From virginie.van.wassenhove at gmail.com Thu Feb 1 11:22:36 2018 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Thu, 1 Feb 2018 11:22:36 +0100 Subject: [FieldTrip] [tenure-track researcher position] Message-ID: Dear all, applications are invited for a tenure-track researcher position in the Cognition and Brain Dynamics research team of Virginie van Wassenhove. The lab is hosted at NeuroSpin (Dir. Prof Stanislas Dehaene) on the plateau de Saclay near Paris, France. See full description attached. Kind regards, Virginie -- Virginie van Wassenhove *https://brainthemind.com/ * -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2018_VvW_JobDescription_CEA.pdf Type: application/pdf Size: 100589 bytes Desc: not available URL: From annekathrinweise at gmail.com Thu Feb 1 14:54:49 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 1 Feb 2018 14:54:49 +0100 Subject: [FieldTrip] Salzburg Mind Brain Annual (SAMBA) Meeting 2018 Message-ID: Dear all, on behalf of myself, my colleagues, and our advisory board, I am happy to announce the *Salzburg Mind Brain Annual Meeting* (*SAMBA*)**which will take place *in Salzburg, Austria* on *July 12 & 13*, *2018*. The*registration* is now *open until March 15*. The mission of SAMBA is to attract the most exciting researchers in the domain of cognitive neuroscience, including related fields (e.g., computational modelling, animal neurophysiology, neurology etc.) that influence or are influenced by developments in cognitive neuroscience. Furthermore, our goal is to make young scientists enthusiastic about this research field. The moderate size of an anticipated ~100 participants will enable an intimate atmosphere with ample opportunity for exchange. Confirmed speakers are: *     Radoslav Cichy (FU Berlin) *     Simon Eickhoff (Jülich) *     Saskia Haegens (Columbia / Donders) *     Jim Haxby (Dartmouth) *     Katharina von Kriegstein (MPI Leipzig) *     Floris de Lange (Donders) *     Tamar Makin (UCL) *     Kia Nobre (Oxford) *     Uta Noppeney (Birmingham) *     Anne-Marike Schiffer (Nature Human Behavior) *     Andreas Wutz (MIT / Salzburg) Attendees have the possibility to present a poster. For more information see the SAMBA website: https://samba.ccns.sbg.ac.at/ Best, Nathan -- Nathan Weisz Centre for Cognitive Neuroscience Division of Physiological Psychology University of Salzburg nathan.weisz at sbg.ac.at www.oboblab.at -- Annekathrin Weise, Dr. Paris-Lodron Universität Salzburg Division of Physiological Psychology Hellbrunnerstraße 34 5020 Salzburg Austria e-mail: annekathrin.weise at sbg.ac.at; annekathrinweise at gmail.com web: http://www.oboblab.at/ https://sites.google.com/site/weiseannekathrin/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From yaocong.duan at gmail.com Thu Feb 1 18:31:56 2018 From: yaocong.duan at gmail.com (Yaocong Duan) Date: Thu, 1 Feb 2018 17:31:56 +0000 Subject: [FieldTrip] Question about Phase locking value Message-ID: Hi All, I am using Phase Locking Value to measure the connectivity between brain regions at the source level. I learned that the PLV is an average value over trails. In the fieldtrip code, I calculated a frequency model first, then do connectivity analysis with this freq model. The problem is I don’t see trails information in the freq model. So how do I get that phase locking result? Below is my code. This code works, but I am confused about the question above. [image: Inline images 1] Thanks in advance, Yaocong -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From stephen.whitmarsh at gmail.com Thu Feb 1 19:02:51 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 1 Feb 2018 19:02:51 +0100 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Dear Yaocong, To understand your question, it would be helpful if you post the output of the freqanalysis, i.e. your *freq *datastructure. It should contain a .*pow *field, which should be an array of structs, numbering your number of trials, right? Cheers, Stephen Virus-free. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On 1 February 2018 at 18:31, Yaocong Duan wrote: > Hi All, > > > > I am using Phase Locking Value to measure the connectivity between brain > regions at the source level. I learned that the PLV is an average value > over trails. In the fieldtrip code, I calculated a frequency model first, > then do connectivity analysis with this freq model. The problem is I don’t > see trails information in the freq model. So how do I get that phase > locking result? > > > > Below is my code. This code works, but I am confused about the question > above. > > [image: Inline images 1] > > Thanks in advance, > Yaocong > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From yaocong.duan at gmail.com Fri Feb 2 01:12:56 2018 From: yaocong.duan at gmail.com (Yaocong Duan) Date: Fri, 2 Feb 2018 00:12:56 +0000 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Hi Stephen, Thank you for your response. I write something wrong in my previous email. the freq structure does have trails information. but then I do a source reconstruction and generate a source structure. phase locking value is calculated from the source structure directly. However, the source structure does not have any trails info (trails seems have been averaged). source = ft_sourceanalysis(cfg, freq); ... plv = ft_connectivityanalysis(cfg, souceSparse); below are the freq structure generated by freq analysis, source structure generated by source analysis as well as the .avg field of source structure. [image: Inline images 1][image: Inline images 2][image: Inline images 3] On 1 February 2018 at 18:02, Stephen Whitmarsh wrote: > Dear Yaocong, > > To understand your question, it would be helpful if you post the output of > the freqanalysis, i.e. your *freq *datastructure. It should contain a .*pow > *field, which should be an array of structs, numbering your number of > trials, right? > > Cheers, > Stephen > > > Virus-free. > www.avast.com > > <#m_6562418138207874494_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On 1 February 2018 at 18:31, Yaocong Duan wrote: > >> Hi All, >> >> >> >> I am using Phase Locking Value to measure the connectivity between brain >> regions at the source level. I learned that the PLV is an average value >> over trails. In the fieldtrip code, I calculated a frequency model first, >> then do connectivity analysis with this freq model. The problem is I don’t >> see trails information in the freq model. So how do I get that phase >> locking result? >> >> >> >> Below is my code. This code works, but I am confused about the question >> above. >> >> [image: Inline images 1] >> >> Thanks in advance, >> Yaocong >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 82049 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 97937 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 92321 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From xiew1202 at gmail.com Fri Feb 2 02:35:59 2018 From: xiew1202 at gmail.com (Xie Wanze) Date: Thu, 1 Feb 2018 20:35:59 -0500 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Hi Yaocong, Two things you may want to try: 1. use the "keep trials" option when you do your source analysis. This method makes a lot of sense, but it did not work for me. 2. Do source reconstruction separately for each individual trial. You may calculate the filter in Fieldtrip using ft_sourceanalysis and then use the filter for source reconstruction for each trial: reconstructed source activity = filter*data (in individual trial). This second option worked for me. Good luck. Wanze 2018-02-01 19:12 GMT-05:00 Yaocong Duan : > Hi Stephen, > > Thank you for your response. I write something wrong in my previous email. > the freq structure does have trails information. but then I do a source > reconstruction and generate a source structure. phase locking value is > calculated from the source structure directly. However, the source > structure does not have any trails info (trails seems have been averaged). > > source = ft_sourceanalysis(cfg, freq); > ... > plv = ft_connectivityanalysis(cfg, souceSparse); > > > below are the freq structure generated by freq analysis, source structure > generated by source analysis as well as the .avg field of source structure. > > > [image: Inline images 1][image: Inline images 2][image: Inline images 3] > > On 1 February 2018 at 18:02, Stephen Whitmarsh < > stephen.whitmarsh at gmail.com> wrote: > >> Dear Yaocong, >> >> To understand your question, it would be helpful if you post the output >> of the freqanalysis, i.e. your *freq *datastructure. It should contain a >> .*pow *field, which should be an array of structs, numbering your number >> of trials, right? >> >> Cheers, >> Stephen >> >> >> Virus-free. >> www.avast.com >> >> <#m_3173352166848949795_m_6562418138207874494_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> On 1 February 2018 at 18:31, Yaocong Duan wrote: >> >>> Hi All, >>> >>> >>> >>> I am using Phase Locking Value to measure the connectivity between brain >>> regions at the source level. I learned that the PLV is an average value >>> over trails. In the fieldtrip code, I calculated a frequency model first, >>> then do connectivity analysis with this freq model. The problem is I don’t >>> see trails information in the freq model. So how do I get that phase >>> locking result? >>> >>> >>> >>> Below is my code. This code works, but I am confused about the question >>> above. >>> >>> [image: Inline images 1] >>> >>> Thanks in advance, >>> Yaocong >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 92321 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 97937 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 82049 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Fri Feb 2 09:07:49 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 2 Feb 2018 08:07:49 +0000 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: <86C3123F-DB4B-4C27-8261-2230D3689ACF@donders.ru.nl> When you call ft_freqanalysis with ‘fourier’ in the cfg.method, followed by ft_sourceanalysis with ‘pcc’ in cfg.method, the source.avg.mom contains the fourier coefficients at the single taper level. A bunch of tapers constitute a single trial, the number of which depends on the smoothing parameter that you used in ft_freqanalysis. Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 2 Feb 2018, at 01:12, Yaocong Duan > wrote: Hi Stephen, Thank you for your response. I write something wrong in my previous email. the freq structure does have trails information. but then I do a source reconstruction and generate a source structure. phase locking value is calculated from the source structure directly. However, the source structure does not have any trails info (trails seems have been averaged). source = ft_sourceanalysis(cfg, freq); ... plv = ft_connectivityanalysis(cfg, souceSparse); below are the freq structure generated by freq analysis, source structure generated by source analysis as well as the .avg field of source structure. On 1 February 2018 at 18:02, Stephen Whitmarsh > wrote: Dear Yaocong, To understand your question, it would be helpful if you post the output of the freqanalysis, i.e. your freq datastructure. It should contain a .pow field, which should be an array of structs, numbering your number of trials, right? Cheers, Stephen [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif] Virus-free. www.avast.com On 1 February 2018 at 18:31, Yaocong Duan > wrote: Hi All, I am using Phase Locking Value to measure the connectivity between brain regions at the source level. I learned that the PLV is an average value over trails. In the fieldtrip code, I calculated a frequency model first, then do connectivity analysis with this freq model. The problem is I don’t see trails information in the freq model. So how do I get that phase locking result? Below is my code. This code works, but I am confused about the question above. Thanks in advance, Yaocong _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmelloni at gmail.com Sun Feb 4 18:37:43 2018 From: lmelloni at gmail.com (Lucia Melloni) Date: Sun, 4 Feb 2018 18:37:43 +0100 Subject: [FieldTrip] Postdoctoral Position in Electrocorticography at NYU Message-ID: <79BBB75B-4A9E-4057-B75F-F069BE96E8BC@gmail.com> Dear All, We have an opening for a POSTDOCTORAL POSITION IN ELECTROCORTICOGRAPHY RESEARCH AT NYU. See below for details. Thanks and all the best, Lucia POSTDOCTORAL POSITION IN ELECTROCORTICOGRAPHY RESEARCH AT NYU NYU School of Medicine has an opening for a Postdoctoral Researcher to conduct Human intracranial EEG and electrocortigoraphy (ECoG) research. The postdoctoral researcher will work with the clinical neurology team to conduct neurophysiological research in surgical patients undergoing treatment for refractory epilepsy implanted with intracranial electrodes (surface, depth). Research approaches will include both recording and stimulation. The postdoctoral fellow will be a member of a collaborative team that includes Lucia Melloni (NYU and Max Planck Institute, Frankfurt), Adeen Flinker (NYU), Charan Ranganath (UC Davis), Sam Gershman (Harvard), Ken Norman & Uri Hasson (Princeton), and Jeff Zacks (Washington University). The goal of the research studies will be to use real-time measures of brain activity to investigate how cortico-hippocampal interactions support event segmentation, schema formation, and memory for complex events. The ideal applicant must have a Ph.D. in neuroscience, psychology, biomedical engineering, or a related field. Proficiency in oral and written English is mandatory. A solid background in programming, statistics, and scientific writing is required. The candidate is expected to be able to work independently, to enjoy interacting within an interdisciplinary team, and to have a track-record of peer-reviewed publications. Previous experience with human electrophysiology or machine learning will be an asset. Start date is negotiable. Interested individuals should send an email to lucia.melloni at nyumc.org , including a cover letter describing research experience and qualifications, an academic CV, and contact information of referees. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jordvink at gmail.com Sun Feb 4 21:13:39 2018 From: jordvink at gmail.com (Jord Vink) Date: Sun, 4 Feb 2018 21:13:39 +0100 Subject: [FieldTrip] Cross spectral density versus coherence Message-ID: Hi all, I am working with functional connectivity between different (EEG) signals. I'm calculating the connectivity strength between different brain regions and correlate the connectivity strength to a certain outcome measure. Among others, I'm using the cross spectral density (CSD) and the coherence. The CSD is not generally used as a measure of connectivity but I don't completely understand why not. Especially since the CSD correlates well with my outcome measure, while the coherence doesn't. I'm trying to undertand whether there is a fundamental reason why I can't use the CSD, and why I should use the coherence. So I'm trying to understand why people use coherence (the normalized version of the cross spectral density) as a measure of connectivity instead of cross spectral density (CSD). Why do you have to normalize the CSD with the autospectral densities to determine connectivity when the CSD by itself is a measure of signal similarity? Is there a fundamental reason to normalize the CSD? Jord -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.smulders at maastrichtuniversity.nl Mon Feb 5 10:38:28 2018 From: f.smulders at maastrichtuniversity.nl (Smulders F (PSYCHOLOGY)) Date: Mon, 5 Feb 2018 09:38:28 +0000 Subject: [FieldTrip] impact of skewed power distributions on data analysis Message-ID: Hi Teresa Madsen, I am new to the Fieldtrip list, and not sure whether I contribute to this older discussion in the appropriate way. Noticing your thread on the distribution of alpha power, this paper might be relevant: http://onlinelibrary.wiley.com/doi/10.1111/ejn.13854/full kind regards, Fren Smulders -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Mon Feb 5 21:28:01 2018 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Mon, 5 Feb 2018 20:28:01 +0000 Subject: [FieldTrip] SPM M/EEG course 2018 Message-ID: Dear all, We are pleased to announce that our annual SPM course for MEG/EEG will take place this year from Monday May 7 to Wednesday May 9 2018. Hosted by University College London, the course will be held at Queen Square (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. For full details see: http://www.fil.ion.ucl.ac.uk/spm/course/london/ where you can also register. Available places are limited so please register as early as possible if you would like to attend! For any administrative questions, please contact Ms Kamlyn Ramikssoon (k.ramkissoon at ucl.ac.uk) very best - Hayriye Cagnan Monday May 7th (12 Queen square, 4th floor) 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources 9.45 - 10.30 What are we measuring with M/EEG? 10.30 - 11.15 Data pre-processing Coffee 11.45 - 12.30 Data pre-processing – demo 12.30 - 13.15 General linear model and classical inference Lunch 14.15 - 15.00 Multiple comparisons problem and solutions 15.00 - 15.45 Bayesian inference Coffee 16.15 - 17.45 Group M/EEG dataset analysis – demo 17.45 - 18.30 Advanced applications of the GLM Tuesday May 8th (33 Queen square, basement) 9.30 - 10.15 M/EEG source analysis 10.15 - 11.15 M/EEG source analysis – demo Coffee 11.45 - 12.30 The principles of dynamic causal modelling 12.30 - 13.15 DCM for evoked responses Lunch 14.15 - 15.00 DCM for steady state responses 15.00 - 15.45 DCM - demo Coffee 16.15 - 17.00 Bayesian model selection and averaging 17.00 - 18.30 Clinic - questions & answers 19.00 - ... Social Event Wednesday May 9th 9.30 - 17.00 Practical hands-on session will take place in UCL computer classrooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. From strautma at uke.de Tue Feb 6 11:25:40 2018 From: strautma at uke.de (Dr. Sina A. Trautmann-Lengsfeld) Date: Tue, 6 Feb 2018 11:25:40 +0100 Subject: [FieldTrip] Invitation: SAGE 2.0 in Hamburg, Germany (http://sfb936.net/SAGE2.0) Message-ID: <57ddc705-6f58-4d6c-80da-20ad7f851b94@uke.de> Dear Fieldtrip Users, dear Colleagues, Do you wonder why so few of your colleagues are female? Do all scientists with comparable skills have equal career opportunities? Why do a lot of people leave their job in science at a certain moment in their career, independent of their skills? Why is it so hard to find a good work-life-family balance? Why we do not care more about diversity and equality of chances in science? For these and many other reasons, we are very happy to announce our *second Science and Gender Equality Symposium “SAGE 2.0”* funded by the DFG Collaborative Research Center 936 (SFB 936). When? *March 23, 2018, 10:00 – 19:00 h* Where? *Erika-Haus, University Medical Center Hamburg-Eppendorf, Hamburg, Germany* There will be talks on neuroscience, astrophysics, equality, and day-to-day issues, as well as round table discussions by and with the following very renowned female scientists: Seats are given away on first-come, first-served basis. Participation is for free. The registration *deadline* is *March 15th 2018*. Please register: http://sfb936.net/SAGE2.0. The symposium is open to all scientists, independent of gender. Please do not hesitate to contact us (s.trautmann-lengsfeld at uke.de) in case of questions. We are looking forward to discussions with a broad variety of people! Sincerely yours, Marina Fiene, Annika Lübbert, Hilke M. Petersen, Bettina Schwab, Alexandra Tinnermann, and Sina A. Trautmann-Lengsfeld (Organizing Team) -- Dr. Sina Alexa Trautmann-Lengsfeld Postdoc & SFB 936 Graduate School Management Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg Germany Phone: +49-40-7410-57238 Fax: +49-40-7410-57752 Email: s.trautmann-lengsfeld at uke.de -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From william.chermanne at hotmail.com Thu Feb 8 15:37:34 2018 From: william.chermanne at hotmail.com (William Chermanne) Date: Thu, 8 Feb 2018 14:37:34 +0000 Subject: [FieldTrip] Problem to connect to the server Message-ID: Hi, Since yesterday, I have been trying to access the server by using the username « anonymous » and my e-mail adress as a password, but it doesn’t seem to work and I can’t connect to the server to download the FielTrip toolbox. Does someone know how to solve this problem? Thank you for your answer, William Chermanne From jan.schoffelen at donders.ru.nl Fri Feb 9 09:30:40 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 9 Feb 2018 08:30:40 +0000 Subject: [FieldTrip] Problem to connect to the server In-Reply-To: References: Message-ID: <4F6B8615-83DE-4D2C-BBAE-57AAA585E60E@donders.ru.nl> Dear William, I don’t know what’s going on with the FTP-server, but there are alternatives to grab the code repository, which I recommend instead. For instance you can find the code on http://github.com/fieldtrip Groeten, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 8 Feb 2018, at 15:37, William Chermanne > wrote: Hi, Since yesterday, I have been trying to access the server by using the username « anonymous » and my e-mail adress as a password, but it doesn’t seem to work and I can’t connect to the server to download the FielTrip toolbox. Does someone know how to solve this problem? Thank you for your answer, William Chermanne _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From william.chermanne at hotmail.com Sun Feb 11 16:31:49 2018 From: william.chermanne at hotmail.com (William Chermanne) Date: Sun, 11 Feb 2018 15:31:49 +0000 Subject: [FieldTrip] Starting from .mat files Message-ID: Hello everyone, I have started reading the documentation about the FieldTrip toolbox. A friend and I implemented a Matlab routine allowing to ‘create’ simulated EEG signals with hand movements for the three different channels C3,C4 and CZ. The routine writes the results in a .mat file where each line represents a channel. I thus have the format channel x time. However, I am not sure about where to begin with the fieldtrip functions. I also do not understand perfectly the concept of ’trials’. Should I define trials in my data? How to read the .mat file with the ft_preprocessing function or the ft_definetrial function? Thank you for your answer, William Chermanne From maximilien.chaumon at gmail.com Mon Feb 12 17:44:04 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Mon, 12 Feb 2018 16:44:04 +0000 Subject: [FieldTrip] scaling signals for joint EOG-MEG ICA decomposition Message-ID: Dear eeglab and FieldTrip users, On our MEG system, we systematically record EOG and EKG along with the MEG data. Running an ICA on the data to remove blinks and EKG works fine most of the time, but every now and then, the output is turned to puzzling complex-valued numbers. I realized that the huge scale discrepancy between the EKG and the MEG data could be what causes the problem, so I just multiplied all my EOG & EKG signals by 1e-6 and ran the ICA again, which returns real-valued numbers. The topographies look fine but I'm stuck trying to find out a way to scale this output to recover my originally scaled data. Is it possible? Any comments are welcome, thanks! Best, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcmackr at tcd.ie Mon Feb 12 21:46:26 2018 From: mcmackr at tcd.ie (Roisin McMackin) Date: Mon, 12 Feb 2018 20:46:26 +0000 Subject: [FieldTrip] Scale of timeseries for dipoles calculated from leadfields and EEG data Message-ID: Hi all, I'm using the method as described in https://mailman.science.ru. nl/pipermail/fieldtrip/2011-April/003690.html to estimate timeseries of activity for a number of dipole positions and moments. These were obtained using ft_dipolefitting to localise EEG recorded event related potentials. Headmodel (BEM) and sensor (128 electrodes) units are in mm and the EEG data (data.avg) is in microV, these are used to make the leadfield whose inverse is used to make weights. The leadfield is not normalised (since the orientation vector is). The amplitudes of the timeseries I'm getting for each dipole are in the range of about +/-500 to 5000. Is the timeseries still in the same units as the input data (i.e. microV, so the timeseries has milliV range amplitude)? If not how can I calculate the units of the leadfield, weights and timeseries? Thanks for any help or suggestions, Roisin -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Feb 13 16:54:18 2018 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 13 Feb 2018 16:54:18 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Dear Team, I am using Matlab 2017 and when I execute the following lines : cfg=[]; cfg.layout = 'biosemi256.lay'; layout = ft_prepare_layout(cfg); I get the following error *Error using nargin* *You can only call nargin/nargout from within a MATLAB function.* *Error in ft_preamble_init (line 34)* *if nargin==0* *Error in ft_preamble (line 56)* * evalin('caller', ['ft_preamble_' cmd]);* *Error in ft_prepare_layout (line 96)* *ft_preamble init* This seems related to the nargin instruction, which cannot be used in scripts anymore and it is MatLab version specific (does not happen if I use Matlab 2015b). Is this a bug? Cris -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at psy.ox.ac.uk Wed Feb 14 10:49:01 2018 From: eelke.spaak at psy.ox.ac.uk (Eelke Spaak) Date: Wed, 14 Feb 2018 10:49:01 +0100 Subject: [FieldTrip] scaling signals for joint EOG-MEG ICA decomposition In-Reply-To: <524555d6-9e22-47bf-91a8-ae39c1576f18@HUB01.ad.oak.ox.ac.uk> References: <524555d6-9e22-47bf-91a8-ae39c1576f18@HUB01.ad.oak.ox.ac.uk> Message-ID: Dear Max, Is there a particular reason you are including the EOG and ECG data in the ICA decomposition? The pipeline that would make most sense to me is to do the ICA decomposition on the MEG data alone, then check the correlation of the EOG/ECG timecourses with individual ICA components to classify which of those likely correspond to artifacts. Doing a joint decomposition will lead to some mixing in of EOG/ECG data into the reconstructed (cleaned) MEG data. Cheers, Eelke On 12 February 2018 at 17:44, Maximilien Chaumon wrote: > Dear eeglab and FieldTrip users, > > On our MEG system, we systematically record EOG and EKG along with the MEG > data. Running an ICA on the data to remove blinks and EKG works fine most of > the time, but every now and then, the output is turned to puzzling > complex-valued numbers. > > I realized that the huge scale discrepancy between the EKG and the MEG data > could be what causes the problem, so I just multiplied all my EOG & EKG > signals by 1e-6 and ran the ICA again, which returns real-valued numbers. > The topographies look fine but I'm stuck trying to find out a way to scale > this output to recover my originally scaled data. Is it possible? > > Any comments are welcome, thanks! > Best, > Max > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Wed Feb 14 11:56:19 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 14 Feb 2018 10:56:19 +0000 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Dear Cris, This is a known issue and has been addressed a while ago. You may need to upgrade your fieldtrip version to an up-to-date version. Best wishes, JM On 13 Feb 2018, at 16:54, Cristiano Micheli > wrote: Dear Team, I am using Matlab 2017 and when I execute the following lines : cfg=[]; cfg.layout = 'biosemi256.lay'; layout = ft_prepare_layout(cfg); I get the following error Error using nargin You can only call nargin/nargout from within a MATLAB function. Error in ft_preamble_init (line 34) if nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_prepare_layout (line 96) ft_preamble init This seems related to the nargin instruction, which cannot be used in scripts anymore and it is MatLab version specific (does not happen if I use Matlab 2015b). Is this a bug? Cris _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jb.eichenlaub at gmail.com Fri Feb 16 10:38:02 2018 From: jb.eichenlaub at gmail.com (Jean-Baptiste Eichenlaub) Date: Fri, 16 Feb 2018 10:38:02 +0100 Subject: [FieldTrip] ft_freqanalysis warning (correcting numerical inaccuracy in time axes) after ft_redefinetrial on continous data Message-ID: Dear Fieldtripers, After having segmented continuous EEG data (ft_redefinetrial, cfg.length = 2; cfg.overlap = 0.5), I compute the power spectrum for each trial/segment (ft_freqanalysis). However, I am getting the following warning message (see below in blue). Based on several sources, it seems to be explained by "the inaccuracy in binary representation of floating point values". I do not get the error message with cfg.length = 5 in the previous step (ft_redefinetrial). Should I be concerned? Thanks! Best, Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_freqanalysis (line 217) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_selectdata (line 134) In ft_freqanalysis (line 232) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) the call to "ft_selectdata" took 1 seconds processing trials processing trial 1199/1199 nfft: 2048 samples, datalength: 2000 samples, 1 tapers -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Sat Feb 17 03:09:51 2018 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Sat, 17 Feb 2018 02:09:51 +0000 Subject: [FieldTrip] Parallel simbio fem Message-ID: At one point there was a suggestion in the maiing list that the computation of the forward model for the Simbio FEM model might add some parallelization. Does anyone know if this has been done. I read through the previous discussion and sympathesize with the users whose jobs take a day or so to compute. I have found it is the size of the source space grid-like 10mm for an adult head goes pretty fast, 3mm for an adult head takes 24 hrs. Anyone know of a parallel implementation? Thanks, 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 ************************************************* [cid:image001.png at 01D23F64.B505C760] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 30144 bytes Desc: image001.png URL: From jan.schoffelen at donders.ru.nl Sat Feb 17 20:35:23 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sat, 17 Feb 2018 19:35:23 +0000 Subject: [FieldTrip] ft_freqanalysis warning (correcting numerical inaccuracy in time axes) after ft_redefinetrial on continous data In-Reply-To: References: Message-ID: <25C04C90-EAB8-47A1-AC70-85A991938CC2@donders.ru.nl> Hi JB, This is indeed nothing to worry about. Your sources are right. Best wishes, JM On 16 Feb 2018, at 10:38, Jean-Baptiste Eichenlaub > wrote: Dear Fieldtripers, After having segmented continuous EEG data (ft_redefinetrial, cfg.length = 2; cfg.overlap = 0.5), I compute the power spectrum for each trial/segment (ft_freqanalysis). However, I am getting the following warning message (see below in blue). Based on several sources, it seems to be explained by "the inaccuracy in binary representation of floating point values". I do not get the error message with cfg.length = 5 in the previous step (ft_redefinetrial). Should I be concerned? Thanks! Best, Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_freqanalysis (line 217) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_selectdata (line 134) In ft_freqanalysis (line 232) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) the call to "ft_selectdata" took 1 seconds processing trials processing trial 1199/1199 nfft: 2048 samples, datalength: 2000 samples, 1 tapers _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From h.park at bham.ac.uk Sun Feb 18 09:37:24 2018 From: h.park at bham.ac.uk (Hyojin Park) Date: Sun, 18 Feb 2018 08:37:24 +0000 Subject: [FieldTrip] Inaugural MEG Symposium at the CHBH, University of Birmingham (11th May) Message-ID: <8EB94CB9BF5FD74FA38E0919D3329E9BD6D113@EX14.adf.bham.ac.uk> Dear all, We are pleased to announce the "Inaugural MEG Symposium at the Centre for Human Brain Health" at the University of Birmingham. *09:30-17:30, 11th May 2018 at The Alan Walters Building, University of Birmingham* We would be delighted if you could join us to celebrate the opening of our new MEG facility. The event will include talks from speakers who are leaders in their field, and will include a tour of the new MEG facility at the University of Birmingham. For a complete list of speakers and to register (free) please visit: https://meg2018.eventbrite.co.uk Best regards, Dr. Hyojin Park and Prof. Ole Jensen School of Psychology|Centre for Human Brain Health, University of Birmingham -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.kristensen at gipsa-lab.grenoble-inp.fr Wed Feb 21 15:39:36 2018 From: emmanuelle.kristensen at gipsa-lab.grenoble-inp.fr (EMMANUELLE KRISTENSEN) Date: Wed, 21 Feb 2018 15:39:36 +0100 Subject: [FieldTrip] reading Brain Vision data : unknown resolution for channel Message-ID: <6709f46f-de1f-6dd5-a4dd-932c2bd91caf@gipsa-lab.grenoble-inp.fr> Dear all When reading a .vhdr file/ .dat file (written by EEGlab), I get this warning message, for each channel: "/Warning: unknown resolution (i.e. recording units) for channel 1 in// //MyFile.vhdr/". In the .vhdr file, the resolution is indicated : /"[Binary Infos]// //BinaryFormat=IEEE_FLOAT_32// // //[Channel Infos]// //; Each entry: Ch=,,// //; ////"/ How can I fix this warning, please? Regards, Emmanuelle -- Emmanuelle Kristensen -------------- next part -------------- An HTML attachment was scrubbed... URL: From dbaeper at upo.es Thu Feb 22 18:31:03 2018 From: dbaeper at upo.es (Daniel Baena Perez) Date: Thu, 22 Feb 2018 18:31:03 +0100 Subject: [FieldTrip] Cluster analysis for across subjects with behavioral data Message-ID: Dear all I would like to use the cluster analysis functions in Fieldtrip on correlation statistics. My data consist on an eeg signal recorded on 8 different channels and 125 time bins for 31 subjects. I would like to do an across subjects correlation for each time bin and each channel with the behavioural results. Which function is more suitable for this purpose? My reasoning so far is to use ft_statfun_intersubcorr in the first place but I'm not sure how to continue with the cluster analysis per se. Can this function be given as an argument to ft_timelockstatistics? Thank you, Daniel -------------- next part -------------- An HTML attachment was scrubbed... URL: From mylenbcn at hotmail.com Fri Feb 23 01:02:38 2018 From: mylenbcn at hotmail.com (D myl) Date: Fri, 23 Feb 2018 00:02:38 +0000 Subject: [FieldTrip] Clustering Statistics with Different Number of Observations Per Channel Message-ID: Subject: Clustering Statistics with Different Number of Observations Per Channel Dear community, My name is Dimitris Mylonas and I am working on coupled oscillations on EEG. Currently I am analyzing a high density EEG dataset where we measure the phase-amplitude coupling of specific oscillations (slow waves (.5-2 Hz) and sleep spindles (12-15 Hz)) at each electrode, for two different groups. The outcome measure is the vector length of the coupling (coupling strength) and the question is whether the two groups show significant difference in coupling strength. In order to estimate reliably the coupling strength for each electrode/subject we need to have a minimum number N of coupled oscillations. If for a given subject and a given electrode there are less than N detected oscillations there will be a missing value in the outcome measure. As a result each electrode has different number of subjects where the coupling strength can be "measured reliably". My question is if I can implement the non-parametric statistical testing (not necessarily as implemented in Fieldtrip) (Maris and Oostenveld, 2007) to test for a group difference under this condition (different degrees of freedom at each electrode). Thank you, Dimitris -------------- next part -------------- An HTML attachment was scrubbed... URL: From pascualm at key.uzh.ch Fri Feb 23 06:41:22 2018 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Fri, 23 Feb 2018 14:41:22 +0900 Subject: [FieldTrip] Comparing EEG/MEG neuroimaging methods based on localization error, false positive activity, and false positive connectivity Message-ID: Dear Colleagues, The preprint entitled: "Comparing EEG/MEG neuroimaging methods based on localization error, false positive activity, and false positive connectivity" at: https://www.biorxiv.org/content/early/2018/02/22/269753 might be of interest to those working in the field of EEG/MEG neuroimaging. The abstract can be found below. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [www.keyinst.uzh.ch/loreta] [scholar.google.com/citations?user=pascualmarqui] ... Abstract: EEG/MEG neuroimaging consists of estimating the cortical distribution of time varying signals of electric neuronal activity, for the study of functional localization and connectivity. Currently, many different imaging methods are being used, with very different capabilities of correct localization of activity and of correct localization of connectivity. The aim here is to provide a guideline for choosing the best (i.e. least bad) imaging method. This first study is limited to the comparison of the following methods for EEG signals: sLORETA and eLORETA (standardized and exact low resolution electromagnetic tomography), MNE (minimum norm estimate), dSPM (dynamic statistical parametric mapping), and LCMVBs (linearly constrained minimum variance beamformers). These methods are linear, except for the LCMVBs that make use of the quadratic EEG covariances. To achieve a fair comparison, it is assumed here that the generators are independent and widely distributed (i.e. not few in number), giving a well-defined theoretical population EEG covariance matrix for use with the LCMVBs. Measures of localization error, false positive activity, and false positive connectivity are defined and computed under ideal no-noise conditions. It is empirically shown with extensive simulations that: (1) MNE, dSPM, and all LCMVBs are in general incapable of correct localization, while sLORETA and eLORETA have exact (zero-error) localization; (2) the brain volume with false positive activity is significantly larger for MN, dSPM, and all LCMVBs, as compared to sLORETA and eLORETA; and (3) the number of false positive connections is significantly larger for MN, dSPM, all LCMVBs, and sLORETA, as compared to eLORETA. Non-vague and fully detailed equations are given. PASCAL program codes and data files are available. It is noted that the results reported here do not apply to the LCMVBs based on EEG covariance matrices generated from extremely few generators, such as only one or two independent point sources. From hesham.elshafei at inserm.fr Mon Feb 26 13:38:50 2018 From: hesham.elshafei at inserm.fr (Hesham ElShafei) Date: Mon, 26 Feb 2018 13:38:50 +0100 Subject: [FieldTrip] Extraction of Amplitude and Phase from PCC sources Message-ID: Hello all , I have computed beamformer sources using the 'pcc' method. In my source.avg structures , I have the 'csd' , 'noisecsd' , 'mom' and 'csdlabel. I was wondering if there are means to extract both phase and amplitude of the source-level signal from these information. Cheers Hesham ElShafei From jan.schoffelen at donders.ru.nl Mon Feb 26 13:54:16 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 26 Feb 2018 12:54:16 +0000 Subject: [FieldTrip] Extraction of Amplitude and Phase from PCC sources In-Reply-To: References: Message-ID: <350B16BA-8244-44DF-9F0D-BDE333E9C8C3@donders.ru.nl> Hi Hesham, The single trial/taper Fourier coefficients with amplitude and phase info are in source.avg.mom. Best wishes, Jan-Mathijs > On 26 Feb 2018, at 13:38, Hesham ElShafei wrote: > > Hello all , > > I have computed beamformer sources using the 'pcc' method. In my source.avg structures , I have the 'csd' , 'noisecsd' , 'mom' and 'csdlabel. > > I was wondering if there are means to extract both phase and amplitude of the source-level signal from these information. > > Cheers > Hesham ElShafei > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tony.w.wilson at gmail.com Tue Feb 27 12:59:34 2018 From: tony.w.wilson at gmail.com (Tony W. Wilson) Date: Tue, 27 Feb 2018 05:59:34 -0600 Subject: [FieldTrip] Tenure-track Faculty Position in Cognitive Neuroscience Message-ID: The Department of Neurological Sciences at the University of Nebraska Medical Center invites applications for a tenure leading faculty position in Clinical Cognitive Neuroscience. This position is part of a new Neuroimaging Section within the department and aims to leverage multiple hires across the School of Medicine in human neuroscience. We welcome applications from any area of cognitive neuroscience, including memory, executive function, visual attention, perception, audition, motor control, emotion, and decision-making. Methodological specialty within neuroimaging is open, but ideally the candidate would benefit from our strong existing program in MEG imaging, and develop a translational, theory-based multimodal neuroimaging program focusing on their area of interest. The successful applicant would join a growing group of cognitive neuroscientists within the department (and across campus) using MEG, fMRI, and other modalities, and hopefully help grow other programs in parallel with building their own. Successful candidates will have a MD, PhD, or MD/PhD in neuroscience, psychology, or computer science, with postdoctoral training and an excellent publication record for their career stage. Candidates should also have an excellent and sustained record of research and evidence of the potential, or demonstrated ability, to generate extramural funding commensurate with their career stage. Applicants should have the ability and interest to teach graduate courses in cognitive neuroscience, and to mentor PhD students in our growing Neuroscience PhD program. The University of Nebraska Medical Center (UNMC) is a vibrant multidisciplinary research environment with major resources and ample opportunities for training and collaboration. Resources include a 306-sensor MEG system, multiple 3T human MRI scanners, high-definition transcranial direct-current and alternating-current stimulation (HD-tDCS/tACS) equipment, eye-tracking equipment, and a state-of-the-art transcranial magnetic stimulation (TMS) suite. The UNMC is located in Omaha, with a metro area population of approximately one million, and major attractions and events such as the College World Series. Please submit a letter detailing current research and teaching interests, a curriculum vitae, a list of the applicant’s five most important publications, and contact information for three individuals who will provide letters of recommendation at a later time. Applications should be submitted online at: https://unmc.peopleadmin.com/postings/36674 . Review of applications will begin immediately and will continue until the position is filled. Start dates are negotiable, but ideally before the close of 2018. Individuals from diverse backgrounds are encouraged to apply. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elinor.tzvi at neuro.uni-luebeck.de Tue Feb 27 17:03:11 2018 From: elinor.tzvi at neuro.uni-luebeck.de (Elinor Tzvi-Minker) Date: Tue, 27 Feb 2018 16:03:11 +0000 Subject: [FieldTrip] PhD position @ Queen Mary University of London Message-ID: <2530B215-C864-40D3-87F5-1F5ED7C5DE7A@neuro.uni-luebeck.de> Dear All, A 3-year PhD studentship for UK and EU citizens is open at Queen Mary University of London. The project will investigate sense of agency, outcome processing and learning under social influence. Application deadline is 12thMarch. More information and link to the application portal can be found under https://www.findaphd.com/search/ProjectDetails.aspx?PJID=94998 Best wishes, Frederike Beyer -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Wed Feb 28 03:27:31 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Wed, 28 Feb 2018 02:27:31 +0000 Subject: [FieldTrip] Alignment problem Message-ID: Dear Experts, I read a Brainweb MRI volume in filedtrip ( by default it doesn’t have any coordinate fields). When I align this data to CTF coordinate system using ft_volumerealign and then apply this alignment using ft_volumereslice; I see I miss some data and I get a very wrong head model using this resliced data. Any Ideas? Thanks in advance, Regards, Fereshte -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 28 08:54:47 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 28 Feb 2018 07:54:47 +0000 Subject: [FieldTrip] Alignment problem In-Reply-To: References: Message-ID: <572A023D-3A85-47BF-A5EB-2DB95DA8B332@donders.ru.nl> Hi Fereshte, No, without any additional information I don’t have any ideas :). What do you mean by “I miss some data”, and “I get a very wrong head model”? Please refer to http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list in phrasing your question. This will maximize the probability that somebody will be inclined and able to point you into the good direction. Best wishes, Jan-Mathijs On 28 Feb 2018, at 03:27, Fereshte > wrote: Dear Experts, I read a Brainweb MRI volume in filedtrip ( by default it doesn’t have any coordinate fields). When I align this data to CTF coordinate system using ft_volumerealign and then apply this alignment using ft_volumereslice; I see I miss some data and I get a very wrong head model using this resliced data. Any Ideas? Thanks in advance, Regards, Fereshte _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Wed Feb 28 12:15:34 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Wed, 28 Feb 2018 12:15:34 +0100 (CET) Subject: [FieldTrip] 1st International Workshop on Predictive Processing (WoPP) In-Reply-To: References: <5a7d686f.ed3fed0a.5f941.c127SMTPIN_ADDED_BROKEN@mx.google.com> <1640004900.9152749.1519247555698.JavaMail.zimbra@bcbl.eu> <1717447392.9286562.1519725808525.JavaMail.zimbra@bcbl.eu> <497399636.9344962.1519815833963.JavaMail.zimbra@bcbl.eu> Message-ID: <1858953218.9345933.1519816534199.JavaMail.zimbra@bcbl.eu> Dear All, We invite you to the " 1st International Workshop on Predictive Processing (WoPP) " organized by Basque Center on Cognition, Brain and Language (BCBL) that will be held in one of most beautiful cities in europe, San Sebastian, Spain from 20 - 22 June 2018 , at Palacio Miramar in Donostia - San Sebastián. The aim of the workshop is to discuss predictive coding and its underlying mechanisms from behaviour to neuroscience. We aim at calling together researchers and students from various domains such as vision, audition and language, to build bridges between various research fields and share this common and exciting interest on prediction. Please visit http://www.bcbl.eu/events/prediction-2018/en/ for details about abstract submission and registration. Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018. -------------- next part -------------- An HTML attachment was scrubbed... URL: From virginie.van.wassenhove at gmail.com Thu Feb 1 11:22:36 2018 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Thu, 1 Feb 2018 11:22:36 +0100 Subject: [FieldTrip] [tenure-track researcher position] Message-ID: Dear all, applications are invited for a tenure-track researcher position in the Cognition and Brain Dynamics research team of Virginie van Wassenhove. The lab is hosted at NeuroSpin (Dir. Prof Stanislas Dehaene) on the plateau de Saclay near Paris, France. See full description attached. Kind regards, Virginie -- Virginie van Wassenhove *https://brainthemind.com/ * -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2018_VvW_JobDescription_CEA.pdf Type: application/pdf Size: 100589 bytes Desc: not available URL: From annekathrinweise at gmail.com Thu Feb 1 14:54:49 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 1 Feb 2018 14:54:49 +0100 Subject: [FieldTrip] Salzburg Mind Brain Annual (SAMBA) Meeting 2018 Message-ID: Dear all, on behalf of myself, my colleagues, and our advisory board, I am happy to announce the *Salzburg Mind Brain Annual Meeting* (*SAMBA*)**which will take place *in Salzburg, Austria* on *July 12 & 13*, *2018*. The*registration* is now *open until March 15*. The mission of SAMBA is to attract the most exciting researchers in the domain of cognitive neuroscience, including related fields (e.g., computational modelling, animal neurophysiology, neurology etc.) that influence or are influenced by developments in cognitive neuroscience. Furthermore, our goal is to make young scientists enthusiastic about this research field. The moderate size of an anticipated ~100 participants will enable an intimate atmosphere with ample opportunity for exchange. Confirmed speakers are: *     Radoslav Cichy (FU Berlin) *     Simon Eickhoff (Jülich) *     Saskia Haegens (Columbia / Donders) *     Jim Haxby (Dartmouth) *     Katharina von Kriegstein (MPI Leipzig) *     Floris de Lange (Donders) *     Tamar Makin (UCL) *     Kia Nobre (Oxford) *     Uta Noppeney (Birmingham) *     Anne-Marike Schiffer (Nature Human Behavior) *     Andreas Wutz (MIT / Salzburg) Attendees have the possibility to present a poster. For more information see the SAMBA website: https://samba.ccns.sbg.ac.at/ Best, Nathan -- Nathan Weisz Centre for Cognitive Neuroscience Division of Physiological Psychology University of Salzburg nathan.weisz at sbg.ac.at www.oboblab.at -- Annekathrin Weise, Dr. Paris-Lodron Universität Salzburg Division of Physiological Psychology Hellbrunnerstraße 34 5020 Salzburg Austria e-mail: annekathrin.weise at sbg.ac.at; annekathrinweise at gmail.com web: http://www.oboblab.at/ https://sites.google.com/site/weiseannekathrin/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From yaocong.duan at gmail.com Thu Feb 1 18:31:56 2018 From: yaocong.duan at gmail.com (Yaocong Duan) Date: Thu, 1 Feb 2018 17:31:56 +0000 Subject: [FieldTrip] Question about Phase locking value Message-ID: Hi All, I am using Phase Locking Value to measure the connectivity between brain regions at the source level. I learned that the PLV is an average value over trails. In the fieldtrip code, I calculated a frequency model first, then do connectivity analysis with this freq model. The problem is I don’t see trails information in the freq model. So how do I get that phase locking result? Below is my code. This code works, but I am confused about the question above. [image: Inline images 1] Thanks in advance, Yaocong -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From stephen.whitmarsh at gmail.com Thu Feb 1 19:02:51 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 1 Feb 2018 19:02:51 +0100 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Dear Yaocong, To understand your question, it would be helpful if you post the output of the freqanalysis, i.e. your *freq *datastructure. It should contain a .*pow *field, which should be an array of structs, numbering your number of trials, right? Cheers, Stephen Virus-free. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On 1 February 2018 at 18:31, Yaocong Duan wrote: > Hi All, > > > > I am using Phase Locking Value to measure the connectivity between brain > regions at the source level. I learned that the PLV is an average value > over trails. In the fieldtrip code, I calculated a frequency model first, > then do connectivity analysis with this freq model. The problem is I don’t > see trails information in the freq model. So how do I get that phase > locking result? > > > > Below is my code. This code works, but I am confused about the question > above. > > [image: Inline images 1] > > Thanks in advance, > Yaocong > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From yaocong.duan at gmail.com Fri Feb 2 01:12:56 2018 From: yaocong.duan at gmail.com (Yaocong Duan) Date: Fri, 2 Feb 2018 00:12:56 +0000 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Hi Stephen, Thank you for your response. I write something wrong in my previous email. the freq structure does have trails information. but then I do a source reconstruction and generate a source structure. phase locking value is calculated from the source structure directly. However, the source structure does not have any trails info (trails seems have been averaged). source = ft_sourceanalysis(cfg, freq); ... plv = ft_connectivityanalysis(cfg, souceSparse); below are the freq structure generated by freq analysis, source structure generated by source analysis as well as the .avg field of source structure. [image: Inline images 1][image: Inline images 2][image: Inline images 3] On 1 February 2018 at 18:02, Stephen Whitmarsh wrote: > Dear Yaocong, > > To understand your question, it would be helpful if you post the output of > the freqanalysis, i.e. your *freq *datastructure. It should contain a .*pow > *field, which should be an array of structs, numbering your number of > trials, right? > > Cheers, > Stephen > > > Virus-free. > www.avast.com > > <#m_6562418138207874494_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On 1 February 2018 at 18:31, Yaocong Duan wrote: > >> Hi All, >> >> >> >> I am using Phase Locking Value to measure the connectivity between brain >> regions at the source level. I learned that the PLV is an average value >> over trails. In the fieldtrip code, I calculated a frequency model first, >> then do connectivity analysis with this freq model. The problem is I don’t >> see trails information in the freq model. So how do I get that phase >> locking result? >> >> >> >> Below is my code. This code works, but I am confused about the question >> above. >> >> [image: Inline images 1] >> >> Thanks in advance, >> Yaocong >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 82049 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 97937 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 92321 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From xiew1202 at gmail.com Fri Feb 2 02:35:59 2018 From: xiew1202 at gmail.com (Xie Wanze) Date: Thu, 1 Feb 2018 20:35:59 -0500 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Hi Yaocong, Two things you may want to try: 1. use the "keep trials" option when you do your source analysis. This method makes a lot of sense, but it did not work for me. 2. Do source reconstruction separately for each individual trial. You may calculate the filter in Fieldtrip using ft_sourceanalysis and then use the filter for source reconstruction for each trial: reconstructed source activity = filter*data (in individual trial). This second option worked for me. Good luck. Wanze 2018-02-01 19:12 GMT-05:00 Yaocong Duan : > Hi Stephen, > > Thank you for your response. I write something wrong in my previous email. > the freq structure does have trails information. but then I do a source > reconstruction and generate a source structure. phase locking value is > calculated from the source structure directly. However, the source > structure does not have any trails info (trails seems have been averaged). > > source = ft_sourceanalysis(cfg, freq); > ... > plv = ft_connectivityanalysis(cfg, souceSparse); > > > below are the freq structure generated by freq analysis, source structure > generated by source analysis as well as the .avg field of source structure. > > > [image: Inline images 1][image: Inline images 2][image: Inline images 3] > > On 1 February 2018 at 18:02, Stephen Whitmarsh < > stephen.whitmarsh at gmail.com> wrote: > >> Dear Yaocong, >> >> To understand your question, it would be helpful if you post the output >> of the freqanalysis, i.e. your *freq *datastructure. It should contain a >> .*pow *field, which should be an array of structs, numbering your number >> of trials, right? >> >> Cheers, >> Stephen >> >> >> Virus-free. >> www.avast.com >> >> <#m_3173352166848949795_m_6562418138207874494_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> On 1 February 2018 at 18:31, Yaocong Duan wrote: >> >>> Hi All, >>> >>> >>> >>> I am using Phase Locking Value to measure the connectivity between brain >>> regions at the source level. I learned that the PLV is an average value >>> over trails. In the fieldtrip code, I calculated a frequency model first, >>> then do connectivity analysis with this freq model. The problem is I don’t >>> see trails information in the freq model. So how do I get that phase >>> locking result? >>> >>> >>> >>> Below is my code. This code works, but I am confused about the question >>> above. >>> >>> [image: Inline images 1] >>> >>> Thanks in advance, >>> Yaocong >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 92321 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 97937 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 82049 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Fri Feb 2 09:07:49 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 2 Feb 2018 08:07:49 +0000 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: <86C3123F-DB4B-4C27-8261-2230D3689ACF@donders.ru.nl> When you call ft_freqanalysis with ‘fourier’ in the cfg.method, followed by ft_sourceanalysis with ‘pcc’ in cfg.method, the source.avg.mom contains the fourier coefficients at the single taper level. A bunch of tapers constitute a single trial, the number of which depends on the smoothing parameter that you used in ft_freqanalysis. Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 2 Feb 2018, at 01:12, Yaocong Duan > wrote: Hi Stephen, Thank you for your response. I write something wrong in my previous email. the freq structure does have trails information. but then I do a source reconstruction and generate a source structure. phase locking value is calculated from the source structure directly. However, the source structure does not have any trails info (trails seems have been averaged). source = ft_sourceanalysis(cfg, freq); ... plv = ft_connectivityanalysis(cfg, souceSparse); below are the freq structure generated by freq analysis, source structure generated by source analysis as well as the .avg field of source structure. On 1 February 2018 at 18:02, Stephen Whitmarsh > wrote: Dear Yaocong, To understand your question, it would be helpful if you post the output of the freqanalysis, i.e. your freq datastructure. It should contain a .pow field, which should be an array of structs, numbering your number of trials, right? Cheers, Stephen [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif] Virus-free. www.avast.com On 1 February 2018 at 18:31, Yaocong Duan > wrote: Hi All, I am using Phase Locking Value to measure the connectivity between brain regions at the source level. I learned that the PLV is an average value over trails. In the fieldtrip code, I calculated a frequency model first, then do connectivity analysis with this freq model. The problem is I don’t see trails information in the freq model. So how do I get that phase locking result? Below is my code. This code works, but I am confused about the question above. Thanks in advance, Yaocong _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmelloni at gmail.com Sun Feb 4 18:37:43 2018 From: lmelloni at gmail.com (Lucia Melloni) Date: Sun, 4 Feb 2018 18:37:43 +0100 Subject: [FieldTrip] Postdoctoral Position in Electrocorticography at NYU Message-ID: <79BBB75B-4A9E-4057-B75F-F069BE96E8BC@gmail.com> Dear All, We have an opening for a POSTDOCTORAL POSITION IN ELECTROCORTICOGRAPHY RESEARCH AT NYU. See below for details. Thanks and all the best, Lucia POSTDOCTORAL POSITION IN ELECTROCORTICOGRAPHY RESEARCH AT NYU NYU School of Medicine has an opening for a Postdoctoral Researcher to conduct Human intracranial EEG and electrocortigoraphy (ECoG) research. The postdoctoral researcher will work with the clinical neurology team to conduct neurophysiological research in surgical patients undergoing treatment for refractory epilepsy implanted with intracranial electrodes (surface, depth). Research approaches will include both recording and stimulation. The postdoctoral fellow will be a member of a collaborative team that includes Lucia Melloni (NYU and Max Planck Institute, Frankfurt), Adeen Flinker (NYU), Charan Ranganath (UC Davis), Sam Gershman (Harvard), Ken Norman & Uri Hasson (Princeton), and Jeff Zacks (Washington University). The goal of the research studies will be to use real-time measures of brain activity to investigate how cortico-hippocampal interactions support event segmentation, schema formation, and memory for complex events. The ideal applicant must have a Ph.D. in neuroscience, psychology, biomedical engineering, or a related field. Proficiency in oral and written English is mandatory. A solid background in programming, statistics, and scientific writing is required. The candidate is expected to be able to work independently, to enjoy interacting within an interdisciplinary team, and to have a track-record of peer-reviewed publications. Previous experience with human electrophysiology or machine learning will be an asset. Start date is negotiable. Interested individuals should send an email to lucia.melloni at nyumc.org , including a cover letter describing research experience and qualifications, an academic CV, and contact information of referees. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jordvink at gmail.com Sun Feb 4 21:13:39 2018 From: jordvink at gmail.com (Jord Vink) Date: Sun, 4 Feb 2018 21:13:39 +0100 Subject: [FieldTrip] Cross spectral density versus coherence Message-ID: Hi all, I am working with functional connectivity between different (EEG) signals. I'm calculating the connectivity strength between different brain regions and correlate the connectivity strength to a certain outcome measure. Among others, I'm using the cross spectral density (CSD) and the coherence. The CSD is not generally used as a measure of connectivity but I don't completely understand why not. Especially since the CSD correlates well with my outcome measure, while the coherence doesn't. I'm trying to undertand whether there is a fundamental reason why I can't use the CSD, and why I should use the coherence. So I'm trying to understand why people use coherence (the normalized version of the cross spectral density) as a measure of connectivity instead of cross spectral density (CSD). Why do you have to normalize the CSD with the autospectral densities to determine connectivity when the CSD by itself is a measure of signal similarity? Is there a fundamental reason to normalize the CSD? Jord -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.smulders at maastrichtuniversity.nl Mon Feb 5 10:38:28 2018 From: f.smulders at maastrichtuniversity.nl (Smulders F (PSYCHOLOGY)) Date: Mon, 5 Feb 2018 09:38:28 +0000 Subject: [FieldTrip] impact of skewed power distributions on data analysis Message-ID: Hi Teresa Madsen, I am new to the Fieldtrip list, and not sure whether I contribute to this older discussion in the appropriate way. Noticing your thread on the distribution of alpha power, this paper might be relevant: http://onlinelibrary.wiley.com/doi/10.1111/ejn.13854/full kind regards, Fren Smulders -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Mon Feb 5 21:28:01 2018 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Mon, 5 Feb 2018 20:28:01 +0000 Subject: [FieldTrip] SPM M/EEG course 2018 Message-ID: Dear all, We are pleased to announce that our annual SPM course for MEG/EEG will take place this year from Monday May 7 to Wednesday May 9 2018. Hosted by University College London, the course will be held at Queen Square (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. For full details see: http://www.fil.ion.ucl.ac.uk/spm/course/london/ where you can also register. Available places are limited so please register as early as possible if you would like to attend! For any administrative questions, please contact Ms Kamlyn Ramikssoon (k.ramkissoon at ucl.ac.uk) very best - Hayriye Cagnan Monday May 7th (12 Queen square, 4th floor) 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources 9.45 - 10.30 What are we measuring with M/EEG? 10.30 - 11.15 Data pre-processing Coffee 11.45 - 12.30 Data pre-processing – demo 12.30 - 13.15 General linear model and classical inference Lunch 14.15 - 15.00 Multiple comparisons problem and solutions 15.00 - 15.45 Bayesian inference Coffee 16.15 - 17.45 Group M/EEG dataset analysis – demo 17.45 - 18.30 Advanced applications of the GLM Tuesday May 8th (33 Queen square, basement) 9.30 - 10.15 M/EEG source analysis 10.15 - 11.15 M/EEG source analysis – demo Coffee 11.45 - 12.30 The principles of dynamic causal modelling 12.30 - 13.15 DCM for evoked responses Lunch 14.15 - 15.00 DCM for steady state responses 15.00 - 15.45 DCM - demo Coffee 16.15 - 17.00 Bayesian model selection and averaging 17.00 - 18.30 Clinic - questions & answers 19.00 - ... Social Event Wednesday May 9th 9.30 - 17.00 Practical hands-on session will take place in UCL computer classrooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. From strautma at uke.de Tue Feb 6 11:25:40 2018 From: strautma at uke.de (Dr. Sina A. Trautmann-Lengsfeld) Date: Tue, 6 Feb 2018 11:25:40 +0100 Subject: [FieldTrip] Invitation: SAGE 2.0 in Hamburg, Germany (http://sfb936.net/SAGE2.0) Message-ID: <57ddc705-6f58-4d6c-80da-20ad7f851b94@uke.de> Dear Fieldtrip Users, dear Colleagues, Do you wonder why so few of your colleagues are female? Do all scientists with comparable skills have equal career opportunities? Why do a lot of people leave their job in science at a certain moment in their career, independent of their skills? Why is it so hard to find a good work-life-family balance? Why we do not care more about diversity and equality of chances in science? For these and many other reasons, we are very happy to announce our *second Science and Gender Equality Symposium “SAGE 2.0”* funded by the DFG Collaborative Research Center 936 (SFB 936). When? *March 23, 2018, 10:00 – 19:00 h* Where? *Erika-Haus, University Medical Center Hamburg-Eppendorf, Hamburg, Germany* There will be talks on neuroscience, astrophysics, equality, and day-to-day issues, as well as round table discussions by and with the following very renowned female scientists: Seats are given away on first-come, first-served basis. Participation is for free. The registration *deadline* is *March 15th 2018*. Please register: http://sfb936.net/SAGE2.0. The symposium is open to all scientists, independent of gender. Please do not hesitate to contact us (s.trautmann-lengsfeld at uke.de) in case of questions. We are looking forward to discussions with a broad variety of people! Sincerely yours, Marina Fiene, Annika Lübbert, Hilke M. Petersen, Bettina Schwab, Alexandra Tinnermann, and Sina A. Trautmann-Lengsfeld (Organizing Team) -- Dr. Sina Alexa Trautmann-Lengsfeld Postdoc & SFB 936 Graduate School Management Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg Germany Phone: +49-40-7410-57238 Fax: +49-40-7410-57752 Email: s.trautmann-lengsfeld at uke.de -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From william.chermanne at hotmail.com Thu Feb 8 15:37:34 2018 From: william.chermanne at hotmail.com (William Chermanne) Date: Thu, 8 Feb 2018 14:37:34 +0000 Subject: [FieldTrip] Problem to connect to the server Message-ID: Hi, Since yesterday, I have been trying to access the server by using the username « anonymous » and my e-mail adress as a password, but it doesn’t seem to work and I can’t connect to the server to download the FielTrip toolbox. Does someone know how to solve this problem? Thank you for your answer, William Chermanne From jan.schoffelen at donders.ru.nl Fri Feb 9 09:30:40 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 9 Feb 2018 08:30:40 +0000 Subject: [FieldTrip] Problem to connect to the server In-Reply-To: References: Message-ID: <4F6B8615-83DE-4D2C-BBAE-57AAA585E60E@donders.ru.nl> Dear William, I don’t know what’s going on with the FTP-server, but there are alternatives to grab the code repository, which I recommend instead. For instance you can find the code on http://github.com/fieldtrip Groeten, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 8 Feb 2018, at 15:37, William Chermanne > wrote: Hi, Since yesterday, I have been trying to access the server by using the username « anonymous » and my e-mail adress as a password, but it doesn’t seem to work and I can’t connect to the server to download the FielTrip toolbox. Does someone know how to solve this problem? Thank you for your answer, William Chermanne _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From william.chermanne at hotmail.com Sun Feb 11 16:31:49 2018 From: william.chermanne at hotmail.com (William Chermanne) Date: Sun, 11 Feb 2018 15:31:49 +0000 Subject: [FieldTrip] Starting from .mat files Message-ID: Hello everyone, I have started reading the documentation about the FieldTrip toolbox. A friend and I implemented a Matlab routine allowing to ‘create’ simulated EEG signals with hand movements for the three different channels C3,C4 and CZ. The routine writes the results in a .mat file where each line represents a channel. I thus have the format channel x time. However, I am not sure about where to begin with the fieldtrip functions. I also do not understand perfectly the concept of ’trials’. Should I define trials in my data? How to read the .mat file with the ft_preprocessing function or the ft_definetrial function? Thank you for your answer, William Chermanne From maximilien.chaumon at gmail.com Mon Feb 12 17:44:04 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Mon, 12 Feb 2018 16:44:04 +0000 Subject: [FieldTrip] scaling signals for joint EOG-MEG ICA decomposition Message-ID: Dear eeglab and FieldTrip users, On our MEG system, we systematically record EOG and EKG along with the MEG data. Running an ICA on the data to remove blinks and EKG works fine most of the time, but every now and then, the output is turned to puzzling complex-valued numbers. I realized that the huge scale discrepancy between the EKG and the MEG data could be what causes the problem, so I just multiplied all my EOG & EKG signals by 1e-6 and ran the ICA again, which returns real-valued numbers. The topographies look fine but I'm stuck trying to find out a way to scale this output to recover my originally scaled data. Is it possible? Any comments are welcome, thanks! Best, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcmackr at tcd.ie Mon Feb 12 21:46:26 2018 From: mcmackr at tcd.ie (Roisin McMackin) Date: Mon, 12 Feb 2018 20:46:26 +0000 Subject: [FieldTrip] Scale of timeseries for dipoles calculated from leadfields and EEG data Message-ID: Hi all, I'm using the method as described in https://mailman.science.ru. nl/pipermail/fieldtrip/2011-April/003690.html to estimate timeseries of activity for a number of dipole positions and moments. These were obtained using ft_dipolefitting to localise EEG recorded event related potentials. Headmodel (BEM) and sensor (128 electrodes) units are in mm and the EEG data (data.avg) is in microV, these are used to make the leadfield whose inverse is used to make weights. The leadfield is not normalised (since the orientation vector is). The amplitudes of the timeseries I'm getting for each dipole are in the range of about +/-500 to 5000. Is the timeseries still in the same units as the input data (i.e. microV, so the timeseries has milliV range amplitude)? If not how can I calculate the units of the leadfield, weights and timeseries? Thanks for any help or suggestions, Roisin -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Feb 13 16:54:18 2018 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 13 Feb 2018 16:54:18 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Dear Team, I am using Matlab 2017 and when I execute the following lines : cfg=[]; cfg.layout = 'biosemi256.lay'; layout = ft_prepare_layout(cfg); I get the following error *Error using nargin* *You can only call nargin/nargout from within a MATLAB function.* *Error in ft_preamble_init (line 34)* *if nargin==0* *Error in ft_preamble (line 56)* * evalin('caller', ['ft_preamble_' cmd]);* *Error in ft_prepare_layout (line 96)* *ft_preamble init* This seems related to the nargin instruction, which cannot be used in scripts anymore and it is MatLab version specific (does not happen if I use Matlab 2015b). Is this a bug? Cris -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at psy.ox.ac.uk Wed Feb 14 10:49:01 2018 From: eelke.spaak at psy.ox.ac.uk (Eelke Spaak) Date: Wed, 14 Feb 2018 10:49:01 +0100 Subject: [FieldTrip] scaling signals for joint EOG-MEG ICA decomposition In-Reply-To: <524555d6-9e22-47bf-91a8-ae39c1576f18@HUB01.ad.oak.ox.ac.uk> References: <524555d6-9e22-47bf-91a8-ae39c1576f18@HUB01.ad.oak.ox.ac.uk> Message-ID: Dear Max, Is there a particular reason you are including the EOG and ECG data in the ICA decomposition? The pipeline that would make most sense to me is to do the ICA decomposition on the MEG data alone, then check the correlation of the EOG/ECG timecourses with individual ICA components to classify which of those likely correspond to artifacts. Doing a joint decomposition will lead to some mixing in of EOG/ECG data into the reconstructed (cleaned) MEG data. Cheers, Eelke On 12 February 2018 at 17:44, Maximilien Chaumon wrote: > Dear eeglab and FieldTrip users, > > On our MEG system, we systematically record EOG and EKG along with the MEG > data. Running an ICA on the data to remove blinks and EKG works fine most of > the time, but every now and then, the output is turned to puzzling > complex-valued numbers. > > I realized that the huge scale discrepancy between the EKG and the MEG data > could be what causes the problem, so I just multiplied all my EOG & EKG > signals by 1e-6 and ran the ICA again, which returns real-valued numbers. > The topographies look fine but I'm stuck trying to find out a way to scale > this output to recover my originally scaled data. Is it possible? > > Any comments are welcome, thanks! > Best, > Max > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Wed Feb 14 11:56:19 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 14 Feb 2018 10:56:19 +0000 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Dear Cris, This is a known issue and has been addressed a while ago. You may need to upgrade your fieldtrip version to an up-to-date version. Best wishes, JM On 13 Feb 2018, at 16:54, Cristiano Micheli > wrote: Dear Team, I am using Matlab 2017 and when I execute the following lines : cfg=[]; cfg.layout = 'biosemi256.lay'; layout = ft_prepare_layout(cfg); I get the following error Error using nargin You can only call nargin/nargout from within a MATLAB function. Error in ft_preamble_init (line 34) if nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_prepare_layout (line 96) ft_preamble init This seems related to the nargin instruction, which cannot be used in scripts anymore and it is MatLab version specific (does not happen if I use Matlab 2015b). Is this a bug? Cris _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jb.eichenlaub at gmail.com Fri Feb 16 10:38:02 2018 From: jb.eichenlaub at gmail.com (Jean-Baptiste Eichenlaub) Date: Fri, 16 Feb 2018 10:38:02 +0100 Subject: [FieldTrip] ft_freqanalysis warning (correcting numerical inaccuracy in time axes) after ft_redefinetrial on continous data Message-ID: Dear Fieldtripers, After having segmented continuous EEG data (ft_redefinetrial, cfg.length = 2; cfg.overlap = 0.5), I compute the power spectrum for each trial/segment (ft_freqanalysis). However, I am getting the following warning message (see below in blue). Based on several sources, it seems to be explained by "the inaccuracy in binary representation of floating point values". I do not get the error message with cfg.length = 5 in the previous step (ft_redefinetrial). Should I be concerned? Thanks! Best, Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_freqanalysis (line 217) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_selectdata (line 134) In ft_freqanalysis (line 232) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) the call to "ft_selectdata" took 1 seconds processing trials processing trial 1199/1199 nfft: 2048 samples, datalength: 2000 samples, 1 tapers -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Sat Feb 17 03:09:51 2018 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Sat, 17 Feb 2018 02:09:51 +0000 Subject: [FieldTrip] Parallel simbio fem Message-ID: At one point there was a suggestion in the maiing list that the computation of the forward model for the Simbio FEM model might add some parallelization. Does anyone know if this has been done. I read through the previous discussion and sympathesize with the users whose jobs take a day or so to compute. I have found it is the size of the source space grid-like 10mm for an adult head goes pretty fast, 3mm for an adult head takes 24 hrs. Anyone know of a parallel implementation? Thanks, 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 ************************************************* [cid:image001.png at 01D23F64.B505C760] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 30144 bytes Desc: image001.png URL: From jan.schoffelen at donders.ru.nl Sat Feb 17 20:35:23 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sat, 17 Feb 2018 19:35:23 +0000 Subject: [FieldTrip] ft_freqanalysis warning (correcting numerical inaccuracy in time axes) after ft_redefinetrial on continous data In-Reply-To: References: Message-ID: <25C04C90-EAB8-47A1-AC70-85A991938CC2@donders.ru.nl> Hi JB, This is indeed nothing to worry about. Your sources are right. Best wishes, JM On 16 Feb 2018, at 10:38, Jean-Baptiste Eichenlaub > wrote: Dear Fieldtripers, After having segmented continuous EEG data (ft_redefinetrial, cfg.length = 2; cfg.overlap = 0.5), I compute the power spectrum for each trial/segment (ft_freqanalysis). However, I am getting the following warning message (see below in blue). Based on several sources, it seems to be explained by "the inaccuracy in binary representation of floating point values". I do not get the error message with cfg.length = 5 in the previous step (ft_redefinetrial). Should I be concerned? Thanks! Best, Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_freqanalysis (line 217) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_selectdata (line 134) In ft_freqanalysis (line 232) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) the call to "ft_selectdata" took 1 seconds processing trials processing trial 1199/1199 nfft: 2048 samples, datalength: 2000 samples, 1 tapers _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From h.park at bham.ac.uk Sun Feb 18 09:37:24 2018 From: h.park at bham.ac.uk (Hyojin Park) Date: Sun, 18 Feb 2018 08:37:24 +0000 Subject: [FieldTrip] Inaugural MEG Symposium at the CHBH, University of Birmingham (11th May) Message-ID: <8EB94CB9BF5FD74FA38E0919D3329E9BD6D113@EX14.adf.bham.ac.uk> Dear all, We are pleased to announce the "Inaugural MEG Symposium at the Centre for Human Brain Health" at the University of Birmingham. *09:30-17:30, 11th May 2018 at The Alan Walters Building, University of Birmingham* We would be delighted if you could join us to celebrate the opening of our new MEG facility. The event will include talks from speakers who are leaders in their field, and will include a tour of the new MEG facility at the University of Birmingham. For a complete list of speakers and to register (free) please visit: https://meg2018.eventbrite.co.uk Best regards, Dr. Hyojin Park and Prof. Ole Jensen School of Psychology|Centre for Human Brain Health, University of Birmingham -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.kristensen at gipsa-lab.grenoble-inp.fr Wed Feb 21 15:39:36 2018 From: emmanuelle.kristensen at gipsa-lab.grenoble-inp.fr (EMMANUELLE KRISTENSEN) Date: Wed, 21 Feb 2018 15:39:36 +0100 Subject: [FieldTrip] reading Brain Vision data : unknown resolution for channel Message-ID: <6709f46f-de1f-6dd5-a4dd-932c2bd91caf@gipsa-lab.grenoble-inp.fr> Dear all When reading a .vhdr file/ .dat file (written by EEGlab), I get this warning message, for each channel: "/Warning: unknown resolution (i.e. recording units) for channel 1 in// //MyFile.vhdr/". In the .vhdr file, the resolution is indicated : /"[Binary Infos]// //BinaryFormat=IEEE_FLOAT_32// // //[Channel Infos]// //; Each entry: Ch=,,// //; ////"/ How can I fix this warning, please? Regards, Emmanuelle -- Emmanuelle Kristensen -------------- next part -------------- An HTML attachment was scrubbed... URL: From dbaeper at upo.es Thu Feb 22 18:31:03 2018 From: dbaeper at upo.es (Daniel Baena Perez) Date: Thu, 22 Feb 2018 18:31:03 +0100 Subject: [FieldTrip] Cluster analysis for across subjects with behavioral data Message-ID: Dear all I would like to use the cluster analysis functions in Fieldtrip on correlation statistics. My data consist on an eeg signal recorded on 8 different channels and 125 time bins for 31 subjects. I would like to do an across subjects correlation for each time bin and each channel with the behavioural results. Which function is more suitable for this purpose? My reasoning so far is to use ft_statfun_intersubcorr in the first place but I'm not sure how to continue with the cluster analysis per se. Can this function be given as an argument to ft_timelockstatistics? Thank you, Daniel -------------- next part -------------- An HTML attachment was scrubbed... URL: From mylenbcn at hotmail.com Fri Feb 23 01:02:38 2018 From: mylenbcn at hotmail.com (D myl) Date: Fri, 23 Feb 2018 00:02:38 +0000 Subject: [FieldTrip] Clustering Statistics with Different Number of Observations Per Channel Message-ID: Subject: Clustering Statistics with Different Number of Observations Per Channel Dear community, My name is Dimitris Mylonas and I am working on coupled oscillations on EEG. Currently I am analyzing a high density EEG dataset where we measure the phase-amplitude coupling of specific oscillations (slow waves (.5-2 Hz) and sleep spindles (12-15 Hz)) at each electrode, for two different groups. The outcome measure is the vector length of the coupling (coupling strength) and the question is whether the two groups show significant difference in coupling strength. In order to estimate reliably the coupling strength for each electrode/subject we need to have a minimum number N of coupled oscillations. If for a given subject and a given electrode there are less than N detected oscillations there will be a missing value in the outcome measure. As a result each electrode has different number of subjects where the coupling strength can be "measured reliably". My question is if I can implement the non-parametric statistical testing (not necessarily as implemented in Fieldtrip) (Maris and Oostenveld, 2007) to test for a group difference under this condition (different degrees of freedom at each electrode). Thank you, Dimitris -------------- next part -------------- An HTML attachment was scrubbed... URL: From pascualm at key.uzh.ch Fri Feb 23 06:41:22 2018 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Fri, 23 Feb 2018 14:41:22 +0900 Subject: [FieldTrip] Comparing EEG/MEG neuroimaging methods based on localization error, false positive activity, and false positive connectivity Message-ID: Dear Colleagues, The preprint entitled: "Comparing EEG/MEG neuroimaging methods based on localization error, false positive activity, and false positive connectivity" at: https://www.biorxiv.org/content/early/2018/02/22/269753 might be of interest to those working in the field of EEG/MEG neuroimaging. The abstract can be found below. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [www.keyinst.uzh.ch/loreta] [scholar.google.com/citations?user=pascualmarqui] ... Abstract: EEG/MEG neuroimaging consists of estimating the cortical distribution of time varying signals of electric neuronal activity, for the study of functional localization and connectivity. Currently, many different imaging methods are being used, with very different capabilities of correct localization of activity and of correct localization of connectivity. The aim here is to provide a guideline for choosing the best (i.e. least bad) imaging method. This first study is limited to the comparison of the following methods for EEG signals: sLORETA and eLORETA (standardized and exact low resolution electromagnetic tomography), MNE (minimum norm estimate), dSPM (dynamic statistical parametric mapping), and LCMVBs (linearly constrained minimum variance beamformers). These methods are linear, except for the LCMVBs that make use of the quadratic EEG covariances. To achieve a fair comparison, it is assumed here that the generators are independent and widely distributed (i.e. not few in number), giving a well-defined theoretical population EEG covariance matrix for use with the LCMVBs. Measures of localization error, false positive activity, and false positive connectivity are defined and computed under ideal no-noise conditions. It is empirically shown with extensive simulations that: (1) MNE, dSPM, and all LCMVBs are in general incapable of correct localization, while sLORETA and eLORETA have exact (zero-error) localization; (2) the brain volume with false positive activity is significantly larger for MN, dSPM, and all LCMVBs, as compared to sLORETA and eLORETA; and (3) the number of false positive connections is significantly larger for MN, dSPM, all LCMVBs, and sLORETA, as compared to eLORETA. Non-vague and fully detailed equations are given. PASCAL program codes and data files are available. It is noted that the results reported here do not apply to the LCMVBs based on EEG covariance matrices generated from extremely few generators, such as only one or two independent point sources. From hesham.elshafei at inserm.fr Mon Feb 26 13:38:50 2018 From: hesham.elshafei at inserm.fr (Hesham ElShafei) Date: Mon, 26 Feb 2018 13:38:50 +0100 Subject: [FieldTrip] Extraction of Amplitude and Phase from PCC sources Message-ID: Hello all , I have computed beamformer sources using the 'pcc' method. In my source.avg structures , I have the 'csd' , 'noisecsd' , 'mom' and 'csdlabel. I was wondering if there are means to extract both phase and amplitude of the source-level signal from these information. Cheers Hesham ElShafei From jan.schoffelen at donders.ru.nl Mon Feb 26 13:54:16 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 26 Feb 2018 12:54:16 +0000 Subject: [FieldTrip] Extraction of Amplitude and Phase from PCC sources In-Reply-To: References: Message-ID: <350B16BA-8244-44DF-9F0D-BDE333E9C8C3@donders.ru.nl> Hi Hesham, The single trial/taper Fourier coefficients with amplitude and phase info are in source.avg.mom. Best wishes, Jan-Mathijs > On 26 Feb 2018, at 13:38, Hesham ElShafei wrote: > > Hello all , > > I have computed beamformer sources using the 'pcc' method. In my source.avg structures , I have the 'csd' , 'noisecsd' , 'mom' and 'csdlabel. > > I was wondering if there are means to extract both phase and amplitude of the source-level signal from these information. > > Cheers > Hesham ElShafei > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tony.w.wilson at gmail.com Tue Feb 27 12:59:34 2018 From: tony.w.wilson at gmail.com (Tony W. Wilson) Date: Tue, 27 Feb 2018 05:59:34 -0600 Subject: [FieldTrip] Tenure-track Faculty Position in Cognitive Neuroscience Message-ID: The Department of Neurological Sciences at the University of Nebraska Medical Center invites applications for a tenure leading faculty position in Clinical Cognitive Neuroscience. This position is part of a new Neuroimaging Section within the department and aims to leverage multiple hires across the School of Medicine in human neuroscience. We welcome applications from any area of cognitive neuroscience, including memory, executive function, visual attention, perception, audition, motor control, emotion, and decision-making. Methodological specialty within neuroimaging is open, but ideally the candidate would benefit from our strong existing program in MEG imaging, and develop a translational, theory-based multimodal neuroimaging program focusing on their area of interest. The successful applicant would join a growing group of cognitive neuroscientists within the department (and across campus) using MEG, fMRI, and other modalities, and hopefully help grow other programs in parallel with building their own. Successful candidates will have a MD, PhD, or MD/PhD in neuroscience, psychology, or computer science, with postdoctoral training and an excellent publication record for their career stage. Candidates should also have an excellent and sustained record of research and evidence of the potential, or demonstrated ability, to generate extramural funding commensurate with their career stage. Applicants should have the ability and interest to teach graduate courses in cognitive neuroscience, and to mentor PhD students in our growing Neuroscience PhD program. The University of Nebraska Medical Center (UNMC) is a vibrant multidisciplinary research environment with major resources and ample opportunities for training and collaboration. Resources include a 306-sensor MEG system, multiple 3T human MRI scanners, high-definition transcranial direct-current and alternating-current stimulation (HD-tDCS/tACS) equipment, eye-tracking equipment, and a state-of-the-art transcranial magnetic stimulation (TMS) suite. The UNMC is located in Omaha, with a metro area population of approximately one million, and major attractions and events such as the College World Series. Please submit a letter detailing current research and teaching interests, a curriculum vitae, a list of the applicant’s five most important publications, and contact information for three individuals who will provide letters of recommendation at a later time. Applications should be submitted online at: https://unmc.peopleadmin.com/postings/36674 . Review of applications will begin immediately and will continue until the position is filled. Start dates are negotiable, but ideally before the close of 2018. Individuals from diverse backgrounds are encouraged to apply. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elinor.tzvi at neuro.uni-luebeck.de Tue Feb 27 17:03:11 2018 From: elinor.tzvi at neuro.uni-luebeck.de (Elinor Tzvi-Minker) Date: Tue, 27 Feb 2018 16:03:11 +0000 Subject: [FieldTrip] PhD position @ Queen Mary University of London Message-ID: <2530B215-C864-40D3-87F5-1F5ED7C5DE7A@neuro.uni-luebeck.de> Dear All, A 3-year PhD studentship for UK and EU citizens is open at Queen Mary University of London. The project will investigate sense of agency, outcome processing and learning under social influence. Application deadline is 12thMarch. More information and link to the application portal can be found under https://www.findaphd.com/search/ProjectDetails.aspx?PJID=94998 Best wishes, Frederike Beyer -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Wed Feb 28 03:27:31 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Wed, 28 Feb 2018 02:27:31 +0000 Subject: [FieldTrip] Alignment problem Message-ID: Dear Experts, I read a Brainweb MRI volume in filedtrip ( by default it doesn’t have any coordinate fields). When I align this data to CTF coordinate system using ft_volumerealign and then apply this alignment using ft_volumereslice; I see I miss some data and I get a very wrong head model using this resliced data. Any Ideas? Thanks in advance, Regards, Fereshte -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 28 08:54:47 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 28 Feb 2018 07:54:47 +0000 Subject: [FieldTrip] Alignment problem In-Reply-To: References: Message-ID: <572A023D-3A85-47BF-A5EB-2DB95DA8B332@donders.ru.nl> Hi Fereshte, No, without any additional information I don’t have any ideas :). What do you mean by “I miss some data”, and “I get a very wrong head model”? Please refer to http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list in phrasing your question. This will maximize the probability that somebody will be inclined and able to point you into the good direction. Best wishes, Jan-Mathijs On 28 Feb 2018, at 03:27, Fereshte > wrote: Dear Experts, I read a Brainweb MRI volume in filedtrip ( by default it doesn’t have any coordinate fields). When I align this data to CTF coordinate system using ft_volumerealign and then apply this alignment using ft_volumereslice; I see I miss some data and I get a very wrong head model using this resliced data. Any Ideas? Thanks in advance, Regards, Fereshte _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Wed Feb 28 12:15:34 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Wed, 28 Feb 2018 12:15:34 +0100 (CET) Subject: [FieldTrip] 1st International Workshop on Predictive Processing (WoPP) In-Reply-To: References: <5a7d686f.ed3fed0a.5f941.c127SMTPIN_ADDED_BROKEN@mx.google.com> <1640004900.9152749.1519247555698.JavaMail.zimbra@bcbl.eu> <1717447392.9286562.1519725808525.JavaMail.zimbra@bcbl.eu> <497399636.9344962.1519815833963.JavaMail.zimbra@bcbl.eu> Message-ID: <1858953218.9345933.1519816534199.JavaMail.zimbra@bcbl.eu> Dear All, We invite you to the " 1st International Workshop on Predictive Processing (WoPP) " organized by Basque Center on Cognition, Brain and Language (BCBL) that will be held in one of most beautiful cities in europe, San Sebastian, Spain from 20 - 22 June 2018 , at Palacio Miramar in Donostia - San Sebastián. The aim of the workshop is to discuss predictive coding and its underlying mechanisms from behaviour to neuroscience. We aim at calling together researchers and students from various domains such as vision, audition and language, to build bridges between various research fields and share this common and exciting interest on prediction. Please visit http://www.bcbl.eu/events/prediction-2018/en/ for details about abstract submission and registration. Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018. -------------- next part -------------- An HTML attachment was scrubbed... URL: From virginie.van.wassenhove at gmail.com Thu Feb 1 11:22:36 2018 From: virginie.van.wassenhove at gmail.com (Virginie van Wassenhove) Date: Thu, 1 Feb 2018 11:22:36 +0100 Subject: [FieldTrip] [tenure-track researcher position] Message-ID: Dear all, applications are invited for a tenure-track researcher position in the Cognition and Brain Dynamics research team of Virginie van Wassenhove. The lab is hosted at NeuroSpin (Dir. Prof Stanislas Dehaene) on the plateau de Saclay near Paris, France. See full description attached. Kind regards, Virginie -- Virginie van Wassenhove *https://brainthemind.com/ * -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: 2018_VvW_JobDescription_CEA.pdf Type: application/pdf Size: 100589 bytes Desc: not available URL: From annekathrinweise at gmail.com Thu Feb 1 14:54:49 2018 From: annekathrinweise at gmail.com (Annekathrin Weise) Date: Thu, 1 Feb 2018 14:54:49 +0100 Subject: [FieldTrip] Salzburg Mind Brain Annual (SAMBA) Meeting 2018 Message-ID: Dear all, on behalf of myself, my colleagues, and our advisory board, I am happy to announce the *Salzburg Mind Brain Annual Meeting* (*SAMBA*)**which will take place *in Salzburg, Austria* on *July 12 & 13*, *2018*. The*registration* is now *open until March 15*. The mission of SAMBA is to attract the most exciting researchers in the domain of cognitive neuroscience, including related fields (e.g., computational modelling, animal neurophysiology, neurology etc.) that influence or are influenced by developments in cognitive neuroscience. Furthermore, our goal is to make young scientists enthusiastic about this research field. The moderate size of an anticipated ~100 participants will enable an intimate atmosphere with ample opportunity for exchange. Confirmed speakers are: *     Radoslav Cichy (FU Berlin) *     Simon Eickhoff (Jülich) *     Saskia Haegens (Columbia / Donders) *     Jim Haxby (Dartmouth) *     Katharina von Kriegstein (MPI Leipzig) *     Floris de Lange (Donders) *     Tamar Makin (UCL) *     Kia Nobre (Oxford) *     Uta Noppeney (Birmingham) *     Anne-Marike Schiffer (Nature Human Behavior) *     Andreas Wutz (MIT / Salzburg) Attendees have the possibility to present a poster. For more information see the SAMBA website: https://samba.ccns.sbg.ac.at/ Best, Nathan -- Nathan Weisz Centre for Cognitive Neuroscience Division of Physiological Psychology University of Salzburg nathan.weisz at sbg.ac.at www.oboblab.at -- Annekathrin Weise, Dr. Paris-Lodron Universität Salzburg Division of Physiological Psychology Hellbrunnerstraße 34 5020 Salzburg Austria e-mail: annekathrin.weise at sbg.ac.at; annekathrinweise at gmail.com web: http://www.oboblab.at/ https://sites.google.com/site/weiseannekathrin/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From yaocong.duan at gmail.com Thu Feb 1 18:31:56 2018 From: yaocong.duan at gmail.com (Yaocong Duan) Date: Thu, 1 Feb 2018 17:31:56 +0000 Subject: [FieldTrip] Question about Phase locking value Message-ID: Hi All, I am using Phase Locking Value to measure the connectivity between brain regions at the source level. I learned that the PLV is an average value over trails. In the fieldtrip code, I calculated a frequency model first, then do connectivity analysis with this freq model. The problem is I don’t see trails information in the freq model. So how do I get that phase locking result? Below is my code. This code works, but I am confused about the question above. [image: Inline images 1] Thanks in advance, Yaocong -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From stephen.whitmarsh at gmail.com Thu Feb 1 19:02:51 2018 From: stephen.whitmarsh at gmail.com (Stephen Whitmarsh) Date: Thu, 1 Feb 2018 19:02:51 +0100 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Dear Yaocong, To understand your question, it would be helpful if you post the output of the freqanalysis, i.e. your *freq *datastructure. It should contain a .*pow *field, which should be an array of structs, numbering your number of trials, right? Cheers, Stephen Virus-free. www.avast.com <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> On 1 February 2018 at 18:31, Yaocong Duan wrote: > Hi All, > > > > I am using Phase Locking Value to measure the connectivity between brain > regions at the source level. I learned that the PLV is an average value > over trails. In the fieldtrip code, I calculated a frequency model first, > then do connectivity analysis with this freq model. The problem is I don’t > see trails information in the freq model. So how do I get that phase > locking result? > > > > Below is my code. This code works, but I am confused about the question > above. > > [image: Inline images 1] > > Thanks in advance, > Yaocong > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From yaocong.duan at gmail.com Fri Feb 2 01:12:56 2018 From: yaocong.duan at gmail.com (Yaocong Duan) Date: Fri, 2 Feb 2018 00:12:56 +0000 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Hi Stephen, Thank you for your response. I write something wrong in my previous email. the freq structure does have trails information. but then I do a source reconstruction and generate a source structure. phase locking value is calculated from the source structure directly. However, the source structure does not have any trails info (trails seems have been averaged). source = ft_sourceanalysis(cfg, freq); ... plv = ft_connectivityanalysis(cfg, souceSparse); below are the freq structure generated by freq analysis, source structure generated by source analysis as well as the .avg field of source structure. [image: Inline images 1][image: Inline images 2][image: Inline images 3] On 1 February 2018 at 18:02, Stephen Whitmarsh wrote: > Dear Yaocong, > > To understand your question, it would be helpful if you post the output of > the freqanalysis, i.e. your *freq *datastructure. It should contain a .*pow > *field, which should be an array of structs, numbering your number of > trials, right? > > Cheers, > Stephen > > > Virus-free. > www.avast.com > > <#m_6562418138207874494_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > On 1 February 2018 at 18:31, Yaocong Duan wrote: > >> Hi All, >> >> >> >> I am using Phase Locking Value to measure the connectivity between brain >> regions at the source level. I learned that the PLV is an average value >> over trails. In the fieldtrip code, I calculated a frequency model first, >> then do connectivity analysis with this freq model. The problem is I don’t >> see trails information in the freq model. So how do I get that phase >> locking result? >> >> >> >> Below is my code. This code works, but I am confused about the question >> above. >> >> [image: Inline images 1] >> >> Thanks in advance, >> Yaocong >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 82049 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 97937 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 92321 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: From xiew1202 at gmail.com Fri Feb 2 02:35:59 2018 From: xiew1202 at gmail.com (Xie Wanze) Date: Thu, 1 Feb 2018 20:35:59 -0500 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: Hi Yaocong, Two things you may want to try: 1. use the "keep trials" option when you do your source analysis. This method makes a lot of sense, but it did not work for me. 2. Do source reconstruction separately for each individual trial. You may calculate the filter in Fieldtrip using ft_sourceanalysis and then use the filter for source reconstruction for each trial: reconstructed source activity = filter*data (in individual trial). This second option worked for me. Good luck. Wanze 2018-02-01 19:12 GMT-05:00 Yaocong Duan : > Hi Stephen, > > Thank you for your response. I write something wrong in my previous email. > the freq structure does have trails information. but then I do a source > reconstruction and generate a source structure. phase locking value is > calculated from the source structure directly. However, the source > structure does not have any trails info (trails seems have been averaged). > > source = ft_sourceanalysis(cfg, freq); > ... > plv = ft_connectivityanalysis(cfg, souceSparse); > > > below are the freq structure generated by freq analysis, source structure > generated by source analysis as well as the .avg field of source structure. > > > [image: Inline images 1][image: Inline images 2][image: Inline images 3] > > On 1 February 2018 at 18:02, Stephen Whitmarsh < > stephen.whitmarsh at gmail.com> wrote: > >> Dear Yaocong, >> >> To understand your question, it would be helpful if you post the output >> of the freqanalysis, i.e. your *freq *datastructure. It should contain a >> .*pow *field, which should be an array of structs, numbering your number >> of trials, right? >> >> Cheers, >> Stephen >> >> >> Virus-free. >> www.avast.com >> >> <#m_3173352166848949795_m_6562418138207874494_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> >> On 1 February 2018 at 18:31, Yaocong Duan wrote: >> >>> Hi All, >>> >>> >>> >>> I am using Phase Locking Value to measure the connectivity between brain >>> regions at the source level. I learned that the PLV is an average value >>> over trails. In the fieldtrip code, I calculated a frequency model first, >>> then do connectivity analysis with this freq model. The problem is I don’t >>> see trails information in the freq model. So how do I get that phase >>> locking result? >>> >>> >>> >>> Below is my code. This code works, but I am confused about the question >>> above. >>> >>> [image: Inline images 1] >>> >>> Thanks in advance, >>> Yaocong >>> >>> _______________________________________________ >>> fieldtrip mailing list >>> fieldtrip at donders.ru.nl >>> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >>> >> >> >> _______________________________________________ >> fieldtrip mailing list >> fieldtrip at donders.ru.nl >> https://mailman.science.ru.nl/mailman/listinfo/fieldtrip >> > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 92321 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 97937 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 184150 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 82049 bytes Desc: not available URL: From jan.schoffelen at donders.ru.nl Fri Feb 2 09:07:49 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 2 Feb 2018 08:07:49 +0000 Subject: [FieldTrip] Question about Phase locking value In-Reply-To: References: Message-ID: <86C3123F-DB4B-4C27-8261-2230D3689ACF@donders.ru.nl> When you call ft_freqanalysis with ‘fourier’ in the cfg.method, followed by ft_sourceanalysis with ‘pcc’ in cfg.method, the source.avg.mom contains the fourier coefficients at the single taper level. A bunch of tapers constitute a single trial, the number of which depends on the smoothing parameter that you used in ft_freqanalysis. Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 2 Feb 2018, at 01:12, Yaocong Duan > wrote: Hi Stephen, Thank you for your response. I write something wrong in my previous email. the freq structure does have trails information. but then I do a source reconstruction and generate a source structure. phase locking value is calculated from the source structure directly. However, the source structure does not have any trails info (trails seems have been averaged). source = ft_sourceanalysis(cfg, freq); ... plv = ft_connectivityanalysis(cfg, souceSparse); below are the freq structure generated by freq analysis, source structure generated by source analysis as well as the .avg field of source structure. On 1 February 2018 at 18:02, Stephen Whitmarsh > wrote: Dear Yaocong, To understand your question, it would be helpful if you post the output of the freqanalysis, i.e. your freq datastructure. It should contain a .pow field, which should be an array of structs, numbering your number of trials, right? Cheers, Stephen [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif] Virus-free. www.avast.com On 1 February 2018 at 18:31, Yaocong Duan > wrote: Hi All, I am using Phase Locking Value to measure the connectivity between brain regions at the source level. I learned that the PLV is an average value over trails. In the fieldtrip code, I calculated a frequency model first, then do connectivity analysis with this freq model. The problem is I don’t see trails information in the freq model. So how do I get that phase locking result? Below is my code. This code works, but I am confused about the question above. Thanks in advance, Yaocong _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From lmelloni at gmail.com Sun Feb 4 18:37:43 2018 From: lmelloni at gmail.com (Lucia Melloni) Date: Sun, 4 Feb 2018 18:37:43 +0100 Subject: [FieldTrip] Postdoctoral Position in Electrocorticography at NYU Message-ID: <79BBB75B-4A9E-4057-B75F-F069BE96E8BC@gmail.com> Dear All, We have an opening for a POSTDOCTORAL POSITION IN ELECTROCORTICOGRAPHY RESEARCH AT NYU. See below for details. Thanks and all the best, Lucia POSTDOCTORAL POSITION IN ELECTROCORTICOGRAPHY RESEARCH AT NYU NYU School of Medicine has an opening for a Postdoctoral Researcher to conduct Human intracranial EEG and electrocortigoraphy (ECoG) research. The postdoctoral researcher will work with the clinical neurology team to conduct neurophysiological research in surgical patients undergoing treatment for refractory epilepsy implanted with intracranial electrodes (surface, depth). Research approaches will include both recording and stimulation. The postdoctoral fellow will be a member of a collaborative team that includes Lucia Melloni (NYU and Max Planck Institute, Frankfurt), Adeen Flinker (NYU), Charan Ranganath (UC Davis), Sam Gershman (Harvard), Ken Norman & Uri Hasson (Princeton), and Jeff Zacks (Washington University). The goal of the research studies will be to use real-time measures of brain activity to investigate how cortico-hippocampal interactions support event segmentation, schema formation, and memory for complex events. The ideal applicant must have a Ph.D. in neuroscience, psychology, biomedical engineering, or a related field. Proficiency in oral and written English is mandatory. A solid background in programming, statistics, and scientific writing is required. The candidate is expected to be able to work independently, to enjoy interacting within an interdisciplinary team, and to have a track-record of peer-reviewed publications. Previous experience with human electrophysiology or machine learning will be an asset. Start date is negotiable. Interested individuals should send an email to lucia.melloni at nyumc.org , including a cover letter describing research experience and qualifications, an academic CV, and contact information of referees. -------------- next part -------------- An HTML attachment was scrubbed... URL: From jordvink at gmail.com Sun Feb 4 21:13:39 2018 From: jordvink at gmail.com (Jord Vink) Date: Sun, 4 Feb 2018 21:13:39 +0100 Subject: [FieldTrip] Cross spectral density versus coherence Message-ID: Hi all, I am working with functional connectivity between different (EEG) signals. I'm calculating the connectivity strength between different brain regions and correlate the connectivity strength to a certain outcome measure. Among others, I'm using the cross spectral density (CSD) and the coherence. The CSD is not generally used as a measure of connectivity but I don't completely understand why not. Especially since the CSD correlates well with my outcome measure, while the coherence doesn't. I'm trying to undertand whether there is a fundamental reason why I can't use the CSD, and why I should use the coherence. So I'm trying to understand why people use coherence (the normalized version of the cross spectral density) as a measure of connectivity instead of cross spectral density (CSD). Why do you have to normalize the CSD with the autospectral densities to determine connectivity when the CSD by itself is a measure of signal similarity? Is there a fundamental reason to normalize the CSD? Jord -------------- next part -------------- An HTML attachment was scrubbed... URL: From f.smulders at maastrichtuniversity.nl Mon Feb 5 10:38:28 2018 From: f.smulders at maastrichtuniversity.nl (Smulders F (PSYCHOLOGY)) Date: Mon, 5 Feb 2018 09:38:28 +0000 Subject: [FieldTrip] impact of skewed power distributions on data analysis Message-ID: Hi Teresa Madsen, I am new to the Fieldtrip list, and not sure whether I contribute to this older discussion in the appropriate way. Noticing your thread on the distribution of alpha power, this paper might be relevant: http://onlinelibrary.wiley.com/doi/10.1111/ejn.13854/full kind regards, Fren Smulders -------------- next part -------------- An HTML attachment was scrubbed... URL: From litvak.vladimir at gmail.com Mon Feb 5 21:28:01 2018 From: litvak.vladimir at gmail.com (Vladimir Litvak) Date: Mon, 5 Feb 2018 20:28:01 +0000 Subject: [FieldTrip] SPM M/EEG course 2018 Message-ID: Dear all, We are pleased to announce that our annual SPM course for MEG/EEG will take place this year from Monday May 7 to Wednesday May 9 2018. Hosted by University College London, the course will be held at Queen Square (UK). The course will present instruction on the analysis of MEG and EEG data. The first two days will combine theoretical presentations with practical demonstrations of the different data analysis methods implemented in SPM. On the last day participants will have the opportunity to work on SPM tutorial data sets under the supervision of the course faculty. We also invite students to bring their own data for analysis. The course is suitable for both beginners and more advanced users. The topics that will be covered range from pre-processing and statistical analysis to source localization and dynamic causal modelling. The program is listed below. Registration is now open. For full details see: http://www.fil.ion.ucl.ac.uk/spm/course/london/ where you can also register. Available places are limited so please register as early as possible if you would like to attend! For any administrative questions, please contact Ms Kamlyn Ramikssoon (k.ramkissoon at ucl.ac.uk) very best - Hayriye Cagnan Monday May 7th (12 Queen square, 4th floor) 9.00 - 9.30 Registration 9.30 - 9.45 SPM introduction and resources 9.45 - 10.30 What are we measuring with M/EEG? 10.30 - 11.15 Data pre-processing Coffee 11.45 - 12.30 Data pre-processing – demo 12.30 - 13.15 General linear model and classical inference Lunch 14.15 - 15.00 Multiple comparisons problem and solutions 15.00 - 15.45 Bayesian inference Coffee 16.15 - 17.45 Group M/EEG dataset analysis – demo 17.45 - 18.30 Advanced applications of the GLM Tuesday May 8th (33 Queen square, basement) 9.30 - 10.15 M/EEG source analysis 10.15 - 11.15 M/EEG source analysis – demo Coffee 11.45 - 12.30 The principles of dynamic causal modelling 12.30 - 13.15 DCM for evoked responses Lunch 14.15 - 15.00 DCM for steady state responses 15.00 - 15.45 DCM - demo Coffee 16.15 - 17.00 Bayesian model selection and averaging 17.00 - 18.30 Clinic - questions & answers 19.00 - ... Social Event Wednesday May 9th 9.30 - 17.00 Practical hands-on session will take place in UCL computer classrooms. Participants can either work on SPM tutorial datasets or on their own data with the help of the faculty. There will also be an opportunity to ask questions in small tutorial groups for further discussions on the topics of the lectures. From strautma at uke.de Tue Feb 6 11:25:40 2018 From: strautma at uke.de (Dr. Sina A. Trautmann-Lengsfeld) Date: Tue, 6 Feb 2018 11:25:40 +0100 Subject: [FieldTrip] Invitation: SAGE 2.0 in Hamburg, Germany (http://sfb936.net/SAGE2.0) Message-ID: <57ddc705-6f58-4d6c-80da-20ad7f851b94@uke.de> Dear Fieldtrip Users, dear Colleagues, Do you wonder why so few of your colleagues are female? Do all scientists with comparable skills have equal career opportunities? Why do a lot of people leave their job in science at a certain moment in their career, independent of their skills? Why is it so hard to find a good work-life-family balance? Why we do not care more about diversity and equality of chances in science? For these and many other reasons, we are very happy to announce our *second Science and Gender Equality Symposium “SAGE 2.0”* funded by the DFG Collaborative Research Center 936 (SFB 936). When? *March 23, 2018, 10:00 – 19:00 h* Where? *Erika-Haus, University Medical Center Hamburg-Eppendorf, Hamburg, Germany* There will be talks on neuroscience, astrophysics, equality, and day-to-day issues, as well as round table discussions by and with the following very renowned female scientists: Seats are given away on first-come, first-served basis. Participation is for free. The registration *deadline* is *March 15th 2018*. Please register: http://sfb936.net/SAGE2.0. The symposium is open to all scientists, independent of gender. Please do not hesitate to contact us (s.trautmann-lengsfeld at uke.de) in case of questions. We are looking forward to discussions with a broad variety of people! Sincerely yours, Marina Fiene, Annika Lübbert, Hilke M. Petersen, Bettina Schwab, Alexandra Tinnermann, and Sina A. Trautmann-Lengsfeld (Organizing Team) -- Dr. Sina Alexa Trautmann-Lengsfeld Postdoc & SFB 936 Graduate School Management Dept. of Neurophysiology and Pathophysiology University Medical Center Hamburg-Eppendorf Martinistr. 52 20246 Hamburg Germany Phone: +49-40-7410-57238 Fax: +49-40-7410-57752 Email: s.trautmann-lengsfeld at uke.de -- _____________________________________________________________________ Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; Gerichtsstand: Hamburg | www.uke.de Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Prof. Dr. Dr. Uwe Koch-Gromus, Joachim Prölß, Martina Saurin (komm.) _____________________________________________________________________ SAVE PAPER - THINK BEFORE PRINTING -------------- next part -------------- An HTML attachment was scrubbed... URL: From william.chermanne at hotmail.com Thu Feb 8 15:37:34 2018 From: william.chermanne at hotmail.com (William Chermanne) Date: Thu, 8 Feb 2018 14:37:34 +0000 Subject: [FieldTrip] Problem to connect to the server Message-ID: Hi, Since yesterday, I have been trying to access the server by using the username « anonymous » and my e-mail adress as a password, but it doesn’t seem to work and I can’t connect to the server to download the FielTrip toolbox. Does someone know how to solve this problem? Thank you for your answer, William Chermanne From jan.schoffelen at donders.ru.nl Fri Feb 9 09:30:40 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Fri, 9 Feb 2018 08:30:40 +0000 Subject: [FieldTrip] Problem to connect to the server In-Reply-To: References: Message-ID: <4F6B8615-83DE-4D2C-BBAE-57AAA585E60E@donders.ru.nl> Dear William, I don’t know what’s going on with the FTP-server, but there are alternatives to grab the code repository, which I recommend instead. For instance you can find the code on http://github.com/fieldtrip Groeten, Jan-Mathijs J.M.Schoffelen, MD PhD Senior Researcher, VIDI-fellow - PI, language in interaction Telephone: +31-24-3614793 Physical location: room 00.028 Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands On 8 Feb 2018, at 15:37, William Chermanne > wrote: Hi, Since yesterday, I have been trying to access the server by using the username « anonymous » and my e-mail adress as a password, but it doesn’t seem to work and I can’t connect to the server to download the FielTrip toolbox. Does someone know how to solve this problem? Thank you for your answer, William Chermanne _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From william.chermanne at hotmail.com Sun Feb 11 16:31:49 2018 From: william.chermanne at hotmail.com (William Chermanne) Date: Sun, 11 Feb 2018 15:31:49 +0000 Subject: [FieldTrip] Starting from .mat files Message-ID: Hello everyone, I have started reading the documentation about the FieldTrip toolbox. A friend and I implemented a Matlab routine allowing to ‘create’ simulated EEG signals with hand movements for the three different channels C3,C4 and CZ. The routine writes the results in a .mat file where each line represents a channel. I thus have the format channel x time. However, I am not sure about where to begin with the fieldtrip functions. I also do not understand perfectly the concept of ’trials’. Should I define trials in my data? How to read the .mat file with the ft_preprocessing function or the ft_definetrial function? Thank you for your answer, William Chermanne From maximilien.chaumon at gmail.com Mon Feb 12 17:44:04 2018 From: maximilien.chaumon at gmail.com (Maximilien Chaumon) Date: Mon, 12 Feb 2018 16:44:04 +0000 Subject: [FieldTrip] scaling signals for joint EOG-MEG ICA decomposition Message-ID: Dear eeglab and FieldTrip users, On our MEG system, we systematically record EOG and EKG along with the MEG data. Running an ICA on the data to remove blinks and EKG works fine most of the time, but every now and then, the output is turned to puzzling complex-valued numbers. I realized that the huge scale discrepancy between the EKG and the MEG data could be what causes the problem, so I just multiplied all my EOG & EKG signals by 1e-6 and ran the ICA again, which returns real-valued numbers. The topographies look fine but I'm stuck trying to find out a way to scale this output to recover my originally scaled data. Is it possible? Any comments are welcome, thanks! Best, Max -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcmackr at tcd.ie Mon Feb 12 21:46:26 2018 From: mcmackr at tcd.ie (Roisin McMackin) Date: Mon, 12 Feb 2018 20:46:26 +0000 Subject: [FieldTrip] Scale of timeseries for dipoles calculated from leadfields and EEG data Message-ID: Hi all, I'm using the method as described in https://mailman.science.ru. nl/pipermail/fieldtrip/2011-April/003690.html to estimate timeseries of activity for a number of dipole positions and moments. These were obtained using ft_dipolefitting to localise EEG recorded event related potentials. Headmodel (BEM) and sensor (128 electrodes) units are in mm and the EEG data (data.avg) is in microV, these are used to make the leadfield whose inverse is used to make weights. The leadfield is not normalised (since the orientation vector is). The amplitudes of the timeseries I'm getting for each dipole are in the range of about +/-500 to 5000. Is the timeseries still in the same units as the input data (i.e. microV, so the timeseries has milliV range amplitude)? If not how can I calculate the units of the leadfield, weights and timeseries? Thanks for any help or suggestions, Roisin -------------- next part -------------- An HTML attachment was scrubbed... URL: From michelic72 at gmail.com Tue Feb 13 16:54:18 2018 From: michelic72 at gmail.com (Cristiano Micheli) Date: Tue, 13 Feb 2018 16:54:18 +0100 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Dear Team, I am using Matlab 2017 and when I execute the following lines : cfg=[]; cfg.layout = 'biosemi256.lay'; layout = ft_prepare_layout(cfg); I get the following error *Error using nargin* *You can only call nargin/nargout from within a MATLAB function.* *Error in ft_preamble_init (line 34)* *if nargin==0* *Error in ft_preamble (line 56)* * evalin('caller', ['ft_preamble_' cmd]);* *Error in ft_prepare_layout (line 96)* *ft_preamble init* This seems related to the nargin instruction, which cannot be used in scripts anymore and it is MatLab version specific (does not happen if I use Matlab 2015b). Is this a bug? Cris -------------- next part -------------- An HTML attachment was scrubbed... URL: From eelke.spaak at psy.ox.ac.uk Wed Feb 14 10:49:01 2018 From: eelke.spaak at psy.ox.ac.uk (Eelke Spaak) Date: Wed, 14 Feb 2018 10:49:01 +0100 Subject: [FieldTrip] scaling signals for joint EOG-MEG ICA decomposition In-Reply-To: <524555d6-9e22-47bf-91a8-ae39c1576f18@HUB01.ad.oak.ox.ac.uk> References: <524555d6-9e22-47bf-91a8-ae39c1576f18@HUB01.ad.oak.ox.ac.uk> Message-ID: Dear Max, Is there a particular reason you are including the EOG and ECG data in the ICA decomposition? The pipeline that would make most sense to me is to do the ICA decomposition on the MEG data alone, then check the correlation of the EOG/ECG timecourses with individual ICA components to classify which of those likely correspond to artifacts. Doing a joint decomposition will lead to some mixing in of EOG/ECG data into the reconstructed (cleaned) MEG data. Cheers, Eelke On 12 February 2018 at 17:44, Maximilien Chaumon wrote: > Dear eeglab and FieldTrip users, > > On our MEG system, we systematically record EOG and EKG along with the MEG > data. Running an ICA on the data to remove blinks and EKG works fine most of > the time, but every now and then, the output is turned to puzzling > complex-valued numbers. > > I realized that the huge scale discrepancy between the EKG and the MEG data > could be what causes the problem, so I just multiplied all my EOG & EKG > signals by 1e-6 and ran the ICA again, which returns real-valued numbers. > The topographies look fine but I'm stuck trying to find out a way to scale > this output to recover my originally scaled data. Is it possible? > > Any comments are welcome, thanks! > Best, > Max > > > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From jan.schoffelen at donders.ru.nl Wed Feb 14 11:56:19 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 14 Feb 2018 10:56:19 +0000 Subject: [FieldTrip] reconstruction of EEG patterns on a 3D shape In-Reply-To: References: Message-ID: Dear Cris, This is a known issue and has been addressed a while ago. You may need to upgrade your fieldtrip version to an up-to-date version. Best wishes, JM On 13 Feb 2018, at 16:54, Cristiano Micheli > wrote: Dear Team, I am using Matlab 2017 and when I execute the following lines : cfg=[]; cfg.layout = 'biosemi256.lay'; layout = ft_prepare_layout(cfg); I get the following error Error using nargin You can only call nargin/nargout from within a MATLAB function. Error in ft_preamble_init (line 34) if nargin==0 Error in ft_preamble (line 56) evalin('caller', ['ft_preamble_' cmd]); Error in ft_prepare_layout (line 96) ft_preamble init This seems related to the nargin instruction, which cannot be used in scripts anymore and it is MatLab version specific (does not happen if I use Matlab 2015b). Is this a bug? Cris _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From jb.eichenlaub at gmail.com Fri Feb 16 10:38:02 2018 From: jb.eichenlaub at gmail.com (Jean-Baptiste Eichenlaub) Date: Fri, 16 Feb 2018 10:38:02 +0100 Subject: [FieldTrip] ft_freqanalysis warning (correcting numerical inaccuracy in time axes) after ft_redefinetrial on continous data Message-ID: Dear Fieldtripers, After having segmented continuous EEG data (ft_redefinetrial, cfg.length = 2; cfg.overlap = 0.5), I compute the power spectrum for each trial/segment (ft_freqanalysis). However, I am getting the following warning message (see below in blue). Based on several sources, it seems to be explained by "the inaccuracy in binary representation of floating point values". I do not get the error message with cfg.length = 5 in the previous step (ft_redefinetrial). Should I be concerned? Thanks! Best, Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_freqanalysis (line 217) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_selectdata (line 134) In ft_freqanalysis (line 232) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) the call to "ft_selectdata" took 1 seconds processing trials processing trial 1199/1199 nfft: 2048 samples, datalength: 2000 samples, 1 tapers -------------- next part -------------- An HTML attachment was scrubbed... URL: From RICHARDS at mailbox.sc.edu Sat Feb 17 03:09:51 2018 From: RICHARDS at mailbox.sc.edu (RICHARDS, JOHN) Date: Sat, 17 Feb 2018 02:09:51 +0000 Subject: [FieldTrip] Parallel simbio fem Message-ID: At one point there was a suggestion in the maiing list that the computation of the forward model for the Simbio FEM model might add some parallelization. Does anyone know if this has been done. I read through the previous discussion and sympathesize with the users whose jobs take a day or so to compute. I have found it is the size of the source space grid-like 10mm for an adult head goes pretty fast, 3mm for an adult head takes 24 hrs. Anyone know of a parallel implementation? Thanks, 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 ************************************************* [cid:image001.png at 01D23F64.B505C760] -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 30144 bytes Desc: image001.png URL: From jan.schoffelen at donders.ru.nl Sat Feb 17 20:35:23 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Sat, 17 Feb 2018 19:35:23 +0000 Subject: [FieldTrip] ft_freqanalysis warning (correcting numerical inaccuracy in time axes) after ft_redefinetrial on continous data In-Reply-To: References: Message-ID: <25C04C90-EAB8-47A1-AC70-85A991938CC2@donders.ru.nl> Hi JB, This is indeed nothing to worry about. Your sources are right. Best wishes, JM On 16 Feb 2018, at 10:38, Jean-Baptiste Eichenlaub > wrote: Dear Fieldtripers, After having segmented continuous EEG data (ft_redefinetrial, cfg.length = 2; cfg.overlap = 0.5), I compute the power spectrum for each trial/segment (ft_freqanalysis). However, I am getting the following warning message (see below in blue). Based on several sources, it seems to be explained by "the inaccuracy in binary representation of floating point values". I do not get the error message with cfg.length = 5 in the previous step (ft_redefinetrial). Should I be concerned? Thanks! Best, Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_freqanalysis (line 217) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) Warning: correcting numerical inaccuracy in the time axes > In ft_warning (line 184) In ft_datatype_raw>fixtimeaxes (line 310) In ft_datatype_raw (line 262) In ft_checkdata (line 236) In ft_selectdata (line 134) In ft_freqanalysis (line 232) In DefineSleepPeriodsBlock>computeSpectrumAveragedChan_fieldtrip (line 237) In DefineSleepPeriodsBlock (line 91) the call to "ft_selectdata" took 1 seconds processing trials processing trial 1199/1199 nfft: 2048 samples, datalength: 2000 samples, 1 tapers _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From h.park at bham.ac.uk Sun Feb 18 09:37:24 2018 From: h.park at bham.ac.uk (Hyojin Park) Date: Sun, 18 Feb 2018 08:37:24 +0000 Subject: [FieldTrip] Inaugural MEG Symposium at the CHBH, University of Birmingham (11th May) Message-ID: <8EB94CB9BF5FD74FA38E0919D3329E9BD6D113@EX14.adf.bham.ac.uk> Dear all, We are pleased to announce the "Inaugural MEG Symposium at the Centre for Human Brain Health" at the University of Birmingham. *09:30-17:30, 11th May 2018 at The Alan Walters Building, University of Birmingham* We would be delighted if you could join us to celebrate the opening of our new MEG facility. The event will include talks from speakers who are leaders in their field, and will include a tour of the new MEG facility at the University of Birmingham. For a complete list of speakers and to register (free) please visit: https://meg2018.eventbrite.co.uk Best regards, Dr. Hyojin Park and Prof. Ole Jensen School of Psychology|Centre for Human Brain Health, University of Birmingham -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuelle.kristensen at gipsa-lab.grenoble-inp.fr Wed Feb 21 15:39:36 2018 From: emmanuelle.kristensen at gipsa-lab.grenoble-inp.fr (EMMANUELLE KRISTENSEN) Date: Wed, 21 Feb 2018 15:39:36 +0100 Subject: [FieldTrip] reading Brain Vision data : unknown resolution for channel Message-ID: <6709f46f-de1f-6dd5-a4dd-932c2bd91caf@gipsa-lab.grenoble-inp.fr> Dear all When reading a .vhdr file/ .dat file (written by EEGlab), I get this warning message, for each channel: "/Warning: unknown resolution (i.e. recording units) for channel 1 in// //MyFile.vhdr/". In the .vhdr file, the resolution is indicated : /"[Binary Infos]// //BinaryFormat=IEEE_FLOAT_32// // //[Channel Infos]// //; Each entry: Ch=,,// //; ////"/ How can I fix this warning, please? Regards, Emmanuelle -- Emmanuelle Kristensen -------------- next part -------------- An HTML attachment was scrubbed... URL: From dbaeper at upo.es Thu Feb 22 18:31:03 2018 From: dbaeper at upo.es (Daniel Baena Perez) Date: Thu, 22 Feb 2018 18:31:03 +0100 Subject: [FieldTrip] Cluster analysis for across subjects with behavioral data Message-ID: Dear all I would like to use the cluster analysis functions in Fieldtrip on correlation statistics. My data consist on an eeg signal recorded on 8 different channels and 125 time bins for 31 subjects. I would like to do an across subjects correlation for each time bin and each channel with the behavioural results. Which function is more suitable for this purpose? My reasoning so far is to use ft_statfun_intersubcorr in the first place but I'm not sure how to continue with the cluster analysis per se. Can this function be given as an argument to ft_timelockstatistics? Thank you, Daniel -------------- next part -------------- An HTML attachment was scrubbed... URL: From mylenbcn at hotmail.com Fri Feb 23 01:02:38 2018 From: mylenbcn at hotmail.com (D myl) Date: Fri, 23 Feb 2018 00:02:38 +0000 Subject: [FieldTrip] Clustering Statistics with Different Number of Observations Per Channel Message-ID: Subject: Clustering Statistics with Different Number of Observations Per Channel Dear community, My name is Dimitris Mylonas and I am working on coupled oscillations on EEG. Currently I am analyzing a high density EEG dataset where we measure the phase-amplitude coupling of specific oscillations (slow waves (.5-2 Hz) and sleep spindles (12-15 Hz)) at each electrode, for two different groups. The outcome measure is the vector length of the coupling (coupling strength) and the question is whether the two groups show significant difference in coupling strength. In order to estimate reliably the coupling strength for each electrode/subject we need to have a minimum number N of coupled oscillations. If for a given subject and a given electrode there are less than N detected oscillations there will be a missing value in the outcome measure. As a result each electrode has different number of subjects where the coupling strength can be "measured reliably". My question is if I can implement the non-parametric statistical testing (not necessarily as implemented in Fieldtrip) (Maris and Oostenveld, 2007) to test for a group difference under this condition (different degrees of freedom at each electrode). Thank you, Dimitris -------------- next part -------------- An HTML attachment was scrubbed... URL: From pascualm at key.uzh.ch Fri Feb 23 06:41:22 2018 From: pascualm at key.uzh.ch (pascualm at key.uzh.ch) Date: Fri, 23 Feb 2018 14:41:22 +0900 Subject: [FieldTrip] Comparing EEG/MEG neuroimaging methods based on localization error, false positive activity, and false positive connectivity Message-ID: Dear Colleagues, The preprint entitled: "Comparing EEG/MEG neuroimaging methods based on localization error, false positive activity, and false positive connectivity" at: https://www.biorxiv.org/content/early/2018/02/22/269753 might be of interest to those working in the field of EEG/MEG neuroimaging. The abstract can be found below. Cordially, Roberto ... Roberto D. Pascual-Marqui, PhD, PD The KEY Institute for Brain-Mind Research, University of Zurich Visiting Professor at Neuropsychiatry, Kansai Medical University, Osaka [www.keyinst.uzh.ch/loreta] [scholar.google.com/citations?user=pascualmarqui] ... Abstract: EEG/MEG neuroimaging consists of estimating the cortical distribution of time varying signals of electric neuronal activity, for the study of functional localization and connectivity. Currently, many different imaging methods are being used, with very different capabilities of correct localization of activity and of correct localization of connectivity. The aim here is to provide a guideline for choosing the best (i.e. least bad) imaging method. This first study is limited to the comparison of the following methods for EEG signals: sLORETA and eLORETA (standardized and exact low resolution electromagnetic tomography), MNE (minimum norm estimate), dSPM (dynamic statistical parametric mapping), and LCMVBs (linearly constrained minimum variance beamformers). These methods are linear, except for the LCMVBs that make use of the quadratic EEG covariances. To achieve a fair comparison, it is assumed here that the generators are independent and widely distributed (i.e. not few in number), giving a well-defined theoretical population EEG covariance matrix for use with the LCMVBs. Measures of localization error, false positive activity, and false positive connectivity are defined and computed under ideal no-noise conditions. It is empirically shown with extensive simulations that: (1) MNE, dSPM, and all LCMVBs are in general incapable of correct localization, while sLORETA and eLORETA have exact (zero-error) localization; (2) the brain volume with false positive activity is significantly larger for MN, dSPM, and all LCMVBs, as compared to sLORETA and eLORETA; and (3) the number of false positive connections is significantly larger for MN, dSPM, all LCMVBs, and sLORETA, as compared to eLORETA. Non-vague and fully detailed equations are given. PASCAL program codes and data files are available. It is noted that the results reported here do not apply to the LCMVBs based on EEG covariance matrices generated from extremely few generators, such as only one or two independent point sources. From hesham.elshafei at inserm.fr Mon Feb 26 13:38:50 2018 From: hesham.elshafei at inserm.fr (Hesham ElShafei) Date: Mon, 26 Feb 2018 13:38:50 +0100 Subject: [FieldTrip] Extraction of Amplitude and Phase from PCC sources Message-ID: Hello all , I have computed beamformer sources using the 'pcc' method. In my source.avg structures , I have the 'csd' , 'noisecsd' , 'mom' and 'csdlabel. I was wondering if there are means to extract both phase and amplitude of the source-level signal from these information. Cheers Hesham ElShafei From jan.schoffelen at donders.ru.nl Mon Feb 26 13:54:16 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Mon, 26 Feb 2018 12:54:16 +0000 Subject: [FieldTrip] Extraction of Amplitude and Phase from PCC sources In-Reply-To: References: Message-ID: <350B16BA-8244-44DF-9F0D-BDE333E9C8C3@donders.ru.nl> Hi Hesham, The single trial/taper Fourier coefficients with amplitude and phase info are in source.avg.mom. Best wishes, Jan-Mathijs > On 26 Feb 2018, at 13:38, Hesham ElShafei wrote: > > Hello all , > > I have computed beamformer sources using the 'pcc' method. In my source.avg structures , I have the 'csd' , 'noisecsd' , 'mom' and 'csdlabel. > > I was wondering if there are means to extract both phase and amplitude of the source-level signal from these information. > > Cheers > Hesham ElShafei > _______________________________________________ > fieldtrip mailing list > fieldtrip at donders.ru.nl > https://mailman.science.ru.nl/mailman/listinfo/fieldtrip From tony.w.wilson at gmail.com Tue Feb 27 12:59:34 2018 From: tony.w.wilson at gmail.com (Tony W. Wilson) Date: Tue, 27 Feb 2018 05:59:34 -0600 Subject: [FieldTrip] Tenure-track Faculty Position in Cognitive Neuroscience Message-ID: The Department of Neurological Sciences at the University of Nebraska Medical Center invites applications for a tenure leading faculty position in Clinical Cognitive Neuroscience. This position is part of a new Neuroimaging Section within the department and aims to leverage multiple hires across the School of Medicine in human neuroscience. We welcome applications from any area of cognitive neuroscience, including memory, executive function, visual attention, perception, audition, motor control, emotion, and decision-making. Methodological specialty within neuroimaging is open, but ideally the candidate would benefit from our strong existing program in MEG imaging, and develop a translational, theory-based multimodal neuroimaging program focusing on their area of interest. The successful applicant would join a growing group of cognitive neuroscientists within the department (and across campus) using MEG, fMRI, and other modalities, and hopefully help grow other programs in parallel with building their own. Successful candidates will have a MD, PhD, or MD/PhD in neuroscience, psychology, or computer science, with postdoctoral training and an excellent publication record for their career stage. Candidates should also have an excellent and sustained record of research and evidence of the potential, or demonstrated ability, to generate extramural funding commensurate with their career stage. Applicants should have the ability and interest to teach graduate courses in cognitive neuroscience, and to mentor PhD students in our growing Neuroscience PhD program. The University of Nebraska Medical Center (UNMC) is a vibrant multidisciplinary research environment with major resources and ample opportunities for training and collaboration. Resources include a 306-sensor MEG system, multiple 3T human MRI scanners, high-definition transcranial direct-current and alternating-current stimulation (HD-tDCS/tACS) equipment, eye-tracking equipment, and a state-of-the-art transcranial magnetic stimulation (TMS) suite. The UNMC is located in Omaha, with a metro area population of approximately one million, and major attractions and events such as the College World Series. Please submit a letter detailing current research and teaching interests, a curriculum vitae, a list of the applicant’s five most important publications, and contact information for three individuals who will provide letters of recommendation at a later time. Applications should be submitted online at: https://unmc.peopleadmin.com/postings/36674 . Review of applications will begin immediately and will continue until the position is filled. Start dates are negotiable, but ideally before the close of 2018. Individuals from diverse backgrounds are encouraged to apply. -------------- next part -------------- An HTML attachment was scrubbed... URL: From elinor.tzvi at neuro.uni-luebeck.de Tue Feb 27 17:03:11 2018 From: elinor.tzvi at neuro.uni-luebeck.de (Elinor Tzvi-Minker) Date: Tue, 27 Feb 2018 16:03:11 +0000 Subject: [FieldTrip] PhD position @ Queen Mary University of London Message-ID: <2530B215-C864-40D3-87F5-1F5ED7C5DE7A@neuro.uni-luebeck.de> Dear All, A 3-year PhD studentship for UK and EU citizens is open at Queen Mary University of London. The project will investigate sense of agency, outcome processing and learning under social influence. Application deadline is 12thMarch. More information and link to the application portal can be found under https://www.findaphd.com/search/ProjectDetails.aspx?PJID=94998 Best wishes, Frederike Beyer -------------- next part -------------- An HTML attachment was scrubbed... URL: From fereshte.ramezani at gmail.com Wed Feb 28 03:27:31 2018 From: fereshte.ramezani at gmail.com (Fereshte) Date: Wed, 28 Feb 2018 02:27:31 +0000 Subject: [FieldTrip] Alignment problem Message-ID: Dear Experts, I read a Brainweb MRI volume in filedtrip ( by default it doesn’t have any coordinate fields). When I align this data to CTF coordinate system using ft_volumerealign and then apply this alignment using ft_volumereslice; I see I miss some data and I get a very wrong head model using this resliced data. Any Ideas? Thanks in advance, Regards, Fereshte -------------- next part -------------- An HTML attachment was scrubbed... URL: From jan.schoffelen at donders.ru.nl Wed Feb 28 08:54:47 2018 From: jan.schoffelen at donders.ru.nl (Schoffelen, J.M. (Jan Mathijs)) Date: Wed, 28 Feb 2018 07:54:47 +0000 Subject: [FieldTrip] Alignment problem In-Reply-To: References: Message-ID: <572A023D-3A85-47BF-A5EB-2DB95DA8B332@donders.ru.nl> Hi Fereshte, No, without any additional information I don’t have any ideas :). What do you mean by “I miss some data”, and “I get a very wrong head model”? Please refer to http://www.fieldtriptoolbox.org/faq/how_to_ask_good_questions_to_the_community?s[]=discussion&s[]=list in phrasing your question. This will maximize the probability that somebody will be inclined and able to point you into the good direction. Best wishes, Jan-Mathijs On 28 Feb 2018, at 03:27, Fereshte > wrote: Dear Experts, I read a Brainweb MRI volume in filedtrip ( by default it doesn’t have any coordinate fields). When I align this data to CTF coordinate system using ft_volumerealign and then apply this alignment using ft_volumereslice; I see I miss some data and I get a very wrong head model using this resliced data. Any Ideas? Thanks in advance, Regards, Fereshte _______________________________________________ fieldtrip mailing list fieldtrip at donders.ru.nl https://mailman.science.ru.nl/mailman/listinfo/fieldtrip -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.nara at bcbl.eu Wed Feb 28 12:15:34 2018 From: s.nara at bcbl.eu (Sanjeev Nara) Date: Wed, 28 Feb 2018 12:15:34 +0100 (CET) Subject: [FieldTrip] 1st International Workshop on Predictive Processing (WoPP) In-Reply-To: References: <5a7d686f.ed3fed0a.5f941.c127SMTPIN_ADDED_BROKEN@mx.google.com> <1640004900.9152749.1519247555698.JavaMail.zimbra@bcbl.eu> <1717447392.9286562.1519725808525.JavaMail.zimbra@bcbl.eu> <497399636.9344962.1519815833963.JavaMail.zimbra@bcbl.eu> Message-ID: <1858953218.9345933.1519816534199.JavaMail.zimbra@bcbl.eu> Dear All, We invite you to the " 1st International Workshop on Predictive Processing (WoPP) " organized by Basque Center on Cognition, Brain and Language (BCBL) that will be held in one of most beautiful cities in europe, San Sebastian, Spain from 20 - 22 June 2018 , at Palacio Miramar in Donostia - San Sebastián. The aim of the workshop is to discuss predictive coding and its underlying mechanisms from behaviour to neuroscience. We aim at calling together researchers and students from various domains such as vision, audition and language, to build bridges between various research fields and share this common and exciting interest on prediction. Please visit http://www.bcbl.eu/events/prediction-2018/en/ for details about abstract submission and registration. Dear Researcher, We are happy to announce the new discussion arena fully centred on predictive processing. The Workshop on Predictive Processing (WoPP) will take place in San Sebastian (Spain) on June 20-22, 2018. The goal of the workshop is to address the role of predictive processing in cognition. Some of the crucial issues in this timely research topic are the extent to which prediction is a fundamental mechanism of brain function, the role of prediction in learning, and, how predictive processing is expressed across distinct cognitive domains. This workshop will gather experts from different fields in cognitive neuroscience including sensory processing, attention and memory, to work alongside the community of language processing, with the aim of furthering our understanding of the role of predictive processing in cognition. The conference will include keynote speakers, regular talks, symposiums and poster sessions. Keynote speakers will be the main sources of discussion: Sophie Scott , University College London Moshe Bar , Bar-Ilan University Pascal Fries, Ernst Strüngmann Institute (ESI) Each keynote will be followed by a symposium on a related topic. Each symposium will be co-organized by two experts in the field, and will last 2 hours. Symposium organizers are Gina Kuperberg, Matt Davis, Craig Richter, Julien Vezoli, Lucia Amoruso and Ruth De Diego Balaguer. For further information please visit: http://www.bcbl.eu/events/prediction-2018/en/ We look forward to seeing you at the conference. Yours sincerely, The Organizing Committee Manuel Carreiras, Clara Martin, Nicola Molinaro & David Soto IMPORTANT DATES TO REMEMBER: Abstract submission and Registration OPEN Abstract deadline: April, 6th, 2018. Notification of abstract acceptance : April 24th, 2018. Early registration deadline: May 11th, 2018. Online registration deadline: May 30th, 2018. Conference dates: June 20-22, 2018. -------------- next part -------------- An HTML attachment was scrubbed... URL: