of Chris Bishop. Begin forwarded message: > We are looking for qualified applicants for a Senior Research Scientist position at the University of Washington. Applicants will need to have a background in EEG and MATLAB. > > The requisition number is 120420. Full description and application details can be found at the link below. > > https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szCategory=jobprofile&szOrderID=120420&szCandidateID=0&szSearchWords=&szReturnToSearch=1 > > Thank you > -Chris Bishop -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri May 1 09:44:26 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 1 May 2015 09:44:26 +0200 Subject: [FieldTrip] postdoc position at NatMEG: Alzheimer's disease diagnostics and treatment evaluation with MEG Message-ID: Post doc, Stockholm, Sweden The position as postdoctoral researcher at NatMEG Applications are invited for a postdoctoral position in MEG within a project aiming at new diagnostics and (evaluation of) treatment for the neuropathological conditions Alzheimer´s disease (AD), Parkinson´s disease (PD) and related prodromal and at-risk stages of these conditions. The position is for 2 years, with the possibility of extension for a maximum of another 2 years. Duties The successful candidate will use MEG during emotion/cognition tasks, activation (motor), stimulation (visual, auditory, somatosensory, olfactory) and resting state protocols to explore functional connectivity measures for characterizing individuals with AD and PD, and for detecting individuals at risk of developing either of these conditions. The successful candidate will also work with methods for evaluating treatment effects within AD, PD and related prodromal cohorts. NatMEG –The National Facility for Magnetoencephalography (MEG) As of September 2013, Karolinska Institutet hosts a superbly equipped MEG lab. The lab, NatMEG, is a national facility, open for researchers from all across Sweden. The fact that NatMEG is a national facility is reflected by the wide array of projects currently ongoing/under initiation at NatMEG, covering areas such as next-generation SQUIDS, computational modelling, epilepsy work-ups, and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson’s and Alzheimer’s disease, and more. The latest equipment installations, entailing microneurography and next-generation high-Tc SQUIDS, makes NatMEG very uniquely equipped. NatMEG offers an open and friendly working environment, in the middle of Karolinska Institutet campus, Stockholm. Please visit http://natmeg.se for more information. Entry requirements A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. It is required that a candidate: A. Has extensive MEG hands-on experience (preferably on an Elekta Neuromag TRIUX or Vectorview system), from MEG data collection, including setting up experiments and peripheral stimulators. B. Has strong skills and expertise in MEG analysis (preferably in at least FieldTrip and/or MNE). C. Has a background and research interest within the cognitive neuroscience domain. D. Is independent, professional, and service minded, and enjoys interacting with researchers and research subjects. E. Masters academic English. It is also highly valued if a candidate: F. Has experience and/or expertise regarding Alzheimer’s disease. G. Has experience and/or expertise regarding Parkinson’s disease. H. Has an expertise in / experience with psychophysiology (e.g. EMG, facial EMG, GSR, HR, respiration) measurements and analysis. H. Karolinska Institutet Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 percent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. See http://ki.se/en/ for more information. The Department of Clinical Neuroscience The Department of Clinical Neuroscience (CNS) conducts research and education in the field of neuroscience from the molecular level to the society level. The clinical research and education is conducted in collaboration with other research groups from the Karolinska Institutet, with other universities as well as the Stockholm County Council. Please visit our website for more information: http://ki.se/en/cns Application process Read more about the application process at https://ki.mynetworkglobal.com/en/what:job/jobID:63833/. Applications are to be submitted in the recruitment system MyNetwork. Application deadline 2015-05-24 Contact information Daniel Lundqvist, Head of Unit daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Fri May 1 09:44:29 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Fri, 1 May 2015 09:44:29 +0200 Subject: [FieldTrip] postdoc position at NatMEG: combined MEG and microneurography Message-ID: <2F1892F1-A625-4919-AB37-43AE8C571093@donders.ru.nl> Post doc, Stockholm, Sweden The position as postdoctoral researcher at NatMEG Applications are invited for a postdoctoral position within two unique and overlapping projects at NatMEG: 1. combined MEG and microneurography (recording and stimulation inside peripheral nerve fibres) measurements, and 2. benchmarking of next-generation high-Tc SQUIDS (head-adjustable, nitrogen-cooled MEG sensors with millimetre sensor-to-scalp-proximity) against today’s state of the art MEG system (Elekta Triux). The position is for a maximum of 4 years. Duties The successful candidate will explore: 1. the (1a) physiology of touch and the (1b) autonomic nervous system by means of combined MEG and microneurography recordings. 2. the spatiotemporal precision and MEG signal characteristics of focal High-TC SQUIDS, benchmarked against the present (a conventional helium-cooled) MEG system for application such as (2a) sensory stimulation (visual, auditory, somatosensory, olfactory) and clinical applications such as (2b) interictal epileptogenic spike detection and (2c) functional mapping. NatMEG –The National Facility for Magnetoencephalography (MEG) As of September 2013, Karolinska Institutet hosts a superbly equipped MEG lab. The lab, NatMEG, is a national facility, open for researchers from all across Sweden. The fact that NatMEG is a national facility is reflected by the wide array of projects currently ongoing/under initiation at NatMEG, covering areas such as next-generation SQUIDS, computational modelling, epilepsy work-ups, and cognitive neuroscience in the areas of memory, language, attention, perception, pain, music, decision making, emotion, autism, schizophrenia, Parkinson’s and Alzheimer’s disease, and more. The latest equipment installations, entailing microneurography and next-generation high-Tc SQUIDS, makes NatMEG very uniquely equipped. NatMEG offers an open and friendly working environment, in the middle of Karolinska Institutet campus, Stockholm. Please visit http://natmeg.se for more information. Entry requirements A person is eligible for a position as postdoctoral research fellow if he or she has obtained a PhD no more than seven years before the last date of employment as postdoc. It is required that a candidate: A. Has a background and research interest within the cognitive neuroscience domain. B. Has extensive MEG hands-on experience (preferably on an Elekta Neuromag TRIUX or Vectorview system), from MEG data collection, including setting up experiments and peripheral stimulators. C. Has very strong skills and expertise in MEG analysis (preferably in at least FieldTrip and/or MNE). D. Is independent, professional, and service minded, and enjoys interacting with researchers and research subjects. E. Masters academic English. It is also highly valued if a candidate: F. Has an expertise in the primary sensory system in one or several sensory modalities. G. Has an expertise in / experience from high-Tc SQUIDS. H. Has an expertise in / experience from microneurography measurements and analysis. I. Has an expertise in / experience with psychophysiology (e.g. EMG, facial EMG, GSR, HR, respiration) measurements and analysis. I. Karolinska Institutet Karolinska Institutet is one of the world´s leading medical universities. Its mission is to contribute to the improvement of human health through research and education. Karolinska Institutet accounts for over 40 percent of the medical academic research conducted in Sweden and offers the country´s broadest range of education in medicine and health sciences. Since 1901 the Nobel Assembly at Karolinska Institutet has selected the Nobel laureates in Physiology or Medicine. See http://ki.se/en/ for more information. The Department of Clinical Neuroscience The Department of Clinical Neuroscience (CNS) conducts research and education in the field of neuroscience from the molecular level to the society level. The clinical research and education is conducted in collaboration with other research groups from the Karolinska Institutet, with other universities as well as the Stockholm County Council. Please visit our website for more information: http://ki.se/en/cns Application process Read more about the application process at https://ki.mynetworkglobal.com/what:job/jobID:63834/. Applications are to be submitted in the recruitment system MyNetwork. Application deadline 2015-05-24 Contact information Daniel Lundqvist, Head of Unit daniel.lundqvist at ki.se -------------- next part -------------- An HTML attachment was scrubbed... URL: From elam4hcp at gmail.com Fri May 1 20:29:09 2015 From: elam4hcp at gmail.com (Jennifer Elam) Date: Fri, 1 May 2015 13:29:09 -0500 Subject: [FieldTrip] Still time to register for the 2015 HCP Course! Message-ID: A reminder that it’s not too late to register for the 2015 HCP Course: “Exploring the Human Connectome” , to be held June 8-12, 2015 at the Marriott Resort Waikiki Beach, in Honolulu, Hawaii, USA. Also, a reminder that you might try http://www.vrbo.com/ or https://www.airbnb.com/ for affordable accommodations in the Waikiki Beach area, near the Marriott. This 5-day intensive course is designed for investigators who are interested in: - using data being collected and distributed by HCP - acquiring and analyzing HCP-style imaging and behavioral data at your own institution - processing your own non-HCP data using HCP pipelines and methods - learning to use Connectome Workbench tools and the CIFTI connectivity data format - learning HCP multi-modal neuroimaging analysis methods, including those that combine MEG and MRI data - positioning yourself to capitalize on HCP-style data from forthcoming large-scale projects (e.g., Lifespan HCP and Connectomes Related to Human Disease) Visit the HCP Course website to register and for Faculty listings and the full schedule of covered topics. We hope to see you in Hawaii! Best, 2015 HCP Course Organizers -------------- next part -------------- An HTML attachment was scrubbed... URL: From haristz at umn.edu Fri May 1 21:58:02 2015 From: haristz at umn.edu (Haris Tzagarakis) Date: Fri, 1 May 2015 14:58:02 -0500 Subject: [FieldTrip] Problems using fieldtrip with Matlab Distributed Computing Server Message-ID: Hi There, I have been trying to use fieldrtip in conjunction with Matlab Distributed Computing Server on a supercomputing resource and have been running into a problem that seems to come from paths/global variables? in detail: I use fieldtrip in conjunction with my own code for an analysis. The analysis works fine on a "normal"/non-parallel call. I then set out to parallelize the code and split the analysis to a different node for every subject I have. I have access to a supercomputing cluster (not uniquely for matlab/biomed use), which runs Matlab Distributed Computing Server, so job scheduling etc can happen from within matlab. I believe this is different from the 'peer distributed' approach described in the faq. I prepared a script which is then run with the matlab 'batch' command : job = batch('parscript3b', 'Profile', 'Itasca_MSI', 'Pool', 10); I attach the script in its current form here. This call should pass the script to a top level node that then distributes the loop in 10 nodes, one for each subject. What always happens however is that I get an error at the top level node saying: Error using ft_hastoolbox (line 469) the FREESURFER toolbox is not installed, see http://surfer.nmr.mgh.harvard.edu/fswiki I have read the help/comments text and some of the code in ft_hastoolbox and ft_defaults (I in fact always call ft_defaults at startup - my startup file is also attached here). This in conjunction with what is mentioned in MATLAB help makes me think that there is something about the way paths and global variables are handled by MDCS that does not agree with Fieldtrip. I have been trying to go around the problem by liberally using ft_defaults in my script code (as can be seen) and I also added some lines to the ft_hastoolbox function (in all its 4 instances in the private folders) to check explicitly for the fieldtrip locations in my system but none of this has worked. I would be grateful for any insight you might have. With Thanks and Best Wishes, Haris -- Charidimos [Haris] Tzagarakis MD, PhD, MRCPsych Senior Research Associate University of Minnesota Dept of Neuroscience office: Brain Sciences Center Minneapolis VA Medical Center Tel:612-467-1363 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: parscript3b.m Type: text/x-csrc Size: 679 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: startup_current.m Type: text/x-csrc Size: 552 bytes Desc: not available URL: From e.maris at donders.ru.nl Mon May 4 17:42:17 2015 From: e.maris at donders.ru.nl (Maris, E.G.G. (Eric)) Date: Mon, 4 May 2015 15:42:17 +0000 Subject: [FieldTrip] symposium on model-based and model-inspired analysis of electrophysiological data Message-ID: <30e5b4c636464fafb45f7de18ae20de5@EXPRD03.hosting.ru.nl> Dear colleague, On June 1, I will organise a symposium on model-based and model-inspired analysis of electrophysiological data, to which I would like to invite you and your colleagues. You can find the program and additional information in the attachment. Please send around this invitation to everyone who might profit from this symposium. About a week before the symposium, I will send around directions on how the get here. best, Eric Maris -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2015-06-01.Model-based and Model-inspired Analysis of Electrophysiological Data.pdf Type: application/pdf Size: 27061 bytes Desc: 2015-06-01.Model-based and Model-inspired Analysis of Electrophysiological Data.pdf URL: From mark.woolrich at ohba.ox.ac.uk Tue May 5 13:14:50 2015 From: mark.woolrich at ohba.ox.ac.uk (Mark Woolrich) Date: Tue, 5 May 2015 11:14:50 +0000 Subject: [FieldTrip] Research postdoc positions in neuroimage analysis and computational neuroscience. Message-ID: <0229ABEF-5744-43AD-8130-CC2567B50AD5@ohba.ox.ac.uk> Applications are invited for two postdoctoral scientists to work on a Wellcome Trust funded project to advance understanding of spontaneous whole-brain activity. The project will use a combination of MRI, M/EEG / LFP recordings, methods development and biophysical modeling to advance understanding of spontaneous whole-brain activity, and provide new insights into the underlying mechanisms. This research will be conducted within the OHBA Analysis Group headed by Mark Woolrich and based at the Oxford Centre for Human Brain Activity (http://www.ohba.ox.ac.uk), and will be in collaboration with colleagues at FMRIB (http://www.fmrib.ox.ac.uk/analysis) and the Centre for Neural Circuits and Behaviour (http://www.cncb.ox.ac.uk). We are looking for excellent researchers with a strong technical background, ideally in computational neuroscience and/or in developing neuroimaging analysis methods, but also with experience in other areas of Engineering/Applied Mathematics, Statistics, Computer Science and Physics (e.g. Machine Learning and Pattern Recognition). Post in Neuroimaging Analysis https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=117895 Post in computational biophysical model development https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_version_4.jobspec?p_id=118123 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cmuehl at gmail.com Tue May 5 17:20:32 2015 From: cmuehl at gmail.com (Christian Muehl) Date: Tue, 5 May 2015 15:20:32 +0000 Subject: [FieldTrip] 2nd Call for Papers - 4th Workshop on Affective Brain-Computer Interfaces @ ACII2015 Message-ID: ** 2nd Call for Papers ** 4th Workshop on Affective Brain-Computer Interfaces (aBCI) Workshop at ACII 2015 (September 21-24), Xi'an, China, September 21, 2015 http://www.affective-sciences.org/aBCI2015 http://www.acii2015.org/ The goal of the aBCI workshop series is to connect researchers from the communities of affective computing, social signal processing, brain-computer interfacing, neuro-ergonomics, and neuroscience around the federating theme of affective brain computer interfaces (aBCI). Affective BCI aim at the development of human-computer interfaces able to react and adapt to users' emotions and related cognitive states as measured from neurophysiological signals. Besides the general solicitation of work toward adaptive HCI applications based on aBCI, this 4th edition of the workshop will focus on two specific aspects of aBCI. Firstly, we welcome papers on ways to alleviate current aBCI limitations, through work on the physiological basis of aBCI, innovative applications resilient to classification error, and methods to increase the robustness of aBCI. Secondly, we would like to explore the social aspects and applications of aBCI by welcoming submissions on topics such as multi-user aBCI and the assessment of social processes from brain signals. The workshop topics include, but are not limited to, * effective emotion elicitation and data collection in social settings; * identification of robust and specific markers of emotional, cognitive and social processes; * methods for the assessment of emotions, cognitive states and social interactions; * methods to measure and process multiple people physiological activity; * applications of central and peripheral signal processing to social situations; * innovative concepts for adaptive interfaces and affective BCI; * demos of affective BCI systems. Submission Instructions: * The papers should feature original empirical work, theoretical work, or a well defendable but arguable position of the authors. * Papers will be published electronically in the proceedings of ACII 2015 by IEEE Xplore. Papers should be limited to 6 pages+1page references. The review is double blind - please remove all author information from the manuscripts. * Further details about the submission instructions and format can be found on the website of ACII 2015. Important Dates: June 5, 2015: Submission of manuscripts July 3, 2015: Acceptance/Rejection notification July 24, 2015: Submission of camera-ready papers September 21, 2015: Date of the Workshop For further information, see our website or contact abci at ewi.utwente.nl Programme Chairs: * Fabien Lotte, Inria Bordeaux Sud-Ouest, Talance, France * Guillaume Chanel, Swiss Center for Affective Sciences, Geneva, Switzerland * Christian Mühl, German Aerospace Center, Cologne, Germany * Anton Nijholt, Universiteit Twente, the Netherlands Programme Committee: Egon L. van den Broek, University of Utrecht, the Netherlands Anne-Marie Brouwer, TNO Perceptual and Cognitive Systems, Soesterberg, the Netherlands Stephen Dunne, Starlab Barcelona, Spain Touradj Ebrahimi, École polytechnique fédérale de Lausanne, Switzerland Stephen Fairclough, John Moores University, Liverpool, UK Tiago H. Falk, Institut National de la Recherche Scientifique (INRS), Montreal, Canada Hayrettin Gürkök, University of Twente, Enschede, the Netherlands Dominic Heger, Karlsruhe Institute of Technology, Germany Klas Ihme, German Aerospace Center, Brunswick, Germany Jonghwa Kim, University of Augsburg, Germany Brent Lance, Army Research Laboratory/TNB, Aberdeen Proving Ground, USA, Grace Leslie, MIT Media Lab, Boston, USA Giulia Liberati, Université catholique de Louvain, Belgium Gary Garcia Molina, Philips Research North America, Briarcliff, USA Scott Makeig, University of California San Diego, USA Tim Mullen, University of California San Diego, USA Domen Novak, University of Wyoming, Laramie, USA Ioannis Patras, Queen Mary University, London, UK Evan Peck, Bucknell University, Lewisburg, USA Mannes Poel, University of Twente, Enschede, the Netherlands Alan Pope, NASA Langley Research Center, Norfolk, USA Thierry Pun, University of Geneva, Switzerland Erin Solovey, Drexel University, Philadelphia, USA Mohammad Soleymani, University of Geneva, Switzerland Aureli Soria-Frisch, Starlab Barcelona, Spain Olga Sourina, NanYang Technological University, Singapore Aleksander Valjamae, Linköping University, Sweden Jan van Erp, University of Twente, Enschede, the Netherlands Chi Thanh Vi, University of Bristol, UK Thorsten Zander, Technische Universität Berlin, Germany From hamzaf at sabanciuniv.edu Tue May 5 18:40:23 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Tue, 5 May 2015 18:40:23 +0200 Subject: [FieldTrip] brick0 Message-ID: Hello, While trying to plot all tissues in one image using ft_sourceplot function as in seg_i = ft_datatype_segmentation(segmentedmri,'segmentationstyle','indexed'); cfg = []; cfg.funparameter = 'seg'; cfg.funcolormap = lines(6); % distinct color per tissue cfg.location = 'center'; cfg.atlas = seg_i; % the segmentation can also be used as atlas ft_sourceplot(cfg, seg_i); I faced the following error: Reference to non-existent field 'brick0' This brick0 is defined in atlas_lookup.m as brick0_val = atlas.brick0(ijk(1), ijk(2), ijk(3)); But the atlas variable that is called for this function is defined as: dim: [256 256 256] transform: [4x4 double] coordsys: 'ctf' unit: 'mm' cfg: [1x1 struct] seg: [256x256x256 double] seglabel: {'gray' 'white' 'csf' 'skull' 'scalp'} I wonder from where this brick0 come? Thanks for help -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Wed May 6 00:01:40 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Tue, 5 May 2015 23:01:40 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy Message-ID: <55493DC4.90601@glasgow.ac.uk> An HTML attachment was scrubbed... URL: From nadine.dijkstra92 at gmail.com Wed May 6 14:20:58 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Wed, 6 May 2015 14:20:58 +0200 Subject: [FieldTrip] labels per grid point Message-ID: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Dear Fieldtrip Users, I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? Thanks in advance for your help, Nadine From tzvetan.popov at uni-konstanz.de Wed May 6 14:37:56 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 6 May 2015 14:37:56 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: Hi Nadine, maybe this is what you need? http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations best tzvetan > Dear Fieldtrip Users, > > I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? > > Thanks in advance for your help, > Nadine > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 14:43:08 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 14:43:08 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: <018c01d087fa$34fa3150$9eee93f0$@artinis.com> Hi Nadine, does the second exercise in this section help (i.e. defining a lookup atlas for source plotting): http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_source s_of_oscillatory_gamma-band_activity ? Best, Jörn -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Nadine > Sent: Wednesday, May 6, 2015 2:21 PM > To: fieldtrip at science.ru.nl > Subject: [FieldTrip] labels per grid point > > Dear Fieldtrip Users, > > I am trying to get anatomical labels for individual source grid points. I can only > find how to parcellate the grid points to get an averaged value of sources for > certain parcellations (e.g. Brodmann areas). But I would like to get an > anatomical label per grid point, so that I can see which grid points belong to > which area. Does anybody have any solution for this? > > Thanks in advance for your help, > Nadine > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 14:49:32 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 14:49:32 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <018c01d087fa$34fa3150$9eee93f0$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> Message-ID: <018f01d087fb$19d25460$4d76fd20$@artinis.com> the correct link is: http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_source s_of_oscillatory_gamma-band_activity not sure why there was a line break introduced... -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > Sent: Wednesday, May 6, 2015 2:43 PM > To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] labels per grid point > > Hi Nadine, > > does the second exercise in this section help (i.e. defining a lookup atlas for > source plotting): > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > ource > s_of_oscillatory_gamma-band_activity > ? > > Best, > Jörn > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems  |  +31 481 350 980 > > > -----Original Message----- > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > bounces at science.ru.nl] On Behalf Of Nadine > > Sent: Wednesday, May 6, 2015 2:21 PM > > To: fieldtrip at science.ru.nl > > Subject: [FieldTrip] labels per grid point > > > > Dear Fieldtrip Users, > > > > I am trying to get anatomical labels for individual source grid > > points. I > can only > > find how to parcellate the grid points to get an averaged value of > > sources > for > > certain parcellations (e.g. Brodmann areas). But I would like to get > > an anatomical label per grid point, so that I can see which grid > > points > belong to > > which area. Does anybody have any solution for this? > > > > Thanks in advance for your help, > > Nadine > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jorn at artinis.com Wed May 6 15:07:24 2015 From: jorn at artinis.com (=?iso-8859-1?Q?J=F6rn_M._Horschig?=) Date: Wed, 6 May 2015 15:07:24 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <018f01d087fb$19d25460$4d76fd20$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> <018f01d087fb$19d25460$4d76fd20$@artinis.com> Message-ID: <019001d087fd$98c7f020$ca57d060$@artinis.com> haha ok, I give up, the link still appears to be broken - please copy the link together yourself or click on 'Plotting sources of oscillatory gamma-band activity' on the navigation tab to the left and look for the second exercise in that section. -- Jörn M. Horschig, Software Engineer Artinis Medical Systems  |  +31 481 350 980 > -----Original Message----- > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > Sent: Wednesday, May 6, 2015 2:50 PM > To: 'FieldTrip discussion list' > Subject: Re: [FieldTrip] labels per grid point > > the correct link is: > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > ource > s_of_oscillatory_gamma-band_activity > not sure why there was a line break introduced... > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems  |  +31 481 350 980 > > > -----Original Message----- > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > bounces at science.ru.nl] On Behalf Of Jörn M. Horschig > > Sent: Wednesday, May 6, 2015 2:43 PM > > To: 'FieldTrip discussion list' > > Subject: Re: [FieldTrip] labels per grid point > > > > Hi Nadine, > > > > does the second exercise in this section help (i.e. defining a lookup > atlas for > > source plotting): > > > http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ > > s > > ource > > s_of_oscillatory_gamma-band_activity > > ? > > > > Best, > > Jörn > > > > > > -- > > > > Jörn M. Horschig, Software Engineer > > Artinis Medical Systems  |  +31 481 350 980 > > > > > -----Original Message----- > > > From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > > > bounces at science.ru.nl] On Behalf Of Nadine > > > Sent: Wednesday, May 6, 2015 2:21 PM > > > To: fieldtrip at science.ru.nl > > > Subject: [FieldTrip] labels per grid point > > > > > > Dear Fieldtrip Users, > > > > > > I am trying to get anatomical labels for individual source grid > > > points. I > > can only > > > find how to parcellate the grid points to get an averaged value of > > > sources > > for > > > certain parcellations (e.g. Brodmann areas). But I would like to get > > > an anatomical label per grid point, so that I can see which grid > > > points > > belong to > > > which area. Does anybody have any solution for this? > > > > > > Thanks in advance for your help, > > > Nadine > > > > > > _______________________________________________ > > > fieldtrip mailing list > > > fieldtrip at donders.ru.nl > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nadine.dijkstra92 at gmail.com Wed May 6 15:51:59 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Wed, 6 May 2015 15:51:59 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: <019001d087fd$98c7f020$ca57d060$@artinis.com> References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> <018c01d087fa$34fa3150$9eee93f0$@artinis.com> <018f01d087fb$19d25460$4d76fd20$@artinis.com> <019001d087fd$98c7f020$ca57d060$@artinis.com> Message-ID: Thanks, the link works fine for me! I am not sure if this solves the problem however, because it only gives the labels for some points in the plot, while I want to have the label for every individual grid point in a list so that I can see which grid points belong to the same area etc. However, this might be a good place to start. Thanks anyway! Best, Nadine On 06 May 2015, at 15:07, Jörn M. Horschig wrote: > haha ok, I give up, the link still appears to be broken - please copy the > link together yourself or click on 'Plotting sources of oscillatory > gamma-band activity' on the navigation tab to the left and look for the > second exercise in that section. > > > -- > > Jörn M. Horschig, Software Engineer > Artinis Medical Systems | +31 481 350 980 > >> -----Original Message----- >> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >> bounces at science.ru.nl] On Behalf Of Jörn M. Horschig >> Sent: Wednesday, May 6, 2015 2:50 PM >> To: 'FieldTrip discussion list' >> Subject: Re: [FieldTrip] labels per grid point >> >> the correct link is: >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s >> ource >> s_of_oscillatory_gamma-band_activity >> not sure why there was a line break introduced... >> >> >> -- >> >> Jörn M. Horschig, Software Engineer >> Artinis Medical Systems | +31 481 350 980 >> >>> -----Original Message----- >>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >>> bounces at science.ru.nl] On Behalf Of Jörn M. Horschig >>> Sent: Wednesday, May 6, 2015 2:43 PM >>> To: 'FieldTrip discussion list' >>> Subject: Re: [FieldTrip] labels per grid point >>> >>> Hi Nadine, >>> >>> does the second exercise in this section help (i.e. defining a lookup >> atlas for >>> source plotting): >>> >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ >>> s >>> ource >>> s_of_oscillatory_gamma-band_activity >>> ? >>> >>> Best, >>> Jörn >>> >>> >>> -- >>> >>> Jörn M. Horschig, Software Engineer >>> Artinis Medical Systems | +31 481 350 980 >>> >>>> -----Original Message----- >>>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- >>>> bounces at science.ru.nl] On Behalf Of Nadine >>>> Sent: Wednesday, May 6, 2015 2:21 PM >>>> To: fieldtrip at science.ru.nl >>>> Subject: [FieldTrip] labels per grid point >>>> >>>> Dear Fieldtrip Users, >>>> >>>> I am trying to get anatomical labels for individual source grid >>>> points. I >>> can only >>>> find how to parcellate the grid points to get an averaged value of >>>> sources >>> for >>>> certain parcellations (e.g. Brodmann areas). But I would like to get >>>> an anatomical label per grid point, so that I can see which grid >>>> points >>> belong to >>>> which area. Does anybody have any solution for this? >>>> >>>> Thanks in advance for your help, >>>> Nadine >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From nadine.dijkstra92 at gmail.com Thu May 7 09:36:34 2015 From: nadine.dijkstra92 at gmail.com (Nadine) Date: Thu, 7 May 2015 09:36:34 +0200 Subject: [FieldTrip] labels per grid point In-Reply-To: References: <93C40CA3-0C1A-48C2-A695-C37A6BDD7726@gmail.com> Message-ID: <306CCF9F-01AC-4036-8B14-C4FFC99AA54E@gmail.com> Hi Tzvetan, Yes, thank you, this is perfect! Best, Nadine On 06 May 2015, at 14:37, Tzvetan Popov wrote: > Hi Nadine, > > maybe this is what you need? > http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations > > best > tzvetan > >> Dear Fieldtrip Users, >> >> I am trying to get anatomical labels for individual source grid points. I can only find how to parcellate the grid points to get an averaged value of sources for certain parcellations (e.g. Brodmann areas). But I would like to get an anatomical label per grid point, so that I can see which grid points belong to which area. Does anybody have any solution for this? >> >> Thanks in advance for your help, >> Nadine >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip From guiraudh at gmail.com Thu May 7 10:21:19 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Thu, 7 May 2015 10:21:19 +0200 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi Till and John, Thank you, this is perfect! Best regards, Hélène 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > We have a template for children‹actually have for infants from 2 weeks > through adults at 89 years. We also have average electrode positions for > EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented > priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have > been using this recently with FT for infants and child/adolescent/adult > ages. > > WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > Fro www site: This is a database of average MRIs and associated MRI > volumes for developmental MRI work. It consists of average MRI templates, > segmented partial volume estimate volumes for GM, WM, T2W-derived CSF > (Description > > > ). The database is separated into head-based and brain-based averages. The > data are separated by ages in months, years, 6-month, or 5-year intervals > (Ages and Templates > < > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm > l>). The templates are grouped into first year (2 weeks through 12 > months), early childhood (15 months through 4 years), childhood (4 years > through 10 years), adolescence (10.5 years through 17.5 years) and adults > (18 years through 89 years). > Tools for cortical source analysis of EEG and ERP are provided. These > tools are based on the average MRI templates, segmenting, and atlases. > > Also see my www site, jerlab.psych.sc.edu for publications describing > this. We have a recent chapter that has a good description of the issues > behind the database (with Wanze Xie). We have a paper accepted at > Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, > Michelle Phillips-Meek, and Wanze Xie). > > John > > > *********************************************** > John E. Richards Carolina Distinguished Professor > Department of Psychology > University of South Carolina > Columbia, SC 29208 > Dept Phone: 803 777 2079 > Fax: 803 777 9558 > Email: richards-john at sc.edu > HTTP: jerlab.psych.sc.edu > *********************************************** > > > > > > > > > On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" > wrote: > > >Send fieldtrip mailing list submissions to > > fieldtrip at science.ru.nl > > > >To subscribe or unsubscribe via the World Wide Web, visit > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >or, via email, send a message with subject or body 'help' to > > fieldtrip-request at science.ru.nl > > > >You can reach the person managing the list at > > fieldtrip-owner at science.ru.nl > > > >When replying, please edit your Subject line so it is more specific > >than "Re: Contents of fieldtrip digest..." > > > > > >Today's Topics: > > > > 1. Search for a template children. (H?l?ne Guiraud) > > 2. Re: Search for a template children. (Till Schneider) > > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > > > > >---------------------------------------------------------------------- > > > >Message: 1 > >Date: Wed, 29 Apr 2015 14:45:56 +0200 > >From: H?l?ne Guiraud > >To: fieldtrip at science.ru.nl > >Subject: [FieldTrip] Search for a template children. > >Message-ID: > > < > CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> > >Content-Type: text/plain; charset="utf-8" > > > >Dear community, > > > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on > >speech perception in children using MEG. > >The children involved in the study don't pass MRI. We want to achieve > >source reconstruction from a template. However I can't find a template > >corresponding to the anatomy of a child (8-12 years). > >Can someone tell me if there are template children and where I can find > >them? > > > >Best, > > > >H?l?ne Guiraud > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e > >9b53e/attachment-0001.html> > > > >------------------------------ > > > >Message: 2 > >Date: Wed, 29 Apr 2015 15:53:13 +0200 > >From: Till Schneider > >To: FieldTrip discussion list > >Subject: Re: [FieldTrip] Search for a template children. > >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> > >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > > >Dear Helene, > > > >McGill University provides MNI brains for different age groups between > >4.5y to 18y. > >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 > >You will probably find the template brain you are searching for in this > >database. > > > >Best regards, > >Till > > > >-- > > > >Till Schneider, PhD > > > >Cognitive and Clinical Neurophysiology Group > >Dept. of Neurophysiology and Pathophysiology > >University Medical Center Hamburg-Eppendorf > >Martinistr. 52 > >20246 Hamburg > >Germany > > > >phone +49-40-7410-53188 > >fax +49-40-7410-57126 > >www.uke.de/neurophysiologie > > > > > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: > >> Dear community, > >> > >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) > >> on speech perception in children using MEG. > >> The children involved in the study don't pass MRI. We want to achieve > >> source reconstruction from a template. However I can't find a template > >> corresponding to the anatomy of a child (8-12 years). > >> Can someone tell me if there are template children and where I can > >> find them? > >> > >> Best, > >> > >> H?l?ne Guiraud > >> > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > >-- > > > >_____________________________________________________________________ > > > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen > >Rechts; Gerichtsstand: Hamburg | www.uke.de > >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. > >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik > >_____________________________________________________________________ > > > >SAVE PAPER - THINK BEFORE PRINTING > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e > >44937/attachment-0001.html> > > > >------------------------------ > > > >Message: 3 > >Date: Wed, 29 Apr 2015 16:25:35 +0200 > >From: Keyvan Mahjoory > >To: FieldTrip discussion list > >Subject: [FieldTrip] ICBM 152 templates in FT > >Message-ID: > > UJp6-+4+7fA at mail.gmail.com> > >Content-Type: text/plain; charset="iso-8859-1" > > > >Dear Fieldtrip Users, > > > >I perform source analysis in Fieldtrip with a template head model ( > >standard_bem ) and a > >template source model (cortex_5124.surf.gii > >) to constarin > >estimated sources on cortex. These templates are based on Colin27, But I > >prefere to use the template ICBM152 instead. > >Does FT include ICBM template? I mean templates for both head model and > >cortical surfe. > > > >Many Thanks in advance, > >Keyvan > >-------------- next part -------------- > >An HTML attachment was scrubbed... > >URL: > >< > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 > >9daf3/attachment-0001.html> > > > >------------------------------ > > > >_______________________________________________ > >fieldtrip mailing list > >fieldtrip at donders.ru.nl > >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > >End of fieldtrip Digest, Vol 53, Issue 23 > >***************************************** > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hélène Guiraud Doctorante Université Lyon 2 Laboratoire Dynamique Du Langage CNRS, UMR 5596 Tel : 04 72 72 65 34 guiraudh at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From sander at mpib-berlin.mpg.de Thu May 7 10:29:39 2015 From: sander at mpib-berlin.mpg.de (Sander, Myriam) Date: Thu, 7 May 2015 08:29:39 +0000 Subject: [FieldTrip] Vacant Predoctoral Position in Lifespan Psychology at the MPI for Human Development in Berlin, Germany Message-ID: ********************************************************* PREDOCTORAL POSITION: CENTER FOR LIFESPAN PSYCHOLOGY, MPI BERLIN The new MINERVA research group headed by Dr. Myriam Sander at the Max Planck Institute for Human Development, Center for Lifespan Psychology (Director: Prof. Dr. Ulman Lindenberger), is seeking applications for a PREDOCTORAL POSITION The doctoral contract will last for 3 years. The position is available from October 1, 2015 or later. Job Description: Future research of the new MINERVA research group (PI: Dr. Myriam Sander) will use a multi-modal imaging approach (EEG with a focus on oscillatory measures in combination with structural and functional MRI) to uncover lifespan differences in the interplay between sensory (visual and auditory) and cognitive abilities influencing memory performance. The MINERVA research group is part of the project „Cognitive and Neural Dynamics of Memory Across the Lifespan (CONMEM)” which investigates lifespan changes in the interplay between associative and strategic components of memory functioning on neural and cognitive levels, with a focus on working and episodic memory (see Sander, et al., Neurosci. Biobehav. Rev., 2012; Shing, et al., Neurosci. Biobehav. Rev., 2010). The successful predoctoral fellow will plan and conduct empirical studies in this domain, analyze the behavioral, EEG, and MRI data, and prepare scientific manuscripts for publication. For further information, please contact: Dr. Myriam Sander (sander at mpib-berlin.mpg.de) Requirements: A successful applicant needs to hold (or expect by summer 2015) a diploma/master degree in psychology, cognitive neuroscience, or related fields. Applicants should have experience with conducting experimental research, knowledge in neuroimaging methods (EEG and/or MRI), and a solid background in at least one programming language (preferably Matlab or R). In addition, the ability to work independently as well as a high proficiency of the English language is required. Experience with age-comparative studies is an advantage. The Max Planck Society is interested in increasing the number of women on its scientific staff. We strongly encourage applications from women and members of minority groups. In addition, the Max Planck Society is committed to employing more handicapped individuals and encourages them to apply. To apply, please send (as ONE FILE and via email only) a statement of research interests, a CV, a copy of relevant certificates, (p)reprints of publications, and a list of two references to Dr. Myriam Sander, MPI for Human Development, Lentzeallee 94, 14195 Berlin (sander at mpib-berlin.mpg.de) preferably by June 30th, 2015. Later applications will be considered until the position is filled. * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu May 7 11:11:54 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Thu, 7 May 2015 11:11:54 +0200 Subject: [FieldTrip] Vgrid Message-ID: Hello, I got the following error when I run these lines: (found in http://www.fieldtriptoolbox.org/development/simbio) cfg = []; cfg.shift = 0.3; cfg.method = 'hexahedral'; mesh = ft_prepare_mesh(cfg,segmentedmri); Error using vgrid (line 16) the vgrid executable is not available for your platform, it was expected to be located at ***\external\vgrid\bin\pcwin64\vgrid.exe I don't have a folder called pcwin64! I have only glnx86 (empty folder) glnxa64 and maci64 in ***\external\vgrid\bin\ I also downloaded a newer version of fieldtrip, but I did not find it! >From where I can get vgrid.exe? Thank you -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From j.vorw01 at gmail.com Thu May 7 11:40:17 2015 From: j.vorw01 at gmail.com (Johannes Vorwerk) Date: Thu, 07 May 2015 11:40:17 +0200 Subject: [FieldTrip] Vgrid In-Reply-To: References: Message-ID: <1430991617.11932.23.camel@biomag43> Hi, vgrid should no longer be needed in recent fieldtrip-versions. It was replaced by a fully matlab-based function (prepare_mesh_hexahedral), that should now also work under windows. A vgrid.exe never existed, it was only available for mac and linux. Did you try updating your fieldtrip-version to a recent release? Best, Johannes Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi Altakroury (Alumni): > Hello, > > > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was > expected to be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > > I don't have a folder called pcwin64! I have only glnx86 (empty > folder) glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > From where I can get vgrid.exe? > > > Thank you > > > > -- > > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -- Dipl.-Math. Johannes Vorwerk e-mail: j.vorwerk at uni-muenster.de Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters Institute for Biomagnetism and Biosignalanalysis, University of Muenster www: http://campus.uni-muenster.de/index.php?id=919&L=1 -------------- next part -------------- An HTML attachment was scrubbed... URL: From haiteng.jiang at gmail.com Thu May 7 12:21:40 2015 From: haiteng.jiang at gmail.com (Haiteng Jiang) Date: Thu, 7 May 2015 12:21:40 +0200 Subject: [FieldTrip] labels per grid point (Nadine) Message-ID: Hi Nadine, Following up Tzvetan's response , you get the label for every grid by doing this : clear all; clc; % read the atlas atlas = ft_read_atlas('/home/common/matlab/fieldtrip/template/atlas/aal/ROI_MNI_V4.nii'); load('standard_sourcemodel3d10mm.mat'); % mni template source model % and call ft_sourceinterpolate: cfg = []; cfg.interpmethod = 'nearest'; cfg.parameter = 'tissue'; sourcemodel2 = ft_sourceinterpolate(cfg, atlas, sourcemodel); % replace NAN with 0 ; sourcemodel2.tissue(isnan(sourcemodel2.tissue)) =0; ids =find(sourcemodel2.tissue); % all interpolate regions id =sourcemodel2.tissue(ids); % all interpolate regions index ROI =atlas.tissuelabel(id); if you want to find Occipital for instance , you just call a few more lines code : occid =find(strncmpi(ROI,'Occipital',9)); % indice OCC =ROI(occid); % label Hope this helps, Hatieng > Message: 6 > Date: Wed, 6 May 2015 15:51:59 +0200 > From: Nadine > To: FieldTrip discussion list > Subject: Re: [FieldTrip] labels per grid point > Message-ID: > Content-Type: text/plain; charset=iso-8859-1 > > Thanks, the link works fine for me! > I am not sure if this solves the problem however, because it only gives > the labels for some points in the plot, while I want to have the label for > every individual grid point in a list so that I can see which grid points > belong to the same area etc. However, this might be a good place to start. > Thanks anyway! > > Best, > Nadine > > On 06 May 2015, at 15:07, J?rn M. Horschig wrote: > > > haha ok, I give up, the link still appears to be broken - please copy the > > link together yourself or click on 'Plotting sources of oscillatory > > gamma-band activity' on the navigation tab to the left and look for the > > second exercise in that section. > > > > > > -- > > > > J?rn M. Horschig, Software Engineer > > Artinis Medical Systems | +31 481 350 980 > > > >> -----Original Message----- > >> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >> bounces at science.ru.nl] On Behalf Of J?rn M. Horschig > >> Sent: Wednesday, May 6, 2015 2:50 PM > >> To: 'FieldTrip discussion list' > >> Subject: Re: [FieldTrip] labels per grid point > >> > >> the correct link is: > >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_s > >> ource > >> s_of_oscillatory_gamma-band_activity > >> not sure why there was a line break introduced... > >> > >> > >> -- > >> > >> J?rn M. Horschig, Software Engineer > >> Artinis Medical Systems | +31 481 350 980 > >> > >>> -----Original Message----- > >>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >>> bounces at science.ru.nl] On Behalf Of J?rn M. Horschig > >>> Sent: Wednesday, May 6, 2015 2:43 PM > >>> To: 'FieldTrip discussion list' > >>> Subject: Re: [FieldTrip] labels per grid point > >>> > >>> Hi Nadine, > >>> > >>> does the second exercise in this section help (i.e. defining a lookup > >> atlas for > >>> source plotting): > >>> > >> http://www.fieldtriptoolbox.org/tutorial/beamformingextended#plotting_ > >>> s > >>> ource > >>> s_of_oscillatory_gamma-band_activity > >>> ? > >>> > >>> Best, > >>> J?rn > >>> > >>> > >>> -- > >>> > >>> J?rn M. Horschig, Software Engineer > >>> Artinis Medical Systems | +31 481 350 980 > >>> > >>>> -----Original Message----- > >>>> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip- > >>>> bounces at science.ru.nl] On Behalf Of Nadine > >>>> Sent: Wednesday, May 6, 2015 2:21 PM > >>>> To: fieldtrip at science.ru.nl > >>>> Subject: [FieldTrip] labels per grid point > >>>> > >>>> Dear Fieldtrip Users, > >>>> > >>>> I am trying to get anatomical labels for individual source grid > >>>> points. I > >>> can only > >>>> find how to parcellate the grid points to get an averaged value of > >>>> sources > >>> for > >>>> certain parcellations (e.g. Brodmann areas). But I would like to get > >>>> an anatomical label per grid point, so that I can see which grid > >>>> points > >>> belong to > >>>> which area. Does anybody have any solution for this? > >>>> > >>>> Thanks in advance for your help, > >>>> Nadine > >>>> > >>>> _______________________________________________ > >>>> fieldtrip mailing list > >>>> fieldtrip at donders.ru.nl > >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >>> > >>> > >>> _______________________________________________ > >>> fieldtrip mailing list > >>> fieldtrip at donders.ru.nl > >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > >> > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > ------------------------------ > > Message: 7 > Date: Thu, 7 May 2015 09:36:34 +0200 > From: Nadine > To: FieldTrip discussion list > Subject: Re: [FieldTrip] labels per grid point > Message-ID: <306CCF9F-01AC-4036-8B14-C4FFC99AA54E at gmail.com> > Content-Type: text/plain; charset=us-ascii > > Hi Tzvetan, > > Yes, thank you, this is perfect! > > Best, > Nadine > On 06 May 2015, at 14:37, Tzvetan Popov > wrote: > > > Hi Nadine, > > > > maybe this is what you need? > > > http://www.fieldtriptoolbox.org/faq/how_can_i_map_source_locations_between_two_different_representations > > > > best > > tzvetan > > > >> Dear Fieldtrip Users, > >> > >> I am trying to get anatomical labels for individual source grid points. > I can only find how to parcellate the grid points to get an averaged value > of sources for certain parcellations (e.g. Brodmann areas). But I would > like to get an anatomical label per grid point, so that I can see which > grid points belong to which area. Does anybody have any solution for this? > >> > >> Thanks in advance for your help, > >> Nadine > >> > >> _______________________________________________ > >> fieldtrip mailing list > >> fieldtrip at donders.ru.nl > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > ------------------------------ > > Message: 8 > Date: Thu, 7 May 2015 10:21:19 +0200 > From: H?l?ne Guiraud > To: FieldTrip discussion list > Subject: Re: [FieldTrip] re template for children > Message-ID: > < > CAJ16KS8BwyAttHC2E23tsdisvjE+Y_T5NAjpMm4F8--0H6HN8g at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Till and John, > > Thank you, this is perfect! > > Best regards, > H?l?ne > > 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > > > We have a template for children?actually have for infants from 2 weeks > > through adults at 89 years. We also have average electrode positions for > > EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented > > priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have > > been using this recently with FT for infants and child/adolescent/adult > > ages. > > > > WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ > > Fro www site: This is a database of average MRIs and associated MRI > > volumes for developmental MRI work. It consists of average MRI templates, > > segmented partial volume estimate volumes for GM, WM, T2W-derived CSF > > (Description > > < > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html > > > > > ). The database is separated into head-based and brain-based averages. > The > > data are separated by ages in months, years, 6-month, or 5-year intervals > > (Ages and Templates > > < > > > http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm > > l>). The templates are grouped into first year (2 weeks through 12 > > months), early childhood (15 months through 4 years), childhood (4 years > > through 10 years), adolescence (10.5 years through 17.5 years) and adults > > (18 years through 89 years). > > Tools for cortical source analysis of EEG and ERP are provided. These > > tools are based on the average MRI templates, segmenting, and atlases. > > > > Also see my www site, jerlab.psych.sc.edu for publications describing > > this. We have a recent chapter that has a good description of the issues > > behind the database (with Wanze Xie). We have a paper accepted at > > Neuroimage for their upcoming ?Data Sharing? issue (with Carmen Sanchez, > > Michelle Phillips-Meek, and Wanze Xie). > > > > John > > > > > > *********************************************** > > John E. Richards Carolina Distinguished Professor > > Department of Psychology > > University of South Carolina > > Columbia, SC 29208 > > Dept Phone: 803 777 2079 > > Fax: 803 777 9558 > > Email: richards-john at sc.edu > > HTTP: jerlab.psych.sc.edu > > *********************************************** > > > > > > > > > > > > > > > > > > On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" > > wrote: > > > > >Send fieldtrip mailing list submissions to > > > fieldtrip at science.ru.nl > > > > > >To subscribe or unsubscribe via the World Wide Web, visit > > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > >or, via email, send a message with subject or body 'help' to > > > fieldtrip-request at science.ru.nl > > > > > >You can reach the person managing the list at > > > fieldtrip-owner at science.ru.nl > > > > > >When replying, please edit your Subject line so it is more specific > > >than "Re: Contents of fieldtrip digest..." > > > > > > > > >Today's Topics: > > > > > > 1. Search for a template children. (H?l?ne Guiraud) > > > 2. Re: Search for a template children. (Till Schneider) > > > 3. ICBM 152 templates in FT (Keyvan Mahjoory) > > > > > > > > >---------------------------------------------------------------------- > > > > > >Message: 1 > > >Date: Wed, 29 Apr 2015 14:45:56 +0200 > > >From: H?l?ne Guiraud > > >To: fieldtrip at science.ru.nl > > >Subject: [FieldTrip] Search for a template children. > > >Message-ID: > > > < > > CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> > > >Content-Type: text/plain; charset="utf-8" > > > > > >Dear community, > > > > > >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on > > >speech perception in children using MEG. > > >The children involved in the study don't pass MRI. We want to achieve > > >source reconstruction from a template. However I can't find a template > > >corresponding to the anatomy of a child (8-12 years). > > >Can someone tell me if there are template children and where I can find > > >them? > > > > > >Best, > > > > > >H?l?ne Guiraud > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e > > >9b53e/attachment-0001.html> > > > > > >------------------------------ > > > > > >Message: 2 > > >Date: Wed, 29 Apr 2015 15:53:13 +0200 > > >From: Till Schneider > > >To: FieldTrip discussion list > > >Subject: Re: [FieldTrip] Search for a template children. > > >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> > > >Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > > > > >Dear Helene, > > > > > >McGill University provides MNI brains for different age groups between > > >4.5y to 18y. > > >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 > > >You will probably find the template brain you are searching for in this > > >database. > > > > > >Best regards, > > >Till > > > > > >-- > > > > > >Till Schneider, PhD > > > > > >Cognitive and Clinical Neurophysiology Group > > >Dept. of Neurophysiology and Pathophysiology > > >University Medical Center Hamburg-Eppendorf > > >Martinistr. 52 > > >20246 Hamburg > > >Germany > > > > > >phone +49-40-7410-53188 > > >fax +49-40-7410-57126 > > >www.uke.de/neurophysiologie > > > > > > > > > > > >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: > > >> Dear community, > > >> > > >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) > > >> on speech perception in children using MEG. > > >> The children involved in the study don't pass MRI. We want to achieve > > >> source reconstruction from a template. However I can't find a template > > >> corresponding to the anatomy of a child (8-12 years). > > >> Can someone tell me if there are template children and where I can > > >> find them? > > >> > > >> Best, > > >> > > >> H?l?ne Guiraud > > >> > > >> > > >> _______________________________________________ > > >> fieldtrip mailing list > > >> fieldtrip at donders.ru.nl > > >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > > > >-- > > > > > >_____________________________________________________________________ > > > > > >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen > > >Rechts; Gerichtsstand: Hamburg | www.uke.de > > >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. > > >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik > > >_____________________________________________________________________ > > > > > >SAVE PAPER - THINK BEFORE PRINTING > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e > > >44937/attachment-0001.html> > > > > > >------------------------------ > > > > > >Message: 3 > > >Date: Wed, 29 Apr 2015 16:25:35 +0200 > > >From: Keyvan Mahjoory > > >To: FieldTrip discussion list > > >Subject: [FieldTrip] ICBM 152 templates in FT > > >Message-ID: > > > > UJp6-+4+7fA at mail.gmail.com> > > >Content-Type: text/plain; charset="iso-8859-1" > > > > > >Dear Fieldtrip Users, > > > > > >I perform source analysis in Fieldtrip with a template head model ( > > >standard_bem ) and > a > > >template source model (cortex_5124.surf.gii > > >) to constarin > > >estimated sources on cortex. These templates are based on Colin27, But > I > > >prefere to use the template ICBM152 instead. > > >Does FT include ICBM template? I mean templates for both head model and > > >cortical surfe. > > > > > >Many Thanks in advance, > > >Keyvan > > >-------------- next part -------------- > > >An HTML attachment was scrubbed... > > >URL: > > >< > > > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 > > >9daf3/attachment-0001.html> > > > > > >------------------------------ > > > > > >_______________________________________________ > > >fieldtrip mailing list > > >fieldtrip at donders.ru.nl > > >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > >End of fieldtrip Digest, Vol 53, Issue 23 > > >***************************************** > > > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > > > -- > H?l?ne Guiraud > Doctorante > Universit? Lyon 2 > Laboratoire Dynamique Du Langage > CNRS, UMR 5596 > Tel : 04 72 72 65 34 > guiraudh at gmail.com > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/0bd0dea8/attachment-0001.html > > > > ------------------------------ > > Message: 9 > Date: Thu, 7 May 2015 08:29:39 +0000 > From: "Sander, Myriam" > To: FieldTrip discussion list ?[fieldtrip at science.ru.nl]? > > Subject: [FieldTrip] Vacant Predoctoral Position in Lifespan > Psychology at the MPI for Human Development in Berlin, Germany > Message-ID: > < > D12CFACF574CEA4498D72B949FF5631C9B20628E at MaxMail04.mpib-berlin.mpg.de> > > Content-Type: text/plain; charset="cp1256" > > ********************************************************* > > PREDOCTORAL POSITION: CENTER FOR LIFESPAN PSYCHOLOGY, MPI BERLIN > > The new MINERVA research group headed by Dr. Myriam Sander at the Max > Planck Institute for Human Development, Center for Lifespan Psychology > (Director: Prof. Dr. Ulman Lindenberger), is seeking applications for a > > PREDOCTORAL POSITION > > The doctoral contract will last for 3 years. The position is available > from October 1, 2015 or later. > > Job Description: Future research of the new MINERVA research group (PI: > Dr. Myriam Sander) will use a multi-modal imaging approach (EEG with a > focus on oscillatory measures in combination with structural and functional > MRI) to uncover lifespan differences in the interplay between sensory > (visual and auditory) and cognitive abilities influencing memory > performance. The MINERVA research group is part of the project ?Cognitive > and Neural Dynamics of Memory Across the Lifespan (CONMEM)? which > investigates lifespan changes in the interplay between associative and > strategic components of memory functioning on neural and cognitive levels, > with a focus on working and episodic memory (see Sander, et al., Neurosci. > Biobehav. Rev., 2012; Shing, et al., Neurosci. Biobehav. Rev., 2010). The > successful predoctoral fellow will plan and conduct empirical studies in > this domain, analyze the behavioral, EEG, and MRI data, and prepare > scientific manuscripts for publication. > > For further information, please contact: Dr. Myriam Sander ( > sander at mpib-berlin.mpg.de) > > Requirements: A successful applicant needs to hold (or expect by summer > 2015) a diploma/master degree in psychology, cognitive neuroscience, or > related fields. Applicants should have experience with conducting > experimental research, knowledge in neuroimaging methods (EEG and/or MRI), > and a solid background in at least one programming language (preferably > Matlab or R). In addition, the ability to work independently as well as a > high proficiency of the English language is required. Experience with > age-comparative studies is an advantage. > > The Max Planck Society is interested in increasing the number of women on > its scientific staff. We strongly encourage applications from women and > members of minority groups. In addition, the Max Planck Society is > committed to employing more handicapped individuals and encourages them to > apply. > > To apply, please send (as ONE FILE and via email only) a statement of > research interests, a CV, a copy of relevant certificates, (p)reprints of > publications, and a list of two references to Dr. Myriam Sander, MPI for > Human Development, Lentzeallee 94, 14195 Berlin (sander at mpib-berlin.mpg.de) > preferably by June 30th, 2015. Later applications will be considered until > the position is filled. > > * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/0579250d/attachment-0001.html > > > > ------------------------------ > > Message: 10 > Date: Thu, 7 May 2015 11:11:54 +0200 > From: "Hamza Fawzi Altakroury (Alumni)" > To: FieldTrip discussion list > Subject: [FieldTrip] Vgrid > Message-ID: > < > CADB5qVBgnCciEmuwJ8ZR3MPRrEuHeWdysTQWek9+aTabP6-GMg at mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was expected to > be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > I don't have a folder called pcwin64! I have only glnx86 (empty folder) > glnxa64 and maci64 in ***\external\vgrid\bin\ > > I also downloaded a newer version of fieldtrip, but I did not find it! > > >From where I can get vgrid.exe? > > Thank you > > > -- > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabanc? University > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/793650e7/attachment-0001.html > > > > ------------------------------ > > Message: 11 > Date: Thu, 07 May 2015 11:40:17 +0200 > From: Johannes Vorwerk > To: fieldtrip at science.ru.nl > Subject: Re: [FieldTrip] Vgrid > Message-ID: <1430991617.11932.23.camel at biomag43> > Content-Type: text/plain; charset="utf-8" > > Hi, > > vgrid should no longer be needed in recent fieldtrip-versions. It was > replaced by a fully matlab-based function (prepare_mesh_hexahedral), > that should now also work under windows. A vgrid.exe never existed, it > was only available for mac and linux. Did you try updating your > fieldtrip-version to a recent release? > > Best, > Johannes > > Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi > Altakroury (Alumni): > > Hello, > > > > > > > > I got the following error when I run these lines: (found in > > http://www.fieldtriptoolbox.org/development/simbio) > > > > cfg = []; > > cfg.shift = 0.3; > > cfg.method = 'hexahedral'; > > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > > > > > > Error using vgrid (line 16) > > the vgrid executable is not available for your platform, it was > > expected to be > > located at > > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > > > > > > I don't have a folder called pcwin64! I have only glnx86 (empty > > folder) glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > > > > From where I can get vgrid.exe? > > > > > > Thank you > > > > > > > > -- > > > > Hamza Fawzi Altakroury > > Graduate student - MA > > Faculty of Engineering and Natural Sciences > > Sabanc? University > > > > _______________________________________________ > > fieldtrip mailing list > > fieldtrip at donders.ru.nl > > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Dipl.-Math. Johannes Vorwerk > e-mail: j.vorwerk at uni-muenster.de > > Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters > Institute for Biomagnetism and Biosignalanalysis, University of Muenster > www: http://campus.uni-muenster.de/index.php?id=919&L=1 > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150507/6c43fe26/attachment-0001.html > > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 5 > **************************************** > -- Haiteng Jiang PhD candidate Donders Institute for Brain, Cognition and Behaviour Neuronal Oscillations Group Computational Cognitive Neuroscience Lab https://sites.google.com/site/haitengjiang/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From thomas.wunderle at esi-frankfurt.de Thu May 7 12:56:27 2015 From: thomas.wunderle at esi-frankfurt.de (Wunderle, Thomas) Date: Thu, 7 May 2015 10:56:27 +0000 Subject: [FieldTrip] Statistics on spike rate Message-ID: <27E5CAD9145EEC41BB9B34C01716A1987FB3B3B3@UM-EXCDAG-A01.um.gwdg.de> Dear community, I’m working on spike/ spike-field analysis and I was wondering if there are statistical comparisons in field trip for spikes. In particular, I would like to test if the spike rate after a stimulus onset is significantly different from the spike rate before stimulus onset (that is, the recorded neurons responds to the stimulus). I tried around with “ft_timelockstatistics”, “ft_statistics_stats” and “ft_spike_rate”, bud did not succeed. I’m not very familiar with statistical testing in FT in general, so I don’t know if statistics for spike rate are implemented in field trip at all. Thanks in advance, Thomas ----- Dr. Thomas Wunderle Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society Deutschordenstrasse 46 60528 Frankfurt am Main, Germany www.esi-frankfurt.de thomas.wunderle at esi-frankfurt.de Tel: +49 69 96769 516 Fax: +49 69 96769 555 Sitz der Gesellschaft: Frankfurt am Main Registergericht: Amtsgericht Frankfurt - HRB 84266 Geschäftsführer: Prof. Dr. Pascal Fries -------------- next part -------------- An HTML attachment was scrubbed... URL: From berdakho at gmail.com Thu May 7 15:56:04 2015 From: berdakho at gmail.com (Berdakh Abibullaev) Date: Thu, 7 May 2015 08:56:04 -0500 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi, I am also using the Dr. Richard's infant database. It took us sometime to figure out to how prepare forward models in FT. If you need I have scripts ready to use to get you started smoothly. ​Just let me know. ​ ​​ Thanks, Berdakh Abibullaev, Postdoctoral Research Scholar , Laboratory for Non-invasive Brain-Machine Interfaces, Department of Electrical Eng. & Computer Science, University of Houston, E413, Engineering Building II, Houston, Texas, 77204-4005. https://www.facebook.com/UHBMIST On Thu, May 7, 2015 at 3:21 AM, Hélène Guiraud wrote: > Hi Till and John, > > Thank you, this is perfect! > > Best regards, > Hélène > > 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : > >> We have a template for children‹actually have for infants from 2 weeks >> through adults at 89 years. We also have average electrode positions for >> EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented >> priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have >> been using this recently with FT for infants and child/adolescent/adult >> ages. >> >> WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ >> Fro www site: This is a database of average MRIs and associated MRI >> volumes for developmental MRI work. It consists of average MRI templates, >> segmented partial volume estimate volumes for GM, WM, T2W-derived CSF >> (Description >> < >> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html >> > >> ). The database is separated into head-based and brain-based averages. The >> data are separated by ages in months, years, 6-month, or 5-year intervals >> (Ages and Templates >> < >> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm >> l>). The templates are grouped into first year (2 weeks through 12 >> months), early childhood (15 months through 4 years), childhood (4 years >> through 10 years), adolescence (10.5 years through 17.5 years) and adults >> (18 years through 89 years). >> Tools for cortical source analysis of EEG and ERP are provided. These >> tools are based on the average MRI templates, segmenting, and atlases. >> >> Also see my www site, jerlab.psych.sc.edu for publications describing >> this. We have a recent chapter that has a good description of the issues >> behind the database (with Wanze Xie). We have a paper accepted at >> Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, >> Michelle Phillips-Meek, and Wanze Xie). >> >> John >> >> >> *********************************************** >> John E. Richards Carolina Distinguished Professor >> Department of Psychology >> University of South Carolina >> Columbia, SC 29208 >> Dept Phone: 803 777 2079 >> Fax: 803 777 9558 >> Email: richards-john at sc.edu >> HTTP: jerlab.psych.sc.edu >> *********************************************** >> >> >> >> >> >> >> >> >> On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" >> wrote: >> >> >Send fieldtrip mailing list submissions to >> > fieldtrip at science.ru.nl >> > >> >To subscribe or unsubscribe via the World Wide Web, visit >> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >or, via email, send a message with subject or body 'help' to >> > fieldtrip-request at science.ru.nl >> > >> >You can reach the person managing the list at >> > fieldtrip-owner at science.ru.nl >> > >> >When replying, please edit your Subject line so it is more specific >> >than "Re: Contents of fieldtrip digest..." >> > >> > >> >Today's Topics: >> > >> > 1. Search for a template children. (H?l?ne Guiraud) >> > 2. Re: Search for a template children. (Till Schneider) >> > 3. ICBM 152 templates in FT (Keyvan Mahjoory) >> > >> > >> >---------------------------------------------------------------------- >> > >> >Message: 1 >> >Date: Wed, 29 Apr 2015 14:45:56 +0200 >> >From: H?l?ne Guiraud >> >To: fieldtrip at science.ru.nl >> >Subject: [FieldTrip] Search for a template children. >> >Message-ID: >> > < >> CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> >> >Content-Type: text/plain; charset="utf-8" >> > >> >Dear community, >> > >> >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >> >speech perception in children using MEG. >> >The children involved in the study don't pass MRI. We want to achieve >> >source reconstruction from a template. However I can't find a template >> >corresponding to the anatomy of a child (8-12 years). >> >Can someone tell me if there are template children and where I can find >> >them? >> > >> >Best, >> > >> >H?l?ne Guiraud >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e >> >9b53e/attachment-0001.html> >> > >> >------------------------------ >> > >> >Message: 2 >> >Date: Wed, 29 Apr 2015 15:53:13 +0200 >> >From: Till Schneider >> >To: FieldTrip discussion list >> >Subject: Re: [FieldTrip] Search for a template children. >> >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" >> > >> >Dear Helene, >> > >> >McGill University provides MNI brains for different age groups between >> >4.5y to 18y. >> >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >> >You will probably find the template brain you are searching for in this >> >database. >> > >> >Best regards, >> >Till >> > >> >-- >> > >> >Till Schneider, PhD >> > >> >Cognitive and Clinical Neurophysiology Group >> >Dept. of Neurophysiology and Pathophysiology >> >University Medical Center Hamburg-Eppendorf >> >Martinistr. 52 >> >20246 Hamburg >> >Germany >> > >> >phone +49-40-7410-53188 >> >fax +49-40-7410-57126 >> >www.uke.de/neurophysiologie >> > >> > >> > >> >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >> >> Dear community, >> >> >> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >> >> on speech perception in children using MEG. >> >> The children involved in the study don't pass MRI. We want to achieve >> >> source reconstruction from a template. However I can't find a template >> >> corresponding to the anatomy of a child (8-12 years). >> >> Can someone tell me if there are template children and where I can >> >> find them? >> >> >> >> Best, >> >> >> >> H?l?ne Guiraud >> >> >> >> >> >> _______________________________________________ >> >> fieldtrip mailing list >> >> fieldtrip at donders.ru.nl >> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> > >> >-- >> > >> >_____________________________________________________________________ >> > >> >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >> >Rechts; Gerichtsstand: Hamburg | www.uke.de >> >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >> >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >> >_____________________________________________________________________ >> > >> >SAVE PAPER - THINK BEFORE PRINTING >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e >> >44937/attachment-0001.html> >> > >> >------------------------------ >> > >> >Message: 3 >> >Date: Wed, 29 Apr 2015 16:25:35 +0200 >> >From: Keyvan Mahjoory >> >To: FieldTrip discussion list >> >Subject: [FieldTrip] ICBM 152 templates in FT >> >Message-ID: >> > > UJp6-+4+7fA at mail.gmail.com> >> >Content-Type: text/plain; charset="iso-8859-1" >> > >> >Dear Fieldtrip Users, >> > >> >I perform source analysis in Fieldtrip with a template head model ( >> >standard_bem ) and a >> >template source model (cortex_5124.surf.gii >> >) to constarin >> >estimated sources on cortex. These templates are based on Colin27, But I >> >prefere to use the template ICBM152 instead. >> >Does FT include ICBM template? I mean templates for both head model and >> >cortical surfe. >> > >> >Many Thanks in advance, >> >Keyvan >> >-------------- next part -------------- >> >An HTML attachment was scrubbed... >> >URL: >> >< >> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 >> >9daf3/attachment-0001.html> >> > >> >------------------------------ >> > >> >_______________________________________________ >> >fieldtrip mailing list >> >fieldtrip at donders.ru.nl >> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > >> >End of fieldtrip Digest, Vol 53, Issue 23 >> >***************************************** >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > Hélène Guiraud > Doctorante > Université Lyon 2 > Laboratoire Dynamique Du Langage > CNRS, UMR 5596 > Tel : 04 72 72 65 34 > guiraudh at gmail.com > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From guiraudh at gmail.com Thu May 7 16:23:54 2015 From: guiraudh at gmail.com (=?UTF-8?B?SMOpbMOobmUgR3VpcmF1ZA==?=) Date: Thu, 7 May 2015 16:23:54 +0200 Subject: [FieldTrip] re template for children In-Reply-To: References: Message-ID: Hi, Thank you. I'm just trying to develop my scripts. A little help would be welcome! I'm taking, thank! Hélène 2015-05-07 15:56 GMT+02:00 Berdakh Abibullaev : > Hi, > > I am also using the Dr. Richard's infant database. It took us sometime to > figure out to how prepare forward models in FT. > If you need I have scripts ready to use to get you started smoothly. > > ​Just let me know. ​ > > ​​ > Thanks, > > Berdakh Abibullaev, > > Postdoctoral Research Scholar , > Laboratory for Non-invasive Brain-Machine Interfaces, > Department of Electrical Eng. & Computer Science, > University of Houston, E413, Engineering Building II, > Houston, Texas, 77204-4005. > https://www.facebook.com/UHBMIST > > On Thu, May 7, 2015 at 3:21 AM, Hélène Guiraud wrote: > >> Hi Till and John, >> >> Thank you, this is perfect! >> >> Best regards, >> Hélène >> >> 2015-04-30 14:12 GMT+02:00 RICHARDS, JOHN : >> >>> We have a template for children‹actually have for infants from 2 weeks >>> through adults at 89 years. We also have average electrode positions for >>> EGI sensor nets (GSN128, HGSN128) and the 10-10 system; and segmented >>> priors, stereotaxic atlases, and segmented heads (BEM, FEM). I also have >>> been using this recently with FT for infants and child/adolescent/adult >>> ages. >>> >>> WWW site: http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/ >>> Fro www site: This is a database of average MRIs and associated MRI >>> volumes for developmental MRI work. It consists of average MRI templates, >>> segmented partial volume estimate volumes for GM, WM, T2W-derived CSF >>> (Description >>> < >>> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/Description.html >>> > >>> ). The database is separated into head-based and brain-based averages. >>> The >>> data are separated by ages in months, years, 6-month, or 5-year intervals >>> (Ages and Templates >>> < >>> http://jerlab.psych.sc.edu/NeurodevelopmentalMRIDatabase/agestemplates.htm >>> l>). The templates are grouped into first year (2 weeks through 12 >>> months), early childhood (15 months through 4 years), childhood (4 years >>> through 10 years), adolescence (10.5 years through 17.5 years) and adults >>> (18 years through 89 years). >>> Tools for cortical source analysis of EEG and ERP are provided. These >>> tools are based on the average MRI templates, segmenting, and atlases. >>> >>> Also see my www site, jerlab.psych.sc.edu for publications describing >>> this. We have a recent chapter that has a good description of the issues >>> behind the database (with Wanze Xie). We have a paper accepted at >>> Neuroimage for their upcoming ³Data Sharing² issue (with Carmen Sanchez, >>> Michelle Phillips-Meek, and Wanze Xie). >>> >>> John >>> >>> >>> *********************************************** >>> John E. Richards Carolina Distinguished Professor >>> Department of Psychology >>> University of South Carolina >>> Columbia, SC 29208 >>> Dept Phone: 803 777 2079 >>> Fax: 803 777 9558 >>> Email: richards-john at sc.edu >>> HTTP: jerlab.psych.sc.edu >>> *********************************************** >>> >>> >>> >>> >>> >>> >>> >>> >>> On 4/30/15, 6:00 AM, "fieldtrip-request at science.ru.nl" >>> wrote: >>> >>> >Send fieldtrip mailing list submissions to >>> > fieldtrip at science.ru.nl >>> > >>> >To subscribe or unsubscribe via the World Wide Web, visit >>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >or, via email, send a message with subject or body 'help' to >>> > fieldtrip-request at science.ru.nl >>> > >>> >You can reach the person managing the list at >>> > fieldtrip-owner at science.ru.nl >>> > >>> >When replying, please edit your Subject line so it is more specific >>> >than "Re: Contents of fieldtrip digest..." >>> > >>> > >>> >Today's Topics: >>> > >>> > 1. Search for a template children. (H?l?ne Guiraud) >>> > 2. Re: Search for a template children. (Till Schneider) >>> > 3. ICBM 152 templates in FT (Keyvan Mahjoory) >>> > >>> > >>> >---------------------------------------------------------------------- >>> > >>> >Message: 1 >>> >Date: Wed, 29 Apr 2015 14:45:56 +0200 >>> >From: H?l?ne Guiraud >>> >To: fieldtrip at science.ru.nl >>> >Subject: [FieldTrip] Search for a template children. >>> >Message-ID: >>> > < >>> CAJ16KS_S7ednTeE2MgaLasRaWD4GK+0ChX0S+nYZzU_-ypdh4w at mail.gmail.com> >>> >Content-Type: text/plain; charset="utf-8" >>> > >>> >Dear community, >>> > >>> >My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) on >>> >speech perception in children using MEG. >>> >The children involved in the study don't pass MRI. We want to achieve >>> >source reconstruction from a template. However I can't find a template >>> >corresponding to the anatomy of a child (8-12 years). >>> >Can someone tell me if there are template children and where I can find >>> >them? >>> > >>> >Best, >>> > >>> >H?l?ne Guiraud >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/03e >>> >9b53e/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >Message: 2 >>> >Date: Wed, 29 Apr 2015 15:53:13 +0200 >>> >From: Till Schneider >>> >To: FieldTrip discussion list >>> >Subject: Re: [FieldTrip] Search for a template children. >>> >Message-ID: <5540E249.3000200 at uke.uni-hamburg.de> >>> >Content-Type: text/plain; charset="windows-1252"; Format="flowed" >>> > >>> >Dear Helene, >>> > >>> >McGill University provides MNI brains for different age groups between >>> >4.5y to 18y. >>> >http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1 >>> >You will probably find the template brain you are searching for in this >>> >database. >>> > >>> >Best regards, >>> >Till >>> > >>> >-- >>> > >>> >Till Schneider, PhD >>> > >>> >Cognitive and Clinical Neurophysiology Group >>> >Dept. of Neurophysiology and Pathophysiology >>> >University Medical Center Hamburg-Eppendorf >>> >Martinistr. 52 >>> >20246 Hamburg >>> >Germany >>> > >>> >phone +49-40-7410-53188 >>> >fax +49-40-7410-57126 >>> >www.uke.de/neurophysiologie >>> > >>> > >>> > >>> >Am 29.04.15 um 14:45 schrieb H?l?ne Guiraud: >>> >> Dear community, >>> >> >>> >> My name is H?l?ne Guiraud and i'm working in DDL lab in Lyon (France) >>> >> on speech perception in children using MEG. >>> >> The children involved in the study don't pass MRI. We want to achieve >>> >> source reconstruction from a template. However I can't find a template >>> >> corresponding to the anatomy of a child (8-12 years). >>> >> Can someone tell me if there are template children and where I can >>> >> find them? >>> >> >>> >> Best, >>> >> >>> >> H?l?ne Guiraud >>> >> >>> >> >>> >> _______________________________________________ >>> >> fieldtrip mailing list >>> >> fieldtrip at donders.ru.nl >>> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> > >>> > >>> >-- >>> > >>> >_____________________________________________________________________ >>> > >>> >Universit?tsklinikum Hamburg-Eppendorf; K?rperschaft des ?ffentlichen >>> >Rechts; Gerichtsstand: Hamburg | www.uke.de >>> >Vorstandsmitglieder: Prof. Dr. Burkhard G?ke (Vorsitzender), Prof. Dr. >>> >Dr. Uwe Koch-Gromus, Joachim Pr?l?, Rainer Schoppik >>> >_____________________________________________________________________ >>> > >>> >SAVE PAPER - THINK BEFORE PRINTING >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/c4e >>> >44937/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >Message: 3 >>> >Date: Wed, 29 Apr 2015 16:25:35 +0200 >>> >From: Keyvan Mahjoory >>> >To: FieldTrip discussion list >>> >Subject: [FieldTrip] ICBM 152 templates in FT >>> >Message-ID: >>> > >> UJp6-+4+7fA at mail.gmail.com> >>> >Content-Type: text/plain; charset="iso-8859-1" >>> > >>> >Dear Fieldtrip Users, >>> > >>> >I perform source analysis in Fieldtrip with a template head model ( >>> >standard_bem ) and >>> a >>> >template source model (cortex_5124.surf.gii >>> >) to constarin >>> >estimated sources on cortex. These templates are based on Colin27, But >>> I >>> >prefere to use the template ICBM152 instead. >>> >Does FT include ICBM template? I mean templates for both head model and >>> >cortical surfe. >>> > >>> >Many Thanks in advance, >>> >Keyvan >>> >-------------- next part -------------- >>> >An HTML attachment was scrubbed... >>> >URL: >>> >< >>> http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20150429/992 >>> >9daf3/attachment-0001.html> >>> > >>> >------------------------------ >>> > >>> >_______________________________________________ >>> >fieldtrip mailing list >>> >fieldtrip at donders.ru.nl >>> >http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> > >>> >End of fieldtrip Digest, Vol 53, Issue 23 >>> >***************************************** >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> Hélène Guiraud >> Doctorante >> Université Lyon 2 >> Laboratoire Dynamique Du Langage >> CNRS, UMR 5596 >> Tel : 04 72 72 65 34 >> guiraudh at gmail.com >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hélène Guiraud Doctorante Université Lyon 2 Laboratoire Dynamique Du Langage CNRS, UMR 5596 Tel : 04 72 72 65 34 guiraudh at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From hamzaf at sabanciuniv.edu Thu May 7 16:39:59 2015 From: hamzaf at sabanciuniv.edu (Hamza Fawzi Altakroury (Alumni)) Date: Thu, 7 May 2015 17:39:59 +0300 Subject: [FieldTrip] Vgrid In-Reply-To: <1430991617.11932.23.camel@biomag43> References: <1430991617.11932.23.camel@biomag43> Message-ID: Thank you Johannes, I'll try to run it using a newer version of fieldtrip. Best, Hamza On Thu, May 7, 2015 at 12:40 PM, Johannes Vorwerk wrote: > Hi, > > vgrid should no longer be needed in recent fieldtrip-versions. It was > replaced by a fully matlab-based function (prepare_mesh_hexahedral), that > should now also work under windows. A vgrid.exe never existed, it was only > available for mac and linux. Did you try updating your fieldtrip-version to > a recent release? > > Best, > Johannes > > Am Donnerstag, den 07.05.2015, 11:11 +0200 schrieb Hamza Fawzi Altakroury > (Alumni): > > Hello, > > > I got the following error when I run these lines: (found in > http://www.fieldtriptoolbox.org/development/simbio) > > cfg = []; > cfg.shift = 0.3; > cfg.method = 'hexahedral'; > mesh = ft_prepare_mesh(cfg,segmentedmri); > > > Error using vgrid (line 16) > the vgrid executable is not available for your platform, it was expected > to be > located at > ***\external\vgrid\bin\pcwin64\vgrid.exe > > > I don't have a folder called pcwin64! I have only glnx86 (empty folder) > glnxa64 and maci64 in ***\external\vgrid\bin\ > > > > I also downloaded a newer version of fieldtrip, but I did not find it! > > > From where I can get vgrid.exe? > > > Thank you > > > > -- > > Hamza Fawzi Altakroury > Graduate student - MA > Faculty of Engineering and Natural Sciences > Sabancı University > > _______________________________________________ > fieldtrip mailing listfieldtrip at donders.ru.nlhttp://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > -- > Dipl.-Math. Johannes Vorwerk > e-mail: j.vorwerk at uni-muenster.de > > Workgroup Methods in Bioelectromagnetism, PD. Dr. Carsten Wolters > Institute for Biomagnetism and Biosignalanalysis, University of Muenster > www: http://campus.uni-muenster.de/index.php?id=919&L=1 > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Hamza Fawzi Altakroury Graduate student - MA Faculty of Engineering and Natural Sciences Sabancı University -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Fri May 8 13:22:56 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Fri, 8 May 2015 12:22:56 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy Message-ID: <554C9C90.4090702@glasgow.ac.uk> An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Fri May 8 13:38:48 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 8 May 2015 11:38:48 +0000 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy In-Reply-To: <554C9C90.4090702@glasgow.ac.uk> References: <554C9C90.4090702@glasgow.ac.uk> Message-ID: <524BB694-AB68-4A2A-BC8B-9A9F515CC75B@fcdonders.ru.nl> May, Have you ensured that the stat.pos field contains the dipole positions, coregistered to the template brain? Best, Jan-Mathijs On May 8, 2015, at 1:22 PM, Heng-Ru May Tan > wrote: Hi Fieldtrippers [The previous email didn't display properly so resending this again.] I am having trouble running ft_sourceinterpolate... I didn't seem to have this issue before. =( The anatomy seems to be missing and so when I subsequently call ft_sourceplot, the brain anatomy is not 'available' for plotting. Here are some example of the things I tried and the errors in hope that someone might be able help! Many thanks in advance, May -- this is a stat structure used: stat = prob: [33480x1 double] cirange: [33480x1 double] mask: [33480x1 logical] stat: [33480x1 double] ref: [33480x1 double] df: 185 critval: [-1.9729 1.9729] dim: [33480 1] inside: [10354x1 double] outside: [23126x1 double] pos: [33480x3 double] freq: 64.9309 cfg: [1x1 struct] grid = xgrid: [1x31 double] ygrid: [1x36 double] zgrid: [1x30 double] dim: [31 36 30] pos: [33480x3 double] inside: [12773x1 double] outside: [20707x1 double] anatpath2 = [unixANALYSEpath 'Matlab_scripts/fieldtrip-20140114/template/anatomy/single_subj_T1.nii'] template_mri = ft_read_mri(anatpath2); cfg = []; cfg.parameter = 'stat'; cfg.interpmethod = 'nearest'; statplot2 = ft_sourceinterpolate(cfg,stat, template_mri); the input is volume data with dimensions [91 109 91] Warning: sphereradius is not used for projmethod 'nearest' > In fieldtrip-20140114/private/interp_ungridded at 86 In ft_sourceinterpolate at 216 the call to "ft_sourceinterpolate" took 37 seconds and required the additional allocation of an estimated 96 MB -- somehow anatomy structure is lost... ?! statplot2 = freq: 64.9309 stat: [902629x1 double] pos: [902629x3 double] dim: [91 109 91] inside: [1x902629 double] outside: [1x0 double] unit: 'mm' cfg: [1x1 struct] cfg = []; cfg.method ='slice'; cfg.nslices = 30 cfg.funparameter = 'stat'; % cfg.maskparameter = 'mask'; cfg.maskparameter = cfg.funparameter; cfg.anaparameter = 'anatomy'; cfg.opacitymap = 'rampup'; ft_sourceplot(cfg, statplot2); the input is source data with 902629 positions on a [91 109 91] grid Warning: do not understand cfg.anaparameter, not plotting anatomy\n > In ft_sourceplot at 350 the call to "ft_sourceplot" took 2 seconds and required the additional allocation of an estimated 3 MB -- If using fieldtrip_new on server --> revision = '$Id: ft_sourceinterpolate.m 10221 2015-02-12 08:28:20Z roboos $'; cfg = parameter: 'stat' interpmethod: 'nearest' statplot1 = ft_sourceinterpolate(stat, template_mri) Undefined function or variable 'abort'. Error in ft_sourceinterpolate (line 106) if abort -- ________________________________________________________________________________________________________________________________________ Heng-Ru May Tan Centre for Cognitive Neuroimaging (CCNi) ▫Institute of Neuroscience and Psychology (INP) ▫ College of Medical, Veterinary and Life Sciences & College of Science and Engineering ▫ University of Glasgow ▫ 58 Hillhead Street, Glasgow G12 8QB, United Kingdom ▫ +44 (0)141-330-5090 ▫ Heng-RuMay.Tan at glasgow.ac.uk _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From christophe.grova at mcgill.ca Sat May 9 12:38:09 2015 From: christophe.grova at mcgill.ca (Christophe Grova) Date: Sat, 9 May 2015 10:38:09 +0000 Subject: [FieldTrip] MSc/PhD positions in Biomedical Physics and at the PERFORM Centre, Concordia University Message-ID: <9E1647EDA3EBB44AADA162CEC4C4222E7510052D@exmbx2010-9.campus.MCGILL.CA> Now available, MSc/PhD positions in Biomedical Physics and at the PERFORM Centre, Concordia University [multi_funkin] We offer two very interesting opportunities for M.Sc or PhD projects in the context of the new Biomedical Physics program proposed at Concordia University by the Department of Physics and at PERFORM. Project 1: Multimodal characterization of resting state functional connectivity. Supervisor: C. Grova, Department of Physics and PERFORM Center The overall project aims at assessing the organization of fluctuations of neuronal bioelectrical signals measured from the scalp using either Electro-EncephaloGraphy (EEG) or Magneto-EncephaloGraphy (MEG), while the subject is resting. The main methodological originality of this project is to consider time-frequency based source localization of EEG and MEG data, using wavelet-based Maximum on the Mean wMEM (Lina et al IEEE TBME 2014) in order to investigate resting state functional connectivity from simultaneous EEG/MEG data and also from simultaneous high-density EEG/fMRI data. These multimodal data will be considered in order to investigate the dynamic of resting state functional connectivity patterns in healthy controls The candidates will join a multidisciplinary team composed of neurologists and methodologists within the Multimodal Functional Imaging Laboratory, directed by Pr. Christophe Grova. Simultaneous EEG/fMRI data will be acquired at PERFORM, while simultaneous EEG/MEG data will be acquired at the Montreal Neurological Institute, McGill University. The key component of this project consists in adapting and validating the performance of EEG/MEG source localization of resting state data in healthy subjects, in order to build a normative database. Requirements: The candidate should have some knowledge in image and signal processing, linear algebra and statistics, as well as experience in computation and programmation, using notably Matlab software. Any experience with neuroimaging softwares would be an asset. Project 2: Multimodal characterization of functional hubs. Supervisor: C. Gauthier, Department of Physics and PERFORM Center Co-Supervisor: C. Grova, Department of Physics and PERFORM Center In the overall context of understanding the organization of brain activity during rest, as in the analysis of any network, the notion of “hub”, their detection and characterization is a key and challenging objective. This project will propose and evaluate new methods to detect these hubs and to charactrize their underlying metabolism using quantitative Magnetic Resonance Imaging (MRI) techniques. Using a new method based on sparse modeling to extract the hubs of such network organization from resting state functional MRI data acquired simultaneously with EEG data, the project will consist in combining these techniques with quantitative MRI to measure the metabolic rate of oxygen consumption. To do so, gas manipulations, i.e. breathing controlled amount of CO2 and O2, will be needed during the MRI acquisition. The objective will be to assess hemodynamic fluctuations, neuronal bioelectrical oscillations and local oxygen consumption of these hubs, within a population of healthy controls of different age ranges. Requirements: The candidate should have some knowledge in image and signal processing, linear algebra and statistics, as well as experience in computation and programmation, using notably Matlab software. Any experience of neuroimaging softwares and in experimental sciences would be an asset More details on the Multimodal Functional Imaging Lab can be found at: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage More details on PERFORM centre can be found at: http://www.concordia.ca/research/perform.html Please send your CV and motivation letter to: christophe.grova at concordia.ca and claudine.gauthier at concordia.ca *************************** Christophe Grova, PhD Assistant Professor, Physics Dpt, Concordia University PERFORM centre, Concordia University, Chair of PERFORM Applied Bio-Imaging Committee (ABC) Adjunct Prof in Biomedical Engineering, and Neurology and Neurosurgery Dpt, McGill University Multimodal Functional Imaging Lab (Multi FunkIm) Montreal Neurological Institute - epilepsy group Centre de Recherches en Mathématiques Physics Dpt Concordia University - Loyola Campus - Office SP 365.12 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Phone: (514) 848-2424 ext.4221 Biomedical Engineering Department McGill University - Room 304 3775 University Street, Montreal, Quebec, Canada, H3A 2B4 Phone : (514) 398 2516 Fax : (514) 398 7461 email : christophe.grova at concordia.ca , christophe.grova at mcgill.ca web: Explore Concordia: http://explore.concordia.ca/christophe-grova Physics, Concordia University: http://physics.concordia.ca/facultyandresearch/bios/grova.php McGill University: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleChristophe MultiFunkIm Lab: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/HomePage *************************** [X] -------------- next part -------------- An HTML attachment was scrubbed... URL: From Heng-RuMay.Tan at glasgow.ac.uk Mon May 11 13:29:03 2015 From: Heng-RuMay.Tan at glasgow.ac.uk (Heng-Ru May Tan) Date: Mon, 11 May 2015 12:29:03 +0100 Subject: [FieldTrip] Issues with ft_sourceinterpolate -- missing anatomy In-Reply-To: References: Message-ID: <5550927F.7080609@glasgow.ac.uk> An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: hjcjfgji.png Type: image/png Size: 213443 bytes Desc: not available URL: From anna.wieczorek.taraday at gmail.com Tue May 12 10:17:40 2015 From: anna.wieczorek.taraday at gmail.com (Anna Wieczorek-Taraday) Date: Tue, 12 May 2015 08:17:40 +0000 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip Message-ID: Dear Fieldtrippers, I have a problem while reading EEG (EGI) electrode location file to FieldTrip. I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? Any support will be appreciated. I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. *************************************** Here is code I used to read these locations: cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; cfg.feedback = 'yes'; layout = ft_prepare_layout(cfg); Here is the code that I used to preprocess my data in Fieldtrip: cfg = []; cfg.trialfun = 'ft_trialfun_general'; cfg.dataset = '136.set'; cfg.trialdef.eventtype = 'trigger'; cfg.trialdef.eventvalue = 'DIN8' cfg.trialdef.prestim = 0.5; cfg.trialdef.poststim = 2.5; cfg = ft_definetrial(cfg); cfg.lpfilter = 'no'; cfg.hpfilter = 'yes'; cfg.hpfreq = 0.3; data = ft_preprocessing(cfg); Anna Wieczorek-Taraday. PhD Student Nencki Institute of Experimental Biology Pasteur Street 3, 02-093 Warsaw, Poland Warsaw University of Social Sciences and Humanities Chodakowska Street 19/31, 03-815 Warsaw, Poland -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Tue May 12 11:05:09 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Tue, 12 May 2015 11:05:09 +0200 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip In-Reply-To: References: Message-ID: Hi Ana The ft_prepare_layout function reads the electrode positions and scales them such that they fit in the sphere that represents the head. I suggest you do cfg.layout = ‘yourfilename’ lay = ft_prepare_layout(cfg); cfg = []; cfg.layout = lay; ft_layoutplot(cfg); and then modify lay.pos repeatedly, every time plotting it again, until you are happy with the result. You probably want to do this for the vertical direction lay.pos(:,2) = (lay.pos(:,2)+shift) .* scale; to shift and scale the electrodes to a better fit inside/outside the sphere, and this for the horizontal lay.pos(:,1) = lay.pos(:,1) .* scale; as they seem to be properly centred along the x-axis alreadly. After this, you can save yourlayout.mat lay and specify “yourlayout.mat” as the layout filename for your future figures. best regards Robert On 12 May 2015, at 10:17, Anna Wieczorek-Taraday wrote: > Dear Fieldtrippers, > > I have a problem while reading EEG (EGI) electrode location file to FieldTrip. > I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. > > When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. > When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). > However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. > > I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? > Any support will be appreciated. > > I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. > > *************************************** > > > Here is code I used to read these locations: > > cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; > cfg.feedback = 'yes'; > layout = ft_prepare_layout(cfg); > > > Here is the code that I used to preprocess my data in Fieldtrip: > > cfg = []; > cfg.trialfun = 'ft_trialfun_general'; > cfg.dataset = '136.set'; > cfg.trialdef.eventtype = 'trigger'; > cfg.trialdef.eventvalue = 'DIN8' > cfg.trialdef.prestim = 0.5; > cfg.trialdef.poststim = 2.5; > cfg = ft_definetrial(cfg); > > cfg.lpfilter = 'no'; > cfg.hpfilter = 'yes'; > cfg.hpfreq = 0.3; > data = ft_preprocessing(cfg); > > Anna Wieczorek-Taraday. > > PhD Student > Nencki Institute of Experimental Biology > Pasteur Street 3, 02-093 Warsaw, Poland > > Warsaw University of Social Sciences and Humanities > Chodakowska Street 19/31, 03-815 Warsaw, Poland > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From anna.wieczorek.taraday at gmail.com Tue May 12 17:25:43 2015 From: anna.wieczorek.taraday at gmail.com (Anna Wieczorek-Taraday) Date: Tue, 12 May 2015 17:25:43 +0200 Subject: [FieldTrip] EGI 64 - channel locations doesn't work in FTrip In-Reply-To: References: Message-ID: <72EDF4F9-1F07-42A1-B1B3-72174896C8A2@gmail.com> Hi Robert, Thank you for your help. Indeed, the location on the sphere looks good after adjusting these parameters. Thank you a lot. Best regards, Anna Sent from my iPad > On 12 May 2015, at 11:05, Robert Oostenveld wrote: > > Hi Ana > > The ft_prepare_layout function reads the electrode positions and scales them such that they fit in the sphere that represents the head. > > I suggest you do > > cfg.layout = ‘yourfilename’ > lay = ft_prepare_layout(cfg); > > cfg = []; > cfg.layout = lay; > ft_layoutplot(cfg); > > and then modify lay.pos repeatedly, every time plotting it again, until you are happy with the result. You probably want to do this for the vertical direction > lay.pos(:,2) = (lay.pos(:,2)+shift) .* scale; > to shift and scale the electrodes to a better fit inside/outside the sphere, and this for the horizontal > lay.pos(:,1) = lay.pos(:,1) .* scale; > as they seem to be properly centred along the x-axis alreadly. > > After this, you can > save yourlayout.mat lay > and specify “yourlayout.mat” as the layout filename for your future figures. > > > best regards > Robert > > > >> On 12 May 2015, at 10:17, Anna Wieczorek-Taraday wrote: >> >> Dear Fieldtrippers, >> >> I have a problem while reading EEG (EGI) electrode location file to FieldTrip. >> I am using EGI Amp 300, 64-channel cap, data were exported to .raw files. >> >> When I read locations to EEGLAB, it works well (lilnk to pictures || see pic. eeglab_chanlocs.jpg). The layout corresponds with the actual electrode placement in the cap. >> When I read the same file into FieldTrip, the electrodes seem to have similar layout (see pic. fieldtrip_chanlocs.jpg). >> However, it seems like the electrodes are confined within the plot too much. Electrodes E61:E64 should be outside of boundaries of the layout plot. >> >> I was wondering whether anybody else had similar issue and did overcome it? Could anybody suggest what is wrong and how can I read the locations properly? >> Any support will be appreciated. >> >> I am using Matlab 2015, eeglab eeglab13_4_4b and the latest version of fieldtrip. >> >> *************************************** >> >> >> Here is code I used to read these locations: >> >> cfg.layout = 'C:\Users\annwie\Documents\awt_chanlocs\GSN-HydroCel_64.sfp'; >> cfg.feedback = 'yes'; >> layout = ft_prepare_layout(cfg); >> >> >> Here is the code that I used to preprocess my data in Fieldtrip: >> >> cfg = []; >> cfg.trialfun = 'ft_trialfun_general'; >> cfg.dataset = '136.set'; >> cfg.trialdef.eventtype = 'trigger'; >> cfg.trialdef.eventvalue = 'DIN8' >> cfg.trialdef.prestim = 0.5; >> cfg.trialdef.poststim = 2.5; >> cfg = ft_definetrial(cfg); >> >> cfg.lpfilter = 'no'; >> cfg.hpfilter = 'yes'; >> cfg.hpfreq = 0.3; >> data = ft_preprocessing(cfg); >> >> Anna Wieczorek-Taraday. >> >> PhD Student >> Nencki Institute of Experimental Biology >> Pasteur Street 3, 02-093 Warsaw, Poland >> >> Warsaw University of Social Sciences and Humanities >> Chodakowska Street 19/31, 03-815 Warsaw, Poland >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Wed May 13 17:28:39 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Wed, 13 May 2015 17:28:39 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI Message-ID: Dear all, I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? If I am right, which command shall I use to organize individual WPLI data, in order to create a correct input for ‘ft_freqstatistics’. According to the tutorial, in case of time-frequency data it is ft_freqgrandaverage. However, if I use it for WPLI data, I have the following error: “This function requires freq data as input”. Could you please recommend me a tutorial, reference documentation or some comment on this issue? Thanks for any suggestions in advanced and let me know if the description of my problem is not clear! Zsolt -- ************************************************************ Ph.D. student Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Wed May 13 19:14:45 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 13 May 2015 19:14:45 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: Message-ID: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Hi Zsolt, > Dear all, > > > I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. > > > I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > You could. Stick with the tutorial you are currently working with. You should organize your data into cell arrays and call ft_freqstatistics like this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise ft_freqstatistics will default to ‘powspctrm’ which will be not present in the data. good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: From zerr.paul at googlemail.com Thu May 14 14:01:07 2015 From: zerr.paul at googlemail.com (Paul Zerr) Date: Thu, 14 May 2015 14:01:07 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found Message-ID: Hi all, I'm new to fieldtrip so forgive me if my mistake is obvious. I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with *cfg = []; * *cfg.dataset = '2.bdf';* *data = ft_preprocessing(cfg)* However, I get *reading and preprocessing* *error opening file: 2.bdf* *One or more output arguments not assigned during call to "read_24bit".* *Error in read_biosemi_bdf>readLowLevel (line 274)* * buf = read_24bit(filename, offset, numwords);* *Error in read_biosemi_bdf (line 242)* * buf = readLowLevel(filename, offset, epochlength); % see below in subfunction* *Error in ft_read_data (line 321)* * dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx);* *Error in ft_preprocessing (line 578)* * dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample,* * 'endsample', endsample, 'chanindx', rawindx, 'checkboundary',* * strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat)* *Error in Untitled (line 19)* *data = ft_preprocessing(cfg) * Using *cfg.trialdef.eventtype = '?';* outputs *"no events were found in the datafile"* for *ft_definetrial* even for datasets with many markers. Converting to EDF+ did not help as it then says *"channels with different sampling rate not supported"*. Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Defining only one channel to preprocess gives the same error. I couldn't find a solution in the archives, the faq, wiki or documentation. I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. Any ideas? Much appreciated, Paul Zerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Thu May 14 16:15:09 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Thu, 14 May 2015 16:15:09 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Message-ID: Hi Tzvetan, thanks for your suggestions. I am still stucked at the ft_freqstatistics, as I keep on receiving the following error and would be glad if you could make a comment on this as well: #### Reference to non-existent field 'label'. Error in ft_freqgrandaverage (line 123) cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); ### Is it because I have labelcomb in the WPLI data? labelcmb: {9x2 cell} dimord: 'chan_freq_time' wplispctrm: [9x7x16 double] freq: [3 4 5 6 7 8 9] time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] cfg: [1x1 struct] And this is my specification (I couldn't fine the option cfg.channelcmb for ft_freqgrandaverage in the reference documentation): cfg = []; cfg.keepindividual = 'yes'; cfg.cfg.foilim = 'all'; cfg.toilim = 'all'; cfg.channel = 'all'; cfg.parameter = 'wplispctrm'; Thanks again for the answer in advance! Best, Zsolt ps.I can provide other parts of my code but I don't want to make this mail too long : 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > > Dear all, > > > I would like to perform a cluster-based permutation test on weighted phase > lag index values by using a within-subjects experimental design. I have two > conditions (congruent and incongruent one) and my goal is to compute WPLI > between certain channel combinations (FCz and F3 for instance) and see the > WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two > conditions. > > > I experienced some difficulties after the point when I calculated the > WPLI data for each participant. To perform the above-mentioned comparison, > shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > > You could. Stick with the tutorial you are currently working with. You > should organize your data into cell arrays and call ft_freqstatistics like > this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). > Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise > ft_freqstatistics will default to ‘powspctrm’ which will be not present in > the data. > good luck > tzvetan > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Fri May 15 10:26:45 2015 From: B.Haendel at gmx.net (Barbara Haendel) Date: Fri, 15 May 2015 10:26:45 +0200 Subject: [FieldTrip] leadfields MNI-coordinates Message-ID: An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: warp_location.JPG Type: image/jpeg Size: 95511 bytes Desc: not available URL: From alexandra.bendixen at physik.tu-chemnitz.de Fri May 15 11:49:52 2015 From: alexandra.bendixen at physik.tu-chemnitz.de (Alexandra Bendixen) Date: Fri, 15 May 2015 11:49:52 +0200 Subject: [FieldTrip] Postdoc position in Chemnitz, Germany: Auditory perception & cognition Message-ID: Dear list, A postdoc position is available in my newly established Cognitive Systems Lab at Chemnitz University of Technology (https://www.tu-chemnitz.de/physik/SFKS/index.html.en). The lab is part of an interdisciplinary research center at the intersection of physics and psychology. Our research is centered around auditory perception and cognition, with extensions towards multisensory processing as well as towards effects of cognitive aging. Within this general framework, there is a great deal of flexibility in the specific research topic(s) pursued by the postdoc. We are looking for candidates with an academic university degree (M.Sc. equivalent) as well as a Ph.D. degree in psychology, neuroscience, cognitive science, or a related field. Good programming skills, good command of English, and prior publications in peer-reviewed journals are required. We use and combine EEG, eyetracking, and psychophysics methods. Candidates should have a strong background in at least one of these methods, or a complementary profile in cognitive/computational modeling. The position involves 4 hours of teaching per week at Bachelor or Master level, covering psychophysics and psychophysiology topics. To fulfill teaching requirements, knowledge of German is advantageous (but not strictly necessary). The position can be filled immediately and runs until March 31, 2018. Salary is determined by German public service regulations for full-term employment with a Ph.D. degree. Chemnitz University of Technology is dedicated to increasing the percentage of women in science. Therefore, female candidates are particularly encouraged to apply. Applicants with disabilities will be employed preferentially if equally qualified. This call is open until June 2nd, 2015. Anybody interested is welcome to contact me (alexandra.bendixen at physik.tu-chemnitz.de). For more information on the position and on how to apply, please visit https://www.tu-chemnitz.de/verwaltung/personal/stellen/212067_4_Ku.php I would be grateful if you could distribute this advert to anyone potentially interested. Many thanks, Alexandra Bendixen --- Prof. Dr. Alexandra Bendixen Cognitive Systems Lab Chemnitz University of Technology Faculty of Natural Sciences Institute of Physics New Physics Building, Room P137 Reichenhainer Str. 70 D-09126 Chemnitz, Germany Tel.: +49-(0)371-531-31681 Fax: +49-(0)371-531-831681 E-mail: alexandra.bendixen at physik.tu-chemnitz.de WWW: https://www.tu-chemnitz.de/physik/SFKS/alexandrabendixen.html.en From michelic72 at gmail.com Sat May 16 16:17:25 2015 From: michelic72 at gmail.com (Cristiano Micheli) Date: Sat, 16 May 2015 16:17:25 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: Message-ID: Dear Zsolt I experienced difficulties and encountered many pitfalls along the way too. What exactly will your metric be? wPLI of post onset versus baseline difference/ratio? wPLI difference of the two conditions? Do you common average re-reference your data before? The statistics that you will use will depend on your design. I would personally try a non-parametric design where you shuffle the index of the trials of one condition (if you do wPLI1-wPLI2) and consider the proportion of iterations exceeding the measured wPLI difference. Please consider though that both conditions should have the same number of trials. Could you attach the programming attempts that you tried so far together with the exact error outputs? I hope this helps so far. Cris Micheli On Wed, May 13, 2015 at 5:28 PM, Zsolt Turi wrote: > Dear all, > > > > I would like to perform a cluster-based permutation test on weighted phase > lag index values by using a within-subjects experimental design. I have two > conditions (congruent and incongruent one) and my goal is to compute WPLI > between certain channel combinations (FCz and F3 for instance) and see the > WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two > conditions. > > > I experienced some difficulties after the point when I calculated the > WPLI data for each participant. To perform the above-mentioned comparison, > shall I use ‘ft_freqstatistics’for the cluster-based permutation test? > > > > If I am right, which command shall I use to organize individual WPLI data, > in order to create a correct input for ‘ft_freqstatistics’. According to > the tutorial, in case of time-frequency data it is ft_freqgrandaverage. > However, if I use it for WPLI data, I have the following error: “This > function requires freq data as input”. > > > > Could you please recommend me a tutorial, reference documentation or some > comment on this issue? > > > > Thanks for any suggestions in advanced and let me know if the description > of my problem is not clear! > > > > Zsolt > > -- > ************************************************************ > Ph.D. student > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 08:18:54 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 08:18:54 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> Message-ID: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Hi Zsolt, > Hi Tzvetan, > > thanks for your suggestions. > I am still stucked at the ft_freqstatistics, as I keep on receiving the following error and would be glad if you could make a comment on this as well: > > #### > Reference to non-existent field 'label'. > > Error in ft_freqgrandaverage (line 123) > cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); > ### > > Is it because I have labelcomb in the WPLI data? yes > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x7x16 double] > freq: [3 4 5 6 7 8 9] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > And this is my specification (I couldn't fine the option cfg.channelcmb for ft_freqgrandaverage in the reference documentation): again try to give cell arrays as input to ft_freqanalysis. I’m still considering the case you mentioned in your initial e-mail, one channel etc. e.g. cfg.channel = ‘FCzF3’; cfg.parameter = ‘wplispctrm’; cfg.neighbours = []; % this will force clustering over time and freq dimension best tzvetan > > cfg = []; > cfg.keepindividual = 'yes'; > cfg.cfg.foilim = 'all'; > cfg.toilim = 'all'; > cfg.channel = 'all'; > cfg.parameter = 'wplispctrm'; > > Thanks again for the answer in advance! > > Best, > Zsolt > > ps.I can provide other parts of my code but I don't want to make this mail too long : > > > > 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > >> Dear all, >> >> >> I would like to perform a cluster-based permutation test on weighted phase lag index values by using a within-subjects experimental design. I have two conditions (congruent and incongruent one) and my goal is to compute WPLI between certain channel combinations (FCz and F3 for instance) and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the two conditions. >> >> >> I experienced some difficulties after the point when I calculated the WPLI data for each participant. To perform the above-mentioned comparison, shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >> > You could. Stick with the tutorial you are currently working with. You should organize your data into cell arrays and call ft_freqstatistics like this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise ft_freqstatistics will default to ‘powspctrm’ which will be not present in the data. > good luck > tzvetan > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 08:19:41 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 08:19:41 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: > > again try to give cell arrays as input to ft_freqanalysis I’m sorry I meant ft_freqstatistics here tz From zsoltturi at gmail.com Mon May 18 11:33:48 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Mon, 18 May 2015 11:33:48 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Hi Tzvetan and Chris, thanks for your emails. Removing channelcmb and adding a new one called label solved my problem. Chris: I'ld like to compare the WPLI difference of two conditions, congruent and incongruent ones by using a within-subjects design (so not a between trials comparison). >From your email I may infer that after running wpli, I should still have my trials. However, I do not have repetitions (trials) anymore in the output structure. Am I doing an illegitimate step during wPLI calculation or miss one specification? cfg = []; cfg.method = 'wpli'; dataWPLI = ft_connectivityanalysis(cfg,TFRhann); labelcmb: {9x2 cell} dimord: 'chan_freq_time' wplispctrm: [9x43x16 double] freq: [1x43 double] time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] cfg: [1x1 struct] Thanks for your help! Best, Zsolt 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : > Hi Zsolt, > > > Hi Tzvetan, > > thanks for your suggestions. > I am still stucked at the ft_freqstatistics, as I keep on receiving the > following error and would be glad if you could make a comment on this as > well: > > #### > Reference to non-existent field 'label'. > > Error in ft_freqgrandaverage (line 123) > cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); > ### > > Is it because I have labelcomb in the WPLI data? > > yes > > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x7x16 double] > freq: [3 4 5 6 7 8 9] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 > 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > And this is my specification (I couldn't fine the option cfg.channelcmb > for ft_freqgrandaverage in the reference documentation): > > again try to give cell arrays as input to ft_freqanalysis. I’m still > considering the case you mentioned in your initial e-mail, one channel etc. > e.g. cfg.channel = ‘FCzF3’; > cfg.parameter = ‘wplispctrm’; > cfg.neighbours = []; % this will force clustering over time and > freq dimension > > best > tzvetan > > > cfg = []; > cfg.keepindividual = 'yes'; > cfg.cfg.foilim = 'all'; > cfg.toilim = 'all'; > cfg.channel = 'all'; > cfg.parameter = 'wplispctrm'; > > Thanks again for the answer in advance! > > Best, > Zsolt > > ps.I can provide other parts of my code but I don't want to make this mail > too long : > > > > 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : > >> Hi Zsolt, >> >> >> Dear all, >> >> >> I would like to perform a cluster-based permutation test on weighted >> phase lag index values by using a within-subjects experimental design. I >> have two conditions (congruent and incongruent one) and my goal is to >> compute WPLI between certain channel combinations (FCz and F3 for instance) >> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >> two conditions. >> >> >> I experienced some difficulties after the point when I calculated the >> WPLI data for each participant. To perform the above-mentioned comparison, >> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >> >> You could. Stick with the tutorial you are currently working with. You >> should organize your data into cell arrays and call ft_freqstatistics like >> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >> the data. >> good luck >> tzvetan >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Mon May 18 18:30:03 2015 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Mon, 18 May 2015 16:30:03 +0000 Subject: [FieldTrip] Source Reconstruction: MNI or subject space Message-ID: <1431966603032.7006@nin.knaw.nl> Dear FieldTrippers, When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Mon May 18 20:02:05 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Mon, 18 May 2015 20:02:05 +0200 Subject: [FieldTrip] Source Reconstruction: MNI or subject space In-Reply-To: <1431966603032.7006@nin.knaw.nl> References: <1431966603032.7006@nin.knaw.nl> Message-ID: Dear Rajat, one option that is widely used by FieldTrip users, I believe, is the computation of source model aligned in MNI space while retaining the individual head model. This FAQ explains how to do this. http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space best tzvetan > Dear FieldTrippers, > > When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? > > > Thank you. > Rajat > > > > > > Rajat Mani Thomas > Social Brain Lab > Netherlands Institute for Neuroscience > Amsterdam > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 18 21:54:08 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 18 May 2015 19:54:08 +0000 Subject: [FieldTrip] problem reading bdf-file References: Message-ID: <4C5E591D-C0B8-4161-8070-80CA60521DB3@fcdonders.ru.nl> Dear all, I want to import a raw, markerless datafile (http://www.filedropper.com/1_20) by using cfg = []; cfg.dataset = '2.bdf'; data = ft_preprocessing(cfg) However, I get reading and preprocessing error opening file: 2.bdf One or more output arguments not assigned during call to "read_24bit". Error in read_biosemi_bdf>readLowLevel (line 274) buf = read_24bit(filename, offset, numwords); Error in read_biosemi_bdf (line 242) buf = readLowLevel(filename, offset, epochlength); % see below in subfunction Error in ft_read_data (line 321) dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 578) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Error in Untitled (line 19) data = ft_preprocessing(cfg) Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Best, Paul -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.thomas at nin.knaw.nl Tue May 19 10:23:19 2015 From: r.thomas at nin.knaw.nl (Rajat Thomas) Date: Tue, 19 May 2015 08:23:19 +0000 Subject: [FieldTrip] using SPM to transform EEG electrode location Message-ID: <1432023799396.61888@nin.knaw.nl> Hi FieldTrippers and users of SPM I have, (i) the coordinates of my EEG electrodes in MNI space (ii) the y_*.nii and iy_*.nii files (deformation fields from SPM segmentation that is used to transform back and forth from subj->MNI. Does anyone know how to use the deformation fields on the 3D coordinates in MNI space to get the electrode locations in subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Tue May 19 11:09:09 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Tue, 19 May 2015 09:09:09 +0000 Subject: [FieldTrip] leadfields MNI-coordinates In-Reply-To: References: Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> Hi Barbara, Your code actually looks fine to me. Some things that I could think of: 1. Did you specify cfg.coordinates=’mni’ before applying ft_volumenormalise? 2. Did you select the right volumes for plotting? So a. For CTF head space: % make a figure of the single subject headmodel cfg=[]; cfg.location=ctfpos(i,:); cfg.locationcoordinates='head'; ft_sourceplot(cfg,mri_realign) b. And for MNI-space: cfg=[]; cfg.location=targets(i,:); cfg.locationcoordinates='head'; ft_sourceplot(cfg,mri_realign_mni) This should lead to the same anatomical locations. Hope this helps! Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Barbara Haendel Sent: vrijdag 15 mei 2015 10:27 To: fieldtrip at science.ru.nl Subject: [FieldTrip] leadfields MNI-coordinates Hi there, I found this very nice thread on warping between spm and ctf space (thanks Jan-Mathijs and Stan) and at first sight it seems to work fine (numbers match after applying warping back and forth) but when I try to navigate to the spot in the plotted figure the point of interest seems not to be the same. mri_realign_mni=ft_volumenormalise([],mri_realign) % Inverse warping mnipos=[-48 -75 8]; % [46 -78 6]; MT posback=ft_warp_apply(mri_realign_mni.params,mnipos,'sn2individual') ctfpos= ft_warp_apply(pinv(mri_realign_mni.initial),posback) -8.6110 55.6190 50.0473 I plotted either (see .jpg) A. the source (source = ft_sourceanalysis(cfg, freq)); B. the interpolated source (sourceInt = ft_sourceinterpolate(cfg, source , mri_realign); C. the normalized source (sourceIntNorm = ft_volumenormalise(cfg, sourceInt); and manually navigated to the respective coordinates. While for the normalized source the location makes sense (area MT) the location for A and B seems different. Is there any obvious mistake I’m overlooking? Thanks a lot! Barbara -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Tue May 19 11:17:25 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Tue, 19 May 2015 09:17:25 +0000 Subject: [FieldTrip] Source Reconstruction: MNI or subject space In-Reply-To: References: <1431966603032.7006@nin.knaw.nl> Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C1793D04F@exprd03.hosting.ru.nl> Dear Rajat, Both options are fine in principle. The only thing to keep in mind is that you used a non-warped volume (with either a CTF or MNI-grid) when computing the leadfields. It is crucial that these are computed based on the actual physical proportions/relations of the brain and sensors. Best, Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Tzvetan Popov Sent: maandag 18 mei 2015 20:02 To: FieldTrip discussion list Subject: Re: [FieldTrip] Source Reconstruction: MNI or subject space Dear Rajat, one option that is widely used by FieldTrip users, I believe, is the computation of source model aligned in MNI space while retaining the individual head model. This FAQ explains how to do this. http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space best tzvetan Dear FieldTrippers, When you have to perform source reconstruction, do you do it in MNI space (after warping the T1 image to MNI coordinates?) or is it better to do it in the individual subject space? Thank you. Rajat Rajat Mani Thomas Social Brain Lab Netherlands Institute for Neuroscience Amsterdam _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue May 19 12:47:43 2015 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 19 May 2015 12:47:43 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Dear Zsolt, please find an answer below. Regards Cris On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > Hi Tzvetan and Chris, > > thanks for your emails. > Removing channelcmb and adding a new one called label solved my problem. > > Chris: > I'ld like to compare the WPLI difference of two conditions, congruent and > incongruent ones by using a within-subjects design (so not a between trials > comparison). > From your email I may infer that after running wpli, I should still have > my trials. However, I do not have repetitions (trials) anymore in the > output structure. Am I doing an illegitimate step during wPLI calculation > or miss one specification? > You did it correctly. After running the wPLI metric ( I suggest the unbiased version of it, use the 'wpli_debiased' method in ft_connectivityanalysis) you are left with no trials. This is because the trials dimension (and tapers) are used to estimate the phase lag index. If I left that implied in the previous mail, I did not communicate it very well. What I meant to say is to be careful in the contrast of two conditions, because the subtraction (or ratio, or else...) will generate fake effects (or false positives) if the trials in condition 1 and condition 2 BEFORE wPLI calculation are different. I hope this helps Cris > cfg = []; > cfg.method = 'wpli'; > dataWPLI = ft_connectivityanalysis(cfg,TFRhann); > > > labelcmb: {9x2 cell} > dimord: 'chan_freq_time' > wplispctrm: [9x43x16 double] > freq: [1x43 double] > time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 > 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] > cfg: [1x1 struct] > > Thanks for your help! > > Best, > Zsolt > > > > > 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : > >> Hi Zsolt, >> >> >> Hi Tzvetan, >> >> thanks for your suggestions. >> I am still stucked at the ft_freqstatistics, as I keep on receiving the >> following error and would be glad if you could make a comment on this as >> well: >> >> #### >> Reference to non-existent field 'label'. >> >> Error in ft_freqgrandaverage (line 123) >> cfg.channel = ft_channelselection(cfg.channel, varargin{i}.label); >> ### >> >> Is it because I have labelcomb in the WPLI data? >> >> yes >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x7x16 double] >> freq: [3 4 5 6 7 8 9] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> And this is my specification (I couldn't fine the option cfg.channelcmb >> for ft_freqgrandaverage in the reference documentation): >> >> again try to give cell arrays as input to ft_freqanalysis. I’m still >> considering the case you mentioned in your initial e-mail, one channel etc. >> e.g. cfg.channel = ‘FCzF3’; >> cfg.parameter = ‘wplispctrm’; >> cfg.neighbours = []; % this will force clustering over time and >> freq dimension >> >> best >> tzvetan >> >> >> cfg = []; >> cfg.keepindividual = 'yes'; >> cfg.cfg.foilim = 'all'; >> cfg.toilim = 'all'; >> cfg.channel = 'all'; >> cfg.parameter = 'wplispctrm'; >> >> Thanks again for the answer in advance! >> >> Best, >> Zsolt >> >> ps.I can provide other parts of my code but I don't want to make this >> mail too long : >> >> >> >> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Dear all, >>> >>> >>> I would like to perform a cluster-based permutation test on weighted >>> phase lag index values by using a within-subjects experimental design. I >>> have two conditions (congruent and incongruent one) and my goal is to >>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >>> two conditions. >>> >>> >>> I experienced some difficulties after the point when I calculated the >>> WPLI data for each participant. To perform the above-mentioned comparison, >>> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >>> >>> You could. Stick with the tutorial you are currently working with. You >>> should organize your data into cell arrays and call ft_freqstatistics like >>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >>> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >>> the data. >>> good luck >>> tzvetan >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, Göttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > > -- > ************************************************************ > Ph.D. > Department of Clinical Neurophysiology > Georg-August University, Göttingen > Robert-Koch-Str. 40 > 37075 Goettingen > Web: http://www.uni-goettingen.de/en/222525.html > ************************************************************ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.Haendel at gmx.net Wed May 20 08:20:09 2015 From: B.Haendel at gmx.net (Barbara Haendel) Date: Wed, 20 May 2015 08:20:09 +0200 Subject: [FieldTrip] leadfields MNI-coordinates In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> References: , <7CCA2706D7A4DA45931A892DF3C2894C1793BFFA@exprd03.hosting.ru.nl> Message-ID: An HTML attachment was scrubbed... URL: From e.caspar at ucl.ac.uk Wed May 20 10:20:57 2015 From: e.caspar at ucl.ac.uk (Caspar, Emilie) Date: Wed, 20 May 2015 08:20:57 +0000 Subject: [FieldTrip] Tiggers added manually Message-ID: Dear Fieldtrippers, I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. Many thanks in advance! Emilie From rb643 at medschl.cam.ac.uk Wed May 20 12:34:32 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Wed, 20 May 2015 10:34:32 +0000 Subject: [FieldTrip] data segmenting and frequency analysis Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> Dear Fieldtrippers, Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. Thus, my questions are: 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? If a: how does freqanalysis handle multiple trials? I currently use this: cfg.method = 'wavelet'; cfg.output = 'powandcsd'; cfg.channel = 1:64; cfg.foilim = [0 70]; cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: cfg.method = 'wpli'; wpli_data = ft_connectivityanalysis(cfg, freq_data); 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? Any help would be much appreciated! Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From spa268 at nyu.edu Wed May 20 12:44:22 2015 From: spa268 at nyu.edu (Stephen Politzer-Ahles) Date: Wed, 20 May 2015 06:44:22 -0400 Subject: [FieldTrip] Tiggers added manually Message-ID: Hi Emilie, You could add new rows to the trial definition matrix (cfg.trl) to add new triggers. See http://www.fieldtriptoolbox.org/reference/ft_definetrial for information on how cfg.trl is organized. There might be more efficient built-in ways to do it, but this is how I add triggers at least. Best, Steve > ------------------------------ > > Message: 3 > Date: Wed, 20 May 2015 08:20:57 +0000 > From: "Caspar, Emilie" > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Tiggers added manually > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. > > Many thanks in advance! > > Emilie > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 17 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From melissa.ralston at gmail.com Wed May 20 20:34:33 2015 From: melissa.ralston at gmail.com (Melissa Smith) Date: Wed, 20 May 2015 11:34:33 -0700 Subject: [FieldTrip] Reading/importing .daq files Message-ID: Hi Fieldtrip community, My name is Melissa and I have a very basic question as I am just starting to use the Fieldtrip toolbox. I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 channels. So, each trial has four .daq data files (one for each amplifier containing 16 channels). What is the best way to import and read this data for analysis using Fieldtrip? Thanks in advance for your time! Best, Melissa -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcantor at umich.edu Wed May 20 20:51:02 2015 From: mcantor at umich.edu (Max Cantor) Date: Wed, 20 May 2015 14:51:02 -0400 Subject: [FieldTrip] Reading/importing .daq files In-Reply-To: References: Message-ID: I don't know about g.tec amps or .daq files specifically, but one way I can think to do it would be to load them each in separately and then use ft_appenddata. Coincidentally, I'm actually heading to Seattle tomorrow to visit a friend of mine at University of Washington! Great place :) Best, Max On Wed, May 20, 2015 at 2:34 PM, Melissa Smith wrote: > Hi Fieldtrip community, > > My name is Melissa and I have a very basic question as I am just starting > to use the Fieldtrip toolbox. > > I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 > channels. So, each trial has four .daq data files (one for each amplifier > containing 16 channels). > > What is the best way to import and read this data for analysis using > Fieldtrip? > > Thanks in advance for your time! > > Best, > Melissa > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Lab Manager Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: From tzvetan.popov at uni-konstanz.de Wed May 20 21:23:26 2015 From: tzvetan.popov at uni-konstanz.de (Tzvetan Popov) Date: Wed, 20 May 2015 21:23:26 +0200 Subject: [FieldTrip] data segmenting and frequency analysis In-Reply-To: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> References: <3188FAB8621D294696F13E80A7BBC97EFF4759E5@me-mbx3.medschl.cam.ac.uk> Message-ID: Dear Richard, > Dear Fieldtrippers, > > Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. you might check this page that illustrates a way to do this. It is in source space yet in your case you’ll stay on the electrode level. http://www.fieldtriptoolbox.org/tutorial/networkanalysis Keep in mind that sensor/electrode level connectivity metrics, regardless of the metric, come with some difficulties that are not trivial to solve. Maybe is good if you consult this lecture first: https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. cfg = []; cfg.dataset = ‘yourdataset'; cfg.trialdef.triallength = 4; cfg.trialdef.ntrials = Inf; cfg = ft_definetrial(cfg); cfg.channel = {‘EEG'}; data = ft_preprocessing(cfg); If you generate several of these data structures corresponding to your 1-minute epochs you can do data = ft_appenddata([],data1,data2). This way you combine them in one data structure. > After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. > > Thus, my questions are: > 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? > If a: how does freqanalysis handle multiple trials? I currently use this: > cfg.method = 'wavelet'; > cfg.output = 'powandcsd'; > cfg.channel = 1:64; > cfg.foilim = [0 70]; > cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] > [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data > > Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? Then for a given frequency in this example 8-12 Hz you could do this: cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.tapsmofrq = 2; cfg.foi = 10; freq_data = ft_freqanalysis(cfg, data); and subsequently use ft_connectivityanalysis with the metric of your choice. > > If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? there are two functions you might want to check: ft_redefinetrial and ft_selectdata > > 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? I would definitely remove the channel but there are certainly other opinions on that. > > 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? You can- cfg.foi = [0:1:100] gives you 0 to 100 Hz in steps of 1 Hz. Whether or not your frequency resolution is 1 Hz is different issue. You might check out this lecture too: https://www.youtube.com/watch?v=vwPpSglPJTE > > 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: > > cfg.method = 'wpli'; > wpli_data = ft_connectivityanalysis(cfg, freq_data); see above > > 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? no, you have to decide what value corresponds to a connection = 1 and what not =0 > Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? ft_selectdata with cfg.avgoverfreq = ‘yes' > Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? I don’t get that one. Good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: From zsoltturi at gmail.com Wed May 20 22:24:38 2015 From: zsoltturi at gmail.com (Zsolt Turi) Date: Wed, 20 May 2015 22:24:38 +0200 Subject: [FieldTrip] cluster-based permutation test on WPLI In-Reply-To: References: <80A8567B-FE52-4CF9-AE99-DE2370A6EE15@uni-konstanz.de> <879D5CD1-4C08-4D90-BC78-8F6795CC7116@uni-konstanz.de> Message-ID: Dear Chris, thanks again for your comment. Cheers, Zsolt 2015-05-19 12:47 GMT+02:00 Cristiano Micheli : > > Dear Zsolt, > please find an answer below. > Regards > Cris > > On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > >> Hi Tzvetan and Chris, >> >> thanks for your emails. >> Removing channelcmb and adding a new one called label solved my problem. >> >> Chris: >> I'ld like to compare the WPLI difference of two conditions, congruent and >> incongruent ones by using a within-subjects design (so not a between trials >> comparison). >> From your email I may infer that after running wpli, I should still have >> my trials. However, I do not have repetitions (trials) anymore in the >> output structure. Am I doing an illegitimate step during wPLI calculation >> or miss one specification? >> > > You did it correctly. > After running the wPLI metric ( I suggest the unbiased version of it, use > the 'wpli_debiased' method in ft_connectivityanalysis) you are left with > no trials. This is because the trials dimension (and tapers) are used to > estimate the phase lag index. If I left that implied in the previous mail, > I did not communicate it very well. What I meant to say is to be careful in > the contrast of two conditions, because the subtraction (or ratio, or > else...) will generate fake effects (or false positives) if the trials in > condition 1 and condition 2 BEFORE wPLI calculation are different. > > I hope this helps > Cris > > >> cfg = []; >> cfg.method = 'wpli'; >> dataWPLI = ft_connectivityanalysis(cfg,TFRhann); >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x43x16 double] >> freq: [1x43 double] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> Thanks for your help! >> >> Best, >> Zsolt >> >> >> >> >> 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Hi Tzvetan, >>> >>> thanks for your suggestions. >>> I am still stucked at the ft_freqstatistics, as I keep on receiving the >>> following error and would be glad if you could make a comment on this as >>> well: >>> >>> #### >>> Reference to non-existent field 'label'. >>> >>> Error in ft_freqgrandaverage (line 123) >>> cfg.channel = ft_channelselection(cfg.channel, >>> varargin{i}.label); >>> ### >>> >>> Is it because I have labelcomb in the WPLI data? >>> >>> yes >>> >>> >>> labelcmb: {9x2 cell} >>> dimord: 'chan_freq_time' >>> wplispctrm: [9x7x16 double] >>> freq: [3 4 5 6 7 8 9] >>> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >>> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >>> cfg: [1x1 struct] >>> >>> And this is my specification (I couldn't fine the option cfg.channelcmb >>> for ft_freqgrandaverage in the reference documentation): >>> >>> again try to give cell arrays as input to ft_freqanalysis. I’m still >>> considering the case you mentioned in your initial e-mail, one channel etc. >>> e.g. cfg.channel = ‘FCzF3’; >>> cfg.parameter = ‘wplispctrm’; >>> cfg.neighbours = []; % this will force clustering over time and >>> freq dimension >>> >>> best >>> tzvetan >>> >>> >>> cfg = []; >>> cfg.keepindividual = 'yes'; >>> cfg.cfg.foilim = 'all'; >>> cfg.toilim = 'all'; >>> cfg.channel = 'all'; >>> cfg.parameter = 'wplispctrm'; >>> >>> Thanks again for the answer in advance! >>> >>> Best, >>> Zsolt >>> >>> ps.I can provide other parts of my code but I don't want to make this >>> mail too long : >>> >>> >>> >>> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov >>> : >>> >>>> Hi Zsolt, >>>> >>>> >>>> Dear all, >>>> >>>> >>>> I would like to perform a cluster-based permutation test on weighted >>>> phase lag index values by using a within-subjects experimental design. I >>>> have two conditions (congruent and incongruent one) and my goal is to >>>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>>> and see the WPLI change let’s say in 3-9 Hz and -100 to 500 ms between the >>>> two conditions. >>>> >>>> >>>> I experienced some difficulties after the point when I calculated the >>>> WPLI data for each participant. To perform the above-mentioned comparison, >>>> shall I use ‘ft_freqstatistics’for the cluster-based permutation test? >>>> >>>> You could. Stick with the tutorial you are currently working with. You >>>> should organize your data into cell arrays and call ft_freqstatistics like >>>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>>> Furthermore you should specify cfg.parameter = ‘wplispctrm’ otherwise >>>> ft_freqstatistics will default to ‘powspctrm’ which will be not present in >>>> the data. >>>> good luck >>>> tzvetan >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> ************************************************************ >>> Ph.D. >>> Department of Clinical Neurophysiology >>> Georg-August University, Göttingen >>> Robert-Koch-Str. 40 >>> 37075 Goettingen >>> Web: http://www.uni-goettingen.de/en/222525.html >>> ************************************************************ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, Göttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, Göttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Thu May 21 14:02:53 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Thu, 21 May 2015 12:02:53 +0000 Subject: [FieldTrip] data segmenting and frequency analysis (Tzvetan Popov) Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF47FDCE@me-mbx3.medschl.cam.ac.uk> Hi Tzvetan and others, Thanks for all the wonderful feedback and links to resources! I did manage to sort out the redefine trials issue now to split the trial up in smaller segments. As for faulty channels, I found the option to repair channels (which I would prefer to keep the matrix sizes the same). When looking at the data this does seem to adequately resolve the one faulty channel I had with the specific subject I was looking at. For some reason however this seems to cause some errors in later on displaying the ICA topoplots (the ICA itself still seems to run fine, but when inspecting the components I only see the timecourses and not the topoplots)? An error in matlabs surf function in using complex numbers is all I get back? As for the frequencies of interest: I would ideally like to use wavelet decomposition rather than fourier transformations to obtain a specific power. I assume I can set this in cfg_foi and then run ft_freqanalysis on the different bands, but at what point would you collapse or average the windows together? As for the connectivity analysis, the reason I would like to use wpli is precisely to get around the volume conduction issue and the fact that I only have the elecrode level metrics. It does seem however as though something is missing in my pipeline before that as the cross and power spectra contains a lot of NaN's? I am also not sure about when to average over the wavelet windows or frequency 'timepoints' (going from the 3D wpli spectrum to a vector or a 2 matrix)? Related to that last point was my question about the adjacency matrix, the connectivity analysis output just list all the wpl indices per channel pair, but I would rather have the 2D matrix (with nothing trilled off) that lists all channels against all channels? Just to sum up my remaining questions: 1. Why would channelrepair result in issues with ICA's topoplot and how to fix that (it would be good to see if the noise from the one faulty channel is really gone)? 2. How to obtain a metric per frequency band (using wavelets)/or alternatively at what point in the analysis should the wavelet decomposition be averaged? 3. How to obtain a 64*64 matrix (all channels*all channels) of the wpl indices? For reference, my entire (under construction) code is here: https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m Cheers, Richard ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of fieldtrip-request at science.ru.nl [fieldtrip-request at science.ru.nl] Sent: 21 May 2015 11:00 To: fieldtrip at science.ru.nl Subject: fieldtrip Digest, Vol 54, Issue 18 Send fieldtrip mailing list submissions to fieldtrip at science.ru.nl To subscribe or unsubscribe via the World Wide Web, visit http://mailman.science.ru.nl/mailman/listinfo/fieldtrip or, via email, send a message with subject or body 'help' to fieldtrip-request at science.ru.nl You can reach the person managing the list at fieldtrip-owner at science.ru.nl When replying, please edit your Subject line so it is more specific than "Re: Contents of fieldtrip digest..." Today's Topics: 1. data segmenting and frequency analysis (Richard Bethlehem) 2. Re: Tiggers added manually (Stephen Politzer-Ahles) 3. Reading/importing .daq files (Melissa Smith) 4. Re: Reading/importing .daq files (Max Cantor) 5. Re: data segmenting and frequency analysis (Tzvetan Popov) 6. Re: cluster-based permutation test on WPLI (Zsolt Turi) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 May 2015 10:34:32 +0000 From: Richard Bethlehem To: "fieldtrip at science.ru.nl" Subject: [FieldTrip] data segmenting and frequency analysis Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4759E5 at me-mbx3.medschl.cam.ac.uk> Content-Type: text/plain; charset="iso-8859-1" Dear Fieldtrippers, Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. Thus, my questions are: 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? If a: how does freqanalysis handle multiple trials? I currently use this: cfg.method = 'wavelet'; cfg.output = 'powandcsd'; cfg.channel = 1:64; cfg.foilim = [0 70]; cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: cfg.method = 'wpli'; wpli_data = ft_connectivityanalysis(cfg, freq_data); 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? Any help would be much appreciated! Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 2 Date: Wed, 20 May 2015 06:44:22 -0400 From: Stephen Politzer-Ahles To: fieldtrip at science.ru.nl Subject: Re: [FieldTrip] Tiggers added manually Message-ID: Content-Type: text/plain; charset="utf-8" Hi Emilie, You could add new rows to the trial definition matrix (cfg.trl) to add new triggers. See http://www.fieldtriptoolbox.org/reference/ft_definetrial for information on how cfg.trl is organized. There might be more efficient built-in ways to do it, but this is how I add triggers at least. Best, Steve > ------------------------------ > > Message: 3 > Date: Wed, 20 May 2015 08:20:57 +0000 > From: "Caspar, Emilie" > To: "fieldtrip at science.ru.nl" > Subject: [FieldTrip] Tiggers added manually > Message-ID: > Content-Type: text/plain; charset="us-ascii" > > Dear Fieldtrippers, > > I have continuous EEG data and I have to add manually new triggers at some point in the signal. I have checked on the website but did not find anything relevant. I was thus wondering whether or not it was possible to add manually triggers with Fieldtrip and if yes (and if there are several ways to do it), what is the most convenient/efficient method. > > Many thanks in advance! > > Emilie > > > ------------------------------ > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > > End of fieldtrip Digest, Vol 54, Issue 17 > ***************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 3 Date: Wed, 20 May 2015 11:34:33 -0700 From: Melissa Smith To: fieldtrip at science.ru.nl Subject: [FieldTrip] Reading/importing .daq files Message-ID: Content-Type: text/plain; charset="utf-8" Hi Fieldtrip community, My name is Melissa and I have a very basic question as I am just starting to use the Fieldtrip toolbox. I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 channels. So, each trial has four .daq data files (one for each amplifier containing 16 channels). What is the best way to import and read this data for analysis using Fieldtrip? Thanks in advance for your time! Best, Melissa -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 4 Date: Wed, 20 May 2015 14:51:02 -0400 From: Max Cantor To: FieldTrip discussion list Subject: Re: [FieldTrip] Reading/importing .daq files Message-ID: Content-Type: text/plain; charset="utf-8" I don't know about g.tec amps or .daq files specifically, but one way I can think to do it would be to load them each in separately and then use ft_appenddata. Coincidentally, I'm actually heading to Seattle tomorrow to visit a friend of mine at University of Washington! Great place :) Best, Max On Wed, May 20, 2015 at 2:34 PM, Melissa Smith wrote: > Hi Fieldtrip community, > > My name is Melissa and I have a very basic question as I am just starting > to use the Fieldtrip toolbox. > > I am analyzing EEG data recorded with g.tec amplifiers. I am recording 64 > channels. So, each trial has four .daq data files (one for each amplifier > containing 16 channels). > > What is the best way to import and read this data for analysis using > Fieldtrip? > > Thanks in advance for your time! > > Best, > Melissa > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- Max Cantor Lab Manager Computational Neurolinguistics Lab University of Michigan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 5 Date: Wed, 20 May 2015 21:23:26 +0200 From: Tzvetan Popov To: FieldTrip discussion list Subject: Re: [FieldTrip] data segmenting and frequency analysis Message-ID: Content-Type: text/plain; charset="windows-1252" Dear Richard, > Dear Fieldtrippers, > > Being somewhat new to using fieldtrip I was hoping someone would be able to help me sort out some parcellation and data-handling issues. In short: I'm working with resting state EEG data, recorded with a 64-channel BioSemi system and would like to do some graph based analyses on this. you might check this page that illustrates a way to do this. It is in source space yet in your case you?ll stay on the electrode level. http://www.fieldtriptoolbox.org/tutorial/networkanalysis Keep in mind that sensor/electrode level connectivity metrics, regardless of the metric, come with some difficulties that are not trivial to solve. Maybe is good if you consult this lecture first: https://www.youtube.com/watch?v=ZBwh0Vm4fh4 > The data is 4 minutes (eyes-open, eyes-closed 1-minute epochs) and ideally I would like to split these two 1 minute eyes-closed parts into 30*4s epochs. cfg = []; cfg.dataset = ?yourdataset'; cfg.trialdef.triallength = 4; cfg.trialdef.ntrials = Inf; cfg = ft_definetrial(cfg); cfg.channel = {?EEG'}; data = ft_preprocessing(cfg); If you generate several of these data structures corresponding to your 1-minute epochs you can do data = ft_appenddata([],data1,data2). This way you combine them in one data structure. > After this I would like to run a wavelet decomposition for the frequency analysis and obtain the adjacency matrix based on weighted phase lag index. > > Thus, my questions are: > 1. How to handle parcellating data? Shoud I use a)"toi" in ft_freqanalysis as a sliding window or b) split at trial definition? > If a: how does freqanalysis handle multiple trials? I currently use this: > cfg.method = 'wavelet'; > cfg.output = 'powandcsd'; > cfg.channel = 1:64; > cfg.foilim = [0 70]; > cfg.toi = [5 10 15 20 25 30 35 40 45 50 55] > [freq_data] = ft_freqanalysis(cfg, data_iccleaned) % run over ICA cleaned data > > Which does give me 11 fragments, but I am not sure how the two 1-minute epochs/trials are handled in this or if they are adequately handles in the subsequent ft_connectivityanalysis? Then for a given frequency in this example 8-12 Hz you could do this: cfg = []; cfg.method = 'mtmfft'; cfg.output = 'fourier'; cfg.keeptrials = 'yes'; cfg.tapsmofrq = 2; cfg.foi = 10; freq_data = ft_freqanalysis(cfg, data); and subsequently use ft_connectivityanalysis with the metric of your choice. > > If b: how can you split trial in different epochs of a certain length and how does ft_freqanalysis handle multiple trials? there are two functions you might want to check: ft_redefinetrial and ft_selectdata > > 2. How to deal with faulty or noisy channels? If there are some noisy channels, do you remove these? Removing channels does not seem ideal as it would mean having to deal with uneven graphs (graphs with different numbers of nodes). Leaving them in might bias the wpli estimation? I would definitely remove the channel but there are certainly other opinions on that. > > 3. Can you set the interval length for ft_freqanalysis (and if so, how)? It currently takes 0.02Hz increments, is that standard? You can- cfg.foi = [0:1:100] gives you 0 to 100 Hz in steps of 1 Hz. Whether or not your frequency resolution is 1 Hz is different issue. You might check out this lecture too: https://www.youtube.com/watch?v=vwPpSglPJTE > > 4. Is it necessary to tell ft_connectivityanalysis to use mutliple trials/segments? I currently get the message saying it needs more than 1 trial, even though ft_freqanalysis returns an x*x*11 matrix (and I'm assuming the 11 are the windows set for the wavelet decomposition). I am just using this: > > cfg.method = 'wpli'; > wpli_data = ft_connectivityanalysis(cfg, freq_data); see above > > 5. Is it possible to automatically obtain the wpli adjacency matrix per frequency band? no, you have to decide what value corresponds to a connection = 1 and what not =0 > Is there a fieldtrip function to average over a range of frequencies (and/or timepoints/trils) from the ft_connectivity analysis output? ft_selectdata with cfg.avgoverfreq = ?yes' > Is there a fieldtrip function to convert individal wpli's back to a complete channel*channel matrix as opposed to the 1D vector is seems to return (that lists each individual wpli)? I don?t get that one. Good luck tzvetan -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ Message: 6 Date: Wed, 20 May 2015 22:24:38 +0200 From: Zsolt Turi To: FieldTrip discussion list Subject: Re: [FieldTrip] cluster-based permutation test on WPLI Message-ID: Content-Type: text/plain; charset="utf-8" Dear Chris, thanks again for your comment. Cheers, Zsolt 2015-05-19 12:47 GMT+02:00 Cristiano Micheli : > > Dear Zsolt, > please find an answer below. > Regards > Cris > > On Mon, May 18, 2015 at 11:33 AM, Zsolt Turi wrote: > >> Hi Tzvetan and Chris, >> >> thanks for your emails. >> Removing channelcmb and adding a new one called label solved my problem. >> >> Chris: >> I'ld like to compare the WPLI difference of two conditions, congruent and >> incongruent ones by using a within-subjects design (so not a between trials >> comparison). >> From your email I may infer that after running wpli, I should still have >> my trials. However, I do not have repetitions (trials) anymore in the >> output structure. Am I doing an illegitimate step during wPLI calculation >> or miss one specification? >> > > You did it correctly. > After running the wPLI metric ( I suggest the unbiased version of it, use > the 'wpli_debiased' method in ft_connectivityanalysis) you are left with > no trials. This is because the trials dimension (and tapers) are used to > estimate the phase lag index. If I left that implied in the previous mail, > I did not communicate it very well. What I meant to say is to be careful in > the contrast of two conditions, because the subtraction (or ratio, or > else...) will generate fake effects (or false positives) if the trials in > condition 1 and condition 2 BEFORE wPLI calculation are different. > > I hope this helps > Cris > > >> cfg = []; >> cfg.method = 'wpli'; >> dataWPLI = ft_connectivityanalysis(cfg,TFRhann); >> >> >> labelcmb: {9x2 cell} >> dimord: 'chan_freq_time' >> wplispctrm: [9x43x16 double] >> freq: [1x43 double] >> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >> cfg: [1x1 struct] >> >> Thanks for your help! >> >> Best, >> Zsolt >> >> >> >> >> 2015-05-18 8:18 GMT+02:00 Tzvetan Popov : >> >>> Hi Zsolt, >>> >>> >>> Hi Tzvetan, >>> >>> thanks for your suggestions. >>> I am still stucked at the ft_freqstatistics, as I keep on receiving the >>> following error and would be glad if you could make a comment on this as >>> well: >>> >>> #### >>> Reference to non-existent field 'label'. >>> >>> Error in ft_freqgrandaverage (line 123) >>> cfg.channel = ft_channelselection(cfg.channel, >>> varargin{i}.label); >>> ### >>> >>> Is it because I have labelcomb in the WPLI data? >>> >>> yes >>> >>> >>> labelcmb: {9x2 cell} >>> dimord: 'chan_freq_time' >>> wplispctrm: [9x7x16 double] >>> freq: [3 4 5 6 7 8 9] >>> time: [-0.5000 -0.4004 -0.3008 -0.1992 -0.0996 0 0.0996 0.1992 >>> 0.3008 0.4004 0.5000 0.5996 0.6992 0.8008 0.9004 1] >>> cfg: [1x1 struct] >>> >>> And this is my specification (I couldn't fine the option cfg.channelcmb >>> for ft_freqgrandaverage in the reference documentation): >>> >>> again try to give cell arrays as input to ft_freqanalysis. I?m still >>> considering the case you mentioned in your initial e-mail, one channel etc. >>> e.g. cfg.channel = ?FCzF3?; >>> cfg.parameter = ?wplispctrm?; >>> cfg.neighbours = []; % this will force clustering over time and >>> freq dimension >>> >>> best >>> tzvetan >>> >>> >>> cfg = []; >>> cfg.keepindividual = 'yes'; >>> cfg.cfg.foilim = 'all'; >>> cfg.toilim = 'all'; >>> cfg.channel = 'all'; >>> cfg.parameter = 'wplispctrm'; >>> >>> Thanks again for the answer in advance! >>> >>> Best, >>> Zsolt >>> >>> ps.I can provide other parts of my code but I don't want to make this >>> mail too long : >>> >>> >>> >>> 2015-05-13 19:14 GMT+02:00 Tzvetan Popov >>> : >>> >>>> Hi Zsolt, >>>> >>>> >>>> Dear all, >>>> >>>> >>>> I would like to perform a cluster-based permutation test on weighted >>>> phase lag index values by using a within-subjects experimental design. I >>>> have two conditions (congruent and incongruent one) and my goal is to >>>> compute WPLI between certain channel combinations (FCz and F3 for instance) >>>> and see the WPLI change let?s say in 3-9 Hz and -100 to 500 ms between the >>>> two conditions. >>>> >>>> >>>> I experienced some difficulties after the point when I calculated the >>>> WPLI data for each participant. To perform the above-mentioned comparison, >>>> shall I use ?ft_freqstatistics?for the cluster-based permutation test? >>>> >>>> You could. Stick with the tutorial you are currently working with. You >>>> should organize your data into cell arrays and call ft_freqstatistics like >>>> this: stat = ft_freqstatistics(cfg, congruent{:}, incongruent{:}). >>>> Furthermore you should specify cfg.parameter = ?wplispctrm? otherwise >>>> ft_freqstatistics will default to ?powspctrm? which will be not present in >>>> the data. >>>> good luck >>>> tzvetan >>>> >>>> >>>> _______________________________________________ >>>> fieldtrip mailing list >>>> fieldtrip at donders.ru.nl >>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>>> >>> >>> >>> >>> -- >>> ************************************************************ >>> Ph.D. >>> Department of Clinical Neurophysiology >>> Georg-August University, G?ttingen >>> Robert-Koch-Str. 40 >>> 37075 Goettingen >>> Web: http://www.uni-goettingen.de/en/222525.html >>> ************************************************************ >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >>> >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> >> -- >> ************************************************************ >> Ph.D. >> Department of Clinical Neurophysiology >> Georg-August University, G?ttingen >> Robert-Koch-Str. 40 >> 37075 Goettingen >> Web: http://www.uni-goettingen.de/en/222525.html >> ************************************************************ >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -- ************************************************************ Ph.D. Department of Clinical Neurophysiology Georg-August University, G?ttingen Robert-Koch-Str. 40 37075 Goettingen Web: http://www.uni-goettingen.de/en/222525.html ************************************************************ -------------- next part -------------- An HTML attachment was scrubbed... URL: ------------------------------ _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip End of fieldtrip Digest, Vol 54, Issue 18 ***************************************** From l.garcia.d at gmail.com Thu May 21 20:02:04 2015 From: l.garcia.d at gmail.com (Luis Garcia Dominguez) Date: Thu, 21 May 2015 14:02:04 -0400 Subject: [FieldTrip] Fwd: clusterplot not plotting for gradiometeres In-Reply-To: References: Message-ID: Dear All, Has anyone been successful in combining magnetometers and gradiometers in dipole fitting. In my experience the results obtained using either grad or mag are very similar and accurate, but the combination of both did not work.... I can offer more details, code and data if needed. Any updates on this? Thank you! -------------- next part -------------- An HTML attachment was scrubbed... URL: From mor2451 at gmail.com Fri May 22 14:00:47 2015 From: mor2451 at gmail.com (moran abilea) Date: Fri, 22 May 2015 15:00:47 +0300 Subject: [FieldTrip] what should i do between two stimulations P300 speller Message-ID: hi there everyone, so quick update and a problem that i need some advice from you guys. as I've already mentioned i'm doing a final project of MALAB p300 speller, i'm currently at the part of the experiment which means recording raw data on my partner's scalp while showing him the flashing 6X6 matrix of letters. we are using Emotiv EPOC device which means that it records 128 samples per sec. so now for my question: in the raw data itself that i record, between two stimulations i have 128 recorded raw data and i don't know what to do with it in order to continue the next step of using p300 detection method. what should i do with the 128 recorded data? should i average it or maybe use any band pass filter on the data i'm stuck and i need ideas in order to continue my project. any help will be welcomed, best regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From a.llera at donders.ru.nl Fri May 22 17:34:25 2015 From: a.llera at donders.ru.nl (Llera Arenas, A. (Alberto)) Date: Fri, 22 May 2015 15:34:25 +0000 Subject: [FieldTrip] what should i do between two stimulations P300 speller In-Reply-To: References: Message-ID: <6F2BEAB2DB977640884026115886A9B3247F9F@exprd01.hosting.ru.nl> Hi Hereby some starting points: I first would recommend reading the following paper: Single-Trial Analysis and Classification of ERP Components – a Tutorial. You can download it for free at http://doc.ml.tu-berlin.de/bbci/publications/BlaLemTreHauMue10.pdf If you want more, check for example: Interactions between pre-processing and classification methods for event-related-potential classification: best-practice guidelines for brain-computer interfacing. http://www.ncbi.nlm.nih.gov/pubmed/23250668 a free pre print of this last one is available at research gate http://www.researchgate.net/publication/234112682_FarquharHill_ERP_Classification_Best_Practice_Author_Pre-print Good luck Alberto Llera ________________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of moran abilea [mor2451 at gmail.com] Sent: Friday, May 22, 2015 2:00 PM To: FieldTrip discussion list Subject: [FieldTrip] what should i do between two stimulations P300 speller hi there everyone, so quick update and a problem that i need some advice from you guys. as I've already mentioned i'm doing a final project of MALAB p300 speller, i'm currently at the part of the experiment which means recording raw data on my partner's scalp while showing him the flashing 6X6 matrix of letters. we are using Emotiv EPOC device which means that it records 128 samples per sec. so now for my question: in the raw data itself that i record, between two stimulations i have 128 recorded raw data and i don't know what to do with it in order to continue the next step of using p300 detection method. what should i do with the 128 recorded data? should i average it or maybe use any band pass filter on the data i'm stuck and i need ideas in order to continue my project. any help will be welcomed, best regards, Moran Abilea From greg at think-now.com Sat May 23 02:11:58 2015 From: greg at think-now.com (Greg Simpson) Date: Fri, 22 May 2015 17:11:58 -0700 Subject: [FieldTrip] RA Position Open Message-ID: Dear Colleagues, I would like to announce an opening for a Research Associate (see ad below). Please spread the word. Thank you, Greg Research Associate – Cognitive Training Think Now Incorporated is seeking a research associate to work on a NIMH funded project testing the effects of mobile software training on attention in adults with ADHD. Duties will include recruiting, screening and testing (both behavioral tests and EEG tests) of adults with ADHD, before and after they train their attention with the mobile software. We are seeking candidates with direct hands-on experience in conducting cognitive/psychological tests or related experience. Experience with collecting EEG data is not required but would be great. Also, experience with MatLab and statistical packages such as SPSS would be a plus. We prefer strongly self-directed individuals with great people-skills to take on this work. The position reports directly to Greg Simpson, Ph.D., a cognitive neuroscientist and Chief Scientific Officer of Think Now. Think Now is located in San Francisco and our research partners for this effort are located at UCLA in Los Angeles. Candidates need to be located in the Los Angeles area. Think Now is focused on creating solutions for the diagnosis and amelioration of neurological disorders with a focus on attention and its control. Please send your CV to jobs at think-now.com with a letter describing your prior experience with conducting studies with adults (and any EEG experience) and your reason for being interested in this position. Gregory V. Simpson, Ph.D. Think Now, Inc. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Ad_Staff Research Associate TNI 2015.docx Type: application/vnd.openxmlformats-officedocument.wordprocessingml.document Size: 15847 bytes Desc: not available URL: From sjaak10101 at gmail.com Sat May 23 21:54:42 2015 From: sjaak10101 at gmail.com (Sjaak Zwart) Date: Sat, 23 May 2015 21:54:42 +0200 Subject: [FieldTrip] EDF+C annotations Message-ID: Dear all, I have an .edf file, according to the header, I think the precise format is EDF+C, and my goal is to convert this file in SPM and see the data with annotations. SPM is able to convert the file, although it does give a warning: Warning: Skipping "EDF Annotations" as continuous data channel because of > inconsistent sampling frequency > > In fileio/private/read_edf at 235 > In ft_read_header at 616 > In spm_eeg_convert at 97 > In spm_eeg_convert at 92 > In spm_eeg_convert_ui at 26 > In spm at 1054 > I further noticed that the EDFBrowser application is able to read the data *and* show the annotations. I could now try to figure out from the source what the EDFBrowser is doing exactly, and try to do something similar in the fieldtrip methods that read the edf. Not sure how far I'd get then. An additional complexity is that I do not have a full Matlab license, so I have the Matlab compiler and I have octave installed. (I'm not 100% sure but I think that means I cannot run Matlab code, but only pre-compiled code). >From the EDFBrowser I am able to export the events. But I don't know how to read that file together with the original file when I convert the edf file in SPM to get everything to show up right. Would be great if anybody has some experience with this already, or somebody who just knows how to get me further, Thanks, Sjaak. -------------- next part -------------- An HTML attachment was scrubbed... URL: From bibi.raquel at gmail.com Sat May 23 22:06:40 2015 From: bibi.raquel at gmail.com (bibi.raquel at gmail.com) Date: Sat, 23 May 2015 20:06:40 +0000 Subject: [FieldTrip] =?utf-8?q?biosemi_bdf_=3E=3E_read=5F24bit_error_+_no_?= =?utf-8?q?events_found?= In-Reply-To: References: Message-ID: <5560dddf.0b91340a.2dab.ffffdae5@mx.google.com> Have you resolved this issue? From: Paul Zerr Sent: ‎Thursday‎, ‎May‎ ‎14‎, ‎2015 ‎8‎:‎01‎ ‎AM To: FieldTrip discussion list Hi all, I'm new to fieldtrip so forgive me if my mistake is obvious. I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with cfg = []; cfg.dataset = '2.bdf'; data = ft_preprocessing(cfg) However, I get reading and preprocessing error opening file: 2.bdf One or more output arguments not assigned during call to "read_24bit". Error in read_biosemi_bdf>readLowLevel (line 274) buf = read_24bit(filename, offset, numwords); Error in read_biosemi_bdf (line 242) buf = readLowLevel(filename, offset, epochlength); % see below in subfunction Error in ft_read_data (line 321) dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); Error in ft_preprocessing (line 578) dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) Error in Untitled (line 19) data = ft_preprocessing(cfg) Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). Defining only one channel to preprocess gives the same error. I couldn't find a solution in the archives, the faq, wiki or documentation. I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. Any ideas? Much appreciated, Paul Zerr -------------- next part -------------- An HTML attachment was scrubbed... URL: From Andreas.Horn at charite.de Sun May 24 10:55:55 2015 From: Andreas.Horn at charite.de (Horn, Andreas) Date: Sun, 24 May 2015 08:55:55 +0000 Subject: [FieldTrip] Elements have wrong orientation or are degenerated Message-ID: Hello everybody, I am new to fieldtrip and want to use it (and simbio) to forward model the current spread of a known dipole. I consider only a small cubic fraction of brain tissue which I so far have divided in gray and white matter. I pass that cubic volume into ft_prepare_mesh and get a hexahedral mesh without error. ft_plot_mesh also shows the correct mesh. However, once I pass the mesh into ft_headmodel_simbio, I get the error ‘Elements have wrong orientation or are degenerated’ Does anyone have an idea of why this could happen and how I could potentially fix the issue? Thanks a lot, Andreas From alizadeh.arezoo88 at gmail.com Sun May 24 22:00:11 2015 From: alizadeh.arezoo88 at gmail.com (Arezoo Alizadeh) Date: Sun, 24 May 2015 09:00:11 -1100 Subject: [FieldTrip] User pass Message-ID: Hello, I have forget both my user name and pass word to ask question from fieldtriper. Could you please help me. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mahjoory86 at gmail.com Sun May 24 22:03:46 2015 From: mahjoory86 at gmail.com (Keyvan Mahjoory) Date: Sun, 24 May 2015 22:03:46 +0200 Subject: [FieldTrip] User pass In-Reply-To: References: Message-ID: http://mailman.science.ru.nl/mailman/listinfo/fieldtrip On Sun, May 24, 2015 at 10:00 PM, Arezoo Alizadeh < alizadeh.arezoo88 at gmail.com> wrote: > Hello, > > I have forget both my user name and pass word to ask question from > fieldtriper. Could you please help me. > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.pedrosa at ndcn.ox.ac.uk Mon May 25 11:19:00 2015 From: david.pedrosa at ndcn.ox.ac.uk (David Pedrosa) Date: Mon, 25 May 2015 09:19:00 +0000 Subject: [FieldTrip] Statistics of coherence (DICS) Message-ID: Dear list, I would be very grateful if someone might answer some questions on the statistics of coherence. Maybe first of all an outline to our experiment. We have measured a 128 channel EEG with additional peripheral signals from the most affected arm on 20 subjects suffering from tremor and the same number of healthy control subjects with a simple motor paradigm (activation condition). In another condition, rest (baseline condition) was also measured (we have about 20-35 trials per condition). For the data analysis we have preprocessed the EEG in a rather standard way. For localizing the cortical sources we created a headmodel from individual MRI and the source reconstruction was obtained using the DICS beamformer (with the peripheral signal as 'refchan' and after computing a common spatial filter). Everything works out well and regarding the activation condition by itself the sources appear to be where we you would suspect it (motor areas) in all individuals. Of course coherence is much bigger during activation (about 1-3 dimensions). But otherwise coherence is never 0, not even in the rest condition (as to be expected). This makes us suspect a permutation test much more valid for testing the 'null-hypothesis' of interchangeable coherence between the conditions. Now we are struggling with the stats of the individual but also the group results. My first question is am I right that averageing over trials per condition is not necessary? And do I need to normalise the coherence after computing it with ft_freqanalysis? I was thinking of computing (activation - baseline)/baseline. And, finally, regarding the stats. The idea is to look individually at differences between the conditions and in a second step perform a group analysis. But what to test if we are not assuming a null-hypothesis, or am I completely on the wrong track? Thanks in advance. Best, David From zerr.paul at googlemail.com Mon May 25 15:51:15 2015 From: zerr.paul at googlemail.com (Paul Zerr) Date: Mon, 25 May 2015 15:51:15 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found Message-ID: I have not. I can read in the header but that's about it. I don't have any older matlab versions here to test it with either. >From what I understand ft_preprocessing should be capable of reading bdf's directly with only the file name as input arg. Greetings, Paul Zerr From: > To: FieldTrip discussion list > Subject: Re: [FieldTrip] biosemi bdf >> read_24bit error + no events > found > Message-ID: <5560dddf.0b91340a.2dab.ffffdae5 at mx.google.com> > Content-Type: text/plain; charset="utf-8" > > Have you resolved this issue? > > > From: Paul Zerr > Sent: ?Thursday?, ?May? ?14?, ?2015 ?8?:?01? ?AM > To: FieldTrip discussion list > > > Hi all, > > I'm new to fieldtrip so forgive me if my mistake is obvious. > I want to import my raw, markerless dataset ( > http://www.filedropper.com/1_20) with > > cfg = []; > cfg.dataset = '2.bdf'; > data = ft_preprocessing(cfg) > > However, I get > > reading and preprocessing > error opening file: 2.bdf > One or more output arguments not assigned during call to "read_24bit". > > Error in read_biosemi_bdf>readLowLevel (line 274) > buf = read_24bit(filename, offset, numwords); > > Error in read_biosemi_bdf (line 242) > buf = readLowLevel(filename, offset, epochlength); % see below in > subfunction > > Error in ft_read_data (line 321) > dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); > > Error in ft_preprocessing (line 578) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', > begsample, > 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) > > Error in Untitled (line 19) > data = ft_preprocessing(cfg) > > Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the > datafile" for ft_definetrial even for datasets with many markers. > Converting to EDF+ did not help as it then says "channels with different > sampling rate not supported". Specifying only one channel makes no > difference. The file itself is fine (opens well in BvA). > > Defining only one channel to preprocess gives the same error. > > I couldn't find a solution in the archives, the faq, wiki or documentation. > > I'm using debian stable & matlab 2014a. Same issue at DCC computers > running windows & matlab 2013a. > > Any ideas? > > Much appreciated, > > Paul Zerr > -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Mon May 25 20:15:04 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Mon, 25 May 2015 18:15:04 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at: https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Mon May 25 20:52:56 2015 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 25 May 2015 18:52:56 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR In-Reply-To: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> References: <3188FAB8621D294696F13E80A7BBC97EFF4A4BB2@me-mbx3.medschl.cam.ac.uk> Message-ID: <0D293943-40CA-45B3-B6E6-0CA403FCFA0B@fcdonders.ru.nl> Hi Richard, Is there a specific reason you would want to do a time-frequency type of analysis (with averaging across ‘epochs’ for resting state data? Since there’s no external event, such analysis does not really make sense. Yet, if you insist on doing this, you need to ensure that the individual ‘pseudo-trial’ time axis (i.e. data_iccleaned.time{x}) contains a ‘pseudo-time-axis’ such that it goes from 0 to 4. Best, Jan-Mathijs On May 25, 2015, at 8:15 PM, Richard Bethlehem > wrote: Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at:https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From rb643 at medschl.cam.ac.uk Tue May 26 11:27:38 2015 From: rb643 at medschl.cam.ac.uk (Richard Bethlehem) Date: Tue, 26 May 2015 09:27:38 +0000 Subject: [FieldTrip] NaN's in Wavelet TFR Message-ID: <3188FAB8621D294696F13E80A7BBC97EFF4AAB5C@me-mbx3.medschl.cam.ac.uk> Hi Jan-Mathijs, Essentially I want to do connectivity analysis using the wpli measure for connectivity and use wavelets to get to the frequency domain, I gathered I needed to do frequency analysis to get the power and crosspectrum info for computing wpli (and to decompose into the different frequency bands), but please let me know if this should be done differently? I thought with such analysis selecting epochs would be fairly standard practice (following van Diessen et al. 2014), but again please do correct me if I misunderstood. If not, what would be the alternative for getting epochs/trials? Following you suggestion I have replaced the time axis with the same 0-4second interval as used in the freqanalysis input: stepSize = 1/1024; timeVector = 0:stepSize:(epochLength-stepSize); for i = 1:size(data_iccleaned.time,2) data_iccleaned.time{:,i} = timeVector; end Unfortunately this still gives me NaN's in the output... Cheers, Richard Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl ________________________________ Hi Richard, Is there a specific reason you would want to do a time-frequency type of analysis (with averaging across ‘epochs’ for resting state data? Since there’s no external event, such analysis does not really make sense. Yet, if you insist on doing this, you need to ensure that the individual ‘pseudo-trial’ time axis (i.e. data_iccleaned.time{x}) contains a ‘pseudo-time-axis’ such that it goes from 0 to 4. Best, Jan-Mathijs On May 25, 2015, at 8:15 PM, Richard Bethlehem >> wrote: Dear Fieldtrippers, This question has undoubtedly been asked before, but I could find clear guidance on how to work around it. When running ft_freqanalysis with wavelet decomposition I keep getting NaN's in all of my output. It would figure that this would be caused by insufficient data at the data borders, but I am (or at least think I am) not using that part of my epochs... So why am I still ending up with NaN's? The data is from a 64-channel BioSemi system, sampled at 1k (and not downsampled), fairly 'standard' preprocessing with the addition of one channel repair and ICA artefact rejection (although in this one example dataset there was no clear ICA artefact component in the eyes-closed phase of the resting state). The data consist of two 50 second trials that are further segmented in 4s epochs). The frequency code is below, the full script can be found at:https://github.com/rb643/fieldtrip_restingState/blob/master/restingstate.m cfg_freq = []; cfg_freq.method = 'wavelet'; cfg_freq.output = 'powandcsd'; cfg_freq.channel = 1:64; cfg_freq.keeptrials ='yes'; %do not return an average of all trials for subsequent wpli analysis cfg_freq.toi = [0.5:0.05:3.5]; %50ms time-window should give enough specificity cfg_freq.foi = [0.5:0.02:4]; %delta range with increments of 0.02Hz [freq_data.delta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [4:0.02:7]; [freq_data.theta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [7:0.02:13]; [freq_data.alpha] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [13:0.02:30]; [freq_data.beta] = ft_freqanalysis(cfg_freq, data_iccleaned); cfg_freq.foi = [30:0.02:60]; [freq_data.gamma] = ft_freqanalysis(cfg_freq, data_iccleaned); Cheers, Richard -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed May 27 11:28:27 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 27 May 2015 11:28:27 +0200 Subject: [FieldTrip] Power Spectra - averaging across samples Message-ID: Dear all, I have a question about spectral power computation. I'm using this code cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 5:1:40; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; freqfourier = ft_freqanalysis(cfg, eeg); and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) X 36 (frequencies), for each subject. My question is: is it correct to average the data across the samples dimension? Thank you in advance! Best, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From stan.vanpelt at donders.ru.nl Wed May 27 11:46:25 2015 From: stan.vanpelt at donders.ru.nl (Pelt, S. van (Stan)) Date: Wed, 27 May 2015 09:46:25 +0000 Subject: [FieldTrip] Power Spectra - averaging across samples In-Reply-To: References: Message-ID: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> Dear Fedrica, Yes it is. You can get to the same outcome directly by just specifying cfg.keeptrials=’no’ (the default), but I assume you want to do some single-trial analysis later on. Best, Stan From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Federica Mauro Sent: woensdag 27 mei 2015 11:28 To: FieldTrip discussion list Subject: [FieldTrip] Power Spectra - averaging across samples Dear all, I have a question about spectral power computation. I'm using this code cfg = []; cfg.output = 'pow'; cfg.method = 'mtmfft'; cfg.taper = 'hanning'; cfg.foi = 5:1:40; cfg.t_ftimwin = 5./cfg.foi; cfg.tapsmofrq = 5; cfg.keeptrials = 'yes'; cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; freqfourier = ft_freqanalysis(cfg, eeg); and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) X 36 (frequencies), for each subject. My question is: is it correct to average the data across the samples dimension? Thank you in advance! Best, Federica -------------- next part -------------- An HTML attachment was scrubbed... URL: From federica.ma at gmail.com Wed May 27 12:09:43 2015 From: federica.ma at gmail.com (Federica Mauro) Date: Wed, 27 May 2015 12:09:43 +0200 Subject: [FieldTrip] Power Spectra - averaging across samples In-Reply-To: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> References: <7CCA2706D7A4DA45931A892DF3C2894C17950DDC@exprd03.hosting.ru.nl> Message-ID: ok, great, thanks! 2015-05-27 11:46 GMT+02:00 Pelt, S. van (Stan) : > Dear Fedrica, > > > > Yes it is. You can get to the same outcome directly by just specifying > cfg.keeptrials=’no’ (the default), but I assume you want to do some > single-trial analysis later on. > > > > Best, > > Stan > > > > *From:* fieldtrip-bounces at science.ru.nl [mailto: > fieldtrip-bounces at science.ru.nl] *On Behalf Of *Federica Mauro > *Sent:* woensdag 27 mei 2015 11:28 > *To:* FieldTrip discussion list > *Subject:* [FieldTrip] Power Spectra - averaging across samples > > > > Dear all, > > I have a question about spectral power computation. > > I'm using this code > > cfg = []; > cfg.output = 'pow'; > cfg.method = 'mtmfft'; > cfg.taper = 'hanning'; > cfg.foi = 5:1:40; > cfg.t_ftimwin = 5./cfg.foi; > cfg.tapsmofrq = 5; > cfg.keeptrials = 'yes'; > cfg.channel = {'Fp1' 'Fp2' 'F7' 'F3' 'Fz' 'F4' 'F8' 'T3' 'C3' 'Cz' 'C4' > 'T4' 'T5' 'P3' 'Pz' 'P4' 'T6' 'O1' 'O2'}; > freqfourier = ft_freqanalysis(cfg, eeg); > > and the power spectrum output is a matrix 138 (samples) X 19 (electrodes) > X 36 (frequencies), for each subject. > > My question is: is it correct to average the data across the samples > dimension? > > Thank you in advance! > > Best, > > Federica > > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: From jonathan.schubert at gmail.com Wed May 27 16:33:26 2015 From: jonathan.schubert at gmail.com (Jonathan Schubert) Date: Wed, 27 May 2015 16:33:26 +0200 Subject: [FieldTrip] postdoc position in Hamburg In-Reply-To: <4E102991-AB38-44E6-AA60-780A723AFCE2@gmail.com> References: <4E102991-AB38-44E6-AA60-780A723AFCE2@gmail.com> Message-ID: <5565D5B6.8020805@gmail.com> Dear all, I'd like to advertise the following postdoc postion. If you have any questions, please do not hesitate to contact Tobias Heed (tobias.heed at uni-hamburg.de). Cheers, Jonathan -------- Weitergeleitete Nachricht -------- Dear friends and colleagues, The Reach & Touch Lab at the University of Hamburg is hiring a PostDoc for a 4-year project about brain connectivity in tactile-visual processing involving EEG, TMS, and eye tracking. I would be thankful if you could pass on this link: http://goo.gl/zhlk4p to anyone who might be interested. Application deadline is June 15, 2015. Thanks! Tobias Heed — Follow the Reach & Touch Lab (@HeedLab ) and myself (@TobiasHeed ) on Twitter Read our news and blog posts on www.reachtouchlab.com View our publications Dr. Tobias Heed Reach & Touch Lab of the Biological Psychology and Neuropsychology Faculty of Psychology & Human Movement Science | University of Hamburg Von-Melle-Park 11, Room 206 | D-20146 Hamburg, Germany Phone: (49) 40 - 42838 5831 | Fax: (49) 40 - 42838 6591 tobias.heed at uni-hamburg.de | Website | Twitter | Google Scholar -------------- next part -------------- An HTML attachment was scrubbed... URL: From lauri.parkkonen at aalto.fi Thu May 28 14:51:18 2015 From: lauri.parkkonen at aalto.fi (Parkkonen Lauri) Date: Thu, 28 May 2015 12:51:18 +0000 Subject: [FieldTrip] Post-doc position in Bayesian estimation & MEG Message-ID: Postdoctoral researcher in Bayesian estimation of functional connectivity from MEG data at Department of Neuroscience and Biomedical Engineering (NBE) of Aalto University School of Science, Finland. The work will be carried out jointly in the teams of prof. Lauri Parkkonen and prof. Simo Särkkä. More information on the position can be found here: http://www.aalto.fi/en/about/careers/jobs/view/515/ Cheers, Lauri -- ----------------------------------------------- Dr. Lauri Parkkonen Assistant Professor (Medical Imaging) Dept. of Neuroscience and Biomedical Engineering (NBE) Aalto University School of Science Street address: Rakentajanaukio 2 C, FI-02150 ESPOO, Finland Postal address: P.O. Box 12200, FI-00076 AALTO, Finland Tel: +358-40-5089712, mailto:lauri.parkkonen at aalto.fi http://nbe.aalto.fi/en -------------- next part -------------- An HTML attachment was scrubbed... URL: From mor2451 at gmail.com Thu May 28 16:56:51 2015 From: mor2451 at gmail.com (moran abilea) Date: Thu, 28 May 2015 17:56:51 +0300 Subject: [FieldTrip] using triggers building my own function Message-ID: hi everyone, so i'm trying to create my own function for using triggers with EEG raw data. i used this tutorial: http://www.fieldtriptoolbox.org/tutorial/preprocessing my question is if i can somehow specify the time i want to record my EEG data? for example i would like my function to get 'time' as parameter to the function and returns the EEG raw data of this specific time+one second. if so, can some one give me a piece of code for example to understand what to do? also 2 more little questions: 1. cfg.trialdef.eventvalue = [3 5 9]; what does the 3 5 9 stands for? i don't understand what is the meaning of those (or any other) numbers. can i get definition for what is event value? 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; does it means it takes exactly one second for the buffer to give me the EEG raw data? or does it means wait one second and then take the data from the buffer or something like that (1 second the trigger will "pop out" and finish taking the data from the buffer after 2 seconds) the triggers are new to me, so i have some problems to understand the concept of it, thus my questions for you guys. i hope i explained myself as clear as possible, i really would like to understand what i'm doing. regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From bmaniscalco at gmail.com Thu May 28 17:30:17 2015 From: bmaniscalco at gmail.com (Brian Maniscalco) Date: Thu, 28 May 2015 11:30:17 -0400 Subject: [FieldTrip] Inverse warping vs interpolating & normalizing for across-subject source space analysis Message-ID: When it comes to conducting across-subject analysis on source space data, I've seen two approaches described on the Field Trip web site and mailing list. 1) for each subject, interpolate the source space data onto the subject's brain anatomy and then normalize the result to a standard template before conducting across-subject analysis 2) for each subject, perform an inverse warp to a template as described in the following link, which then allows across-subject analysis without having to interpolate and normalize http://www.fieldtriptoolbox.org/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space I have seen approach (2) recommended for Field Trip users but I have not been able to find an in depth discussion of the pros and cons of doing (1) vs (2). I gather that (2) is computationally simpler and may save computation time. But aside from computational considerations, is there any theoretical or statistical benefit to using approach (2) over approach (1) or vice versa? thanks, Brian -------------- next part -------------- An HTML attachment was scrubbed... URL: From n.lam at donders.ru.nl Fri May 29 11:59:33 2015 From: n.lam at donders.ru.nl (Lam, N.H.L. (Nietzsche)) Date: Fri, 29 May 2015 09:59:33 +0000 Subject: [FieldTrip] using triggers building my own function In-Reply-To: References: Message-ID: Hi Moran, It was a bit difficult to understand your question, but I've tried to answer them below. For your main question: Yes, it is possible to cut up your EEG data into individual trials, with the time (i.e. 1 second) that you specify. The function that cuts up your EEG data is known as ft_definetrial. However, ft_definetrial needs to read information from another function that explicitly tells it how to do the cutting. Usually, that function is "ft_trialfun_general" (this is the tutorial link you mentioned). However, if you have a complicated set of triggers or ways you want to cut up your data, you will be better off writing your own trialfun (" trial function"). If you need to write your trialfun, you should check out these example scripts / tutorials: http://www.fieldtriptoolbox.org/example/making_your_own_trialfun_for_conditional_trial_definitionhttp://www.fieldtriptoolbox.org/example/making_your_own_trialfun_for_conditional_trial_definition http://www.fieldtriptoolbox.org/tutorial/eeg_preprocessing_erphttp://www.fieldtriptoolbox.org/tutorial/eeg_preprocessing_erp To answer your " little " questions 1. cfg.trialdef.eventvalue = [3 5 9]; 3 5 9 are trigger codes. This tells your function to go into your data, look for these trigger codes, and cut your data with respect to the location of these triggers E.g., your data trigger codes look like this ----1 ----- 3 ------ 4 ------5 ----- 9 ----. In this case, the ft_definetrial will only use triggers 3, 5, and 9 as relative points for cutting your data, trigger 1 and 4 will be ignored. N.B. The data at trigger 1 might end up in your time window that contains trigger 3 if you define your time window to be very. To understand this, see below. 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; These 2 parameters are important. The values are defined in seconds. So cfg.trialdef.prestim refers to 1s before your trigger (i.e. prestim = prestimulus onset, where stimulus onset is referred to the sample point of your chosen trigger). cfg.trialdef.poststim refers to 2s after your trigger. In this way you would end up with a 3 second time window (1 second before trigger, and 2 seconds after). You mentioned you wanted " specific time [in data] + one second". So you 1) determine which triggers mark the " specific time [in your data]" 2) specify cfg.trialdef.poststim = 1. Hope this helps and good luck, Nietzsche ________________________________ From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of moran abilea [mor2451 at gmail.com] Sent: 28 May 2015 16:56 To: FieldTrip discussion list Subject: [FieldTrip] using triggers building my own function hi everyone, so i'm trying to create my own function for using triggers with EEG raw data. i used this tutorial: http://www.fieldtriptoolbox.org/tutorial/preprocessing my question is if i can somehow specify the time i want to record my EEG data? for example i would like my function to get 'time' as parameter to the function and returns the EEG raw data of this specific time+one second. if so, can some one give me a piece of code for example to understand what to do? also 2 more little questions: 1. cfg.trialdef.eventvalue = [3 5 9]; what does the 3 5 9 stands for? i don't understand what is the meaning of those (or any other) numbers. can i get definition for what is event value? 2. cfg.trialdef.prestim = 1; cfg.trialdef.poststim = 2; does it means it takes exactly one second for the buffer to give me the EEG raw data? or does it means wait one second and then take the data from the buffer or something like that (1 second the trigger will "pop out" and finish taking the data from the buffer after 2 seconds) the triggers are new to me, so i have some problems to understand the concept of it, thus my questions for you guys. i hope i explained myself as clear as possible, i really would like to understand what i'm doing. regards, Moran Abilea -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun May 31 22:16:45 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 31 May 2015 22:16:45 +0200 Subject: [FieldTrip] biosemi bdf >> read_24bit error + no events found In-Reply-To: References: Message-ID: <82B38BFA-DF5F-4364-B7A5-7D1D754A75F7@donders.ru.nl> Hi Paul, I suppose it is an incompatibility between your particular BDF file and the code. I suggest you use MATLAB debugging facilities to check what is wrong in the lower-level code. See http://tinyurl.com/oy7b496. best regards, Robert On 25 May 2015, at 15:51, Paul Zerr wrote: > I have not. I can read in the header but that's about it. > I don't have any older matlab versions here to test it with either. > > From what I understand ft_preprocessing should be capable of reading bdf's directly with only the file name as input arg. > > Greetings, > Paul Zerr > > > From: > To: FieldTrip discussion list > Subject: Re: [FieldTrip] biosemi bdf >> read_24bit error + no events > found > Message-ID: <5560dddf.0b91340a.2dab.ffffdae5 at mx.google.com> > Content-Type: text/plain; charset="utf-8" > > Have you resolved this issue? > > > From: Paul Zerr > Sent: ?Thursday?, ?May? ?14?, ?2015 ?8?:?01? ?AM > To: FieldTrip discussion list > > > Hi all, > > I'm new to fieldtrip so forgive me if my mistake is obvious. > I want to import my raw, markerless dataset (http://www.filedropper.com/1_20) with > > cfg = []; > cfg.dataset = '2.bdf'; > data = ft_preprocessing(cfg) > > However, I get > > reading and preprocessing > error opening file: 2.bdf > One or more output arguments not assigned during call to "read_24bit". > > Error in read_biosemi_bdf>readLowLevel (line 274) > buf = read_24bit(filename, offset, numwords); > > Error in read_biosemi_bdf (line 242) > buf = readLowLevel(filename, offset, epochlength); % see below in subfunction > > Error in ft_read_data (line 321) > dat = read_biosemi_bdf(filename, hdr, begsample, endsample, chanindx); > > Error in ft_preprocessing (line 578) > dat = ft_read_data(cfg.datafile, 'header', hdr, 'begsample', begsample, > 'endsample', endsample, 'chanindx', rawindx, 'checkboundary', > strcmp(cfg.continuous, 'no'), 'dataformat', cfg.dataformat) > > Error in Untitled (line 19) > data = ft_preprocessing(cfg) > > Using cfg.trialdef.eventtype = '?'; outputs "no events were found in the datafile" for ft_definetrial even for datasets with many markers. Converting to EDF+ did not help as it then says "channels with different sampling rate not supported". Specifying only one channel makes no difference. The file itself is fine (opens well in BvA). > > Defining only one channel to preprocess gives the same error. > > I couldn't find a solution in the archives, the faq, wiki or documentation. > > I'm using debian stable & matlab 2014a. Same issue at DCC computers running windows & matlab 2013a. > > Any ideas? > > Much appreciated, > > Paul Zerr > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From r.oostenveld at donders.ru.nl Sun May 31 22:18:38 2015 From: r.oostenveld at donders.ru.nl (Robert Oostenveld) Date: Sun, 31 May 2015 22:18:38 +0200 Subject: [FieldTrip] Research Scientist Position at University of Washington References: Message-ID: Please see the message below on behalf of Chris Bishop. Begin forwarded message: > We are looking for qualified applicants for a Senior Research Scientist position at the University of Washington. Applicants will need to have a background in EEG and MATLAB. > > The requisition number is 120420. Full description and application details can be found at the link below. > > https://uwhires.admin.washington.edu/eng/candidates/default.cfm?szCategory=jobprofile&szOrderID=120420&szCandidateID=0&szSearchWords=&szReturnToSearch=1 > > Thank you > -Chris Bishop -------------- next part -------------- An HTML attachment was scrubbed... URL: